Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014171.1 Kokia drynarioides strain JFW-HI SEQ_129204, 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: 96643
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Warning! 130 characters in sequence are not A, C, G, or T
Found at i:3330 original size:73 final size:73
Alignment explanation
Indices: 3211--3358 Score: 278
Period size: 73 Copynumber: 2.0 Consensus size: 73
3201 AAAGCTACTA
3211 CTTAATAACATTAATTAAAGACTCAACTAATTAAAAGTAAAAGCTTTAGAATCTTGCTAATTGCT
1 CTTAATAACATTAATTAAAGACTCAACTAATTAAAAGTAAAAGCTTTAGAATCTTGCTAATTGCT
3276 ATAATTAC
66 ATAATTAC
* *
3284 CTTAATAACATTAATTAAAGACTCGATTAATTAAAAGTAAAAGCTTTAGAATCTTGCTAATTGCT
1 CTTAATAACATTAATTAAAGACTCAACTAATTAAAAGTAAAAGCTTTAGAATCTTGCTAATTGCT
3349 ATAATTAC
66 ATAATTAC
3357 CT
1 CT
3359 GTGAAGGGAA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.35
Consensus pattern (73 bp):
CTTAATAACATTAATTAAAGACTCAACTAATTAAAAGTAAAAGCTTTAGAATCTTGCTAATTGCT
ATAATTAC
Found at i:9996 original size:4 final size:4
Alignment explanation
Indices: 9987--10016 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
9977 TTCTCTTTCC
9987 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CT
10017 CTCTCTCTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (4 bp):
CTTT
Found at i:10025 original size:12 final size:12
Alignment explanation
Indices: 9974--10025 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
9964 TTTCTGTTTA
*
9974 TCTTTCTCTTTC
1 TCTTTCTCTCTC
* * *
9986 CCTTTCTTTCTT
1 TCTTTCTCTCTC
* *
9998 TCTTTCTTTCTT
1 TCTTTCTCTCTC
10010 TCTTTCTCTCTC
1 TCTTTCTCTCTC
10022 TCTT
1 TCTT
10026 AATTAAAAGC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (12 bp):
TCTTTCTCTCTC
Found at i:11445 original size:3 final size:3
Alignment explanation
Indices: 11437--11461 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
11427 ATTTTAAAGA
11437 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
11462 TGATCGTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:12334 original size:23 final size:23
Alignment explanation
Indices: 12302--12379 Score: 102
Period size: 23 Copynumber: 3.4 Consensus size: 23
12292 TGCTTTCGCA
* *
12302 GCACGCTTTTCCTCTATCTTGTG
1 GCACGTTTTTTCTCTATCTTGTG
* *
12325 GTACGTTTTTTCTCTGTCTTGTG
1 GCACGTTTTTTCTCTATCTTGTG
*
12348 GCACGTTTTTTCTCTACCTTGTG
1 GCACGTTTTTTCTCTATCTTGTG
*
12371 ACACGTTTT
1 GCACGTTTT
12380 GCCTACCTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.09, C:0.24, G:0.18, T:0.49
Consensus pattern (23 bp):
GCACGTTTTTTCTCTATCTTGTG
Found at i:12385 original size:21 final size:23
Alignment explanation
Indices: 12303--12388 Score: 68
Period size: 23 Copynumber: 3.8 Consensus size: 23
12293 GCTTTCGCAG
* * * *
12303 CACGCTTTTCCTCTATCTTGTGG
1 CACGTTTTTGCTCTACCTTGTGA
* * ** *
12326 TACGTTTTTTCTCTGTCTTGTGG
1 CACGTTTTTGCTCTACCTTGTGA
*
12349 CACGTTTTTTCTCTACCTTGTGA
1 CACGTTTTTGCTCTACCTTGTGA
12372 CACG-TTTTGC-CTACCTT
1 CACGTTTTTGCTCTACCTT
12389 TATGGTAGAT
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
21 7 0.13
22 5 0.09
23 42 0.78
ACGTcount: A:0.09, C:0.27, G:0.16, T:0.48
Consensus pattern (23 bp):
CACGTTTTTGCTCTACCTTGTGA
Found at i:13740 original size:21 final size:21
Alignment explanation
Indices: 13703--13750 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
13693 TTGTATTATA
*
13703 TATTTTAATTAATATTATTTT
1 TATTTTAAGTAATATTATTTT
13724 TATTGTTAAGTAA-ATTATTTT
1 TATT-TTAAGTAATATTATTTT
13745 TATTTT
1 TATTTT
13751 TTTAATTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 2 0.08
21 16 0.64
22 7 0.28
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (21 bp):
TATTTTAAGTAATATTATTTT
Found at i:14096 original size:20 final size:21
Alignment explanation
Indices: 14071--14116 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
14061 ATTTTTATCT
14071 TGAAAAAAATAAAATTCA-AA
1 TGAAAAAAATAAAATTCAGAA
***
14091 TGAAAATCTTAAAATTCAGAA
1 TGAAAAAAATAAAATTCAGAA
14112 TGAAA
1 TGAAA
14117 TTATTAATGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.61, C:0.07, G:0.09, T:0.24
Consensus pattern (21 bp):
TGAAAAAAATAAAATTCAGAA
Found at i:14123 original size:21 final size:20
Alignment explanation
Indices: 14080--14123 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
14070 TTGAAAAAAA
*
14080 TAAAATTCAAATGAAAATCT
1 TAAAATTCAAATGAAAATAT
*
14100 TAAAATTCAGAATGAAATTAT
1 TAAAATTCA-AATGAAAATAT
14121 TAA
1 TAA
14124 TGTAACATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.32
Consensus pattern (20 bp):
TAAAATTCAAATGAAAATAT
Found at i:16405 original size:24 final size:26
Alignment explanation
Indices: 16367--16414 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
16357 TCTACATGGG
16367 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
