Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010188.1 Kokia drynarioides strain JFW-HI SEQ_124999, 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: 22750
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35
Found at i:90 original size:13 final size:14
Alignment explanation
Indices: 66--109 Score: 65
Period size: 13 Copynumber: 3.3 Consensus size: 14
56 ATCCTTTATT
66 TTTAGGGTTTAGGG
1 TTTAGGGTTTAGGG
*
80 TTTAGTG-TTAGGG
1 TTTAGGGTTTAGGG
93 -TTAGGGTTTAGGG
1 TTTAGGGTTTAGGG
106 TTTA
1 TTTA
110 TGGTCAGGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 5 0.19
13 12 0.46
14 9 0.35
ACGTcount: A:0.16, C:0.00, G:0.39, T:0.45
Consensus pattern (14 bp):
TTTAGGGTTTAGGG
Found at i:95 original size:6 final size:7
Alignment explanation
Indices: 66--109 Score: 65
Period size: 7 Copynumber: 6.6 Consensus size: 7
56 ATCCTTTATT
66 TTTAGGG
1 TTTAGGG
73 TTTAGGG
1 TTTAGGG
*
80 TTTAGTG
1 TTTAGGG
87 -TTAGGG
1 TTTAGGG
93 -TTAGGG
1 TTTAGGG
99 TTTAGGG
1 TTTAGGG
106 TTTA
1 TTTA
110 TGGTCAGGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
6 11 0.32
7 23 0.68
ACGTcount: A:0.16, C:0.00, G:0.39, T:0.45
Consensus pattern (7 bp):
TTTAGGG
Found at i:118 original size:26 final size:26
Alignment explanation
Indices: 67--119 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
57 TCCTTTATTT
*
67 TTAGGGTTTAGGGTTTAGTGTTAGGG
1 TTAGGGTTTAGGGTTTAGTGTCAGGG
93 TTAGGGTTTAGGGTTTA-TGGTCAGGG
1 TTAGGGTTTAGGGTTTAGT-GTCAGGG
119 T
1 T
120 CTAAAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 1 0.04
26 24 0.96
ACGTcount: A:0.15, C:0.02, G:0.42, T:0.42
Consensus pattern (26 bp):
TTAGGGTTTAGGGTTTAGTGTCAGGG
Found at i:408 original size:7 final size:7
Alignment explanation
Indices: 393--459 Score: 79
Period size: 7 Copynumber: 10.1 Consensus size: 7
383 ATCCTTTATT
393 TTTAGGG
1 TTTAGGG
*
400 TTTAAGG
1 TTTAGGG
407 TTTAGGG
1 TTTAGGG
*
414 -TTAGTG
1 TTTAGGG
*
420 -TCAGGG
1 TTTAGGG
426 -TTAGGG
1 TTTAGGG
432 TTTAGGG
1 TTTAGGG
439 TTTAGGG
1 TTTAGGG
446 TTTAGGG
1 TTTAGGG
453 -TTAGGG
1 TTTAGGG
459 T
1 T
460 CTAAAAATTT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
6 20 0.38
7 32 0.62
ACGTcount: A:0.16, C:0.01, G:0.42, T:0.40
Consensus pattern (7 bp):
TTTAGGG
Found at i:431 original size:6 final size:6
Alignment explanation
Indices: 394--459 Score: 60
Period size: 6 Copynumber: 10.2 Consensus size: 6
384 TCCTTTATTT
* * *
394 TTAGGG TTTAAGGT TTAGGG TTAGTG TCAGGG TTAGGG TTTAGGG TTTAGGG
1 TTAGGG -TT-AGGG TTAGGG TTAGGG TTAGGG TTAGGG -TTAGGG -TTAGGG
446 TTTAGGG TTAGGG T
1 -TTAGGG TTAGGG T
460 CTAAAAATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
6 24 0.47
7 24 0.47
8 3 0.06
ACGTcount: A:0.17, C:0.02, G:0.42, T:0.39
Consensus pattern (6 bp):
TTAGGG
