Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011858.1 Kokia drynarioides strain JFW-HI SEQ_126855, 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: 158970
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 35 characters in sequence are not A, C, G, or T
Found at i:671 original size:22 final size:23
Alignment explanation
Indices: 646--708 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 23
636 GTATTTAGTT
646 TATAATAAATT-TTAATTTATCA
1 TATAATAAATTATTAATTTATCA
**
668 TATAATAATATTATTTGTTTATCA
1 TATAATAA-ATTATTAATTTATCA
692 TATTAAATAAATATATT
1 TA-T-AATAAAT-TATT
709 TTTATTAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
22 8 0.24
23 3 0.09
24 11 0.32
25 3 0.09
26 9 0.26
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (23 bp):
TATAATAAATTATTAATTTATCA
Found at i:10852 original size:169 final size:169
Alignment explanation
Indices: 10573--10910 Score: 631
Period size: 169 Copynumber: 2.0 Consensus size: 169
10563 CAACTCCTGC
10573 TGCAGTCAGTCAAGCTATTTGGCTGAGAAAACTTTTGAAGGATTTAAATGTGTACCAAGGAGAAG
1 TGCAGTCAGTCAAGCTATTTGGCTGAGAAAACTTTTGAAGGATTTAAATGTGTACCAAGGAGAAG
* *
10638 TAACAGAGATCAAATGTGATAACCAATCTGCTGTTGCAATTCCAAAGAATCCAGTGTTTCATGAC
66 CAACAGAGATCAAATGTGATAACCAATCTGCTATTGCAATTCCAAAGAATCCAGTGTTTCATGAC
10703 AAAACCAAACATGTTAAGATTAAATTTCACTTTGTAAGG
131 AAAACCAAACATGTTAAGATTAAATTTCACTTTGTAAGG
*
10742 TGCAGTCAGTCAAGCTATTTGGCTGAGAAAATTTTTGAAGGATTTAAATGTGTACCAAGGAGAAG
1 TGCAGTCAGTCAAGCTATTTGGCTGAGAAAACTTTTGAAGGATTTAAATGTGTACCAAGGAGAAG
10807 CAACAGAGATCAAATGTGATAACCAATCTGCTATTGCAATTCCAAAGAATCCAGTGTTTCATGAC
66 CAACAGAGATCAAATGTGATAACCAATCTGCTATTGCAATTCCAAAGAATCCAGTGTTTCATGAC
* *
10872 CAAACCAAACATTTTAAGATTAAATTTCACTTTGTAAGG
131 AAAACCAAACATGTTAAGATTAAATTTCACTTTGTAAGG
10911 GAGGCTGAGC
Statistics
Matches: 164, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
169 164 1.00
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.29
Consensus pattern (169 bp):
TGCAGTCAGTCAAGCTATTTGGCTGAGAAAACTTTTGAAGGATTTAAATGTGTACCAAGGAGAAG
CAACAGAGATCAAATGTGATAACCAATCTGCTATTGCAATTCCAAAGAATCCAGTGTTTCATGAC
AAAACCAAACATGTTAAGATTAAATTTCACTTTGTAAGG
Found at i:20098 original size:31 final size:30
Alignment explanation
Indices: 20057--20114 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
20047 TATATAATTG
20057 CATTAAATCAA-ATTTCATATATTAAATTACA
1 CATTAAATCAAGA-TTCATATA-TAAATTACA
* *
20088 CATTAGATCAAGATTCATGTATAAATT
1 CATTAAATCAAGATTCATATATAAATT
20115 TAAATTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 6 0.25
31 17 0.71
32 1 0.04
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (30 bp):
CATTAAATCAAGATTCATATATAAATTACA
Found at i:20623 original size:23 final size:23
Alignment explanation
Indices: 20564--20620 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
20554 TTAATATTTG
20564 TATTTTTATTTTTAAGAATTTAT
1 TATTTTTATTTTTAAGAATTTAT
*
20587 TATTTTTATTTTTAGGAATTTA-
1 TATTTTTATTTTTAAGAATTTAT
*
20609 -GTTTTTATTTTT
1 TATTTTTATTTTT
20621 TTAAATTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 11 0.34
23 21 0.66
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (23 bp):
TATTTTTATTTTTAAGAATTTAT
Found at i:24868 original size:25 final size:25
Alignment explanation
Indices: 24840--24890 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
24830 CCATGAACCC
24840 ATTCGACTCTACTCGAAGTAGGAAG
1 ATTCGACTCTACTCGAAGTAGGAAG
24865 ATTCGACTCTACTCGAAGTAGGAAG
1 ATTCGACTCTACTCGAAGTAGGAAG
24890 A
1 A
24891 CATAACACAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.24
Consensus pattern (25 bp):
ATTCGACTCTACTCGAAGTAGGAAG
Found at i:25857 original size:21 final size:20
Alignment explanation
Indices: 25815--25890 Score: 68
Period size: 19 Copynumber: 3.9 Consensus size: 20
25805 ACAATAAAAG
* *
25815 TTATAAAATTAT--TAAATT
1 TTATAAAATTATAAAAAATA
25833 TTAATAAAATTATAAAAAATA
1 TT-ATAAAATTATAAAAAATA
* *
25854 TTA-AAAATTAGAAAAAAAA
1 TTATAAAATTATAAAAAATA
*
25873 TTATAAAAATCATAAAAA
1 TTAT-AAAATTATAAAAA
25891 TATAAAAAGT
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
18 2 0.04
19 27 0.57
20 1 0.02
21 17 0.36
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (20 bp):
TTATAAAATTATAAAAAATA
Found at i:25860 original size:19 final size:19
Alignment explanation
Indices: 25838--25898 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
25828 AAATTTTAAT
25838 AAAATTATAAAAAATATTA
1 AAAATTATAAAAAATATTA
* *
25857 AAAATTAGAAAAAAAATTATA
1 AAAATTATAAAAAATA-T-TA
*
25878 AAAATCAT-AAAAATA-TA
1 AAAATTATAAAAAATATTA
25895 AAAA
1 AAAA
25899 GTTTGTAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
17 6 0.17
19 14 0.40
20 7 0.20
21 8 0.23
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.25
Consensus pattern (19 bp):
AAAATTATAAAAAATATTA
Found at i:25880 original size:9 final size:9
Alignment explanation
Indices: 25794--25939 Score: 68
Period size: 9 Copynumber: 15.7 Consensus size: 9
25784 ACATGTGGCA
25794 AAAAATTAT
1 AAAAATTAT
*
25803 AAACA--AT
1 AAAAATTAT
*
25810 AAAAGTTAT
1 AAAAATTAT
25819 -AAAATTAT
1 AAAAATTAT
* *
25827 -TAAATTTT
1 AAAAATTAT
25835 AATAAAATTAT
1 -A-AAAATTAT
*
25846 AAAAAATATT
1 AAAAATTA-T
*
25856 AAAAATTAGAAA
1 AAAAATT---AT
25868 AAAAATTAT
1 AAAAATTAT
*
25877 AAAAATCAT
1 AAAAATTAT
25886 AAAAA-TAT
