Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013771.1 Kokia drynarioides strain JFW-HI SEQ_128799, 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: 58529
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.35
Warning! 11 characters in sequence are not A, C, G, or T
Found at i:565 original size:29 final size:30
Alignment explanation
Indices: 531--929 Score: 315
Period size: 29 Copynumber: 13.5 Consensus size: 30
521 TAAAACAGTA
*
531 ATTTTTAGAGGTTTCGGGGTTAAAAATGAG
1 ATTTTTAGAAGTTTCGGGGTTAAAAATGAG
* * * *
561 ATTTTTGGAAATTT-GGGGGTAAAAAT-AA
1 ATTTTTAGAAGTTTCGGGGTTAAAAATGAG
* * *
589 ATTTTTGGAAGTTTTAGGGTTTAAAAATGAG
1 ATTTTTAGAAG-TTTCGGGGTTAAAAATGAG
**
620 ATTTTTAGAAGTTTTAGGG-TAAAAATG-G
1 ATTTTTAGAAGTTTCGGGGTTAAAAATGAG
* * *
648 AATTTTTAGAAGTTTCAGGG-TCAAAATGGG
1 -ATTTTTAGAAGTTTCGGGGTTAAAAATGAG
* * * *
678 ATTTTTGGAAGTTTCGAGGTCAAAAATGGG
1 ATTTTTAGAAGTTTCGGGGTTAAAAATGAG
*
708 ATTTTTGGAAG-TTCGAGGG-TAAAAAT-AG
1 ATTTTTAGAAGTTTCG-GGGTTAAAAATGAG
* * *
736 AATTTTTAGAAGTTTTGGGGTCAAAAATGGG
1 -ATTTTTAGAAGTTTCGGGGTTAAAAATGAG
*
767 ATTTTTGGAAGTTT-GGGAG-TAAAAATG-G
1 ATTTTTAGAAGTTTCGGG-GTTAAAAATGAG
* ** * *
795 AATTTTTGGAAGTTTTAGGGTTAGAAATGGG
1 -ATTTTTAGAAGTTTCGGGGTTAAAAATGAG
*
826 ATTTTTAGAAG-TTCGGGGGTAAAAATAGAG
1 ATTTTTAGAAGTTTCGGGGTTAAAAAT-GAG
*
856 TTTTTTAGAAGTTT-GGGGTTAAAAAT-ATG
1 ATTTTTAGAAGTTTCGGGGTTAAAAATGA-G
* * * * *
885 ATTTTTGGAAG-ATCGGGGATAAAAATAAA
1 ATTTTTAGAAGTTTCGGGGTTAAAAATGAG
914 ATTTTTAGAAGTTTCG
1 ATTTTTAGAAGTTTCG
930 AGGACCTTCA
Statistics
Matches: 301, Mismatches: 46, Indels: 44
0.77 0.12 0.11
Matches are distributed among these distances:
28 16 0.05
29 153 0.51
30 117 0.39
31 15 0.05
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.36
Consensus pattern (30 bp):
ATTTTTAGAAGTTTCGGGGTTAAAAATGAG
Found at i:823 original size:118 final size:118
Alignment explanation
Indices: 589--927 Score: 391
Period size: 118 Copynumber: 2.9 Consensus size: 118
579 GTAAAAATAA
** * *
589 ATTTTTGGAAGTTTTAGGGTTTAAAAAT-GAGATTTTTAGAAGTTTTAGGGTAAAAATGGAATTT
1 ATTTTTGGAAGTTCGAGGG--TAAAAATAGAGATTTTTAGAAGTTTTGGGGTAAAAATGGGATTT
* * * * *
653 TTAGAAGTTTCAGGGTCAAAATGGGATTTTTGGAAG-TTTCGAGGTCAAAAATGGG
64 TTGGAAGTTT-GGGGTAAAAATGGAATTTTTGGAAGTTTTAGAGGTCAAAAATGGG
708 ATTTTTGGAAGTTCGAGGGTAAAAATAGA-ATTTTTAGAAGTTTTGGGGTCAAAAATGGGATTTT
1 ATTTTTGGAAGTTCGAGGGTAAAAATAGAGATTTTTAGAAGTTTTGGGGT-AAAAATGGGATTTT
* *
772 TGGAAGTTTGGGAGTAAAAATGGAATTTTTGGAAGTTTTAG-GGTTAGAAATGGG
65 TGGAAGTTTGGG-GTAAAAATGGAATTTTTGGAAGTTTTAGAGGTCAAAAATGGG
* * * **
826 ATTTTTAGAAGTTCGGGGGTAAAAATAGAGTTTTTTAGAAG-TTTGGGGTTAAAAATATGATTTT
1 ATTTTTGGAAGTTCGAGGGTAAAAATAGAGATTTTTAGAAGTTTTGGGG-TAAAAATGGGATTTT
* * ** *
890 TGGAAGATCGGGGATAAAAATAAAATTTTTAGAAGTTT
65 TGGAAGTTTGGGG-TAAAAATGGAATTTTTGGAAGTTT
928 CGAGGACCTT
Statistics
Matches: 192, Mismatches: 21, Indels: 15
0.84 0.09 0.07
Matches are distributed among these distances:
117 29 0.15
118 131 0.68
119 32 0.17
ACGTcount: A:0.34, C:0.02, G:0.27, T:0.37
Consensus pattern (118 bp):
ATTTTTGGAAGTTCGAGGGTAAAAATAGAGATTTTTAGAAGTTTTGGGGTAAAAATGGGATTTTT
GGAAGTTTGGGGTAAAAATGGAATTTTTGGAAGTTTTAGAGGTCAAAAATGGG
Found at i:901 original size:59 final size:58
Alignment explanation
Indices: 543--927 Score: 348
Period size: 59 Copynumber: 6.6 Consensus size: 58
533 TTTTAGAGGT
* * * * **
543 TTCGGGGTTAAAAATGAGATTTTTGGAAATTTGGGGGTAAAAAT-AAATTTTTGGAAG
