Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004867.1 Kokia drynarioides strain JFW-HI SEQ_118535, 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: 63157
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Warning! 20 characters in sequence are not A, C, G, or T
Found at i:1538 original size:29 final size:29
Alignment explanation
Indices: 1479--1539 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
1469 TTCAAATTAT
*
1479 TTAAATAATAAAAAATAATGTTATTTCAA
1 TTAAATAATAAAAAATAATATTATTTCAA
*
1508 TTAAATAATAATTTAAATAATATT-TTT-AA
1 TTAAATAATAA--AAAATAATATTATTTCAA
1537 TTA
1 TTA
1540 TTTGTCTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 16 0.57
30 3 0.11
31 9 0.32
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (29 bp):
TTAAATAATAAAAAATAATATTATTTCAA
Found at i:7961 original size:30 final size:30
Alignment explanation
Indices: 7904--7961 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
7894 TTCATATTTT
* *
7904 AATTTTTTTTTATAAATTTTAGAATTTTCA
1 AATTATTTTTTATAAATTTTAAAATTTTCA
*
7934 AATTATTTTTTAT-ATTTTTAAAGATTTT
1 AATTATTTTTTATAAATTTTAAA-ATTTT
7962 TAGTGTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 7 0.29
30 17 0.71
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (30 bp):
AATTATTTTTTATAAATTTTAAAATTTTCA
Found at i:10829 original size:29 final size:29
Alignment explanation
Indices: 10796--10855 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
10786 GTAACGTAGT
10796 ATATAAAATTGCCTCGAAAGCAATAGTGA
1 ATATAAAATTGCCTCGAAAGCAATAGTGA
*
10825 ATATAAAATTGCCTCGAAAGCAGTAGTGA
1 ATATAAAATTGCCTCGAAAGCAATAGTGA
10854 AT
1 AT
10856 CGATTTCAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.43, C:0.13, G:0.18, T:0.25
Consensus pattern (29 bp):
ATATAAAATTGCCTCGAAAGCAATAGTGA
Found at i:12257 original size:109 final size:108
Alignment explanation
Indices: 12116--12322 Score: 317
Period size: 109 Copynumber: 1.9 Consensus size: 108
12106 ACACTTGTCA
* * *
12116 ATTTTAAATTGAATATTCAATTACTTAGGTTCAAAGAAAAATCATACCCA-ATACGTTAGGGCAC
1 ATTTTAAATAGAATATTCAATTACTTAAGTTCAAAGAAAAACCATACCCACATA--TTAGGGCAC
*
12180 AATTTCTCGAGTTCCCTAAAATAATAGAACATTAAACATTTATCG
64 AATTTCTCGAGTTCCCTAAAATAAAAGAACATTAAACATTTATCG
* *
12225 ATTTTAAATAGGATATTCAATTACTTAAGTTCAAAGAAAAACCATACTCAGCATATTAGGGCACA
1 ATTTTAAATAGAATATTCAATTACTTAAGTTCAAAGAAAAACCATACCCA-CATATTAGGGCACA
*
12290 ATTTCTCGAGTTCCCTAAAATAAAATAACATTA
65 ATTTCTCGAGTTCCCTAAAATAAAAGAACATTA
12323 CCTTGATTTT
Statistics
Matches: 89, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
109 86 0.97
111 3 0.03
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.31
Consensus pattern (108 bp):
ATTTTAAATAGAATATTCAATTACTTAAGTTCAAAGAAAAACCATACCCACATATTAGGGCACAA
TTTCTCGAGTTCCCTAAAATAAAAGAACATTAAACATTTATCG
Found at i:12945 original size:28 final size:27
Alignment explanation
Indices: 12889--12954 Score: 64
Period size: 27 Copynumber: 2.4 Consensus size: 27
12879 AAATGAAATA