Found at i:716 original size:342 final size:338
Alignment explanation
Indices: 1--751 Score: 1308
Period size: 342 Copynumber: 2.2 Consensus size: 338
*
1 ATTATTAAGGATAAATTTATGCGTACAATAACTAGAATGCTGTAAATAATGATTGATCC-TT-TA
1 ATTATTAAGGATAAATTTATGCATACAATAACTAGAATGCTGTAAATAATGATTGATCCTTTATA
* * *
64 TTT----TTAGGGTTTAGGG-T--T-T-AGTGTTAGGGTTAGGGTTTAGGGTTTATGGTCAGGGT
66 TTTAGGGTTAAGGTTTAGGGTTAGTGTCAGGGTTAGGGTTAGGGTTTAGGGTTTAGGGTCAGGGT
120 CTAAAAATTTTGAATTTGAAGCTTATAACATGTACTCCAAAGACATAGACATACAAAAAACTTCA
131 CTAAAAATTTTGAATTTGAAGCTTATAACATGTACTCCAAAGACATAGACATACAAAAAACTTCA
185 AACAATTTCATTGCACACATGTGCAAAAACAGTTAACAGCCACTTTTGTGCTAAAACAGGCTTAA
196 AACAATTTCATTGCACACATGTGCAAAAACAGTTAACAGCCACTTTTGTGCTAAAACAGGCTTAA
*
250 GCAAAATGGCTTACGAACCATGTTAGATTCAACCCCAATAGTATAGCACCTAATAAACATATGGG
261 GCAAAATGGCTTACAAACCATGTTAGATTCAACCCCAATAGTATAGCACCTAATAAACATATGGG
315 TGGATGTATAGTG
326 TGGATGTATAGTG
* *
328 ATTATTAAGGATAAATTTATGCGTACAATAACTAGAATGCTGTAAATAATGATTGATCCTTTATT
1 ATTATTAAGGATAAATTTATGCATACAATAACTAGAATGCTGTAAATAATGATTGATCCTTTATA
*
393 TTTAGGGTTTAAGGTTTAGGGTTAGTGTCAGGGTTAGGGTTTAGGGTTTAGGGTTTAGGGTTAGG
66 TTTAGGG-TTAAGGTTTAGGGTTAGTGTCAGGGTTAGGG-TTAGGGTTTAGGGTTTAGGGTCAGG
458 GTCTAAAAATTTTGAATTTGAAGCTTATATAACATGTACTCCAAAGACATAGACATACAAAAAAC
129 GTCTAAAAATTTTGAATTTGAAGC-T-TATAACATGTACTCCAAAGACATAGACATACAAAAAAC
523 TTCAAACAATTTCATTGCACACATGTGCAAAAACAGTTAACAGCCACTTTTGTGCTAAAACAGGC
192 TTCAAACAATTTCATTGCACACATGTGCAAAAACAGTTAACAGCCACTTTTGTGCTAAAACAGGC
588 TTAAGCAAAATGGCTTACAAACCATGTTAGATTCAACCCCAATAGTATAGCACCTAATAAACATA
257 TTAAGCAAAATGGCTTACAAACCATGTTAGATTCAACCCCAATAGTATAGCACCTAATAAACATA
653 TGGGTGGATGTATAGTG
322 TGGGTGGATGTATAGTG
670 ATTATTAAGGATAAATTTATGCATACAATAACTAGAATGCTGTAAATAATGATTGATCCTTTATA
1 ATTATTAAGGATAAATTTATGCATACAATAACTAGAATGCTGTAAATAATGATTGATCCTTTATA
*
735 TTTAGGGTTAGGGTTTA
66 TTTAGGGTTAAGGTTTA
752 TGATTTATGG
Statistics
Matches: 400, Mismatches: 9, Indels: 16
0.94 0.02 0.04
Matches are distributed among these distances:
327 59 0.15
328 2 0.00
329 4 0.01
334 12 0.03
335 1 0.00
337 1 0.00
338 1 0.00
339 9 0.02
340 47 0.12
341 10 0.03
342 254 0.63
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (338 bp):
ATTATTAAGGATAAATTTATGCATACAATAACTAGAATGCTGTAAATAATGATTGATCCTTTATA
TTTAGGGTTAAGGTTTAGGGTTAGTGTCAGGGTTAGGGTTAGGGTTTAGGGTTTAGGGTCAGGGT
CTAAAAATTTTGAATTTGAAGCTTATAACATGTACTCCAAAGACATAGACATACAAAAAACTTCA
AACAATTTCATTGCACACATGTGCAAAAACAGTTAACAGCCACTTTTGTGCTAAAACAGGCTTAA
GCAAAATGGCTTACAAACCATGTTAGATTCAACCCCAATAGTATAGCACCTAATAAACATATGGG
TGGATGTATAGTG
Found at i:786 original size:7 final size:7
Alignment explanation
Indices: 746--1058 Score: 166
Period size: 7 Copynumber: 47.0 Consensus size: 7
736 TTAGGGTTAG
746 GGTTTAT
1 GGTTTAT
*
753 GATTTAT
1 GGTTTAT