1 TTCGGGGGTAAAAATGAGATTTTTAGAAGTTTGGGGTTAAAAATGGGATTTTTGGAAG
* ** * * *
600 TTTTAGGGTTTAAAAATGAGATTTTTAGAAGTTTTAGGG-TAAAAATGGAATTTTTAGAAG
1 --TTCGGGGGTAAAAATGAGATTTTTAGAAG-TTTGGGGTTAAAAATGGGATTTTTGGAAG
* * * * * *
660 TTTC-AGGGTCAAAATGGGATTTTTGGAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAG
1 -TTCGGGGGTAAAAATGAGATTTTTAGAAGTTT-GGGGTTAAAAATGGGATTTTTGGAAG
* *
719 TTCGAGGGTAAAAAT-AGAATTTTTAGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAG
1 TTCGGGGGTAAAAATGAG-ATTTTTAGAAG-TTTGGGGTTAAAAATGGGATTTTTGGAAG
* * * * * *
778 TTTGGGAGTAAAAATG-GAATTTTTGGAAGTTTTAGGGTTAGAAATGGGATTTTTAGAAG
1 TTCGGGGGTAAAAATGAG-ATTTTTAGAAG-TTTGGGGTTAAAAATGGGATTTTTGGAAG
* **
837 TTCGGGGGTAAAAATAGAGTTTTTTAGAAGTTTGGGGTTAAAAATATGATTTTTGGAAG
1 TTCGGGGGTAAAAAT-GAGATTTTTAGAAGTTTGGGGTTAAAAATGGGATTTTTGGAAG
* * * *
896 ATCGGGGATAAAAATAAAATTTTTAGAAGTTT
1 TTCGGGGGTAAAAATGAGATTTTTAGAAGTTT
928 CGAGGACCTT
Statistics
Matches: 271, Mismatches: 45, Indels: 21
0.80 0.13 0.06
Matches are distributed among these distances:
57 3 0.01
58 39 0.14
59 198 0.73
60 30 0.11
61 1 0.00
ACGTcount: A:0.34, C:0.02, G:0.28, T:0.36
Consensus pattern (58 bp):
TTCGGGGGTAAAAATGAGATTTTTAGAAGTTTGGGGTTAAAAATGGGATTTTTGGAAG
Found at i:2780 original size:6 final size:6
Alignment explanation
Indices: 2771--2826 Score: 82
Period size: 6 Copynumber: 9.8 Consensus size: 6
2761 AATTTTGAAG
*
2771 TTAAAT TTAAAT TTAAAT TTAAAT TT-AAT TTAAAT TTAGA- TT-AAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
2816 TTAAAT TTAAA
1 TTAAAT TTAAA
2827 ATAAATTAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
4 1 0.02
5 9 0.20
6 35 0.78
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (6 bp):
TTAAAT
Found at i:2831 original size:11 final size:11
Alignment explanation
Indices: 2771--2833 Score: 65
Period size: 11 Copynumber: 5.6 Consensus size: 11
2761 AATTTTGAAG
2771 TTAAATTTAAA
1 TTAAATTTAAA
2782 TTTAAATTTAAA
1 -TTAAATTTAAA
*
2794 TTTAATTTAAA
1 TTAAATTTAAA
* *
2805 TTTAGA-TTAAT
1 -TTAAATTTAAA
2816 TTAAATTTAAA
1 TTAAATTTAAA
*
2827 ATAAATT
1 TTAAATT
2834 AAAAAGGGGG
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
10 4 0.10
11 24 0.57
12 14 0.33
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:2835 original size:16 final size:16
Alignment explanation
Indices: 2771--2836 Score: 69
Period size: 16 Copynumber: 3.9 Consensus size: 16
2761 AATTTTGAAG
2771 TTAAATTTAAATTTAAAT
1 TTAAA-TTAAA-TTAAAT
*
2789 TTAAATTTAATTTAAAT
1 TTAAA-TTAAATTAAAT
* *
2806 TTAGATTAATTTAAAT
1 TTAAATTAAATTAAAT
*
2822 TTAAAATAAATTAAA
1 TTAAATTAAATTAAA
2837 AAGGGGGCCC
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
16 23 0.53
17 10 0.23
18 10 0.23
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (16 bp):
TTAAATTAAATTAAAT
Found at i:3679 original size:206 final size:207
Alignment explanation
Indices: 3321--3778 Score: 633
Period size: 206 Copynumber: 2.2 Consensus size: 207
3311 AGGAAGTTGG
* * * * *
3321 GCTTCTCGGTGTCTTATCAGGAAGCTAGGGTTC-GAAGATTTTGCTTGCTTTGAGCGTGGTTTTG
1 GCTTCTCGGTGTCTCATCAGGAAGCTGGGGTTCAG-AGATTTTGCTCGCATTGAGCGTGGTTCTG
* * * * *
3385 ATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGATCGCATCTCTTGTTTCAATCCGCTTCTC
65 ATTTGGTCTTCCTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTATTTCAATCCACTTCTC
*
3450 TGTATCTCATCAGGAGAACGAATTTGG-TTCACTTCTCAGTATCTCATCAGGAAGCTAACCG-TT
130 TGTATCTCACCAGGAGAACGAATTTGGCTT-ACTTCTCAGTATCTCATCAGGAAGCTAACCGTTT
