Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012763.1 Kokia drynarioides strain JFW-HI SEQ_127775, 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: 269682
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Warning! 30 characters in sequence are not A, C, G, or T
Found at i:2016 original size:27 final size:27
Alignment explanation
Indices: 1958--2018 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
1948 CGATTTGTGG
* *
1958 TAGCACTGGAGGAACTCCATCTTGCCG
1 TAGCACTAGAGGAACTCCATCTTGCCA
* *
1985 CAGCACTAGAGGAACTCCATCTTGTCA
1 TAGCACTAGAGGAACTCCATCTTGCCA
2012 TAGCACT
1 TAGCACT
2019 GGTGGTAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (27 bp):
TAGCACTAGAGGAACTCCATCTTGCCA
Found at i:6676 original size:34 final size:35
Alignment explanation
Indices: 6637--6737 Score: 98
Period size: 35 Copynumber: 2.8 Consensus size: 35
6627 ACTACCAATA
6637 GTTATTCCAAAATTTTAGGGAAA-AACACCAACTT
1 GTTATTCCAAAATTTTAGGGAAAGAACACCAACTT
* * * * *
6671 TTTATTCTCAAATTTTTA-CGAAAGAGCACTAACTT
1 GTTATTC-CAAAATTTTAGGGAAAGAACACCAACTT
*
6706 GCTATTCCCAAAATTTTAGCGGAAAGTAACAC
1 GTTATT-CCAAAATTTTAG-GGAAAG-AACAC
6738 ATGCTCTTCC
Statistics
Matches: 51, Mismatches: 10, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
34 10 0.20
35 31 0.61
36 1 0.02
37 5 0.10
38 4 0.08
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.32
Consensus pattern (35 bp):
GTTATTCCAAAATTTTAGGGAAAGAACACCAACTT
Found at i:7423 original size:15 final size:16
Alignment explanation
Indices: 7396--7425 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
7386 CCATTGTTTG
7396 GAACAACTTGTATTTA
1 GAACAACTTGTATTTA
7412 GAACAA-TTGTATTT
1 GAACAACTTGTATTT
7426 TTTCAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.40
Consensus pattern (16 bp):
GAACAACTTGTATTTA
Found at i:13701 original size:9 final size:9
Alignment explanation
Indices: 13675--13704 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
13665 CACCCAAAAC
*
13675 CTTCATCAC
1 CTTCATCAT
13684 CTTCATCAT
1 CTTCATCAT
13693 CTTCATCAT
1 CTTCATCAT
13702 CTT
1 CTT
13705 TTAACGTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.20, C:0.37, G:0.00, T:0.43
Consensus pattern (9 bp):
CTTCATCAT
Found at i:13820 original size:21 final size:22
Alignment explanation
Indices: 13794--13838 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
13784 TTAAACGATA
* *
13794 TTTAGTCCTTTAAA-GTAAGTT
1 TTTAGTCATTAAAATGTAAGTT
13815 TTTAGTCATTAAAATGTAAGTT
1 TTTAGTCATTAAAATGTAAGTT
13837 TT
1 TT
13839 GAATAAAAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.31, C:0.07, G:0.13, T:0.49
Consensus pattern (22 bp):
TTTAGTCATTAAAATGTAAGTT
Found at i:21648 original size:96 final size:96
Alignment explanation
Indices: 21497--21674 Score: 293
Period size: 96 Copynumber: 1.9 Consensus size: 96
21487 TAATAAATTA
* * *
21497 GGAGTGTGTTGGACTGAGTAATCGGGATGAAGTGCTTGGGTTGTCATTTCATTTCGTGTCAAAAG
1 GGAGTATGTTGGACTGAGTAACCGGGATGAAGTGATTGGGTTGTCATTTCATTTCGTGTCAAAAG
21562 GGCTAATACATTCTTAAATAAAAAATGATTG
66 GGCTAATACATTCTTAAATAAAAAATGATTG
* *
21593 GGAGTATGTTGGGCTGAGTAACCGGGATGGAGTGATTGGGTTGTCATTTCATTTCGTGTCAAAAG
1 GGAGTATGTTGGACTGAGTAACCGGGATGAAGTGATTGGGTTGTCATTTCATTTCGTGTCAAAAG
* *
21658 GTCTAATATATTCTTAA
66 GGCTAATACATTCTTAA
21675 GGAAAAAAAA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
96 75 1.00
ACGTcount: A:0.27, C:0.11, G:0.28, T:0.34
Consensus pattern (96 bp):
GGAGTATGTTGGACTGAGTAACCGGGATGAAGTGATTGGGTTGTCATTTCATTTCGTGTCAAAAG
GGCTAATACATTCTTAAATAAAAAATGATTG
Found at i:23350 original size:23 final size:23
Alignment explanation
Indices: 23319--23484 Score: 215
Period size: 23 Copynumber: 7.2 Consensus size: 23
23309 ACGATGCATC
* *
23319 AAATTTTAATATGATTTATGCTT
1 AAATATTAATGTGATTTATGCTT
* *
23342 AAATATTAATGTGATTTGTGCTA
1 AAATATTAATGTGATTTATGCTT
* *
23365 AAATATTAAAGTGATTTATACTT
1 AAATATTAATGTGATTTATGCTT
* * *
23388 AAATATTAATATGATTTGTGCTC
1 AAATATTAATGTGATTTATGCTT
*
23411 AAATATTAATGTGATGTATGCTT
1 AAATATTAATGTGATTTATGCTT
**
23434 AAATATTAATGTGATTTACACTT
1 AAATATTAATGTGATTTATGCTT
23457 AAATATTAATGTGATTTATGCTT
1 AAATATTAATGTGATTTATGCTT
*
23480 CAATA
1 AAATA
23485 ATATGTAACA
Statistics
Matches: 120, Mismatches: 23, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 120 1.00
ACGTcount: A:0.37, C:0.06, G:0.12, T:0.45
Consensus pattern (23 bp):
AAATATTAATGTGATTTATGCTT
Found at i:23438 original size:69 final size:69
Alignment explanation
Indices: 23319--23478 Score: 239
Period size: 69 Copynumber: 2.3 Consensus size: 69
23309 ACGATGCATC
* * * * *
23319 AAATTTTAATATGATTTATGCTTAAATATTAATGTGATTTGTGCTAAAATATTAAAGTGATTTAT
1 AAATATTAATATGATTTATGCTCAAATATTAATGTGATGTATGCTAAAATATTAAAGTGATTTAC
23384 ACTT
66 ACTT
* * *
23388 AAATATTAATATGATTTGTGCTCAAATATTAATGTGATGTATGCTTAAATATTAATGTGATTTAC
1 AAATATTAATATGATTTATGCTCAAATATTAATGTGATGTATGCTAAAATATTAAAGTGATTTAC
23453 ACTT
66 ACTT
*
23457 AAATATTAATGTGATTTATGCT
1 AAATATTAATATGATTTATGCT
23479 TCAATAATAT
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
69 81 1.00
ACGTcount: A:0.37, C:0.06, G:0.12, T:0.45
Consensus pattern (69 bp):
AAATATTAATATGATTTATGCTCAAATATTAATGTGATGTATGCTAAAATATTAAAGTGATTTAC
ACTT
Found at i:28190 original size:80 final size:81
Alignment explanation
Indices: 27875--28189 Score: 370