1 AAAAATTAT
*
25894 AAAAAGTTTGT
1 AAAAA--TTAT
*
25905 AAAATTTTAT
1 AAAA-ATTAT
*
25915 AAAAATCAT
1 AAAAATTAT
*
25924 AAAAATGCAT
1 AAAAAT-TAT
25934 AAAAAT
1 AAAAAT
25940 GGGCTTTAAC
Statistics
Matches: 104, Mismatches: 19, Indels: 27
0.69 0.13 0.18
Matches are distributed among these distances:
7 5 0.05
8 20 0.19
9 35 0.34
10 24 0.23
11 12 0.12
12 7 0.07
13 1 0.01
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:26130 original size:18 final size:18
Alignment explanation
Indices: 26105--26280 Score: 73
Period size: 19 Copynumber: 9.7 Consensus size: 18
26095 CTTTTGGTAC
26105 TATAATTTTTAT-ATTTT
1 TATAATTTTTATAATTTT
26122 TATACATTTTTATAATTTT
1 TATA-ATTTTTATAATTTT
*
26141 CT-TACGA-TTTTATAAAGTTT
1 -TATA--ATTTTTAT-AATTTT
* * *
26161 AATAAAATTTTACAA-TTT
1 TAT-AATTTTTATAATTTT
*
26179 TAT-A-TTTTATTATTTT
1 TATAATTTTTATAATTTT
* **
26195 TATAAAATTTTATGTTTTT
1 TAT-AATTTTTATAATTTT
* *
26214 TTTAATTTTATACAATTTT
1 TATAATTTT-TATAATTTT
*
26233 TATAATTTGTTTCTAATTTGT
1 TATAA-TT-TTTATAATTT-T
* *
26254 TATAA-ATTTA-ATTTTT
1 TATAATTTTTATAATTTT
26270 TAT-ATTTTTAT
1 TATAATTTTTAT
26281 TAAAAAATAT
Statistics
Matches: 120, Mismatches: 21, Indels: 36
0.68 0.12 0.20
Matches are distributed among these distances:
15 7 0.06
16 15 0.12
17 8 0.07
18 22 0.18
19 38 0.32
20 21 0.17
21 9 0.08
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (18 bp):
TATAATTTTTATAATTTT
Found at i:26132 original size:10 final size:9
Alignment explanation
Indices: 26105--26280 Score: 73
Period size: 10 Copynumber: 19.3 Consensus size: 9
26095 CTTTTGGTAC
26105 TATAATTTT
1 TATAATTTT
26114 TAT-ATTTT
1 TATAATTTT
26122 TATACATTTT
1 TATA-ATTTT
26132 TATAATTTT
1 TATAATTTT
26141 CT-TACGA-TTT
1 -TATA--ATTTT
*
26151 TATAAAGTTT
1 TAT-AATTTT
* *
26161 AATAAAATTT
1 TAT-AATTTT
*
26171 TACAA-TTT
1 TATAATTTT
26179 TAT-A-TTT
1 TATAATTTT
*
26186 TATTATTTT
1 TATAATTTT
*
26195 TATAAAATTT
1 TAT-AATTTT
**
26205 TATGTTTTT
1 TATAATTTT
*
26214 TTTAATTTT
1 TATAATTTT
*
26223 ATACAATTTT
1 -TATAATTTT
26233 TATAATTTGTT
1 TATAA-TT-TT
*
26244 TCTAATTTGT
1 TATAATTT-T
*
26254 TATAA-ATT
1 TATAATTTT
*
26262 TA-ATTTTT
1 TATAATTTT
26270 TAT-ATTTT
1 TATAATTTT
26278 TAT
1 TAT
26281 TAAAAAATAT
Statistics
Matches: 128, Mismatches: 22, Indels: 35
0.69 0.12 0.19
Matches are distributed among these distances:
7 8 0.06
8 28 0.22
9 35 0.27
10 49 0.38
11 8 0.06
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (9 bp):
TATAATTTT
Found at i:26222 original size:27 final size:26
Alignment explanation
Indices: 26174--26232 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
26164 AAAATTTTAC
*
26174 AATTTTATATTTTATTATTTTTATAA
1 AATTTTATATTTTATTAATTTTATAA
* * *
26200 AATTTTATGTTTTTTTTAATTTTATAC
1 AATTTTAT-ATTTTATTAATTTTATAA
26227 AATTTT
1 AATTTT
26233 TATAATTTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.29
27 20 0.71
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (26 bp):
AATTTTATATTTTATTAATTTTATAA
Found at i:31635 original size:21 final size:19
Alignment explanation
Indices: 31597--31635 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
31587 TGTAAATGTA
*
31597 ATTTTATTTATTAAATATT
1 ATTTTATTTATGAAATATT
31616 ATTTCTATTTAATGAAATAT
1 ATTT-TATTT-ATGAAATAT
31636 AATTATTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 5 0.29
21 8 0.47
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (19 bp):
ATTTTATTTATGAAATATT
Found at i:34683 original size:61 final size:60
Alignment explanation
Indices: 34605--34726 Score: 165
Period size: 61 Copynumber: 2.0 Consensus size: 60
34595 CCTAAATCTA
** *
34605 AAAAGATCAACAAATTTAACCCTCAATGTTTACAAAAGTTTATCATTTTAGTTCA-AATTCT
1 AAAAGATCAACAAATTTAACCCTCAACATTTACAAAA-TTTATCAATTTAGTT-ATAATTCT
* * *
34666 AAAAGTTCAATAAATTTAACCCTCAACATTTACAAAATTTGTCAATTTAGTTATAATTCT
1 AAAAGATCAACAAATTTAACCCTCAACATTTACAAAATTTATCAATTTAGTTATAATTCT
34726 A
1 A
34727 TTTTTCTTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
59 1 0.02
60 20 0.37
61 33 0.61
ACGTcount: A:0.42, C:0.16, G:0.06, T:0.37
Consensus pattern (60 bp):
AAAAGATCAACAAATTTAACCCTCAACATTTACAAAATTTATCAATTTAGTTATAATTCT
Found at i:37563 original size:219 final size:219
Alignment explanation
Indices: 37184--37626 Score: 841
Period size: 219 Copynumber: 2.0 Consensus size: 219
37174 TTTAATATAT
37184 ATATGATTAATCATGATGAAAATGAGATGTTTAATTATAAGTATGATAATTATGTGTGATTAAAT
1 ATATGATTAATCATGATGAAAATGAGATGTTTAATTATAAGTATGATAATTATGTGTGATTAAAT
*
37249 GAAATTTAGTGTAAACAGACATGAAAAAGGAAGCATGTCCATTAAAACAGTTTGGACAGAACAGA
66 GAAATTTAGTGTAAACAGACAAGAAAAAGGAAGCATGTCCATTAAAACAGTTTGGACAGAACAGA
*
37314 AGACTAACTTCGAAAATTCACTAAAAATTGTATAAAAAGAGTTAAGAGTTGAATTAAATATGTAA
131 AGACTAACTTCGAAAATTCACCAAAAATTGTATAAAAAGAGTTAAGAGTTGAATTAAATATGTAA
*
37379 TTAAATTTTATTGAATTTAGTTTC
196 TTAAATATTATTGAATTTAGTTTC
37403 ATATGATTAATCATGATGAAAATGAGATGTTTAATTATAAGTATGATAATTATGTGTGATTAAAT
1 ATATGATTAATCATGATGAAAATGAGATGTTTAATTATAAGTATGATAATTATGTGTGATTAAAT
*
37468 GAAATTTAGTGTAAAGAGACAAGAAAAAGGAAGCATGTCCATTAAAACAGTTTGGACAGAACAGA
66 GAAATTTAGTGTAAACAGACAAGAAAAAGGAAGCATGTCCATTAAAACAGTTTGGACAGAACAGA
*
37533 AGACTAACTTCGAAAATTCACCAAAAATTGTATAAAAAGAGTTAAGAGTTGAATTAATTATGTAA
131 AGACTAACTTCGAAAATTCACCAAAAATTGTATAAAAAGAGTTAAGAGTTGAATTAAATATGTAA
