Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009571.1 Kokia drynarioides strain JFW-HI SEQ_124285, 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: 144364
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:101 original size:61 final size:61
Alignment explanation
Indices: 5--139 Score: 198
Period size: 61 Copynumber: 2.2 Consensus size: 61
1 TTGG
* ** * * *
5 TTTGTGTTTCTTTTTGATTAATTAGATTCAGCTGCTATTTGAAATCCTGAATACTGATTTGA
1 TTTGTATTTC-TTTTGATTAATTAGATTCAGCTGCTATTCAAAACCCTGAATAATGAGTTGA
*
67 TTTGTATTTCTTTTGATTCATTAGATTCAGCTGCTATTCAAAACCCTGAATAATGAGTTGA
1 TTTGTATTTCTTTTGATTAATTAGATTCAGCTGCTATTCAAAACCCTGAATAATGAGTTGA
128 TTTGTATTTCTT
1 TTTGTATTTCTT
140 CCTAAATGCT
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
61 57 0.86
62 9 0.14
ACGTcount: A:0.24, C:0.13, G:0.15, T:0.48
Consensus pattern (61 bp):
TTTGTATTTCTTTTGATTAATTAGATTCAGCTGCTATTCAAAACCCTGAATAATGAGTTGA
Found at i:2382 original size:34 final size:34
Alignment explanation
Indices: 2310--2382 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 34
2300 ATTTGTGATG
* *
2310 TTTTTAAATGTCACCAAAATTATTTTTCATGACA
1 TTTTTAAATGTCACCAAAACTATTTTTCACGACA
* * * *
2344 TTTTTAAATGTCATCATAACTATTTTTCGCGACT
1 TTTTTAAATGTCACCAAAACTATTTTTCACGACA
2378 TTTTT
1 TTTTT
2383 GTAATTTGTG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.29, C:0.15, G:0.07, T:0.49
Consensus pattern (34 bp):
TTTTTAAATGTCACCAAAACTATTTTTCACGACA
Found at i:9805 original size:18 final size:19
Alignment explanation
Indices: 9773--9813 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
9763 CAACCTCAAA
9773 ACCCGAAAACCTGGCAACG
1 ACCCGAAAACCTGGCAACG
*
9792 ACCCG-AAACTTGGCAACG
1 ACCCGAAAACCTGGCAACG
9810 ACCC
1 ACCC
9814 AGCAATCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.34, C:0.39, G:0.20, T:0.07
Consensus pattern (19 bp):
ACCCGAAAACCTGGCAACG
Found at i:11108 original size:29 final size:28
Alignment explanation
Indices: 11040--11109 Score: 70
Period size: 29 Copynumber: 2.5 Consensus size: 28
11030 ACAGCCATGG
* * * *
11040 TAATCAATT-ATTACTAAATTTATACTT
1 TAATCACTTAATTACTAAAATTACAATT
* *
11067 TAATTACTAAATTACTAAAAATTACAATT
1 TAATCACTTAATTACTAAA-ATTACAATT
11096 TAATCACTTAATTA
1 TAATCACTTAATTA
11110 TTTGAAATTC
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
27 6 0.18
28 9 0.27
29 18 0.55
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (28 bp):
TAATCACTTAATTACTAAAATTACAATT
Found at i:13808 original size:27 final size:27
Alignment explanation
Indices: 13777--13865 Score: 106
Period size: 27 Copynumber: 3.3 Consensus size: 27
13767 TGGATTCTAA
* * **
13777 CTCGAAAGAGCGTTGTTTTGATTCTGG
1 CTCGAAAGAGCGATATTCAGATTCTGG
*
13804 TTCGAAAGAGCGATATTCAGATTCTGG
1 CTCGAAAGAGCGATATTCAGATTCTGG
* *
13831 CTCGAAAGAGCAATATTCTAGACTCTGG
1 CTCGAAAGAGCGATATTC-AGATTCTGG
13859 CTCGAAA
1 CTCGAAA
13866 AGGGCGTTAC
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
27 38 0.72
28 15 0.28
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (27 bp):
CTCGAAAGAGCGATATTCAGATTCTGG
Found at i:13967 original size:27 final size:27
Alignment explanation
Indices: 13903--13967 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
13893 AGAGCGAAAA
*
13903 TCTGTTCTGGGCTCAAATGAGCAATAC
1 TCTGTTATGGGCTCAAATGAGCAATAC
* * * *
13930 ACTATTATGGGCTCAAATGAGTAATTC
1 TCTGTTATGGGCTCAAATGAGCAATAC
*
13957 TCTGTTGTGGG
1 TCTGTTATGGG
13968 GGTCTAATAA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.34
Consensus pattern (27 bp):
TCTGTTATGGGCTCAAATGAGCAATAC
Found at i:17877 original size:27 final size:27
Alignment explanation
Indices: 17839--17941 Score: 143
Period size: 27 Copynumber: 3.8 Consensus size: 27
17829 AGTGGTTTCG
* *
17839 AGCTCGAAAGAGTGTTATTCTGATTCT
1 AGCTCAAAAGAGTGATATTCTGATTCT
17866 AGCTCAAAAGAGTGATATTCTGATTCT
1 AGCTCAAAAGAGTGATATTCTGATTCT
*
17893 AGCTCAAAAGAGCGATATTCTGATTCT
1 AGCTCAAAAGAGTGATATTCTGATTCT
* * * *
17920 GGCTCATAAGAGCGATAATCTG
1 AGCTCAAAAGAGTGATATTCTG
17942 GACTTTGGCT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 70 1.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (27 bp):
AGCTCAAAAGAGTGATATTCTGATTCT
Found at i:17904 original size:54 final size:55
Alignment explanation
Indices: 17839--17989 Score: 164
Period size: 54 Copynumber: 2.7 Consensus size: 55