Period size: 80 Copynumber: 3.9 Consensus size: 81
27865 ATCAACTGAA
* * * * * * *
27875 TCCGTTAATTCATGGCACTCT-GTGTCTAGTGGATAAACCGTGATAAGTGAGTCCAGCTCTAGTT
1 TCCGTCAATTCATGGCACGCTAGTGCCTAGCGGATAAACCGTAATAAATGAGCCCAGCTCTAGTT
*
27939 GGATTAACCAACCAAT
66 GGATTAACCAACAAAT
* ** *
27955 TCCGTCAATTCATGGCACGC-AGTGCCTAGCGAATAAACCACAATAAATGAGCCCAACTCTAGTT
1 TCCGTCAATTCATGGCACGCTAGTGCCTAGCGGATAAACCGTAATAAATGAGCCCAGCTCTAGTT
28019 GGATTAACCAACAAAT
66 GGATTAACCAACAAAT
* * * ** *
28035 TCCATCAATTCATGGCAC-CCAGTGCCTAACGGATAAA-TTTCAATAAATGAGCCTAGCTCTAGT
1 TCCGTCAATTCATGGCACGCTAGTGCCTAGCGGATAAACCGT-AATAAATGAGCCCAGCTCTAGT
*
28098 TGGATTAACCAATAAAT
65 TGGATTAACCAACAAAT
* * * * *
28115 TCCGTCAATTCATCGCAC-CTAGTGCCTAGCGGATAAACTGTAATAAATTAGCCCAGTTATAGTT
1 TCCGTCAATTCATGGCACGCTAGTGCCTAGCGGATAAACCGTAATAAATGAGCCCAGCTCTAGTT
28179 GGATTAACCAA
66 GGATTAACCAA
28190 TGGTTTGCGC
Statistics
Matches: 201, Mismatches: 30, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
79 1 0.00
80 198 0.99
81 2 0.01
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (81 bp):
TCCGTCAATTCATGGCACGCTAGTGCCTAGCGGATAAACCGTAATAAATGAGCCCAGCTCTAGTT
GGATTAACCAACAAAT
Found at i:29720 original size:23 final size:23
Alignment explanation
Indices: 29694--30010 Score: 445
Period size: 23 Copynumber: 13.8 Consensus size: 23
29684 CGTTACATAA
*
29694 TAATATGATTTGTGCTTAAATAT
1 TAATGTGATTTGTGCTTAAATAT
* *
29717 TAATGTGATTTATGTTTAAATAT
1 TAATGTGATTTGTGCTTAAATAT
*
29740 TAATATGATTTGTGCTTAAATAT
1 TAATGTGATTTGTGCTTAAATAT
29763 TAATGTGATTTGTGCTTAAATAT
1 TAATGTGATTTGTGCTTAAATAT
* * * *
29786 TGATATGATTTATGCTTAAATTT
1 TAATGTGATTTGTGCTTAAATAT
29809 TAATGTGATTTGTGCTTAAATAT
1 TAATGTGATTTGTGCTTAAATAT
*
29832 TAATGTGATTTGTGCTTAAATAA
1 TAATGTGATTTGTGCTTAAATAT
*
29855 TAATGTGATTTGTGCTTAAATAA
1 TAATGTGATTTGTGCTTAAATAT
29878 TAATGTGATTTGTGCTTAAATAT
1 TAATGTGATTTGTGCTTAAATAT
*
29901 TAATGTGATTTGTGCTTAAATAC
1 TAATGTGATTTGTGCTTAAATAT
* ** * *
29924 TAATATGGCTTGTGCTCAAATAC
1 TAATGTGATTTGTGCTTAAATAT
* * *
29947 TAATGTAATTTATGCTTAAATTT
1 TAATGTGATTTGTGCTTAAATAT
*
29970 TAATGTGGTTTGTGCTTAAATAT
1 TAATGTGATTTGTGCTTAAATAT
*
29993 TAATGTGATTTTTGCTTA
1 TAATGTGATTTGTGCTTA
30011 TGCTAAAGAT
Statistics
Matches: 258, Mismatches: 36, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 258 1.00
ACGTcount: A:0.32, C:0.05, G:0.16, T:0.47
Consensus pattern (23 bp):
TAATGTGATTTGTGCTTAAATAT
Found at i:30476 original size:25 final size:25
Alignment explanation
Indices: 30442--30616 Score: 196
Period size: 25 Copynumber: 7.0 Consensus size: 25
30432 GTAGACACAC
30442 ATGAAAAGAAAGCCTTTGTGGCAAA
1 ATGAAAAGAAAGCCTTTGTGGCAAA
* *
30467 ATGAAAAGAAAACCTTTGTGGCAAT
1 ATGAAAAGAAAGCCTTTGTGGCAAA
* *
30492 ATGAAAAGAAAGCCTTTATGAGAAAA
1 ATGAAAAGAAAGCCTTTGTG-GCAAA
* *
30518 ATAAAAAG-AAGCCTTTTTGG-AAA
1 ATGAAAAGAAAGCCTTTGTGGCAAA
* *
30541 TATGAAAAGAAAGCTTTTGTGGAAAAA
1 -ATGAAAAGAAAGCCTTTGTGG-CAAA
* *
30568 ACG-AAAGAAAACCTTTGTGG-AAA
1 ATGAAAAGAAAGCCTTTGTGGCAAA
30591 TATGAAAAGAAAGCCTTTGTGGCAAA
1 -ATGAAAAGAAAGCCTTTGTGGCAAA
30617 GCCTGAATAG
Statistics
Matches: 126, Mismatches: 16, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
23 6 0.05
24 10 0.08
25 92 0.73
26 15 0.12
27 3 0.02
ACGTcount: A:0.47, C:0.10, G:0.21, T:0.22
Consensus pattern (25 bp):
ATGAAAAGAAAGCCTTTGTGGCAAA
Found at i:30533 original size:50 final size:50
Alignment explanation
Indices: 30442--30612 Score: 238
Period size: 50 Copynumber: 3.4 Consensus size: 50
30432 GTAGACACAC
* * *
30442 ATGAAAAGAAAGCCTTTGTGGCAAAATGAAAAGAAAACCTTTGTGGCAAT
1 ATGAAAAGAAAGCCTTTGTGGAAAAATAAAAAGAAAACCTTTGTGGAAAT
* * *
30492 ATGAAAAGAAAGCCTTTATGAGAAAAATAAAAAG-AAGCCTTTTTGGAAAT
1 ATGAAAAGAAAGCCTTTGTG-GAAAAATAAAAAGAAAACCTTTGTGGAAAT
* *
30542 ATGAAAAGAAAGCTTTTGTGGAAAAA-ACGAAAGAAAACCTTTGTGGAAAT
1 ATGAAAAGAAAGCCTTTGTGGAAAAATA-AAAAGAAAACCTTTGTGGAAAT
30592 ATGAAAAGAAAGCCTTTGTGG
1 ATGAAAAGAAAGCCTTTGTGG
30613 CAAAGCCTGA
Statistics
Matches: 106, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
48 1 0.01
49 10 0.09
50 84 0.79
51 11 0.10
ACGTcount: A:0.46, C:0.09, G:0.22, T:0.23
Consensus pattern (50 bp):
ATGAAAAGAAAGCCTTTGTGGAAAAATAAAAAGAAAACCTTTGTGGAAAT
Found at i:33971 original size:18 final size:16
Alignment explanation
Indices: 33941--33974 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 16
33931 AAATTGGTTG
33941 AATTTTTTTAATTTTT
1 AATTTTTTTAATTTTT
33957 AATTTTTATTGAATTTTT
1 AATTTTT-TT-AATTTTT
33975 TATTACGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 2 0.12
18 7 0.44
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (16 bp):
AATTTTTTTAATTTTT
Found at i:39503 original size:42 final size:42
Alignment explanation
Indices: 39456--39540 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
39446 TGGAGAATAA
* *
39456 AAATGGTGTTTGGAAATAGAGAAAATGAGAGAGAAAAATGAC
1 AAATGGTGTTTGGAAAGAGAGAAAATAAGAGAGAAAAATGAC
*
39498 AAATGGTGTTTGGCAAGAGAGAAAATAAGAGAGAAAAATGAC
1 AAATGGTGTTTGGAAAGAGAGAAAATAAGAGAGAAAAATGAC
39540 A
1 A
39541 GCCGGTAGTG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.51, C:0.04, G:0.28, T:0.18
Consensus pattern (42 bp):
AAATGGTGTTTGGAAAGAGAGAAAATAAGAGAGAAAAATGAC
Found at i:47918 original size:43 final size:44
Alignment explanation
Indices: 47845--47978 Score: 128
