Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009969.1 Kokia drynarioides strain JFW-HI SEQ_124718, 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: 130369
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 30 characters in sequence are not A, C, G, or T
Found at i:80 original size:20 final size:21
Alignment explanation
Indices: 55--97 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
45 TACTTACTAC
55 TACTAAC-AACAAAATAAAAT
1 TACTAACTAACAAAATAAAAT
* *
75 TACTAACTAATAAAATTAAAT
1 TACTAACTAACAAAATAAAAT
96 TA
1 TA
98 AAGTAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (21 bp):
TACTAACTAACAAAATAAAAT
Found at i:781 original size:13 final size:13
Alignment explanation
Indices: 763--797 Score: 56
Period size: 11 Copynumber: 2.8 Consensus size: 13
753 AGGGTGTCAG
763 GTATTTTTTTGTC
1 GTATTTTTTTGTC
776 GTA--TTTTTGTC
1 GTATTTTTTTGTC
787 GTATTTTTTTG
1 GTATTTTTTTG
798 AAAAAAACCC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 11 0.55
13 9 0.45
ACGTcount: A:0.09, C:0.06, G:0.17, T:0.69
Consensus pattern (13 bp):
GTATTTTTTTGTC
Found at i:887 original size:11 final size:11
Alignment explanation
Indices: 871--895 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
861 TTAAATATAT
871 AAAAATAAAAA
1 AAAAATAAAAA
882 AAAAATAAAAA
1 AAAAATAAAAA
893 AAA
1 AAA
896 CACGTGTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (11 bp):
AAAAATAAAAA
Found at i:2177 original size:16 final size:15
Alignment explanation
Indices: 2137--2179 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
2127 TGTCAATATA
* *
2137 AAATTAT-ATTTTAT
1 AAATTATAATTATGT
2151 AAATTATAATTATGT
1 AAATTATAATTATGT
2166 AAATTAATAATTAT
1 AAATT-ATAATTAT
2180 TTGAAATGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 7 0.28
15 10 0.40
16 8 0.32
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (15 bp):
AAATTATAATTATGT
Found at i:8529 original size:18 final size:17
Alignment explanation
Indices: 8485--8529 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
8475 ATTATTATTC
* *
8485 AAATAAAATTTGAAATT
1 AAATTAAATTTAAAATT
8502 AAATTGAAATTTAAAATT
1 AAATT-AAATTTAAAATT
8520 AAAATTAAAT
1 -AAATTAAAT
8530 AAAACTTGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 4 0.17
18 15 0.62
19 5 0.21
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (17 bp):
AAATTAAATTTAAAATT
Found at i:8570 original size:17 final size:17
Alignment explanation
Indices: 8550--8586 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
8540 GAAGAAAAAT
*
8550 AAATTGAAATGAAATGA
1 AAATTCAAATGAAATGA
*
8567 AAATTCAAATTAAATGA
1 AAATTCAAATGAAATGA
8584 AAA
1 AAA
8587 AATAATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.11, T:0.24
Consensus pattern (17 bp):
AAATTCAAATGAAATGA
Found at i:8811 original size:11 final size:11
Alignment explanation
Indices: 8785--8848 Score: 83
Period size: 11 Copynumber: 5.7 Consensus size: 11
8775 AGCTTCAGAC
*
8785 ATGAAATTTAAA
1 ATGAAA-TTCAA
8797 ATGAAATTCAA
1 ATGAAATTCAA
8808 ATGAAATTCAA
1 ATGAAATTCAA
* *
8819 TTGAAATTAAA
1 ATGAAATTCAA
*
8830 ATGAAAATCAA
1 ATGAAATTCAA
8841 ATGAAATT
1 ATGAAATT
8849 TAACTAAATT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
11 39 0.87
12 6 0.13
ACGTcount: A:0.56, C:0.05, G:0.09, T:0.30
Consensus pattern (11 bp):
ATGAAATTCAA
Found at i:8862 original size:33 final size:34
Alignment explanation
Indices: 8786--8864 Score: 117
Period size: 33 Copynumber: 2.4 Consensus size: 34
8776 GCTTCAGACA
* *
8786 TGAAATTTAAAATGAAATTCAAATGAAATTCAAT
1 TGAAATTTAAAATGAAAATCAAATGAAATTCAAC
*
8820 TGAAA-TTAAAATGAAAATCAAATGAAATTTAAC
1 TGAAATTTAAAATGAAAATCAAATGAAATTCAAC
8853 T-AAATTTAAAAT
1 TGAAATTTAAAAT
8865 TTAATGGGTG
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
32 3 0.07
33 33 0.80
34 5 0.12
ACGTcount: A:0.56, C:0.05, G:0.08, T:0.32
Consensus pattern (34 bp):
TGAAATTTAAAATGAAAATCAAATGAAATTCAAC
Found at i:8899 original size:24 final size:24
Alignment explanation
Indices: 8872--8927 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
8862 AATTTAATGG
*
8872 GTGGCAGGCCTAAACCTGCGTCAA
1 GTGGCAGGCCTAAACCCGCGTCAA
* * * *
8896 GTGGTAGGCTTAAGCCCGCGTCAG
1 GTGGCAGGCCTAAACCCGCGTCAA
8920 GTGGCAGG
1 GTGGCAGG
8928 TGCGTGAGGT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.20, C:0.25, G:0.38, T:0.18
Consensus pattern (24 bp):
GTGGCAGGCCTAAACCCGCGTCAA
Found at i:27748 original size:52 final size:52
Alignment explanation
Indices: 27666--27960 Score: 466
Period size: 52 Copynumber: 5.7 Consensus size: 52
27656 AATGAAAAAG
* * * *
27666 GGTCCGATGACTAAGTGTCATCGTGAGTATACGAATCCTTTACAGATTATGA
1 GGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
* *
27718 GGTTCGATGGCTATGTGTCATTGTGAGTATATGAATCCTTTACGGATTATGA
1 GGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
* *
27770 GGTCCGATGGCTATGTGTCATCGTAAGTATATGAAACCTTTACGGATTATGA
1 GGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
*
27822 GGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATGA
1 GGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
* * *
27874 GGTCCGATGGCTATGTGCCATCATGATTATATGAATCCTTTACGGATTATGA
1 GGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
*
27926 GGTCCGATGACTATGT-TCATCGTGAGTATATGAAT
1 GGTCCGATGGCTATGTGTCATCGTGAGTATATGAAT
27961 GAAATGAAAT
Statistics
Matches: 222, Mismatches: 21, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
51 16 0.07
52 206 0.93
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (52 bp):
GGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
Found at i:30872 original size:32 final size:33
Alignment explanation
Indices: 30812--30890 Score: 92
Period size: 32 Copynumber: 2.4 Consensus size: 33
30802 ATTATAATTA
30812 AAATTTAACTTCTTAATTTTCAAATTTTAT-TTAAT
1 AAATTTAAC-T-TT-ATTTTCAAATTTTATATTAAT
**
30847 AAATTTAACTTTATTTTCATTTTTTATATTAAT
1 AAATTTAACTTTATTTTCAAATTTTATATTAAT