37598 TTAAATATTATTGAATTTAGTTTC
196 TTAAATATTATTGAATTTAGTTTC
37622 ATATG
1 ATATG
37627 GAAGAAACAG
Statistics
Matches: 219, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
219 219 1.00
ACGTcount: A:0.44, C:0.07, G:0.17, T:0.33
Consensus pattern (219 bp):
ATATGATTAATCATGATGAAAATGAGATGTTTAATTATAAGTATGATAATTATGTGTGATTAAAT
GAAATTTAGTGTAAACAGACAAGAAAAAGGAAGCATGTCCATTAAAACAGTTTGGACAGAACAGA
AGACTAACTTCGAAAATTCACCAAAAATTGTATAAAAAGAGTTAAGAGTTGAATTAAATATGTAA
TTAAATATTATTGAATTTAGTTTC
Found at i:38179 original size:6 final size:6
Alignment explanation
Indices: 38168--38206 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
38158 TGATCAAAAT
* * *
38168 TGAAAG TGAAAG TGAAAA TGAAAT TGAAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
38207 TATGAATTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.51, C:0.00, G:0.26, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:38195 original size:18 final size:19
Alignment explanation
Indices: 38163--38202 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
38153 ATTTGTGATC
38163 AAAATTGAAAGTGAAAGTG
1 AAAATTGAAAGTGAAAGTG
* *
38182 AAAA-TGAAATTGAAATTG
1 AAAATTGAAAGTGAAAGTG
38200 AAA
1 AAA
38203 GTGATATGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (19 bp):
AAAATTGAAAGTGAAAGTG
Found at i:38402 original size:37 final size:38
Alignment explanation
Indices: 38305--38411 Score: 108
Period size: 37 Copynumber: 2.8 Consensus size: 38
38295 CTTCGACCTT
* *
38305 GAGTCGATAAGACACTGGGTATCATTATTTTACTTCGGATA
1 GAGTCGATGAGACACTGGGTATC---ACTTTACTTCGGATA
* ** * *
38346 GATTCGATGAGGTATTGGGTATCACTTTACTTCGGCTA
1 GAGTCGATGAGACACTGGGTATCACTTTACTTCGGATA
*
38384 G-GTCGATGAGACACTGGGTGTCACTTTA
1 GAGTCGATGAGACACTGGGTATCACTTTA
38412 TTGCTTCGAA
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
37 22 0.41
38 14 0.26
41 18 0.33
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (38 bp):
GAGTCGATGAGACACTGGGTATCACTTTACTTCGGATA
Found at i:39746 original size:25 final size:24
Alignment explanation
Indices: 39715--39769 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 24
39705 TTATATTAAG
*
39715 TTATTTGTTTTGTTTAATTTAA-TTT
1 TTATTTGATTTG-TT-ATTTAATTTT
39740 TTATTTGATTTGTTATTTAATTTT
1 TTATTTGATTTGTTATTTAATTTT
39764 TTATTT
1 TTATTT
39770 AGTAGAGTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 6 0.21
24 11 0.39
25 11 0.39
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (24 bp):
TTATTTGATTTGTTATTTAATTTT
Found at i:39755 original size:12 final size:12
Alignment explanation
Indices: 39731--39770 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
39721 GTTTTGTTTA
39731 ATTTAATTT-TT
1 ATTTAATTTGTT
*
39742 ATTTGATTTGTT
1 ATTTAATTTGTT
*
39754 ATTTAATTTTTT
1 ATTTAATTTGTT
39766 ATTTA
1 ATTTA
39771 GTAGAGTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
11 8 0.32
12 17 0.68
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (12 bp):
ATTTAATTTGTT
Found at i:39849 original size:21 final size:21
Alignment explanation
Indices: 39823--39863 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
39813 ATTTTTAATT
39823 TAATTTAATTTTGTTAGTAAG
1 TAATTTAATTTTGTTAGTAAG
*
39844 TAATTTTATTTTGTTAGTAA
1 TAATTTAATTTTGTTAGTAA
39864 TAAGTAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (21 bp):
TAATTTAATTTTGTTAGTAAG
Found at i:41123 original size:23 final size:23
Alignment explanation
Indices: 40978--41111 Score: 162
Period size: 23 Copynumber: 5.8 Consensus size: 23
40968 GCTGGGGAAA
*
40978 CAGTAAGCACACACAATGCAAAT
1 CAGTAAGCACACACAGTGCAAAT
* *
41001 CAGTAGGTACACACAGTGCAAAT
1 CAGTAAGCACACACAGTGCAAAT
* *
41024 CAGTAGGCACACACAATGCAAAAT
1 CAGTAAGCACACACAGTGC-AAAT
* *
41048 -AATAAGCACACACAGTGTAAAT
1 CAGTAAGCACACACAGTGCAAAT
* * *
41070 CAGTAAGCACATATAGTGCGAAT
1 CAGTAAGCACACACAGTGCAAAT
41093 CAGTAAGCACACACAGTGC
1 CAGTAAGCACACACAGTGC
41112 TGAACAGTAA
Statistics
Matches: 93, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
22 4 0.04
23 85 0.91
24 4 0.04
ACGTcount: A:0.43, C:0.23, G:0.18, T:0.16
Consensus pattern (23 bp):
CAGTAAGCACACACAGTGCAAAT
Found at i:41123 original size:69 final size:69
Alignment explanation
Indices: 40975--41123 Score: 181
Period size: 69 Copynumber: 2.2 Consensus size: 69
40965 AGTGCTGGGG
* * *
40975 AAACAGTAAGCACACACAATGCAAATCAGTAGGTACACACAGTGCAAATCAGTAGGCACACACAA
1 AAACAGTAAGCACACACAATGCAAATCAGTAAGCACACACAGTGCAAATCAGTAAGCACACACAA
41040 TGCA
66 TGCA
* * * * * * * *
41044 AAATAATAAGCACACACAGTGTAAATCAGTAAGCACATATAGTGCGAATCAGTAAGCACACACAG
1 AAACAGTAAGCACACACAATGCAAATCAGTAAGCACACACAGTGCAAATCAGTAAGCACACACAA
*
41109 TGCT
66 TGCA
*
41113 GAACAGTAAGC
1 AAACAGTAAGC
41124 GCGTTAATGT
Statistics
Matches: 65, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
69 65 1.00
ACGTcount: A:0.44, C:0.22, G:0.18, T:0.15
Consensus pattern (69 bp):
AAACAGTAAGCACACACAATGCAAATCAGTAAGCACACACAGTGCAAATCAGTAAGCACACACAA
TGCA
Found at i:43665 original size:6 final size:5
Alignment explanation
Indices: 43631--43665 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
43621 TACTACTAAC
43631 AAAAT AAAAT AAAAT AAAAT AAAACT AAAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAA-T -AAAAT AAA
43666 CAAACTTATC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 22 0.79
6 2 0.07
7 4 0.14
