Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013998.1 Kokia drynarioides strain JFW-HI SEQ_129029, 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: 301293
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Warning! 177 characters in sequence are not A, C, G, or T
Found at i:14534 original size:5 final size:5
Alignment explanation
Indices: 14524--14548 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
14514 AGAATCTTAT
14524 ACAGA ACAGA ACAGA ACAGA ACAGA
1 ACAGA ACAGA ACAGA ACAGA ACAGA
14549 GGCTTATTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.20, G:0.20, T:0.00
Consensus pattern (5 bp):
ACAGA
Found at i:16779 original size:18 final size:17
Alignment explanation
Indices: 16756--16791 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
16746 TGAATTTCTA
*
16756 TCCAATTTATATCTTAAT
1 TCCAATTTA-ATCCTAAT
16774 TCCAATTTAATCCTAAT
1 TCCAATTTAATCCTAAT
16791 T
1 T
16792 AACTCATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.47
Consensus pattern (17 bp):
TCCAATTTAATCCTAAT
Found at i:17953 original size:17 final size:17
Alignment explanation
Indices: 17931--17974 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
17921 TTACAAGAAT
17931 ATGAAAGGTTGAGGAAG
1 ATGAAAGGTTGAGGAAG
17948 ATGAAAGGTTGAGGAAG
1 ATGAAAGGTTGAGGAAG
*
17965 ATGGAAGGTT
1 ATGAAAGGTT
17975 AAAGGTCAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.41, T:0.20
Consensus pattern (17 bp):
ATGAAAGGTTGAGGAAG
Found at i:18008 original size:17 final size:17
Alignment explanation
Indices: 17931--18011 Score: 76
Period size: 17 Copynumber: 4.7 Consensus size: 17
17921 TTACAAGAAT
*
17931 ATGAAAGGTTGAGGAAG
1 ATGAAAGGTTAAGGAAG
*
17948 ATGAAAGGTTGAGGAAG
1 ATGAAAGGTTAAGGAAG
*
17965 ATGGAAGGTTAAAGGTCAAG
1 ATGAAAGGTT-AAGG--AAG
**
17985 --GGGAGGTTAAGGAAG
1 ATGAAAGGTTAAGGAAG
18000 ATGAAAGGTTAA
1 ATGAAAGGTTAA
18012 AAGTAAAGGA
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
15 3 0.06
17 38 0.70
18 10 0.19
20 3 0.06
ACGTcount: A:0.41, C:0.01, G:0.40, T:0.19
Consensus pattern (17 bp):
ATGAAAGGTTAAGGAAG
Found at i:37858 original size:34 final size:36
Alignment explanation
Indices: 37784--37861 Score: 99
Period size: 36 Copynumber: 2.2 Consensus size: 36
37774 TAGGAAGTTA
* *
37784 AATTGATCAATTTTCCAATTAGTTCAATTTTGCTCTT
1 AATT-ATCAATTTTCCAATTAGATCAATTTTGATCTT
37821 AATTATCAATTTATCCAA-TAGAT-AATTTT-ATCTT
1 AATTATCAATTT-TCCAATTAGATCAATTTTGATCTT
37855 AATTATC
1 AATTATC
37862 TCTCGATCTC
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
34 11 0.29
35 6 0.16
36 12 0.32
37 9 0.24
ACGTcount: A:0.33, C:0.14, G:0.05, T:0.47
Consensus pattern (36 bp):
AATTATCAATTTTCCAATTAGATCAATTTTGATCTT
Found at i:46659 original size:20 final size:22
Alignment explanation
Indices: 46619--46662 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
46609 GTCAAAATAT
46619 AATTTTATATTTATTAATTTAA
1 AATTTTATATTTATTAATTTAA
*
46641 AATTTTAT-TTT-TTACTTTAA
1 AATTTTATATTTATTAATTTAA
46661 AA
1 AA
46663 CCATATATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.48
21 3 0.14
22 8 0.38
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
AATTTTATATTTATTAATTTAA
Found at i:46971 original size:23 final size:23
Alignment explanation
Indices: 46919--46972 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
46909 AAAAAAATCG
* *
46919 AAATTAAATTGTAATTTTTAATA
1 AAATTAAAATGTAATTTTTAAAA
* *
46942 TAGTTAAAATGTAATTTTTAAAA
1 AAATTAAAATGTAATTTTTAAAA
46965 AAATTAAA
1 AAATTAAA
46973 TCAAAATTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.43
Consensus pattern (23 bp):
AAATTAAAATGTAATTTTTAAAA
Found at i:53784 original size:2 final size:2
Alignment explanation
Indices: 53777--53801 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
53767 ATCAAACAAT
53777 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
53802 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:61419 original size:22 final size:22
Alignment explanation
Indices: 61394--61451 Score: 71
Period size: 23 Copynumber: 2.6 Consensus size: 22
61384 ATTTGCGCTT
*
61394 TGTGCGCCTACTGATTGCACTA
1 TGTGTGCCTACTGATTGCACTA
* *
61416 TGTGTGCCTATTGGATTGCACTG
1 TGTGTGCCTACT-GATTGCACTA
*
61439 TGTGTGCTTACTG
1 TGTGTGCCTACTG
61452 TTAAGTACTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 11 0.37
23 19 0.63
ACGTcount: A:0.14, C:0.21, G:0.28, T:0.38
Consensus pattern (22 bp):
TGTGTGCCTACTGATTGCACTA
Found at i:62458 original size:22 final size:22
Alignment explanation
Indices: 62407--62486 Score: 97
Period size: 23 Copynumber: 3.5 Consensus size: 22
62397 AAGTACTTAA
* *
62407 CAGTAAGCACACATAATGCAAT
1 CAGTAGGCACACATAGTGCAAT
*
62429 CCAGTAGGCACACACAGTGCAAT
1 -CAGTAGGCACACATAGTGCAAT
* *
62452 CAGTAGGCGCACATAGCGCAAAT
1 CAGTAGGCACACATAGTGC-AAT
62475 CAGTAGGCACAC
1 CAGTAGGCACAC
62487 GAGATGCGAA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
22 16 0.33
23 33 0.67
ACGTcount: A:0.38, C:0.28, G:0.21, T:0.14
Consensus pattern (22 bp):
CAGTAGGCACACATAGTGCAAT
Found at i:62502 original size:23 final size:23
Alignment explanation
Indices: 62471--62528 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
62461 CACATAGCGC
*
62471 AAATCAGTAGGCACACG-AGATGCG
1 AAAT-AGTAAGCACACGAAG-TGCG
*
62495 AAATAGTAAGCACATGAAGTGCG
1 AAATAGTAAGCACACGAAGTGCG
*
62518 AAACAGTAAGC
1 AAATAGTAAGC
62529 GCGCTTGCGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 24 0.80
24 6 0.20
ACGTcount: A:0.43, C:0.17, G:0.26, T:0.14
Consensus pattern (23 bp):
AAATAGTAAGCACACGAAGTGCG
Found at i:64292 original size:60 final size:59
Alignment explanation
Indices: 64216--64357 Score: 205
Period size: 60 Copynumber: 2.4 Consensus size: 59
64206 AACACACGGA
* *
64216 TGTTACA-AGCCTCTATAATGCTTCTATATAAGGTTTATACGTATAAATCGGGTATAGGGG
1 TGTTACAGA-CCTCTATAATGCTTCTATATAAGGTTTATACCTATAAA-CGGATATAGGGG
* **
64276 TGTTACAGACTTCTATAATGCTTCTATATAAGGTTTATACCTATAAACTTATATAGGGG
1 TGTTACAGACCTCTATAATGCTTCTATATAAGGTTTATACCTATAAACGGATATAGGGG
*
64335 TGTTACATACCTCTATAATGCTT
1 TGTTACAGACCTCTATAATGCTT
64358 TTACCTAAAC
Statistics
Matches: 74, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
59 30 0.41
60 43 0.58
61 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (59 bp):
TGTTACAGACCTCTATAATGCTTCTATATAAGGTTTATACCTATAAACGGATATAGGGG
Found at i:83730 original size:2 final size:2
Alignment explanation
Indices: 83723--83748 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