* *
12889 AAATAGATAAAATGCCAAGATAAATAAC
1 AAATA-ATAAAATACCAAGATAAACAAC
*
12917 AAATAATAAAATACCAA-ATAGAC-AC
1 AAATAATAAAATACCAAGATAAACAAC
12942 AACATAAATAAAA
1 AA-AT-AATAAAA
12955 GGATAATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
25 4 0.12
26 6 0.18
27 18 0.55
28 5 0.15
ACGTcount: A:0.65, C:0.12, G:0.06, T:0.17
Consensus pattern (27 bp):
AAATAATAAAATACCAAGATAAACAAC
Found at i:14420 original size:17 final size:20
Alignment explanation
Indices: 14384--14421 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
14374 TGGGTAGCTT
14384 AGGTTTTAGTGGGTCATTTA
1 AGGTTTTAGTGGGTCATTTA
14404 AGGTTTT-G-GGGTC-TTTA
1 AGGTTTTAGTGGGTCATTTA
14421 A
1 A
14422 TCTTTGCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.28
18 5 0.28
19 1 0.06
20 7 0.39
ACGTcount: A:0.18, C:0.05, G:0.32, T:0.45
Consensus pattern (20 bp):
AGGTTTTAGTGGGTCATTTA
Found at i:15128 original size:17 final size:18
Alignment explanation
Indices: 15096--15129 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
15086 AAAAAGTAAC
*
15096 CACAAATCATGTTGCAAA
1 CACAAATCATGATGCAAA
15114 CACAAA-CATGATGCAA
1 CACAAATCATGATGCAA
15130 TGCACCCAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.47, C:0.24, G:0.12, T:0.18
Consensus pattern (18 bp):
CACAAATCATGATGCAAA
Found at i:15427 original size:22 final size:22
Alignment explanation
Indices: 15408--15456 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
15398 ATGCTCAAAG
*
15408 TAAATGCATGACATGGTCAACA
1 TAAATGAATGACATGGTCAACA
*
15430 TAAATTAATGACATGGTCAACA
1 TAAATGAATGACATGGTCAACA
15452 TAAAT
1 TAAAT
15457 TACTCAACTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.27
Consensus pattern (22 bp):
TAAATGAATGACATGGTCAACA
Found at i:15457 original size:22 final size:22
Alignment explanation
Indices: 15415--15458 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
15405 AAGTAAATGC
15415 ATGACATGGTCAACATAAATTA
1 ATGACATGGTCAACATAAATTA
15437 ATGACATGGTCAACATAAATTA
1 ATGACATGGTCAACATAAATTA
15459 CTCAACTCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.27
Consensus pattern (22 bp):
ATGACATGGTCAACATAAATTA
Found at i:16011 original size:7 final size:7
Alignment explanation
Indices: 15999--16037 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
15989 TTCAGAAAAA
15999 GTCAACG
1 GTCAACG
16006 GTCAACG
1 GTCAACG
*
16013 GTCAACA
1 GTCAACG
*
16020 GTCAACA
1 GTCAACG
*
16027 GTTAACG
1 GTCAACG
16034 GTCA
1 GTCA
16038 GTCAACAGCC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.18
Consensus pattern (7 bp):
GTCAACG
Found at i:16024 original size:21 final size:21
Alignment explanation
Indices: 15998--16037 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
15988 TTTCAGAAAA
*
15998 AGTCAACGGTCAACGGTCAAC
1 AGTCAACAGTCAACGGTCAAC
*
16019 AGTCAACAGTTAACGGTCA
1 AGTCAACAGTCAACGGTCA
16038 GTCAACAGCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.25, G:0.23, T:0.17
Consensus pattern (21 bp):
AGTCAACAGTCAACGGTCAAC
