Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014362.1 Kokia drynarioides strain JFW-HI SEQ_129399, 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: 144876
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:5053 original size:22 final size:22
Alignment explanation
Indices: 5025--5081 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
5015 TGCACAAATG
*
5025 AACAGAGAGCACTGAGGTGCTA
1 AACAGAGAGCACTAAGGTGCTA
* *
5047 AACAGAGAGCACAAATGTGCTA
1 AACAGAGAGCACTAAGGTGCTA
*
5069 AACGGAGAGCACT
1 AACAGAGAGCACT
5082 TTACGTGCTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.40, C:0.19, G:0.28, T:0.12
Consensus pattern (22 bp):
AACAGAGAGCACTAAGGTGCTA
Found at i:7756 original size:61 final size:61
Alignment explanation
Indices: 7638--7910 Score: 299
Period size: 60 Copynumber: 4.5 Consensus size: 61
7628 TTTAATCTGA
* *
7638 CAAAAAAA-TTGATTTTTTTATCAGATAAAAAGAGGGTGTCGGCCAATGCATAG-CAACAC
1 CAAAAAAATTTGAATTTTTTATCAGATAAAAAGAGGGTGTCGACCAATGCATAGCCAACAC
* *** * *
7697 CAAAAAAATTTGAATTTTTTATCAGATAAAAAAAACATGTCGACC-ATGCAATGGTCAACAC
1 CAAAAAAATTTGAATTTTTTATCAGATAAAAAGAGGGTGTCGACCAATGC-ATAGCCAACAC
* ** *
7758 C-AAAATATTTGAAATTTTTTATCTCATAAAAAG-GTGGTGTCGACCAATGCATGGCCAACAC
1 CAAAAAAATTTG-AATTTTTTATCAGATAAAAAGAG-GGTGTCGACCAATGCATAGCCAACAC
* ** * *
7819 C-AAAAAATTTGATTTTTTTATCAGATAAAAAGAGGGTGTCGGTCAATACAAAGCCAACA-
1 CAAAAAAATTTGAATTTTTTATCAGATAAAAAGAGGGTGTCGACCAATGCATAGCCAACAC
*
7878 CAAAAAAAATTGAATTTTTTTATCAGATAAAAA
1 CAAAAAAATTTGAA-TTTTTTATCAGATAAAAA
7911 AGATGAAAAA
Statistics
Matches: 179, Mismatches: 26, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
59 13 0.07
60 90 0.50
61 72 0.40
62 4 0.02
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.28
Consensus pattern (61 bp):
CAAAAAAATTTGAATTTTTTATCAGATAAAAAGAGGGTGTCGACCAATGCATAGCCAACAC
Found at i:7877 original size:121 final size:121
Alignment explanation
Indices: 7639--7910 Score: 318
Period size: 121 Copynumber: 2.3 Consensus size: 121
7629 TTAATCTGAC
* *
7639 AAAAAAATTG-ATTTTTTTATCAGATAAAAAGAGGGTGTCGGCCAATGCATAGCAACACCAAAAA
1 AAAAAAATTGAAATTTTTTATCAGATAAAAAGAGGGTGTCGACCAATGCATAGCAACACCAAAAA
* * * * *
7703 AATTTGAATTTTTTATCAGATAAAAAAAACATGTCGACCATGCAATGGTCAACACC
66 AATTTGAATTTTTTATCAGATAAAAAAAACATGTCGACAATACAATAGCCAACACA
* * ** *
7759 AAAATATTTGAAATTTTTTATCTCATAAAAAG-GTGGTGTCGACCAATGCATGGCCAACACC-AA
1 AAAAAAATTGAAATTTTTTATCAGATAAAAAGAG-GGTGTCGACCAATGCATAG-CAACACCAAA
* * *** *
7822 AAAATTTGATTTTTTTATCAGATAAAAAGAGGGTGTCGGTCAATACAA-AGCCAACACA
64 AAAATTTGAATTTTTTATCAGATAAAAAAAACATGTC-GACAATACAATAGCCAACACA
*
7880 AAAAAAATTGAATTTTTTTATCAGATAAAAA
1 AAAAAAATTGAAATTTTTTATCAGATAAAAA
7911 AGATGAAAAA
Statistics
Matches: 125, Mismatches: 23, Indels: 7
0.81 0.15 0.05
Matches are distributed among these distances:
120 9 0.07
121 102 0.82
122 14 0.11
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (121 bp):
AAAAAAATTGAAATTTTTTATCAGATAAAAAGAGGGTGTCGACCAATGCATAGCAACACCAAAAA
AATTTGAATTTTTTATCAGATAAAAAAAACATGTCGACAATACAATAGCCAACACA
Found at i:9639 original size:24 final size:24
Alignment explanation
Indices: 9590--9639 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
9580 TTTAATGTAA
* *
9590 TTTTATTATTTTAATAATTTATAT
1 TTTTATAATTTTAATAATTTAAAT
9614 TTTTATAATTTTAA-AATATTAAAT
1 TTTTATAATTTTAATAAT-TTAAAT
9638 TT
1 TT
9640 AATTTTTATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 3 0.13
24 20 0.87
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
TTTTATAATTTTAATAATTTAAAT
Found at i:9657 original size:30 final size:31
Alignment explanation
Indices: 9605--9688 Score: 93
Period size: 31 Copynumber: 2.7 Consensus size: 31
9595 TTATTTTAAT
* * *
9605 AATTTATATTTTTATAATTTT-AAAATAT-TA
1 AATTTA-ATTTTTATCATTTTAAAAAAATAAA
9635 AATTTAATTTTTATCATCTTTAAAAAAATAAA
1 AATTTAATTTTTATCAT-TTTAAAAAAATAAA
9667 AATTTAA-TTTTATCATTATTAA
1 AATTTAATTTTTATCATT-TTAA
9689 TTTAAAATTT
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
29 10 0.21
30 10 0.21
31 19 0.40
32 8 0.17
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (31 bp):
AATTTAATTTTTATCATTTTAAAAAAATAAA
Found at i:14779 original size:149 final size:148
Alignment explanation
Indices: 14504--14803 Score: 519
Period size: 149 Copynumber: 2.0 Consensus size: 148
14494 TCTTATTTCA
14504 TAATTTCTAGTGGTATCCCCCACTAATATAGTATATTGTCCCATATATTTTTTCATATCTTCATA
1 TAATTTCTAGTGGTATCCCCCACTAATATAGTATATTGTCCCATATATTTTTTCATATCTTCATA
* * * * *
14569 TGGTACATCATCGGATTTCTCTTCAAAGTTAGTCACTAATTAAACCTCATATGATGGCCTGATAG
66 TGGTACATCATCGAATTCCTCTTCAAAGTTAATCACTAATTAAACCACATATGATGCCCTGATAG
14634 TTAAAGGTGTTTATAATCT
131 TTAAAGGTGTTTATAAT-T
*
14653 TAATTTCTAGTGGTATCCCCCACTAATATAGTATATTGTCCTATATATTTTTTCATATCTTCATA