83713 TTTAAGACAA
83723 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
83749 GATCAAAAAT
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:83760 original size:12 final size:12
Alignment explanation
Indices: 83745--83782 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
83735 ATATATATAT
83745 ATATGATCAAAA
1 ATATGATCAAAA
83757 ATATGATCAAAA
1 ATATGATCAAAA
* *
83769 ATTTTATCAAAA
1 ATATGATCAAAA
83781 AT
1 AT
83783 TTTCAAAGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.55, C:0.08, G:0.05, T:0.32
Consensus pattern (12 bp):
ATATGATCAAAA
Found at i:84789 original size:19 final size:19
Alignment explanation
Indices: 84765--84804 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
84755 TCCTTCACTC
84765 CTAAATGAAGAAAACAACT
1 CTAAATGAAGAAAACAACT
84784 CTAAATGAAGAAAACAACT
1 CTAAATGAAGAAAACAACT
84803 CT
1 CT
84805 GATTGGAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.55, C:0.17, G:0.10, T:0.17
Consensus pattern (19 bp):
CTAAATGAAGAAAACAACT
Found at i:90476 original size:21 final size:21
Alignment explanation
Indices: 90437--90476 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
90427 CAAGTAACGT
*
90437 AAAATGAACTTGGAAACAAGA
1 AAAATGAACTTCGAAACAAGA
90458 AAAATGAAC-TCGAATACAA
1 AAAATGAACTTCGAA-ACAA
90477 TTGCTGAGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.57, C:0.12, G:0.15, T:0.15
Consensus pattern (21 bp):
AAAATGAACTTCGAAACAAGA
Found at i:95864 original size:25 final size:25
Alignment explanation
Indices: 95812--95864 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
95802 GTAAACAAAT
*
95812 ATATTTATAAAAAATATATAAATCA
1 ATATTTATAAAAAATATATAAATAA
* *
95837 ATATTTATATAAAATTTATGAAA-AA
1 ATATTTATAAAAAATATAT-AAATAA
95862 ATA
1 ATA
95865 AATGAGATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 21 0.88
26 3 0.12
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (25 bp):
ATATTTATAAAAAATATATAAATAA
Found at i:98548 original size:11 final size:11
Alignment explanation
Indices: 98532--98566 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
98522 TTAGAATTCA
98532 TTTATTATTAG
1 TTTATTATTAG
*
98543 TTTATT-TTAA
1 TTTATTATTAG
98553 TTTATTATTAG
1 TTTATTATTAG
98564 TTT
1 TTT
98567 TAAATATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.69
Consensus pattern (11 bp):
TTTATTATTAG
Found at i:111416 original size:3 final size:3
Alignment explanation
Indices: 111408--111441 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
111398 GAAGGATATT
111408 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
111442 CTGTTTCCAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:113679 original size:30 final size:29
Alignment explanation
Indices: 113645--113736 Score: 148
Period size: 30 Copynumber: 3.1 Consensus size: 29
113635 CTTAACAAAT
*
113645 AAATGTCTCTAAAATAATAATAAAATTAAC
1 AAATG-CTCTAAAATAATAACAAAATTAAC
113675 AAATGCATCTAAAATAATAACAAAATTAAC
1 AAATGC-TCTAAAATAATAACAAAATTAAC
113705 AAATGCCTCTAAAATAATAACAAAATTAAC
1 AAATG-CTCTAAAATAATAACAAAATTAAC
113735 AA
1 AA
113737 TAAAATAAGT
Statistics
Matches: 59, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
29 1 0.02
30 57 0.97
31 1 0.02
ACGTcount: A:0.59, C:0.13, G:0.03, T:0.25
Consensus pattern (29 bp):
AAATGCTCTAAAATAATAACAAAATTAAC
Found at i:114635 original size:20 final size:20
Alignment explanation
Indices: 114601--114645 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
114591 AATATTTTAT
114601 ATTTA-AAATAATAAA-AATA
1 ATTTATAAATAATAAATAA-A
*
114620 ATTTATAAATACTAAATAAA
1 ATTTATAAATAATAAATAAA
114640 ATTTAT
1 ATTTAT
114646 TTTTGATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 5 0.22
20 16 0.70
21 2 0.09
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (20 bp):
ATTTATAAATAATAAATAAA
Found at i:119014 original size:3 final size:3
Alignment explanation
Indices: 119006--119041 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
118996 ATGTTACATG
119006 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
119042 ACAACAACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:120405 original size:16 final size:16
Alignment explanation
Indices: 120381--120423 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
120371 CAAACCCGAT
*
120381 AAAATCTGAACCTGAA
1 AAAACCTGAACCTGAA
*
120397 AAGAA-CTGAATCTGAA
1 AA-AACCTGAACCTGAA
120413 AAAACCTGAAC
1 AAAACCTGAAC
120424 TCAAAAAGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 2 0.09
16 19 0.83
17 2 0.09
ACGTcount: A:0.51, C:0.19, G:0.14, T:0.16
Consensus pattern (16 bp):
AAAACCTGAACCTGAA
Found at i:129173 original size:60 final size:58
Alignment explanation
Indices: 129100--129399 Score: 209
Period size: 60 Copynumber: 5.0 Consensus size: 58
129090 AAAAAAAAAA
* *
129100 TTGGTGTTGGCCATTGC-ATGGTCAACACTCACTTTTAATCTGATAAAAAAATCAAATTT
1 TTGGTGTTGGCCA-TGCAATGGTCGACACTC-CTTTTTATCTGATAAAAAAATCAAATTT
**
129159 TTGGGTGTTGGCCATGCAATGACCGACA-TCCTTATTTATCTGATAAAAAAAATCAAAATTT
1 TT-GGTGTTGGCCATGCAATGGTCGACACTCCTT-TTTATCTGAT-AAAAAAATC-AAATTT
* * * * *
129220 TTTGTGTTGGCCATGCGATGGTTGACACCTCCTTTTT-TCAGATAAAAAATTTCAAATGTT
1 TTGGTGTTGGCCATGCAATGGTCGACA-CTCCTTTTTATCTGATAAAAAA-ATCAAAT-TT
* * * *
129280 TTAGGTATTGGCCATTG-TATGG-CTGACACCCCTTTTTATCTGA-ATAAAAAATCAATTTT
1 TT-GGTGTTGGCCA-TGCAATGGTC-GACACTCCTTTTTATCTGATA-AAAAAATCAAATTT
** * * * * * * * *
129339 TTTATGTTGGTCATACCATGATCGACATCTCTTTTTTGT-TAGATAAAAAATTCGAATTT
1 TTGGTGTTGGCCATGCAATGGTCGACA-CTCCTTTTTATCT-GATAAAAAAATCAAATTT
129398 TT
1 TT
129400 TTACCTCCAT
Statistics
Matches: 190, Mismatches: 32, Indels: 38
0.73 0.12 0.15
Matches are distributed among these distances:
57 1 0.01
58 18 0.09
59 54 0.28
60 73 0.38
61 37 0.19
62 7 0.04
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.39
Consensus pattern (58 bp):
TTGGTGTTGGCCATGCAATGGTCGACACTCCTTTTTATCTGATAAAAAAATCAAATTT
Found at i:129711 original size:59 final size:59
Alignment explanation
Indices: 129407--129848 Score: 270
Period size: 59 Copynumber: 7.3 Consensus size: 59
129397 TTTTTACCTC
* * * * * * * *
129407 CATTGTATGGCTAACA-CAAAAAAAATGA-TTTTTTACCAGCTAAAAAAAAGGGTGTTGAC
1 CATTGCATGGCCAACACCAAAAAAATTGATTTTTTTATCAG--ATAAAAAGGGGTGTCGAT
* * * * * * * *
129466 CATCGCATGACCAACACAAAAAAAAATTCGAATTTTTATCTCACA-AAAAGGGGGTGTTGAT
1 CATTGCATGGCCAACAC-CAAAAAAATT-G-ATTTTTTTATCAGATAAAAAGGGGTGTCGAT
* * * * **
129527 TA-TGACATGGCCAACATCC-AAAAATTTGATTTTTTTTTATTCAAATAAAAAGGGATGTCGGC