3513 TATTGCTTCGACCT
194 TATTGCTTCGACCT
3527 GCTTCTCGAG-GTCTCATCAGGAAGCTGGGGTTCAGAGATTTTGCTCGCATTGAGCGTGAG-TCT
1 GCTTCTCG-GTGTCTCATCAGGAAGCTGGGGTTCAGAGATTTTGCTCGCATTGAGCGTG-GTTCT
* **
3590 GATTTGGTCTTCCTCTCAGTATCTCATTAGGAAGATGACCGCATCGCTTATTTCAATTTACTTCT
64 GATTTGGTCTTCCTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTATTTCAATCCACTTCT
3655 CTGTATCTCACCAGGA-AGACGAATTTGGCTTACTTCTCAGTATCTCATCAGGAAGCTAACCGTT
129 CTGTATCTCACCAGGAGA-ACGAATTTGGCTTACTTCTCAGTATCTCATCAGGAAGCTAACCGTT
* *
3719 TTATTGCTTTGATCT
193 TTATTGCTTCGACCT
* * * * *
3734 ACTTCTCGGTATCTCATCAAGAAGCTGGGATTCAAAGA-TTTGCTC
1 GCTTCTCGGTGTCTCATCAGGAAGCTGGGGTTCAGAGATTTTGCTC
3779 ATTTTGAGCC
Statistics
Matches: 224, Mismatches: 21, Indels: 14
0.86 0.08 0.05
Matches are distributed among these distances:
205 1 0.00
206 173 0.77
207 50 0.22
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (207 bp):
GCTTCTCGGTGTCTCATCAGGAAGCTGGGGTTCAGAGATTTTGCTCGCATTGAGCGTGGTTCTGA
TTTGGTCTTCCTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTATTTCAATCCACTTCTCT
GTATCTCACCAGGAGAACGAATTTGGCTTACTTCTCAGTATCTCATCAGGAAGCTAACCGTTTTA
TTGCTTCGACCT
Found at i:4344 original size:23 final size:23
Alignment explanation
Indices: 4318--4364 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
4308 AGAATTCTAT
*
4318 TAAAAAAGTATCAAAGG-AAACAA
1 TAAAAAAGGATC-AAGGAAAACAA
*
4341 TAAAAGAGGATCAAGGAAAACAA
1 TAAAAAAGGATCAAGGAAAACAA
4364 T
1 T
4365 TACTAGTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.62, C:0.09, G:0.17, T:0.13
Consensus pattern (23 bp):
TAAAAAAGGATCAAGGAAAACAA
Found at i:14315 original size:97 final size:96
Alignment explanation
Indices: 14130--14322 Score: 223
Period size: 97 Copynumber: 2.0 Consensus size: 96
14120 TTTTTGGGAA
* ** *
14130 AAGGATATTTGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
*
14195 GAATCGAATATAAGGAAACATTGCCTCGATT
66 GAATCGAATATAAAGAAACATTGCCTCGATT
* * * *
14226 AAGGGTATTCGATTATTTCGATTTGAGGAAAAAATTGCACCTAGTAAGTTAAGTCACAA-ATTTT
1 AAGGATATTCGATTATCTCGATTTGAAG-AAAAATTGCACCTAGTAAGTTAAGGCACAATA-TTT
*
14290 C-GAAACTCGAA-ATAAA-AGAATATTGCCTCGATT
64 CAG-AA-TCGAATATAAAGA-AACATTGCCTCGATT
14323 TTAAAGTTTT
Statistics
Matches: 82, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
96 27 0.33
97 50 0.61
98 5 0.06
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
GAATCGAATATAAAGAAACATTGCCTCGATT
Found at i:14585 original size:29 final size:28
Alignment explanation
Indices: 14553--15077 Score: 348
Period size: 29 Copynumber: 18.0 Consensus size: 28
14543 GGATACCCAA
* *
14553 GGGTAAAATAGTAATTTTTGGAGGTTTCG
1 GGGTAAAA-AGGAATTTTTGGAAGTTTCG
*
14582 GGGTCAAAAATGGAATTTTTGGAAGTTTAG
1 GGGT-AAAAA-GGAATTTTTGGAAGTTTCG
**
14612 GACTAAAAATGGAATTTTTGGAAGTTTCG
1 GGGTAAAAA-GGAATTTTTGGAAGTTTCG
* *
14641 AGGTTAAAAATGAGATTTTTGGAAG-TTCGG
1 -GGGTAAAAAGGA-ATTTTTGGAAGTTTC-G
** *
14671 GGGTAAAATTGAATTTTTGGAAGTTTTG
1 GGGTAAAAAGGAATTTTTGGAAGTTTCG
* * *
14699 GGGTTAAAAATGGGATTTTTAGAAG-TTCAT
1 GGG-TAAAAA-GGAATTTTTGGAAGTTTC-G
* * *
14729 GGATAAAAATGAAATTTTTAGAAGTTTCG
1 GGGTAAAAA-GGAATTTTTGGAAGTTTCG
* *
14758 AGGTCAAAAATGGGATTTTTGGAAG-TTCG
1 GGGT-AAAAA-GGAATTTTTGGAAGTTTCG
* *
14787 GGGTAAAAATGGAATTTTTAGAAGTTTTG
1 GGGTAAAAA-GGAATTTTTGGAAGTTTCG
* * * *
14816 GGTTCAAAATGGGATTTTTTGAAGTTTCG
1 GGGT-AAAAAGGAATTTTTGGAAGTTTCG
* *
14845 AGGTTAAAAATAGG-ATTTTTGGAAGTTTAG
1 -GGGT-AAAA-AGGAATTTTTGGAAGTTTCG
*