1 TAATTTCTAGTGGTATCCCCCACTAATATAGTATATTGTCCCATATATTTTTTCATATCTTCATA
*
14718 TGGTACATCATCGAATTCCTCTTCAAAGTTAATCACTAATTGAACCACATATGATGCCCTGATAG
66 TGGTACATCATCGAATTCCTCTTCAAAGTTAATCACTAATTAAACCACATATGATGCCCTGATAG
*
14783 TTAAGGGTGTTTATAATT
131 TTAAAGGTGTTTATAATT
14801 TAA
1 TAA
14804 AGTGTGATTT
Statistics
Matches: 143, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
148 4 0.03
149 139 0.97
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.40
Consensus pattern (148 bp):
TAATTTCTAGTGGTATCCCCCACTAATATAGTATATTGTCCCATATATTTTTTCATATCTTCATA
TGGTACATCATCGAATTCCTCTTCAAAGTTAATCACTAATTAAACCACATATGATGCCCTGATAG
TTAAAGGTGTTTATAATT
Found at i:16763 original size:29 final size:30
Alignment explanation
Indices: 16716--16772 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
16706 TGTACCAGCT
16716 CCACACGAACTAGACACACG-GTCGTGTGGC
1 CCACACGAACTAGACACACGAG-CGTGTGGC
* *
16746 CCACACG-AGTAGAGACACGAGCGTGTG
1 CCACACGAACTAGACACACGAGCGTGTG
16773 TCGAGGCATG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.28, C:0.30, G:0.30, T:0.12
Consensus pattern (30 bp):
CCACACGAACTAGACACACGAGCGTGTGGC
Found at i:22416 original size:30 final size:30
Alignment explanation
Indices: 22371--22489 Score: 132
Period size: 30 Copynumber: 4.0 Consensus size: 30
22361 TTCAGATACA
* * *
22371 ACAAGCTAACTTTATAAT-GAAGTTACTCAC
1 ACAAGCTGACATTATAATAGAA-TTGCTCAC
* *
22401 ACAAGTTGACATTATAATAGAATTGCTTAC
1 ACAAGCTGACATTATAATAGAATTGCTCAC
* *
22431 ACAAGCTAAGATTATAATAGAATTGCTCAC
1 ACAAGCTGACATTATAATAGAATTGCTCAC
* * *
22461 ACAAACTGACATTATAATAGGATTACTCA
1 ACAAGCTGACATTATAATAGAATTGCTCA
22490 GTCGAGAATC
Statistics
Matches: 74, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
30 71 0.96
31 3 0.04
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (30 bp):
ACAAGCTGACATTATAATAGAATTGCTCAC
Found at i:23608 original size:10 final size:10
Alignment explanation
Indices: 23593--23641 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
23583 CTTATATACT
23593 TTAATTAAAC
1 TTAATTAAAC
*
23603 TTAATTAATC
1 TTAATTAAAC
* **
23613 CTAATTAAGT
1 TTAATTAAAC
23623 TTAATTAAAC
1 TTAATTAAAC
23633 TATAATTAA
1 T-TAATTAA
23642 CCAATCCTTA
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
10 24 0.77
11 7 0.23
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (10 bp):
TTAATTAAAC
Found at i:30149 original size:25 final size:24
Alignment explanation
Indices: 30102--30157 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
30092 TTGAATTTTA
* * *
30102 GTTTGTTTTTTGACACGAGAGTTT
1 GTTTGTCTTTTGACAAGAAAGTTT
30126 GTTTGTCTTTTGACAAGAAAAGTTT
1 GTTTGTCTTTTGACAAG-AAAGTTT
30151 GTCTTGT
1 GT-TTGT
30158 TTTGTCTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 15 0.56
25 8 0.30
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.23, T:0.48
Consensus pattern (24 bp):
GTTTGTCTTTTGACAAGAAAGTTT
Found at i:33963 original size:30 final size:30
Alignment explanation
Indices: 33941--34082 Score: 214
Period size: 30 Copynumber: 4.8 Consensus size: 30
33931 TTTGACCCTT
* *
33941 AAACTTTTCTAAAATTACATTTTGA-CACC
1 AAACTTTTCTAAAATTACATTTTAACCCCC
*
33970 AAACTTTTCTAAAATTACATTTTAACCCTC
1 AAACTTTTCTAAAATTACATTTTAACCCCC
* * *
34000 AAACTTCTCCAAAATTACATTTTAACCCCT
1 AAACTTTTCTAAAATTACATTTTAACCCCC
34030 AAACTTTTCTAAAATTACATTTTAACCCCC
1 AAACTTTTCTAAAATTACATTTTAACCCCC
*
34060 AAACTTTCCTAAAATTACATTTT
1 AAACTTTTCTAAAATTACATTTT
34083 GATCCTCGAG
Statistics
Matches: 101, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
29 24 0.24
30 77 0.76
ACGTcount: A:0.37, C:0.24, G:0.01, T:0.38
Consensus pattern (30 bp):
AAACTTTTCTAAAATTACATTTTAACCCCC
Found at i:46421 original size:39 final size:39
Alignment explanation
Indices: 46378--46453 Score: 143
Period size: 39 Copynumber: 1.9 Consensus size: 39
46368 CCATCAGTCA
46378 ATCTCTTACCCCGAGCTTGGGGCATATAAAAACCATCTG
1 ATCTCTTACCCCGAGCTTGGGGCATATAAAAACCATCTG
*
46417 ATCTCTTACCCCGAGCTTGGGGCATATAGAAACCATC
1 ATCTCTTACCCCGAGCTTGGGGCATATAAAAACCATC
46454 CTGGGCAGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCTTGGGGCATATAAAAACCATCTG
Found at i:46595 original size:78 final size:78
Alignment explanation
Indices: 46454--46799 Score: 345
Period size: 78 Copynumber: 4.4 Consensus size: 78
46444 AGAAACCATC
* * * *
46454 CTGG-GCAGATCACCATCAGCCTATCTCTTACCCCGAGCCTAAGGCAAATTACAGCCATTCGATC
1 CTGGAGCAGATCACCATAAGCCAATCTCTTACCCCAAGCCTAGGGCAAATTACAGCCATTCGATC
46518 TCTTACCCCGAGT
66 TCTTACCCCGAGT
* * * * * * ** * *
46531 TTGGGGTAGATCACCATAAGCCAATCTCTTACCTCAAGCCTGGGGCATATTGTAGTCATCCGATC
1 CTGGAGCAGATCACCATAAGCCAATCTCTTACCCCAAGCCTAGGGCAAATTACAGCCATTCGATC
*
46596 TCTTACCCCGAGC
66 TCTTACCCCGAGT
* * * * * *