*
760 GGTTTGT
1 GGTTTAT
*
767 GGTTTGT
1 GGTTTAT
774 GGTTTAT
1 GGTTTAT
781 GGTTTA-
1 GGTTTAT
* *
787 GGGTTAA
1 GGTTTAT
794 GGTTTAT
1 GGTTTAT
801 GGTTTAT
1 GGTTTAT
808 GGTTTAT
1 GGTTTAT
815 GGTTTAT
1 GGTTTAT
* *
822 GATTTAG
1 GGTTTAT
829 GGTTTAT
1 GGTTTAT
836 GG-TTAT
1 GGTTTAT
842 GG-TTA-
1 GGTTTAT
*
847 -GTTTAG
1 GGTTTAT
853 GGTTTAT
1 GGTTTAT
860 GGTTTAGT
1 GGTTTA-T
868 GTTAGTTTA-
1 G---GTTTAT
*
877 GGGTTA-
1 GGTTTAT
*
883 GG-TTAG
1 GGTTTAT
889 GGTTTAT
1 GGTTTAT
*
896 AGTTTA-
1 GGTTTAT
*
902 GGGTTA-
1 GGTTTAT
*
908 GG-TTAA
1 GGTTTAT
*
914 GGTTTAG
1 GGTTTAT
921 GGTTTAT
1 GGTTTAT
928 GGTTTA-
1 GGTTTAT
934 GGTTT-T
1 GGTTTAT
*
940 AGTGTTA-
1 GGT-TTAT
*
947 GGGTTAT
1 GGTTTAT
954 -GTTTAT
1 GGTTTAT
*
960 GG-TTAG
1 GGTTTAT
*
966 GGTTTAG
1 GGTTTAT
973 GGTTTA-
1 GGTTTAT
979 GGTTTA-
1 GGTTTAT
*
985 GGGTTA-
1 GGTTTAT
*
991 AGTTTA-
1 GGTTTAT
* *
997 GGGTTAG
1 GGTTTAT
*
1004 GGTTTAG
1 GGTTTAT
1011 GGTTTAT
1 GGTTTAT
*
1018 GGTTAAT
1 GGTTTAT
1025 -GTTTAT
1 GGTTTAT
* *
1031 CGTGTA-
1 GGTTTAT
*
1037 GGATTTAG
1 GG-TTTAT
*
1045 GGTTTAG
1 GGTTTAT
1052 GGTTTAT
1 GGTTTAT
1059 ATATATAGTT
Statistics
Matches: 247, Mismatches: 37, Indels: 44
0.75 0.11 0.13
Matches are distributed among these distances:
4 1 0.00
5 9 0.04
6 75 0.30
7 152 0.62
8 4 0.02
9 1 0.00
11 5 0.02
ACGTcount: A:0.17, C:0.00, G:0.34, T:0.49
Consensus pattern (7 bp):
GGTTTAT
Found at i:787 original size:48 final size:46
Alignment explanation
Indices: 735--989 Score: 164
Period size: 48 Copynumber: 5.3 Consensus size: 46
725 ATCCTTTATA
*
735 TTTAGGGTTAGGGTTTATGATTTATGGTTTGTGGTTTGTGGTTTATGG
1 TTTAGGGTTAGGGTTTATG-TTTATGGTTTATGGTTTGTGGTTTA-GG
* * *
783 TTTAGGGTTAAGGTTTATGGTTTATGGTTTATGGTTTATGATTTAGGG
1 TTTAGGGTTAGGGTTTAT-GTTTATGGTTTATGGTTTGTGGTTTA-GG
* * *
831 TTTATGGTTATGG-TTA-GTTTAGGGTTTATGGTTTAGTGTTAGTTTAGG
1 TTTAGGGTTAGGGTTTATGTTTATGGTTTATGGTTT-GTG---GTTTAGG
* * *
879 GTTA-GGTTAGGGTTTATAGTTTAGGGTTAGGTTAAGGTTTAG-GGTTTATGG
1 TTTAGGGTTAGGGTTTAT-GTTTATGG-T---TTATGGTTT-GTGGTTTA-GG
* * * * *
930 TTTAGGTTTTAGTG-TTAGGGTTAT-GTTTATGGTTAG-GGTTTAGGG
1 TTTAGG-GTTAGGGTTTATGTTTATGGTTTATGGTTTGTGGTTTA-GG
*
975 TTTAGGTTTAGGGTT
1 TTTAGGGTTAGGGTT
990 AAGTTTAGGG
Statistics
Matches: 168, Mismatches: 23, Indels: 35
0.74 0.10 0.15
Matches are distributed among these distances:
44 6 0.04
45 33 0.20
46 9 0.05
47 10 0.06
48 60 0.36
49 6 0.04
50 14 0.08
51 10 0.06
52 4 0.02
53 6 0.04
54 10 0.06
ACGTcount: A:0.16, C:0.00, G:0.34, T:0.49
Consensus pattern (46 bp):
TTTAGGGTTAGGGTTTATGTTTATGGTTTATGGTTTGTGGTTTAGG
Found at i:866 original size:14 final size:14
Alignment explanation
Indices: 742--1058 Score: 228
Period size: 14 Copynumber: 23.8 Consensus size: 14
732 ATATTTAGGG
*
742 TTAGGGTTTATGAT
1 TTAGGGTTTATGGT
* *