1 CATTG-CATGGCCAACA-CCAAAAAAATTGA--TTTTTTTA-TCAGATAAAAAGGGGTGTCGAT
* * * * * * * * *
129589 CA-TCCAATGACCAATACCAAAAAAAATTGAAACTTTTTTACCTGAAAAAAAGGAGTGTTGAT
1 CATTGC-ATGGCCAACACC-AAAAAAATTG--ATTTTTTTATCAGATAAAAAGGGGTGTCGAT
* * *
129651 CATTACATGGCCAATACCAAAAAAATTGATTTTTTTATCAGATAAATAGGGGTGTCGAT
1 CATTGCATGGCCAACACCAAAAAAATTGATTTTTTTATCAGATAAAAAGGGGTGTCGAT
* * * *
129710 CATGGCATGGCCAACACCAAAAAAATTGAATTTTTTATCTGACAAAAAGGGTGTGTC-AGT
1 CATTGCATGGCCAACACCAAAAAAATTGATTTTTTTATCAGATAAAAAGGG-GTGTCGA-T
* * * * *
129770 CATTGCATGGCCAACACCCAAAAATTTGATTTTTTTATCAAATTAAAAGGGGTGTCG-G
1 CATTGCATGGCCAACACCAAAAAAATTGATTTTTTTATCAGATAAAAAGGGGTGTCGAT
**
129828 CCCTGCAATGGCCAACACCAA
1 CATTGC-ATGGCCAACACCAA
129849 TTTTTTTTTT
Statistics
Matches: 293, Mismatches: 69, Indels: 42
0.73 0.17 0.10
Matches are distributed among these distances:
58 5 0.02
59 100 0.34
60 63 0.22
61 49 0.17
62 50 0.17
63 18 0.06
64 7 0.02
65 1 0.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (59 bp):
CATTGCATGGCCAACACCAAAAAAATTGATTTTTTTATCAGATAAAAAGGGGTGTCGAT
Found at i:129779 original size:119 final size:116
Alignment explanation
Indices: 129451--129848 Score: 367
Period size: 119 Copynumber: 3.3 Consensus size: 116
129441 ACCAGCTAAA
* * * *
129451 AAAAAGGGTGTTGACCATCGC-ATGACCAACACAAAAAAAAATTCGAA-TTTTTATCTCACAAAA
1 AAAAGGGGTGTCGACCAT-GCAATGACCAACAC-CAAAAAAATT-GAATTTTTTATCTGACAAAA
* * *
129514 AGGGGGTGTTGATTA-TGACATGGCCAACATCCAAAAATTTGATTTTTTTTTATTCAAAT
63 AGGGTGTGTAG-TCATTG-CATGGCCAACA-CCAAAAATTTGA--TTTTTTTA-TCAAAT
* * * * * *
129573 AAAAAGGGATGTCGGCCATCCAATGACCAATACCAAAAAAAATTGAAACTTTTTTACCTGAAAAA
1 -AAAAGGGGTGTCGACCATGCAATGACCAACACC-AAAAAAATTG-AA-TTTTTTATCTGACAAA
* * * *
129638 AAGGAGTGT-T-GATCATTACATGGCCAATACCAAAAAAATTGATTTTTTTATCAGAT
62 AAGG-GTGTGTAG-TCATTGCATGGCCAACACC-AAAAATTTGATTTTTTTATCAAAT
* *
129694 AAATAGGGGTGTCGATCATGGC-ATGGCCAACACCAAAAAAATTGAATTTTTTATCTGACAAAAA
1 AAA-AGGGGTGTCGACCAT-GCAATGACCAACACCAAAAAAATTGAATTTTTTATCTGACAAAAA
129758 GGGTGTGTCAGTCATTGCATGGCCAACACCCAAAAATTTGATTTTTTTATCAAATT
64 GGGTGTGT-AGTCATTGCATGGCCAACA-CCAAAAATTTGATTTTTTTATCAAA-T
* * *
129814 AAAAGGGGTGTCGGCCCTGCAATGGCCAACACCAA
1 AAAAGGGGTGTCGACCATGCAATGACCAACACCAA
129849 TTTTTTTTTT
Statistics
Matches: 228, Mismatches: 31, Indels: 36
0.77 0.11 0.12
Matches are distributed among these distances:
117 4 0.02
118 21 0.09
119 64 0.28
120 20 0.09
121 27 0.12
122 11 0.05
123 37 0.16
124 23 0.10
125 18 0.08
126 3 0.01
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (116 bp):
AAAAGGGGTGTCGACCATGCAATGACCAACACCAAAAAAATTGAATTTTTTATCTGACAAAAAGG
GTGTGTAGTCATTGCATGGCCAACACCAAAAATTTGATTTTTTTATCAAAT
Found at i:137240 original size:11 final size:11
Alignment explanation
Indices: 137224--137259 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
137214 GCATTATATA
137224 TATTTAAAAAT
1 TATTTAAAAAT
137235 TATTTAAAAAT
1 TATTTAAAAAT
*
137246 AATATTAAAAAT
1 TAT-TTAAAAAT
137258 TA
1 TA
137260 ATATAAGTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 13 0.59
12 9 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
TATTTAAAAAT
Found at i:137256 original size:13 final size:13
Alignment explanation
Indices: 137223--137263 Score: 52
Period size: 11 Copynumber: 3.3 Consensus size: 13
137213 TGCATTATAT
137223 ATATTTAAAAAT-
1 ATATTTAAAAATA
137235 -TATTTAAAAATA
1 ATATTTAAAAATA
137247 ATA-TTAAAAATTA
1 ATATTTAAAAA-TA
137260 ATAT
1 ATAT
137264 AAGTAGACCG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 11 0.44
12 7 0.28
13 7 0.28
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
ATATTTAAAAATA
Found at i:139103 original size:25 final size:25
Alignment explanation
Indices: 139069--139116 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
139059 TGAAGTACTT
139069 AATAGAAGCACATAAGTGCTGGGGA
1 AATAGAAGCACATAAGTGCTGGGGA
139094 AATAGAAGCACATAAGTGCTGGG
1 AATAGAAGCACATAAGTGCTGGG
139117 AAACAGTAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.12, G:0.31, T:0.17
Consensus pattern (25 bp):
AATAGAAGCACATAAGTGCTGGGGA
Found at i:139157 original size:22 final size:22
Alignment explanation
Indices: 139129--139191 Score: 99
Period size: 22 Copynumber: 2.9 Consensus size: 22
139119 ACAGTAGGCG
*
139129 CACACAGTGCCGAACAGAAGCA
1 CACACAGTGCTGAACAGAAGCA
*
139151 CACACAGTGCTGAACAAAAGCA
1 CACACAGTGCTGAACAGAAGCA
*
139173 CACACAGTGCTTAACAGAA
1 CACACAGTGCTGAACAGAA
139192 AGCGCACTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.43, C:0.29, G:0.19, T:0.10
Consensus pattern (22 bp):
CACACAGTGCTGAACAGAAGCA
Found at i:142021 original size:28 final size:27
Alignment explanation
Indices: 141980--142041 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 27
141970 ATTGATAATG
141980 TTTTATAATAATTA-ATATATTTAATAAAA
1 TTTTATAATAATTATA-ATATTTAAT--AA
142009 TTTTATAAT-ATTATAATATTTAATAA
1 TTTTATAATAATTATAATATTTAATAA
142035 TTTTATA
1 TTTTATA
142042 GTTTTTTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
26 9 0.28
28 13 0.41
29 10 0.31
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
TTTTATAATAATTATAATATTTAATAA
Found at i:142024 original size:18 final size:18
Alignment explanation
Indices: 141982--142041 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
141972 TGATAATGTT
141982 TTATAATAA-TTAAT-ATA
1 TTATAA-AATTTAATAATA
*
141999 TTTAATAAAATTTTATAATA
1 -TT-ATAAAATTTAATAATA
* *
142019 TTATAATATTTAATAATT
1 TTATAAAATTTAATAATA
142037 TTATA
1 TTATA
142042 GTTTTTTTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
18 22 0.63
19 10 0.29
20 3 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TTATAAAATTTAATAATA
Found at i:142035 original size:10 final size:10
Alignment explanation
Indices: 141974--142039 Score: 59
Period size: 10 Copynumber: 7.0 Consensus size: 10
141964 TATTATATTG
* *
141974 ATAATGTTTT
1 ATAATATTTA
*
141984 ATAATAATTA
1 ATAATATTTA
141994 AT-ATATTTA
1 ATAATATTTA
* *
142003 ATAAAATTTT
1 ATAATATTTA
142013 ATAATA-TT-
1 ATAATATTTA
142021 ATAATATTTA
1 ATAATATTTA
142031 ATAAT-TTTA
1 ATAATATTTA
142040 TAGTTTTTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
8 6 0.13
9 16 0.35
10 24 0.52
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (10 bp):
ATAATATTTA
Found at i:151913 original size:24 final size:27
Alignment explanation
Indices: 151856--151908 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
151846 TTTTAAATAT
*
151856 TATATAA-AAAATAAATATTATAAAAA