Period size: 45 Copynumber: 3.0 Consensus size: 44
47835 GTGGTTGAAG
* * * * *
47845 CCACCAATATTTGCAGACAAGCTTCCATGTAGGTTGTGGATAAA
1 CCACCAATAATCGTAGACAAGATACCATGTAGGTTGTGGATAAA
* ** * *
47889 CCATCAA-AATCGTA-ATCAAGATGTCATGTAGGTTATGGATGAAG
1 CCACCAATAATCGTAGA-CAAGATACCATGTAGGTTGTGGAT-AAA
* *
47933 CCACCAATATTCGTAGACAAGCTACCATGTAGGTTGTGGATAAA
1 CCACCAATAATCGTAGACAAGATACCATGTAGGTTGTGGATAAA
47977 CC
1 CC
47979 CCTAATTTTG
Statistics
Matches: 70, Mismatches: 16, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
42 1 0.01
43 24 0.34
44 18 0.26
45 26 0.37
46 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (44 bp):
CCACCAATAATCGTAGACAAGATACCATGTAGGTTGTGGATAAA
Found at i:48008 original size:88 final size:88
Alignment explanation
Indices: 47840--48026 Score: 234
Period size: 88 Copynumber: 2.1 Consensus size: 88
47830 TATATGTGGT
* *
47840 TGAAGCCACCAATATTTGCAGACAAGCTTCCATGTAGGTTGTGGATAAACCATCAAAATCGTAAT
1 TGAAGCCACCAATATTCGCAGACAAGCTACCATGTAGGTTGTGGATAAACCATCAAAATCGTAAT
* *
47905 CAAGATGTCATGTAGGTTATGGA
66 CAAGATGGCAAGTAGGTTATGGA
* * ** *
47928 TGAAGCCACCAATATTCGTAGACAAGCTACCATGTAGGTTGTGGATAAACC-CCTAATTTTGTAG
1 TGAAGCCACCAATATTCGCAGACAAGCTACCATGTAGGTTGTGGATAAACCATC-AAAATCGTA-
* *
47992 AT-AAGCTGGCAAGTAGGTTGTGGA
64 ATCAAGATGGCAAGTAGGTTATGGA
*
48016 TGAAGCTACCA
1 TGAAGCCACCA
48027 TGTAGGTTGT
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
87 1 0.01
88 82 0.96
89 2 0.02
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.27
Consensus pattern (88 bp):
TGAAGCCACCAATATTCGCAGACAAGCTACCATGTAGGTTGTGGATAAACCATCAAAATCGTAAT
CAAGATGGCAAGTAGGTTATGGA
Found at i:48021 original size:24 final size:23
Alignment explanation
Indices: 47986--48037 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
47976 ACCCCTAATT
* **
47986 TTGTAGATAAGCTGGCAAGTAGG
1 TTGTGGATAAGCTACCAAGTAGG
*
48009 TTGTGGATGAAGCTACCATGTAGG
1 TTGTGGAT-AAGCTACCAAGTAGG
48033 TTGTG
1 TTGTG
48038 AACGAGCCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.25, C:0.10, G:0.35, T:0.31
Consensus pattern (23 bp):
TTGTGGATAAGCTACCAAGTAGG
Found at i:57760 original size:22 final size:22
Alignment explanation
Indices: 57729--57775 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
57719 ACTGGTGAAA
57729 AATTACTATTTGAAGTTCAATT
1 AATTACTATTTGAAGTTCAATT
*
57751 AATTATTATTTGAAGTTCAATT
1 AATTACTATTTGAAGTTCAATT
57773 AAT
1 AAT
57776 CATATTGAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (22 bp):
AATTACTATTTGAAGTTCAATT
Found at i:60971 original size:12 final size:12
Alignment explanation
Indices: 60956--60993 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
60946 AATTAAAGAA
60956 ATAATAGCATTC
1 ATAATAGCATTC
* *
60968 ATAATAGTAGTC
1 ATAATAGCATTC
60980 ATAATAGCATTC
1 ATAATAGCATTC
60992 AT
1 AT
60994 CATGATGACA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (12 bp):
ATAATAGCATTC
Found at i:63721 original size:25 final size:25
Alignment explanation
Indices: 63687--63750 Score: 94
Period size: 25 Copynumber: 2.6 Consensus size: 25
63677 AAGTCTTCCA
*
63687 TCTTACGAGCCAGATAG-AATATTGC
1 TCTTACGAGCCAGATAGAAATA-CGC
63712 TCTTACGAGCCAGATAGAAATACGC
1 TCTTACGAGCCAGATAGAAATACGC
*
63737 TCTTATGAGCCAGA
1 TCTTACGAGCCAGA
63751 ATCAGAATGC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
25 32 0.89
26 4 0.11
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (25 bp):
TCTTACGAGCCAGATAGAAATACGC
Found at i:78965 original size:17 final size:17
Alignment explanation
Indices: 78943--78990 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
78933 TGTCATCTAG
78943 TTGTCATTACATTTTAA
1 TTGTCATTACATTTTAA
* * *
78960 TTGTCACTGCATTTTAC
1 TTGTCATTACATTTTAA
* *
78977 TTGTTATCACATTT
1 TTGTCATTACATTT
78991 GCATTATAGT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.23, C:0.17, G:0.08, T:0.52
Consensus pattern (17 bp):
TTGTCATTACATTTTAA
Found at i:84727 original size:22 final size:22
Alignment explanation
Indices: 84702--84743 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
84692 AGTTGTCGAA
84702 GAAATA-GATTGAAAATAAAAAT
1 GAAATATGATT-AAAATAAAAAT
*
84724 GAAATATGATTATAATAAAA
1 GAAATATGATTAAAATAAAA
84744 TGGGGCCCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.26
Consensus pattern (22 bp):
GAAATATGATTAAAATAAAAAT
Found at i:95146 original size:21 final size:21
Alignment explanation
Indices: 95120--95162 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
95110 TGCTTTCTTT
95120 TCTGTTATTTTATATCACACA
1 TCTGTTATTTTATATCACACA
95141 TCTGTTATTTTATATCACACA
1 TCTGTTATTTTATATCACACA
95162 T
1 T
95163 AGAGGGCAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.19, G:0.05, T:0.49
Consensus pattern (21 bp):
TCTGTTATTTTATATCACACA
Found at i:100808 original size:18 final size:18
Alignment explanation
Indices: 100785--100819 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
100775 CCATAAATGA
*
100785 TCTTACGAGCCGGTATGC
1 TCTTACGAACCGGTATGC
100803 TCTTACGAACCGGTATG
1 TCTTACGAACCGGTATG
100820 ATACTCCTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.29
Consensus pattern (18 bp):
TCTTACGAACCGGTATGC
Found at i:107223 original size:11 final size:11
Alignment explanation
Indices: 107199--107236 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
107189 AAGAAATAGG