Found at i:16098 original size:15 final size:16
Alignment explanation
Indices: 16080--16114 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
16070 GGGTTTGGAG
16080 TTGGTTC-CTTTGGGT
1 TTGGTTCACTTTGGGT
16095 TTGGTTCACTTTGGGT
1 TTGGTTCACTTTGGGT
16111 TTGG
1 TTGG
16115 GTTATTGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.03, C:0.11, G:0.34, T:0.51
Consensus pattern (16 bp):
TTGGTTCACTTTGGGT
Found at i:19552 original size:22 final size:22
Alignment explanation
Indices: 19524--19569 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
19514 CCTAAACACA
19524 AATATCTTATATTAGTAATCCC
1 AATATCTTATATTAGTAATCCC
19546 AATATCTTATATTAGTAATCCC
1 AATATCTTATATTAGTAATCCC
19568 AA
1 AA
19570 ATTAAAACTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.39, C:0.17, G:0.04, T:0.39
Consensus pattern (22 bp):
AATATCTTATATTAGTAATCCC
Found at i:19775 original size:22 final size:21
Alignment explanation
Indices: 19750--19816 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 21
19740 TTAAAGTCAA
*
19750 TGGTCAGCGGTCAGTCAACGGT
1 TGGTCAACGGTC-GTCAACGGT
* *
19772 TGGTCAAAGGTCGATCAACGAT
1 TGGTCAACGGTCG-TCAACGGT
*
19794 TGGTCAACGGTCGGTTAACGGT
1 TGGTCAACGGTC-GTCAACGGT
19816 T
1 T
19817 TGACTTCGTT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
21 1 0.03
22 35 0.95
23 1 0.03
ACGTcount: A:0.22, C:0.19, G:0.33, T:0.25
Consensus pattern (21 bp):
TGGTCAACGGTCGTCAACGGT
Found at i:19777 original size:11 final size:11
Alignment explanation
Indices: 19763--19816 Score: 54
Period size: 11 Copynumber: 4.9 Consensus size: 11
19753 TCAGCGGTCA
19763 GTCAACGGTTG
1 GTCAACGGTTG
* *
19774 GTCAAAGGTCG
1 GTCAACGGTTG
* *
19785 ATCAACGATTG
1 GTCAACGGTTG
*
19796 GTCAACGGTCG
1 GTCAACGGTTG
*
19807 GTTAACGGTT
1 GTCAACGGTT
19817 TGACTTCGTT
Statistics
Matches: 32, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
11 32 1.00
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (11 bp):
GTCAACGGTTG
Found at i:19858 original size:15 final size:16
Alignment explanation
Indices: 19838--19872 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
19828 GGGTTTAGAC
19838 TTGGTTCA-ATTGGGT
1 TTGGTTCACATTGGGT
*
19853 TTGGTTCACTTTGGGT
1 TTGGTTCACATTGGGT
19869 TTGG
1 TTGG
19873 GTTATTGGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.09, C:0.09, G:0.34, T:0.49
Consensus pattern (16 bp):
TTGGTTCACATTGGGT
Found at i:23731 original size:26 final size:26
Alignment explanation
Indices: 23695--23769 Score: 114
Period size: 26 Copynumber: 2.9 Consensus size: 26
23685 CATAAGAGCG
* *
23695 ATACTACACTGGCTCGTAAGAGCAAT
1 ATACTACACTGACTCGTAAGAGCAAC
23721 ATACTACACTGACTCGTAAGAGCAAC
1 ATACTACACTGACTCGTAAGAGCAAC
* *
23747 ATACTATACTGACTCATAAGAGC
1 ATACTACACTGACTCGTAAGAGC
23770 GATTTATTGA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 45 1.00
ACGTcount: A:0.37, C:0.24, G:0.16, T:0.23
Consensus pattern (26 bp):
ATACTACACTGACTCGTAAGAGCAAC