30880 -AATTTAA-TTTA
1 AAATTTAACTTTA
30891 ATTATCTTCA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
31 4 0.10
32 20 0.49
33 7 0.17
34 1 0.02
35 9 0.22
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (33 bp):
AAATTTAACTTTATTTTCAAATTTTATATTAAT
Found at i:30932 original size:17 final size:17
Alignment explanation
Indices: 30912--30948 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
30902 AAATTATTTT
*
30912 TTTTCATTTAATTTGAA
1 TTTTCATTTAATTTCAA
*
30929 TTTTCATTTCATTTCAA
1 TTTTCATTTAATTTCAA
30946 TTT
1 TTT
30949 CTTTTTCTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.24, C:0.11, G:0.03, T:0.62
Consensus pattern (17 bp):
TTTTCATTTAATTTCAA
Found at i:30986 original size:12 final size:12
Alignment explanation
Indices: 30969--31027 Score: 50
Period size: 12 Copynumber: 4.9 Consensus size: 12
30959 CTCAACTTTT
30969 ATTTAATTTTAA
1 ATTTAATTTTAA
* *
30981 ATTTAAATTTCA
1 ATTTAATTTTAA
* *
30993 ACTTAATTTCAA
1 ATTTAATTTTAA
31005 ATTGT-A-TTTAA
1 ATT-TAATTTTAA
31016 ATATTAATTTTA
1 AT-TTAATTTTA
31028 TTTCATTAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 7
0.70 0.16 0.14
Matches are distributed among these distances:
11 7 0.20
12 23 0.66
13 5 0.14
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.53
Consensus pattern (12 bp):
ATTTAATTTTAA
Found at i:34132 original size:42 final size:41
Alignment explanation
Indices: 34054--34136 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 41
34044 ACAAAACACT
* *
34054 TATATATATATACTACTAGGGTGCTAGAGATTTATAGGATA
1 TATATATATATACTACTAGGGTGCCAGAGATCTATAGGATA
* * *
34095 TATATATATCTACTACCTAGGGTGCCGGTGATCTATAGGATA
1 TATATATATATACTA-CTAGGGTGCCAGAGATCTATAGGATA
34137 AAAAACCAGC
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 14 0.39
42 22 0.61
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (41 bp):
TATATATATATACTACTAGGGTGCCAGAGATCTATAGGATA
Found at i:34487 original size:56 final size:55
Alignment explanation
Indices: 34319--34487 Score: 139
Period size: 55 Copynumber: 3.0 Consensus size: 55
34309 TCAAAGATCC
* * * * * *
34319 AAAAAATATTTTTTAATCTAAGTTTTTTTGTGTTTG-CCAATAGGTGTCAAAAATCCAA
1 AAAAAATATTTTTT-AT-TCA-TTTTTTGGTG-TCGACCATTAGGTGGCAAACATCCAA
* * *
34377 AAAAAATATTTTTTATTCATTTTTTGGTGTCGACTATTAGCT-GCTAAACGTCCAA
1 AAAAAATATTTTTTATTCATTTTTTGGTGTCGACCATTAGGTGGC-AAACATCCAA
**
34432 AAAATAAT-TTTTTTATTC-TTTTTTTTTGTGCAGACCATTAGGTGGCAAACATCCAA
1 AAAA-AATATTTTTTATTCATTTTTTGGTGT-C-GACCATTAGGTGGCAAACATCCAA
34488 TTTTTTCAAA
Statistics
Matches: 91, Mismatches: 14, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
54 12 0.13
55 38 0.42
56 23 0.25
57 4 0.04
58 14 0.15
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (55 bp):
AAAAAATATTTTTTATTCATTTTTTGGTGTCGACCATTAGGTGGCAAACATCCAA
Found at i:36858 original size:27 final size:27
Alignment explanation
Indices: 36828--36882 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
36818 TACTTGACAC
*
36828 CCAATGGAGGAACA-CGAAGTGGCGGCA
1 CCAATGGAAGAACATC-AAGTGGCGGCA
*
36855 CCAATGGAAGAATATCAAGTGGCGGCA
1 CCAATGGAAGAACATCAAGTGGCGGCA
36882 C
1 C
36883 TAAGGGGTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 24 0.96
28 1 0.04
ACGTcount: A:0.35, C:0.22, G:0.33, T:0.11
Consensus pattern (27 bp):
CCAATGGAAGAACATCAAGTGGCGGCA
Found at i:37226 original size:16 final size:16
Alignment explanation
Indices: 37181--37230 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
37171 TAAACTTAGC
*
37181 TAATTAATTACCAAAA
1 TAATTAATTATCAAAA
*
37197 T-A-TAA-TATAAAAAA
1 TAATTAATTAT-CAAAA
37211 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
37227 TAAT
1 TAAT
37231 ATCCCCATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 2 0.07
16 12 0.44
17 3 0.11
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Found at i:37253 original size:59 final size:59
Alignment explanation
Indices: 37190--37424 Score: 425
Period size: 59 Copynumber: 4.0 Consensus size: 59
37180 CTAATTAATT
37190 ACCAAAATATAATATAAAAAATAATTAATTATCAAAATAATATCCCCATCATATTATTG
1 ACCAAAATATAATATAAAAAATAATTAATTATCAAAATAATATCCCCATCATATTATTG
****
37249 ACCAAAATATAATATAAAAAATAATTAATTATCAAAATAATATTYYYATCATATTATTG
1 ACCAAAATATAATATAAAAAATAATTAATTATCAAAATAATATCCCCATCATATTATTG
37308 ACCAAAATATAATATAAAAAATAATTAATTATCAAAATAATATCCCCATCATATTATTG
1 ACCAAAATATAATATAAAAAATAATTAATTATCAAAATAATATCCCCATCATATTATTG
*
37367 ACCAAAATATAATATAAAAAATAATTAATTATGAAAATAATATCCCCATCATATTATT
1 ACCAAAATATAATATAAAAAATAATTAATTATCAAAATAATATCCCCATCATATTATT
37425 TTATCTTATC
Statistics
Matches: 167, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 167 1.00
ACGTcount: A:0.53, C:0.11, G:0.02, T:0.33
Consensus pattern (59 bp):
ACCAAAATATAATATAAAAAATAATTAATTATCAAAATAATATCCCCATCATATTATTG
Found at i:37603 original size:28 final size:28
Alignment explanation
Indices: 37545--37600 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
37535 ACACTCCTTA
* *
37545 GTGCCGCCACTTGATATTTCCTCTATTG
1 GTGCCGCCACTTGATAGTTCCTCCATTG
37573 GTGCCGCCACTTCG-T-GTTCCTCCATTG
1 GTGCCGCCACTT-GATAGTTCCTCCATTG
37600 G
1 G
37601 GTGTCAGGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 11 0.44
28 13 0.52
29 1 0.04
ACGTcount: A:0.11, C:0.32, G:0.21, T:0.36
Consensus pattern (28 bp):
GTGCCGCCACTTGATAGTTCCTCCATTG
Found at i:41582 original size:164 final size:162
Alignment explanation
Indices: 41047--41629 Score: 456
Period size: 164 Copynumber: 3.6 Consensus size: 162
41037 TTGTTAGTAG
* * * * *
41047 TAGTAATTATTATAAAATGTTTTTTTA--ATTTTAATGTTTAATGTGATTTGTTA-TAATTTTAT
1 TAGTAATTATTATAAATTATTTATTTAGTTTTTTAAT-TTTTATGTGATTTGTTATTAATTTT-T
* * * * * * * *
41109 CTGTTTAGTAG-ATATATT-AAGGGA-AAAAAAAGCTAAAAGAAAGATAAATATTTTGTTGTTT-
64 TTATTTAGTAGAATAGATTAAAAGAAGAAAAAAAGCTAAAAGAAAGGTAATTATTTTGTTATTTG
*
41170 TTTA---TAA---AATTGAATTTAAAGTTATTTTT
129 TTTAGTTTAATTTAATTTAATTTAAAGTTA-TTTT
* * * *