756 TTATGGTTTGTGGT
1 TTAGGGTTTATGGT
770 TT-GTGGTTTATGGT
1 TTAG-GGTTTATGGT
*
784 TTAGGG-TTAAGGT
1 TTAGGGTTTATGGT
*
797 TTATGGTTTATGGT
1 TTAGGGTTTATGGT
* *
811 TTATGGTTTATGAT
1 TTAGGGTTTATGGT
825 TTAGGGTTTATGG-
1 TTAGGGTTTATGGT
*
838 TTATGG-TTA--GT
1 TTAGGGTTTATGGT
849 TTAGGGTTTATGGT
1 TTAGGGTTTATGGT
*
863 TTAGTG-TTA--GT
1 TTAGGGTTTATGGT
874 TTAGGG-TTA-GG-
1 TTAGGGTTTATGGT
*
885 TTAGGGTTTATAGT
1 TTAGGGTTTATGGT
*
899 TTAGGGTTAGGTTAAGGT
1 TTAGGG-T---TTATGGT
917 TTAGGGTTTATGGT
1 TTAGGGTTTATGGT
*
931 TTA-GGTTT-TAGT
1 TTAGGGTTTATGGT
943 GTTAGGG-TTAT-GT
1 -TTAGGGTTTATGGT
* *
956 TTATGG-TTAGGGT
1 TTAGGGTTTATGGT
969 TTAGGGTTTA-GGT
1 TTAGGGTTTATGGT
*
982 TTAGGG-TTA-AGT
1 TTAGGGTTTATGGT
*
994 TTAGGG-TTAGGGT
1 TTAGGGTTTATGGT
1007 TTAGGGTTTATGG-
1 TTAGGGTTTATGGT
** *
1020 TTAATGTTTATCGT
1 TTAGGGTTTATGGT
* * *
1034 GTAGGATTTAGGGT
1 TTAGGGTTTATGGT
1048 TTAGGGTTTAT
1 TTAGGGTTTAT
1059 ATATATAGTT
Statistics
Matches: 242, Mismatches: 38, Indels: 46
0.74 0.12 0.14
Matches are distributed among these distances:
10 1 0.00
11 21 0.09
12 35 0.14
13 66 0.27
14 105 0.43
15 2 0.01
17 1 0.00
18 11 0.05
ACGTcount: A:0.17, C:0.00, G:0.34, T:0.49
Consensus pattern (14 bp):
TTAGGGTTTATGGT
Found at i:875 original size:11 final size:11
Alignment explanation
Indices: 842--1014 Score: 93
Period size: 13 Copynumber: 14.4 Consensus size: 11
832 TTATGGTTAT
842 GGTTAGTTTAG
1 GGTTAGTTTAG
853 GGTTTATGGTTTAG
1 GG-TTA--GTTTAG
*
867 TGTTAGTTTAG
1 GGTTAGTTTAG
*
878 GGTTAGGTTAG
1 GGTTAGTTTAG
889 GGTTTATAGTTTAG
1 GG--T-TAGTTTAG
*
903 GGTTAGGTTA-
1 GGTTAGTTTAG
*
913 AG---GTTTAG
1 GGTTAGTTTAG
921 GGTTTATGGTTTAG
1 GG-TTA--GTTTAG
*
935 GTTTTAGTGTTAG
1 G-GTTAGT-TTAG
*
948 GGTTATGTTTAT
1 GGTTA-GTTTAG
960 GGTTAGGGTTTAG
1 GGTTA--GTTTAG
973 GGTTTAGGTTTAG
1 GG-TTA-GTTTAG
986 GGTTAAGTTTAG
1 GGTT-AGTTTAG
998 GGTTAGGGTTTAG
1 GGTTA--GTTTAG
1011 GGTT
1 GGTT
1015 TATGGTTAAT
Statistics
Matches: 128, Mismatches: 13, Indels: 40
0.71 0.07 0.22
Matches are distributed among these distances:
7 4 0.03
8 1 0.01
10 1 0.01
11 26 0.20
12 29 0.23
13 38 0.30
14 29 0.23
ACGTcount: A:0.17, C:0.00, G:0.36, T:0.46
Consensus pattern (11 bp):
GGTTAGTTTAG
Found at i:883 original size:6 final size:6
Alignment explanation
Indices: 825--1014 Score: 82
Period size: 6 Copynumber: 30.3 Consensus size: 6
815 GGTTTATGAT
* * * * * *
825 TTAGGG TTTATGG TTATGG TTA-GT TTAGGG TTTATGGT TTAGTG TTA-GT
1 TTAGGG -TTAGGG TTAGGG TTAGGG TTAGGG -TTA-GGG TTAGGG TTAGGG
* * *
874 TTAGGG TTA-GG TTAGGG TTTATAGT TTAGGG TTA-GG TTAAGGT TTAGGG
1 TTAGGG TTAGGG TTAGGG -TTA-GGG TTAGGG TTAGGG TT-AGGG TTAGGG
* * * * * *
923 TTTATGGT TTAGGTT TTAGTG TTAGGG TTATGT TTATGG TTAGGG TTTAGGG
1 -TTA-GGG TTAGG-G TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG -TTAGGG