Found at i:29308 original size:52 final size:52
Alignment explanation
Indices: 29225--29461 Score: 291
Period size: 52 Copynumber: 4.6 Consensus size: 52
29215 TGAAAAAGGA
* * *
29225 TCCGCTGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGAGG
1 TCCGATGACTATATGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGG
* *
29277 TCCGATGACTATATGTCATCGTGAGTATATGAATCTTTTATGGATTATGAGG
1 TCCGATGACTATATGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGG
* * * * *
29329 TCCAATGACTATATGTTATCGCGAATATATGAATCCTTTATGGATTATGAGG
1 TCCGATGACTATATGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGG
** *
29381 TCCGATGACTATGA-GTCATCGTGAGTATAT-AATTCCGAATACGGATTA-AAGG
1 TCCGATGACTAT-ATGTCATCGTGAGTATATGAA-TCC-TTTACGGATTATGAGG
* *
29433 TCCGATGACTTTGTGTCATCGTGAGTATA
1 TCCGATGACTATATGTCATCGTGAGTATA
29462 AAAAAATGCA
Statistics
Matches: 161, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
51 2 0.01
52 150 0.93
53 9 0.06
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (52 bp):
TCCGATGACTATATGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGG
Found at i:32113 original size:52 final size:52
Alignment explanation
Indices: 32032--32257 Score: 303
Period size: 52 Copynumber: 4.4 Consensus size: 52
32022 ATTTTATTTA
** * *
32032 ATACTCACAATGACACATAGTCATGGGACCTCTTAATCCGTAAAGGAATCAT
1 ATACTCATGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGAATCAT
*
32084 ATACTCATGATGACACATAATCATCGGACCTCATAATCCGTAAAGG-ATCAT
1 ATACTCATGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGAATCAT
* * * *
32135 ATACTCACGATGACACATAGTTATCAGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCATGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGAATCAT
* * *
32187 A-AGCTCATGATGACACATAGTCATCGAACCTCTTAATCCGTAAAGGATTCAT
1 ATA-CTCATGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGAATCAT
* *
32239 ATATTAATGATGACACATA
1 ATACTCATGATGACACATA
32258 ATTATCAGAC
Statistics
Matches: 154, Mismatches: 17, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
51 48 0.31
52 105 0.68
53 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (52 bp):
ATACTCATGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGAATCAT
Found at i:32211 original size:103 final size:104
Alignment explanation
Indices: 32032--32269 Score: 336
Period size: 103 Copynumber: 2.3 Consensus size: 104
32022 ATTTTATTTA
* * ** *
32032 ATACTCACAATGACACATAGTCATGGGACCTCTTAATCCGTAAAGGAATCATATACTCATGATGA
1 ATACTCACGATGACACATAGTTATCAGACCTCATAATCCGTAAAGGAATCATATACTCATGATGA
*
32097 CACATAATCATCGGACCTCATAATCCGTAAAGGA-TCAT
66 CACATAATCATCGAACCTCATAATCCGTAAAGGATTCAT
*
32135 ATACTCACGATGACACATAGTTATCAGACCTCATAATCCGTAAAGGATTCATA-AGCTCATGATG
1 ATACTCACGATGACACATAGTTATCAGACCTCATAATCCGTAAAGGAATCATATA-CTCATGATG
* *
32199 ACACATAGTCATCGAACCTCTTAATCCGTAAAGGATTCAT
65 ACACATAATCATCGAACCTCATAATCCGTAAAGGATTCAT
* * * *
32239 ATATTAATGATGACACATAATTATCAGACCT
1 ATACTCACGATGACACATAGTTATCAGACCT
32270 TTTTCATTTA