14875 GGGTAAAAATGGAA-TTTTAGAAGTTTCG
1 GGGTAAAAA-GGAATTTTTGGAAGTTTCG
* * *
14903 AGGTCAAAATGGGATTTTTGGAAG-TTCGG
1 GGGT-AAAAAGGAATTTTTGGAAGTTTC-G
*
14932 GGGTGAAAATGGAATTTTTGGAAGTTTCG
1 GGGT-AAAAAGGAATTTTTGGAAGTTTCG
* * * * **
14961 GTGTTGAAATGAAATTTTTAAAAG-TTCAG
1 G-GGTAAAAAGGAATTTTTGGAAGTTTC-G
* *
14990 GGGTAAAAATGGAGTTTTTTTGAAGTTTCG
1 GGGTAAAAA-GGA-ATTTTTGGAAGTTTCG
*
15020 GGGTTAAAAATGGGATTTTTGGAAG-TTCG
1 GGG-TAAAAA-GGAATTTTTGGAAGTTTCG
*
15049 TGGGTAAAAACGGAA-TTTTAGAAGTTTCG
1 -GGGTAAAAA-GGAATTTTTGGAAGTTTCG
15078 AGAACTTCCT
Statistics
Matches: 399, Mismatches: 68, Indels: 58
0.76 0.13 0.11
Matches are distributed among these distances:
27 1 0.00
28 76 0.19
29 179 0.45
30 129 0.32
31 14 0.04
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.36
Consensus pattern (28 bp):
GGGTAAAAAGGAATTTTTGGAAGTTTCG
Found at i:14704 original size:58 final size:59
Alignment explanation
Indices: 14565--15077 Score: 437
Period size: 58 Copynumber: 8.8 Consensus size: 59
14555 GTAAAATAGT
* * * **
14565 AATTTTTGGAGGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTT-AGGACTAAAAATGG
1 AATTTTTGGAAGTTTCGGGGTTAAAAATGG-ATTTTTGGAAGTTTCGGGGGTAAAAATGG
* *
14624 AATTTTTGGAAGTTTCGAGGTTAAAAATGAGATTTTTGGAAG-TTCGGGGGT-AAAATTG
1 AATTTTTGGAAGTTTCGGGGTTAAAAATG-GATTTTTGGAAGTTTCGGGGGTAAAAATGG
* * ** * *
14682 AATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTAGAAG-TTCATGGATAAAAATGA
1 AATTTTTGGAAGTTTCGGGGTTAAAAAT-GGATTTTTGGAAGTTTCGGGGGTAAAAATGG
* * *
14741 AATTTTTAGAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAG-TTC-GGGGTAAAAATGG
1 AATTTTTGGAAGTTTCGGGGTTAAAAAT-GGATTTTTGGAAGTTTCGGGGGTAAAAATGG
* * * * * *
14799 AATTTTTAGAAGTTT-TGGGTTCAAAATGGGATTTTTTGAAGTTTCGAGGTTAAAAATAGG
1 AATTTTTGGAAGTTTCGGGGTTAAAAAT-GGATTTTTGGAAGTTTCGGGGGTAAAAAT-GG
* * * * *
14859 -ATTTTTGGAAGTTTAGGGG-TAAAAATGGAATTTTAGAAGTTTC-GAGGTCAAAATGG
1 AATTTTTGGAAGTTTCGGGGTTAAAAATGGATTTTTGGAAGTTTCGGGGGTAAAAATGG
* * * * ** *
14915 GATTTTTGGAAG-TTCGGGGGTGAAAATGGAATTTTTGGAAGTTTC-GGTGTTGAAATGA
1 AATTTTTGGAAGTTTCGGGGTTAAAAATGG-ATTTTTGGAAGTTTCGGGGGTAAAAATGG
** * *
14973 AATTTTTAAAAG-TTCAGGGG-TAAAAATGGAGTTTTTTTGAAGTTTCGGGGTTAAAAATGG
1 AATTTTTGGAAGTTTC-GGGGTTAAAAATGGA--TTTTTGGAAGTTTCGGGGGTAAAAATGG
* * * *
15033 GATTTTTGGAAG-TTCGTGGG-TAAAAACGGAATTTTAGAAGTTTCG
1 AATTTTTGGAAGTTTCG-GGGTTAAAAATGGATTTTTGGAAGTTTCG
15078 AGAACTTCCT
Statistics
Matches: 374, Mismatches: 64, Indels: 33
0.79 0.14 0.07
Matches are distributed among these distances:
56 8 0.02
57 48 0.13
58 148 0.40
59 132 0.35
60 38 0.10
ACGTcount: A:0.32, C:0.04, G:0.28, T:0.36
Consensus pattern (59 bp):
AATTTTTGGAAGTTTCGGGGTTAAAAATGGATTTTTGGAAGTTTCGGGGGTAAAAATGG
Found at i:14738 original size:87 final size:87
Alignment explanation
Indices: 14566--15074 Score: 509
Period size: 87 Copynumber: 5.8 Consensus size: 87
14556 TAAAATAGTA
* * **
14566 ATTTTTGGAGGTTTC-GGGGTCAAAAATGGAATTTTTGGAAGTTTAGGACTAAAAATGGAATTTT
1 ATTTTTGGAAGTTTCGGGGGT-AAAAATGGAATTTTTGGAAGTTTCGGGGTAAAAATGGAATTTT
*
14630 TGGAAGTTTCGAGGTTAAAAATGAG
65 TAGAAG-TTC-AGGTTAAAAATGAG
* * *
14655 ATTTTTGGAAG-TTCGGGGGT-AAAATTGAATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTT
1 ATTTTTGGAAGTTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTCGGGG-TAAAAATGGAATTTT
* *
14718 TAGAAGTTCATGGATAAAAATGAA
65 TAGAAGTTCA-GGTTAAAAATGAG
* * *
14742 ATTTTTAGAAGTTTC-GAGGTCAAAAATGGGATTTTTGGAAG-TTCGGGGTAAAAATGGAATTTT