1 TATATAATGAAATAAATATTATAAAAA
* *
151882 TATATAATGAAATTAATATTAAAAAAA
1 TATATAATGAAATAAATATTATAAAAA
151909 ATAATCATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (27 bp):
TATATAATGAAATAAATATTATAAAAA
Found at i:156492 original size:22 final size:22
Alignment explanation
Indices: 156449--156491 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
156439 TTTTAAAAAA
156449 AATATTTATATTATATTATTTT
1 AATATTTATATTATATTATTTT
156471 AATATTTAATATT-T-TTATTTT
1 AATATTT-ATATTATATTATTTT
156492 TTTTATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 7 0.35
22 8 0.40
23 5 0.25
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
AATATTTATATTATATTATTTT
Found at i:162019 original size:23 final size:21
Alignment explanation
Indices: 161977--162019 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
161967 GAGTTGAATA
* *
161977 GGTATAATTTTAAAATATTAT
1 GGTATAAATTTAAAAGATTAT
161998 GGTATAAAATTTAAATAGATTA
1 GGTAT-AAATTTAAA-AGATTA
162020 AAAAATTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.28
22 8 0.44
23 5 0.28
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.42
Consensus pattern (21 bp):
GGTATAAATTTAAAAGATTAT
Found at i:165768 original size:104 final size:105
Alignment explanation
Indices: 165646--165855 Score: 395
Period size: 105 Copynumber: 2.0 Consensus size: 105
165636 CACATTATCT
*
165646 TCCTATCTATAAGTTGAGGAGGGACTATAAATAATTCTAAGGATTGAAT-AAAAAAAGGATTATA
1 TCCTATCTATAAGTTGAGGAGGGACTATAAATAATTCTAAGGATTGAATAAAAAAAAAGATTATA
165710 TGATGAGTTGGAATTTGTGACTTGTTGCACCAACAATGCA
66 TGATGAGTTGGAATTTGTGACTTGTTGCACCAACAATGCA
165750 TCCTATCTATAAGTTGAGGAGGGACTATAAATAATTCTAAGGATTGAATAAAAAAAAAGATTATA
1 TCCTATCTATAAGTTGAGGAGGGACTATAAATAATTCTAAGGATTGAATAAAAAAAAAGATTATA
*
165815 TGATGAGTTGGAATTTGTGACTTGTTGCATCAACAATGCA
66 TGATGAGTTGGAATTTGTGACTTGTTGCACCAACAATGCA
165855 T
1 T
165856 GGTAGGACTT
Statistics
Matches: 103, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
104 49 0.48
105 54 0.52
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.31
Consensus pattern (105 bp):
TCCTATCTATAAGTTGAGGAGGGACTATAAATAATTCTAAGGATTGAATAAAAAAAAAGATTATA
TGATGAGTTGGAATTTGTGACTTGTTGCACCAACAATGCA
Found at i:167580 original size:6 final size:6
Alignment explanation
Indices: 167569--167635 Score: 55
Period size: 6 Copynumber: 11.0 Consensus size: 6
167559 TCAAATTTGA
** * *
167569 TTAAAT TTAAAT TTAAA- GCAAAT TTAAAT TTAAAAAG ATAAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TT--AAAT TTAAAT TTAAAT
* *
167618 TTAAAA ATAAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT
167636 CAATTTAAAC
Statistics
Matches: 46, Mismatches: 12, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
5 3 0.07
6 39 0.85
8 4 0.09
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (6 bp):
TTAAAT
Found at i:167654 original size:22 final size:23
Alignment explanation
Indices: 167615--167661 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
167605 GATAAATTTA
167615 AATTTAAAAATAAATTT-AAATC
1 AATTTAAAAATAAATTTAAAATC
** *
167637 AATTTAAACCTAATTTTAAAATC
1 AATTTAAAAATAAATTTAAAATC
167660 AA
1 AA
167662 AATTTGATCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (23 bp):
AATTTAAAAATAAATTTAAAATC
Found at i:170243 original size:3 final size:3
Alignment explanation
Indices: 170235--170261 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
170225 TCAAGTAAGA
170235 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
170262 ATTGATTGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:170703 original size:19 final size:20
Alignment explanation
Indices: 170681--170730 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
170671 AAAATATAAT
170681 AAATATTAAAA-TATTCAAA
1 AAATATTAAAAGTATTCAAA
* *
170700 AAATCTTAAAAGTGTTCAAA
1 AAATATTAAAAGTATTCAAA
*
170720 AAATAATAAAA
1 AAATATTAAAA
170731 ATATATAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.62, C:0.06, G:0.04, T:0.28
Consensus pattern (20 bp):
AAATATTAAAAGTATTCAAA
Found at i:177003 original size:3 final size:3
Alignment explanation
Indices: 176995--177037 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
176985 ATTAAAATTA
*
176995 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
177038 GAGTTTAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:177493 original size:127 final size:127
Alignment explanation
Indices: 177267--177519 Score: 452
Period size: 127 Copynumber: 2.0 Consensus size: 127
177257 TTTGAGTATT
* *
177267 ATCATATTCTCCCTACTTAGTTCATGCTTGCCCTCAAGTATGATTCTTAATCCACTAAGTAATTT
1 ATCATATTCTCCCTACTTAGTCCATGCTTGCCCTCAAGTATGATTCCTAATCCACTAAGTAATTT
*
177332 AGATTTTACCATGGAAAGAAGTATCACTCCAAAGTTTTACAAACAATTAAGCATAATGCATC
66 AGATTTTACCATGGAAAGAAGTATCACCCCAAAGTTTTACAAACAATTAAGCATAATGCATC
* *
177394 ATCATATTCTCCTTACTTAGTCCATGCTTGCTCTCAAGTATGATTCCTAATCCACTAAGTAATTT
1 ATCATATTCTCCCTACTTAGTCCATGCTTGCCCTCAAGTATGATTCCTAATCCACTAAGTAATTT
*
177459 AGATTTTACCATGGAAAGAAGTATCACCCCAAAGTTTTACAAACAATTAAGCATGATGCAT
66 AGATTTTACCATGGAAAGAAGTATCACCCCAAAGTTTTACAAACAATTAAGCATAATGCAT
177520 ATGAAAATGA
Statistics
Matches: 120, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
127 120 1.00
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (127 bp):
ATCATATTCTCCCTACTTAGTCCATGCTTGCCCTCAAGTATGATTCCTAATCCACTAAGTAATTT
AGATTTTACCATGGAAAGAAGTATCACCCCAAAGTTTTACAAACAATTAAGCATAATGCATC
Found at i:177718 original size:19 final size:19
Alignment explanation
Indices: 177690--177735 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
177680 AATTTTCTTA
*
177690 CTTTTATTTTATCGA-TTTT
1 CTTTT-TTTTTTCGACTTTT
*
177709 CTTTTTTTTTTCTACTTTT
1 CTTTTTTTTTTCGACTTTT
177728 -TTTTTTTT
1 CTTTTTTTT
177736 GCTTAAGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.09, C:0.11, G:0.02, T:0.78
Consensus pattern (19 bp):
CTTTTTTTTTTCGACTTTT
Found at i:179958 original size:46 final size:46
Alignment explanation
Indices: 179905--179996 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
179895 TGTGACATAA
179905 GCTAACTTCATGATGATTTCATTAGCCAAATAAACCTTAAAAAATC
1 GCTAACTTCATGATGATTTCATTAGCCAAATAAACCTTAAAAAATC
179951 GCTAACTTCATGATGATTTCATTAGCCAAATAAACCTTAAAAAATC
1 GCTAACTTCATGATGATTTCATTAGCCAAATAAACCTTAAAAAATC
179997 ATTAAAATTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (46 bp):
GCTAACTTCATGATGATTTCATTAGCCAAATAAACCTTAAAAAATC
Found at i:180027 original size:19 final size:18
Alignment explanation