Statistics
Matches: 120, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
102 1 0.01
103 88 0.73
104 31 0.26
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (104 bp):
ATACTCACGATGACACATAGTTATCAGACCTCATAATCCGTAAAGGAATCATATACTCATGATGA
CACATAATCATCGAACCTCATAATCCGTAAAGGATTCAT
Found at i:37309 original size:21 final size:21
Alignment explanation
Indices: 37282--37328 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
37272 GATTTATGTA
37282 ATTTGGATTTATAAACTTTAT
1 ATTTGGATTTATAAACTTTAT
* *
37303 GTTTGGATTTCTAAACTTTAT
1 ATTTGGATTTATAAACTTTAT
37324 ATTTG
1 ATTTG
37329 AATTATGCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.28, C:0.06, G:0.13, T:0.53
Consensus pattern (21 bp):
ATTTGGATTTATAAACTTTAT
Found at i:37858 original size:31 final size:29
Alignment explanation
Indices: 37818--37887 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
37808 ATATGAAAGT
*
37818 TATATATGAACTATGGTTTAATGTGCAATTG
1 TATACATGAACTATGGTTT--TGTGCAATTG
* * * *
37849 TATACATGAATTTTGGTTTTGTGTAATTT
1 TATACATGAACTATGGTTTTGTGCAATTG
37878 TATACATGAA
1 TATACATGAA
37888 ATTTTGATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 18 0.53
31 16 0.47
ACGTcount: A:0.31, C:0.06, G:0.17, T:0.46
Consensus pattern (29 bp):
TATACATGAACTATGGTTTTGTGCAATTG
Found at i:37898 original size:29 final size:29
Alignment explanation
Indices: 37839--37898 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
37829 TATGGTTTAA
*
37839 TGTGCAATTGTATACATGAATTTTGGTTT
1 TGTGCAATTGTATACATGAATTTTGGATT
* *
37868 TGTGTAATTTTATACATGAAATTTT-GATT
1 TGTGCAATTGTATACATG-AATTTTGGATT
37897 TG
1 TG
37899 ATCCAATTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 21 0.78
30 6 0.22
ACGTcount: A:0.27, C:0.05, G:0.18, T:0.50
Consensus pattern (29 bp):
TGTGCAATTGTATACATGAATTTTGGATT
Found at i:42969 original size:57 final size:57
Alignment explanation
Indices: 42906--43019 Score: 219
Period size: 57 Copynumber: 2.0 Consensus size: 57
42896 TGATCTCCTA
42906 AAATATTTAGAGATAAAAATTAATTAGTTTATCTTCACAACTTAACAAACATTGAAT
1 AAATATTTAGAGATAAAAATTAATTAGTTTATCTTCACAACTTAACAAACATTGAAT
*
42963 AAATATTTAGAGATAAAAATTAATTAGTTTATCTTCACAACTTAATAAACATTGAAT
1 AAATATTTAGAGATAAAAATTAATTAGTTTATCTTCACAACTTAACAAACATTGAAT
43020 TCTTAGTAAT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.36
Consensus pattern (57 bp):
AAATATTTAGAGATAAAAATTAATTAGTTTATCTTCACAACTTAACAAACATTGAAT
Found at i:46901 original size:31 final size:33
Alignment explanation
Indices: 46863--46927 Score: 89
Period size: 31 Copynumber: 2.0 Consensus size: 33
46853 CTCATAAAAA
*
46863 TTTTAAAAATTTTAATTAAA-TC-CAATTTTTT
1 TTTTAAAAATTCTAATTAAACTCTCAATTTTTT
* *
46894 TTTTAAAAATTCTCATTAAACTCTTAATTTTTT
1 TTTTAAAAATTCTAATTAAACTCTCAATTTTTT
46927 T
1 T
46928 AAAAATTACT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 18 0.62
32 2 0.07
33 9 0.31
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.55
Consensus pattern (33 bp):