16393 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
16415 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Found at i:17937 original size:23 final size:23
Alignment explanation
Indices: 17905--17982 Score: 102
Period size: 23 Copynumber: 3.4 Consensus size: 23
17895 TGCTTTCGCA
* *
17905 GCACGCTTTTCCTCTATCTTGTG
1 GCACGTTTTTTCTCTATCTTGTG
* *
17928 GTACGTTTTTTCTCTGTCTTGTG
1 GCACGTTTTTTCTCTATCTTGTG
*
17951 GCACGTTTTTTCTCTACCTTGTG
1 GCACGTTTTTTCTCTATCTTGTG
*
17974 ACACGTTTT
1 GCACGTTTT
17983 GCCTACCTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.09, C:0.24, G:0.18, T:0.49
Consensus pattern (23 bp):
GCACGTTTTTTCTCTATCTTGTG
Found at i:17988 original size:21 final size:23
Alignment explanation
Indices: 17906--17991 Score: 68
Period size: 23 Copynumber: 3.8 Consensus size: 23
17896 GCTTTCGCAG
* * * *
17906 CACGCTTTTCCTCTATCTTGTGG
1 CACGTTTTTGCTCTACCTTGTGA
* * ** *
17929 TACGTTTTTTCTCTGTCTTGTGG
1 CACGTTTTTGCTCTACCTTGTGA
*
17952 CACGTTTTTTCTCTACCTTGTGA
1 CACGTTTTTGCTCTACCTTGTGA
17975 CACG-TTTTGC-CTACCTT
1 CACGTTTTTGCTCTACCTT
17992 TATGGTAGAT
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
21 7 0.13
22 5 0.09
23 42 0.78
ACGTcount: A:0.09, C:0.27, G:0.16, T:0.48
Consensus pattern (23 bp):
CACGTTTTTGCTCTACCTTGTGA
Found at i:19343 original size:21 final size:21
Alignment explanation
Indices: 19306--19353 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
19296 TTGTATTATA
*
19306 TATTTTAATTAATATTATTTT
1 TATTTTAAGTAATATTATTTT
19327 TATTGTTAAGTAA-ATTATTTT
1 TATT-TTAAGTAATATTATTTT
19348 TATTTT
1 TATTTT
19354 TTTAATTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 2 0.08
21 16 0.64
22 7 0.28
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (21 bp):
TATTTTAAGTAATATTATTTT
Found at i:19699 original size:20 final size:21
Alignment explanation
Indices: 19674--19719 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
19664 ATTTTTATCT
19674 TGAAAAAAATAAAATTCA-AA
1 TGAAAAAAATAAAATTCAGAA
***
19694 TGAAAATCTTAAAATTCAGAA
1 TGAAAAAAATAAAATTCAGAA
19715 TGAAA
1 TGAAA
19720 TTATTAATGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.61, C:0.07, G:0.09, T:0.24
Consensus pattern (21 bp):
TGAAAAAAATAAAATTCAGAA
Found at i:19726 original size:21 final size:20
Alignment explanation
Indices: 19683--19726 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
19673 TTGAAAAAAA
*
19683 TAAAATTCAAATGAAAATCT
1 TAAAATTCAAATGAAAATAT
*
19703 TAAAATTCAGAATGAAATTAT
1 TAAAATTCA-AATGAAAATAT
19724 TAA
1 TAA
19727 TGTAACATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.32
Consensus pattern (20 bp):
TAAAATTCAAATGAAAATAT
Found at i:22008 original size:24 final size:26
Alignment explanation
Indices: 21970--22017 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
21960 TCTACATGGG
21970 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
21996 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
22018 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Found at i:28847 original size:24 final size:24
Alignment explanation
Indices: 28820--28875 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 24
28810 TATAGAGGTA
28820 ATTATGAATTTTTTTAATAAT-TTT
1 ATTAT-AATTTTTTTAATAATATTT
*
28844 ATTATAA--CTTTTAATAATATTT
1 ATTATAATTTTTTTAATAATATTT
28866 ATT-TAATTTT
1 ATTATAATTTT
28876 AAAATTAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
21 13 0.48
22 6 0.22
23 3 0.11
24 5 0.19
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (24 bp):
ATTATAATTTTTTTAATAATATTT
Found at i:28855 original size:21 final size:19
Alignment explanation
Indices: 28831--28881 Score: 68
Period size: 21 Copynumber: 2.6 Consensus size: 19
28821 TTATGAATTT
28831 TTTTAATAATTTTATTATAA
1 TTTTAATAATTTTATT-TAA
28851 CTTTTAATAATATTTATTTAA
1 -TTTTAATAAT-TTTATTTAA
28872 TTTTAA-AATT
1 TTTTAATAATT
28882 AAGTATACTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 1 0.03
19 3 0.10
20 6 0.21
21 13 0.45
22 6 0.21
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTAATAATTTTATTTAA
Found at i:29716 original size:10 final size:11
Alignment explanation
Indices: 29700--29728 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
29690 TGCTCAAAAC
29700 ATACCAAAATG
1 ATACCAAAATG
29711 AT-CCAAAATG
1 ATACCAAAATG
29721 ATACCAAA
1 ATACCAAA
29729 CATATAACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.55, C:0.21, G:0.07, T:0.17
Consensus pattern (11 bp):
ATACCAAAATG
Found at i:36970 original size:28 final size:28
Alignment explanation
Indices: 36901--36957 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
36891 ATTTAATTTC
* * *
36901 ATTAATATAAGTACTTATTAGTTGATTGA
1 ATTAA-ATAAATATTTATTAGTTGATAGA
36930 ATTAAATAAATATTTATTAGTTGATAGA
1 ATTAAATAAATATTTATTAGTTGATAGA
36958 TATAATAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 20 0.80