46609 CTGAAGCAGATCACCATCAGCCAATCTCTTACCCCAAGCTTGGGGCAAATTACGGCCATTCGATA
1 CTGGAGCAGATCACCATAAGCCAATCTCTTACCCCAAGCCTAGGGCAAATTACAGCCATTCGATC
* *
46674 TTTTACCCCGAGA
66 TCTTACCCCGAGT
* * * * * * *
46687 CTGGGGAAGATCACCATCAA-CCAATCTCTTACCCCGACCCTAGGGCAGATTGCAACCATTCGAT
1 CTGGAGCAGATCACCAT-AAGCCAATCTCTTACCCCAAGCCTAGGGCAAATTACAGCCATTCGAT
* *
46751 CTTTTACCCCGATT
65 CTCTTACCCCGAGT
* * * *
46765 ATGGAGCAGATCATCGTTAGCCAATCTCTTACCCC
1 CTGGAGCAGATCACCATAAGCCAATCTCTTACCCC
46800 GACCCAAGGT
Statistics
Matches: 215, Mismatches: 51, Indels: 5
0.79 0.19 0.02
Matches are distributed among these distances:
77 4 0.02
78 210 0.98
79 1 0.00
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.25
Consensus pattern (78 bp):
CTGGAGCAGATCACCATAAGCCAATCTCTTACCCCAAGCCTAGGGCAAATTACAGCCATTCGATC
TCTTACCCCGAGT
Found at i:46636 original size:39 final size:39
Alignment explanation
Indices: 46458--46643 Score: 117
Period size: 39 Copynumber: 4.8 Consensus size: 39
46448 ACCATCCTGG
*
46458 GCAGATCACCATCAGCCTATCTCTTACCCCGAGCCT-AA
1 GCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGAA
* * * ** * ** **
46496 GGCAAATTA-CAGCCATTCGATCTCTTACCCCGAGTTTGGG
1 -GCAGATCACCA-TCAGCCAATCTCTTACCCCGAGCCTGAA
* * * * **
46536 GTAGATCACCATAAGCCAATCTCTTACCTCAAGCCTGGG
1 GCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGAA
* *** * *
46575 GCATAT-TGTAGTCATCCGATCTCTTACCCCGAGCCTGAA
1 GCAGATCACCA-TCAGCCAATCTCTTACCCCGAGCCTGAA
46614 GCAGATCACCATCAGCCAATCTCTTACCCC
1 GCAGATCACCATCAGCCAATCTCTTACCCC
46644 AAGCTTGGGG
Statistics
Matches: 102, Mismatches: 40, Indels: 10
0.67 0.26 0.07
Matches are distributed among these distances:
38 3 0.03
39 96 0.94
40 3 0.03
ACGTcount: A:0.25, C:0.34, G:0.17, T:0.24
Consensus pattern (39 bp):
GCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGAA
Found at i:46719 original size:39 final size:39
Alignment explanation
Indices: 46515--46723 Score: 118
Period size: 39 Copynumber: 5.4 Consensus size: 39
46505 CAGCCATTCG
** *
46515 ATCTCTTACCCCGAGTTTGGGGTAGATCACCAT-AAGCCA
1 ATCTCTTACCCCGAGCCTGGGGAAGATCACCATCAA-CCA
* * * * *** * *
46554 ATCTCTTACCTCAAGCCTGGGGCATAT-TGTAGTCATCCG
1 ATCTCTTACCCCGAGCCTGGGGAAGATCACCA-TCAACCA
** * *
46593 ATCTCTTACCCCGAGCCTGAAGCAGATCACCATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGAAGATCACCATCAACCA
* * * *** ** *
46632 ATCTCTTACCCCAAGCTTGGGGCAA-ATTACGGCCATTCG
1 ATCTCTTACCCCGAGCCTGGGG-AAGATCACCATCAACCA
* * *
46671 ATATTTTACCCCGAGACTGGGGAAGATCACCATCAACCA
1 ATCTCTTACCCCGAGCCTGGGGAAGATCACCATCAACCA
46710 ATCTCTTACCCCGA
1 ATCTCTTACCCCGA
46724 CCCTAGGGCA
Statistics
Matches: 118, Mismatches: 47, Indels: 10
0.67 0.27 0.06
Matches are distributed among these distances:
38 3 0.03
39 112 0.95
40 3 0.03
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCCTGGGGAAGATCACCATCAACCA
Found at i:46751 original size:156 final size:156
Alignment explanation
Indices: 46458--46799 Score: 416
Period size: 156 Copynumber: 2.2 Consensus size: 156
46448 ACCATCCTGG
* * *
46458 GCAGATCACCATCAGCCTATCTCTTACCCCGAGCCTAAGGCAAATTACAGCCATTCGATCTCTTA
1 GCAGATCACCATCAGCCAATCTCTTACCCCAAGCCTAAGGCAAATTACAGCCATTCGATATCTTA
** * * * * * * **
46523 CCCCGAGTTTGGGGTAGATCACCATAAGCCAATCTCTTACCTCAAGCCTGGGGCATATTGTAGTC
66 CCCCGAGACTGGGGAAGATCACCATAAGCCAATCTCTTACCCCAACCCTAGGGCAGATTGCAACC
*
46588 ATCCGATCTCTTACCCCGAGCCTGAA
131 ATCCGATCTCTTACCCCGAGCATGAA
* ** * *
46614 GCAGATCACCATCAGCCAATCTCTTACCCCAAGCTTGGGGCAAATTACGGCCATTCGATATTTTA
1 GCAGATCACCATCAGCCAATCTCTTACCCCAAGCCTAAGGCAAATTACAGCCATTCGATATCTTA
*
46679 CCCCGAGACTGGGGAAGATCACCATCAA-CCAATCTCTTACCCCGACCCTAGGGCAGATTGCAAC
66 CCCCGAGACTGGGGAAGATCACCAT-AAGCCAATCTCTTACCCCAACCCTAGGGCAGATTGCAAC
* * ** *
46743 CATTCGATCTTTTACCCCGATTATGGA
130 CATCCGATCTCTTACCCCGAGCATGAA
* * *
46770 GCAGATCATCGTTAGCCAATCTCTTACCCC
1 GCAGATCACCATCAGCCAATCTCTTACCCC
46800 GACCCAAGGT
Statistics
Matches: 157, Mismatches: 28, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
156 155 0.99
157 2 0.01
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.25
Consensus pattern (156 bp):
GCAGATCACCATCAGCCAATCTCTTACCCCAAGCCTAAGGCAAATTACAGCCATTCGATATCTTA
CCCCGAGACTGGGGAAGATCACCATAAGCCAATCTCTTACCCCAACCCTAGGGCAGATTGCAACC
ATCCGATCTCTTACCCCGAGCATGAA
Found at i:48895 original size:20 final size:20
Alignment explanation
Indices: 48870--48912 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
48860 TTTTCTTTCA
*
48870 AAAATCACATTTTAACTCCT
1 AAAATCACATTTTAACCCCT
*
48890 AAAATCATATTTTAACCCCT
1 AAAATCACATTTTAACCCCT
48910 AAA
1 AAA
48913 CTTTTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.23, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAATCACATTTTAACCCCT
Found at i:48979 original size:31 final size:30