*
107199 GAAAGCAAATAA
1 GAAA-CAAAAAA
107211 GAAACAAAAAA
1 GAAACAAAAAA
107222 GAAACAAAAAA
1 GAAACAAAAAA
107233 GAAA
1 GAAA
107237 GGAAATAGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
11 21 0.84
12 4 0.16
ACGTcount: A:0.76, C:0.08, G:0.13, T:0.03
Consensus pattern (11 bp):
GAAACAAAAAA
Found at i:107992 original size:42 final size:42
Alignment explanation
Indices: 107919--108326 Score: 440
Period size: 42 Copynumber: 10.0 Consensus size: 42
107909 GGGTACACAG
*
107919 GGTGTGAAGGTCCATTTAC-TTTCATTGCATTTAGAGGCCCA
1 GGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCA
** * *
107960 GGTGTGGAGGTTGATTTAGTTTTCATTACATTTAGAGGCCCA
1 GGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCA
* * * *
108002 GGTGTGGAGG------T--TTTTCATCGCATTTAAATGCCAA
1 GGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCA
* ** *
108036 GGTGTGAAGGTCCATTTACTTTTCATTATATTTAAAGGCCCA
1 GGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCA
* * * *
108078 AGTGTGGAGGTTCATTTACTTTTCATCGCATTTAGAGGCCTA
1 GGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCA
* * *
108120 GATGTGGAGGTCCATTTACTTTTCATTGCATTTAAAGGCACA
1 GGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCA
* * * * * *
108162 AGTGTAGAAGTTCATTTACTGTTCATTACATTTAGAGGCCCA
1 GGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCA
* * * *
108204 TGTGTGGAGGTTCATTTACTTTTTATTGAATTTAGAGGCCCA
1 GGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCA
** * *
108246 AATGTGGAGGTCCATTTACATTTCATTG-ATATAGAGGCCCA
1 GGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCA
108287 GGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCC
1 GGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCC
108327 TAAGCATAGA
Statistics
Matches: 300, Mismatches: 57, Indels: 19
0.80 0.15 0.05
Matches are distributed among these distances:
34 27 0.09
36 1 0.00
40 1 0.00
41 52 0.17
42 219 0.73
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.37
Consensus pattern (42 bp):
GGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCA
Found at i:108026 original size:34 final size:34
Alignment explanation
Indices: 107979--108046 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
107969 GTTGATTTAG
* * * *
107979 TTTTCATTACATTTAGAGGCCCAGGTGTGGAGGT
1 TTTTCATCACATTTAAAGGCCAAGGTGTGAAGGT
* *
108013 TTTTCATCGCATTTAAATGCCAAGGTGTGAAGGT
1 TTTTCATCACATTTAAAGGCCAAGGTGTGAAGGT
108047 CCATTTACTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (34 bp):
TTTTCATCACATTTAAAGGCCAAGGTGTGAAGGT
Found at i:108069 original size:76 final size:76
Alignment explanation
Indices: 107938--108166 Score: 233
Period size: 76 Copynumber: 2.9 Consensus size: 76
107928 GTCCATTTAC
* * * * ** * * *
107938 TTTCATTGCATTTAGAGGCCCAGGTGTGGAGGTTGATTTAGTTTTCATTACATTTAGAGGCCCAG
1 TTTCATCGCATTTAAAGGCCAAGGTGTGAAGGTCCATTTACTTTTCATTACATTTAAAGGCCCAA
108003 GTGTGGAGGTT
66 GTGTGGAGGTT
* *
108014 TTTCATCGCATTTAAATGCCAAGGTGTGAAGGTCCATTTACTTTTCATTATATTTAAAGGCCCAA
1 TTTCATCGCATTTAAAGGCCAAGGTGTGAAGGTCCATTTACTTTTCATTACATTTAAAGGCCCAA
108079 GTGTGGAGGTTCATTTACT
66 GTGTGGAGG------T--T
* * * * * *
108098 TTTCATCGCATTTAGAGGCCTAGATGTGGAGGTCCATTTACTTTTCATTGCATTTAAAGGCACAA
1 TTTCATCGCATTTAAAGGCCAAGGTGTGAAGGTCCATTTACTTTTCATTACATTTAAAGGCCCAA
108163 GTGT
66 GTGT
108167 AGAAGTTCAT
Statistics
Matches: 126, Mismatches: 19, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
76 63 0.50
82 1 0.01
84 62 0.49
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.37
Consensus pattern (76 bp):
TTTCATCGCATTTAAAGGCCAAGGTGTGAAGGTCCATTTACTTTTCATTACATTTAAAGGCCCAA
GTGTGGAGGTT
Found at i:109458 original size:19 final size:19
Alignment explanation
Indices: 109434--109496 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 19
109424 TATTCAAAAT
109434 AAAAGTTTTGATTTTTAAG
1 AAAAGTTTTGATTTTTAAG
**
109453 AAAAGTAATGATTTTTTAAAAG
1 AAAAGTTTTGA-TTTTT--AAG
* *
109475 AAAA-TTTAGATTTTTAAT
1 AAAAGTTTTGATTTTTAAG
109493 AAAA
1 AAAA
109497 AATCTATTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
18 6 0.17
19 9 0.26
20 10 0.29
21 3 0.09
22 7 0.20
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (19 bp):
AAAAGTTTTGATTTTTAAG
Found at i:109570 original size:140 final size:144
Alignment explanation
Indices: 109193--109607 Score: 574
Period size: 140 Copynumber: 2.9 Consensus size: 144
109183 TAAGAAAATA
* * * *
109193 TAGATTTTTAAAAAAATAAAAAAATTTGTTTTTAGTCATTTTAAAGGGAAAAG-TAAAATATTTA
1 TAGATTTTT-AAAAAATAAAAATATGT-TTTTTAGTCATTTTAAAGGAAAAAGTTTAAATATTTA
*
109257 AACAAAGTTTGATTTTTTTAACTATTTCTAAATAAAAGTTTTGATTTTTAAGAAAAGTAGTGATT
64 AACAAAGTTTG-TTTTTTTAACTATTTCAAAATAAAAGTTTTGATTTTTAAGAAAAGTAGTGATT
*
109322 TAAAAAAAAATAAACTT
128 TTAAAAAAAATAAACTT
109339 TAGATTTTTAAAAAATAAAAATATGTTTTTTAGTCATTTTAAAGGAAAAAGTTTAAAT-TTGTAA
1 TAGATTTTTAAAAAATAAAAATATGTTTTTTAGTCATTTTAAAGGAAAAAGTTTAAATATT-TAA
* *
109403 ACAAAGTTTTGATTTTTTAACTA-TTCAAAATAAAAGTTTTGATTTTTAAGAAAAGTAATGATTT
65 ACAAAG-TTTGTTTTTTTAACTATTTCAAAATAAAAGTTTTGATTTTTAAGAAAAGTAGTGATTT
** *
109467 TTTAAAAGA-AAA-TT
129 TAAAAAAAATAAACTT
* ** * *
109481 TAGATTTTTAATAAA-AAATCTAT-TTTTTTAGTCATTTTAAAAGAAAAAGTTTAAATAATTAAA
1 TAGATTTTTAAAAAATAAAAATATGTTTTTTAGTCATTTTAAAGGAAAAAGTTTAAATATTTAAA
* *
109544 CAAAGTTTGTTTTTTTAACCATTTCAAAATAAAAGTTTTGATTTTTAAGAAAAATAGTGATTTT