29 5 0.20
ACGTcount: A:0.42, C:0.02, G:0.12, T:0.44
Consensus pattern (28 bp):
ATTAAATAAATATTTATTAGTTGATAGA
Found at i:40956 original size:15 final size:16
Alignment explanation
Indices: 40927--40960 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
40917 ATGGAAACAT
40927 AATAATTTGAATATAA
1 AATAATTTGAATATAA
40943 AATAATTT-AATATAA
1 AATAATTTGAATATAA
40958 AAT
1 AAT
40961 TTAATTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
AATAATTTGAATATAA
Found at i:42617 original size:30 final size:30
Alignment explanation
Indices: 42599--42836 Score: 250
Period size: 30 Copynumber: 8.0 Consensus size: 30
42589 GAGAAGTTCG
*
42599 AGGGTCAAAATGTGATTTTGG-AAAGTTT-
1 AGGGTCAAAATATGATTTTGGAAAAGTTTA
* * *
42627 GGAGGTTAAAGTATGATTTTGGAAAAGTTTA
1 AG-GGTCAAAATATGATTTTGGAAAAGTTTA
* *
42658 AAGATCAAAATATGATTTTGGAAAAGTTTA
1 AGGGTCAAAATATGATTTTGGAAAAGTTTA
* * *
42688 AGGGTCAAAGTGTAATTTTGGAAAAGTTTA
1 AGGGTCAAAATATGATTTTGGAAAAGTTTA
42718 AGGGTCAAAATATGATTTTGGAAAAGTTTA
1 AGGGTCAAAATATGATTTTGGAAAAGTTTA
* * *
42748 GGGGTTAAAATATGATTTTGGAAATG-TTA
1 AGGGTCAAAATATGATTTTGGAAAAGTTTA
* * * *
42777 GGGGTTAAAATGTAATTTTGGAAAAGTTT-
1 AGGGTCAAAATATGATTTTGGAAAAGTTTA
* * * *
42806 AGGTGTTAAAATGTAATTTTGAAAAAGTTTA
1 AGG-GTCAAAATATGATTTTGGAAAAGTTTA
42837 GGGACCTTTT
Statistics
Matches: 179, Mismatches: 25, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
28 1 0.01
29 44 0.25
30 134 0.75
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.36
Consensus pattern (30 bp):
AGGGTCAAAATATGATTTTGGAAAAGTTTA
Found at i:42837 original size:30 final size:29
Alignment explanation
Indices: 42575--42839 Score: 228
Period size: 30 Copynumber: 8.9 Consensus size: 29
42565 ACTTGGGATG
* * * * *
42575 AAAATGAAATTTTAGAGAAGTTCGAGGGTC
1 AAAATGTAATTTTGGAAAAGTT-TAGGGTT
* *
42605 AAAATGTGATTTTGG-AAAGTTTGGAGGTT
1 AAAATGTAATTTTGGAAAAGTTTAG-GGTT
* * * * * *
42634 AAAGTATGATTTTGGAAAAGTTTAAAGATC
1 AAAATGTAATTTTGGAAAAGTTT-AGGGTT
* * *
42664 AAAATATGATTTTGGAAAAGTTTAAGGGTC
1 AAAATGTAATTTTGGAAAAGTTT-AGGGTT
* *
42694 AAAGTGTAATTTTGGAAAAGTTTAAGGGTC
1 AAAATGTAATTTTGGAAAAGTTT-AGGGTT
* *
42724 AAAATATGATTTTGGAAAAGTTTAGGGGTT
1 AAAATGTAATTTTGGAAAAGTTTA-GGGTT
* * *
42754 AAAATATGATTTTGGAAATG-TTAGGGGTT
1 AAAATGTAATTTTGGAAAAGTTTA-GGGTT
42783 AAAATGTAATTTTGGAAAAGTTTAGGTGTT
1 AAAATGTAATTTTGGAAAAGTTTAGG-GTT
*
42813 AAAATGTAATTTTGAAAAAGTTTAGGG
1 AAAATGTAATTTTGGAAAAGTTTAGGG
42840 ACCTTTTGAG
Statistics
Matches: 201, Mismatches: 28, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
28 1 0.00
29 51 0.25
30 149 0.74
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.35
Consensus pattern (29 bp):
AAAATGTAATTTTGGAAAAGTTTAGGGTT
Found at i:44856 original size:42 final size:41
Alignment explanation
Indices: 44800--44942 Score: 162
Period size: 42 Copynumber: 3.4 Consensus size: 41
44790 CTTGACTTAG
* * **
44800 GGGTAAAAGATTGGATGAGGTCTTCAATCTGTCTTATGATC
1 GGGTAAGAGATTGGATGAGGTCTTCAATCTGCCCCATGATC
* *
44841 GGGATAAGAGATTGGATGATGG-CTGCAATATGCCCCATGATC
1 GGG-TAAGAGATTGGATGA-GGTCTTCAATCTGCCCCATGATC
* * *
44883 GAGGTAAGAGATTGGATGATGTTTTCAATCTGCCCCATGATTG
1 G-GGTAAGAGATTGGATGAGGTCTTCAATCTGCCCCATGA-TC
44926 GGGTAAGAGATTGGATG
1 GGGTAAGAGATTGGATG
44943 GTGACGTAAC
Statistics
Matches: 86, Mismatches: 11, Indels: 9
0.81 0.10 0.08
Matches are distributed among these distances:
41 4 0.05
42 76 0.88
43 6 0.07
ACGTcount: A:0.27, C:0.13, G:0.31, T:0.29
Consensus pattern (41 bp):
GGGTAAGAGATTGGATGAGGTCTTCAATCTGCCCCATGATC
Found at i:45332 original size:49 final size:49
Alignment explanation
Indices: 45279--45967 Score: 531
Period size: 49 Copynumber: 14.1 Consensus size: 49
45269 ATGTTTTTGA
* * * * *
45279 GGTACAAGGTTCGTCATTACGACTTAAACCTTTCCCTTCAAATCTTCGT
1 GGTACAAGGTTCGCCGTTGCGACTTAAATCTTTCCCTTCATATCTTCGT
* * * * * * * *
45328 GGTACTAGATTCGCCGTAGCGGCTTAAATCTTTCCCTTCATTTTTTTGA
1 GGTACAAGGTTCGCCGTTGCGACTTAAATCTTTCCCTTCATATCTTCGT
* * * * *
45377 GGTACAAGGTTCGCCGCTACGACTTGAACCTTTCCCTCCATATCTTCGT
1 GGTACAAGGTTCGCCGTTGCGACTTAAATCTTTCCCTTCATATCTTCGT
* * * * * *
45426 GGTACTAGAG-TCGCCGTTGTGGCTAAAATCTTTCCCTTCAT-GCTTCTGA
1 GGTACAAG-GTTCGCCGTTGCGACTTAAATCTTTCCCTTCATATCTTC-GT
* * * *
45475 GGTACAAGGTTCGTCATTGCGACTTAAATCTTTCCCTCCATATCCTCGT
1 GGTACAAGGTTCGCCGTTGCGACTTAAATCTTTCCCTTCATATCTTCGT
* * *
45524 GGTACTGAA--TTCGCCGTTGCGACTTAAATCTTTCTCTTCAT-GCTTTTGT
1 GGTAC--AAGGTTCGCCGTTGCGACTTAAATCTTTCCCTTCATATC-TTCGT
* * * * *
45573 GGTACAAGGTTCGTCGTTGCAACTTAAACCTTTCCCTCCATATCCTCGT
1 GGTACAAGGTTCGCCGTTGCGACTTAAATCTTTCCCTTCATATCTTCGT
* * * *
45622 GGTAC-TGGATTCGCCGTTGCGACTTAAATCTTTCTCTTCAT-TCTTTTGA
1 GGTACAAGG-TTCGCCGTTGCGACTTAAATCTTTCCCTTCATATC-TTCGT
* * * * * * *
45671 GGTACAAGGTTTGCTGTTACAATTTAAACCTTTCCC-TCTATATCCTCGT
1 GGTACAAGGTTCGCCGTTGCGACTTAAATCTTTCCCTTC-ATATCTTCGT