17829 AGTGGTTTCG
* * * *
17839 AGCTCGAAAGAGTGTTATTCTGATTCTAGCTCAAAAGAGTGATATTCT-GA-TTCT
1 AGCTCAAAAGAGTGTTATTCTGATTCTGGCTCATAAGAGTGATAATCTGGACTT-T
* * *
17893 AGCTCAAAAGAGCGATATTCTGATTCTGGCTCATAAGAGCGATAATCTGGACTTT
1 AGCTCAAAAGAGTGTTATTCTGATTCTGGCTCATAAGAGTGATAATCTGGACTTT
* * *
17948 GGCTCGAAAAGGGTGTTACTT-TGTTTCTGGCTCATAAGAGTG
1 AGCTC-AAAAGAGTGTTA-TTCTGATTCTGGCTCATAAGAGTG
17990 GAAATTTGTT
Statistics
Matches: 80, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
54 41 0.51
55 7 0.09
56 30 0.38
57 2 0.03
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (55 bp):
AGCTCAAAAGAGTGTTATTCTGATTCTGGCTCATAAGAGTGATAATCTGGACTTT
Found at i:18024 original size:27 final size:27
Alignment explanation
Indices: 17994--18045 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
17984 AGAGTGGAAA
17994 TTTGTTCCAG-GCTCAAATGAGCAATAC
1 TTTGTT-CAGAGCTCAAATGAGCAATAC
*
18021 TTTGTTCTGAGCTCAAATGAGCAAT
1 TTTGTTCAGAGCTCAAATGAGCAAT
18046 TCTATGTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 2 0.09
27 21 0.91
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (27 bp):
TTTGTTCAGAGCTCAAATGAGCAATAC
Found at i:18063 original size:27 final size:27
Alignment explanation
Indices: 18006--18079 Score: 69
Period size: 27 Copynumber: 2.7 Consensus size: 27
17996 TGTTCCAGGC
* * * *
18006 TCAAATGAGCAATACTTTGTTCTGAGC
1 TCAAATGAGCAATTCTATGTTATGAGA
18033 TCAAATGAGCAATTCTATGTTAT-AGGA
1 TCAAATGAGCAATTCTATGTTATGA-GA
*
18060 TCAAATAAGCTATATTCTAT
1 TCAAATGAGC-A-ATTCTAT
18080 TATGGTGCAC
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
26 1 0.03
27 30 0.77
28 1 0.03
29 7 0.18
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (27 bp):
TCAAATGAGCAATTCTATGTTATGAGA
Found at i:20504 original size:19 final size:19
Alignment explanation
Indices: 20480--20517 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
20470 AATTTTTACA
20480 AAGCCC-AAAAATAAAAAAT
1 AAGCCCTAAAAA-AAAAAAT
*
20499 AAGCCCTAAACAAAAAAAT
1 AAGCCCTAAAAAAAAAAAT
20518 GAAAAAACCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.66, C:0.18, G:0.05, T:0.11
Consensus pattern (19 bp):
AAGCCCTAAAAAAAAAAAT
Found at i:21406 original size:14 final size:14
Alignment explanation
Indices: 21389--21423 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
21379 TCTTCTTCTT
21389 TTATTTATTTATTA
1 TTATTTATTTATTA
*
21403 TTATTTATTTTTTA
1 TTATTTATTTATTA
21417 TGTATTT
1 T-TATTT
21424 TATATTCTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.74
15 5 0.26
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (14 bp):
TTATTTATTTATTA
Found at i:25927 original size:13 final size:13
Alignment explanation
Indices: 25894--25944 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
25884 CTAAAAATAG
*
25894 AAATTAAAAGGATT
1 AAATTAAAA-AATT
*
25908 TAATTAAAAAATT
1 AAATTAAAAAATT
*
25921 AAATT-AAAAGTT
1 AAATTAAAAAATT
25933 AAAATTAAAAAA
1 -AAATTAAAAAA
25945 AAATAGAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
12 6 0.20
13 12 0.40
14 12 0.40
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (13 bp):
AAATTAAAAAATT
Found at i:27885 original size:101 final size:102
Alignment explanation
Indices: 27714--27925 Score: 279
Period size: 101 Copynumber: 2.1 Consensus size: 102
27704 CTTCAAAGTG
*
27714 ATAAGATTT-TCTGTTGTAGCTTCACTCCATTCCACTGCAACCCTAAGGAGATTGAGATTCGCTA
1 ATAAGATTTGTCTGTTGTAACTTCACTCCATTCCACTGCAACCCTAAGGAGATTGAGATTCGCTA
*
27778 TCGTAGTTTTAATCCGATCCACTGCAACTTCAGGGAT
66 TCGTAGTTTTAATCCGATCCACTACAACTTCAGGGAT
* * * * *
27815 ATAAGATTTGT-TGTTGTAACTTCACTCCATTCCATTGTAA-CTTCAGGGAGATTGAGATTTGCT
1 ATAAGATTTGTCTGTTGTAACTTCACTCCATTCCACTGCAACCCT-AAGGAGATTGAGATTCGCT
* *
27878 A-CTGTAGTTTTAATCTGATCCACTACAACTTTAGGGAT
65 ATC-GTAGTTTTAATCCGATCCACTACAACTTCAGGGAT
* *
27916 GTAGGATTTG
1 ATAAGATTTG
27926 ATGGTTATAA
Statistics
Matches: 97, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
100 3 0.03
101 93 0.96
102 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (102 bp):
ATAAGATTTGTCTGTTGTAACTTCACTCCATTCCACTGCAACCCTAAGGAGATTGAGATTCGCTA
TCGTAGTTTTAATCCGATCCACTACAACTTCAGGGAT
Found at i:27908 original size:51 final size:49
Alignment explanation
Indices: 27760--27914 Score: 123
Period size: 51 Copynumber: 3.1 Consensus size: 49
27750 GCAACCCTAA