* * *
975 TTTAGGT TTAGGG TTAAGT TTAGGG TTAGGG TTTAGGG TT
1 -TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG -TTAGGG TT
1015 TATGGTTAAT
Statistics
Matches: 140, Mismatches: 29, Indels: 29
0.71 0.15 0.15
Matches are distributed among these distances:
5 16 0.11
6 70 0.50
7 49 0.35
8 5 0.04
ACGTcount: A:0.17, C:0.00, G:0.36, T:0.47
Consensus pattern (6 bp):
TTAGGG
Found at i:1011 original size:25 final size:23
Alignment explanation
Indices: 781--1014 Score: 140
Period size: 25 Copynumber: 9.5 Consensus size: 23
771 TGTGGTTTAT
*
781 GGTTTAGGGTTAAGGTTTATGGTTTA
1 GGTTTAGGGTT-A-GTTTA-GGGTTA
*
807 TGGTTTATGGTTTATGATTTAGGGTTTA
1 -GGTTTA-GGGTTA-G-TTTAGGG-TTA
*
835 TGG-TTATGGTTAGTTTAGGGTTTA
1 -GGTTTAGGGTTAGTTTAGGG-TTA
*
859 TGGTTTAGTGTTAGTTTAGGGTTA
1 -GGTTTAGGGTTAGTTTAGGGTTA
883 GG-TTAGGGTTTATAGTTTAGGGTTA
1 GGTTTAGGG--T-TAGTTTAGGGTTA
*
908 GG-TTA-AG---GTTTAGGGTTTA
1 GGTTTAGGGTTAGTTTAGGG-TTA
*
927 TGGTTTAGGTTTTAGTGTTAGGGTTA
1 -GGTTTAGG-GTTAGT-TTAGGGTTA
* *
953 TGTTTATGGTTAGGGTTTAGGGTTTA
1 GGTTTAGGGTTA--GTTTAGGG-TTA
979 GGTTTAGGGTTAAGTTTAGGGTTA
1 GGTTTAGGGTT-AGTTTAGGGTTA
1003 GGGTTTAGGGTT
1 -GGTTTAGGGTT
1015 TATGGTTAAT
Statistics
Matches: 170, Mismatches: 16, Indels: 44
0.74 0.07 0.19
Matches are distributed among these distances:
18 8 0.05
19 3 0.02
20 2 0.01
21 3 0.02
22 5 0.03
23 2 0.01
24 25 0.15
25 65 0.38
26 23 0.14
27 20 0.12
28 14 0.08
ACGTcount: A:0.18, C:0.00, G:0.35, T:0.47
Consensus pattern (23 bp):
GGTTTAGGGTTAGTTTAGGGTTA
Found at i:1360 original size:21 final size:21
Alignment explanation
Indices: 1270--1361 Score: 75
Period size: 21 Copynumber: 4.4 Consensus size: 21
1260 ACGAATAACA
*
1270 GATAACGGATAACCGGAAATG
1 GATAACGGATAACGGGAAATG
* *
1291 GATAACGGATAATGGGAAATA
1 GATAACGGATAACGGGAAATG
* *
1312 GATAACGGGA-AA-TGGATA-G
1 GATAAC-GGATAACGGGAAATG
1331 CCTGA-AACGGATAACGGGAAATG
1 ---GATAACGGATAACGGGAAATG
1354 GATAACGG
1 GATAACGG
1362 GAAACGAAAG
Statistics
Matches: 55, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
20 9 0.16
21 36 0.65
22 9 0.16
23 1 0.02
ACGTcount: A:0.42, C:0.11, G:0.32, T:0.15
Consensus pattern (21 bp):
GATAACGGATAACGGGAAATG
Found at i:1367 original size:28 final size:28
Alignment explanation
Indices: 1297--1367 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
1287 AATGGATAAC
* **
1297 GGATAATGGGAAATAGATAACGGGAAAT
1 GGATAACGGGAAACGGATAACGGGAAAT
* **
1325 GGATAGCCTGAAACGGATAACGGGAAAT
1 GGATAACGGGAAACGGATAACGGGAAAT
1353 GGATAACGGGAAACG
1 GGATAACGGGAAACG
1368 AAAGGAAATG
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.42, C:0.10, G:0.34, T:0.14
Consensus pattern (28 bp):
GGATAACGGGAAACGGATAACGGGAAAT
Found at i:1842 original size:18 final size:18
Alignment explanation