TTTTAAAAATTCTAATTAAACTCTCAATTTTTT
Found at i:47140 original size:19 final size:18
Alignment explanation
Indices: 47096--47143 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
47086 ATTAAATATA
* *
47096 TATAAAAATATATAATAT
1 TATAATAATATATAAAAT
*
47114 TTTAATAATATACTAAAAT
1 TATAATAATATA-TAAAAT
47133 TATAATAATAT
1 TATAATAATAT
47144 GTAATAACAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (18 bp):
TATAATAATATATAAAAT
Found at i:47837 original size:71 final size:72
Alignment explanation
Indices: 47700--47843 Score: 182
Period size: 71 Copynumber: 2.0 Consensus size: 72
47690 TGAAACTTTC
** * * * * * *
47700 CAAGTCAGTAGCTAAAGGTTTCTTTCTCCTGTACATTCTATCGATATTTCATTGAGTTGTTCCGA
1 CAAGTCAGTAGCTAAAGCATTCCTTCCCCCGTACATTCTATCAATACTTCATAGAGTTGTTCCGA
47765 AACAACT
66 AACAACT
* * *
47772 CAAGTCAGTAGCTGAAGCATTCCTTCCCCCGTAC-TTCTATCAATACTTCCTAGAGTTGTTTCGA
1 CAAGTCAGTAGCTAAAGCATTCCTTCCCCCGTACATTCTATCAATACTTCATAGAGTTGTTCCGA
47836 AACAACT
66 AACAACT
47843 C
1 C
47844 GAGTTAATAT
Statistics
Matches: 61, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
71 33 0.54
72 28 0.46
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (72 bp):
CAAGTCAGTAGCTAAAGCATTCCTTCCCCCGTACATTCTATCAATACTTCATAGAGTTGTTCCGA
AACAACT
Found at i:48435 original size:24 final size:24
Alignment explanation
Indices: 48386--48472 Score: 102
Period size: 24 Copynumber: 3.6 Consensus size: 24
48376 TCAGAGAGCG
* * *
48386 TACATTTATGCTTGTCAATCATTA
1 TACATTTATGCTCGTCAGTCACTA
*
48410 TACATTTATGCTCGTCAGCCACTA
1 TACATTTATGCTCGTCAGTCACTA
* * *
48434 TACGTTTATGTTCATCAGTCACTA
1 TACATTTATGCTCGTCAGTCACTA
*
48458 TACGTTTATGCTCGT
1 TACATTTATGCTCGT
48473 GTATTTTAGT
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.24, C:0.22, G:0.13, T:0.41
Consensus pattern (24 bp):
TACATTTATGCTCGTCAGTCACTA
Found at i:48728 original size:10 final size:10
Alignment explanation
Indices: 48699--48728 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
48689 TGAGGAGATT
*
48699 CTCAAAATCT
1 CTCAAAATCA
48709 CTCAAAATCA
1 CTCAAAATCA
48719 CTCAAAATCA
1 CTCAAAATCA
48729 TTGGCCTTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (10 bp):
CTCAAAATCA
Found at i:53378 original size:60 final size:60
Alignment explanation
Indices: 53282--53394 Score: 174
Period size: 60 Copynumber: 1.9 Consensus size: 60
53272 TTAAAAAAAA
* *
53282 AAAAAAAGCTTAGGTACCAAATTAGGAAAATATGTCAAGTTCAGGTACCAAATTGGGTCC
1 AAAAAAAGCTTAGGTACCAAATTAAGAAAATATGTCAAGTTCAAGTACCAAATTGGGTCC
* *
53342 AAAAAAAGTTTAGGTACCAAGTTAAGAAAA-AGTGTCAAGTTCAAGTACCAAAT
1 AAAAAAAGCTTAGGTACCAAATTAAGAAAATA-TGTCAAGTTCAAGTACCAAAT
53395 GTTATATTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
59 1 0.02
60 47 0.98
ACGTcount: A:0.45, C:0.13, G:0.19, T:0.23
Consensus pattern (60 bp):
AAAAAAAGCTTAGGTACCAAATTAAGAAAATATGTCAAGTTCAAGTACCAAATTGGGTCC
Found at i:54331 original size:12 final size:12
Alignment explanation
Indices: 54314--54340 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