*
27760 GGAGATTGAGATTCGCTATCGTAGTTTTAATCCGATCCACTGCAACTTCAG
1 GGAGATTGAGATTTGCTAT-GTAGTTTTAAT-CGATCCACTGCAACTTCAG
* * * * ** * * * * *
27811 GGATA-TAAGATTTGTTGTTGTAACTTCACTCCATTCCATTGTAACTTCAG
1 GGAGATTGAGATTTGCT-ATGTAGTTTTAATCGA-TCCACTGCAACTTCAG
* *
27861 GGAGATTGAGATTTGCTACTGTAGTTTTAATCTGATCCACTACAACTTTAG
1 GGAGATTGAGATTTGCTA-TGTAGTTTTAATC-GATCCACTGCAACTTCAG
27912 GGA
1 GGA
27915 TGTAGGATTT
Statistics
Matches: 74, Mismatches: 25, Indels: 10
0.68 0.23 0.09
Matches are distributed among these distances:
49 2 0.03
50 33 0.45
51 38 0.51
52 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.35
Consensus pattern (49 bp):
GGAGATTGAGATTTGCTATGTAGTTTTAATCGATCCACTGCAACTTCAG
Found at i:29519 original size:68 final size:68
Alignment explanation
Indices: 29440--29578 Score: 224
Period size: 68 Copynumber: 2.0 Consensus size: 68
29430 TATTTTTCTT
* * *
29440 TTTGTTACTACTTTTACATTTTATTTTAGGTGTTTTATAACCTATAGAAATTTGTAATTTATTGT
1 TTTGTTACTACTTTTACATTTTATTTTAGGTGTTTTATAACCCAGAGAAATTTGAAATTTATTGT
29505 TGG
66 TGG
* * *
29508 TTTGTTTCTACTTTTACATTTTATTTTAGGTGTTTTATGACCCGGAGAAATTTGAAATTTATTGT
1 TTTGTTACTACTTTTACATTTTATTTTAGGTGTTTTATAACCCAGAGAAATTTGAAATTTATTGT
29573 TGG
66 TGG
29576 TTT
1 TTT
29579 AGATCTAGAA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
68 65 1.00
ACGTcount: A:0.23, C:0.08, G:0.15, T:0.54
Consensus pattern (68 bp):
TTTGTTACTACTTTTACATTTTATTTTAGGTGTTTTATAACCCAGAGAAATTTGAAATTTATTGT
TGG
Found at i:31732 original size:92 final size:92
Alignment explanation
Indices: 31575--31851 Score: 448
Period size: 92 Copynumber: 3.0 Consensus size: 92
31565 TAAGTTGCCA
* *
31575 CCCAAAATGAAAGATCTAGGAAGCTTTACTATCCCATGTTCAATTGACAACCACTACTTGGGTAA
1 CCCAAAATGAAAGATCTAGGAAGCTTTACGATCCCATGTTCAATTGGCAACCACTACTTGGGTAA
*
31640 AGCTTTATGTGATCTGGGTACTAGCAT
66 AGCTTTATGTGATTTGGGTACTAGCAT
*
31667 CCCAAAATGAAAGAGCTAGGAAGCTTTACGATCCCATGTTCAATTGGCAACCACTACTTGGGTAA
1 CCCAAAATGAAAGATCTAGGAAGCTTTACGATCCCATGTTCAATTGGCAACCACTACTTGGGTAA
31732 AGCTTTATGTGATTTGGG-AGCTAGCAT
66 AGCTTTATGTGATTTGGGTA-CTAGCAT
* * * *
31759 CCCAAAATGAATGATCCAAGAAGCTTTACGATCCTATGTTCAATTGGCAACCACTACTTGGGTAA
1 CCCAAAATGAAAGATCTAGGAAGCTTTACGATCCCATGTTCAATTGGCAACCACTACTTGGGTAA
* *
31824 AACTTTATGTGATTTGGGTGCTAGCAT
66 AGCTTTATGTGATTTGGGTACTAGCAT
31851 C
1 C
31852 AACCTTATGC
Statistics
Matches: 172, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
91 1 0.01
92 171 0.99
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (92 bp):
CCCAAAATGAAAGATCTAGGAAGCTTTACGATCCCATGTTCAATTGGCAACCACTACTTGGGTAA
AGCTTTATGTGATTTGGGTACTAGCAT
Found at i:37576 original size:17 final size:17
Alignment explanation
Indices: 37547--37594 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
37537 CACATTCCCG
*
37547 TTGTCAGTT-CATTTTAA
1 TTGTCA-TTGCATTTGAA
*
37564 TTGTCATTGCATTTGCA
1 TTGTCATTGCATTTGAA
*
37581 TTTTCATTGCATTT
1 TTGTCATTGCATTT
37595 CCATCTGTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 2 0.07
17 25 0.93
ACGTcount: A:0.19, C:0.15, G:0.12, T:0.54
Consensus pattern (17 bp):
TTGTCATTGCATTTGAA
Found at i:38496 original size:64 final size:64
Alignment explanation
Indices: 38391--38532 Score: 250
Period size: 64 Copynumber: 2.2 Consensus size: 64
38381 CTTGCTAGTT
*
38391 TTGATTT-TACTTGAGGACAAATAAAAACTCAAGTTTAGGGGTGTGATAGTATTAGAAAGAACCA
1 TTGATTTCTCCTT-AGGACAAATAAAAACTCAAGTTTAGGGGTGTGATAGTATTAGAAAGAACCA
*
38455 TTGATTTCTCCTTAGGACAAATAAAAACTCAAGTTTGGGGGTGTGATAGTATTAGAAAGAACCA
1 TTGATTTCTCCTTAGGACAAATAAAAACTCAAGTTTAGGGGTGTGATAGTATTAGAAAGAACCA
38519 TTGATTTCTCCTTA
1 TTGATTTCTCCTTA
38533 CTTTTTGTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
64 71 0.95
65 4 0.05
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.32
Consensus pattern (64 bp):
TTGATTTCTCCTTAGGACAAATAAAAACTCAAGTTTAGGGGTGTGATAGTATTAGAAAGAACCA
Found at i:40547 original size:36 final size:36
Alignment explanation
Indices: 40500--40571 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
40490 TATTCAAGAA
40500 CAAGTGGATTAAATTCCTTCAATCCCCAAGCAACTT
1 CAAGTGGATTAAATTCCTTCAATCCCCAAGCAACTT
40536 CAAGTGGATTAAATTCCTTCAATCCCCAAGCAACTT
1 CAAGTGGATTAAATTCCTTCAATCCCCAAGCAACTT
40572 TTGTTATCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.33, C:0.28, G:0.11, T:0.28