* * *
45720 GGTACTAGATTCGTCGTTGCGACTTAAATCTTTCCCTTCATATCTTCGT
1 GGTACAAGGTTCGCCGTTGCGACTTAAATCTTTCCCTTCATATCTTCGT
* * * * * * *
45769 GGTACTAGATTCGTCATTGCGGCTTAAATCTTTCCCTTCAT-GCTTCTGA
1 GGTACAAGGTTCGCCGTTGCGACTTAAATCTTTCCCTTCATATCTTC-GT
* * *
45818 GGTATAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGT
1 GGTACAAGGTTCGCCGTTGCGACTTAAATCTTTCCCTTCATATCTTCGT
** ** * *
45867 GGTA-TTGGATTCGCCGTTGTAACTTAAATATTTCCCTTCATGCAT-TT-GA
1 GGTACAAGG-TTCGCCGTTGCGACTTAAATCTTTCCCTTCAT--ATCTTCGT
* * ** *
45916 GGTACAAAGTTCGCCATTGTAACTTAAATCTTTCCCTCCATATCCTT-GT
1 GGTACAAGGTTCGCCGTTGCGACTTAAATCTTTCCCTTCATAT-CTTCGT
45965 GGT
1 GGT
45968 GATGAAAACT
Statistics
Matches: 495, Mismatches: 121, Indels: 48
0.75 0.18 0.07
Matches are distributed among these distances:
47 4 0.01
48 18 0.04
49 451 0.91
50 18 0.04
51 4 0.01
ACGTcount: A:0.20, C:0.25, G:0.17, T:0.37
Consensus pattern (49 bp):
GGTACAAGGTTCGCCGTTGCGACTTAAATCTTTCCCTTCATATCTTCGT
Found at i:45387 original size:98 final size:98
Alignment explanation
Indices: 45261--45854 Score: 667
Period size: 98 Copynumber: 6.1 Consensus size: 98
45251 AGCCTCAACC
* * * * *
45261 TTCCCTTTATGTTTTTGAGGTACAAGGTTCGTCATTACGACTTAAACCTTTCCCTTCAAATCTTC
1 TTCCCTTCATGCTTTTGAGGTACAAGGTTCGTCATTACGACTTAAACCTTTCCCTCCATATCCTC
* *
45326 GTGGTACTAGATTCGCCGTAGCGGCTTAAATCT
66 GTGGTACTAGATTCGCCGTTGCGACTTAAATCT
** * ** * *
45359 TTCCCTTCATTTTTTTGAGGTACAAGGTTCGCCGCTACGACTTGAACCTTTCCCTCCATATCTTC
1 TTCCCTTCATGCTTTTGAGGTACAAGGTTCGTCATTACGACTTAAACCTTTCCCTCCATATCCTC
* * * *
45424 GTGGTACTAGAGTCGCCGTTGTGGCTAAAATCT
66 GTGGTACTAGATTCGCCGTTGCGACTTAAATCT
* * *
45457 TTCCCTTCATGCTTCTGAGGTACAAGGTTCGTCATTGCGACTTAAATCTTTCCCTCCATATCCTC
1 TTCCCTTCATGCTTTTGAGGTACAAGGTTCGTCATTACGACTTAAACCTTTCCCTCCATATCCTC
45522 GTGGTACT-GAATTCGCCGTTGCGACTTAAATCT
66 GTGGTACTAG-ATTCGCCGTTGCGACTTAAATCT
* * * * *
45555 TTCTCTTCATGCTTTTGTGGTACAAGGTTCGTCGTTGCAACTTAAACCTTTCCCTCCATATCCTC
1 TTCCCTTCATGCTTTTGAGGTACAAGGTTCGTCATTACGACTTAAACCTTTCCCTCCATATCCTC
*
45620 GTGGTACTGGATTCGCCGTTGCGACTTAAATCT
66 GTGGTACTAGATTCGCCGTTGCGACTTAAATCT
* * * * * * *
45653 TTCTCTTCATTCTTTTGAGGTACAAGGTTTG-CTGTTACAATTTAAACCTTTCCCTCTATATCCT
1 TTCCCTTCATGCTTTTGAGGTACAAGGTTCGTC-ATTACGACTTAAACCTTTCCCTCCATATCCT
*
45717 CGTGGTACTAGATTCGTCGTTGCGACTTAAATCT
65 CGTGGTACTAGATTCGCCGTTGCGACTTAAATCT
* * * * * * * * * * *
45751 TTCCCTTCAT-ATCTTCGTGGTACTAGATTCGTCATTGCGGCTTAAATCTTTCCCTTCAT-GCTT
1 TTCCCTTCATGCT-TTTGAGGTACAAGGTTCGTCATTACGACTTAAACCTTTCCCTCCATATCCT
* * *
45814 CTGAGGTA-TAAGGTTCGCCGTTGCGACTTAAACCT
65 C-GTGGTACT-AGATTCGCCGTTGCGACTTAAATCT
45849 TTCCCT
1 TTCCCT
45855 CCATATCTTC
Statistics
Matches: 428, Mismatches: 61, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
97 7 0.02
98 419 0.98
99 2 0.00
ACGTcount: A:0.19, C:0.26, G:0.18, T:0.38
Consensus pattern (98 bp):
TTCCCTTCATGCTTTTGAGGTACAAGGTTCGTCATTACGACTTAAACCTTTCCCTCCATATCCTC
GTGGTACTAGATTCGCCGTTGCGACTTAAATCT
Found at i:47840 original size:14 final size:14
Alignment explanation
Indices: 47823--47855 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
47813 TCATCTTGAC
47823 CTTTTCTTTCTT-TT
1 CTTTTC-TTCTTCTT
47837 CTTTTCTTCTTCTT
1 CTTTTCTTCTTCTT
47851 CTTTT
1 CTTTT
47856 TTTTATATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (14 bp):
CTTTTCTTCTTCTT
Found at i:52467 original size:58 final size:58
Alignment explanation
Indices: 52347--52499 Score: 166
Period size: 58 Copynumber: 2.6 Consensus size: 58
52337 TTAAAATGAG
* * * *
52347 TTTTTAGACATCCGAGGGTAAAACGGTAAATTTTTAGAAAAATCGGGATAAAAAATAGAA
1 TTTTTAGACATTCGAGGGTAAAATGGT-AATTTTT-GAAAAATCGAGATAAAAAAGAGAA
* * *
52407 TTTTTAGATATTCGGGGGTAAAATGGTAATTTTTGGAAAATCGAGATAAAAAACGA-AA
1 TTTTTAGACATTCGAGGGTAAAATGGTAATTTTTGAAAAATCGAGATAAAAAA-GAGAA
* ***
52465 TTTTTGGACATTTTTGGGTAAAAT-GTAATTTTTGA
1 TTTTTAGACATTCGAGGGTAAAATGGTAATTTTTGA
52500 GAGTTTAGGG
Statistics
Matches: 79, Mismatches: 13, Indels: 5
0.81 0.13 0.05
Matches are distributed among these distances:
57 10 0.13
58 38 0.48
59 8 0.10
60 23 0.29
ACGTcount: A:0.39, C:0.06, G:0.21, T:0.34
Consensus pattern (58 bp):
TTTTTAGACATTCGAGGGTAAAATGGTAATTTTTGAAAAATCGAGATAAAAAAGAGAA
Found at i:52525 original size:30 final size:29
Alignment explanation
Indices: 52453--52656 Score: 148
Period size: 30 Copynumber: 6.9 Consensus size: 29
52443 AAAATCGAGA
* * * *
52453 TAAAAAACGAAATTTTTGGACATTTTTGGG
1 TAAAAAATGGAATTTTTGGA-AGTTTAGGG
*
52483 T--AAAATGTAATTTTT-GAGAGTTTAGGG
1 TAAAAAATGGAATTTTTGGA-AGTTTAGGG
* *
52510 TAAAAAAATGGAATTTTTGGAGGTTTGGGGG
1 T-AAAAAATGGAATTTTTGGAAGTTT-AGGG
* *
52541 T-AAAAATGTAATTTTTTGGAAGTTTCGAGG
1 TAAAAAATGGAA-TTTTTGGAAGTTTAG-GG
* *
52571 TCAAAAATGGAATTTTTGGAAGTTCGAGGG
1 TAAAAAATGGAATTTTTGGAAGTT-TAGGG
** * *
52601 T-AAAAATAAAATTTTTAGAAGTTTCGAGG