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:43734 original size:12 final size:11
Alignment explanation
Indices: 43712--43745 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
43702 TACTAAATAA
43712 AAAAATTAAAT
1 AAAAATTAAAT
*
43723 AATAAATCAAAT
1 AA-AAATTAAAT
43735 AAAAATTAAAT
1 AAAAATTAAAT
43746 TCAACAAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (11 bp):
AAAAATTAAAT
Found at i:43758 original size:25 final size:23
Alignment explanation
Indices: 43712--43761 Score: 64
Period size: 25 Copynumber: 2.1 Consensus size: 23
43702 TACTAAATAA
* *
43712 AAAAATTAAATAATAAATCAAAT
1 AAAAATTAAATAACAAAACAAAT
43735 AAAAATTAAATTCAACAAAACAAAT
1 AAAAATTAAA-T-AACAAAACAAAT
43760 AA
1 AA
43762 CTTAAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 10 0.43
24 1 0.04
25 12 0.52
ACGTcount: A:0.70, C:0.08, G:0.00, T:0.22
Consensus pattern (23 bp):
AAAAATTAAATAACAAAACAAAT
Found at i:44046 original size:22 final size:22
Alignment explanation
Indices: 44020--44062 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
44010 TTCTCCTCCT
*
44020 TTCTTTCTTTT-TTTTTTCCTTA
1 TTCTTT-TTTTCTTTCTTCCTTA
44042 TTCTTTTTTTCTTTCTTCCTT
1 TTCTTTTTTTCTTTCTTCCTT
44063 TCTTCTTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (22 bp):
TTCTTTTTTTCTTTCTTCCTTA
Found at i:51678 original size:23 final size:23
Alignment explanation
Indices: 51613--51678 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
51603 TAATATTATC
*
51613 CGTGAACATGTTCAATTATATGTT
1 CGTGAACATGTTCGATTA-ATGTT
* * *
51637 CATGAACATGTTTGTTTAATGTT
1 CGTGAACATGTTCGATTAATGTT
*
51660 TGTGAACATGTTCGATTAA
1 CGTGAACATGTTCGATTAA
51679 GTTAAATAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
23 20 0.59
24 14 0.41
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.42
Consensus pattern (23 bp):
CGTGAACATGTTCGATTAATGTT
Found at i:51758 original size:26 final size:28
Alignment explanation
Indices: 51703--51765 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 28
51693 TTCGTAAACA
*
51703 TTAAATAAATAAACATGAACACACGTAATT
1 TTAAATAAACAAACATGAACACAC--AATT
51733 TTAAATAAACAAACATGAACA-A-AATT
1 TTAAATAAACAAACATGAACACACAATT
51759 TTGAAAT
1 TT-AAAT
51766 TCTTAACAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
26 6 0.19
27 4 0.13
29 1 0.03
30 20 0.65
ACGTcount: A:0.56, C:0.11, G:0.06, T:0.27
Consensus pattern (28 bp):
TTAAATAAACAAACATGAACACACAATT
Found at i:52948 original size:2 final size:2
Alignment explanation
Indices: 52941--52966 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
52931 CAAACTTACA
52941 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
52967 GTAAAGATAT
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:60781 original size:2 final size:2
Alignment explanation
Indices: 60774--60817 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
60764 ACAAACTAAT
* *
60774 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC CC TC TC CC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
60816 TC
1 TC
60818 CCTTCCCTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (2 bp):
TC
Found at i:60818 original size:6 final size:6
Alignment explanation
Indices: 60777--60830 Score: 58
Period size: 6 Copynumber: 9.3 Consensus size: 6
60767 AACTAATTCT
* * * *
60777 CTCTCT CTCTCT CTCTCT CTCTCT CTCTCC CTCTCC CTCTCC CT-TCC
1 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC
60824 CT-TCC CT
1 CTCTCC CT
60831 TATGTTGTAT
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
5 10 0.21
6 37 0.79
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (6 bp):
CTCTCC
Found at i:64975 original size:21 final size:21
Alignment explanation
Indices: 64951--64995 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
64941 CGGAACTAAT
64951 AGTAAGTACCGAAGTACTATC
1 AGTAAGTACCGAAGTACTATC
64972 AGTAAGTACCGAAGTACTATC
1 AGTAAGTACCGAAGTACTATC
64993 AGT
1 AGT
64996 GAGCACATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (21 bp):
AGTAAGTACCGAAGTACTATC
Found at i:65007 original size:21 final size:21
Alignment explanation
Indices: 64951--65007 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
64941 CGGAACTAAT
* *
64951 AGTAAGTACCGAAGTACTATC
1 AGTAAGCACAGAAGTACTATC
* *
64972 AGTAAGTACCGAAGTACTATC
1 AGTAAGCACAGAAGTACTATC
* *
64993 AGTGAGCACATAAGT
1 AGTAAGCACAGAAGT
65008 GCTGGGGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.23
Consensus pattern (21 bp):
AGTAAGCACAGAAGTACTATC
Found at i:65058 original size:23 final size:23
Alignment explanation
Indices: 65018--65118 Score: 118
Period size: 23 Copynumber: 4.5 Consensus size: 23
65008 GCTGGGGAAA
65018 CAGTAAGCAC--ACAGTGCAAAT
1 CAGTAAGCACATACAGTGCAAAT
*
65039 CAGTAGGCACATACAGTGCAAAAT
1 CAGTAAGCACATACAGTGC-AAAT
* * *
65063 -AGTAAGAACACACAGTACAAAT
1 CAGTAAGCACATACAGTGCAAAT
* *
65085 CAGTAAGCACATATAGTGCGAAT
1 CAGTAAGCACATACAGTGCAAAT
65108 CAGTAAGCACA
1 CAGTAAGCACA
65119 CACAATACTG
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
21 9 0.14
22 4 0.06
23 49 0.74
24 4 0.06
ACGTcount: A:0.45, C:0.21, G:0.19, T:0.16
Consensus pattern (23 bp):
CAGTAAGCACATACAGTGCAAAT
Found at i:65084 original size:46 final size:46
Alignment explanation
Indices: 65018--65122 Score: 135
Period size: 46 Copynumber: 2.3 Consensus size: 46