54304 ATTCAGCCAA
54314 CAATTGCACCAT
1 CAATTGCACCAT
54326 CAATTGCACCAT
1 CAATTGCACCAT
54338 CAA
1 CAA
54341 AATGAGAGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.33, G:0.07, T:0.22
Consensus pattern (12 bp):
CAATTGCACCAT
Found at i:56145 original size:26 final size:26
Alignment explanation
Indices: 56116--56271 Score: 115
Period size: 25 Copynumber: 6.2 Consensus size: 26
56106 AGCTCATATA
*
56116 AGCCTAGACAGAGT-TTAACTCTTACG
1 AGCCTAGACAGAATATT-ACTCTTACG
*
56142 AGCCTAGACAGAATATTGCTCTTACG
1 AGCCTAGACAGAATATTACTCTTACG
* ***
56168 AGCC-AGTCAGAATACCGCTCTTACG
1 AGCCTAGACAGAATATTACTCTTACG
* * *
56193 AG-CTAGATAGAATATTGCTCTTATG
1 AGCCTAGACAGAATATTACTCTTACG
* * * *
56218 AGCC-AAATAGAATATTTCTCTTACA
1 AGCCTAGACAGAATATTACTCTTACG
* * * *
56243 AGCC-AAATAGAATATTGCTGTTACG
1 AGCCTAGACAGAATATTACTCTTACG
56268 AGCC
1 AGCC
56272 AGAGTTCAAA
Statistics
Matches: 110, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
24 1 0.01
25 81 0.74
26 26 0.24
27 2 0.02
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.28
Consensus pattern (26 bp):
AGCCTAGACAGAATATTACTCTTACG
Found at i:56187 original size:25 final size:25
Alignment explanation
Indices: 56134--56273 Score: 133
Period size: 25 Copynumber: 5.6 Consensus size: 25
56124 CAGAGTTTAA
*
56134 CTCTTACGAGCCTAGACAGAATATTG
1 CTCTTACGAGCC-AGTCAGAATATTG
**
56160 CTCTTACGAGCCAGTCAGAATACCG
1 CTCTTACGAGCCAGTCAGAATATTG
*
56185 CTCTTACGAGCTAGAT-AGAATATTG
1 CTCTTACGAGCCAG-TCAGAATATTG
* * *
56210 CTCTTATGAGCCAAAT-AGAATATTT
1 CTCTTACGAGCC-AGTCAGAATATTG
* *
56235 CTCTTACAAGCCAAAT-AGAATATTG
1 CTCTTACGAGCC-AGTCAGAATATTG
*
56260 CTGTTACGAGCCAG
1 CTCTTACGAGCCAG
56274 AGTTCAAAAA
Statistics
Matches: 96, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
24 1 0.01
25 81 0.84
26 14 0.15
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (25 bp):
CTCTTACGAGCCAGTCAGAATATTG
Found at i:56210 original size:50 final size:49
Alignment explanation
Indices: 56134--56273 Score: 163
Period size: 50 Copynumber: 2.8 Consensus size: 49
56124 CAGAGTTTAA
*
56134 CTCTTACGAGCCTAGACAGAATATTGCTCTTACGAGCCAGTCAGAATACCG
1 CTCTTACGAG-CTAGATAGAATATTGCTCTTACGAGCCAGT-AGAATACCG
* * ***
56185 CTCTTACGAGCTAGATAGAATATTGCTCTTATGAGCCAAATAGAATATTT
1 CTCTTACGAGCTAGATAGAATATTGCTCTTACGAGCC-AGTAGAATACCG
* * * *
56235 CTCTTACAAGCCAAATAGAATATTGCTGTTACGAGCCAG
1 CTCTTACGAGCTAGATAGAATATTGCTCTTACGAGCCAG
56274 AGTTCAAAAA
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
49 1 0.01
50 63 0.83
51 12 0.16
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (49 bp):
CTCTTACGAGCTAGATAGAATATTGCTCTTACGAGCCAGTAGAATACCG
Found at i:56341 original size:28 final size:28
Alignment explanation
Indices: 56292--56471 Score: 179
Period size: 28 Copynumber: 6.5 Consensus size: 28
56282 AATTTCTCCA
*
56292 CCGAGCCAGAATCAGAATATCGCTCTTT
1 CCGAGCCAGAATCAGAACATCGCTCTTT
* * *
56320 CCGAGCCAAAATTAAAACATCGCTCTTT