66 CAAAGTTTGTTTTTTTAACTATTTCAAAATAAAAGTTTTGATTTTTAAGAAAAGTAGTGATTTT
109608 GTTTAAGAAA
Statistics
Matches: 244, Mismatches: 20, Indels: 16
0.87 0.07 0.06
Matches are distributed among these distances:
139 14 0.06
140 81 0.33
141 7 0.03
142 16 0.07
143 3 0.01
144 70 0.29
145 40 0.16
146 13 0.05
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.42
Consensus pattern (144 bp):
TAGATTTTTAAAAAATAAAAATATGTTTTTTAGTCATTTTAAAGGAAAAAGTTTAAATATTTAAA
CAAAGTTTGTTTTTTTAACTATTTCAAAATAAAAGTTTTGATTTTTAAGAAAAGTAGTGATTTTA
AAAAAAATAAACTT
Found at i:110196 original size:16 final size:15
Alignment explanation
Indices: 110165--110205 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
110155 TTTTTTATTC
*
110165 TTATTTTATCTTTAT
1 TTATTTTATATTTAT
110180 TTATTTTCATATTTAT
1 TTATTTT-ATATTTAT
110196 TTATATTTAT
1 TTAT-TTTAT
110206 GTTTTTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 7 0.30
16 13 0.57
17 3 0.13
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (15 bp):
TTATTTTATATTTAT
Found at i:110314 original size:9 final size:9
Alignment explanation
Indices: 110300--110324 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
110290 TGTATTATTG
110300 TTATCATTA
1 TTATCATTA
110309 TTATCATTA
1 TTATCATTA
110318 TTATCAT
1 TTATCAT
110325 CATGTCAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.12, G:0.00, T:0.56
Consensus pattern (9 bp):
TTATCATTA
Found at i:110938 original size:3 final size:3
Alignment explanation
Indices: 110932--110961 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
110922 TTAAATCTTT
110932 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
110962 AAGATCAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:138500 original size:40 final size:40
Alignment explanation
Indices: 138413--138501 Score: 97
Period size: 40 Copynumber: 2.2 Consensus size: 40
138403 CTATGTTGCA
* *
138413 ACAAACCCCCCTATGTCGCAACATATAATATCTATGTCACG
1 ACAAA-CCCCCTATGTCGCAACACAGAATATCTATGTCACG
* * * * **
138454 AAAAACCCCCTATGTCGCAACACAGCATGTTTATGTCGTG
1 ACAAACCCCCTATGTCGCAACACAGAATATCTATGTCACG
138494 ACAAACCC
1 ACAAACCC
138502 TTGAAGATGT
Statistics
Matches: 39, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
40 35 0.90
41 4 0.10
ACGTcount: A:0.34, C:0.31, G:0.12, T:0.22
Consensus pattern (40 bp):
ACAAACCCCCTATGTCGCAACACAGAATATCTATGTCACG
Found at i:144358 original size:18 final size:18
Alignment explanation
Indices: 144335--144370 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
144325 ATCACTAACT
144335 AATACTAATAGAATAGAA
1 AATACTAATAGAATAGAA
*
144353 AATACTAATATAATAGAA
1 AATACTAATAGAATAGAA
144371 TGAAAAGAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.61, C:0.06, G:0.08, T:0.25
Consensus pattern (18 bp):
AATACTAATAGAATAGAA
Found at i:144369 original size:23 final size:23
Alignment explanation
Indices: 144332--144376 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
144322 GGGATCACTA
144332 ACTAATACTAATAGAATAGAAAAT
1 ACTAATACTAATAGAAT-GAAAAT
144356 ACTAATA-TAATAGAATGAAAA
1 ACTAATACTAATAGAATGAAAA
144377 GAACTATCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 5 0.24
23 9 0.43
24 7 0.33
ACGTcount: A:0.60, C:0.07, G:0.09, T:0.24
Consensus pattern (23 bp):
ACTAATACTAATAGAATGAAAAT
Found at i:144382 original size:23 final size:24
Alignment explanation
Indices: 144331--144382 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
144321 CGGGATCACT
144331 AACTAATACTAATAGAATAGAAAA
1 AACTAATACTAATAGAATAGAAAA
*
144355 TACTAATA-TAATAGAAT-GAAAA
1 AACTAATACTAATAGAATAGAAAA
144377 GAACTA
1 -AACTA
144383 TCTTTTCTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 5 0.20
23 13 0.52
24 7 0.28
ACGTcount: A:0.60, C:0.08, G:0.10, T:0.23
Consensus pattern (24 bp):
AACTAATACTAATAGAATAGAAAA
Found at i:146674 original size:15 final size:15
Alignment explanation
Indices: 146650--146679 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
146640 TCTGTATATC
*
146650 TCAATCGAAAAAGAA
1 TCAATAGAAAAAGAA
146665 TCAATAGAAAAAGAA
1 TCAATAGAAAAAGAA
146680 AGAATCAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.10, G:0.13, T:0.13
Consensus pattern (15 bp):
TCAATAGAAAAAGAA
Found at i:149486 original size:18 final size:18
Alignment explanation
Indices: 149463--149504 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
149453 TTGGTTAATT
149463 AGAGTTCTAATATACTTA
1 AGAGTTCTAATATACTTA
149481 AGAGTTCTAATATACTTA
1 AGAGTTCTAATATACTTA
*
149499 ACAGTT
1 AGAGTT
149505 TTATTTAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AGAGTTCTAATATACTTA
Found at i:155496 original size:18 final size:17
Alignment explanation
Indices: 155454--155496 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
155444 GTTTTAAGTT
*
155454 TATAATATTTTATATTA
1 TATAATTTTTTATATTA
* *
155471 TGTTATTTTTATATATTA
1 TATAATTTTT-TATATTA
155489 TATAATTT
1 TATAATTT
155497 AGAACACATT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
TATAATTTTTTATATTA
Found at i:155641 original size:21 final size:20
Alignment explanation
Indices: 155606--155644 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
155596 ATAAAAACTG
*
155606 TATAAAATTAATAAATATAA
1 TATAAAATAAATAAATATAA
155626 TATAAAATAAAATAAATAT
1 TATAAAAT-AAATAAATAT
155645 TTTTTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