Consensus pattern (36 bp):
CAAGTGGATTAAATTCCTTCAATCCCCAAGCAACTT
Found at i:41513 original size:37 final size:37
Alignment explanation
Indices: 41472--41544 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
41462 GTCCTCAAGG
*
41472 AAAATAGAAATTAGCAAGACTATATCAAAATTTTAAA
1 AAAATAGAAATTAGCAAGACTATATCAAAACTTTAAA
41509 AAAATAGAAATTAGCAAGACTATATCAAAACTTTAA
1 AAAATAGAAATTAGCAAGACTATATCAAAACTTTAA
41545 CAAGGTAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.56, C:0.10, G:0.08, T:0.26
Consensus pattern (37 bp):
AAAATAGAAATTAGCAAGACTATATCAAAACTTTAAA
Found at i:55967 original size:71 final size:76
Alignment explanation
Indices: 55815--56002 Score: 228
Period size: 71 Copynumber: 2.5 Consensus size: 76
55805 AGGAGATCCA
* ** *
55815 AAGAACAAATGGAA-TTAAGAATGATTGACCGTATGGTATGAGTATGAATGAAAGTAAAATGTTT
1 AAGAACAAAT-GAATTTAAGAATGATTAATTGTATGGTATGAATATGAATGAAAGTAAAATGTTT
*
55879 GTTAAATTGGAG
65 GTCAAATTGGAG
* *
55891 AAGAACAAATGAATTTAAGATTGATTAATTGTATGGTATGAATAT-AA-G-AAG-AATA-GTTTG
1 AAGAACAAATGAATTTAAGAATGATTAATTGTATGGTATGAATATGAATGAAAGTAAAATGTTTG
55951 TCAAATTGGACG
66 TCAAATTGGA-G
* *
55963 -AGAACAAATGAATTTAAGAATGATTAATTGTGTGGAATGA
1 AAGAACAAATGAATTTAAGAATGATTAATTGTATGGTATGA
56003 GTAAGATATT
Statistics
Matches: 100, Mismatches: 10, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
71 51 0.51
72 4 0.04
73 3 0.03
74 1 0.01
75 5 0.05
76 36 0.36
ACGTcount: A:0.43, C:0.04, G:0.23, T:0.30
Consensus pattern (76 bp):
AAGAACAAATGAATTTAAGAATGATTAATTGTATGGTATGAATATGAATGAAAGTAAAATGTTTG
TCAAATTGGAG
Found at i:60825 original size:38 final size:38
Alignment explanation
Indices: 60724--60834 Score: 100
Period size: 38 Copynumber: 3.0 Consensus size: 38
60714 GTACATGTTC
* * * * *
60724 ATGCAGCGACATTCTTGGTTGCAA-TTGCAGAATACTT
1 ATGCAGCGACAGTATTGGATGCAATTTGAAGAATATTT
* * * * *
60761 ATGTAGTGATAGTTTTGGATGAAATTTGAAGAATATTT
1 ATGCAGCGACAGTATTGGATGCAATTTGAAGAATATTT
* *
60799 ATGCAGCGACAGTATTGGGTGCAATTTGGA-AATATT
1 ATGCAGCGACAGTATTGGATGCAATTTGAAGAATATT
60835 CCTGCGACGA
Statistics
Matches: 57, Mismatches: 16, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
37 23 0.40
38 34 0.60
ACGTcount: A:0.31, C:0.10, G:0.24, T:0.35
Consensus pattern (38 bp):
ATGCAGCGACAGTATTGGATGCAATTTGAAGAATATTT
Found at i:60857 original size:36 final size:37
Alignment explanation
Indices: 60805--60902 Score: 108
Period size: 36 Copynumber: 2.6 Consensus size: 37
60795 ATTTATGCAG
* * *
60805 CGACAGTATTGGGTGCAATTTGGAAATATTCCTGCGA
1 CGACAGTTTTGGGTGCAATTTGGAAATACTCATGCGA
* * * * *
60842 CGATAGTTTT-GGTGCAATCTAGAAGTGCTCATGCGA
1 CGACAGTTTTGGGTGCAATTTGGAAATACTCATGCGA
60878 CGACAGTTTTGGGTGCAAATTTGGA
1 CGACAGTTTTGGGTGC-AATTTGGA
60903 TGTTATTCTG
Statistics
Matches: 48, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
36 29 0.60
37 13 0.27
38 6 0.12
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.31
Consensus pattern (37 bp):
CGACAGTTTTGGGTGCAATTTGGAAATACTCATGCGA
Found at i:62068 original size:17 final size:17
Alignment explanation
Indices: 62048--62094 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
62038 GACAATGTAG
*
62048 ATGCAGTGGCAATAAAA
1 ATGCAGTGACAATAAAA
62065 ATGCAGTGACAATAAAA
1 ATGCAGTGACAATAAAA
* *
62082 ATGTAGAGACAAT
1 ATGCAGTGACAAT
62095 TATACTACAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.49, C:0.11, G:0.21, T:0.19
Consensus pattern (17 bp):
ATGCAGTGACAATAAAA
Found at i:78306 original size:5 final size:5
Alignment explanation
Indices: 78296--78321 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
78286 GGACATAAAG
78296 ATTTT ATTTT ATTTT ATTTT ATTTT A
1 ATTTT ATTTT ATTTT ATTTT ATTTT A
78322 AAACTCTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
ATTTT
Found at i:78484 original size:60 final size:61
Alignment explanation
Indices: 78370--78485 Score: 155
Period size: 60 Copynumber: 1.9 Consensus size: 61
78360 ATTAGGATAT
* * * *
78370 TGTTTATATTTAATTGATATTTATCTTTTAAAGTTTAAATTGTATCCAATTAGGGAATTAA
1 TGTTTAGATTTAATTGATAATTATCTTTTAAAGTTTAAATTGGATCCAACTAGGGAATTAA
* *
78431 TGTTTAGATTTAATT-ATAATTATCTTTTAGAA-TTTAGATTGGATTCAACTAGGGA
1 TGTTTAGATTTAATTGATAATTATCTTTTA-AAGTTTAAATTGGATCCAACTAGGGA
78486 TTTCTATGTA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
60 32 0.67
61 16 0.33