Indices: 179997--180043 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
179987 TTAAAAAATC
179997 ATTAAAAT-TATTAATAA
1 ATTAAAATATATTAATAA
**
180014 ATTATAAATATATTTTTAA
1 ATTA-AAATATATTAATAA
180033 ATTAGAAATAT
1 ATTA-AAATAT
180044 GTTATAATTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 4 0.16
18 4 0.16
19 17 0.68
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTAAAATATATTAATAA
Found at i:180113 original size:9 final size:9
Alignment explanation
Indices: 180101--180173 Score: 53
Period size: 9 Copynumber: 8.0 Consensus size: 9
180091 AAAACTTTCA
180101 AAAAATTAT
1 AAAAATTAT
*
180110 AAAATTTATT
1 AAAAATTA-T
* *
180120 AGAAATTGT
1 AAAAATTAT
180129 AAAATATTAT
1 AAAA-ATTAT
180139 AAAAA-TATT
1 AAAAATTA-T
*
180148 AAAAACTA-
1 AAAAATTAT
180156 AAAAA-TAGT
1 AAAAATTA-T
180165 AAAAATTAT
1 AAAAATTAT
180174 TGTATCTTAA
Statistics
Matches: 51, Mismatches: 6, Indels: 14
0.72 0.08 0.20
Matches are distributed among these distances:
7 2 0.04
8 7 0.14
9 24 0.47
10 18 0.35
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.33
Consensus pattern (9 bp):
AAAAATTAT
Found at i:180119 original size:33 final size:32
Alignment explanation
Indices: 180056--180120 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
180046 TATAATTCTC
*
180056 TTAAAAATTTCTAAAAATAATAATAATTATTA
1 TTAAAAATTTCAAAAAATAATAATAATTATTA
*
180088 TTAAAAACTTTCAAAAAATTATAA-AATTTATTA
1 TTAAAAA-TTTCAAAAAATAATAATAA-TTATTA
180121 GAAATTGTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 9 0.31
33 20 0.69
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (32 bp):
TTAAAAATTTCAAAAAATAATAATAATTATTA
Found at i:180144 original size:19 final size:18
Alignment explanation
Indices: 180101--180173 Score: 60
Period size: 19 Copynumber: 4.0 Consensus size: 18
180091 AAAACTTTCA
* *
180101 AAAAATTATAAAATTTATT
1 AAAAATTGTAAAAATTA-T
*
180120 AGAAATTGTAAAATATTAT
1 AAAAATTGTAAAA-ATTAT
*
180139 AAAAATAT-TAAAAACTA-
1 AAAAAT-TGTAAAAATTAT
*
180156 AAAAATAGTAAAAATTAT
1 AAAAATTGTAAAAATTAT
180174 TGTATCTTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
17 14 0.33
18 3 0.07
19 22 0.51
20 4 0.09
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.33
Consensus pattern (18 bp):
AAAAATTGTAAAAATTAT
Found at i:181743 original size:14 final size:13
Alignment explanation
Indices: 181709--181746 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
181699 CTTTTCCAAT
181709 AAAAA-TTAATTG
1 AAAAATTTAATTG
*
181721 CAAAATTTAATTG
1 AAAAATTTAATTG
181734 AAAGAATTTAATT
1 AAA-AATTTAATT
181747 ATTACAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 4 0.18
13 9 0.41
14 9 0.41
ACGTcount: A:0.53, C:0.03, G:0.08, T:0.37
Consensus pattern (13 bp):
AAAAATTTAATTG
Found at i:185889 original size:41 final size:41
Alignment explanation
Indices: 185828--185909 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 41
185818 AATACTAATA
* *
185828 TAATTTGTAATCTAGCCCTTACATAATTGGGAAAACGATTT
1 TAATTTATAATCTAGCCCTTACATAATTAGGAAAACGATTT
* * *
185869 TAATTTATAATCTAGTCCTTATATAATTAGGAAAAGGATTT
1 TAATTTATAATCTAGCCCTTACATAATTAGGAAAACGATTT
185910 ATTAGTTTCA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (41 bp):
TAATTTATAATCTAGCCCTTACATAATTAGGAAAACGATTT
Found at i:200994 original size:57 final size:58
Alignment explanation
Indices: 200921--201041 Score: 183
Period size: 57 Copynumber: 2.1 Consensus size: 58
200911 ATTTCCAAGT
*
200921 CATTTTCATTTCCATTTTGGAGAAAACCACATTCATTGT-CAAATGTTTCT-ATTTCTC
1 CATTTTCATTTCCATTTTGAAGAAAACCACATTCATT-TCCAAATGTTTCTCATTTCTC
* * *
200978 TATTTTCATTTTCATTTTGAAGAAAATCACATTCATTTCCAAATGTTTCTCATTTCTC
1 CATTTTCATTTCCATTTTGAAGAAAACCACATTCATTTCCAAATGTTTCTCATTTCTC
201036 CATTTT
1 CATTTT
201042 GACCATTTCT
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
56 1 0.02
57 44 0.77
58 12 0.21
ACGTcount: A:0.26, C:0.20, G:0.07, T:0.47
Consensus pattern (58 bp):
CATTTTCATTTCCATTTTGAAGAAAACCACATTCATTTCCAAATGTTTCTCATTTCTC
Found at i:211260 original size:29 final size:29
Alignment explanation
Indices: 211227--211325 Score: 83
Period size: 29 Copynumber: 3.2 Consensus size: 29
211217 AAAATTTACT
211227 TAATTATTGAATTTGAATGTAATTATAAA
1 TAATTATTGAATTTGAATGTAATTATAAA
* ** * *
211256 TAATTA-TGTATTTGAATAACAATGAAAAATTA
1 TAATTATTGAATTTGAAT-GTAAT-TATAA--A
*
211288 TTTAATAATTGAATTTGAATGTAATTATAAA
1 --TAATTATTGAATTTGAATGTAATTATAAA
211319 TAATTAT
1 TAATTAT
211326 GTATTTAAAT
Statistics
Matches: 51, Mismatches: 12, Indels: 14
0.66 0.16 0.18
Matches are distributed among these distances:
28 10 0.20
29 15 0.29
30 3 0.06
31 1 0.02
32 1 0.02
33 3 0.06
34 8 0.16
35 10 0.20
ACGTcount: A:0.46, C:0.01, G:0.09, T:0.43
Consensus pattern (29 bp):
TAATTATTGAATTTGAATGTAATTATAAA
Found at i:211293 original size:63 final size:63
Alignment explanation
Indices: 211215--211337 Score: 210
Period size: 63 Copynumber: 2.0 Consensus size: 63
211205 GTTTTCTATT
* * *
211215 TGAAAATTTACTTAATTATTGAATTTGAATGTAATTATAAATAATTATGTATTTGAATAACAA
1 TGAAAAATTACTTAATAATTGAATTTGAATGTAATTATAAATAATTATGTATTTAAATAACAA
*
211278 TGAAAAATTATTTAATAATTGAATTTGAATGTAATTATAAATAATTATGTATTTAAATAA
1 TGAAAAATTACTTAATAATTGAATTTGAATGTAATTATAAATAATTATGTATTTAAATAA
211338 TTATTGTAAT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 56 1.00
ACGTcount: A:0.46, C:0.02, G:0.09, T:0.43
Consensus pattern (63 bp):
TGAAAAATTACTTAATAATTGAATTTGAATGTAATTATAAATAATTATGTATTTAAATAACAA
Found at i:214123 original size:20 final size:20
Alignment explanation
Indices: 214087--214124 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
214077 ATGATTTTTG
*
214087 TTAATTAAATTAACATTAGT
1 TTAATTAAATCAACATTAGT
214107 TTAATT-AATCAACCATTA
1 TTAATTAAATCAA-CATTA
214125 ACTATACCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.45, C:0.11, G:0.03, T:0.42
Consensus pattern (20 bp):
TTAATTAAATCAACATTAGT
Found at i:214455 original size:22 final size:23
Alignment explanation
Indices: 214429--214486 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
214419 ATGCTATATA
214429 TTATAAAAAATAATAT-ATTTAT
1 TTATAAAAAATAATATAATTTAT
* * *
214451 TTATAAAAAGTACTATAATTTTT
1 TTATAAAAAATAATATAATTTAT
*
214474 TTATAAGAAATAA
1 TTATAAAAAATAA
214487 ATTTTCTAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
22 14 0.48
23 15 0.52
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (23 bp):
TTATAAAAAATAATATAATTTAT
Found at i:215039 original size:18 final size:16
Alignment explanation