Alignment explanation
Indices: 48898--49055 Score: 228
Period size: 30 Copynumber: 5.2 Consensus size: 30
48888 CTAAAATCAT
* * *
48898 ATTTTAACCCCTAAACTTTTCAAAAATCAC
1 ATTTTAACCCTTAAACTTTTCCAAAATTAC
*
48928 ATTTTAACCCCTAAACTTTTCCAAAATTAC
1 ATTTTAACCCTTAAACTTTTCCAAAATTAC
*
48958 ATTTTAACCCTTAAATTTTTTCCAAAATTAC
1 ATTTTAACCCTTAAA-CTTTTCCAAAATTAC
48989 ATTTTAACCCTTAAA-TTTTCCTAAAATTAC
1 ATTTTAACCCTTAAACTTTTCC-AAAATTAC
* *
49019 ATTTTAATCCTTAAACTTTTCTAAAATTAC
1 ATTTTAACCCTTAAACTTTTCCAAAATTAC
49049 ATTTTAA
1 ATTTTAA
49056 TCATCGAATT
Statistics
Matches: 119, Mismatches: 6, Indels: 6
0.91 0.05 0.05
Matches are distributed among these distances:
29 6 0.05
30 79 0.66
31 34 0.29
ACGTcount: A:0.37, C:0.21, G:0.00, T:0.42
Consensus pattern (30 bp):
ATTTTAACCCTTAAACTTTTCCAAAATTAC
Found at i:48991 original size:61 final size:60
Alignment explanation
Indices: 48886--49055 Score: 234
Period size: 61 Copynumber: 2.8 Consensus size: 60
48876 ACATTTTAAC
* * * *
48886 TCCTAAAATCATATTTTAACCCCTAAACTTTTCAAAAATCACATTTTAACCCCTAAACTTT
1 TCCTAAAATTACATTTTAACCCTTAAACTTTTCAAAAATTACATTTTAACCCCTAAA-TTT
* * *
48947 TCC-AAAATTACATTTTAACCCTTAAATTTTTTCCAAAATTACATTTTAACCCTTAAATTT
1 TCCTAAAATTACATTTTAACCCTTAAA-CTTTTCAAAAATTACATTTTAACCCCTAAATTT
* *
49007 TCCTAAAATTACATTTTAATCCTTAAACTTTTCTAAAATTACATTTTAA
1 TCCTAAAATTACATTTTAACCCTTAAACTTTTCAAAAATTACATTTTAA
49056 TCATCGAATT
Statistics
Matches: 97, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
60 46 0.47
61 51 0.53
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (60 bp):
TCCTAAAATTACATTTTAACCCTTAAACTTTTCAAAAATTACATTTTAACCCCTAAATTT
Found at i:54462 original size:14 final size:14
Alignment explanation
Indices: 54443--54485 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
54433 TCTAGGTTGG
54443 TTTGGTTTTGGGTA
1 TTTGGTTTTGGGTA
54457 TTTGGTTTT-GGT-
1 TTTGGTTTTGGGTA
54469 TTTGGTTTTAGGGTA
1 TTTGGTTTT-GGGTA
54484 TT
1 TT
54486 AGATTTGGGC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 9 0.35
13 3 0.12
14 12 0.46
15 2 0.08
ACGTcount: A:0.07, C:0.00, G:0.33, T:0.60
Consensus pattern (14 bp):
TTTGGTTTTGGGTA
Found at i:54466 original size:6 final size:6
Alignment explanation
Indices: 54439--54477 Score: 53
Period size: 6 Copynumber: 6.3 Consensus size: 6
54429 GGCATCTAGG
54439 TTGG-T TTGGTT TTGGGTAT TTGGTT TTGGTT TTGGTT TT
1 TTGGTT TTGGTT TT-GGT-T TTGGTT TTGGTT TTGGTT TT
54478 AGGGTATTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
5 4 0.13
6 18 0.58
7 6 0.19
8 3 0.10
ACGTcount: A:0.03, C:0.00, G:0.33, T:0.64
Consensus pattern (6 bp):
TTGGTT
Found at i:54492 original size:26 final size:25
Alignment explanation
Indices: 54439--54493 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
54429 GGCATCTAGG
* *
54439 TTGGTTTGGTTTTGGGTATTTGGTT
1 TTGGTTTGGTTTTGGGTATTTAGAT
54464 TTGGTTTTGGTTTTAGGGTA-TTAGAT
1 TTGG-TTTGGTTTT-GGGTATTTAGAT
54490 TTGG
1 TTGG
54494 GCTCTTGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 4 0.15
26 17 0.65
27 5 0.19
ACGTcount: A:0.09, C:0.00, G:0.35, T:0.56
Consensus pattern (25 bp):
TTGGTTTGGTTTTGGGTATTTAGAT
Found at i:64873 original size:20 final size:20
Alignment explanation
Indices: 64844--64882 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
64834 GTATCGATCT
64844 AGTATCGATACTTTTTATTA
1 AGTATCGATACTTTTTATTA
* *
64864 AGTATTGATAGTTTTTATT
1 AGTATCGATACTTTTTATT
64883 GAATACTGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.05, G:0.13, T:0.54
Consensus pattern (20 bp):
AGTATCGATACTTTTTATTA
Found at i:64892 original size:20 final size:20
Alignment explanation
Indices: 64850--64894 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
64840 ATCTAGTATC
* *
64850 GATACTTTTTATTAAGTATT
1 GATAGTTTTTATTAAGTACT
64870 GATAGTTTTTATTGAA-TACT
1 GATAGTTTTTATT-AAGTACT
64890 GATAG
1 GATAG
64895 AATCAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.31, C:0.04, G:0.16, T:0.49
Consensus pattern (20 bp):
GATAGTTTTTATTAAGTACT
Found at i:79232 original size:105 final size:105
Alignment explanation
Indices: 79050--79265 Score: 414
Period size: 105 Copynumber: 2.1 Consensus size: 105
79040 CTTTTACTTA
79050 TATCAAAGTATATGAGTCACATATACATAGTTTATCATTTACTCAAGATTAAATTAAGACACACT
1 TATCAAAGTATATGAGTCACATATACATAGTTTATCATTTACTCAAGATTAAATTAAGACACACT
*
79115 ATGAACGTCACAAGTGCATCAAATTGATACATGGGCTATC
66 ATGAACGTCACAAGTGCATCAAATTGATACATAGGCTATC
79155 TATCAAAGTATATGAGTCACATATACATAGTTTATCATTTACTCAAGATTAAATTAAGACACACT
1 TATCAAAGTATATGAGTCACATATACATAGTTTATCATTTACTCAAGATTAAATTAAGACACACT
*
79220 ATGAACGTCACAAGTGTATCAAATTGATACATAGGCTATC
66 ATGAACGTCACAAGTGCATCAAATTGATACATAGGCTATC
79260 TATCAA
1 TATCAA
79266 GCTCCCATTA