Indices: 1821--1857 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1811 GAACTATGAG
1821 AACAAATATAACTCGTGT
1 AACAAATATAACTCGTGT
1839 AACAAATATAACTCGTGT
1 AACAAATATAACTCGTGT
1857 A
1 A
1858 CCTTCTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.16, G:0.11, T:0.27
Consensus pattern (18 bp):
AACAAATATAACTCGTGT
Found at i:3793 original size:41 final size:41
Alignment explanation
Indices: 3747--3826 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
3737 CTTCAATTTT
*
3747 TAAAGATTTTGAATGGAGAAAGAA-AGAATTTGGGATTTATC
1 TAAAGAATTTGAATGGAG-AAGAAGAGAATTTGGGATTTATC
3788 TAAAGAATTTGAATGGAGAAGAAGAGAATTTGGGATTTA
1 TAAAGAATTTGAATGGAGAAGAAGAGAATTTGGGATTTA
3827 GGATTCTTCG
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
40 5 0.14
41 32 0.86
ACGTcount: A:0.42, C:0.01, G:0.26, T:0.30
Consensus pattern (41 bp):
TAAAGAATTTGAATGGAGAAGAAGAGAATTTGGGATTTATC
Found at i:3805 original size:115 final size:115
Alignment explanation
Indices: 3671--3900 Score: 372
Period size: 115 Copynumber: 2.0 Consensus size: 115
3661 AGCTTTAATT
*
3671 TCTAAAGAATTTGAATGGAGAATG-AGAGAATTTGAGATTTAGGGTTCTTCAAAGGAGAGTTTCA
1 TCTAAAGAATTTGAATGGAGAA-GAAGAGAATTTGAGATTTAGGATTCTTCAAAGGAGAGTTTCA
* *
3735 AGCTTCAATTTTTAAAGATTTTGAATGGAGAAAGAAAGAATTTGGGATTTA
65 AGCTTCAATTTCTAAAGAATTTGAATGGAGAAAGAAAGAATTTGGGATTTA
* * *
3786 TCTAAAGAATTTGAATGGAGAAGAAGAGAATTTGGGATTTAGGATTCTTCGAAGGGGAGTTTCAA
1 TCTAAAGAATTTGAATGGAGAAGAAGAGAATTTGAGATTTAGGATTCTTCAAAGGAGAGTTTCAA
* *
3851 GCTTCAATTTCTAAAGAATTTGAATGGAGAAGGGAAGAATTTGGGATTTA
66 GCTTCAATTTCTAAAGAATTTGAATGGAGAAAGAAAGAATTTGGGATTTA
3901 GGGTTCTTCA
Statistics
Matches: 106, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
114 1 0.01
115 105 0.99
ACGTcount: A:0.37, C:0.06, G:0.26, T:0.32
Consensus pattern (115 bp):
TCTAAAGAATTTGAATGGAGAAGAAGAGAATTTGAGATTTAGGATTCTTCAAAGGAGAGTTTCAA
GCTTCAATTTCTAAAGAATTTGAATGGAGAAAGAAAGAATTTGGGATTTA
Found at i:4009 original size:18 final size:18
Alignment explanation
Indices: 3988--4027 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
3978 TTTTTTTTTT
*
3988 TTTTTAA-TTTTAATTATG
1 TTTTTAAGTTTAAATT-TG
4006 TTTTTAAGTTTAAATTTG
1 TTTTTAAGTTTAAATTTG
4024 TTTT
1 TTTT
4028 GTTGACGTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (18 bp):
TTTTTAAGTTTAAATTTG
Found at i:6260 original size:18 final size:17
Alignment explanation
Indices: 6237--6270 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
6227 AATAATAGTA
*
6237 TAGATTCTTATTCTAATT
1 TAGATTATTATT-TAATT
6255 TAGATTATTATTTAAT
1 TAGATTATTATTTAAT
6271 AATTATGATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.56
Consensus pattern (17 bp):
TAGATTATTATTTAATT
Found at i:7929 original size:7 final size:7
Alignment explanation
Indices: 7891--7915 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