Indices: 215007--215042 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 16
214997 GTAAATGAGT
215007 AATTTAAAAAAATGTA
1 AATTTAAAAAAATGTA
215023 AATTTAAAATTAAATGTA
1 AATTTAAAA--AAATGTA
215041 AA
1 AA
215043 ACTAAAATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
18 9 0.50
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (16 bp):
AATTTAAAAAAATGTA
Found at i:215048 original size:18 final size:18
Alignment explanation
Indices: 215016--215050 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
215006 TAATTTAAAA
**
215016 AAATGTAAATTTAAAATT
1 AAATGTAAAACTAAAATT
215034 AAATGTAAAACTAAAAT
1 AAATGTAAAACTAAAAT
215051 ACCTTTTTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.03, G:0.06, T:0.31
Consensus pattern (18 bp):
AAATGTAAAACTAAAATT
Found at i:215858 original size:23 final size:23
Alignment explanation
Indices: 215796--215858 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 23
215786 TTAAACTAAT
** *
215796 TTAAATATAAAATATTTTTTTATA
1 TTAAATA-AAAATATAATTATATA
215820 TT--ATAAAAA-ATGAATTATATA
1 TTAAATAAAAATAT-AATTATATA
215841 TTAAATAAAAATATAATT
1 TTAAATAAAAATATAATT
215859 CGATTAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
20 2 0.06
21 12 0.38
22 3 0.09
23 11 0.34
24 4 0.12
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
TTAAATAAAAATATAATTATATA
Found at i:225584 original size:30 final size:30
Alignment explanation
Indices: 225531--225609 Score: 106
Period size: 30 Copynumber: 2.6 Consensus size: 30
225521 TACGATTTAA
*
225531 TATGTAATTATATACAT-AAATTTTGATTT
1 TATGTAATTTTATACATAAAATTTTGATTT
225560 TATGTAATTTTATACATAAAATTTTGATTT
1 TATGTAATTTTATACATAAAATTTTGATTT
* * *
225590 AATTTAATTTTTATAAATAA
1 TATGTAA-TTTTATACATAA
225610 TTAAGACAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 16 0.36
30 17 0.39
31 11 0.25
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.52
Consensus pattern (30 bp):
TATGTAATTTTATACATAAAATTTTGATTT
Found at i:225602 original size:31 final size:30
Alignment explanation
Indices: 225524--225609 Score: 102
Period size: 31 Copynumber: 2.8 Consensus size: 30
225514 CATTAATTAC
*
225524 GATTTAATATGTAATTATATACAT-AAATTTT
1 GATTTAAT-T-TAATTTTATACATAAAATTTT
* *
225555 GATTTTATGTAATTTTATACATAAAATTTT
1 GATTTAATTTAATTTTATACATAAAATTTT
*
225585 GATTTAATTTAATTTTTATAAATAA
1 GATTTAATTTAA-TTTTATACATAA
225610 TTAAGACAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
29 12 0.26
30 17 0.36
31 18 0.38
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (30 bp):
GATTTAATTTAATTTTATACATAAAATTTT
Found at i:225683 original size:23 final size:21
Alignment explanation
Indices: 225657--225698 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 21
225647 TATATTGAAT
225657 ATATAAATAATTATATTTATTCA
1 ATATAAAT-ATT-TATTTATTCA
225680 ATATAAATATTTATTTATT
1 ATATAAATATTTATTTATT
225699 TAAATGTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 8 0.42
22 3 0.16
23 8 0.42
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
ATATAAATATTTATTTATTCA
Found at i:240335 original size:493 final size:493
Alignment explanation
Indices: 239409--240397 Score: 1924
Period size: 493 Copynumber: 2.0 Consensus size: 493
239399 AAATCTTTTT
239409 ATACAACTTTTACCATCAGAGGAAATTATAAGTAGTTCTACAAACTTATACAAACAATATCAAGA
1 ATACAACTTTTACCATCAGAGGAAATTATAAGTAGTTCTACAAACTTATACAAACAATATCAAGA
239474 TAAATACTTTCTCTGTCCAGGATACCTCAAGTAAAGATGCACTGAAGTCGAACCAATTAAGGTCT
66 TAAATACTTTCTCTGTCCAGGATACCTCAAGTAAAGATGCACTGAAGTCGAACCAATTAAGGTCT
239539 AGCTCTGCAGCATATTCTTAACAGACCACATGAATACAAGGAAATATATACTCTTGCACCAATTT
131 AGCTCTGCAGCATATTCTTAACAGACCACATGAATACAAGGAAATATATACTCTTGCACCAATTT
*
239604 TCCATGTCATATATTCCAAAATGGAAAATTAATATAAAAACTAATCCAAGATATCTAAACAAGTC
196 TCCATGTCATATATTCCAAAAAGGAAAATTAATATAAAAACTAATCCAAGATATCTAAACAAGTC
239669 CCTGGTTACACACACCATGCCATTGTATATAACATTTGACCTCCAAGCATCAAACACTTGCAGCA
261 CCTGGTTACACACACCATGCCATTGTATATAACATTTGACCTCCAAGCATCAAACACTTGCAGCA
239734 CCATATGGCAATGGATGCCAAAGGCACTCTGCAGTAATTTGAGATAAATGATTCTCCTCTAACAG
326 CCATATGGCAATGGATGCCAAAGGCACTCTGCAGTAATTTGAGATAAATGATTCTCCTCTAACAG
239799 TTGCTAGCAAGGAGAGCACCAAATACCTAATACCACATCCACCAATTTTTGCAGCAACCATACTT
391 TTGCTAGCAAGGAGAGCACCAAATACCTAATACCACATCCACCAATTTTTGCAGCAACCATACTT
*
239864 TGTATGCCACAATAATAGAAAGCAAGAAGTAAGAGCTA
456 TATATGCCACAATAATAGAAAGCAAGAAGTAAGAGCTA
239902 ATACAACTTTTACCATCAGAGGAAATTATAAGTAGTTCTACAAACTTATACAAACAATATCAAGA
1 ATACAACTTTTACCATCAGAGGAAATTATAAGTAGTTCTACAAACTTATACAAACAATATCAAGA
*
239967 TAAATACTTTCTCTGTCCAGGATACCTCAAGTAAAGATGCACTGAAGTCGAACCGATTAAGGTCT
66 TAAATACTTTCTCTGTCCAGGATACCTCAAGTAAAGATGCACTGAAGTCGAACCAATTAAGGTCT
240032 AGCTCTGCAGCATATTCTTAACAGACCACATGAATACAAGGAAATATATACTCTTGCACCAATTT
131 AGCTCTGCAGCATATTCTTAACAGACCACATGAATACAAGGAAATATATACTCTTGCACCAATTT
240097 TCCATGTCATATATTCCAAAAAGGAAAATTAATATAAAAACTAATCCAAGATATCTAAACAAGTC
196 TCCATGTCATATATTCCAAAAAGGAAAATTAATATAAAAACTAATCCAAGATATCTAAACAAGTC
* *
240162 CCTGGTTACACACACCATGCCATTGTATATAACATTTGACCTCCAAGCTTCAAACATTTGCAGCA
261 CCTGGTTACACACACCATGCCATTGTATATAACATTTGACCTCCAAGCATCAAACACTTGCAGCA
*
240227 CCATATGGCAATGGATGCCAAAGGCACTCTGCAGTAATTTGAGATAAATGATTCTCCTCTAAGAG
326 CCATATGGCAATGGATGCCAAAGGCACTCTGCAGTAATTTGAGATAAATGATTCTCCTCTAACAG
240292 TTGCTAGCAAGGAGAGCACCAAATACCTAATACCACATCCACCAATTTTTGCAGCAACCATACTT
391 TTGCTAGCAAGGAGAGCACCAAATACCTAATACCACATCCACCAATTTTTGCAGCAACCATACTT
240357 TATATGCCACAATAATAGAAAGCAAGAAGTAAGAGCTA
456 TATATGCCACAATAATAGAAAGCAAGAAGTAAGAGCTA
240395 ATA
1 ATA
240398 AAAGCATGCA
Statistics
Matches: 490, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
493 490 1.00
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.26
Consensus pattern (493 bp):
ATACAACTTTTACCATCAGAGGAAATTATAAGTAGTTCTACAAACTTATACAAACAATATCAAGA
TAAATACTTTCTCTGTCCAGGATACCTCAAGTAAAGATGCACTGAAGTCGAACCAATTAAGGTCT
AGCTCTGCAGCATATTCTTAACAGACCACATGAATACAAGGAAATATATACTCTTGCACCAATTT
TCCATGTCATATATTCCAAAAAGGAAAATTAATATAAAAACTAATCCAAGATATCTAAACAAGTC
CCTGGTTACACACACCATGCCATTGTATATAACATTTGACCTCCAAGCATCAAACACTTGCAGCA
CCATATGGCAATGGATGCCAAAGGCACTCTGCAGTAATTTGAGATAAATGATTCTCCTCTAACAG
TTGCTAGCAAGGAGAGCACCAAATACCTAATACCACATCCACCAATTTTTGCAGCAACCATACTT
TATATGCCACAATAATAGAAAGCAAGAAGTAAGAGCTA
Found at i:262676 original size:24 final size:25
Alignment explanation
Indices: 262630--262676 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
262620 ATTTTTTTCG
*
262630 AAAAAATAATCATCAAATTTAACTA