1 TAAAAAATGGAATTTTTGGAAGTTTAG-GG
*
52630 TCAAAAATGGAATTTTTGGACAGTTTA
1 TAAAAAATGGAATTTTTGGA-AGTTTA
52657 TGAACCTTCA
Statistics
Matches: 139, Mismatches: 23, Indels: 23
0.75 0.12 0.12
Matches are distributed among these distances:
27 10 0.07
28 13 0.09
29 32 0.23
30 63 0.45
31 21 0.15
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.36
Consensus pattern (29 bp):
TAAAAAATGGAATTTTTGGAAGTTTAGGG
Found at i:52546 original size:29 final size:30
Alignment explanation
Indices: 52484--52655 Score: 156
Period size: 30 Copynumber: 5.7 Consensus size: 30
52474 ATTTTTGGGT
* *
52484 AAAATGTAATTTTT-GAGAGTTT-AGGGTAAA
1 AAAATGGAATTTTTGGA-AGTTTCGGGGT-AA
* *
52514 AAAATGGAATTTTTGGAGGTTTGGGGGT-A
1 AAAATGGAATTTTTGGAAGTTTCGGGGTAA
* * *
52543 AAAATGTAATTTTTTGGAAGTTTCGAGGTCA
1 AAAATGGAA-TTTTTGGAAGTTTCGGGGTAA
52574 AAAATGGAATTTTTGGAAG-TTCGAGGGT-A
1 AAAATGGAATTTTTGGAAGTTTCG-GGGTAA
** * * *
52603 AAAATAAAATTTTTAGAAGTTTCGAGGTCA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTAA
52633 AAAATGGAATTTTTGGACAGTTT
1 AAAATGGAATTTTTGGA-AGTTT
52656 ATGAACCTTC
Statistics
Matches: 118, Mismatches: 16, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
29 33 0.28
30 65 0.55
31 20 0.17
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.35
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAGTTTCGGGGTAA
Found at i:52556 original size:59 final size:60
Alignment explanation
Indices: 52480--52654 Score: 225
Period size: 60 Copynumber: 3.0 Consensus size: 60
52470 GGACATTTTT
* * * * *
52480 GGGT-AAAATGTAATTTTTGAG-AGTTTAG-GGTAAAAAAATGGAATTTTTGGAGGTTTGG
1 GGGTAAAAATGTAATTTTTGAGAAGTTTCGAGGT-CAAAAATGGAATTTTTGGAAGTTCGA
52538 GGGTAAAAATGTAATTTTTTG-GAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTCGA
1 GGGTAAAAATGTAA-TTTTTGAGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTCGA
**
52598 GGGTAAAAATAAAATTTTT-AGAAGTTTCGAGGTCAAAAATGGAATTTTTGGACAGTT
1 GGGTAAAAATGTAATTTTTGAGAAGTTTCGAGGTCAAAAATGGAATTTTTGGA-AGTT
52655 TATGAACCTT
Statistics
Matches: 104, Mismatches: 7, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
58 4 0.04
59 47 0.45
60 50 0.48
61 3 0.03
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (60 bp):
GGGTAAAAATGTAATTTTTGAGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTCGA
Found at i:54392 original size:17 final size:17
Alignment explanation
Indices: 54372--54448 Score: 91
Period size: 17 Copynumber: 4.5 Consensus size: 17
54362 AATAATTTTT
*
54372 AATTCAAAATAAATTCA
1 AATTTAAAATAAATTCA
*
54389 AATTTAAAATAAATTTA
1 AATTTAAAATAAATTCA
* * ** *
54406 AATTCAACACGAATTTA
1 AATTTAAAATAAATTCA
54423 AATTTAAAATAAATTCA
1 AATTTAAAATAAATTCA
54440 AATTTAAAA
1 AATTTAAAA
54449 ATTAAAAGTT
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 49 1.00
ACGTcount: A:0.57, C:0.08, G:0.01, T:0.34
Consensus pattern (17 bp):
AATTTAAAATAAATTCA
Found at i:54400 original size:34 final size:34
Alignment explanation
Indices: 54362--54448 Score: 102
Period size: 34 Copynumber: 2.6 Consensus size: 34
54352 TTTTAATATT
* * *
54362 AATAATTTTTAATTCAAAATAAATTCAAATTTAA
1 AATAAATTTAAATTCAAAACAAATTCAAATTTAA
* * *
54396 AATAAATTTAAATTCAACACGAATTTAAATTTAA
1 AATAAATTTAAATTCAAAACAAATTCAAATTTAA
* *
54430 AATAAATTCAAATTTAAAA
1 AATAAATTTAAATTCAAAA
54449 ATTAAAAGTT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.37
Consensus pattern (34 bp):
AATAAATTTAAATTCAAAACAAATTCAAATTTAA
Found at i:58694 original size:15 final size:15
Alignment explanation
Indices: 58670--58703 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
58660 GGCCCATCAT
*
58670 CACCACCCACGCAAG
1 CACCAACCACGCAAG
*
58685 CACCAACCACTCAAG
1 CACCAACCACGCAAG
58700 CACC
1 CACC
58704 GCCCATGCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.53, G:0.09, T:0.03
Consensus pattern (15 bp):
CACCAACCACGCAAG
Found at i:61271 original size:24 final size:24
Alignment explanation
Indices: 61217--61278 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 24
61207 AAAAATTCAA
61217 AAAAATAATTTATTAGAAAAATATG
1 AAAAATAA-TTATTAGAAAAATATG
*
61242 AGAAATAATTATTAGAATTAAAT-T-
1 AAAAATAATTATTAGAA--AAATATG
61266 AAAAATAATTATT
1 AAAAATAATTATT
61279 GAGGCTGCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
24 21 0.64
25 8 0.24
26 4 0.12
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (24 bp):
AAAAATAATTATTAGAAAAATATG
Found at i:63121 original size:6 final size:6
Alignment explanation
Indices: 63112--63230 Score: 106
Period size: 6 Copynumber: 20.3 Consensus size: 6
63102 TTAGATTAGT
* *
63112 TTTAAA TTT-AT TTCTAAA TTTAAA TTT-AC TTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TT-TAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
63159 TTT-AC TTTAAA TTTAAA TTTAAA TTT-AG TTTAAA TTTGAAA --TAAT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA
* *