7881 ACTAAACCCT
7891 TTTAAAA
1 TTTAAAA
7898 TTTAAAA
1 TTTAAAA
7905 TTTAAAA
1 TTTAAAA
7912 TTTA
1 TTTA
7916 TTGAAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (7 bp):
TTTAAAA
Found at i:8167 original size:34 final size:36
Alignment explanation
Indices: 8103--8171 Score: 97
Period size: 34 Copynumber: 2.0 Consensus size: 36
8093 AAATTATAAT
* **
8103 TTTATAATTTTATAGCTTTTTTTTTTATAAATTTTG
1 TTTATAATTTTATAGCATTTTTTTAAATAAATTTTG
8139 TTTATAATTTTAT-G-ATTTTTTTAAATAAATTTT
1 TTTATAATTTTATAGCATTTTTTTAAATAAATTTT
8172 AAAATTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 16 0.53
35 1 0.03
36 13 0.43
ACGTcount: A:0.29, C:0.01, G:0.04, T:0.65
Consensus pattern (36 bp):
TTTATAATTTTATAGCATTTTTTTAAATAAATTTTG
Found at i:8512 original size:76 final size:76
Alignment explanation
Indices: 8394--8534 Score: 228
Period size: 76 Copynumber: 1.9 Consensus size: 76
8384 ACGTGCACGG
* **
8394 GCTAATTTGCCCATTTTTTTAATGGAGGGGCTAAAATGTAATTTATGGTATTGTACATGAGGAGT
1 GCTAATTTGCCCATTTTTTCAATGGAGGGGCTAAAATGTAATTTATGGTATAATACATGAGGAGT
8459 AATGTGCATGA
66 AATGTGCATGA
* * *
8470 GCTAATTTGTCCATTTTTTCAGTGGAGGGGCTAAAATGTAATTTATGGTATAATACATGGGGAGT
1 GCTAATTTGCCCATTTTTTCAATGGAGGGGCTAAAATGTAATTTATGGTATAATACATGAGGAGT
8535 GTTGTGATAT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
76 59 1.00
ACGTcount: A:0.28, C:0.09, G:0.26, T:0.37
Consensus pattern (76 bp):
GCTAATTTGCCCATTTTTTCAATGGAGGGGCTAAAATGTAATTTATGGTATAATACATGAGGAGT
AATGTGCATGA
Found at i:9335 original size:31 final size:31
Alignment explanation
Indices: 9296--9362 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 31
9286 TTAATTGAAT
* *
9296 TTTTAAAAAAATTAGAAG-GTATGATGAAAA
1 TTTTAAAAAAATTAAAAGAGTATAATGAAAA
* *
9326 TTTTAAAAAAATTAAAAGAGTCTAATTAAAA
1 TTTTAAAAAAATTAAAAGAGTATAATGAAAA
9357 TTTTAA
1 TTTTAA
9363 TGGAGGGAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 17 0.53
31 15 0.47
ACGTcount: A:0.54, C:0.01, G:0.10, T:0.34
Consensus pattern (31 bp):
TTTTAAAAAAATTAAAAGAGTATAATGAAAA
Found at i:20450 original size:18 final size:17
Alignment explanation
Indices: 20419--20452 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
20409 TACCTAAGGT
*
20419 ATTTTATATTTATATAA
1 ATTTTATATGTATATAA
20436 ATTTTAATATGTATATA
1 ATTTT-ATATGTATATA
20453 TATTGATGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
ATTTTATATGTATATAA
Found at i:21902 original size:23 final size:23
Alignment explanation
Indices: 21876--21981 Score: 131
Period size: 23 Copynumber: 4.5 Consensus size: 23
21866 AGTGTTTGGC
*
21876 AACAGAGAGCACACATAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
21899 AACAGAGAGTACACAAAGTACTA
1 AACAGAGAGCACACAAAGTGCTA
*
21922 ATCAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* * *