1 AAAAAATAATCATCAAATGTAACTA
*
262655 AAAAAATAATGATCAAA-GTAAC
1 AAAAAATAATCATCAAATGTAAC
262677 AATAAATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.62, C:0.11, G:0.04, T:0.23
Consensus pattern (25 bp):
AAAAAATAATCATCAAATGTAACTA
Found at i:278263 original size:97 final size:96
Alignment explanation
Indices: 278090--278380 Score: 422
Period size: 97 Copynumber: 3.0 Consensus size: 96
278080 AACCTTGGAA
* * * *
278090 AAGGGTATTCAATTATCCCAATTTGAAGAAAAGTCTCGCCTAGTAAGTTAAGGCACAAATTTTCA
1 AAGGGTATTCGATTAT-CCAATTTGAAGAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTTA
* *
278155 AAACCAAAGATAAAGAAACATTGCCTCGATTT
65 AAACTAGAGATAAAGAAACATTGCCTCGATTT
* * *
278187 AAGGGTATTTGATTATCCTGATTTGAAGAAAAATCGCGCCTAGTAAGTTGAGGCACAAATTTTTA
1 AAGGGTATTCGATTATCC-AATTTGAAGAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTTA
278252 AAACTAGAGATAAAGAAACATTGCCTCGATTT
65 AAACTAGAGATAAAGAAACATTGCCTCGATTT
* *
278284 AAGGGTATTCGATTATCCCAGTTTGAAGAAAAATCGTGCCTAGTAAGTTAAGGCACAAATTTTTA
1 AAGGGTATTCGATTAT-CCAATTTGAAGAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTTA
* *
278349 AAACTCGAGATAAA-AGAATATTGCCTCGATTT
65 AAACTAGAGATAAAGA-AACATTGCCTCGATTT
278381 TAAAGGTTTA
Statistics
Matches: 175, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
96 3 0.02
97 170 0.97
98 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (96 bp):
AAGGGTATTCGATTATCCAATTTGAAGAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTTAA
AACTAGAGATAAAGAAACATTGCCTCGATTT
Found at i:278762 original size:28 final size:28
Alignment explanation
Indices: 278728--278832 Score: 131
Period size: 28 Copynumber: 3.8 Consensus size: 28
278718 AAACGTCTAA
* * *
278728 GGGCAAAATTGTAATTTTAGATGTTC-G
1 GGGCAAAATGGTAATTTTGGATGCTCAG
278755 GGGACAAAATGGTAATTTTGGATGCTCAG
1 GGG-CAAAATGGTAATTTTGGATGCTCAG
* * *
278784 GGGTAAAATGGTAATTTTGGATGCTTAA
1 GGGCAAAATGGTAATTTTGGATGCTCAG
*
278812 GGGTAAAATGGTAATTTTGGA
1 GGGCAAAATGGTAATTTTGGA
278833 AAGTTCGGAA
Statistics
Matches: 70, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
27 3 0.04
28 63 0.90
29 4 0.06
ACGTcount: A:0.31, C:0.06, G:0.30, T:0.33
Consensus pattern (28 bp):
GGGCAAAATGGTAATTTTGGATGCTCAG
Found at i:278877 original size:29 final size:29
Alignment explanation
Indices: 278811--279241 Score: 205
Period size: 29 Copynumber: 14.8 Consensus size: 29
278801 TGGATGCTTA
278811 AGGGT-AAAATGGTAA-TTTTGGAAAGTTCG
1 AGGGTAAAAAT-GTAATTTTTGG-AAGTTCG
** * *
278840 -GAATAAAAAATGCAATTTTTAGAAGTTCG
1 AGGGT-AAAAATGTAATTTTTGGAAGTTCG
*
278869 AGGGT-AAAATGGTAATTTTTGAAAGTTCG
1 AGGGTAAAAAT-GTAATTTTTGGAAGTTCG
*
278898 -GGAGTAAAAATGTAATTTTTGGAAAGTTTG
1 AGG-GTAAAAATGTAATTTTTGG-AAGTTCG
** *
278928 -GGGTCAAAAATACAATTTTTGGATA-TCTTG
1 AGGGT-AAAAATGTAATTTTTGGA-AGT-TCG
* *
278958 A-GGT-AAAATAGTAATTTTAGAAAGTTC-
1 AGGGTAAAAAT-GTAATTTTTGGAAGTTCG
278985 AGGGTCAAAAATGTAATTTTTGGACA-TTCG
1 AGGGT-AAAAATGTAATTTTTGGA-AGTTCG
* *
279015 AGAGT-AAAATGATAA-TTTTGGATGTTCG
1 AGGGTAAAAATG-TAATTTTTGGAAGTTCG
* * *
279043 AGGGTAAAAATATAATTTTTGAGAAATT-T
1 AGGGTAAAAATGTAATTTTTG-GAAGTTCG
* * * *
279072 AGGGTCAAAATGTGATTTTTGGTAGTT-T
1 AGGGTAAAAATGTAATTTTTGGAAGTTCG
* * *
279100 AGGGGTCAAAATATAATTTTTGAAAAGTT--
1 A-GGGTAAAAATGTAATTTTTG-GAAGTTCG
* * * * *
279129 AGGAGTCAATATATAATTTTTGAAAGTT-T
1 AGG-GTAAAAATGTAATTTTTGGAAGTTCG
* * * *
279158 AGAGGTTAAAATATAATTTTTGTAAAGTTTG
1 AG-GGTAAAAATGTAATTTTTG-GAAGTTCG
* * *
279189 AGGGTCAAAATATAATTTTTGGAAAGTTCA
1 AGGGTAAAAATGTAATTTTTGG-AAGTTCG
* * * *
279219 ATGGTCAAAATATGATTTTTGGA
1 AGGGTAAAAATGTAATTTTTGGA
279242 CAATTCAGGG
Statistics
Matches: 324, Mismatches: 46, Indels: 64
0.75 0.11 0.15
Matches are distributed among these distances:
27 1 0.00
28 57 0.18
29 149 0.46
30 115 0.35
31 2 0.01
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.36
Consensus pattern (29 bp):
AGGGTAAAAATGTAATTTTTGGAAGTTCG
Found at i:278937 original size:88 final size:86
Alignment explanation
Indices: 278811--279239 Score: 283
Period size: 88 Copynumber: 4.9 Consensus size: 86
278801 TGGATGCTTA
* ** *
278811 AGGGT-AAAATGGTAA-TTTTGGAAAGTTCGGAATAAAAAATGCAATTTTTAGAAGTTCGAGGGT
1 AGGGTAAAAAT-GTAATTTTTGGAAAGTTTGGGGTCAAAAATG-AATTTTTAGAAGTTCGAGGGT
*
278874 -AAAATGGTAATTTTTGAAAGTTC
64 AAAAAT-ATAATTTTTGAAAGTTC
* * * *
278897 GGGAGTAAAAATGTAATTTTTGGAAAGTTTGGGGTCAAAAATACAATTTTTGGATA-TCTTGA-G
1 AGG-GTAAAAATGTAATTTTTGGAAAGTTTGGGGTCAAAAAT-GAATTTTTAGA-AGT-TCGAGG
*
278960 GT-AAAATAGTAATTTTAGAAAGTTC
62 GTAAAAATA-TAATTTTTGAAAGTTC
* * * * * *
278985 AGGGTCAAAAATGTAATTTTTGGACA-TTCGAGAGT--AAAATGATAATTTTGGATGTTCGAGGG
1 AGGGT-AAAAATGTAATTTTTGGAAAGTTTG-GGGTCAAAAATGA-ATTTTTAGAAGTTCGAGGG
* *
279047 TAAAAATATAATTTTTGAGAAATTT
63 TAAAAATATAATTTTTGA-AAGTTC
* * * *
279072 AGGGTCAAAATGTGATTTTTGG-TAGTTTAGGGGTCAAAATAT-AATTTTTGAAAAGTT--AGGA
1 AGGGTAAAAATGTAATTTTTGGAAAGTTT-GGGGTCAAAA-ATGAATTTTT-AGAAGTTCGAGG-
* * *
279133 GTCAATATATAATTTTTGAAAGTTT
62 GTAAAAATATAATTTTTGAAAGTTC
* * * * * *
279158 AGAGGTTAAAATATAATTTTTGTAAAGTTTGAGGGTCAAAATAT-AATTTTTGGAAAGTTCAATG
1 AG-GGTAAAAATGTAATTTTTGGAAAGTTTG-GGGTCAAAA-ATGAATTTTTAG-AAGTTCGAGG
* *
279222 GTCAAAATATGATTTTTG
62 GTAAAAATATAATTTTTG
279240 GACAATTCAG
Statistics
Matches: 273, Mismatches: 43, Indels: 51
0.74 0.12 0.14
Matches are distributed among these distances:
85 5 0.02
86 58 0.21
87 66 0.24
88 120 0.44
89 22 0.08
90 2 0.01
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.36
Consensus pattern (86 bp):
AGGGTAAAAATGTAATTTTTGGAAAGTTTGGGGTCAAAAATGAATTTTTAGAAGTTCGAGGGTAA
AAATATAATTTTTGAAAGTTC
Found at i:279033 original size:28 final size:29
Alignment explanation
Indices: 278991--279061 Score: 85
Period size: 28 Copynumber: 2.5 Consensus size: 29
278981 GTTCAGGGTC
278991 AAAAATG-TAATTTTTGGACATTCGAGAGT
1 AAAAATGATAA-TTTTGGACATTCGAGAGT
** *
279020 -AAAATGATAATTTTGGATGTTCGAGGGT
1 AAAAATGATAATTTTGGACATTCGAGAGT
279048 AAAAAT-ATAATTTT
1 AAAAATGATAATTTT
279062 TGAGAAATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 29 0.78
29 8 0.22
ACGTcount: A:0.39, C:0.04, G:0.20, T:0.37
Consensus pattern (29 bp):
AAAAATGATAATTTTGGACATTCGAGAGT
Found at i:279187 original size:30 final size:29
Alignment explanation
Indices: 278881--279239 Score: 210
Period size: 29 Copynumber: 12.3 Consensus size: 29
278871 GGTAAAATGG
* * * *
278881 TAATTTTTGAAAG-TTCGGGAGTAAAAATG
1 TAATTTTTGAAAGTTTAGAG-GTCAAAATA
*
278910 TAATTTTTGGAAAGTTT-GGGGTCAAAAATA