65008 GCTGGGGAAA
* *
65018 CAGTAAG--CACACAGTGCAAATCAGTAGGCACATACAGTGCAAAAT
1 CAGTAAGAACACACAGTACAAATCAGTAAGCACATACAGTGC-AAAT
* *
65063 -AGTAAGAACACACAGTACAAATCAGTAAGCACATATAGTGCGAAT
1 CAGTAAGAACACACAGTACAAATCAGTAAGCACATACAGTGCAAAT
*
65108 CAGTAAGCACACACA
1 CAGTAAGAACACACA
65123 ATACTGAACA
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
44 6 0.12
45 3 0.06
46 43 0.83
ACGTcount: A:0.45, C:0.22, G:0.18, T:0.15
Consensus pattern (46 bp):
CAGTAAGAACACACAGTACAAATCAGTAAGCACATACAGTGCAAAT
Found at i:68064 original size:105 final size:105
Alignment explanation
Indices: 67869--68079 Score: 257
Period size: 105 Copynumber: 2.0 Consensus size: 105
67859 ATATAAAAAA
* * * *
67869 TAAAGGTTAATATACTAATTGGTACTTGAGATTAATTTCAATATTCAATTTAGTATTTGATTTTA
1 TAAAGGCTAATATACTAATTGGTACTTAAGATCAATTTCAATATTCAATTGAGTATTTGATTTTA
** * *
67934 TTTTCTAATTTAGCACCTAAGTTTGGCTTTAATGTTAAAT
66 TTCCCCAATTTAGCACCTAAATTTGGCTTTAATGTTAAAT
* *
67974 TAAAGGCTAATATACTATTTGGTACTTAAGATCAATTTCAATGTTCAAATTGA-TATTTGAGTTT
1 TAAAGGCTAATATACTAATTGGTACTTAAGATCAATTTCAATATTC-AATTGAGTATTTGA-TTT
* * *
68038 T-TTCCCCAATTT-GTTACTTAAATTTGGCTTTAATGTTCAAT
64 TATTCCCCAATTTAG-CACCTAAATTTGGCTTTAATGTTAAAT
68079 T
1 T
68080 TGGCACTTAA
Statistics
Matches: 90, Mismatches: 13, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
104 1 0.01
105 80 0.89
106 9 0.10
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.46
Consensus pattern (105 bp):
TAAAGGCTAATATACTAATTGGTACTTAAGATCAATTTCAATATTCAATTGAGTATTTGATTTTA
TTCCCCAATTTAGCACCTAAATTTGGCTTTAATGTTAAAT
Found at i:72092 original size:23 final size:23
Alignment explanation
Indices: 72048--72111 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
72038 TAGCACGTCT
72048 CGTGCTCTTTTGTTATTAGCACTATG
1 CGTGCTC-TTTG--ATTAGCACTATG
*
72074 CGTGCTCTTTGATTAGCACTTTG
1 CGTGCTCTTTGATTAGCACTATG
* *
72097 TGTGCTCTCTGATTA
1 CGTGCTCTTTGATTA
72112 ATACTTTGTG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
23 24 0.69
25 4 0.11
26 7 0.20
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.45
Consensus pattern (23 bp):
CGTGCTCTTTGATTAGCACTATG
Found at i:72117 original size:23 final size:23
Alignment explanation
Indices: 72062--72203 Score: 116
Period size: 23 Copynumber: 6.2 Consensus size: 23
72052 CTCTTTTGTT
* * *
72062 ATTAGCACTATGCGTGCTCTTTG
1 ATTAGCACTTTGTGTGCTCTCTG
72085 ATTAGCACTTTGTGTGCTCTCTG
1 ATTAGCACTTTGTGTGCTCTCTG
** *
72108 ATTAATACTTTGTGTACTCTCT-
1 ATTAGCACTTTGTGTGCTCTCTG
*
72130 ATTTAGCACTGTGTGTGCTCTCTG
1 A-TTAGCACTTTGTGTGCTCTCTG
*
72154 -TTACCCAGCAC-TTATGTGCTCTCTG
1 ATT----AGCACTTTGTGTGCTCTCTG
*
72179 -TTAGTACTTTG-GTGCTCTCTG
1 ATTAGCACTTTGTGTGCTCTCTG
72200 -TTAG
1 ATTAG
72204 TAACGGTTCT
Statistics
Matches: 98, Mismatches: 14, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
21 18 0.18
22 5 0.05
23 56 0.57
25 14 0.14
26 5 0.05
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.43
Consensus pattern (23 bp):
ATTAGCACTTTGTGTGCTCTCTG
Found at i:78300 original size:18 final size:17
Alignment explanation
Indices: 78277--78317 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
78267 TTTAGTAATA
*
78277 TTTTTATTTCAAAAATG
1 TTTTTATCTCAAAAATG
*
78294 CTTTTTATCTCAAAAGTG
1 -TTTTTATCTCAAAAATG
78312 TTTTTA
1 TTTTTA
78318 AAAAAGAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.29, C:0.10, G:0.07, T:0.54
Consensus pattern (17 bp):
TTTTTATCTCAAAAATG
Found at i:83175 original size:3 final size:3
Alignment explanation
Indices: 83169--83198 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
83159 TCTTTTCCAA
83169 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
83199 TTTATAGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:87726 original size:35 final size:35
Alignment explanation
Indices: 87687--87757 Score: 81
Period size: 35 Copynumber: 2.0 Consensus size: 35
87677 TTTTAGTTTT
87687 TATTAAA-ACAAGTATAAAAATTAACCGAATTAAAG
1 TATTAAACA-AAGTATAAAAATTAACCGAATTAAAG
** * **
87722 TATTACCCAAATTATTCAAATTAACCGAATTAAAG
1 TATTAAACAAAGTATAAAAATTAACCGAATTAAAG
87757 T
1 T
87758 TTTTAATTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
35 29 0.97
36 1 0.03
ACGTcount: A:0.51, C:0.13, G:0.07, T:0.30
Consensus pattern (35 bp):
TATTAAACAAAGTATAAAAATTAACCGAATTAAAG
Found at i:87878 original size:19 final size:18
Alignment explanation
Indices: 87839--87874 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
87829 TTTAGAATTT
*
87839 TTATTTTTATTTATTAAA
1 TTATTTGTATTTATTAAA
*
87857 TTATTTGTATTTTTTAAA
1 TTATTTGTATTTATTAAA
87875 ATTAAGTTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (18 bp):
TTATTTGTATTTATTAAA
Found at i:103557 original size:4 final size:4
Alignment explanation
Indices: 103548--103592 Score: 81
Period size: 4 Copynumber: 11.0 Consensus size: 4
103538 GAGCTACATC
103548 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT GCTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT -CTTT
103593 ATCTTTAGCA
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
4 36 0.90
5 4 0.10
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.73
Consensus pattern (4 bp):
CTTT
Found at i:109385 original size:41 final size:42
Alignment explanation
Indices: 109317--109403 Score: 140
Period size: 41 Copynumber: 2.1 Consensus size: 42