TATAAAATAAATAAATATAA
Found at i:161505 original size:2 final size:2
Alignment explanation
Indices: 161500--161531 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
161490 ATATATTTTG
161500 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
161532 CCATGTTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:161636 original size:24 final size:24
Alignment explanation
Indices: 161607--161716 Score: 76
Period size: 24 Copynumber: 4.4 Consensus size: 24
161597 TAAGTTTACG
161607 AGCGTAAACGAGTGCAAGCTGACA
1 AGCGTAAACGAGTGCAAGCTGACA
* * ** *
161631 AGCGTAAATGCATATATTTATAGCTGACG
1 AGCGTAAA--C-GA-GTGCA-AGCTGACA
* *
161660 AGCGTAAACGTGTGCAAGCTGGCA
1 AGCGTAAACGAGTGCAAGCTGACA
* * * *
161684 AGTGTAAACGTGTGCAAGCTGGCG
1 AGCGTAAACGAGTGCAAGCTGACA
161708 AGCGTAAAC
1 AGCGTAAAC
161717 ACATTTATAT
Statistics
Matches: 66, Mismatches: 15, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
24 44 0.67
25 2 0.03
26 1 0.02
27 2 0.03
28 2 0.03
29 15 0.23
ACGTcount: A:0.33, C:0.18, G:0.29, T:0.20
Consensus pattern (24 bp):
AGCGTAAACGAGTGCAAGCTGACA
Found at i:161758 original size:76 final size:77
Alignment explanation
Indices: 161610--161761 Score: 216
Period size: 77 Copynumber: 2.0 Consensus size: 77
161600 GTTTACGAGC
** * *
161610 GTAAACGAGTGCAAGCTGACAAGCGTAAATGCATATATTTATAGCTGACGAGCGTAAACGTGTGC
1 GTAAACGAGTGCAAGCTGACAAGCGTAAACACATATATATATAGCTGACGAGCATAAACGTGTGC
161675 AAGCTGGCAAGT
66 AAGCTGGCAAGT
* * * * *
161687 GTAAACGTGTGCAAGCTGGCGAGCGTAAACACATTTATATA-AGCTGACGAGCATAAATGTGTGC
1 GTAAACGAGTGCAAGCTGACAAGCGTAAACACATATATATATAGCTGACGAGCATAAACGTGTGC
161751 AAGCTGGCAAG
66 AAGCTGGCAAG
161762 CATAAATGCA
Statistics
Matches: 66, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
76 32 0.48
77 34 0.52
ACGTcount: A:0.34, C:0.17, G:0.28, T:0.22
Consensus pattern (77 bp):
GTAAACGAGTGCAAGCTGACAAGCGTAAACACATATATATATAGCTGACGAGCATAAACGTGTGC
AAGCTGGCAAGT
Found at i:161763 original size:24 final size:24
Alignment explanation
Indices: 161664--161769 Score: 68
Period size: 24 Copynumber: 4.2 Consensus size: 24
161654 CTGACGAGCG
* **
161664 TAAACGTGTGCAAGCTGGCAAGTG
1 TAAATGTGTGCAAGCTGGCAAGCA
* *
161688 TAAACGTGTGCAAGCTGGCGAGCGTA
1 TAAATGTGTGCAAGCTGGCAAGC--A
* * * ** * *
161714 AACACATTTATATAAGCTGACGAGCA
1 TA-A-ATGTGTGCAAGCTGGCAAGCA
161740 TAAATGTGTGCAAGCTGGCAAGCA
1 TAAATGTGTGCAAGCTGGCAAGCA
161764 TAAATG
1 TAAATG
161770 CATATATATA
Statistics
Matches: 61, Mismatches: 17, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
24 42 0.69
25 1 0.02
26 3 0.05
27 1 0.02
28 14 0.23
ACGTcount: A:0.34, C:0.17, G:0.27, T:0.22
Consensus pattern (24 bp):
TAAATGTGTGCAAGCTGGCAAGCA
Found at i:161881 original size:56 final size:56
Alignment explanation
Indices: 161771--161883 Score: 147
Period size: 56 Copynumber: 2.0 Consensus size: 56
161761 GCATAAATGC
* * * *
161771 ATATATATAAGCTAACGAGCGTAAACGTGTGCAAGTTGGCAAGTGCAAATGCATAT
1 ATATATATAAACTAACGAGCGTAAACGTGTGCAAGCTGGCAAGCGCAAACGCATAT
* * *
161827 ATATATATAAACTGACGAGTGTAAACGTGTGCAAGCTGG-AGAGCGTAAACGCATAT
1 ATATATATAAACTAACGAGCGTAAACGTGTGCAAGCTGGCA-AGCGCAAACGCATAT
161883 A
1 A
161884 CATAAGCTGA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
55 1 0.02
56 48 0.98
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.24
Consensus pattern (56 bp):
ATATATATAAACTAACGAGCGTAAACGTGTGCAAGCTGGCAAGCGCAAACGCATAT
Found at i:161916 original size:52 final size:52
Alignment explanation
Indices: 161687--161906 Score: 253
Period size: 52 Copynumber: 4.2 Consensus size: 52
161677 GCTGGCAAGT
* * *
161687 GTAAACGTGTGCAAGCTGGCGAGCGTAAACACATTTATATAAGCTGACGAGC
1 GTAAACGTGTGCAAGCTGGCAAGCGTAAACGCATATATATAAGCTGACGAGC
* * * * *
161739 ATAAATGTGTGCAAGCTGGCAAGCATAAATGCATATATATAAGCTAACGAGC
1 GTAAACGTGTGCAAGCTGGCAAGCGTAAACGCATATATATAAGCTGACGAGC
* * * * * *
161791 GTAAACGTGTGCAAGTTGGCAAGTGCAAATGCATATATATATATAAACTGACGAGT
1 GTAAACGTGTGCAAGCTGGCAAGCGTAAACGC----ATATATATAAGCTGACGAGC
*
161847 GTAAACGTGTGCAAGCTGG-AGAGCGTAAACGCATATACATAAGCTGACGAGC
1 GTAAACGTGTGCAAGCTGGCA-AGCGTAAACGCATATATATAAGCTGACGAGC
161899 GTAAACGT
1 GTAAACGT
161907 ACGAAAGCTG
Statistics
Matches: 139, Mismatches: 24, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
52 95 0.68
55 1 0.01
56 43 0.31
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.22
Consensus pattern (52 bp):
GTAAACGTGTGCAAGCTGGCAAGCGTAAACGCATATATATAAGCTGACGAGC
Found at i:169766 original size:37 final size:38
Alignment explanation
Indices: 169716--169794 Score: 90
Period size: 37 Copynumber: 2.1 Consensus size: 38
169706 TTCGAAGCAA
* *
169716 TAAAGTGACACCCAGTGTCC-CATCG-GTCTAGCCGAAG
1 TAAAGTGACACCCAGT-ACCTCATCGAATCTAGCCGAAG
** *
169753 TAAAGTGGTACCCAGTACCTCATCGAATCTATCCGAAG
1 TAAAGTGACACCCAGTACCTCATCGAATCTAGCCGAAG
169791 TAAA
1 TAAA
169795 ATAATGACAC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
36 2 0.06
37 19 0.54
38 14 0.40
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.22
Consensus pattern (38 bp):
TAAAGTGACACCCAGTACCTCATCGAATCTAGCCGAAG
Found at i:170590 original size:14 final size:14
Alignment explanation
Indices: 170571--170597 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
170561 CTTTTTCTTT
170571 TTCCTTCCCTTTTC
1 TTCCTTCCCTTTTC
170585 TTCCTTCCCTTTT