Statistics
Matches: 109, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 109 1.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (105 bp):
TATCAAAGTATATGAGTCACATATACATAGTTTATCATTTACTCAAGATTAAATTAAGACACACT
ATGAACGTCACAAGTGCATCAAATTGATACATAGGCTATC
Found at i:84928 original size:25 final size:25
Alignment explanation
Indices: 84893--84951 Score: 91
Period size: 25 Copynumber: 2.4 Consensus size: 25
84883 TAAATTGAGA
* *
84893 ATATTAGAACAAAATTGTATAAAAT
1 ATATTAAAACAAAACTGTATAAAAT
84918 ATATTAAAACAAAACTGTATAAAAT
1 ATATTAAAACAAAACTGTATAAAAT
*
84943 GTATTAAAA
1 ATATTAAAA
84952 TGAAATTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.58, C:0.05, G:0.07, T:0.31
Consensus pattern (25 bp):
ATATTAAAACAAAACTGTATAAAAT
Found at i:93331 original size:59 final size:58
Alignment explanation
Indices: 93249--93683 Score: 430
Period size: 59 Copynumber: 7.4 Consensus size: 58
93239 CTCGAGGATG
* * * *
93249 AAATGGTAA-TTTTGGAAAATTTTGGGGTAAAAAATGGGATATTTAGGAGTTCGAGGGTAA
1 AAATGG-AATTTTTGG-AAGTTTTGGGGTTAAAAATGGGAT-TTTTGGAGTTCGGGGGTAA
* * * * *
93309 AAATGGGATTTTTAGAAGTTTTGGGGTTAAAAATGGGATTTTTTGAAGTTTGGGGGTTTA
1 AAATGGAATTTTTGGAAGTTTTGGGGTTAAAAATGGGA-TTTTTGGAGTTCGGGGG-TAA
* * * ** *
93369 AAATGGGATTTTTTTGAAGTTTCT-GGGTTAAAAATGGGATTTTTAGAAGTTTTGGGGTTA
1 AAAT-GGAATTTTTGGAAGTTT-TGGGGTTAAAAATGGGATTTTT-GGAGTTCGGGGGTAA
** * * *
93429 AAATGGAATTTTTAAAAG-TTTGGGGGTAAAAATGAGATTTTTGGAAGTTCGGGGGTAG
1 AAATGGAATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTGG-AGTTCGGGGGTAA
* ** **
93487 AAATGGAATTTTTGGAA-TTTTTGGGTT-AAAATGGGATTTTTAAAAGTTTAGGGGTAA
1 AAATGGAATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTT-GGAGTTCGGGGGTAA
*
93544 AAATGGAATTTTTGGAAGTTTTGGGGTTGAAAATGGGATTTTTGGAAGTTCGGGGGTAA
1 AAATGGAATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTGG-AGTTCGGGGGTAA
* * ** *
93603 AAATGAAATTTTTGGAAGTTTCGGGGTCGAAAATGGGATTTTTGGAAGTTTGGGGGTAA
1 AAATGGAATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTGG-AGTTCGGGGGTAA
*
93662 AAATGAAATTTTTGGACAGTTT
1 AAATGGAATTTTTGGA-AGTTT
93684 AGGGACCTCC
Statistics
Matches: 319, Mismatches: 42, Indels: 28
0.82 0.11 0.07
Matches are distributed among these distances:
57 42 0.13
58 60 0.19
59 141 0.44
60 35 0.11
61 40 0.13
62 1 0.00
ACGTcount: A:0.31, C:0.02, G:0.31, T:0.37
Consensus pattern (58 bp):
AAATGGAATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTGGAGTTCGGGGGTAA
Found at i:93683 original size:30 final size:29
Alignment explanation
Indices: 93249--93683 Score: 406
Period size: 29 Copynumber: 14.7 Consensus size: 29
93239 CTCGAGGATG
* * * *
93249 AAATGGTAATTTTGGAAAATTTTGGGGTAAA
1 AAATGGGATTTTTGG-AAGTTTGGGGGT-AA
* * *
93280 AAATGGGATATTTAGG-AGTTCGAGGGTAA
1 AAATGGGAT-TTTTGGAAGTTTGGGGGTAA
* *
93309 AAATGGGATTTTTAGAAGTTTTGGGGTTAA
1 AAATGGGATTTTTGGAAG-TTTGGGGGTAA
* *
93339 AAATGGGATTTTTTGAAGTTTGGGGGTTTA
1 AAATGGGATTTTTGGAAGTTTGGGGG-TAA
* * *
93369 AAATGGGATTTTTTTGAAGTTTCTGGGTTAA
1 AAATGGGA-TTTTTGGAAGTTT-GGGGGTAA
* * *
93400 AAATGGGATTTTTAGAAGTTTTGGGGTTA
1 AAATGGGATTTTTGGAAGTTTGGGGGTAA
* **
93429 AAATGGAATTTTTAAAAGTTTGGGGGTAA
1 AAATGGGATTTTTGGAAGTTTGGGGGTAA
* * *
93458 AAATGAGATTTTTGGAAGTTCGGGGGTAG
1 AAATGGGATTTTTGGAAGTTTGGGGGTAA
* ** *
93487 AAATGGAATTTTTGGAA-TTTTTGGGTTA
1 AAATGGGATTTTTGGAAGTTTGGGGGTAA
** *
93515 AAATGGGATTTTTAAAAGTTTAGGGGTAA
1 AAATGGGATTTTTGGAAGTTTGGGGGTAA
* * *
93544 AAATGGAATTTTTGGAAGTTTTGGGGTTGA
1 AAATGGGATTTTTGGAAG-TTTGGGGGTAA
*
93574 AAATGGGATTTTTGGAAGTTCGGGGGTAA
1 AAATGGGATTTTTGGAAGTTTGGGGGTAA
** * *
93603 AAATGAAATTTTTGGAAGTTTCGGGGTCGA
1 AAATGGGATTTTTGGAAGTTTGGGGGT-AA
93633 AAATGGGATTTTTGGAAGTTTGGGGGTAA
1 AAATGGGATTTTTGGAAGTTTGGGGGTAA
**
93662 AAATGAAATTTTTGGACAGTTT
1 AAATGGGATTTTTGGA-AGTTT
93684 AGGGACCTCC
Statistics
Matches: 329, Mismatches: 65, Indels: 21
0.79 0.16 0.05
Matches are distributed among these distances:
28 24 0.07
29 158 0.48
30 109 0.33
31 30 0.09
32 8 0.02
ACGTcount: A:0.31, C:0.02, G:0.31, T:0.37
Consensus pattern (29 bp):
AAATGGGATTTTTGGAAGTTTGGGGGTAA
Found at i:95629 original size:17 final size:17
Alignment explanation
Indices: 95584--95681 Score: 115
Period size: 17 Copynumber: 5.6 Consensus size: 17
95574 TTGTTTATTT
95584 TAAATTTTAAATTTGAAAA
1 TAAA-TTTAAATTT-AAAA
* * *
95603 TAATTTTAAACTTAAAT
1 TAAATTTAAATTTAAAA
95620 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
95637 TAAATTTAAATTTTTAAA
1 TAAATTTAAA-TTTAAAA
* *
95655 CAAATTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
95672 TAAATTTAAA
1 TAAATTTAAA
95682 GGGAGCATGG
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
17 41 0.62
18 22 0.33
19 3 0.05
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:95631 original size:35 final size:35