63204 TTTAAA CTTAAA CTTTAAA ATTAAA TT
1 TTTAAA TTTAAA -TTTAAA TTTAAA TT
63231 CAAAATCCGA
Statistics
Matches: 90, Mismatches: 14, Indels: 18
0.74 0.11 0.15
Matches are distributed among these distances:
4 2 0.02
5 16 0.18
6 61 0.68
7 11 0.12
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:63144 original size:23 final size:23
Alignment explanation
Indices: 63126--63200 Score: 132
Period size: 23 Copynumber: 3.2 Consensus size: 23
63116 AATTTATTTC
63126 TAAATTTAAATTTACTTTAAATT
1 TAAATTTAAATTTACTTTAAATT
63149 TAAATTTAAATTTACTTTAAATT
1 TAAATTTAAATTTACTTTAAATT
*
63172 TAAATTTAAATTTAGTTTAAATT
1 TAAATTTAAATTTACTTTAAATT
63195 TGAAAT
1 T-AAAT
63201 AATTTTAAAC
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
23 46 0.92
24 4 0.08
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (23 bp):
TAAATTTAAATTTACTTTAAATT
Found at i:63190 original size:17 final size:16
Alignment explanation
Indices: 63112--63200 Score: 71
Period size: 17 Copynumber: 5.4 Consensus size: 16
63102 TTAGATTAGT
63112 TTTAAATTTATTTCTAAA
1 TTTAAATTTA-TT-TAAA
63130 TTTAAATTTACTTTAAA
1 TTTAAATTTA-TTTAAA
63147 TTT-AA---ATTTAAA
1 TTTAAATTTATTTAAA
*
63159 TTT-ACTTTAAATTTAAA
1 TTTAAATTT--ATTTAAA
63176 TTTAAATTTAGTTTAAA
1 TTTAAATTTA-TTTAAA
63193 TTTGAAAT
1 TTT-AAAT
63201 AATTTTAAAC
Statistics
Matches: 60, Mismatches: 3, Indels: 16
0.76 0.04 0.20
Matches are distributed among these distances:
12 10 0.17
13 1 0.02
16 3 0.05
17 26 0.43
18 20 0.33
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (16 bp):
TTTAAATTTATTTAAA
Found at i:64789 original size:58 final size:59
Alignment explanation
Indices: 64727--64872 Score: 190
Period size: 58 Copynumber: 2.5 Consensus size: 59
64717 TTTTAATAAG
* *
64727 ATTATTATTAAATATAATTTAATAAAAATAACAAATAATTTAATTATA-TTTTAACATA
1 ATTATTATTAAATATAATTTAATAAAAATAACAAATAATTTAATAACATTTTTAACATA
* * * *
64785 ATTATTATTAAATACAATTTAAT-AAAATAATATATAATTTAATAACATTTTTAATATA
1 ATTATTATTAAATATAATTTAATAAAAATAACAAATAATTTAATAACATTTTTAACATA
*
64843 ATTATTATTAAAATATGAA-TTAGTAAAAAT
1 ATTATTATT-AAATAT-AATTTAATAAAAAT
64873 TATAATATAT
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
57 20 0.26
58 40 0.53
59 9 0.12
60 7 0.09
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (59 bp):
ATTATTATTAAATATAATTTAATAAAAATAACAAATAATTTAATAACATTTTTAACATA
Found at i:68661 original size:29 final size:29
Alignment explanation
Indices: 68629--68841 Score: 186
Period size: 29 Copynumber: 7.3 Consensus size: 29
68619 AAAAATTATA
68629 TTTTACCCTCGAACTTTCCAAAATTCCAT
1 TTTTACCCTCGAACTTTCCAAAATTCCAT
* * *
68658 TTTTAACCTC-AATTTTTTCCAAAAATTACA-
1 TTTTACCCTCGAA--CTTTCC-AAAATTCCAT
*
68688 TTTTACCCTTGAACTTTCCAAAATTCCATT
1 TTTTACCCTCGAACTTTCCAAAATTCCA-T
* *
68718 TTTTA-CCTCG-ATTTTCCAAAATTACAT
1 TTTTACCCTCGAACTTTCCAAAATTCCAT
* *
68745 TTTTACCCCCAAACTTTCCAAAATTCCAT
1 TTTTACCCTCGAACTTTCCAAAATTCCAT
** * *
68774 TTTTGA-CCT-GATTTTTTCAAAAATTACAT
1 TTTT-ACCCTCGA-ACTTTCCAAAATTCCAT
* **
68803 TTTTACCCTCAAACTTTTTAAAATTCCAT
1 TTTTACCCTCGAACTTTCCAAAATTCCAT
68832 TTTTAACCCT
1 TTTT-ACCCT
68842 AATTTTTTCA
Statistics
Matches: 145, Mismatches: 26, Indels: 25
0.74 0.13 0.13
Matches are distributed among these distances:
27 6 0.04
28 29 0.20
29 75 0.52
30 25 0.17
31 10 0.07
ACGTcount: A:0.30, C:0.25, G:0.02, T:0.43
Consensus pattern (29 bp):
TTTTACCCTCGAACTTTCCAAAATTCCAT
Found at i:68816 original size:58 final size:58
Alignment explanation
Indices: 68619--68929 Score: 333
Period size: 59 Copynumber: 5.3 Consensus size: 58
68609 TAAACTATCT
* *
68619 AAAAATTATATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCTCAATTTTTTCC
1 AAAAATTACATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCTCAATTTTTT-C
** * *
68678 AAAAATTACATTTTACCCTTGAACTTTCCAAAATTCCATTTTTTACCTCGA--TTTTC
1 AAAAATTACATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCTCAATTTTTTC
* * * *
68734 CAAAATTACATTTTTACCCCCAAACTTTCCAAAATTCCATTTTTGACCT-GATTTTTTC
1 AAAAATTACA-TTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCTCAATTTTTTC
**
68792 AAAAATTACATTTTTACCCTCAAACTTTTTAAAATTCCATTTTTAACC-CTAATTTTTTC
1 AAAAATTACA-TTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCTC-AATTTTTTC
* * * ** * * * *
68851 AAAAGTTACCATTTTACCCCCAAACCTTCCAAAAATTTTATTTTTGACCGCAATTCTTCC
1 AAAAATTA-CATTTTACCCTCAAACTTTCC-AAAATTCCATTTTTAACCTCAATTTTTTC
*
68911 AAAAAGTACCATTTTACCC
1 AAAAATTA-CATTTTACCC
68930 CTTAGATGTC
Statistics
Matches: 217, Mismatches: 27, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
56 12 0.06
57 38 0.18
58 48 0.22
59 77 0.35
60 41 0.19
61 1 0.00
ACGTcount: A:0.32, C:0.24, G:0.03, T:0.41
Consensus pattern (58 bp):
AAAAATTACATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCTCAATTTTTTC
Found at i:68849 original size:29 final size:28
Alignment explanation