1 ATTTTTGGAAGTTTCGGGGGT-AAAAATGGAATTTTTGGAAGTTTCGGGGTAAAAATGGAATTTT
** * *
14805 TAGAAGTTTTGGGTTCAAAATGGG
65 TAGAAG-TTCAGGTTAAAAATGAG
* * * *
14829 ATTTTTTGAAGTTTCGAGGTTAAAAATAGG-ATTTTTGGAAGTTTAGGGGTAAAAATGGAA-TTT
1 ATTTTTGGAAGTTTCGGGGGTAAAAAT-GGAATTTTTGGAAGTTTCGGGGTAAAAATGGAATTTT
* *
14892 TAGAAGTTTCGAGG-TCAAAATGGG
65 TAGAAG-TTC-AGGTTAAAAATGAG
* * ** *
14916 ATTTTTGGAAG-TTCGGGGGTGAAAATGGAATTTTTGGAAGTTTCGGTGTTGAAATGAAATTTTT
1 ATTTTTGGAAGTTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTAAAAATGGAATTTTT
* *
14980 AAAAGTTCAGGGGTAAAAATGGAG
66 AGAAGTTCA-GGTTAAAAAT-GAG
* * * * *
15004 TTTTTTTGAAGTTTCGGGGTTAAAAATGGGATTTTTGGAAG-TTCGTGGGTAAAAACGGAA-TTT
1 ATTTTTGGAAGTTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTCG-GGGTAAAAATGGAATTTT
15067 TAGAAGTT
65 TAGAAGTT
15075 TCGAGAACTT
Statistics
Matches: 351, Mismatches: 51, Indels: 37
0.80 0.12 0.08
Matches are distributed among these distances:
85 3 0.01
86 43 0.12
87 157 0.45
88 81 0.23
89 67 0.19
ACGTcount: A:0.32, C:0.04, G:0.28, T:0.36
Consensus pattern (87 bp):
ATTTTTGGAAGTTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTAAAAATGGAATTTTT
AGAAGTTCAGGTTAAAAATGAG
Found at i:14745 original size:117 final size:115
Alignment explanation
Indices: 14565--15067 Score: 468
Period size: 117 Copynumber: 4.3 Consensus size: 115
14555 GTAAAATAGT
* * * *
14565 AATTTTTGGAGGTTTCGGGGTCAAAAATGGAATTTTTGGAAGTTTAGGACTAAAAATGGAATTTT
1 AATTTTTGGAAGTTTCGGGGTTAAAAATGGAATTTTTGGAAGTTCAGGA-TAAAAATGAAATTTT
*
14630 TGGAAGTTTCGAGGTTAAAAATGAGATTTTTGGAAGTTCGGGGGT-AAAATTG
65 TGGAAGTTTCGAGGTTAAAAATG-GATTTTTGGAAGTTC-GGGGTAAAAATGG
* * *
14682 AATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTAGAAGTTCATGGATAAAAATGAAATTTT
1 AATTTTTGGAAGTTTCGGGGTTAAAAATGGAATTTTTGGAAGTTCA-GGATAAAAATGAAATTTT
* *
14747 TAGAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGTAAAAATGG
65 TGGAAGTTTCGAGGTTAAAAAT-GGATTTTTGGAAGTTCGGGGTAAAAATGG
* * * * * * *
14799 AATTTTTAGAAGTTT-TGGGTTCAAAATGGGATTTTTTGAAGTTTCGAGGTTAAAAAT-AGGATT
1 AATTTTTGGAAGTTTCGGGGTTAAAAATGGAATTTTTGGAAG-TTC-AGGATAAAAATGA-AATT
* * * * * *
14862 TTTGGAAGTTTAG-GGGTAAAAATGGAATTTTAGAAGTTTCGAGGTCAAAATGG
63 TTTGGAAGTTTCGAGGTTAAAAATGGATTTTTGGAAG-TTCGGGGTAAAAATGG
* * * * **
14915 GATTTTTGGAAG-TTCGGGGGTGAAAATGGAATTTTTGGAAGTTTC-GGTGTTGAAATGAAATTT
1 AATTTTTGGAAGTTTCGGGGTTAAAAATGGAATTTTTGGAAG-TTCAGG-ATAAAAATGAAATTT
** * *
14978 TTAAAAG-TTC-AGGGGTAAAAATGGAGTTTTTTTGAAGTTTCGGGGTTAAAAATGG
64 TTGGAAGTTTCGA-GGTTAAAAATGGA--TTTTTGGAAG-TTCGGGG-TAAAAATGG
* *
15033 GATTTTTGGAAG-TTCGTGGG-TAAAAACGGAATTTT
1 AATTTTTGGAAGTTTCG-GGGTTAAAAATGGAATTTT
15068 AGAAGTTTCG
Statistics
Matches: 326, Mismatches: 44, Indels: 31
0.81 0.11 0.08
Matches are distributed among these distances:
114 4 0.01
115 40 0.12
116 87 0.27
117 150 0.46
118 42 0.13
119 3 0.01
ACGTcount: A:0.32, C:0.04, G:0.28, T:0.36
Consensus pattern (115 bp):
AATTTTTGGAAGTTTCGGGGTTAAAAATGGAATTTTTGGAAGTTCAGGATAAAAATGAAATTTTT
GGAAGTTTCGAGGTTAAAAATGGATTTTTGGAAGTTCGGGGTAAAAATGG
Found at i:23021 original size:17 final size:16
Alignment explanation
Indices: 22994--23064 Score: 52
Period size: 17 Copynumber: 4.2 Consensus size: 16
22984 TTTTAATTCA
*
22994 ATTTAAGTTTAAATTT
1 ATTTAAATTTAAATTT
**
23010 ATTGTAAATTTAAGCTT
1 ATT-TAAATTTAAATTT
* *
23027 ATTTGGAGTTTAAATTT
1 ATTT-AAATTTAAATTT
* *
23044 ATTTTAAATATATATTT
1 A-TTTAAATTTAAATTT
23061 ATTT
1 ATTT