Alignment explanation
Indices: 95583--95681 Score: 121
Period size: 35 Copynumber: 2.8 Consensus size: 35
95573 TTTGTTTATT
*
95583 TTAAATTTTAAATTTGAAAATAATTTTAAA-CTTAAA
1 TTAAA-TTTAAATTT-AAAATAAATTTAAATCTTAAA
*
95619 TTAAATTTAAATTTAAAATAAATTTAAATTTTTAAA
1 TTAAATTTAAATTTAAAATAAATTTAAA-TCTTAAA
* *
95655 -CAAATTTAATTTTAAAATAAATTTAAA
1 TTAAATTTAAATTTAAAATAAATTTAAA
95682 GGGAGCATGG
Statistics
Matches: 57, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
34 13 0.23
35 34 0.60
36 10 0.18
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (35 bp):
TTAAATTTAAATTTAAAATAAATTTAAATCTTAAA
Found at i:95681 original size:6 final size:6
Alignment explanation
Indices: 95582--95649 Score: 61
Period size: 6 Copynumber: 11.5 Consensus size: 6
95572 CTTTGTTTAT
* * *
95582 TTTAAA TTTTAAA TTTGAAA -ATAAT TTTAAA CTTAAA -TTAAA TTTAAA
1 TTTAAA -TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
95630 TTTAAA -ATAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTT
95650 TTAAACAAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
5 11 0.22
6 30 0.60
7 9 0.18
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (6 bp):
TTTAAA
Found at i:105479 original size:30 final size:30
Alignment explanation
Indices: 105445--105567 Score: 119
Period size: 30 Copynumber: 4.1 Consensus size: 30
105435 TTATGGGTTC
105445 GAGGGTCAAAATGTAATTTTGGAAAAGTTT
1 GAGGGTCAAAATGTAATTTTGGAAAAGTTT
*
105475 GAGGGTCAAAAATG--ACTTTGGAAAAGTTT
1 GAGGGTC-AAAATGTAATTTTGGAAAAGTTT
** **
105504 G-GAGGTCAAAATGTAATTTTTAAAAAAATT
1 GAG-GGTCAAAATGTAATTTTGGAAAAGTTT
* * *
105534 -AGGGGTCAAAATATGATTTTGGAAAAGTTC
1 GA-GGGTCAAAATGTAATTTTGGAAAAGTTT
105564 GAGG
1 GAGG
105568 ACCTTCTAAG
Statistics
Matches: 73, Mismatches: 13, Indels: 14
0.73 0.13 0.14
Matches are distributed among these distances:
28 7 0.10
29 19 0.26
30 39 0.53
31 8 0.11
ACGTcount: A:0.39, C:0.05, G:0.26, T:0.30
Consensus pattern (30 bp):
GAGGGTCAAAATGTAATTTTGGAAAAGTTT
Found at i:105515 original size:59 final size:60
Alignment explanation
Indices: 105448--105562 Score: 162
Period size: 59 Copynumber: 1.9 Consensus size: 60
105438 TGGGTTCGAG
* * *
105448 GGTCAAAATGTAATTTTG-GAAAAGTTTGAGGGTCAAAA-ATGACTTTGGAAAAGTTTGGA
1 GGTCAAAATGTAATTTTGAAAAAAATTAG-GGGTCAAAATATGACTTTGGAAAAGTTTGGA
* *
105507 GGTCAAAATGTAATTTTTAAAAAAATTAGGGGTCAAAATATGATTTTGGAAAAGTT
1 GGTCAAAATGTAATTTTGAAAAAAATTAGGGGTCAAAATATGACTTTGGAAAAGTT
105563 CGAGGACCTT
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 26 0.53
60 23 0.47
ACGTcount: A:0.40, C:0.04, G:0.23, T:0.32
Consensus pattern (60 bp):
GGTCAAAATGTAATTTTGAAAAAAATTAGGGGTCAAAATATGACTTTGGAAAAGTTTGGA
Found at i:105528 original size:29 final size:29
Alignment explanation
Indices: 105445--105528 Score: 100
Period size: 29 Copynumber: 2.9 Consensus size: 29
105435 TTATGGGTTC
105445 GAGGGTCAAAATGTAATTTTGGAAAAGTTT
1 GAGGGTCAAAATGTAATTTT-GAAAAGTTT
* *
105475 GAGGGTCAAAAATG-ACTTTGGAAAAGTTT
1 GAGGGTC-AAAATGTAATTTTGAAAAGTTT
*
105504 G-GAGGTCAAAATGTAATTTTTAAAA
1 GAG-GGTCAAAATGTAATTTTGAAAA
105529 AAATTAGGGG
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
28 7 0.15
29 22 0.48
30 11 0.24
31 6 0.13
ACGTcount: A:0.39, C:0.05, G:0.25, T:0.31
Consensus pattern (29 bp):
GAGGGTCAAAATGTAATTTTGAAAAGTTT
Found at i:107063 original size:14 final size:14
Alignment explanation
Indices: 107046--107102 Score: 53
Period size: 14 Copynumber: 3.8 Consensus size: 14
107036 GTTTGGGTTA
107046 TTGGGTTTGTAACT
1 TTGGGTTTGTAACT
*
107060 TTGGGTTATGGGTAATAT
1 TTGGGTT-T--GTAA-CT
107078 TTGGGTTT-TAGACT
1 TTGGGTTTGTA-ACT
107092 TTGGGTTTGTA
1 TTGGGTTTGTA
107103 TGTAATTGGA
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
14 18 0.51
15 4 0.11
17 5 0.14
18 8 0.23
ACGTcount: A:0.16, C:0.04, G:0.32, T:0.49
Consensus pattern (14 bp):
TTGGGTTTGTAACT
Found at i:107142 original size:18 final size:18
Alignment explanation
Indices: 107115--107158 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
107105 TAATTGGACA
*
107115 TTAAAATAAATT-TAAAAT
1 TTAAATTAAATTCT-AAAT
107133 TTAAATTAAATTCTAAAT
1 TTAAATTAAATTCTAAAT
107151 TTCAAATT
1 TT-AAATT
107159 TATTTTTGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (18 bp):
TTAAATTAAATTCTAAAT
Found at i:108008 original size:85 final size:84
Alignment explanation
Indices: 107904--108075 Score: 245
Period size: 85 Copynumber: 2.0 Consensus size: 84
107894 TTTGCTTCAT
* * * *
107904 TGAATTGGTCTTCTTCTCTGTATCTCATCAGGAAGATGATCGCTTCATTGATTTAATCCACTTCT
1 TGAATTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTGATTTAACCCACTTCT
* *
107969 CTGTATCTGATCAGGAAGA
66 ATGTATCTCATCAGGAAGA
* * * *