1 TTCCTTCCCTTTT
170598 TCATTTAAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (14 bp):
TTCCTTCCCTTTTC
Found at i:178393 original size:17 final size:18
Alignment explanation
Indices: 178359--178394 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
178349 TGAATTTCTA
178359 TCCAATTTATACCCTAAT
1 TCCAATTTATACCCTAAT
*
178377 TCCAATTTA-ATCCTAAT
1 TCCAATTTATACCCTAAT
178394 T
1 T
178395 AATTCATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCAATTTATACCCTAAT
Found at i:178859 original size:21 final size:21
Alignment explanation
Indices: 178820--178859 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
178810 ATTCTATTCC
* * *
178820 TTCTTTTGTTTCTTTTTTTTT
1 TTCTTTTCTTTATTCTTTTTT
178841 TTCTTTTCTTTATTCTTTT
1 TTCTTTTCTTTATTCTTTT
178860 ATATTATATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.03, C:0.12, G:0.03, T:0.82
Consensus pattern (21 bp):
TTCTTTTCTTTATTCTTTTTT
Found at i:182068 original size:10 final size:11
Alignment explanation
Indices: 182049--182090 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
182039 TTTAAAATAT
*
182049 AAATTTTTTTA
1 AAATTATTTTA
182060 AAA-TATTTTA
1 AAATTATTTTA
*
182070 AAATTAATTTA
1 AAATTATTTTA
182081 AAATTATTTT
1 AAATTATTTT
182091 TTAAATATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
AAATTATTTTA
Found at i:182074 original size:21 final size:21
Alignment explanation
Indices: 182016--182090 Score: 61
Period size: 22 Copynumber: 3.7 Consensus size: 21
182006 CAGCAAATGA
*
182016 TTTTAAAAT-TATTAAAATTATT
1 TTTTAAAATATTTTAAAA-T-TT
182038 TTTTAAAATA---T-AAATTT
1 TTTTAAAATATTTTAAAATTT
*
182055 TTTTAAAATATTTTAAAATTA
1 TTTTAAAATATTTTAAAATTT
*
182076 ATTTAAAATTATTTT
1 TTTTAAAA-TATTTT
182091 TTAAATATAA
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
17 12 0.27
18 1 0.02
19 3 0.07
20 2 0.04
21 12 0.27
22 15 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTTAAAATATTTTAAAATTT
Found at i:183247 original size:16 final size:16
Alignment explanation
Indices: 183188--183248 Score: 54
Period size: 17 Copynumber: 3.8 Consensus size: 16
183178 AAAGATAAGA
* *
183188 TTAAAATTATTTAATAA
1 TTAAAATAATTTAAT-T
*
183205 TTATAATAATTTTATATT
1 TTAAAATAA-TTTA-ATT
183223 TT-AAA-AATTTAATT
1 TTAAAATAATTTAATT
183237 TTAAAATAATTT
1 TTAAAATAATTT
183249 TAAATCGTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
14 5 0.14
15 7 0.19
16 7 0.19
17 9 0.25
18 6 0.17
19 2 0.06
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAAAATAATTTAATT
Found at i:191403 original size:39 final size:39
Alignment explanation
Indices: 191360--191456 Score: 140
Period size: 44 Copynumber: 2.4 Consensus size: 39
191350 TGCAATGAGT
*
191360 TCGAGACCTCAAGGAGCATTGCCAAGAAACACGAAAAAC
1 TCGAGATCTCAAGGAGCATTGCCAAGAAACACGAAAAAC
191399 TCGAGATCTCAAGGGAAGGAGCATTGCCAAGAAACACGAAAAAC
1 TCGAGATCTC-----AAGGAGCATTGCCAAGAAACACGAAAAAC
191443 TCGAGATCTCAAGG
1 TCGAGATCTCAAGG
191457 GAAGGAGCAT
Statistics
Matches: 52, Mismatches: 1, Indels: 10
0.83 0.02 0.16
Matches are distributed among these distances:
39 13 0.25
44 39 0.75
ACGTcount: A:0.41, C:0.23, G:0.24, T:0.12
Consensus pattern (39 bp):
TCGAGATCTCAAGGAGCATTGCCAAGAAACACGAAAAAC
Found at i:191433 original size:44 final size:44
Alignment explanation
Indices: 191370--191467 Score: 196
Period size: 44 Copynumber: 2.2 Consensus size: 44
191360 TCGAGACCTC
191370 AAGGAGCATTGCCAAGAAACACGAAAAACTCGAGATCTCAAGGG
1 AAGGAGCATTGCCAAGAAACACGAAAAACTCGAGATCTCAAGGG
191414 AAGGAGCATTGCCAAGAAACACGAAAAACTCGAGATCTCAAGGG
1 AAGGAGCATTGCCAAGAAACACGAAAAACTCGAGATCTCAAGGG
191458 AAGGAGCATT
1 AAGGAGCATT
191468 ACAAAGCTAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 54 1.00
ACGTcount: A:0.43, C:0.19, G:0.26, T:0.12
Consensus pattern (44 bp):
AAGGAGCATTGCCAAGAAACACGAAAAACTCGAGATCTCAAGGG
Found at i:192592 original size:115 final size:114
Alignment explanation
Indices: 192389--192618 Score: 442
Period size: 115 Copynumber: 2.0 Consensus size: 114
192379 GAGCAAAAGT
*
192389 GGAGATGGAGAGTTGTGCTATTTTACACTGCAGAGAGAGGACAGTTAGTCTGCATCCAATAAATG
1 GGAGATGGAGAGTTGTGCTATTTTACACTGCAGAGAGAGGACAGTCAGTCTGCATCCAATAAATG
192454 TGTCCACTCAGATTGCCCTTTTTAAATCGATCCAACGGTTAGGGGATAG
66 TGTCCACTCAGATTGCCCTTTTTAAATCGATCCAACGGTTAGGGGATAG
192503 GNGAGATGGAGAGTTGTGCTATTTTACACTGCAGAGAGAGGACAGTCAGTCTGCATCCAATAAAT
1 G-GAGATGGAGAGTTGTGCTATTTTACACTGCAGAGAGAGGACAGTCAGTCTGCATCCAATAAAT
192568 GTGTCCACTCAGATTGCCCTTTTTAAATCGATCCAACGGTTAGGGGATAG
65 GTGTCCACTCAGATTGCCCTTTTTAAATCGATCCAACGGTTAGGGGATAG
192618 G
1 G
192619 TGCTTGAAAT
Statistics
Matches: 114, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
114 1 0.01
115 113 0.99
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (114 bp):
GGAGATGGAGAGTTGTGCTATTTTACACTGCAGAGAGAGGACAGTCAGTCTGCATCCAATAAATG
TGTCCACTCAGATTGCCCTTTTTAAATCGATCCAACGGTTAGGGGATAG
Found at i:199436 original size:22 final size:22
Alignment explanation
Indices: 199408--199463 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
199398 CTAACATTCT
199408 CCGGCTGTACAAGTTGGTTATA
1 CCGGCTGTACAAGTTGGTTATA
199430 CCGGCTGTACAAGTTGGTTATA
1 CCGGCTGTACAAGTTGGTTATA
*
199452 CCAGCTGTACAA
1 CCGGCTGTACAA
199464 CTCATACATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (22 bp):
CCGGCTGTACAAGTTGGTTATA