41199 TAGTAATTATTATAAATTTTTTGTTTTGTTTTGTTTAATTTTTATGTGATTTGTTATTAATTTTG
1 TAGTAATTATTATAAATTATTTATTTAG-TTT-TTTAATTTTTATGTGATTTGTTATTAATTTTT
* * ** * * *
41264 TTATTTTGTAGAGTAGATTGAAGGGGAGAAAGATAAA-TTTAAAGAAAGGTAAGTT-TTGTTGTT
64 TTATTTAGTAGAATAGATT-AAAAGAAGAAA-A-AAAGCTAAAAGAAAGGTAA-TTATT-TTGTT
* * * *
41327 GTTGTTGTTGTTGTTTTTAATTTAATTTAATTT---TTTTTTTGT
124 -AT-TTGTT-TAG--TTTAATTTAATTTAATTTAAAGTTATTT-T
* * * *
41369 TAGTAATTATTATAAAATATTTTTTTAG---TTTAATGTTTATATGATTTGTTA-TAATTGTTTT
1 TAGTAATTATTATAAATTATTTATTTAGTTTTTTAATTTTTATGTGATTTGTTATTAATT-TTTT
* * *
41430 TGGTTTAGTAG-GTAGATTAAAAGAAGAAAAAAAGCTAAAAGAAAGGTAATTATTTTAAATTATT
65 T-ATTTAGTAGAATAGATTAAAAGAAGAAAAAAAGCTAAAAGAAAGGTAATTATTTT--GTTATT
41494 TGTTTAGTTTAATTTAATTTAATTTAAAGTTATTTT
127 TGTTTAGTTTAATTTAATTTAATTTAAAGTTATTTT
* *
41530 TAGTAATTATTATAAATTAATTAATTAGTTTTTTAATTTTTATGTGATTTGTTATTAATTTTTTT
1 TAGTAATTATTATAAATTATTTATTTAGTTTTTTAATTTTTATGTGATTTGTTATTAATTTTTTT
*
41595 ATTTAGTAGAATAGATTAAATAGATAGAAAGAAAG
66 ATTTAGTAGAATAGATTAAA-AGA-AGAAAAAAAG
41630 GTAAGTTTTA
Statistics
Matches: 339, Mismatches: 50, Indels: 70
0.74 0.11 0.15
Matches are distributed among these distances:
152 23 0.07
155 25 0.07
156 18 0.05
158 5 0.01
159 21 0.06
160 15 0.04
161 36 0.11
162 18 0.05
163 27 0.08
164 52 0.15
165 41 0.12
166 16 0.05
169 3 0.01
170 30 0.09
173 9 0.03
ACGTcount: A:0.35, C:0.01, G:0.14, T:0.51
Consensus pattern (162 bp):
TAGTAATTATTATAAATTATTTATTTAGTTTTTTAATTTTTATGTGATTTGTTATTAATTTTTTT
ATTTAGTAGAATAGATTAAAAGAAGAAAAAAAGCTAAAAGAAAGGTAATTATTTTGTTATTTGTT
TAGTTTAATTTAATTTAATTTAAAGTTATTTT
Found at i:42944 original size:37 final size:38
Alignment explanation
Indices: 42856--42949 Score: 102
Period size: 43 Copynumber: 2.4 Consensus size: 38
42846 TGTTATTCGT
42856 TGACATGTTATTAAATTATAATACTTGACCCGTGTTAATATCG
1 TGACATGTTATTAAATTATAATACTTGA--C---TTAATATCG
* *
42899 TGGA-ATGTTATTAAATTATATTACTTGA-TTAATATTG
1 T-GACATGTTATTAAATTATAATACTTGACTTAATATCG
42936 TGACATGTTATTAA
1 TGACATGTTATTAA
42950 TCGTGCTCAT
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
36 2 0.04
37 19 0.40
43 24 0.51
44 2 0.04
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.44
Consensus pattern (38 bp):
TGACATGTTATTAAATTATAATACTTGACTTAATATCG
Found at i:43345 original size:43 final size:43
Alignment explanation
Indices: 43284--43373 Score: 144
Period size: 43 Copynumber: 2.1 Consensus size: 43
43274 AACTGCACAA
* *
43284 TTAATAATATATCACGATATTAATAAGGGTCAAGTAATATAAT
1 TTAATAACATATCACGATATTAACAAGGGTCAAGTAATATAAT
* *
43327 TTAATAACATGTCACGATATTAACACGGGTCAAGTAATATAAT
1 TTAATAACATATCACGATATTAACAAGGGTCAAGTAATATAAT
43370 TTAA
1 TTAA
43374 CATGTAAAGG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.33
Consensus pattern (43 bp):
TTAATAACATATCACGATATTAACAAGGGTCAAGTAATATAAT
Found at i:48381 original size:7 final size:7
Alignment explanation
Indices: 48369--48468 Score: 64
Period size: 7 Copynumber: 14.4 Consensus size: 7
48359 ATGTATATGT
48369 TTTAAGG
1 TTTAAGG
48376 TTTAAGG
1 TTTAAGG
48383 TTTTAA-G
1 -TTTAAGG
*
48390 TTTAGGG
1 TTTAAGG
48397 TTTAAGG
1 TTTAAGG
*
48404 TTTAGGG
1 TTTAAGG
*
48411 TTTATGG
1 TTTAAGG
* *
48418 TTTATGA
1 TTTAAGG
* *
48425 TTTATGAC
1 TTTAAG-G
48433 TTTAA-G
1 TTTAAGG
*
48439 TTTAAGA
1 TTTAAGG
*
48446 TTTAAGAT
1 TTTAAG-G
48454 TTTAA-G
1 TTTAAGG
48460 TTT-AGG
1 TTTAAGG
48466 TTT
1 TTT
48469 TTTGATTTTT
Statistics
Matches: 76, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
5 1 0.01
6 16 0.21
7 45 0.59
8 14 0.18
ACGTcount: A:0.26, C:0.01, G:0.23, T:0.50
Consensus pattern (7 bp):
TTTAAGG
Found at i:48414 original size:14 final size:14
Alignment explanation
Indices: 48369--48421 Score: 72
Period size: 14 Copynumber: 3.8 Consensus size: 14
48359 ATGTATATGT
*
48369 TTTAAGGTTTAAGGT
1 TTTAAGGTTT-AGGG
48384 TTTAA-GTTTAGGG
1 TTTAAGGTTTAGGG
48397 TTTAAGGTTTAGGG
1 TTTAAGGTTTAGGG
*
48411 TTTATGGTTTA
1 TTTAAGGTTTA
48422 TGATTTATGA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
13 8 0.23
14 22 0.63
15 5 0.14
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.49
Consensus pattern (14 bp):
TTTAAGGTTTAGGG
Found at i:50719 original size:26 final size:26
Alignment explanation
Indices: 50690--50777 Score: 68
Period size: 29 Copynumber: 3.2 Consensus size: 26
50680 CGGTACAAAA
50690 TAAATATTTATTTTGTATCATTTTGG
1 TAAATATTTATTTTGTATCATTTTGG
* *** *
50716 TAAATAATATGATGGGGATATTATTTTGG
1 TAAAT-AT-TTATTTTG-TATCATTTTGG
* * *
50745 TTAAATATATATTTTGTACCATTTTAG
1 -TAAATATTTATTTTGTATCATTTTGG
50772 TAAATA
1 TAAATA
50778 ACTCATTTTG
Statistics
Matches: 45, Mismatches: 13, Indels: 8
0.68 0.20 0.12
Matches are distributed among these distances:
26 11 0.24
27 10 0.22
28 7 0.16
29 12 0.27
30 5 0.11
ACGTcount: A:0.34, C:0.03, G:0.14, T:0.49
Consensus pattern (26 bp):
TAAATATTTATTTTGTATCATTTTGG
Found at i:52019 original size:43 final size:43
Alignment explanation
Indices: 51937--52021 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
51927 ATTAACATGT
* * *
51937 TAAATTATATTACTTGACTCGTGTTAATATGGTTGCATGTTAC
1 TAAATTATATTACTTGACTCGTATTAATATGCTTACATGTTAC
* *
51980 TAAATTATATTACTTTACTCTTATTAATAT-CTTCACATGTTA
1 TAAATTATATTACTTGACTCGTATTAATATGCTT-ACATGTTA
52022 TTAATTGTGC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
42 2 0.06
43 34 0.94
ACGTcount: A:0.31, C:0.13, G:0.09, T:0.47
Consensus pattern (43 bp):
TAAATTATATTACTTGACTCGTATTAATATGCTTACATGTTAC
Found at i:52951 original size:28 final size:27
Alignment explanation
Indices: 52920--53021 Score: 114
Period size: 28 Copynumber: 3.6 Consensus size: 27
52910 TTCATAACAC
52920 TAAACCTTAAACTTAAAATCGTAAACCG
1 TAAACCTTAAACTTAAAATCGTAAA-CG
* * * *
52948 TAAACCTTTAACTTTAAACCTTAAACG
1 TAAACCTTAAACTTAAAATCGTAAACG
* *
52975 TTAAACCTTAAACTTAGAATCGTAAACT
1 -TAAACCTTAAACTTAAAATCGTAAACG
53003 TAAAACCTTAAACCTTAAA
1 T-AAACCTTAAA-CTTAAA
53022 TTTGAAATCG
Statistics