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.47
Consensus pattern (61 bp):
TGTTTAGATTTAATTGATAATTATCTTTTAAAGTTTAAATTGGATCCAACTAGGGAATTAA
Found at i:79560 original size:41 final size:38
Alignment explanation
Indices: 79492--79627 Score: 98
Period size: 41 Copynumber: 3.3 Consensus size: 38
79482 ATTAAATAAA
* * *
79492 AAAT-AATAAAAAAGAAAAAATACATAAAATTTAATGAT
1 AAATAAATAAAAAACAAAAAATACATAAAAATAAATG-T
79530 AAATAAATAAATAAACAAACAAGATA-ATAAAAATAAATGT
1 AAATAAATAAA-AAACAAA-AA-ATACATAAAAATAAATGT
* *
79570 AAATTAAATAAAAATAATAAAAGAGATAACA-ATAAAATAACATGA
1 AAA-TAAAT-AAAA-AACAAAA-A-AT-ACATA-AAAATAA-ATGT
79615 AAATAAATAAAAA
1 AAATAAATAAAAA
79628 TAAAATAAAT
Statistics
Matches: 81, Mismatches: 5, Indels: 20
0.76 0.05 0.19
Matches are distributed among these distances:
38 4 0.05
39 6 0.07
40 10 0.12
41 20 0.25
42 16 0.20
43 6 0.07
44 13 0.16
45 6 0.07
ACGTcount: A:0.71, C:0.04, G:0.05, T:0.21
Consensus pattern (38 bp):
AAATAAATAAAAAACAAAAAATACATAAAAATAAATGT
Found at i:79622 original size:15 final size:14
Alignment explanation
Indices: 79559--79645 Score: 52
Period size: 15 Copynumber: 5.9 Consensus size: 14
79549 CAAGATAATA
*
79559 AAAATAAATGTAAAT
1 AAAATAAAT-AAAAT
*
79574 TAAATAAA-AATAAT
1 AAAATAAATAA-AAT
* *
79588 AAAAGAGATAACAAT
1 AAAATAAATAA-AAT
79603 AAAATAACATGAAAAT
1 AAAATAA-AT-AAAAT
*
79619 AAATAAAAATAAAAT
1 AAA-ATAAATAAAAT
*
79634 -AAATAAACAAAA
1 AAAATAAATAAAA
79646 AAATAAAAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
13 9 0.16
14 10 0.18
15 22 0.39
16 10 0.18
17 5 0.09
ACGTcount: A:0.72, C:0.03, G:0.05, T:0.20
Consensus pattern (14 bp):
AAAATAAATAAAAT
Found at i:79647 original size:15 final size:16
Alignment explanation
Indices: 79530--79652 Score: 64
Period size: 16 Copynumber: 7.8 Consensus size: 16
79520 ATTTAATGAT
79530 AAAT-AAATAAATAAA
1 AAATAAAATAAATAAA
* *
79545 CAAACAAGAT-AAT-AA
1 -AAATAAAATAAATAAA
* *
79560 AAATAAATGTAAATTAA
1 AAATAAA-ATAAATAAA
*
79577 ATA-AAAAT-AATAAA
1 AAATAAAATAAATAAA
*
79591 AGAGATAACAATAAA-ATA
1 A-A-ATAA-AATAAATAAA
*
79609 ACATGAAAATAAAT-AA
1 AAAT-AAAATAAATAAA
79625 AAATAAAATAAATAAA
1 AAATAAAATAAATAAA
79641 CAAA-AAAATAAA
1 -AAATAAAATAAA
79653 AAATTAAATG
Statistics
Matches: 81, Mismatches: 13, Indels: 26
0.68 0.11 0.22
Matches are distributed among these distances:
14 11 0.14
15 13 0.16
16 35 0.43
17 14 0.17
18 6 0.07
19 2 0.02
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.19
Consensus pattern (16 bp):
AAATAAAATAAATAAA
Found at i:79660 original size:20 final size:20
Alignment explanation
Indices: 79623--79689 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 20
79613 GAAAATAAAT
*
79623 AAAAATAAAATAAATAAACAA
1 AAAAATAAAA-AATTAAACAA
79644 AAAAATAAAAAATTAAATGCTAA
1 AAAAATAAAAAATTAAA--C-AA
79667 AATAAATAAACAAATATAAACAA
1 AA-AAATAAA-AAAT-TAAACAA
79690 TGAAAATAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
20 6 0.15
21 10 0.26
22 1 0.03
23 6 0.15
24 8 0.21
25 4 0.10
26 4 0.10
ACGTcount: A:0.75, C:0.06, G:0.01, T:0.18
Consensus pattern (20 bp):
AAAAATAAAAAATTAAACAA
Found at i:79676 original size:4 final size:4
Alignment explanation
Indices: 79443--79661 Score: 51
Period size: 4 Copynumber: 51.5 Consensus size: 4
79433 TTTCATACAT
* * * *
79443 ATAA ATAA AAAA ATCA ATGA ATAA ATAT ATGAA ATGCAA ATTAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT-AA AT--AA A-TAA ATAA
* * * *
79491 A-AA AT-A ATAA A-AA AGAA A-AA ATAC ATAAA ATTTA AT-G ATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT-AA A-TAA ATAA ATAA ATAA
* * * *
79536 ATAA ATAA ACAA ACAA GATAA TAAAA ATAA ATGTAA ATTAA ATAA AAATA
1 ATAA ATAA ATAA ATAA -ATAA -ATAA ATAA A--TAA A-TAA ATAA ATA-A
79586 ATAA A-AGA GATAACA ATAAA ATAA CATGAAA ATAA AT-A A-AA ATAAA
1 ATAA ATA-A -AT-A-A AT-AA ATAA -AT--AA ATAA ATAA ATAA AT-AA
* *
79632 ATAA ATAA ACAA AAAA ATAA A-AA ATTAA AT
1 ATAA ATAA ATAA ATAA ATAA ATAA A-TAA AT
79662 GCTAAAATAA
Statistics
Matches: 164, Mismatches: 25, Indels: 52
0.68 0.10 0.22
Matches are distributed among these distances:
3 22 0.13
4 87 0.53
5 36 0.22
6 14 0.09
7 5 0.03
ACGTcount: A:0.70, C:0.04, G:0.05, T:0.21
Consensus pattern (4 bp):
ATAA
Found at i:79681 original size:12 final size:11
Alignment explanation
Indices: 79484--79682 Score: 63