21945 ATCAAAGAGCACACACAGTGCTAA
1 AACAGAGAGCACACAAAGTGCT-A
21969 TAACAGAGAGCAC
1 -AACAGAGAGCAC
21982 GAGACGTGCT
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
23 60 0.85
24 1 0.01
25 10 0.14
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.12
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTGCTA
Found at i:21928 original size:46 final size:47
Alignment explanation
Indices: 21877--22002 Score: 148
Period size: 46 Copynumber: 2.7 Consensus size: 47
21867 GTGTTTGGCA
* * *
21877 ACAGAGAGCACACATAGTGCTAAACAGAGAGTACACAAAGTACTAAT
1 ACAGAGAGCACACAAAGTGCTAAACAAAGAGCACACAAAGTACTAAT
* * *
21924 -CAGAGAGCACACAAAGTGCTAATCAAAGAGCACACACAGTGCTAAT
1 ACAGAGAGCACACAAAGTGCTAAACAAAGAGCACACAAAGTACTAAT
* *
21970 AACAGAGAGCACGA-GACGTGCTAAACAAAGAGC
1 -ACAGAGAGCAC-ACAAAGTGCTAAACAAAGAGC
22003 GTGCTAGTGT
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
46 40 0.60
48 26 0.39
49 1 0.01
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.12
Consensus pattern (47 bp):
ACAGAGAGCACACAAAGTGCTAAACAAAGAGCACACAAAGTACTAAT
Found at i:21954 original size:69 final size:68
Alignment explanation
Indices: 21829--21978 Score: 171
Period size: 69 Copynumber: 2.1 Consensus size: 68
21819 TATACGGAAC
* * * * *
21829 AAACAGAGAGTACCAAAGTAGTAACAGAGAGCACATAAGTGTTTGGCAACAGAGAGCACACATAG
1 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGTCT-G-AACAAAGAGCACACACAG
21894 TGCT-
64 TGCTA
21898 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTG-CT-AATCAAAGAGCACACAC
1 AAACAGAGAGTAC-CAAAGTACTAA-CAGAGAGCACA-AAAGTGTCTGAA-CAAAGAGCACACAC
21961 AGTGCTA
62 AGTGCTA
21968 ATAACAGAGAG
1 A-AACAGAGAG
21979 CACGAGACGT
Statistics
Matches: 70, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
68 2 0.03
69 31 0.44
70 11 0.16
71 21 0.30
72 5 0.07
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.14
Consensus pattern (68 bp):
AAACAGAGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGTCTGAACAAAGAGCACACACAGTG
CTA
Found at i:21996 original size:23 final size:23
Alignment explanation
Indices: 21876--22002 Score: 112
Period size: 23 Copynumber: 5.4 Consensus size: 23
21866 AGTGTTTGGC
* *
21876 AACAGAGAGCACACATAGTGCTA
1 AACAAAGAGCACACACAGTGCTA
* * * *
21899 AACAGAGAGTACACAAAGTACTA
1 AACAAAGAGCACACACAGTGCTA
* * *
21922 ATCAGAGAGCACACAAAGTGCTA
1 AACAAAGAGCACACACAGTGCTA
*
21945 ATCAAAGAGCACACACAGTGCTAA
1 AACAAAGAGCACACACAGTGCT-A
* *
21969 TAACAGAGAGCACGAGAC-GTGCTA
1 -AACAAAGAGCAC-ACACAGTGCTA
21993 AACAAAGAGC
1 AACAAAGAGC
22003 GTGCTAGTGT
Statistics
Matches: 89, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
23 69 0.78
24 2 0.02
25 15 0.17
26 3 0.03
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.12
Consensus pattern (23 bp):
AACAAAGAGCACACACAGTGCTA
Done.