Matches: 60, Mismatches: 11, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
27 3 0.05
28 52 0.87
29 5 0.08
ACGTcount: A:0.45, C:0.21, G:0.05, T:0.29
Consensus pattern (27 bp):
TAAACCTTAAACTTAAAATCGTAAACG
Found at i:52971 original size:7 final size:7
Alignment explanation
Indices: 52920--53075 Score: 88
Period size: 7 Copynumber: 22.3 Consensus size: 7
52910 TTCATAACAC
52920 TAAACCT
1 TAAACCT
52927 TAAA-CT
1 TAAACCT
* *
52933 TAAAATCG
1 T-AAACCT
*
52941 TAAACCG
1 TAAACCT
52948 TAAACCT
1 TAAACCT
* *
52955 TTAACTT
1 TAAACCT
52962 TAAACCT
1 TAAACCT
*
52969 TAAACGT
1 TAAACCT
52976 TAAACCT
1 TAAACCT
52983 TAAA-CT
1 TAAACCT
* *
52989 TAGAATCG
1 TA-AACCT
52997 TAAA-CT
1 TAAACCT
53003 TAAAACCT
1 T-AAACCT
53011 TAAACCT
1 TAAACCT
*
53018 TAAA-TT
1 TAAACCT
* *
53024 TGAAATCG
1 T-AAACCT
**
53032 TAAACAA
1 TAAACCT
53039 TAAACCT
1 TAAACCT
53046 TAAA-CT
1 TAAACCT
* *
53052 AAAAACCC
1 -TAAACCT
53060 TAAACCT
1 TAAACCT
*
53067 TAAATCT
1 TAAACCT
53074 TA
1 TA
53076 TACATGAAAC
Statistics
Matches: 115, Mismatches: 24, Indels: 20
0.72 0.15 0.13
Matches are distributed among these distances:
6 13 0.11
7 92 0.80
8 10 0.09
ACGTcount: A:0.46, C:0.21, G:0.04, T:0.29
Consensus pattern (7 bp):
TAAACCT
Found at i:53001 original size:35 final size:35
Alignment explanation
Indices: 52962--53050 Score: 110
Period size: 35 Copynumber: 2.5 Consensus size: 35
52952 CCTTTAACTT
*
52962 TAAACCTTAAACGTTAAACCTTAAACTTAG-AATCG
1 TAAACCTTAAACCTTAAACCTTAAA-TTAGAAATCG
*
52997 TAAA-CTTAAAACCTTAAACCTTAAATTTGAAATCG
1 TAAACCTT-AAACCTTAAACCTTAAATTAGAAATCG
**
53032 TAAACAATAAACCTTAAAC
1 TAAACCTTAAACCTTAAAC
53051 TAAAAACCCT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
34 6 0.13
35 40 0.85
36 1 0.02
ACGTcount: A:0.47, C:0.19, G:0.06, T:0.28
Consensus pattern (35 bp):
TAAACCTTAAACCTTAAACCTTAAATTAGAAATCG
Found at i:53871 original size:21 final size:21
Alignment explanation
Indices: 53845--53884 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
53835 ATTACCATGC
*
53845 TATTGACCGTGTTTGATATTT
1 TATTGACCGTATTTGATATTT
*
53866 TATTGACTGTATTTGATAT
1 TATTGACCGTATTTGATAT
53885 GTGAGGATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.07, G:0.17, T:0.53
Consensus pattern (21 bp):
TATTGACCGTATTTGATATTT
Found at i:54194 original size:19 final size:19
Alignment explanation
Indices: 54170--54266 Score: 54
Period size: 19 Copynumber: 5.0 Consensus size: 19
54160 ATTAAAAACA
54170 AAATAACTTTAAAATAAAT
1 AAATAACTTTAAAATAAAT
***
54189 AAATAACAACAAAATAAAGCT
1 AAATAACTTTAAAATAAA--T
** * *
54210 TTATAA-TTTATAATAATT
1 AAATAACTTTAAAATAAAT
* *
54228 ATAATAA-TTAAAAACAAAAT
1 A-AATAACTTTAAAA-TAAAT
*
54248 AAATAACTTTAAATTAAAT
1 AAATAACTTTAAAATAAAT
54267 TAAAGACAAC
Statistics
Matches: 54, Mismatches: 19, Indels: 10
0.65 0.23 0.12
Matches are distributed among these distances:
18 1 0.02
19 33 0.61
20 15 0.28
21 5 0.09
ACGTcount: A:0.61, C:0.06, G:0.01, T:0.32
Consensus pattern (19 bp):
AAATAACTTTAAAATAAAT
Found at i:54423 original size:147 final size:139
Alignment explanation
Indices: 54248--54863 Score: 579
Period size: 146 Copynumber: 4.2 Consensus size: 139
54238 AAAACAAAAT
* * * * * *
54248 AAATAACTTTAAATTAAATTAAAGACAACAAAACAATTTACCTTTGTTTTAGCTTTTTTTCCATT
1 AAATAATTTTAAATTAAATTAAAAACAACAAAACAAATTACCTCTCTTTTAGCTTTTTTTCCCTT
* *
54313 TAATCTA-TCCTACTAAACAAAAATTTCATAATAAATCTCATAAAAATTAAGCTAAACAAATAAT
66 TAATCTACT-CTACTAAACAAAAATTT-ATAACAAA-CTCATAAAAATTAAACT----AAAT--T
54377 TTATAATAATTACTAACA
122 TTATAATAATTACTAACA
* * * *
54395 AAATAACTTTAAATTAAATTAAAAACAACAAAACAATTTACCTTTGTTTTAGCTTTTTTTTTTCC
1 AAATAATTTTAAATTAAATTAAAAACAACAAAACAAATTACCTCTCTTTTAGC---TTTTTTTCC
* *
54460 CTTTAATCTA-TCCTACTAAACAAAATTTTTTATAACAAA-TCATATAAAAATTAAGCTAAACAA
63 CTTTAATCTACT-CTACTAAACAAAA--ATTTATAACAAACTC--ATAAAAATTAAACT----AA
54523 ATAATTTATAATAATTACTAACA
119 AT--TTTATAATAATTACTAACA
* *
54546 AAATAATTTTAAATTAAATTAAAAACAACAAAAAAAAAATTACCTCTCTTTTGGC-TTTTTT-CC
1 AAATAATTTTAAATTAAATTAAAAACAAC--AAAACAAATTACCTCTCTTTTAGCTTTTTTTCCC
* *
54609 TTTAATTTACTCTACTAAACATGAAAATTTATAACAAA-TCATAAACATTAAACTAAATTTTATA
64 TTTAATCTACTCTACTAAACA--AAAATTTATAACAAACTCATAAAAATTAAACTAAATTTTATA
*
54673 ATAATTA--AAAA
127 ATAATTACTAACA
*
54684 ATAATAATTTTAAAATAAATTAACAACAACAACAACAACAACAAAATTACCTCTCTTTTAG-TTT
1 A-AATAATTTTAAATTAAATT----A-AA-AACAACAA-AAC-AAATTACCTCTCTTTTAGCTTT
* *
54748 TTTTCCCTTTAATCTACTCTACTAAACAAAAAAATTTATAATAAAC-CATAAACATTAAACTAAA
57 TTTTCCCTTTAATCTACTCTACTAAAC--AAAAATTTATAACAAACTCATAAAAATTAAACTAAA
** *
54812 TTTTATAAT-ATTAAAAATA
120 TTTTATAATAATTACTAACA
*
54831 AAATAATTTTAAAATAAATTAAAAACAACAAAA
1 AAATAATTTTAAATTAAATTAAAAACAACAAAA
54864 AAACACCTTC
Statistics
Matches: 420, Mismatches: 21, Indels: 64
0.83 0.04 0.13
Matches are distributed among these distances:
138 4 0.01
139 20 0.05
140 21 0.05
141 2 0.00
142 5 0.01
143 3 0.01
144 4 0.01
145 33 0.08
146 93 0.22
147 56 0.13
148 34 0.08
149 9 0.02
150 36 0.09
151 78 0.19
152 3 0.01
153 19 0.05
ACGTcount: A:0.49, C:0.14, G:0.02, T:0.36
Consensus pattern (139 bp):
AAATAATTTTAAATTAAATTAAAAACAACAAAACAAATTACCTCTCTTTTAGCTTTTTTTCCCTT
TAATCTACTCTACTAAACAAAAATTTATAACAAACTCATAAAAATTAAACTAAATTTTATAATAA
TTACTAACA
Found at i:54538 original size:27 final size:25
Alignment explanation
Indices: 54502--54558 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 25
54492 TAACAAATCA
54502 TATAAAAATTAAGCTAA-ACAAATAATT
1 TATAAAAATT-A-CTAACA-AAATAATT
*
54529 TATAATAATTACTAACAAAATAATT
1 TATAAAAATTACTAACAAAATAATT
54554 T-TAAA
1 TATAAA
54559 TTAAATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 3 0.11
25 13 0.48
26 2 0.07
27 9 0.33
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (25 bp):
TATAAAAATTACTAACAAAATAATT
Found at i:54965 original size:15 final size:15
Alignment explanation
Indices: 54945--54984 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