Indices: 68648--68869 Score: 98
Period size: 29 Copynumber: 7.6 Consensus size: 28
68638 CGAACTTTCC
*
68648 AAAATTCCATTTTTAACCTCAATTTTTTCCA
1 AAAATTCCATTTTTACCCT-AATTTTTT--A
* * **
68679 AAAATTACA-TTTTACCCTTGAA-CTTTCC
1 AAAATTCCATTTTTACCC-T-AATTTTTTA
* **
68707 AAAATTCCATTTTTTA-CCTCGA-TTTTCC
1 AAAATTCCA-TTTTTACCCT-AATTTTTTA
* * ** **
68735 AAAATTACATTTTTACCCCCAAACTTTCC
1 AAAATTCCATTTTTA-CCCTAATTTTTTA
*
68764 AAAATTCCATTTTTGA-CCTGATTTTTTCA
1 AAAATTCCATTTTT-ACCCTAATTTTTT-A
* *
68793 AAAATTACATTTTTACCCTCAAACTTTTT-
1 AAAATTCCATTTTTACCCT--AATTTTTTA
68822 AAAATTCCATTTTTAACCCTAATTTTTTCA
1 AAAATTCCATTTTT-ACCCTAATTTTTT-A
*
68852 AAAGTTACCA-TTTTACCC
1 AAAATT-CCATTTTTACCC
68870 CCAAACCTTC
Statistics
Matches: 149, Mismatches: 27, Indels: 32
0.72 0.13 0.15
Matches are distributed among these distances:
27 6 0.04
28 38 0.26
29 55 0.37
30 30 0.20
31 20 0.13
ACGTcount: A:0.32, C:0.23, G:0.02, T:0.43
Consensus pattern (28 bp):
AAAATTCCATTTTTACCCTAATTTTTTA
Found at i:68981 original size:60 final size:59
Alignment explanation
Indices: 68620--68990 Score: 243
Period size: 59 Copynumber: 6.3 Consensus size: 59
68610 AAACTATCTA
* * * * * *
68620 AAAATTA-TATTTTACCCTCGAACTTTCC-AAAATTCCATTTTTAACCTC-AATTTTTTCC
1 AAAATTACCATTTTACCCCCAAAC-TTCCAAAAATTCCATTTTTGACCCCTAATTTTCT-C
*** * * *
68678 AAAAATTA-CATTTTACCCTTGAACTTTCC-AAAATTCCATTTTTTACCTC-GATTTTC-C
1 -AAAATTACCATTTTACCCCCAAAC-TTCCAAAAATTCCATTTTTGACCCCTAATTTTCTC
* *
68735 AAAATTA-CATTTTTACCCCCAAACTTTCC-AAAATTCCATTTTTGA--CCTGATTTTTTC
1 AAAATTACCA-TTTTACCCCCAAAC-TTCCAAAAATTCCATTTTTGACCCCTAATTTTCTC
* *** * *
68792 AAAAATTA-CATTTTTACCCTCAAACTTTTTAAAATTCCATTTTT-AACCCTAATTTTTTC
1 -AAAATTACCA-TTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCCCTAATTTTCTC
** *
68851 AAAAGTTACCATTTTACCCCCAAACCTTCCAAAAATTTTATTTTTGACCGC-AATTCTTC-C
1 AAAA-TTACCATTTTACCCCCAAA-CTTCCAAAAATTCCATTTTTGACCCCTAATT-TTCTC
* * * * *
68911 AAAAAGTACCATTTTACCCCTTAGA-TGTCTAAAAATTCCATTTTTGACCCCTAACTTTCTC
1 -AAAATTACCATTTTACCCC-CAAACT-TCCAAAAATTCCATTTTTGACCCCTAATTTTCTC
*
68972 AAAATTACCATTTTGCCCC
1 AAAATTACCATTTTACCCC
68991 GAGTGACCAA
Statistics
Matches: 261, Mismatches: 34, Indels: 33
0.80 0.10 0.10
Matches are distributed among these distances:
55 1 0.00
56 15 0.06
57 36 0.14
58 41 0.16
59 77 0.30
60 76 0.29
61 15 0.06
ACGTcount: A:0.31, C:0.25, G:0.04, T:0.40
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCCCTAATTTTCTC
Found at i:68986 original size:30 final size:29
Alignment explanation
Indices: 68673--68990 Score: 94
Period size: 29 Copynumber: 10.9 Consensus size: 29
68663 ACCTCAATTT
*
68673 TTTCCAAAAATTA-CATTTT-ACCCTTGAAC
1 TTTCC-AAAATTACCATTTTGACCCCT-AAC
* * * *
68702 TTTCCAAAATT-CCATTTTTTACCTC-GAT
1 TTTCCAAAATTACCA-TTTTGACCCCTAAC
* *
68730 TTTCCAAAATTA-CATTTTTACCCCCAAAC
1 TTTCCAAAATTACCATTTTGA-CCCCTAAC
**
68759 TTTCCAAAATT-CCATTTTTGA--CCTGATTT
1 TTTCCAAAATTACCA-TTTTGACCCCT-A-AC
* * *
68788 TTTCAAAAATTA-CATTTTTACCCTCAAAC
1 TTTCCAAAATTACCATTTTGACCC-CTAAC
** * * *
68817 TTTTTAAAATT-CCATTTTTAACCCTAATT
1 TTTCCAAAATTACCATTTTGACCCCTAA-C
* *
68846 TTTTCAAAAGTTACCATTTT-ACCCCCAAAC
1 TTTCCAAAA-TTACCATTTTGA-CCCCTAAC
* ** * *
68876 CTTCCAAAAATT-TTATTTTTGACCGC-AAT
1 TTTCC-AAAATTACCA-TTTTGACCCCTAAC
*
68905 TCTTCCAAAAAGTACCATTTT-ACCCCTTAGA-
1 T-TTCC-AAAATTACCATTTTGACCCC-TA-AC
* *
68936 TGTCTAAAAATT-CCATTTTTGACCCCTAAC
1 TTTC-CAAAATTACCA-TTTTGACCCCTAAC
68966 TTTCTCAAAATTACCATTTTG-CCCC
1 TTTC-CAAAATTACCATTTTGACCCC
68991 GAGTGACCAA
Statistics
Matches: 216, Mismatches: 41, Indels: 64
0.67 0.13 0.20
Matches are distributed among these distances:
27 8 0.04
28 34 0.16
29 77 0.36
30 67 0.31
31 29 0.13
32 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.04, T:0.40
Consensus pattern (29 bp):
TTTCCAAAATTACCATTTTGACCCCTAAC
Found at i:74642 original size:235 final size:238
Alignment explanation
Indices: 74232--74877 Score: 1149
Period size: 235 Copynumber: 2.7 Consensus size: 238
74222 ATTAAAAAAA
74232 AATTAAAATTTTAACTTTATTACGTATAAAAATCATAAAAATATATTTTAAAA-TTTAAATGAAA
1 AATTAAAATTTTAACTTTATTACGTATAAAAATCATAAAAATATATTTTAAAATTTTAAATGAAA
*
74296 TCATTTTTAATTCTTTTATAAAATTGAATTATTTAAAACATTTAAACTAATAGAAGTTAAATTTG
66 TCATTTTTAATTCTTTTATAAAATTGAATTATTTAAAACATTTAAAATAATAGAAGTTAAATTTG
*
74361 ATAGAAGAAAACTAATAATCACATTATACTTGAGATAAAGAGAGCAATACCATTTTGAATTCA-A
131 ATAGAAGAAAACTAATAATCACATTTTACTTGAGATAAAGAGAGCAATACCATTTTGAATTCAGA
74425 AA-GA-TTTTTTTTATTGATTTAAAGTCATAACTGGGTACCTG
196 AATGATTTTTTTTTATTGATTTAAAGTCATAACTGGGTACCTG
*
74466 AATTAAAATTTTAGCTTTATTACGTATAAAAATCATAAAAATATATTTTAAAATTTTAAATGAAA
1 AATTAAAATTTTAACTTTATTACGTATAAAAATCATAAAAATATATTTTAAAATTTTAAATGAAA
* *
74531 TTATTTTTAATTCTTTTATAAAATTGAATTATTTAAAACATTTAAAATAATATAAGTTAAATTTG
66 TCATTTTTAATTCTTTTATAAAATTGAATTATTTAAAACATTTAAAATAATAGAAGTTAAATTTG