109307 GTCACTGCCA
109317 AAAGCTAAACATTATTACATTATTATTACTAACTCAATGTAGG
1 AAAGCTAAACA-TATTACATTATTATTACTAACTCAATGTAGG
**
109360 AAAGCTAAAC-TATTGTATTATTATTACTAACTCAATGTAGG
1 AAAGCTAAACATATTACATTATTATTACTAACTCAATGTAGG
109401 AAA
1 AAA
109404 ACAAGTGGGT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
41 32 0.76
43 10 0.24
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.34
Consensus pattern (42 bp):
AAAGCTAAACATATTACATTATTATTACTAACTCAATGTAGG
Found at i:112263 original size:99 final size:99
Alignment explanation
Indices: 112143--112340 Score: 369
Period size: 99 Copynumber: 2.0 Consensus size: 99
112133 GAGTCGGATT
* *
112143 TAAGTATGATATTAACATATTTTATGTTTGTTTAAATCCGACTCGAAATTTGAGCCTAAAATTTT
1 TAAGCATGATATTAACATATTTTATGTTTGTTCAAATCCGACTCGAAATTTGAGCCTAAAATTTT
*
112208 GTCCAAATCCGTTTATATTTACAAAAGATTAATC
66 GTCCAAATCCGCTTATATTTACAAAAGATTAATC
112242 TAAGCATGATATTAACATATTTTATGTTTGTTCAAATCCGACTCGAAATTTGAGCCTAAAATTTT
1 TAAGCATGATATTAACATATTTTATGTTTGTTCAAATCCGACTCGAAATTTGAGCCTAAAATTTT
112307 GTCCAAATCCGCTTATATTTACAAAAGATTAATC
66 GTCCAAATCCGCTTATATTTACAAAAGATTAATC
112341 CAAACTCATT
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
99 96 1.00
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (99 bp):
TAAGCATGATATTAACATATTTTATGTTTGTTCAAATCCGACTCGAAATTTGAGCCTAAAATTTT
GTCCAAATCCGCTTATATTTACAAAAGATTAATC
Found at i:112375 original size:5 final size:5
Alignment explanation
Indices: 112365--112389 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
112355 GACTAATCAT
112365 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
112390 ATATTTAATA
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:120320 original size:59 final size:58
Alignment explanation
Indices: 120246--120443 Score: 186
Period size: 59 Copynumber: 3.3 Consensus size: 58
120236 TATTTATCTG
120246 ATAAAAAATCAAATTTTTTGGTGTTGATCATGCAATGGCCGACATCTCCTTTTTCAGAT-A
1 ATAAAAAATCAAATTTTTTGGTGTTGATCATGC-ATGGCCGACAT-TCCTTTTT-AGATGA
* * * * *
120306 A-AAAAATTTCAATTTTTTTTGGTGTTGACCATTGCATGGTCGACATTCCTTTTTATATGA
1 ATAAAAA-ATCAA-ATTTTTTGGTGTTGATCA-TGCATGGCCGACATTCCTTTTTAGATGA
* * ** * *
120366 ATAAAAAATCAAATTTTTTGGTGTTGGTCATGCTATGACTTACATTCCCTTTTAG-TCAA
1 ATAAAAAATCAAATTTTTTGGTGTTGATCATGC-ATGGCCGACATTCCTTTTTAGAT-GA
* *
120425 ATAAAAATTCGAATTTTTT
1 ATAAAAAATCAAATTTTTT
120444 TTGTGTTGGT
Statistics
Matches: 113, Mismatches: 18, Indels: 15
0.77 0.12 0.10
Matches are distributed among these distances:
58 4 0.04
59 56 0.50
60 19 0.17
61 31 0.27
62 3 0.03
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (58 bp):
ATAAAAAATCAAATTTTTTGGTGTTGATCATGCATGGCCGACATTCCTTTTTAGATGA
Found at i:120372 original size:61 final size:59
Alignment explanation
Indices: 120248--120391 Score: 177
Period size: 61 Copynumber: 2.4 Consensus size: 59
120238 TTTATCTGAT
*
120248 AAAAAATCAAATTTTTTGGTGTTGATCATGCAATGGCCGACATCTCCTTTTTCAGATAA
1 AAAAAATCAAATTTTTTGGTGTTGACCATGCAATGGCCGACATCTCCTTTTTCAGATAA
* * * *
120307 AAAAATTTCAATTTTTTTTGGTGTTGACCATTGC-ATGGTCGACAT-TCCTTTTT-ATATGAA
1 AAAAA-ATCAA-ATTTTTTGGTGTTGACCA-TGCAATGGCCGACATCTCCTTTTTCAGAT-AA
120367 TAAAAAATCAAATTTTTTGGTGTTG
1 -AAAAAATCAAATTTTTTGGTGTTG
120392 GTCATGCTAT
Statistics
Matches: 73, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
59 21 0.29
60 18 0.25
61 31 0.42
62 3 0.04
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (59 bp):
AAAAAATCAAATTTTTTGGTGTTGACCATGCAATGGCCGACATCTCCTTTTTCAGATAA
Found at i:120479 original size:120 final size:119
Alignment explanation
Indices: 120238--120503 Score: 283
Period size: 120 Copynumber: 2.2 Consensus size: 119
120228 GTTGGCCATA
* *
120238 TTTATCTGATAAAAAATCAAATTTTTTGGTGTTGATCATGCAATGGCCGACATCTCCTTTTTCAG
1 TTTATCTGATAAAAAATCAAATTTTTTGGTGTTGATCATGCAATGACCGACATCTCCCTTTTCAG
* * *
120303 ATAAAAAAATTTCAATTTTTTTTGGTGTTGACCATTGCATGGTCGACATTCCTT
66 ATAAAAAAAATTCAATTTTTTTTGGTGTTGACCATTGCACGGTCGACATCCCTT
* * * **
120357 TTTATATGAATAAAAAATCAAATTTTTTGGTGTTGGTCATGCTATGACTTACAT-TCCCTTTT-A
1 TTTATCTG-ATAAAAAATCAAATTTTTTGGTGTTGATCATGCAATGACCGACATCTCCCTTTTCA
*** *
120420 G-TCAAATAAAAATTCGAATTTTTTTT-GTGTTGGTTA-TGTCACGGTCGATA-CCCTTTT
65 GAT-AAA-AAAAATTC-AATTTTTTTTGGTGTTGACCATTG-CACGGTCGACATCCC--TT
* *
120477 TTTATCTGATAAAAAATTAATTTTTTT
1 TTTATCTGATAAAAAATCAAATTTTTT
120504 ATGTTGGCCA
Statistics
Matches: 123, Mismatches: 17, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
117 1 0.01
118 9 0.07
119 54 0.44
120 59 0.48
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.44
Consensus pattern (119 bp):
TTTATCTGATAAAAAATCAAATTTTTTGGTGTTGATCATGCAATGACCGACATCTCCCTTTTCAG
ATAAAAAAAATTCAATTTTTTTTGGTGTTGACCATTGCACGGTCGACATCCCTT
Found at i:120489 original size:60 final size:61
Alignment explanation
Indices: 120427--120561 Score: 152
Period size: 58 Copynumber: 2.3 Consensus size: 61
120417 TTAGTCAAAT
* ** * * * *
120427 AAAAATTCGAATTTTTTTTGTGTTGGTTATGTC-ACGGTCGATACCCTTTTTTTATCTGATA
1 AAAAATTCGAATTTTTTTTATGTTGGCCAT-ACAACGGTCAATACCCCTTTTTTATCAGATA
* *
120488 AAAAATT--AA-TTTTTTTATGTTGGCCATACAATGGTCAATACCCCTTTTTTGTCAGATA
1 AAAAATTCGAATTTTTTTTATGTTGGCCATACAACGGTCAATACCCCTTTTTTATCAGATA
120546 AAAAATTCGAATTTTT
1 AAAAATTCGAATTTTT
120562 GGTGTTAGCC
Statistics