54935 ACAAAGTCCC
54945 TAAGGTCCCCCCTTA
1 TAAGGTCCCCCCTTA
54960 TAAGGTCCCCCCTTA
1 TAAGGTCCCCCCTTA
*
54975 TAAGATCCCC
1 TAAGGTCCCC
54985 TACCTCCCCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.23, C:0.40, G:0.12, T:0.25
Consensus pattern (15 bp):
TAAGGTCCCCCCTTA
Found at i:55296 original size:192 final size:186
Alignment explanation
Indices: 54966--55323 Score: 432
Period size: 192 Copynumber: 1.9 Consensus size: 186
54956 CTTATAAGGT
** * * *
54966 CCCCCCTTATAAGATCCCCTACCTCCCCCACACCACTGCCTTGCTTGCCTATGCATGCATGTCAT
1 CCCCCCTTATAAGATCCCCTACCTCCCCCACACCACAACCCTGCTAGCCTATGCATGCATGCCAT
* ** * * *
55031 GCATGTCCTCATGCCATTTTCCCATCCACCTTCGGCAAACCACTTGCCTTGATGGGACAAAGGTG
66 GCATGTCCCCACACCATTTCCCCATCCACCTTCGGCAAACCACTTGCCATGATAGGACAAAGGTG
* * *
55096 TTGCCTATGAGATAGGTGTTTTTGGTGCCACTTATTTCATGAAACACNNNNNNCCTAAAGTC
131 TCGCCTATGAGATAGGTATTTTTGGTGCCACCTATTTCATGAAACAC------CCTAAAGTC
* * * * *
55158 CCCCCCTTATAAGGTTCCCTCCCTCCCCCACGCCACAACCCTGCTAGCCTCTGCATGCATGCCAT
1 CCCCCCTTATAAGATCCCCTACCTCCCCCACACCACAACCCTGCTAGCCTATGCATGCATGCCAT
* * *
55223 GCAT-TCCCCCACACCATTTCCCCGTGCACCTTCGGCAAACCACCTT-CCATGATAGGACAAGGG
66 GCATGT-CCCCACACCATTTCCCCATCCACCTTCGGCAAACCA-CTTGCCATGATAGGACAAAGG
55286 TGTCGCCTATGAGATAGGTATTTTTGGTGCCACCTATT
129 TGTCGCCTATGAGATAGGTATTTTTGGTGCCACCTATT
55324 GAATGGCCAC
Statistics
Matches: 142, Mismatches: 22, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
191 1 0.01
192 138 0.97
193 3 0.02
ACGTcount: A:0.20, C:0.35, G:0.16, T:0.27
Consensus pattern (186 bp):
CCCCCCTTATAAGATCCCCTACCTCCCCCACACCACAACCCTGCTAGCCTATGCATGCATGCCAT
GCATGTCCCCACACCATTTCCCCATCCACCTTCGGCAAACCACTTGCCATGATAGGACAAAGGTG
TCGCCTATGAGATAGGTATTTTTGGTGCCACCTATTTCATGAAACACCCTAAAGTC
Found at i:57171 original size:25 final size:26
Alignment explanation
Indices: 57125--57181 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
57115 TTACTTTACT
*
57125 AAATAAAAAAAAATTAATAACAAACC
1 AAATAAAAAAAAATTAATAACAAAAC
*
57151 AAATAAAAATTAAATT-A-AACAAAAC
1 AAATAAAAA-AAAATTAATAACAAAAC
57176 AAATAA
1 AAATAA
57182 CTTATAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 13 0.46
26 10 0.36
27 5 0.18
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.18
Consensus pattern (26 bp):
AAATAAAAAAAAATTAATAACAAAAC
Found at i:58898 original size:42 final size:42
Alignment explanation
Indices: 58843--58960 Score: 175
Period size: 42 Copynumber: 2.8 Consensus size: 42
58833 GACGCTTATT
* * *
58843 CCGAGTCACGAGTCTTCCTTTAATCATATTCTCATTTTCATC
1 CCGAGACATGAGTCTTCCTTTAATCATATTCTCATTCTCATC
58885 CCGAGACATGAGTCTTCCTTTAATCATATTCTCATTCTCATC
1 CCGAGACATGAGTCTTCCTTTAATCATATTCTCATTCTCATC
* * *
58927 CCAAGACATGAGTCTTCCTTAAAT-ATATCCTCAT
1 CCGAGACATGAGTCTTCCTTTAATCATATTCTCAT
58961 GCTCGTTTCG
Statistics
Matches: 70, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
41 9 0.13
42 61 0.87
ACGTcount: A:0.25, C:0.28, G:0.09, T:0.37
Consensus pattern (42 bp):
CCGAGACATGAGTCTTCCTTTAATCATATTCTCATTCTCATC
Found at i:67728 original size:22 final size:22
Alignment explanation
Indices: 67701--67746 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
67691 AGGGAAATCC
67701 ACGTTATAACCAGCCATTCCAA
1 ACGTTATAACCAGCCATTCCAA
67723 ACGTTATAACCAGCCATTCCAA
1 ACGTTATAACCAGCCATTCCAA
67745 AC
1 AC
67747 AAGCGTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.37, C:0.33, G:0.09, T:0.22
Consensus pattern (22 bp):
ACGTTATAACCAGCCATTCCAA
Found at i:79314 original size:25 final size:26
Alignment explanation
Indices: 79286--79336 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
79276 AAAATAAAAG
**
79286 AATAAAAGGAAA-AAGGAGAGTTAAA
1 AATAAAAGGAAAGAAAAAGAGTTAAA
*
79311 AATAAAATGAAAGAAAAAGAGTTAAA
1 AATAAAAGGAAAGAAAAAGAGTTAAA
79337 TTGCTAAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.67, C:0.00, G:0.20, T:0.14
Consensus pattern (26 bp):
AATAAAAGGAAAGAAAAAGAGTTAAA
Found at i:79570 original size:10 final size:10
Alignment explanation
Indices: 79555--79585 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
79545 TTTAAGTAAC
79555 TATTTATATA
1 TATTTATATA
79565 TATTTATATA
1 TATTTATATA
*
79575 TATATATATA
1 TATTTATATA
79585 T
1 T
79586 TGCTTTCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
TATTTATATA
Found at i:80231 original size:24 final size:25
Alignment explanation
Indices: 80184--80232 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
80174 ATTCAAAATA
* **
80184 TTTATAAAAATTCTAAAATTTATAT
1 TTTATAAAAAATCTAAAAAATATAT
80209 TTTA-AAAAAATCTAAAAAATATAT
1 TTTATAAAAAATCTAAAAAATATAT
80233 AAAAAATTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (25 bp):
TTTATAAAAAATCTAAAAAATATAT
Found at i:83544 original size:20 final size:20
Alignment explanation
Indices: 83507--83547 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
83497 AATATCAAAA
*
83507 TATATAATTTTATGTTAAAT
1 TATATAATTTTATATTAAAT
83527 TATAT-ATTTTATAATTAAAT
1 TATATAATTTTAT-ATTAAAT
83547 T
1 T
83548 TAAATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
TATATAATTTTATATTAAAT
Found at i:88795 original size:414 final size:414
Alignment explanation
Indices: 88025--88850 Score: 1598
Period size: 414 Copynumber: 2.0 Consensus size: 414
88015 TATTGTTGGG
88025 CCAATTCTTCCTTAACAAAAACATCAGTTGGTCACAGTTCCGTCAGGCAGTGGTGGAAGGGCATC
1 CCAATTCTTCCTTAACAAAAACATCAGTTGGTCACAGTTCCGTCAGGCAGTGGTGGAAGGGCATC
*
88090 AAAACAGACAAGGGCAACTCAGGTTAAGGAAACCAAAACAGTCCATATATACATATCCTGCTCCT
66 AAAACAGACAAGGGCAACTCAGGTTAAGGAAACCAAAACAGTCCATACATACATATCCTGCTCCT
88155 GATTGCATGTGCCATGCTTAAGCCTTATATACCCAAAGAAGCCAAAATGCCTATACCATTGATAT
131 GATTGCATGTGCCATGCTTAAGCCTTATATACCCAAAGAAGCCAAAATGCCTATACCATTGATAT
*
88220 CGTAAAAAAGCAACAAAGAGAAATCCTTTCTATAGTTCCAAGCTGTAGTTTCATTTGTACCCATA
196 CGTAAAAAAGCAACAAAGAGAAACCCTTTCTATAGTTCCAAGCTGTAGTTTCATTTGTACCCATA
88285 ATGTTAATAAGCAGCAATCCCATTTCTCTTCTCCCCTTTGGATAGAAGTATTATTACATCTAGCG