1 TAATTTTT-GAAAGTTTAGAGGTC-AAAATA
* *
278940 CAATTTTTGGATA-TCTT-GAGGT-AAAATA
1 TAATTTTT-GAAAGT-TTAGAGGTCAAAATA
* * *
278968 GTAATTTTAGAAAGTTCAG-GGTCAAAAATG
1 -TAATTTTTGAAAGTTTAGAGGTC-AAAATA
* *
278998 TAATTTTTGGACA--TTCGAGAGT-AAAATGA
1 TAATTTTT-GAAAGTTTAGAG-GTCAAAAT-A
* * * *
279027 TAA-TTTTGGATG-TTCGAGGGTAAAAATA
1 TAATTTTTGAAAGTTTAGA-GGTCAAAATA
* *
279055 TAATTTTTGAGAAATTTAG-GGTCAAAATG
1 TAATTTTTGA-AAGTTTAGAGGTCAAAATA
* ** *
279084 TGATTTTTGGTAGTTTAGGGGTCAAAATA
1 TAATTTTTGAAAGTTTAGAGGTCAAAATA
*
279113 TAATTTTTGAAAAG-TTAG-GAGTCAATATA
1 TAATTTTTG-AAAGTTTAGAG-GTCAAAATA
*
279142 TAATTTTTGAAAGTTTAGAGGTTAAAATA
1 TAATTTTTGAAAGTTTAGAGGTCAAAATA
279171 TAATTTTTGTAAAGTTT-GAGGGTCAAAATA
1 TAATTTTTG-AAAGTTTAGA-GGTCAAAATA
*
279201 TAATTTTTGGAAAGTTCA-ATGGTCAAAATA
1 TAATTTTT-GAAAGTTTAGA-GGTCAAAATA
*
279231 TGATTTTTG
1 TAATTTTTG
279240 GACAATTCAG
Statistics
Matches: 263, Mismatches: 39, Indels: 56
0.73 0.11 0.16
Matches are distributed among these distances:
27 1 0.00
28 46 0.17
29 118 0.45
30 92 0.35
31 6 0.02
ACGTcount: A:0.37, C:0.04, G:0.21, T:0.38
Consensus pattern (29 bp):
TAATTTTTGAAAGTTTAGAGGTCAAAATA
Found at i:279240 original size:30 final size:30
Alignment explanation
Indices: 278904--279241 Score: 233
Period size: 30 Copynumber: 11.6 Consensus size: 30
278894 TTCGGGAGTA
* *
278904 AAAATGTAATTTTTGGAAAGTTT-GGGGTC
1 AAAATATAATTTTTGGAAAGTTTAAGGGTC
* * *
278933 AAAAATACAATTTTTGGATA-TCTTGA-GGT-
1 -AAAATATAATTTTTGGAAAGT-TTAAGGGTC
* *
278962 AAAATAGTAA-TTTTAGAAAG-TTCAGGGTC
1 AAAATA-TAATTTTTGGAAAGTTTAAGGGTC
* * ** *
278991 AAAAATGTAATTTTTGGACA-TTCGAGAGT-
1 -AAAATATAATTTTTGGAAAGTTTAAGGGTC
* ** *
279020 AAAATGATAA-TTTTGG-ATGTTCGAGGGTA
1 AAAAT-ATAATTTTTGGAAAGTTTAAGGGTC
279049 AAAATATAATTTTTGAGAAA-TTT-AGGGTC
1 AAAATATAATTTTTG-GAAAGTTTAAGGGTC
* * * *
279078 AAAATGTGATTTTTGG-TAGTTTAGGGGTC
1 AAAATATAATTTTTGGAAAGTTTAAGGGTC
*
279107 AAAATATAATTTTTGAAAAG-TT-AGGAGTC
1 AAAATATAATTTTTGGAAAGTTTAAGG-GTC
* *
279136 AATATATAATTTTT-GAAAGTTT-AGAGGTT
1 AAAATATAATTTTTGGAAAGTTTAAG-GGTC
* *
279165 AAAATATAATTTTTGTAAAGTTTGAGGGTC
1 AAAATATAATTTTTGGAAAGTTTAAGGGTC
* *
279195 AAAATATAATTTTTGGAAAGTTCAATGGTC
1 AAAATATAATTTTTGGAAAGTTTAAGGGTC
*
279225 AAAATATGATTTTTGGA
1 AAAATATAATTTTTGGA
279242 CAATTCAGGG
Statistics
Matches: 244, Mismatches: 41, Indels: 46
0.74 0.12 0.14
Matches are distributed among these distances:
27 4 0.02
28 49 0.20
29 92 0.38
30 96 0.39
31 3 0.01
ACGTcount: A:0.37, C:0.04, G:0.21, T:0.38
Consensus pattern (30 bp):
AAAATATAATTTTTGGAAAGTTTAAGGGTC
Found at i:280977 original size:11 final size:11
Alignment explanation
Indices: 280963--281016 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
280953 AATTAAATTC
280963 AAATTTAAAAT
1 AAATTTAAAAT
*
280974 AAATTTAAACT
1 AAATTTAAAAT
* **
280985 AAAAGTTAATTT
1 -AAATTTAAAAT
*
280997 AAATTTATAAT
1 AAATTTAAAAT
281008 AAATTTAAA
1 AAATTTAAA
281017 CTTAAAATAA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
11 25 0.76
12 8 0.24
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (11 bp):
AAATTTAAAAT
Found at i:280978 original size:17 final size:17
Alignment explanation
Indices: 280956--281040 Score: 100
Period size: 17 Copynumber: 5.0 Consensus size: 17
280946 ATTTTTTAAT
*
280956 TAAATTCAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
280973 TAAATTTAAA-CTAAAA
1 TAAATTTAAATTTAAAA
* *
280989 GTTAATTTAAATTTATAA
1 -TAAATTTAAATTTAAAA
*
281007 TAAATTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
*
281024 TAAATTAAAATTTAAAA
1 TAAATTTAAATTTAAAA
281041 ATTTGGGCTT
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
16 5 0.09
17 47 0.84
18 4 0.07
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.38
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:280982 original size:23 final size:23
Alignment explanation
Indices: 280955--281040 Score: 70
Period size: 23 Copynumber: 3.8 Consensus size: 23
280945 CATTTTTTAA
*
280955 TTAAATTCAAATTTAAAATAAAT
1 TTAAATTAAAATTTAAAATAAAT
* * **
280978 TTAAACTAAAAGTTAATTTAAAT
1 TTAAATTAAAATTTAAAATAAAT
*
281001 TTATAA-T-AAATTTAAACTTAAA-
1 TTA-AATTAAAATTTAAA-ATAAAT
*
281023 ATAAATTAAAATTTAAAA
1 TTAAATTAAAATTTAAAA
281041 ATTTGGGCTT
Statistics
Matches: 50, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
21 2 0.04
22 10 0.20
23 36 0.72
24 2 0.04
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.38
Consensus pattern (23 bp):
TTAAATTAAAATTTAAAATAAAT
Found at i:281009 original size:34 final size:34
Alignment explanation
Indices: 280956--281040 Score: 118
Period size: 34 Copynumber: 2.5 Consensus size: 34
280946 ATTTTTTAAT
*
280956 TAAATTCAAATTTAAAATAAATTTAAAC-TAAAA
1 TAAATTAAAATTTAAAATAAATTTAAACTTAAAA
* * *
280989 GTTAATTTAAATTTATAATAAATTTAAACTTAAAA
1 -TAAATTAAAATTTAAAATAAATTTAAACTTAAAA
281024 TAAATTAAAATTTAAAA
1 TAAATTAAAATTTAAAA
281041 ATTTGGGCTT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
34 39 0.89
35 5 0.11
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.38
Consensus pattern (34 bp):
TAAATTAAAATTTAAAATAAATTTAAACTTAAAA
Found at i:283985 original size:32 final size:32
Alignment explanation
Indices: 283907--283988 Score: 110
Period size: 32 Copynumber: 2.6 Consensus size: 32
283897 TTGCTAAATA
* *
283907 TCTTCCTTGAAATTAATGTTTTTTGCCTAATT
1 TCTTCATTGAAATTAATGTTTTTGGCCTAATT
* *
283939 TCCTCATTGGAATTAATGTTTTTGGCCTAATT
1 TCTTCATTGAAATTAATGTTTTTGGCCTAATT
* *
283971 TCTTCTTTAAAATTAATG
1 TCTTCATTGAAATTAATG
283989 CCTTTATGAT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.24, C:0.15, G:0.11, T:0.50
Consensus pattern (32 bp):
TCTTCATTGAAATTAATGTTTTTGGCCTAATT
Found at i:290588 original size:30 final size:29
Alignment explanation
Indices: 290492--290593 Score: 85
Period size: 30 Copynumber: 3.7 Consensus size: 29
290482 CTATTAAAAA
* *
290492 AAATATAATTTTATAATTTT-AATAGATT
1 AAATATAATTTTATATTTTTAAAAAGATT
290520 --ATAT--TTTTATAATTTTTAAAAA-ATT
1 AAATATAATTTTAT-ATTTTTAAAAAGATT
*
290545 AAATCA-ATTTTTTATATTTTTAAAAAGATT
1 AAAT-ATA-ATTTTATATTTTTAAAAAGATT
290575 AAAATATAATTTTAT-TTTT
1 -AAATATAATTTTATATTTT
290594 ATTAATTTAA
Statistics
Matches: 60, Mismatches: 3, Indels: 21
0.71 0.04 0.25
Matches are distributed among these distances:
24 6 0.10
25 8 0.13
26 7 0.12
27 2 0.03
28 1 0.02
29 15 0.25
30 16 0.27
31 5 0.08
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (29 bp):
AAATATAATTTTATATTTTTAAAAAGATT
Done.