Matches: 61, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
57 1 0.02
58 45 0.74
59 2 0.03
60 2 0.03
61 11 0.18
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.44
Consensus pattern (61 bp):
AAAAATTCGAATTTTTTTTATGTTGGCCATACAACGGTCAATACCCCTTTTTTATCAGATA
Found at i:120573 original size:59 final size:58
Alignment explanation
Indices: 120462--120573 Score: 136
Period size: 58 Copynumber: 1.9 Consensus size: 58
120452 GTTATGTCAC
* * * * *
120462 GGTCGATACCCTTTTTTTATCTGATAAAAAATTAATTTTTTTATGTTGGCCATACAAT
1 GGTCAATACCCCTTTTTTATCAGATAAAAAATTAATTTTTTGATGTTAGCCATACAAT
* *
120520 GGTCAATACCCCTTTTTTGTCAGATAAAAAATTCGAA-TTTTTGGTGTTAGCCAT
1 GGTCAATACCCCTTTTTTATCAGATAAAAAATT--AATTTTTTGATGTTAGCCAT
120574 TGCCAAATAA
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
58 29 0.64
59 14 0.31
60 2 0.04
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.42
Consensus pattern (58 bp):
GGTCAATACCCCTTTTTTATCAGATAAAAAATTAATTTTTTGATGTTAGCCATACAAT
Found at i:120674 original size:59 final size:59
Alignment explanation
Indices: 120583--121001 Score: 257
Period size: 60 Copynumber: 7.0 Consensus size: 59
120573 TTGCCAAATA
* * * * *
120583 AAAAAGGGGTGTCGACCA-TACAATGACCAACAC-CAAAAATTTGAATTTTTTATCTGAC
1 AAAAAGGGGTGTCGATCATTGC-ATGGCCAACACAAAAAAATTTGAATTTTTTATCAGAC
* * *
120641 AAAAAGGGAGTGTCGACCATTGCATGGTCAACACAAAAAAATTT-AATTTTTTA-CAAGATA
1 AAAAAGGG-GTGTCGATCATTGCATGGCCAACACAAAAAAATTTGAATTTTTTATC-AGA-C
* * *
120701 AAAAAGGGGGTGTCGGTCATGGCATAGCCAACACAAAAAAATATTCGAATTTTTTATCTA-AC
1 AAAAA-GGGGTGTCGATCATTGCATGGCCAACACAAAAAAAT-TT-GAATTTTTTATC-AGAC
* * ** * * ** *
120763 AAAAAGGGGTTGTCGGTCATGGCATGATCGATACTCAAAAATTTG-ATTTTTTATTCAGAT
1 AAAAAGGGG-TGTCGATCATTGCATGGCCAACACAAAAAAATTTGAATTTTTTA-TCAGAC
* * *
120823 AAAAAGGAGTGTCTG-TCA-TGCAATGACCAACACAAAAAAAATTGAAATTTTGTTATCAGA-
1 AAAAAGGGGTGTC-GATCATTGC-ATGGCCAACACAAAAAAATTTG-AATTTT-TTATCAGAC
* * * * * * * * *
120883 TAAAAGGGGTGT-TAGCCATGGCATGACAAACATAAAAAAAAATTGAATTTTTTATCTGAC
1 AAAAAGGGGTGTCGA-TCATTGCATGGCCAACA-CAAAAAAATTTGAATTTTTTATCAGAC
* * * * **
120943 AAAAAGGAAGTGTCGATCATTGTATTGCCAATACTCAAAAATTTG-ATTTGTTTATCAGA
1 AAAAAGG-GGTGTCGATCATTGCATGGCCAACACAAAAAAATTTGAATTT-TTTATCAGA
121002 TTAAAAGGAA
Statistics
Matches: 283, Mismatches: 52, Indels: 50
0.74 0.14 0.13
Matches are distributed among these distances:
58 11 0.04
59 73 0.26
60 105 0.37
61 48 0.17
62 34 0.12
63 10 0.04
64 2 0.01
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.29
Consensus pattern (59 bp):
AAAAAGGGGTGTCGATCATTGCATGGCCAACACAAAAAAATTTGAATTTTTTATCAGAC
Found at i:120777 original size:122 final size:119
Alignment explanation
Indices: 120583--120962 Score: 316
Period size: 121 Copynumber: 3.2 Consensus size: 119
120573 TTGCCAAATA
* ** * * *
120583 AAAAAGGGGTGTCGACCATACAATGACCAACAC-CAAAAAT-TTGAATTTTTTATCTGACAAAAA
1 AAAAAGGAGTGTCGGTCATGCAATGACCAACACAAAAAAATATTGAATTTTTTATCTAACAAAAA
* *
120646 GGGAGTGTCGACCATTGCATGGTCAACACAAAAAAATTTAATTTTTTA-CAAGAT
66 GGGAGTGTCGACCATGGCATGATCAACACAAAAAAATTTAATTTTTTATC-AGAT
*
120700 AAAAAAGGGGGTGTCGGTCATGGC-AT-AGCCAACACAAAAAAATATTCGAATTTTTTATCTAAC
1 -AAAAA-GGAGTGTCGGTCAT-GCAATGA-CCAACACAAAAAAATATT-GAATTTTTTATCTAAC
** * * ** *
120763 AAAAAGGG-GTTGTCGGTCATGGCATGATCGATACTCAAAAATTTGATTTTTTATTCAGAT
61 AAAAAGGGAG-TGTCGACCATGGCATGATCAACACAAAAAAATTTAATTTTTTA-TCAGAT
* *
120823 AAAAAGGAGTGTCTGTCATGCAATGACCAACACAAAAAAA-ATTGAAATTTTGTTATC-AGA-TA
1 AAAAAGGAGTGTCGGTCATGCAATGACCAACACAAAAAAATATTG-AATTTT-TTATCTA-ACAA
* * * * *
120885 AAAGGG-GTGT-TAGCCATGGCATGA-CAAACATAAAAAAAAATTGAATTTTTTATCTGAC
63 AAAGGGAGTGTCGA-CCATGGCATGATC-AAC--ACAAAAAAATTTAATTTTTTATCAGAT
*
120943 AAAAAGGAAGTGTCGATCAT
1 AAAAAGG-AGTGTCGGTCAT
120963 TGTATTGCCA
Statistics
Matches: 212, Mismatches: 31, Indels: 35
0.76 0.11 0.13
Matches are distributed among these distances:
118 7 0.03
119 36 0.17
120 38 0.18
121 63 0.30
122 63 0.30
123 4 0.02
124 1 0.00
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.27
Consensus pattern (119 bp):
AAAAAGGAGTGTCGGTCATGCAATGACCAACACAAAAAAATATTGAATTTTTTATCTAACAAAAA
GGGAGTGTCGACCATGGCATGATCAACACAAAAAAATTTAATTTTTTATCAGAT
Found at i:120856 original size:181 final size:178
Alignment explanation
Indices: 120616--121036 Score: 444
Period size: 181 Copynumber: 2.3 Consensus size: 178
120606 TGACCAACAC
* * *
120616 CAAAAATTTGAATTTTTTATCTGACAAAAAGGGAGTGTCGACCATTGC-ATGGTCAACAC-AAAA
1 CAAAAATTTG-ATTTTTTATCAGATAAAAA-GGAGTGTCG-CCA-TGCAATGGCCAACACAAAAA
* * * *
120679 AAATT-TAATTTT-TTA-CAAGATAAAAAAGGGGGTGTCGGTCATGGCAT-AGCCAACACAAAAA
62 AAATTGAAATTTTGTTATC-AGAT--AAAA-GGGGTGTCAGCCATGGCATGA-CAAACACAAAAA
* * * * *
120740 AATATTCGAATTTTTTATCTAACAAAAAGG-GGTTGTCGGTCATGGCA-TGATCGATACT
122 AAAATT-GAATTTTTTATCTAACAAAAAGGAAG-TGTCGATCATGGCATTG-CCAATACT
* *
120798 CAAAAATTTGATTTTTTATTCAGATAAAAAGGAGTGTCTGTCATGCAATGACCAACACAAAAAAA
1 CAAAAATTTGATTTTTTA-TCAGATAAAAAGGAGTGTC-GCCATGCAATGGCCAACACAAAAAAA
* *
120863 ATTGAAATTTTGTTATCAGATAAAAGGGGTGTTAGCCATGGCATGACAAACATAAAAAAAAATTG
64 ATTGAAATTTTGTTATCAGATAAAAGGGGTGTCAGCCATGGCATGACAAACACAAAAAAAAATTG
* * *
120928 AATTTTTTATCTGACAAAAAGGAAGTGTCGATCATTGTATTGCCAATACT
129 AATTTTTTATCTAACAAAAAGGAAGTGTCGATCATGGCATTGCCAATACT
* *
120978 CAAAAATTTGATTTGTTTATCAGATTAAAAGGAAGTGCCAGCCATGCAATGGCCAACAC