261 ATGTTAATAAGCAGCAATCCCATTTCTCTTCTCCCCTTTGGATAGAAGTATTATTACATCTAGCG
88350 TTCGTAGTGTGCATTGTGCACTGTATTGACGGTTGTATTTTATATAGAGAGCTGTGGTGTTGAAC
326 TTCGTAGTGTGCATTGTGCACTGTATTGACGGTTGTATTTTATATAGAGAGCTGTGGTGTTGAAC
*
88415 ATGTTTCGTGTTTATATAATTCCT
391 ATGTTTCATGTTTATATAATTCCT
*
88439 CCAATTCTTCCTTAACAAAAACATCAGTTGGTCACAGTTCCGTCAGGCAGTGGTGGGAGGGCATC
1 CCAATTCTTCCTTAACAAAAACATCAGTTGGTCACAGTTCCGTCAGGCAGTGGTGGAAGGGCATC
*
88504 AAAACAGACAAGGGCAACTCAGGTTAAGGAAACCAAAACAGTCCATACATGCATATCCTGCTCCT
66 AAAACAGACAAGGGCAACTCAGGTTAAGGAAACCAAAACAGTCCATACATACATATCCTGCTCCT
88569 GATTGCATGTGCCATGCTTAAGCCTTATATACCCAAAGAAGCCAAAATGCCTATACCATTGATAT
131 GATTGCATGTGCCATGCTTAAGCCTTATATACCCAAAGAAGCCAAAATGCCTATACCATTGATAT
*
88634 CGTAAAAAAGCAACAAAGAGAAACCCTTTCTATAGTTCCAAGCTGTAGTTTCATTTGTACCCGTA
196 CGTAAAAAAGCAACAAAGAGAAACCCTTTCTATAGTTCCAAGCTGTAGTTTCATTTGTACCCATA
88699 ATGTTAATAAGCAGCAATCCCATTTCTCTTCTCCCCTTTGGATAGAAGTATTATTACATCTAGCG
261 ATGTTAATAAGCAGCAATCCCATTTCTCTTCTCCCCTTTGGATAGAAGTATTATTACATCTAGCG
88764 TTCGTAGTGTGCATTGTGCACTGTATTGACGGTTGTATTTTATATAGAGAGCTGTGGTGTTGAAC
326 TTCGTAGTGTGCATTGTGCACTGTATTGACGGTTGTATTTTATATAGAGAGCTGTGGTGTTGAAC
88829 ATGTTTCATGTTTATATAATTC
391 ATGTTTCATGTTTATATAATTC
88851 ATCGGCCGAT
Statistics
Matches: 406, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
414 406 1.00
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (414 bp):
CCAATTCTTCCTTAACAAAAACATCAGTTGGTCACAGTTCCGTCAGGCAGTGGTGGAAGGGCATC
AAAACAGACAAGGGCAACTCAGGTTAAGGAAACCAAAACAGTCCATACATACATATCCTGCTCCT
GATTGCATGTGCCATGCTTAAGCCTTATATACCCAAAGAAGCCAAAATGCCTATACCATTGATAT
CGTAAAAAAGCAACAAAGAGAAACCCTTTCTATAGTTCCAAGCTGTAGTTTCATTTGTACCCATA
ATGTTAATAAGCAGCAATCCCATTTCTCTTCTCCCCTTTGGATAGAAGTATTATTACATCTAGCG
TTCGTAGTGTGCATTGTGCACTGTATTGACGGTTGTATTTTATATAGAGAGCTGTGGTGTTGAAC
ATGTTTCATGTTTATATAATTCCT
Found at i:114120 original size:138 final size:138
Alignment explanation
Indices: 113938--114220 Score: 494
Period size: 138 Copynumber: 2.1 Consensus size: 138
113928 TCTGACCTAC
113938 ATAGAGGTCCATCAAAGCATAACCTACAGGTTTCATTACCATATAATGGCAAAATGAACCAAGAA
1 ATAGAGGTCCATCAAAGCATAACCTACAGGTTTCATTACCATATAATGGCAAAATGAACCAAGAA
* *
114003 AACATGAAGATTTAAAGGGAAAGGTTGAGGCCGCAATGGCGAACCCGACAGCTTAAAAGATGAGA
66 AACATGAAGATTTAAAGGAAAAGGTTGAGGCCGCAATGGCGAACCCGACACCTTAAAAGATGAGA
114068 TGAGAAGG
131 TGAGAAGG
* * *
114076 ATAGAGGTCCATTAAAGCATAACCTACAGGTTTTATTACCATATAATGGCGAAATGAACCAAGAA
1 ATAGAGGTCCATCAAAGCATAACCTACAGGTTTCATTACCATATAATGGCAAAATGAACCAAGAA
* *
114141 AACATTAAGATTTAAAGGAAAAGGTTGAGGCCGCAATGGCGAACCCGGCACCTTAAAAGATGAGA
66 AACATGAAGATTTAAAGGAAAAGGTTGAGGCCGCAATGGCGAACCCGACACCTTAAAAGATGAGA
114206 TGAGAAGG
131 TGAGAAGG
*
114214 ATTGAGG
1 ATAGAGG
114221 CTGTAATGGT
Statistics
Matches: 137, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
138 137 1.00
ACGTcount: A:0.41, C:0.16, G:0.24, T:0.19
Consensus pattern (138 bp):
ATAGAGGTCCATCAAAGCATAACCTACAGGTTTCATTACCATATAATGGCAAAATGAACCAAGAA
AACATGAAGATTTAAAGGAAAAGGTTGAGGCCGCAATGGCGAACCCGACACCTTAAAAGATGAGA
TGAGAAGG
Found at i:114623 original size:78 final size:78
Alignment explanation
Indices: 114524--115597 Score: 993
Period size: 78 Copynumber: 13.8 Consensus size: 78
114514 GAAGATTTCG
* * ** * * * * ** *
114524 ATCTCTTACCCCGATCATGGGGCAGATCACGGTCATCCGATCTTTTACCCCAAGTTTAAGGTAAA
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTGGGGTAGA
*
114589 TCACCATCAACCA
66 TCACCATCAGCCA
* * *
114602 ATCTCTTACCCCGAGCTTGGGGCAAATTGCAGCCATCCGATCTTTTACCTCGAGCTTGGGGCAGA
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTGGGGTAGA
**
114667 TCACCATCAGTGA
66 TCACCATCAGCCA
* * * * * * * * * *
114680 ATCTCTTACCCCAAGCCTAGGGCAGATTGCAACCATTCAATCTTTTACCCCAAGCTTGAGGCATA
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTGGGGTAGA
*
114745 TCACCATCAGCTA
66 TCACCATCAGCCA
* * * * * *
114758 ATCTCTTACCCCGAGCCTGGGGTAGATTGCAGTCATTCGATCTTTTACCTCGAGCTTAGGGTAGA
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTGGGGTAGA
** * *
114823 TCATAATTAGTCA
66 TCACCATCAGCCA
* * * * * * * * * * *
114836 ATCTCTTACCCCAAGCCTCGGGTAGATTGTAACAATCCGATCATTTATCCCGAGCTTGGGGCAAA
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTGGGGTAGA
* * *
114901 TCACTATCAACTA
66 TCACCATCAGCCA
* ** * * * **
114914 ATCTCTTACCCCGAGCCTGATGCAGATTACAACCATCCGATCTTTTACCTCGAGCTTGGGACAGA
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTGGGGTAGA
114979 TCACCATCAGCCA
66 TCACCATCAGCCA
* * * * * *
114992 ATCTTTTACTCCGAGCTT-GGGCAGATTGCAACCATCCGATCTTTTACCTCGAGCTTGAGGCAGA
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTGGGGTAGA
* *
115056 TCACCATCAGTCG
66 TCACCATCAGCCA
* * * * *
115069 ATCTCTTACCCTGAGCTTAGGGCAGATTACAGCCATCCAATCTTTTACCCCGAGCCT-GGGTAGA
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTGGGGTAGA
* *
115133 TCACAATCAACCA
66 TCACCATCAGCCA
* * * * * **
115146 ATCTCTTACCCCGAGCCTGGGGCAGATTGTAGTCATCTGATCTTTTACCCCGAACTTAAGGTAGA
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTGGGGTAGA
* *
115211 TCACCATTAGTCA
66 TCACCATCAGCCA
* * * ** * * * * * *
115224 TTCGAT-TTATCCCGACCTTGGGAAAGATTACAACCATCTGATTTTTTATCCCGAGCTTGGGGCA
1 ATC--TCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTGGGGTA
115288 GATCACCATCAGCCA
64 GATCACCATCAGCCA
* * * * *
115303 ATCTCTTACCCTGAACTTGGGGCAGATTGCAACCATCCGATCTTTTACCCCAAGCTTGGGGTATA
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTGGGGTAGA
**
115368 TCACCATCAGTTA
66 TCACCATCAGCCA
* * * * ***
115381 ATATCTTACCCCGAGCTTAGGGCAAATTACAGCCATCCGATCTTTTACCCCGAGCTTGGAACAGA
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTGGGGTAGA
* * *
115446 TCACTATAAACCA
66 TCACCATCAGCCA
* * * *
115459 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCAATCTTTTACCTCGAGCTTGGGATAAA
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTGGGGTAGA
*
115524 TCACCATCAGTCA
66 TCACCATCAGCCA
* *** * **