23065 TGAAATAAAA
Statistics
Matches: 41, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
16 7 0.17
17 31 0.76
18 3 0.07
ACGTcount: A:0.35, C:0.01, G:0.08, T:0.55
Consensus pattern (16 bp):
ATTTAAATTTAAATTT
Found at i:23077 original size:17 final size:17
Alignment explanation
Indices: 23037--23077 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
23027 ATTTGGAGTT
23037 TAAATTTATTTTAAATA
1 TAAATTTATTTTAAATA
*
23054 TATATTTATTTTGAAATA
1 TAAATTTATTTT-AAATA
23072 -AAATTT
1 TAAATTT
23078 TAAAATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (17 bp):
TAAATTTATTTTAAATA
Found at i:23887 original size:25 final size:25
Alignment explanation
Indices: 23840--23887 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
23830 TAAATGTTTT
**
23840 ATTAATAATAATAATTAACAATTTC
1 ATTAATAATAATAAGGAACAATTTC
23865 ATTAATAATAATAAAGGAA-AATT
1 ATTAATAATAAT-AAGGAACAATT
23888 AGTGGTCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.35
Consensus pattern (25 bp):
ATTAATAATAATAAGGAACAATTTC
Found at i:24938 original size:29 final size:29
Alignment explanation
Indices: 24897--25323 Score: 297
Period size: 29 Copynumber: 14.8 Consensus size: 29
24887 GATATCCCTA
*
24897 AACTGTCCGAAAATTACCATTTTACCCTCG
1 AACT-TCCAAAAATTACCATTTTACCCTCG
24927 AACTTCCAAAAATT-CCATTTTTCACCC-CG
1 AACTTCCAAAAATTACCA-TTTT-ACCCTCG
* * *
24956 AAACTTCCAAAAATTACCAATTTACCCCCA
1 -AACTTCCAAAAATTACCATTTTACCCTCG
* *
24986 AACTTCCAAAAATT-TCATTTTTGACCC-CAA
1 AACTTCCAAAAATTACCA-TTTT-ACCCTC-G
*
25016 AACTTCCTAAAATTACCATTTTACCCTCG
1 AACTTCCAAAAATTACCATTTTACCCTCG
* * *
25045 AACTTCCAAAAA-TCCCATTTTTGA-TCTCAA
1 AACTTCCAAAAATTACCA-TTTT-ACCCTC-G
* *
25075 AACTCCCAAAAATTACCATTTTACCCCCG
1 AACTTCCAAAAATTACCATTTTACCCTCG
* *
25104 AACTTCCAAAAA-TCCCATTTTTGACCC-CAA
1 AACTTCCAAAAATTACCA-TTTT-ACCCTC-G
*
25134 AAC-TCCCAAAATTACCATTTTACCCTCG
1 AACTTCCAAAAATTACCATTTTACCCTCG
*
25162 AACTTCC-AAAATTCCCATTTT----T-G
1 AACTTCCAAAAATTACCATTTTACCCTCG
* *
25185 -AC-CCCAAAAATTACCATTTTACCCCCG
1 AACTTCCAAAAATTACCATTTTACCCTCG
* * *
25212 AACTTACAAAAA-TCCCATTTTTGA-CCTCAA
1 AACTTCCAAAAATTACCA-TTTT-ACCCTC-G
* *
25242 AACTCCCAAAAATTACCATTTTACCCCCG
1 AACTTCCAAAAATTACCATTTTACCCTCG
25271 AACTT-CAAAAA-T-CTCATTTTTAACCC-CG
1 AACTTCCAAAAATTAC-CA-TTTT-ACCCTCG
*
25299 ACACTTCTAAAAATTACCATTTTAC
1 A-ACTTCCAAAAATTACCATTTTAC
25324 TCTCAGATGT
Statistics
Matches: 317, Mismatches: 39, Indels: 83
0.72 0.09 0.19
Matches are distributed among these distances:
21 2 0.01
22 15 0.05
23 1 0.00
24 1 0.00
26 1 0.00
27 4 0.01
28 52 0.16
29 119 0.38
30 105 0.33
31 16 0.05
32 1 0.00
ACGTcount: A:0.35, C:0.32, G:0.04, T:0.30
Consensus pattern (29 bp):
AACTTCCAAAAATTACCATTTTACCCTCG
Found at i:24998 original size:59 final size:59
Alignment explanation
Indices: 24896--25323 Score: 522
Period size: 59 Copynumber: 7.4 Consensus size: 59
24886 GGATATCCCT
* * * *
24896 AAACTGTCCGAAAATTACCATTTTACCCTCGAACTTCCAAAAATTCCATTTTTCACCCCG
1 AAACT-TCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCCCA
* * *
24956 AAACTTCCAAAAATTACCAATTTACCCCCAAACTTCCAAAAATTTCATTTTTGACCCCA
1 AAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCCCA
* * * * *
25015 AAACTTCCTAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGATCTCA
1 AAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCCCA
* *
25074 AAACTCCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCA
1 AAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCCCA
* *
25133 AAAC-TCCCAAAATTACCATTTTACCCTCGAACTTCC-AAAATTCCCATTTTTGA---C-
1 AAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATT-CCATTTTTGACCCCA
* * *
25187 ---C--CCAAAAATTACCATTTTACCCCCGAACTTACAAAAATCCCATTTTTGACCTCA
1 AAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCCCA
* * *
25241 AAACTCCCAAAAATTACCATTTTACCCCCGAACTT-CAAAAA-TCTCATTTTTAACCCCG
1 AAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATTC-CATTTTTGACCCCA
* *
25299 ACACTTCTAAAAATTACCATTTTAC
1 AAACTTCCAAAAATTACCATTTTAC
25324 TCTCAGATGT
Statistics
Matches: 321, Mismatches: 35, Indels: 26
0.84 0.09 0.07
Matches are distributed among these distances:
50 38 0.12
51 6 0.02
53 1 0.00
55 1 0.00
57 7 0.02
58 78 0.24
59 185 0.58
60 5 0.02
ACGTcount: A:0.35, C:0.32, G:0.04, T:0.30
Consensus pattern (59 bp):
AAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCCCA
Found at i:25280 original size:108 final size:108
Alignment explanation
Indices: 25079--25297 Score: 368
Period size: 108 Copynumber: 2.0 Consensus size: 108
25069 TCTCAAAACT
*
25079 CCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTCCCAAA
1 CCCAAAAATTACCATTTTACCCCCGAACTTACAAAAATCCCATTTTTGACCCCAAAACTCCCAAA
* * *
25144 ATTACCATTTTACCCTCGAACTTCCAAAATTCCCATTTTTGAC
66 ATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAAC
*
25187 CCCAAAAATTACCATTTTACCCCCGAACTTACAAAAATCCCATTTTTGACCTCAAAACTCCCAAA
1 CCCAAAAATTACCATTTTACCCCCGAACTTACAAAAATCCCATTTTTGACCCCAAAACTCCC-AA
*
25252 AATTACCATTTTACCCCCGAACTT-CAAAAATCTCATTTTTAAC
65 AATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAAC
25295 CCC
1 CCC
25298 GACACTTCTA
Statistics
Matches: 104, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
108 79 0.76
109 25 0.24
ACGTcount: A:0.35, C:0.34, G:0.03, T:0.28
Consensus pattern (108 bp):
CCCAAAAATTACCATTTTACCCCCGAACTTACAAAAATCCCATTTTTGACCCCAAAACTCCCAAA
ATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAAC
Found at i:33820 original size:12 final size:13
Alignment explanation
Indices: 33782--33823 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
33772 ATGATGTTTG
33782 ATAAGTTTTTATTT
1 ATAAGTTTTTA-TT
*
33796 ATAAATTTATTATT
1 ATAAGTTT-TTATT
33810 -TAAGTTTTTATT
1 ATAAGTTTTTATT
33822 AT
1 AT
33824 TGTTGTCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
12 5 0.21
13 7 0.29
14 9 0.38
15 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (13 bp):
ATAAGTTTTTATT
Found at i:35425 original size:25 final size:26
Alignment explanation
Indices: 35397--35450 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
35387 AAATGTGAAC
* * *
35397 AATCATAAATATGTGGAC-AAATTAA
1 AATCACAAAAATGTGAACAAAATTAA
35422 AATCACAAAAATGTGAACTAAAATTAA
1 AATCACAAAAATGTGAAC-AAAATTAA
35449 AA
1 AA
35451 ATAAAATAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 15 0.62
27 9 0.38
ACGTcount: A:0.57, C:0.09, G:0.09, T:0.24
Consensus pattern (26 bp):
AATCACAAAAATGTGAACAAAATTAA
Found at i:36802 original size:150 final size:150
Alignment explanation
Indices: 36619--36918 Score: 582
Period size: 150 Copynumber: 2.0 Consensus size: 150
36609 TATAAAGAAA
*
36619 GGTTGGATTGTATTAGCATGTTACATATTTTATAACTTCAATCATAAATGGAATTGAGATAATCT
1 GGTTGGATTGTACTAGCATGTTACATATTTTATAACTTCAATCATAAATGGAATTGAGATAATCT
36684 ATAATTCGAAGAGTACATGGAAGAAGGGTATCTTGATAATCTTATTGATTCAGATTAAAATTCAG
66 ATAATTCGAAGAGTACATGGAAGAAGGGTATCTTGATAATCTTATTGATTCAGATTAAAATTCAG