Period size: 12 Copynumber: 17.2 Consensus size: 11
79474 AAATGCAAAT
79484 TAAATAAAAAA
1 TAAATAAAAAA
79495 T-AATAAAAAA
1 TAAATAAAAAA
* *
79505 GAAA-AAATACA
1 TAAATAAA-AAA
* **
79516 TAAAATTTAATGA
1 T-AAA-TAAAAAA
79529 TAAATAAATAAA
1 TAAATAAA-AAA
*
79541 TAAACAAACAAGA
1 TAAATAAA-AA-A
79554 T-AAT-AAAAA
1 TAAATAAAAAA
** *
79563 TAAATGTAAAT
1 TAAATAAAAAA
79574 TAAAT-AAAAA
1 TAAATAAAAAA
79584 T-AATAAAAGAGA
1 TAAATAAAA-A-A
*
79596 TAACA-ATAAAA
1 TAA-ATAAAAAA
79607 TAACATGAAAATAAA
1 TAA-AT--AAA-AAA
79622 TAAA-AATAAAA
1 TAAATAA-AAAA
79633 TAAATAAACAAA
1 TAAATAAA-AAA
*
79645 AAAATAAAAAA
1 TAAATAAAAAA
**
79656 TTAAATGCTAAAA
1 -TAAAT-AAAAAA
79669 TAAATAAACAAA
1 TAAATAAA-AAA
79681 TA
1 TA
79683 TAAACAATGA
Statistics
Matches: 140, Mismatches: 24, Indels: 47
0.66 0.11 0.22
Matches are distributed among these distances:
9 5 0.04
10 24 0.17
11 39 0.28
12 48 0.34
13 12 0.09
14 6 0.04
15 6 0.04
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.21
Consensus pattern (11 bp):
TAAATAAAAAA
Found at i:80625 original size:49 final size:50
Alignment explanation
Indices: 80546--80688 Score: 155
Period size: 49 Copynumber: 2.9 Consensus size: 50
80536 TTCGCCGTTG
*
80546 TGGCTTCAATCTGTTCCCTCTTTGGTTTTAAGGTGTTAGATCCGTCA-TCA
1 TGGCTTCAATCT-ATCCCTCTTTGGTTTTAAGGTGTTAGATCCGTCATTCA
* * * *
80596 TGGCTTCAATCTATCCCTCTTTGGTTTTAAGGTATTAGGTCTGTCATTGA
1 TGGCTTCAATCTATCCCTCTTTGGTTTTAAGGTGTTAGATCCGTCATTCA
* * * ** * *
80646 -GGCTTAAACCTATCCTTCTTCAGTTTTAAGGTGTAAGACCCGT
1 TGGCTTCAATCTATCCCTCTTTGGTTTTAAGGTGTTAGATCCGT
80689 TATTACGACT
Statistics
Matches: 77, Mismatches: 15, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
49 63 0.82
50 14 0.18
ACGTcount: A:0.19, C:0.21, G:0.20, T:0.41
Consensus pattern (50 bp):
TGGCTTCAATCTATCCCTCTTTGGTTTTAAGGTGTTAGATCCGTCATTCA
Found at i:80750 original size:49 final size:49
Alignment explanation
Indices: 80697--80828 Score: 149
Period size: 49 Copynumber: 2.7 Consensus size: 49
80687 GTTATTACGA
* *
80697 CTTTAATCTTTCCCTATTCAGTTTTAGGGTGTTAGGTTCATCATCACGG
1 CTTTAATCTTTCCCTATTCAGTTTTAGGGTGTTAGGTCCACCATCACGG
* * * * *
80746 CTTTAA-CTTATCCCTCTTCAATTTTAGGGTGTAAGGTCCACCGTTACGG
1 CTTTAATCTT-TCCCTATTCAGTTTTAGGGTGTTAGGTCCACCATCACGG
* * **
80795 CTTTAATCTTTCCTTTTTTGGTTTTAGGGTGTTA
1 CTTTAATCTTTCCCTATTCAGTTTTAGGGTGTTA
80829 AATCTACCGT
Statistics
Matches: 68, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
48 3 0.04
49 62 0.91
50 3 0.04
ACGTcount: A:0.17, C:0.20, G:0.18, T:0.45
Consensus pattern (49 bp):
CTTTAATCTTTCCCTATTCAGTTTTAGGGTGTTAGGTCCACCATCACGG
Found at i:80863 original size:49 final size:49
Alignment explanation
Indices: 80766--80869 Score: 122
Period size: 49 Copynumber: 2.1 Consensus size: 49
80756 TCCCTCTTCA
* * *
80766 ATTTTAGGGTGTAAGGTCCACCGTTACGGCTTTAATCTTTCCTTTTTTG
1 ATTTTAGGGTGTAAGATCCACCGTTACGGCTTTAATCTTGCCTCTTTTG
* * *
80815 GTTTTAGGGTGTTAA-ATCTACCGTTATGGCTTTAATCTATGCC-CTTTTG
1 ATTTTAGGGTG-TAAGATCCACCGTTACGGCTTTAATCT-TGCCTCTTTTG
80864 ATTTTA
1 ATTTTA
80870 AGGTACTAGG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
49 40 0.87
50 6 0.13
ACGTcount: A:0.18, C:0.16, G:0.19, T:0.46
Consensus pattern (49 bp):
ATTTTAGGGTGTAAGATCCACCGTTACGGCTTTAATCTTGCCTCTTTTG
Found at i:81063 original size:88 final size:87
Alignment explanation
Indices: 80895--81063 Score: 216
Period size: 88 Copynumber: 1.9 Consensus size: 87
80885 CGTTGCGACT
*
80895 TCAACCTATCCCTCTTCGGTTTAAGGTGTAAGATCCGTCGTTACGAATTCAATCTTTCCCTCTTC
1 TCAACCTATCCCTCTTAGGTTTAAGGTGTAAGATCCGTCGTTACGAATTCAATCTTTCCCTCTTC
**
80960 GATTTTTGGGCGTTAGGTCTAC
66 GATTTTAAGGCGTTAGGTCTAC
* * * **
80982 TCAACCTATCCCTCTTTAGTTTTAAGGTGTAAGATCTG-CTGTTGCGGCTTCAATCTTTCCCTCT
1 TCAACCTATCCCTC-TTAGGTTTAAGGTGTAAGATCCGTC-GTTACGAATTCAATCTTTCCCTCT
*
81046 TC-AGTTTTAAGGTGTTAG
64 TCGA-TTTTAAGGCGTTAG
81064 ATTTGTTATT
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
87 16 0.23
88 54 0.77
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (87 bp):
TCAACCTATCCCTCTTAGGTTTAAGGTGTAAGATCCGTCGTTACGAATTCAATCTTTCCCTCTTC
GATTTTAAGGCGTTAGGTCTAC
Found at i:81076 original size:49 final size:49
Alignment explanation
Indices: 80982--81161 Score: 155
Period size: 49 Copynumber: 3.7 Consensus size: 49
80972 TTAGGTCTAC
* * * * * *