1 CAAAAATTTGATTT-TTTATCAGATAAAAAGG-AGTGTC-GCCATGCAATGGCCAACAC
121037 CAAATTTTTT
Statistics
Matches: 203, Mismatches: 24, Indels: 25
0.81 0.10 0.10
Matches are distributed among these distances:
180 68 0.33
181 87 0.43
182 34 0.17
183 6 0.03
184 7 0.03
185 1 0.00
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (178 bp):
CAAAAATTTGATTTTTTATCAGATAAAAAGGAGTGTCGCCATGCAATGGCCAACACAAAAAAAAT
TGAAATTTTGTTATCAGATAAAAGGGGTGTCAGCCATGGCATGACAAACACAAAAAAAAATTGAA
TTTTTTATCTAACAAAAAGGAAGTGTCGATCATGGCATTGCCAATACT
Found at i:123090 original size:24 final size:24
Alignment explanation
Indices: 123063--123116 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
123053 TGCAAGTTTG
123063 GGTGCTTTACCTAATTACTAATTA
1 GGTGCTTTACCTAATTACTAATTA
123087 GGTGCTTTACCTAATTACTAATTA
1 GGTGCTTTACCTAATTACTAATTA
123111 GGTGCT
1 GGTGCT
123117 CTGTCTTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.41
Consensus pattern (24 bp):
GGTGCTTTACCTAATTACTAATTA
Found at i:142444 original size:86 final size:86
Alignment explanation
Indices: 142299--142470 Score: 326
Period size: 86 Copynumber: 2.0 Consensus size: 86
142289 GAGGATCACA
*
142299 TAACGTTTTTTACATTATGATGAGATGTAGCCTGCACATTAGTCCATTTGCACATCAATGTTGAC
1 TAACGTTTTCTACATTATGATGAGATGTAGCCTGCACATTAGTCCATTTGCACATCAATGTTGAC
*
142364 AGGTTGAGGTTGGCTGGACAT
66 AGGCTGAGGTTGGCTGGACAT
142385 TAACGTTTTCTACATTATGATGAGATGTAGCCTGCACATTAGTCCATTTGCACATCAATGTTGAC
1 TAACGTTTTCTACATTATGATGAGATGTAGCCTGCACATTAGTCCATTTGCACATCAATGTTGAC
142450 AGGCTGAGGTTGGCTGGACAT
66 AGGCTGAGGTTGGCTGGACAT
142471 GACCTGACCG
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
86 84 1.00
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (86 bp):
TAACGTTTTCTACATTATGATGAGATGTAGCCTGCACATTAGTCCATTTGCACATCAATGTTGAC
AGGCTGAGGTTGGCTGGACAT
Found at i:152002 original size:24 final size:23
Alignment explanation
Indices: 151975--152047 Score: 60
Period size: 24 Copynumber: 3.1 Consensus size: 23
151965 AAAATTTATA
*
151975 TTTATATTATTAAAA-TATTAATAT
1 TTTATACTA-TAAAATTATTAAT-T
*
151999 TTTATGCTATAAAATTATTAATT
1 TTTATACTATAAAATTATTAATT
* * *
152022 TATTATACGATTAAA-TACTAATT
1 T-TTATACTATAAAATTATTAATT
152045 TTT
1 TTT
152048 TAACTAGAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
22 2 0.05
23 15 0.37
24 24 0.59
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.52
Consensus pattern (23 bp):
TTTATACTATAAAATTATTAATT
Found at i:154940 original size:24 final size:24
Alignment explanation
Indices: 154913--154991 Score: 83
Period size: 24 Copynumber: 3.4 Consensus size: 24
154903 ATTAAAAATG
*
154913 TTATTAAATTATATATTATTATTA
1 TTATTAAATTATATATTATAATTA
*
154937 TTATTAAA-T-TATATTA-AAATA
1 TTATTAAATTATATATTATAATTA
* * * *
154958 TAATTAAATTATTTATTATCATTT
1 TTATTAAATTATATATTATAATTA
154982 TTATTAAATT
1 TTATTAAATT
154992 GTATTCAATG
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
21 10 0.23
22 8 0.18
23 7 0.16
24 19 0.43
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (24 bp):
TTATTAAATTATATATTATAATTA
Found at i:154964 original size:45 final size:46
Alignment explanation
Indices: 154897--154996 Score: 139
Period size: 45 Copynumber: 2.2 Consensus size: 46
154887 AATATAAAAT
* * *
154897 AATTATATTAAAAATGTTATTAAATTATATATTATTATTATTATTA
1 AATTATATTAAAAATATAATTAAATTATATATTATCATTATTATTA
* *
154943 AATTATATT-AAAATATAATTAAATTATTTATTATCATTTTTATTA
1 AATTATATTAAAAATATAATTAAATTATATATTATCATTATTATTA
*
154988 AATTGTATT
1 AATTATATT
154997 CAATGATAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
45 39 0.81
46 9 0.19
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (46 bp):
AATTATATTAAAAATATAATTAAATTATATATTATCATTATTATTA
Found at i:156153 original size:15 final size:15
Alignment explanation
Indices: 156109--156154 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
156099 TCATATTACA
*
156109 TTTTAATCATTAATG
1 TTTTAATCATTTATG
*
156124 TTTGAA--ATGTTATG
1 TTTTAATCAT-TTATG
156138 TTTTAATCATTTATG
1 TTTTAATCATTTATG
156153 TT
1 TT
156155 ATCGTTTTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
13 2 0.08
14 9 0.36
15 12 0.48
16 2 0.08
ACGTcount: A:0.28, C:0.04, G:0.11, T:0.57
Consensus pattern (15 bp):
TTTTAATCATTTATG
Found at i:157071 original size:23 final size:23
Alignment explanation
Indices: 157041--157090 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
157031 TTTTTATTTT
* *
157041 TTATTTTTAC-ATTTTCATTATTA
1 TTATTTTT-CTATTTTAATGATTA
157064 TTATTTTTCTATTTTAATGATTA
1 TTATTTTTCTATTTTAATGATTA
157087 TTAT
1 TTAT
157091 ATGAAATGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 1 0.04
23 23 0.96
ACGTcount: A:0.26, C:0.06, G:0.02, T:0.66
Consensus pattern (23 bp):
TTATTTTTCTATTTTAATGATTA
Found at i:158362 original size:44 final size:44
Alignment explanation
Indices: 158313--158402 Score: 162
Period size: 44 Copynumber: 2.0 Consensus size: 44
158303 CAACAAAATC
*
158313 ATTTTTGCTTAACTCAGTCAAAAATTTTACAATTATATTCGCTG
1 ATTTTTGCTTAACTCAATCAAAAATTTTACAATTATATTCGCTG
*
158357 ATTTTTGTTTAACTCAATCAAAAATTTTACAATTATATTCGCTG
1 ATTTTTGCTTAACTCAATCAAAAATTTTACAATTATATTCGCTG
158401 AT
1 AT
158403 CGTGAAATGT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.33, C:0.14, G:0.08, T:0.44
Consensus pattern (44 bp):
ATTTTTGCTTAACTCAATCAAAAATTTTACAATTATATTCGCTG
Done.