36749 ATGATAATAAAAAACCTATG
131 ATGATAATAAAAAACCTATG
*
36769 GGTTGGATTGTACTAGCATGTTACATATTTTATAACTTCAATCATAAATGGAATTGAGATCATCT
1 GGTTGGATTGTACTAGCATGTTACATATTTTATAACTTCAATCATAAATGGAATTGAGATAATCT
36834 ATAATTCGAAGAGTACATGGAAGAAGGGTATCTTGATAATCTTATTGATTCAGATTAAAATTCAG
66 ATAATTCGAAGAGTACATGGAAGAAGGGTATCTTGATAATCTTATTGATTCAGATTAAAATTCAG
36899 ATGATAATAAAAAACCTATG
131 ATGATAATAAAAAACCTATG
36919 TTAAATATTA
Statistics
Matches: 148, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
150 148 1.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.34
Consensus pattern (150 bp):
GGTTGGATTGTACTAGCATGTTACATATTTTATAACTTCAATCATAAATGGAATTGAGATAATCT
ATAATTCGAAGAGTACATGGAAGAAGGGTATCTTGATAATCTTATTGATTCAGATTAAAATTCAG
ATGATAATAAAAAACCTATG
Found at i:46687 original size:60 final size:60
Alignment explanation
Indices: 46604--46732 Score: 183
Period size: 60 Copynumber: 2.1 Consensus size: 60
46594 GTATTTGAAC
*
46604 TTTTTTTTACCCAATTTGATACCTGAACTTGACACTTTTTT-CTAATTTGGTACCTAA-A
1 TTTTTTTTACCCAATTTGATACCTAAACTTGACACTTTTTTCCTAATTTGGTACCTAAGA
* *
46662 TTTTTTTTGGACCCAATTTTG-TACCTAAACTTGACATTTTTTTCCTAATTTGGTACCTAAGC
1 TTTTTTTT--ACCCAA-TTTGATACCTAAACTTGACACTTTTTTCCTAATTTGGTACCTAAGA
46724 TTTTTTTTA
1 TTTTTTTTA
46733 AAACTCAATT
Statistics
Matches: 63, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
58 8 0.13
60 27 0.43
61 20 0.32
62 8 0.13
ACGTcount: A:0.23, C:0.18, G:0.09, T:0.50
Consensus pattern (60 bp):
TTTTTTTTACCCAATTTGATACCTAAACTTGACACTTTTTTCCTAATTTGGTACCTAAGA
Found at i:48525 original size:22 final size:22
Alignment explanation
Indices: 48492--48545 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
48482 GTAGCAAAAT
*
48492 TAATAATA-AAACAAGAGTTATA
1 TAAT-ATACAAACAAAAGTTATA
*
48514 TAATATACAAACAAAATTTATA
1 TAATATACAAACAAAAGTTATA
*
48536 AAATAT-CAAA
1 TAATATACAAA
48546 ATAATGACGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 7 0.25
22 21 0.75
ACGTcount: A:0.61, C:0.07, G:0.04, T:0.28
Consensus pattern (22 bp):
TAATATACAAACAAAAGTTATA
Found at i:51513 original size:18 final size:18
Alignment explanation
Indices: 51490--51524 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
51480 GTTTTAAACA
51490 TCATGAATTTACGAATCG
1 TCATGAATTTACGAATCG
*
51508 TCATGAATTTATGAATC
1 TCATGAATTTACGAATC
51525 AAAATTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.37
Consensus pattern (18 bp):
TCATGAATTTACGAATCG
Found at i:57522 original size:25 final size:26
Alignment explanation
Indices: 57494--57545 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
57484 AAATACTTAA
*
57494 TTATAATT-AAAGTGAAATATATAAT
1 TTATAATTAAAAGTCAAATATATAAT
*
57519 TTATATTTAAAAAGTCAAATATATAAT
1 TTATAATT-AAAAGTCAAATATATAAT
57546 CAATTTTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 7 0.30
27 16 0.70
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (26 bp):
TTATAATTAAAAGTCAAATATATAAT
Found at i:57558 original size:27 final size:27
Alignment explanation
Indices: 57502--57558 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
57492 AATTATAATT
* **
57502 AAAGTGAAATATATAATTTATATTTAA
1 AAAGTCAAATATATAATCAATATTTAA
57529 AAAGTCAAATATATAATCAAT-TTTATA
1 AAAGTCAAATATATAATCAATATTTA-A
57556 AAA
1 AAA
57559 CTTCAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 4 0.15
27 22 0.85
ACGTcount: A:0.54, C:0.04, G:0.05, T:0.37
Consensus pattern (27 bp):
AAAGTCAAATATATAATCAATATTTAA
Done.