115537 ATCTCTTATCCCGAGCTTGGCAAAGATTTCAGCCATCCGATCTTTTACCTTGAGCTTGGGG
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTGGGG
115598 CAAATTACAC
Statistics
Matches: 799, Mismatches: 192, Indels: 10
0.80 0.19 0.01
Matches are distributed among these distances:
77 129 0.16
78 611 0.76
79 58 0.07
80 1 0.00
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.27
Consensus pattern (78 bp):
ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTGGGGTAGA
TCACCATCAGCCA
Found at i:114650 original size:39 final size:37
Alignment explanation
Indices: 114522--115798 Score: 416
Period size: 39 Copynumber: 32.8 Consensus size: 37
114512 CTGAAGATTT
* * *
114522 CGATCTCTTACCCCGATCATGGGGCAGA-TCACGGTCATC
1 CGATCTTTTACCCCGAGCTTGGGGCAGATTCAC---CATC
* * ** * *
114561 CGATCTTTTACCCCAAGTTTAAGGTA-AATCACCATCAAC
1 CGATCTTTTACCCCGAGCTTGGGGCAGATTCACCAT---C
* * *
114600 CAATCTCTTACCCCGAGCTTGGGGCAAATTGCAGCCATC
1 CGATCTTTTACCCCGAGCTTGGGGCAGATT-CA-CCATC
*
114639 CGATCTTTTACCTCGAGCTTGGGGCAGA-TCACCATC
1 CGATCTTTTACCCCGAGCTTGGGGCAGATTCACCATC
* * * * * *
114675 AGTGAATCTCTTACCCCAAGCCTAGGGCAGATTGCAACCATT
1 --CG-ATCTTTTACCCCGAGCTTGGGGCAGATT-C-ACCATC
* * * *
114717 CAATCTTTTACCCCAAGCTTGAGGCATA-TCACCATC
1 CGATCTTTTACCCCGAGCTTGGGGCAGATTCACCATC
* * * * * *
114753 AGCTAATCTCTTACCCCGAGCCTGGGGTAGATTGCAGTCATT
1 --C-GATCTTTTACCCCGAGCTTGGGGCAGATT-CA-CCATC
* * * ** *
114795 CGATCTTTTACCTCGAGCTTAGGGTAGA-TCATAATTAGT
1 CGATCTTTTACCCCGAGCTTGGGGCAGATTCACCA-T--C
* * * * * * * *
114834 CAATCTCTTACCCCAAGCCTCGGGTAGATTGTAACAATC
1 CGATCTTTTACCCCGAGCTTGGGGCAGA-T-TCACCATC
* * * *
114873 CGATCATTTATCCCGAGCTTGGGGCA-AATCACTATC
1 CGATCTTTTACCCCGAGCTTGGGGCAGATTCACCATC
* * * **
114909 AACTAATCTCTTACCCCGAGCCTGATGCAGATTACAACCATC
1 --C-GATCTTTTACCCCGAGCTTGGGGCAGATT-C-ACCATC
* *
114951 CGATCTTTTACCTCGAGCTTGGGACAGA-TCACCATCAGC
1 CGATCTTTTACCCCGAGCTTGGGGCAGATTCACCAT---C
* *
114990 CAATCTTTTACTCCGAGCTT-GGGCAGATTGCAACCATC
1 CGATCTTTTACCCCGAGCTTGGGGCAGATT-C-ACCATC
* *
115028 CGATCTTTTACCTCGAGCTTGAGGCAGA-TCACCATC
1 CGATCTTTTACCCCGAGCTTGGGGCAGATTCACCATC
* * *
115064 AGTCGATCTCTTACCCTGAGCTTAGGGCAGATTACAGCCATC
1 ---CGATCTTTTACCCCGAGCTTGGGGCAGATT-CA-CCATC
* * * *
115106 CAATCTTTTACCCCGAGCCT-GGGTAGA-TCACAATCAAC
1 CGATCTTTTACCCCGAGCTTGGGGCAGATTCAC---CATC
* * * * *
115144 CAATCTCTTACCCCGAGCCTGGGGCAGATTGTAGTCATC
1 CGATCTTTTACCCCGAGCTTGGGGCAGATT-CA-CCATC
* * ** * *
115183 TGATCTTTTACCCCGAACTTAAGGTAGA-TCACCATT
1 CGATCTTTTACCCCGAGCTTGGGGCAGATTCACCATC
* * * * **
115219 AGTCATTCGATTTATCCCGACCTTGGGAAAGATTACAACCATC
1 CG--A-TC-TTTTACCCCGAGCTTGGGGCAGATT-C-ACCATC
* * *
115262 TGATTTTTTATCCCGAGCTTGGGGCAGA-TCACCATCAGC
1 CGATCTTTTACCCCGAGCTTGGGGCAGATTCACCAT---C
* * * *
115301 CAATCTCTTACCCTGAACTTGGGGCAGATTGCAACCATC
1 CGATCTTTTACCCCGAGCTTGGGGCAGATT-C-ACCATC
* * *
115340 CGATCTTTTACCCCAAGCTTGGGGTATA-TCACCATC
1 CGATCTTTTACCCCGAGCTTGGGGCAGATTCACCATC
* * * * *
115376 AGTTAATATCTTACCCCGAGCTTAGGGCAAATTACAGCCATC
1 CG---ATCTTTTACCCCGAGCTTGGGGCAGATT-CA-CCATC
** *
115418 CGATCTTTTACCCCGAGCTTGGAACAGA-TCACTATAAAC
1 CGATCTTTTACCCCGAGCTTGGGGCAGATTCACCAT---C
* *
115457 CAATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATC
1 CGATCTTTTACCCCGAGCTTGGGGCAGATT-CA-CCATC
* * ** *
115496 CAATCTTTTACCTCGAGCTTGGGATA-AATCACCATC
1 CGATCTTTTACCCCGAGCTTGGGGCAGATTCACCATC
* * * ***
115532 AGTCAATCTCTTATCCCGAGCTTGGCAAAGATTTCAGCCATC
1 ---CGATCTTTTACCCCGAGCTTGGGGCAGA-TTCA-CCATC
** *
115574 CGATCTTTTACCTTGAGCTTGGGGCAAATTACACTCATC
1 CGATCTTTTACCCCGAGCTTGGGGCAGATT-CAC-CATC
* ** * *
115613 TGATCTTTTACCCTAAGCTTGGGGTAGATT-ACCGTCAGC
1 CGATCTTTTACCCCGAGCTTGGGGCAGATTCA-C--CATC
* * * * *
115652 CAATCTCTTACCCCGCGAC-AGAGGCAGATTGCAACCATC
1 CGATCTTTTACCCCGAG-CTTGGGGCAGATT-C-ACCATC
** * * * *
115691 TAATCTTTTACCCCGATCATGAGGCA-AATCACTGTCAGT-
1 CGATCTTTTACCCCGAGCTTGGGGCAGATTCAC---CA-TC
* * * *
115730 CAATCTTCTACCCCGAGCTTGAGGCAGATTATAACCATC
1 CGATCTTTTACCCCGAGCTTGGGGCAGA-T-TCACCATC
* **
115769 CGATCTTTTACCCCAAGCTTAAGGCAGATT
1 CGATCTTTTACCCCGAGCTTGGGGCAGATT
115799 ACCGTCAGTC
Statistics
Matches: 918, Mismatches: 221, Indels: 200
0.69 0.17 0.15
Matches are distributed among these distances:
35 1 0.00
36 60 0.07
37 19 0.02
38 78 0.08
39 643 0.70
40 35 0.04
41 26 0.03
42 50 0.05
43 6 0.01
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (37 bp):
CGATCTTTTACCCCGAGCTTGGGGCAGATTCACCATC
Found at i:115691 original size:78 final size:78
Alignment explanation
Indices: 115609--115897 Score: 269
Period size: 78 Copynumber: 3.7 Consensus size: 78
115599 AAATTACACT
* * * * * *
115609 CATCTGATCTTTTACCCTAAGCTTGGGGTAGATTACCGTCAGCCAATCTCTTACCCCGCGACAGA
1 CATCCGATCTTTTACCCCAAGCTTGAGGCAGATTACCGTCAGTCAATCTCTTACCCCGAGACAGA
*
115674 GGCAGATTGCAAC
66 GGCAGATTGTAAC
** * * * * * * *
115687 CATCTAATCTTTTACCCCGATCATGAGGCAAATCACTGTCAGTCAATCT-TCTACCCCGAG-CTT
1 CATCCGATCTTTTACCCCAAGCTTGAGGCAGATTACCGTCAGTCAATCTCT-TACCCCGAGAC-A
*
115750 GAGGCAGATTATAAC
64 GAGGCAGATTGTAAC
* * * *
115765 CATCCGATCTTTTACCCCAAGCTTAAGGCAGATTACCGTCAGTCAATCTCTTACCCTGTGATAG-
1 CATCCGATCTTTTACCCCAAGCTTGAGGCAGATTACCGTCAGTCAATCTCTTACCCCGAGACAGA
115829 GGACAGATTGTAAC
66 GG-CAGATTGTAAC
* * * * * * * *
115843 CATCCGATCTTTTATCCCGATCATGGGGCAGATCACAGTCATTCAATCTCTTACC
1 CATCCGATCTTTTACCCCAAGCTTGAGGCAGATTACCGTCAGTCAATCTCTTACC
115898 TCGATCATGG
Statistics
Matches: 168, Mismatches: 38, Indels: 10
0.78 0.18 0.05
Matches are distributed among these distances:
77 4 0.02
78 163 0.97
79 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.28
Consensus pattern (78 bp):
CATCCGATCTTTTACCCCAAGCTTGAGGCAGATTACCGTCAGTCAATCTCTTACCCCGAGACAGA
GGCAGATTGTAAC
Found at i:115696 original size:156 final size:156
Alignment explanation
Indices: 115588--115891 Score: 378
Period size: 156 Copynumber: 1.9 Consensus size: 156
115578 CTTTTACCTT
* * * * ** *
115588 GAGCTTGGGGCAAATTA-CACTCATCTGATCTTTTACCCTAAGCTTGGGGTAGATTACCGTCAGC