Found at i:214208 original size:50 final size:50
Alignment explanation
Indices: 214102--214244 Score: 146
Period size: 50 Copynumber: 2.8 Consensus size: 50
214092 CAAAAATTTA
* * * * *
214102 GCTCATACAAGCCCAGACAAAATATCGCTCTTACGAGTCAATTAGAACATC
1 GCTCTTACAAG-CCAGATAGAATATCTCTCTTACGAGTCAATCAGAACATC
* ** * *
214153 TCTCTTATGAGCTAGATAGATTATCTCTCTTACGAGTCAGA-CAGAACATC
1 GCTCTTACAAGCCAGATAGAATATCTCTCTTACGAGTCA-ATCAGAACATC
*
214203 GCTCTTACAAGCCAGATAGAATAT-TGCTCTTACGAGCCAATC
1 GCTCTTACAAGCCAGATAGAATATCT-CTCTTACGAGTCAATC
214245 TTCAGTAAAT
Statistics
Matches: 73, Mismatches: 16, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
49 2 0.03
50 63 0.86
51 8 0.11
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (50 bp):
GCTCTTACAAGCCAGATAGAATATCTCTCTTACGAGTCAATCAGAACATC
Found at i:214240 original size:25 final size:25
Alignment explanation
Indices: 214122--214241 Score: 93
Period size: 25 Copynumber: 4.8 Consensus size: 25
214112 GCCCAGACAA
* *
214122 AATATCGCTCTTACGAGTCA-ATTAG
1 AATATTGCTCTTACGAGCCAGA-TAG
* * *
214147 AACATCT-CTCTTATGAGCTAGATAG
1 AATAT-TGCTCTTACGAGCCAGATAG
* * *
214172 ATTATCT-CTCTTACGAGTCAGACAG
1 AATAT-TGCTCTTACGAGCCAGATAG
* * *
214197 AACATCGCTCTTACAAGCCAGATAG
1 AATATTGCTCTTACGAGCCAGATAG
214222 AATATTGCTCTTACGAGCCA
1 AATATTGCTCTTACGAGCCA
214242 ATCTTCAGTA
Statistics
Matches: 72, Mismatches: 20, Indels: 6
0.73 0.20 0.06
Matches are distributed among these distances:
25 71 0.99
26 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (25 bp):
AATATTGCTCTTACGAGCCAGATAG
Found at i:221501 original size:5 final size:5
Alignment explanation
Indices: 221485--221523 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
221475 TTGGTCTTAA
* *
221485 AAAAG GAAAG AACAG AAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
221524 TATCCTCACA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.77, C:0.03, G:0.21, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:245438 original size:28 final size:28
Alignment explanation
Indices: 245406--245487 Score: 119
Period size: 28 Copynumber: 2.9 Consensus size: 28
245396 GAGGTGGAAG
**
245406 ATGTGACCATTTTTTTCAATTATGTGAT
1 ATGTGACCATTTTTGACAATTATGTGAT
* *
245434 ATGTGATCATTTTTGGCAATTATGTGAT
1 ATGTGACCATTTTTGACAATTATGTGAT
*
245462 ATGTGACCATTTATGACAATTATGTG
1 ATGTGACCATTTTTGACAATTATGTG
245488 GCAATTTATC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 48 1.00
ACGTcount: A:0.27, C:0.10, G:0.18, T:0.45
Consensus pattern (28 bp):
ATGTGACCATTTTTGACAATTATGTGAT
Found at i:246721 original size:76 final size:76
Alignment explanation
Indices: 246595--246745 Score: 293
Period size: 76 Copynumber: 2.0 Consensus size: 76
246585 CAACTATCGT
*
246595 ACGTATGACCTTGAATTAGTTGTTATGGTCTTTACCCTTAAGATCTGAAGAGACTATCTCTATAA
1 ACGTATGACCTTGAATTAGTTGTTATGGTCTTTACCCATAAGATCTGAAGAGACTATCTCTATAA
246660 GAGAAGTGTAA
66 GAGAAGTGTAA
246671 ACGTATGACCTTGAATTAGTTGTTATGGTCTTTACCCATAAGATCTGAAGAGACTATCTCTATAA
1 ACGTATGACCTTGAATTAGTTGTTATGGTCTTTACCCATAAGATCTGAAGAGACTATCTCTATAA
246736 GAGAAGTGTA
66 GAGAAGTGTA
246746 CTATCTTCAC
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 74 1.00
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.34
Consensus pattern (76 bp):
ACGTATGACCTTGAATTAGTTGTTATGGTCTTTACCCATAAGATCTGAAGAGACTATCTCTATAA
GAGAAGTGTAA
Found at i:249605 original size:18 final size:17
Alignment explanation
Indices: 249571--249618 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
249561 AACTAAGTTA
*
249571 ACAAAAT-AATGCGATG
1 ACAAAATAAATGCAATG
249587 ACAAAATAAAATGCAATG
1 ACAAAAT-AAATGCAATG
* *
249605 ATAATATAAATGCA
1 ACAAAATAAATGCA
249619 TTAAAACTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 7 0.26
17 7 0.26
18 13 0.48
ACGTcount: A:0.56, C:0.10, G:0.12, T:0.21
Consensus pattern (17 bp):
ACAAAATAAATGCAATG
Found at i:260700 original size:14 final size:14
Alignment explanation
Indices: 260662--260703 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
260652 CGTGGAAGCC
*
260662 TCTCCTCTTCTCTT
1 TCTCCTCTTTTCTT
* *
260676 TTTCTTC-TTTCTT
1 TCTCCTCTTTTCTT
260689 TCTCCTCTTTTCTT
1 TCTCCTCTTTTCTT
260703 T
1 T
260704 TATTTATCTT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (14 bp):
TCTCCTCTTTTCTT
Found at i:260721 original size:29 final size:26
Alignment explanation
Indices: 260660--260722 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
260650 GTCGTGGAAG
260660 CCTCTCCTCTTCTCTTTTTCTTCTTT
1 CCTCTCCTCTTCTCTTTTTCTTCTTT
* * *
260686 CTTTCTCCTCTTTTCTTTTATTTATCTTCT
1 C-CTCTCCTCTTCTCTTTT-TCT-TCTT-T
260716 CCTCTCC
1 CCTCTCC
260723 CCTAACCTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
26 1 0.03
27 15 0.52
28 2 0.07
29 9 0.31
30 2 0.07
ACGTcount: A:0.03, C:0.37, G:0.00, T:0.60
Consensus pattern (26 bp):
CCTCTCCTCTTCTCTTTTTCTTCTTT
Found at i:261127 original size:13 final size:12
Alignment explanation
Indices: 261104--261135 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
261094 GGTTTTACAT
261104 AAAATAAAAGAG
1 AAAATAAAAGAG
261116 AAAATAAAA-AG
1 AAAATAAAAGAG
261127 -AAATAAAAG
1 AAAATAAAAG
261136 CAAGGTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 8 0.42
11 2 0.11
12 9 0.47
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.09
Consensus pattern (12 bp):
AAAATAAAAGAG
Done.