107988 TGAATTTGGTCTACTTCTCTGTGTCTCATCAAGAAGATGACCGCTTTATTGCTTTGACCCACTTC
1 TGAA-TTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTGATTTAACCCACTTC
108053 TATGTATCTCATCAGGAAGA
65 TATGTATCTCATCAGGAAGA
108073 TGA
1 TGA
108076 GGTTCGAAAG
Statistics
Matches: 77, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
84 4 0.05
85 73 0.95
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (84 bp):
TGAATTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTGATTTAACCCACTTCT
ATGTATCTCATCAGGAAGA
Found at i:119866 original size:14 final size:15
Alignment explanation
Indices: 119837--119889 Score: 65
Period size: 14 Copynumber: 3.6 Consensus size: 15
119827 AACGAACTAT
119837 TATACGAATGAATAAA
1 TATACGAAT-AATAAA
119853 TATACGAA-AATAAA
1 TATACGAATAATAAA
* *
119867 CATAAGAATAATAAA
1 TATACGAATAATAAA
119882 -ATACGAAT
1 TATACGAAT
119890 CATGAATCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
14 19 0.58
15 6 0.18
16 8 0.24
ACGTcount: A:0.60, C:0.08, G:0.09, T:0.23
Consensus pattern (15 bp):
TATACGAATAATAAA
Found at i:120148 original size:30 final size:29
Alignment explanation
Indices: 119986--120165 Score: 175
Period size: 30 Copynumber: 6.0 Consensus size: 29
119976 AAAAAAAAAA
* *
119986 TGGGGTCGAAAAATGAAATTTT-GAAGAGTT
1 TGGGGTC--AAAATGTAATTTTGGAAAAGTT
*
120016 TGGGGTCAAAAATGTGATTTT-GAGAAAGTT
1 TGGGGTC-AAAATGTAATTTTGGA-AAAGTT
120046 TGAGGGTCAAAATGTAATTTTGGAAAAGTT
1 TG-GGGTCAAAATGTAATTTTGGAAAAGTT
* * *
120076 CGAGGGTCAAAATATAACTTTGGAAAAGTT
1 TG-GGGTCAAAATGTAATTTTGGAAAAGTT
* *
120106 TGGAGGTTAAAATGTAATTTTGAAAAAGTT
1 TGG-GGTCAAAATGTAATTTTGGAAAAGTT
* * *
120136 CAGGGGTCAAAATATGATTTTGGAAAAGTT
1 -TGGGGTCAAAATGTAATTTTGGAAAAGTT
120166 CGAAGACCTT
Statistics
Matches: 128, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
29 15 0.12
30 104 0.81
31 9 0.07
ACGTcount: A:0.37, C:0.04, G:0.27, T:0.32
Consensus pattern (29 bp):
TGGGGTCAAAATGTAATTTTGGAAAAGTT
Found at i:121831 original size:18 final size:18
Alignment explanation
Indices: 121804--121847 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
121794 TAATTGGACA
*
121804 TTAAAATAAATT-TAAAAT
1 TTAAATTAAATTCT-AAAT
121822 TTAAATTAAATTCTAAAT
1 TTAAATTAAATTCTAAAT
121840 TCTAAATT
1 T-TAAATT
121848 TATTTTTGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (18 bp):
TTAAATTAAATTCTAAAT
Found at i:122044 original size:11 final size:12
Alignment explanation
Indices: 122029--122061 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
122019 TTATATAAAA
122029 ATTAAAAAAATT
1 ATTAAAAAAATT
122041 -TTAAAAAAATT
1 ATTAAAAAAATT
122052 AATTAAAAAA
1 -ATTAAAAAA
122062 CAAATAACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 11 0.58
13 8 0.42
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
ATTAAAAAAATT
Found at i:123692 original size:18 final size:17
Alignment explanation
Indices: 123650--123692 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
123640 TTTATACTAA
123650 TATTTCTCTTAAAAAATT
1 TATTT-TCTTAAAAAATT
*
123668 AATTTTTCTTAAAAAATGT
1 TA-TTTTCTTAAAAAAT-T
123687 TATTTT
1 TATTTT
123693 TAAAATTCCG
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.53
Consensus pattern (17 bp):
TATTTTCTTAAAAAATT
Found at i:129107 original size:28 final size:28
Alignment explanation
Indices: 129067--129123 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
129057 CCTTAACATG
129067 TCACCATTTATCTTAATTTGACCCGTTA
1 TCACCATTTATCTTAATTTGACCCGTTA
129095 TCACCATTTATCTTAATTTGACCCGTTA
1 TCACCATTTATCTTAATTTGACCCGTTA
129123 T
1 T
129124 TAAGCTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.25, C:0.25, G:0.07, T:0.44
Consensus pattern (28 bp):
TCACCATTTATCTTAATTTGACCCGTTA
Found at i:137190 original size:2 final size:2
Alignment explanation
Indices: 137183--137219 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
137173 ACCACACCAA
137183 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
137220 ATTAAATCGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:139360 original size:14 final size:15
Alignment explanation
Indices: 139343--139375 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
139333 ACACAAAAAA
139343 AAAAAATAA-CAAAT
1 AAAAAATAAGCAAAT
*
139357 AAAAACTAAGCAAAT
1 AAAAAATAAGCAAAT
139372 AAAA
1 AAAA
139376 GACAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.76, C:0.09, G:0.03, T:0.12
Consensus pattern (15 bp):
AAAAAATAAGCAAAT
Found at i:141231 original size:14 final size:13
Alignment explanation
Indices: 141197--141231 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
141187 ACGATTTCCC
141197 TTTTGAAACCATT
1 TTTTGAAACCATT
*
141210 TGTTGAAACCATTT
1 TTTTGAAACCA-TT
141224 TTTTGAAA
1 TTTTGAAA
141232 AAAATCCTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.46