74596 ATAGAAGAAAACTAATAATCACATTTTACTTGAGATAAAGAGAGCAATACCATTTTGAATTCAGA
131 ATAGAAGAAAACTAATAATCACATTTTACTTGAGATAAAGAGAGCAATACCATTTTGAATTCAGA
74661 AATTGATTTTTTTTTATTGATTTAAAGTCATAACTGGGTACCTG
196 AA-TGATTTTTTTTTATTGATTTAAAGTCATAACTGGGTACCTG
* * *
74705 AACTAATATTTTAACTTTATTACGTATAAAAATCAT-AAAATATATTTTAAAATTTTAAATAAAA
1 AATTAAAATTTTAACTTTATTACGTATAAAAATCATAAAAATATATTTTAAAATTTTAAATGAAA
*
74769 TCATTTTTAATTCTTTTATAAAATTGAATTATTTAAAACATTTAAAATAATAGAAATTAAATTTG
66 TCATTTTTAATTCTTTTATAAAATTGAATTATTTAAAACATTTAAAATAATAGAAGTTAAATTTG
* *
74834 ATAGAAAAAAACTAATAATCACATTTTACTTGAGAAAAAGAGAG
131 ATAGAAGAAAACTAATAATCACATTTTACTTGAGATAAAGAGAG
74878 ATTTAAAGTC
Statistics
Matches: 393, Mismatches: 14, Indels: 6
0.95 0.03 0.01
Matches are distributed among these distances:
234 52 0.13
235 135 0.34
236 3 0.01
238 133 0.34
239 70 0.18
ACGTcount: A:0.45, C:0.07, G:0.08, T:0.39
Consensus pattern (238 bp):
AATTAAAATTTTAACTTTATTACGTATAAAAATCATAAAAATATATTTTAAAATTTTAAATGAAA
TCATTTTTAATTCTTTTATAAAATTGAATTATTTAAAACATTTAAAATAATAGAAGTTAAATTTG
ATAGAAGAAAACTAATAATCACATTTTACTTGAGATAAAGAGAGCAATACCATTTTGAATTCAGA
AATGATTTTTTTTTATTGATTTAAAGTCATAACTGGGTACCTG
Found at i:75017 original size:198 final size:198
Alignment explanation
Indices: 74679--75072 Score: 727
Period size: 198 Copynumber: 2.0 Consensus size: 198
74669 TTTTTTTATT
74679 GATTTAAAGTCATAACTGGGTACCTGAACTAATATTTTAACTTTATTACGTATAAAAATCATAAA
1 GATTTAAAGTCATAACTGGGTACCTGAACTAATATTTTAACTTTATTACGTATAAAAATCATAAA
74744 ATATATTTTAAAATTTTAAATAAAATCATTTTTAATTCTTTTATAAAATTGAATTATTTAAAACA
66 ATATATTTTAAAATTTTAAATAAAATCATTTTTAATTCTTTTATAAAATTGAATTATTTAAAACA
74809 TTTAAAATAATAGAAATTAAATTTGATAGAAAAAAACTAATAATCACATTTTACTTGAGAAAAAG
131 TTTAAAATAATAGAAATTAAATTTGATAGAAAAAAACTAATAATCACATTTTACTTGAGAAAAAG
74874 AGA
196 AGA
74877 GATTTAAAGTCATAACTGGGTACCTGAACTAATATTTTAACTTTATTACGTATAAAAATCATAAA
1 GATTTAAAGTCATAACTGGGTACCTGAACTAATATTTTAACTTTATTACGTATAAAAATCAT-AA
* *
74942 AATATATTTTAAAA-TTTAAATGAAATCATTTTTAATTCTTTTATAAAATTTAATTATTTAAAAC
65 AATATATTTTAAAATTTTAAATAAAATCATTTTTAATTCTTTTATAAAATTGAATTATTTAAAAC
* * *
75006 ATTTAAAATAATAGAAGTTAAATTTGATAGAAGAAAACTAATAATCACATTTTACTTGAGATAAA
130 ATTTAAAATAATAGAAATTAAATTTGATAGAAAAAAACTAATAATCACATTTTACTTGAGAAAAA
75071 GA
195 GA
75073 ATAAAAACAG
Statistics
Matches: 190, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
198 174 0.92
199 16 0.08
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.38
Consensus pattern (198 bp):
GATTTAAAGTCATAACTGGGTACCTGAACTAATATTTTAACTTTATTACGTATAAAAATCATAAA
ATATATTTTAAAATTTTAAATAAAATCATTTTTAATTCTTTTATAAAATTGAATTATTTAAAACA
TTTAAAATAATAGAAATTAAATTTGATAGAAAAAAACTAATAATCACATTTTACTTGAGAAAAAG
AGA
Found at i:75351 original size:35 final size:36
Alignment explanation
Indices: 75292--75359 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 36
75282 ATGAAATTAA
75292 CAAAAAGAATAAAAACAAAAGGAGAGGAGGAGATGG
1 CAAAAAGAATAAAAACAAAAGGAGAGGAGGAGATGG
***
75328 CAAAAAGAAT-AAAACAGTGGGAGAGGAGGAGA
1 CAAAAAGAATAAAAACAAAAGGAGAGGAGGAGA
75360 CAACAAGGGA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 19 0.66
36 10 0.34
ACGTcount: A:0.56, C:0.06, G:0.32, T:0.06
Consensus pattern (36 bp):
CAAAAAGAATAAAAACAAAAGGAGAGGAGGAGATGG
Found at i:82372 original size:6 final size:6
Alignment explanation
Indices: 82361--82399 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
82351 GGGAAGCGTC
82361 AGCAAT AGCAAT AGCAAT AGCAAT AGCAAT AGCAAT AGC
1 AGCAAT AGCAAT AGCAAT AGCAAT AGCAAT AGCAAT AGC
82400 GGGAGAGGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.49, C:0.18, G:0.18, T:0.15
Consensus pattern (6 bp):
AGCAAT
Found at i:82748 original size:17 final size:16
Alignment explanation
Indices: 82726--82757 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
82716 CAACTTTTTG
82726 ATAATTATACATTTAAA
1 ATAATTATA-ATTTAAA
82743 ATAATTATAATTTAA
1 ATAATTATAATTTAA
82758 TTAAAAAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
ATAATTATAATTTAAA
Found at i:91820 original size:6 final size:6
Alignment explanation
Indices: 91809--91840 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
91799 ACATTTGACC
*
91809 CCACCG CCACCG CCACCG CCACCG CAACCG CC
1 CCACCG CCACCG CCACCG CCACCG CCACCG CC
91841 TGGCGACAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.19, C:0.66, G:0.16, T:0.00
Consensus pattern (6 bp):
CCACCG
Found at i:93840 original size:15 final size:14
Alignment explanation
Indices: 93820--93850 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
93810 CTTAAACTCG
93820 AACCATGAACCTCAA
1 AACCATGAACC-CAA
93835 AACCATGAACCCAA
1 AACCATGAACCCAA
93849 AA
1 AA
93851 TCTAAACCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.52, C:0.32, G:0.06, T:0.10
Consensus pattern (14 bp):
AACCATGAACCCAA
Done.