1 GAGCTTGAGGCAAATTATAAC-CATCCGATCTTTTACCCCAAGCTTAAGGCAGATTACCGTCAGC
* * *
115652 CAATCTCTTACCCCGCGACAGAGG-CAGATTGCAACCATCTAATCTTTTACCCCGATCATGAGGC
65 CAATCTCTTACCCCGCGACAG-GGACAGATTGCAACCATCCAATCTTTTATCCCGAGCATGAGGC
115716 AAATCACTGTCAGTCAATCTTCTACCCC
129 AAATCACTGTCAGTCAATCTTCTACCCC
* *
115744 GAGCTTGAGGCAGATTATAACCATCCGATCTTTTACCCCAAGCTTAAGGCAGATTACCGTCAGTC
1 GAGCTTGAGGCAAATTATAACCATCCGATCTTTTACCCCAAGCTTAAGGCAGATTACCGTCAGCC
* * * * * * * *
115809 AATCTCTTACCCTGTGATAGGGACAGATTGTAACCATCCGATCTTTTATCCCGATCATGGGGCAG
66 AATCTCTTACCCCGCGACAGGGACAGATTGCAACCATCCAATCTTTTATCCCGAGCATGAGGCAA
* *
115874 ATCACAGTCATTCAATCT
131 ATCACTGTCAGTCAATCT
115892 CTTACCTCGA
Statistics
Matches: 126, Mismatches: 20, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
155 2 0.02
156 122 0.97
157 2 0.02
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (156 bp):
GAGCTTGAGGCAAATTATAACCATCCGATCTTTTACCCCAAGCTTAAGGCAGATTACCGTCAGCC
AATCTCTTACCCCGCGACAGGGACAGATTGCAACCATCCAATCTTTTATCCCGAGCATGAGGCAA
ATCACTGTCAGTCAATCTTCTACCCC
Found at i:118745 original size:39 final size:40
Alignment explanation
Indices: 118687--118772 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 40
118677 ATCACAAAAA
118687 AAAAAGATAACTTTCCATTAACTCTATAATTGAAATCGAT
1 AAAAAGATAACTTTCCATTAACTCTATAATTGAAATCGAT
*
118727 AAAAA-ATAACTTTTCATTAACTCTATAATTGAAATCGAT
1 AAAAAGATAACTTTCCATTAACTCTATAATTGAAATCGAT
118766 AAAAAGA
1 AAAAAGA
118773 AAACAATCAT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
39 38 0.86
40 6 0.14
ACGTcount: A:0.49, C:0.13, G:0.07, T:0.31
Consensus pattern (40 bp):
AAAAAGATAACTTTCCATTAACTCTATAATTGAAATCGAT
Found at i:120331 original size:69 final size:69
Alignment explanation
Indices: 120220--120357 Score: 276
Period size: 69 Copynumber: 2.0 Consensus size: 69
120210 TGAGTTGGTG
120220 TCACGAGTCAATCAAGCCCCAACTCGATCAATAAAATTACAGAAATATCTTTCCGTTATTAACGG
1 TCACGAGTCAATCAAGCCCCAACTCGATCAATAAAATTACAGAAATATCTTTCCGTTATTAACGG
120285 AAAT
66 AAAT
120289 TCACGAGTCAATCAAGCCCCAACTCGATCAATAAAATTACAGAAATATCTTTCCGTTATTAACGG
1 TCACGAGTCAATCAAGCCCCAACTCGATCAATAAAATTACAGAAATATCTTTCCGTTATTAACGG
120354 AAAT
66 AAAT
120358 CATATTTTAT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.26
Consensus pattern (69 bp):
TCACGAGTCAATCAAGCCCCAACTCGATCAATAAAATTACAGAAATATCTTTCCGTTATTAACGG
AAAT
Found at i:121798 original size:242 final size:237
Alignment explanation
Indices: 121334--121950 Score: 668
Period size: 240 Copynumber: 2.6 Consensus size: 237
121324 TTAGTAATGT
* ** ** * *
121334 ATTTAATCT-TTTTTTAAATTTTAATATTGTACATATTTTATGTGTTTTTATTAATTAGTTTCAA
1 ATTTAATCTATTTTTT-AATTGTAATATCATACATATTTTATAAGTTATTATTAATCAGTTTCAA
* * * ** * * **
121398 ACCATATGTTTCACTATTTATTGTAGGTTA-TTTTAAACACGCATTT-ATGTTCTGAATTT-TTT
65 ACCATAAGTCTCACTATTTATAGTATATTATTTTTAAACACACATTTGA-GTTCTAAATTTGTGG
* * * *
121460 ATTTTTACACGCATACACATGTGATAGAAATTTTAGTATTAATGTATTCGATTAAGTTGTTGTCA
129 A-TTCTATATGCATACAC-----ATAGAAATTCTAGTATTAATGTATTCGATTAAGTTGTTGTCA
** * * *
121525 CAAGTTAACTCGACACCAACTCAAGATTGATGACAACACATTGATAAACA
188 CAAGTTAACTAAACAACAACTCAACATTGATGACAACACAATGATAAACA
* *
121575 ATTTAATCTAATTTTTTAAATTGTAATATCATGCAT-TTTTCATAAGTTATTATTAATCCGTTTC
1 ATTTAATCT-ATTTTTT-AATTGTAATATCATACATATTTT-ATAAGTTATTATTAATCAGTTTC
* * * * * *
121639 AAACTATATGTGTCACTATTTATAGTGTATTATTTTTAAGCACACATTTGTGTTCTAAATTTGTG
63 AAACCATAAGTCTCACTATTTATAGTATATTATTTTTAAACACACATTTGAGTTCTAAATTTGTG
*
121704 GATTCTATATGCATACACATAGAAATTCTAGTATTAGTAATGTATTCGATTGAGTTGTTGTCACA
128 GATTCTATATGCATACACATAGAAATTCTAGTA-T--TAATGTATTCGATTAAGTTGTTGTCACA
*
121769 AGTTAACTAAACAACAACTCAACATTGATGACAACATAATGATAAACA
190 AGTTAACTAAACAACAACTCAACATTGATGACAACACAATGATAAACA
* ** **
121817 ATTTAATCTATTTTTTAATTTTAATATTGTACATATTTTATGTGTTATTATTAATCAGTTTCAAA
1 ATTTAATCTATTTTTTAATTGTAATATCATACATATTTTATAAGTTATTATTAATCAGTTTCAAA
* * * * *
121882 CCATAAGTCTCATTATTTATTGTATGTTATTTTTAAACATACATTTGAGTTCTAAATTTGTGGTT
66 CCATAAGTCTCACTATTTATAGTATATTATTTTTAAACACACATTTGAGTTCTAAATTTGTGGAT
121947 TCTA
131 TCTA
121951 CAGACATAAG
Statistics
Matches: 316, Mismatches: 50, Indels: 21
0.82 0.13 0.05
Matches are distributed among these distances:
239 14 0.04
240 96 0.30
241 20 0.06
242 82 0.26
243 65 0.21
244 37 0.12
245 2 0.01
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (237 bp):
ATTTAATCTATTTTTTAATTGTAATATCATACATATTTTATAAGTTATTATTAATCAGTTTCAAA
CCATAAGTCTCACTATTTATAGTATATTATTTTTAAACACACATTTGAGTTCTAAATTTGTGGAT
TCTATATGCATACACATAGAAATTCTAGTATTAATGTATTCGATTAAGTTGTTGTCACAAGTTAA
CTAAACAACAACTCAACATTGATGACAACACAATGATAAACA
Found at i:125952 original size:42 final size:42
Alignment explanation
Indices: 125865--125945 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
125855 ACAATTCAGA
*
125865 TTTAGTTTATTAATGTTTTTTAAGAATAAAATTATATTTGAG
1 TTTAGTTTATGAATGTTTTTTAAGAATAAAATTATATTTGAG
*
125907 TTTAGTTTATGAGTGTTTTTTAAGAATAAAATTATATTT
1 TTTAGTTTATGAATGTTTTTTAAGAATAAAATTATATTT
125946 TGGTTTAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (42 bp):
TTTAGTTTATGAATGTTTTTTAAGAATAAAATTATATTTGAG
Found at i:126967 original size:22 final size:22
Alignment explanation
Indices: 126928--126970 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
126918 TATTTTAAAT
*
126928 TAAAATTTAATTACAAAATATA
1 TAAAATTCAATTACAAAATATA
126950 TAAAATATCAATTA-AAAATAT
1 TAAAAT-TCAATTACAAAATAT
126971 TTTTTAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (22 bp):
TAAAATTCAATTACAAAATATA
Found at i:129140 original size:15 final size:14
Alignment explanation
Indices: 129120--129151 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
129110 ATCTAAGATT
129120 TTCTCTTCTCTTATC
1 TTCTCTTCTCTT-TC
129135 TTCTCTTCTCTTTC
1 TTCTCTTCTCTTTC
129149 TTC
1 TTC
129152 GCTTATTCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.03, C:0.34, G:0.00, T:0.62
Consensus pattern (14 bp):
TTCTCTTCTCTTTC
Done.