Consensus pattern (13 bp):
TTTTGAAACCATT
Found at i:141723 original size:109 final size:110
Alignment explanation
Indices: 141527--141725 Score: 278
Period size: 109 Copynumber: 1.8 Consensus size: 110
141517 AAAATTAAAC
* * *
141527 AGGATGTTCAATTATTTAGGTTCAAAGAAAAAACTATACCCAACACGTTAAGGCATGATTTTTCG
1 AGGATATTCAATTATTTAGATTCAAAGAAAAAACTATACCCAACACGTTAAGGCATAATTTTTCG
* * *
141592 AGTTCCTTAAAATAACCAAACATTGAGCACTTATCGATTTTAAGA
66 AATTCCCTAAAATAACAAAACATTGAGCACTTATCGATTTTAAGA
* * *
141637 AGGATATTCAATTATTTAGATTCAAAG-AAAAATTGTACCCAGCACGTT-AGGACATAATTTTTC
1 AGGATATTCAATTATTTAGATTCAAAGAAAAAACTATACCCAACACGTTAAGG-CATAATTTTTC
141700 GAATTCCCTAAAATAA-AATAACATTG
65 GAATTCCCTAAAATAACAA-AACATTG
141726 CCTTTATTTT
Statistics
Matches: 78, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
108 4 0.05
109 49 0.63
110 25 0.32
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.31
Consensus pattern (110 bp):
AGGATATTCAATTATTTAGATTCAAAGAAAAAACTATACCCAACACGTTAAGGCATAATTTTTCG
AATTCCCTAAAATAACAAAACATTGAGCACTTATCGATTTTAAGA
Found at i:144061 original size:90 final size:91
Alignment explanation
Indices: 143909--144086 Score: 225
Period size: 90 Copynumber: 2.0 Consensus size: 91
143899 TAAATCTACC
* * * * * *
143909 CCTCTTGATTAAGGGGTAAAATATTGGACAGTGACTTTAATCTGCCCCTCTTGACAATGGGTAAA
1 CCTCTTGACTAAGGGGTAAAAGATTGGACAGTGAATTCAATCTACCCCTCTTAACAATGGGTAAA
143974 AGATTGGACGGTGACTTTAATCTTCT
66 AGATTGGACGGTGACTTTAATCTTCT
* * *
144000 CCTCTTGACTAA-GGGTAAAAGATTGGATAGTGAATTCAATCTACCCTTCTTAATTAA-GGGTAA
1 CCTCTTGACTAAGGGGTAAAAGATTGGACAGTGAATTCAATCTACCCCTCTTAA-CAATGGGTAA
* * *
144063 AAGATTGGATGGTGGCTTTGATCT
65 AAGATTGGACGGTGACTTTAATCT
144087 GCCCTCTGGT
Statistics
Matches: 74, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
90 61 0.82
91 13 0.18
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (91 bp):
CCTCTTGACTAAGGGGTAAAAGATTGGACAGTGAATTCAATCTACCCCTCTTAACAATGGGTAAA
AGATTGGACGGTGACTTTAATCTTCT
Found at i:144072 original size:45 final size:46
Alignment explanation
Indices: 143901--144071 Score: 204
Period size: 45 Copynumber: 3.8 Consensus size: 46
143891 TGATAGCTTA
*
143901 AATCTACCCCTCTTGATTAAGGGGTAAAATATTGGACAGTGACTTT
1 AATCTACCCCTCTTGATTAAGGGGTAAAAGATTGGACAGTGACTTT
* * * *
143947 AATCTGCCCCTCTTGA-CAATGGGTAAAAGATTGGACGGTGACTTT
1 AATCTACCCCTCTTGATTAAGGGGTAAAAGATTGGACAGTGACTTT
* * * * * *
143992 AATCTTCTCCTCTTGACTAA-GGGTAAAAGATTGGATAGTGAATTC
1 AATCTACCCCTCTTGATTAAGGGGTAAAAGATTGGACAGTGACTTT
* *
144037 AATCTACCCTTCTTAATTAA-GGGTAAAAGATTGGA
1 AATCTACCCCTCTTGATTAAGGGGTAAAAGATTGGA
144072 TGGTGGCTTT
Statistics
Matches: 107, Mismatches: 17, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
45 90 0.84
46 17 0.16
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (46 bp):
AATCTACCCCTCTTGATTAAGGGGTAAAAGATTGGACAGTGACTTT
Found at i:144186 original size:42 final size:42
Alignment explanation
Indices: 144059--144238 Score: 158
Period size: 39 Copynumber: 4.4 Consensus size: 42
144049 TTAATTAAGG
* *
144059 GTAAAAGATTGGATGGTGGCTTTGATCTGCCCTCTGGTTAGA
1 GTAAGAGATTGGATGGTGGCTTTAATCTGCCCTCTGGTTAGA
* * * * *
144101 GTAAGAGATT-GA--ATGACTTTAATCTGTCCTATGGTTAGG
1 GTAAGAGATTGGATGGTGGCTTTAATCTGCCCTCTGGTTAGA
* * * *
144140 GTAAGAGATTGGATGGTGGCTTCAATCTGCCCTCTAGTCAGC
1 GTAAGAGATTGGATGGTGGCTTTAATCTGCCCTCTGGTTAGA
* * * * *
144182 GTAAGAGATTGGA---TGACTTCAATCTGCCC-CATGGATGGG
1 GTAAGAGATTGGATGGTGGCTTTAATCTGCCCTC-TGGTTAGA
144221 GTAAGAGATTGGATGGTG
1 GTAAGAGATTGGATGGTG
144239 ATGTAACTTC
Statistics
Matches: 110, Mismatches: 21, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
38 1 0.01
39 62 0.56
40 2 0.02
41 2 0.02
42 43 0.39
ACGTcount: A:0.24, C:0.14, G:0.31, T:0.31
Consensus pattern (42 bp):
GTAAGAGATTGGATGGTGGCTTTAATCTGCCCTCTGGTTAGA
Found at i:144191 original size:81 final size:81
Alignment explanation
Indices: 144056--144238 Score: 258
Period size: 81 Copynumber: 2.3 Consensus size: 81
144046 TTCTTAATTA
* ** * * *
144056 AGGGTAAAAGATTGGATGGTGGCTTTGATCTGCCCTCTGGTTAGAGTAAGAGATTGAATGACTTT
1 AGGGTAAGAGATTGGATGGTGGCTTCAATCTGCCCTCTAGTCAGAGTAAGAGATTGAATGACTTC
* * *
144121 AATCTGTCCTATGGTT
66 AATCTGCCCCATGGAT
* *
144137 AGGGTAAGAGATTGGATGGTGGCTTCAATCTGCCCTCTAGTCAGCGTAAGAGATTGGATGACTTC
1 AGGGTAAGAGATTGGATGGTGGCTTCAATCTGCCCTCTAGTCAGAGTAAGAGATTGAATGACTTC
144202 AATCTGCCCCATGGAT
66 AATCTGCCCCATGGAT
*
144218 GGGGTAAGAGATTGGATGGTG
1 AGGGTAAGAGATTGGATGGTG
144239 ATGTAACTTC
Statistics
Matches: 90, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 90 1.00
ACGTcount: A:0.25, C:0.14, G:0.31, T:0.30
Consensus pattern (81 bp):
AGGGTAAGAGATTGGATGGTGGCTTCAATCTGCCCTCTAGTCAGAGTAAGAGATTGAATGACTTC
AATCTGCCCCATGGAT
Done.