1 CCGAGCCAGAATCAGAACATCGCTCTTT
* *
56348 TCGAGCCAGAATCAGAACATCACTCTTT
1 CCGAGCCAGAATCAGAACATCGCTCTTT
* ** **
56376 CCAAGCCAGAATCAGAAGTTCATTC-TT
1 CCGAGCCAGAATCAGAACATCGCTCTTT
*
56403 CCTGGGCCA-AA-CAGAACATCGCTCTTT
1 CC-GAGCCAGAATCAGAACATCGCTCTTT
* **
56430 TCGAGCCAGAATCAGAATTTCGCTC-TT
1 CCGAGCCAGAATCAGAACATCGCTCTTT
56457 CCTGAGCCAGAATCA
1 CC-GAGCCAGAATCA
56472 AAGTAGCTAT
Statistics
Matches: 122, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 14 0.11
27 14 0.11
28 94 0.77
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (28 bp):
CCGAGCCAGAATCAGAACATCGCTCTTT
Found at i:56428 original size:54 final size:54
Alignment explanation
Indices: 56350--56465 Score: 151
Period size: 54 Copynumber: 2.1 Consensus size: 54
56340 CGCTCTTTTC
*
56350 GAGCCAGAATCAGAACATCACTCTTTCCAAGCCAGAATCAGAAGTTCATTCTTCCT
1 GAGCCA-AA-CAGAACATCACTCTTTCCAAGCCAGAATCAGAAGTTCACTCTTCCT
* * * * * *
56406 GGGCCAAACAGAACATCGCTCTTTTCGAGCCAGAATCAGAATTTCGCTCTTCCT
1 GAGCCAAACAGAACATCACTCTTTCCAAGCCAGAATCAGAAGTTCACTCTTCCT
56460 GAGCCA
1 GAGCCA
56466 GAATCAAAGT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
54 45 0.87
55 2 0.04
56 5 0.10
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.24
Consensus pattern (54 bp):
GAGCCAAACAGAACATCACTCTTTCCAAGCCAGAATCAGAAGTTCACTCTTCCT
Found at i:56826 original size:12 final size:12
Alignment explanation
Indices: 56809--56833 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
56799 TTAAAATCAT
56809 CCAATATTATAA
1 CCAATATTATAA
56821 CCAATATTATAA
1 CCAATATTATAA
56833 C
1 C
56834 ACTTCAATAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (12 bp):
CCAATATTATAA
Found at i:61351 original size:25 final size:25
Alignment explanation
Indices: 61307--61369 Score: 90
Period size: 25 Copynumber: 2.5 Consensus size: 25
61297 AGTTTAGCTT
*
61307 TTACAAGCCCAGACAGAATATCGCTC
1 TTACAAG-CTAGACAGAATATCGCTC
* *
61333 TTACAAGCTAGACATAATATCTCTC
1 TTACAAGCTAGACAGAATATCGCTC
61358 TTACAAGCTAGA
1 TTACAAGCTAGA
61370 GTTCAAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
25 27 0.79
26 7 0.21
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.25
Consensus pattern (25 bp):
TTACAAGCTAGACAGAATATCGCTC
Found at i:61429 original size:28 final size:28
Alignment explanation
Indices: 61389--61515 Score: 148
Period size: 28 Copynumber: 4.5 Consensus size: 28
61379 ATTTCTCCAC
61389 CGAGCCAAAATCAGAACATCGCTCTTTT
1 CGAGCCAAAATCAGAACATCGCTCTTTT
* *
61417 CGAGCAAAAATCAGAACATCACTCTTTT
1 CGAGCCAAAATCAGAACATCGCTCTTTT
* *
61445 CGAGTCAGAATCAGAACATCGCTC-TTT
1 CGAGCCAAAATCAGAACATCGCTCTTTT
* * * **
61472 CTGAGCCAGAATCAGAACTTAGCTCTTCC
1 C-GAGCCAAAATCAGAACATCGCTCTTTT
*
61501 CGAGCCAGAATCAGA
1 CGAGCCAAAATCAGA
61516 GTAGTTATTA
Statistics
Matches: 86, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
27 4 0.05
28 80 0.93
29 2 0.02
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.23
Consensus pattern (28 bp):
CGAGCCAAAATCAGAACATCGCTCTTTT
Done.