80982 TCAACCTATCCCTCTTTAGTTTTAAGGTGTAAGATCTGCTGTTGCGGCT
1 TCAATCTATCCCTCTTCAGTTTTAAGGTGTTAGATTTGTTATTGCGGCT
*
81031 TCAATCTTTCCCTCTTCAGTTTTAAGGTGTTAGATTTGTTATTGCGGCT
1 TCAATCTATCCCTCTTCAGTTTTAAGGTGTTAGATTTGTTATTGCGGCT
* * ** * * * * ** *
81080 TTAATCTATCCATCAACAATTTTAGGGTTTTAGATTCGTTATTATGACT
1 TCAATCTATCCCTCTTCAGTTTTAAGGTGTTAGATTTGTTATTGCGGCT
* **
81129 TCAACCTATCCCTCTTTGGTTTT-AGGATGTTAG
1 TCAATCTATCCCTCTTCAGTTTTAAGG-TGTTAG
81162 GTCCGTCGTT
Statistics
Matches: 101, Mismatches: 29, Indels: 2
0.77 0.22 0.02
Matches are distributed among these distances:
48 2 0.02
49 99 0.98
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.43
Consensus pattern (49 bp):
TCAATCTATCCCTCTTCAGTTTTAAGGTGTTAGATTTGTTATTGCGGCT
Found at i:88608 original size:93 final size:93
Alignment explanation
Indices: 88438--88617 Score: 220
Period size: 93 Copynumber: 1.9 Consensus size: 93
88428 GGTGCCATCG
* * * * * * *
88438 CGACTTCAACCTATCCCTCTTCAGTTTTAAGGTGTAAGATTCGTAGTTGTGATTTCAATCTTTCC
1 CGACTTCAACCTATCCCTCTTCAATTTAAAGGTGTAAGAGTCGTAATTGCGACTTCAACCTTTCC
*
88503 CTCTTCAATTTTAGGGTGTTAGGTCCGT
66 CTCTTCAATTTTAAGGTGTTAGGTCCGT
*
88531 CGACTTCAACCTATCCCTCTTCAATTTAAAGGTGTAAG-GTC-TATCATTGCGGCTTCAACCTTT
1 CGACTTCAACCTATCCCTCTTCAATTTAAAGGTGTAAGAGTCGTA--ATTGCGACTTCAACCTTT
***
88594 CCCTCTTTGGTTTTAAGGTGTTAG
64 CCCTCTTCAATTTTAAGGTGTTAG
88618 ATCTATCATT
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
91 2 0.03
92 2 0.03
93 69 0.95
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.39
Consensus pattern (93 bp):
CGACTTCAACCTATCCCTCTTCAATTTAAAGGTGTAAGAGTCGTAATTGCGACTTCAACCTTTCC
CTCTTCAATTTTAAGGTGTTAGGTCCGT
Found at i:88612 original size:49 final size:49
Alignment explanation
Indices: 88531--88698 Score: 185
Period size: 49 Copynumber: 3.4 Consensus size: 49
88521 TTAGGTCCGT
** * *
88531 CGACTTCAACCTATCCCTCTTCAATTTAAAGGTGTAAGGTCTATCATTG
1 CGACTTCAACCTATCCCTCTTTGATTTTAAGGTGTTAGGTCTATCATTG
* * * * *
88580 CGGCTTCAACCTTTCCCTCTTTGGTTTTAAGGTGTTAGATCTATCATTA
1 CGACTTCAACCTATCCCTCTTTGATTTTAAGGTGTTAGGTCTATCATTG
* * ** *
88629 CAACCTCAACCTATCCCTCTTTGATTTT-AGGATGTTAGGTCTGCCGTTG
1 CGACTTCAACCTATCCCTCTTTGATTTTAAGG-TGTTAGGTCTATCATTG
*
88678 CGACTTCAACCTATTCCTCTT
1 CGACTTCAACCTATCCCTCTT
88699 CAAACTTTAT
Statistics
Matches: 96, Mismatches: 22, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
48 3 0.03
49 93 0.97
ACGTcount: A:0.21, C:0.26, G:0.15, T:0.38
Consensus pattern (49 bp):
CGACTTCAACCTATCCCTCTTTGATTTTAAGGTGTTAGGTCTATCATTG
Found at i:90023 original size:79 final size:79
Alignment explanation
Indices: 89892--90050 Score: 300
Period size: 79 Copynumber: 2.0 Consensus size: 79
89882 AGATCTGGTG
89892 TGAACTTCTTGGATCTGCAGGTTGTCGCGACATCGCTAGGCGTAATCTAAAACCTTCAATTGCGG
1 TGAACTTCTTGGATCTGCAGGTTGTCGCGACATCGCTAGGCGTAATCTAAAACCTTCAATTGCGG
89957 TGACAACGTGCTCT
66 TGACAACGTGCTCT
*
89971 TGAACTTCTTGGATCTGCAGGTTGTCGCGACATCGCTAGGCGTAATCTAAAACCTTCAATTGTGG
1 TGAACTTCTTGGATCTGCAGGTTGTCGCGACATCGCTAGGCGTAATCTAAAACCTTCAATTGCGG
*
90036 TGACAACGTTCTCT
66 TGACAACGTGCTCT
90050 T
1 T
90051 ACCCTACGTT
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
79 78 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (79 bp):
TGAACTTCTTGGATCTGCAGGTTGTCGCGACATCGCTAGGCGTAATCTAAAACCTTCAATTGCGG
TGACAACGTGCTCT
Found at i:115890 original size:23 final size:21
Alignment explanation
Indices: 115852--115896 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 21
115842 TTAAATGAAG
115852 ACAATAAAATACAATTAATAAC
1 ACAATAAAATACAATT-ATAAC
115874 ACAATAAAA-ATCTAATTATAAC
1 ACAATAAAATA-C-AATTATAAC
115896 A
1 A
115897 TTAAATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 1 0.05
22 16 0.76
23 4 0.19
ACGTcount: A:0.62, C:0.13, G:0.00, T:0.24
Consensus pattern (21 bp):
ACAATAAAATACAATTATAAC
Found at i:116339 original size:4 final size:4
Alignment explanation
Indices: 116332--116452 Score: 61
Period size: 4 Copynumber: 29.0 Consensus size: 4
116322 TATCAACAAT
* * *
116332 ATAA ATAA ATAA ATAA ATAAA ATAA AT-G CTAAA ATAA ACAA ATAA AT--
1 ATAA ATAA ATAA ATAA AT-AA ATAA ATAA AT-AA ATAA ATAA ATAA ATAA
* * * *
116379 ATAA ATAA TAAAA ATAA TTGAG ATCAA GCATGAAA ATAA AT-G ATAA ATAA
1 ATAA ATAA -ATAA ATAA AT-AA AT-AA --AT--AA ATAA ATAA ATAA ATAA
*
116429 ATAA ATAA ATAA ATAA ATCA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA
116453 CTTAAATGTT
Statistics
Matches: 88, Mismatches: 18, Indels: 22
0.69 0.14 0.17
Matches are distributed among these distances:
2 2 0.02
3 3 0.03
4 66 0.75
5 11 0.12
6 2 0.02
7 2 0.02
8 2 0.02
ACGTcount: A:0.67, C:0.04, G:0.05, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:116375 original size:56 final size:59
Alignment explanation
Indices: 116315--116439 Score: 141
Period size: 56 Copynumber: 2.2 Consensus size: 59
116305 AATAGCATGA
* * *
116315 AAATAAATATCAACAATATAAATAAAT-AAAT-AA-AT-AAAATAAATGCTAAAATAAAC
1 AAATAAATATAAACAATAAAAATAAATGAAATCAACATGAAAATAAATGAT-AAATAAAC
* * * *
116371 AAATAAATATAAATAATAAAAATAATTGAGATCAAGCATGAAAATAAATGATAAATAAAT
1 AAATAAATATAAACAATAAAAATAAATGAAATCAA-CATGAAAATAAATGATAAATAAAC
116431 AAATAAATA
1 AAATAAATA
116440 AATAAATCAA
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
56 23 0.40
57 3 0.05
58 2 0.04
60 18 0.32
61 11 0.19
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (59 bp):
AAATAAATATAAACAATAAAAATAAATGAAATCAACATGAAAATAAATGATAAATAAAC
Found at i:116383 original size:93 final size:96
Alignment explanation
Indices: 116231--116484 Score: 247
Period size: 97 Copynumber: 2.6 Consensus size: 96
116221 TTAATGATAA
* * * * *
116231 ATAAATAAATAAACAAACAAGAT-AATAAAACTAAATGC-AAATTAAATAAAT-AATAATAAAAG
1 ATAAACAAATAAATAAATAA-ATAAATAAAACTAAATGCTAAAATAAACAAATAAAT-ATAAAAG
*
116293 AGATAACAATAA-A-AT-AGCATGAAAATAAAT-
64 A-ATAAAAATAATAGATAAGCATGAAAATAAATG
* *
116323 ATCAACAATATAAATAAATAAATAAATAAAA-TAAATGCTAAAATAAACAAATAAATAT-AAATA
1 ATAAACAA-ATAAATAAATAAATAAATAAAACTAAATGCTAAAATAAACAAATAAATATAAAAGA
116386 ATAAAAATAATTGAGATCAAGCATGAAAATAAATG
65 ATAAAAATAA-T-AGAT-AAGCATGAAAATAAATG
* * * *
116421 ATAAATAAATAAATAAATAAATAAATCAATAACTTAAATGTTAAAATAAACAACTAAATGTAAA
1 ATAAACAAATAAATAAATAAATAAAT-AA-AAC-TAAATGCTAAAATAAACAAATAAATATAAA
116485 TAATAATAAT
Statistics
Matches: 133, Mismatches: 13, Indels: 22
0.79 0.08 0.13
Matches are distributed among these distances:
91 9 0.07
92 19 0.14
93 30 0.23
94 4 0.03
95 2 0.02
97 33 0.25
98 8 0.06
99 2 0.02
101 24 0.18
102 2 0.02
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.23
Consensus pattern (96 bp):
ATAAACAAATAAATAAATAAATAAATAAAACTAAATGCTAAAATAAACAAATAAATATAAAAGAA
TAAAAATAATAGATAAGCATGAAAATAAATG
Found at i:116469 original size:101 final size:97
Alignment explanation
Indices: 116308--116496 Score: 272
Period size: 101 Copynumber: 1.9 Consensus size: 97
116298 ACAATAAAAT
*
116308 AGCATGAAAATAAATATCAACAATATAAATAAATAAATAAATAAAATAAATGCTAAAATAAACAA
1 AGCATGAAAATAAATATAAACAATATAAATAAATAAATAAATAAAATAAATGCTAAAATAAACAA
116373 ATAAATATAAATAATAAAAATAATTGAGATCA
66 ATAAATATAAATAATAAAAATAATTGAGATCA
* *
116405 AGCATGAAAATAAATGATAAATAA-ATAAATAAATAAATAAATCAATAACTTAAATGTTAAAATA
1 AGCATGAAAATAAAT-ATAAACAATATAAATAAATAAATAAAT-AA-AA--TAAATGCTAAAATA
* * *
116469 AACAACTAAATGTAAATAATAATAATAA
61 AACAAATAAATATAAATAATAAAAATAA
116497 AAAGAAGACG
Statistics
Matches: 81, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
97 33 0.41
98 8 0.10
99 2 0.02
101 38 0.47
ACGTcount: A:0.64, C:0.06, G:0.05, T:0.25
Consensus pattern (97 bp):
AGCATGAAAATAAATATAAACAATATAAATAAATAAATAAATAAAATAAATGCTAAAATAAACAA
ATAAATATAAATAATAAAAATAATTGAGATCA
Found at i:116723 original size:26 final size:25
Alignment explanation
Indices: 116694--116769 Score: 63
Period size: 26 Copynumber: 3.1 Consensus size: 25
116684 ATTTTCTTTA
116694 AATGTATGTCTCAAAAAAATTCTCTG
1 AATGTATGTCTCAAAAAAA-TCTCTG
*
116720 AATGT-TGTAT--AAAAAATCTCTG
1 AATGTATGTCTCAAAAAAATCTCTG
*
116742 AATCTTAT-TC-CAAAAACAACTCTCTG
1 AAT-GTATGTCTCAAAAA-AA-TCTCTG
116768 AA
1 AA
116770 CAAATGAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
22 9 0.22
23 8 0.20
24 5 0.12
25 6 0.15
26 13 0.32
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (25 bp):
AATGTATGTCTCAAAAAAATCTCTG
Found at i:140250 original size:13 final size:13
Alignment explanation
Indices: 140232--140256 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
140222 TAAGTTAAAA
140232 ATGCTAAAAATGC
1 ATGCTAAAAATGC
140245 ATGCTAAAAATG
1 ATGCTAAAAATG
140257 ATGAAATGGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.12, G:0.16, T:0.24
Consensus pattern (13 bp):
ATGCTAAAAATGC
Done.