Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015137.1 Kokia drynarioides strain JFW-HI SEQ_130181, 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: 154352
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Warning! 87 characters in sequence are not A, C, G, or T
Found at i:771 original size:13 final size:13
Alignment explanation
Indices: 753--790 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
743 TCTTCTCTAG
753 TGTTTTCTTTAAA
1 TGTTTTCTTTAAA
*
766 TGTTTTCTCTAAA
1 TGTTTTCTTTAAA
779 TGTTTTCTTTAA
1 TGTTTTCTTTAA
791 TGAATCATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.21, C:0.11, G:0.08, T:0.61
Consensus pattern (13 bp):
TGTTTTCTTTAAA
Found at i:1352 original size:17 final size:17
Alignment explanation
Indices: 1322--1355 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1312 GTTTAGACCC
**
1322 TTTAAATTTTTAAAAAT
1 TTTAAATTAATAAAAAT
1339 TTTAAATTAATAAAAAT
1 TTTAAATTAATAAAAAT
1356 AAAATTACAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTAAATTAATAAAAAT
Found at i:11935 original size:46 final size:46
Alignment explanation
Indices: 11868--11959 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
11858 TTAGCTGTTG
11868 GCTATTGCAGCTGAAATCATAGGCCATGTGACCTGTTGTTTAACTT
1 GCTATTGCAGCTGAAATCATAGGCCATGTGACCTGTTGTTTAACTT
11914 GCTATTGCAGCTGAAATCATAGGCCATGTGACCTGTTGTTTAACTT
1 GCTATTGCAGCTGAAATCATAGGCCATGTGACCTGTTGTTTAACTT
11960 ATCTTCTTGG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.35
Consensus pattern (46 bp):
GCTATTGCAGCTGAAATCATAGGCCATGTGACCTGTTGTTTAACTT
Found at i:14972 original size:31 final size:30
Alignment explanation
Indices: 14928--14985 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
14918 TAAAATATTG
* *
14928 TTTTTCAATTTTTAAGGGTCCAAAAAAAAA
1 TTTTTCAACTTTTAAGGATCCAAAAAAAAA
*
14958 TTTTATCAACTTTTAAGGATCTAAAAAA
1 TTTT-TCAACTTTTAAGGATCCAAAAAA
14986 TATTCTCTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 4 0.17
31 20 0.83
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.38
Consensus pattern (30 bp):
TTTTTCAACTTTTAAGGATCCAAAAAAAAA
Found at i:41473 original size:23 final size:23
Alignment explanation
Indices: 41443--41490 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
41433 TTTACTCTTG
41443 TTCTTTCATTTCCTCTAATTTTT
1 TTCTTTCATTTCCTCTAATTTTT
41466 TTCTTTCATTTCCTCTAATTTTT
1 TTCTTTCATTTCCTCTAATTTTT
41489 TT
1 TT
41491 TCCACAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.12, C:0.21, G:0.00, T:0.67
Consensus pattern (23 bp):
TTCTTTCATTTCCTCTAATTTTT
Found at i:42133 original size:15 final size:17
Alignment explanation
Indices: 42102--42136 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
42092 ATAATAATGG
42102 AAAAAAATGAAACAAGA
1 AAAAAAATGAAACAAGA
42119 AAAAAAAT-AAA-AAGA
1 AAAAAAATGAAACAAGA
42134 AAA
1 AAA
42137 TGAAAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
16 3 0.17
17 8 0.44
ACGTcount: A:0.83, C:0.03, G:0.09, T:0.06
Consensus pattern (17 bp):
AAAAAAATGAAACAAGA
Found at i:42760 original size:15 final size:13
Alignment explanation
Indices: 42728--42768 Score: 57
Period size: 14 Copynumber: 3.1 Consensus size: 13
42718 CGAAAAAGGG
42728 AAAAAA-GAGAAA
1 AAAAAATGAGAAA
42740 AAAAAATGATGAAA
1 AAAAAATGA-GAAA
42754 AAGAAAATGAGAAA
1 AA-AAAATGAGAAA
42768 A
1 A
42769 GAGCATATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 6 0.23
13 2 0.08
14 11 0.42
15 7 0.27
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (13 bp):
AAAAAATGAGAAA
Found at i:59180 original size:16 final size:17
Alignment explanation
Indices: 59145--59183 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
59135 GGGTTTAGAG
*
59145 ATAAAATGCTAAACTAAA
1 ATAAAATGC-AAAATAAA
59163 ATAAAATG-AAAATAAA
1 ATAAAATGCAAAATAAA
59179 ATAAA
1 ATAAA
59184 TAAAGTGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
18 8 0.40
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.21
Consensus pattern (17 bp):
ATAAAATGCAAAATAAA
Found at i:60461 original size:11 final size:12
Alignment explanation
Indices: 60445--60474 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
60435 TTATATATAC
60445 ATTTTTTCTTG-
1 ATTTTTTCTTGT
60456 ATTTTTTCTTGT
1 ATTTTTTCTTGT
60468 ATTTTTT
1 ATTTTTT
60475 ATTTACACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.10, C:0.07, G:0.07, T:0.77
Consensus pattern (12 bp):
ATTTTTTCTTGT
Found at i:60736 original size:128 final size:128
Alignment explanation
Indices: 60501--60814 Score: 475
Period size: 128 Copynumber: 2.4 Consensus size: 128
60491 AGACCTAATC
* * *
60501 AATTCTTTTTACGCGAATTGAGATGACAAGCTAAGCACCTCAACCCGGTTACTCAATTTGAAAAG
1 AATT-TTTTTACGCAAATTGAGATGACAAGCCAAACACCTCAACCCGGTTACTCAATTTGAAAAG
* * * * * *
60566 TCTTTATCTTATTTTTCAAGGTAGCTCGGTTAGTGGAGTGTTACAAGTTTTGGTTCATCACTTG
65 TCTTTAGCTTATTTTTCAAGGTAGCTCGGTTAGTGGAATGTTACAAGCTTCGATTCATCACTCG
*
60630 AATTTTTTTACGCAAATTGAGATGATAAGCCAAACACCTCAACCCGGTTACTCAATTTGAAAAGT
1 AATTTTTTTACGCAAATTGAGATGACAAGCCAAACACCTCAACCCGGTTACTCAATTTGAAAAGT
* *
60695 CTTTAGCTTATTTTTCAAGGTAGCTCTGTTAGTGGAATGTTACAAGCTTCGATTCGTCACTCG
66 CTTTAGCTTATTTTTCAAGGTAGCTCGGTTAGTGGAATGTTACAAGCTTCGATTCATCACTCG
* * **
60758 AATCTTTTTACGCTAATTGAGATGACAAGCCAAACACCTCAACCCAATTACTCAATT
1 AATTTTTTTACGCAAATTGAGATGACAAGCCAAACACCTCAACCCGGTTACTCAATT
60815 CGATTAGATT
Statistics
Matches: 168, Mismatches: 17, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
128 164 0.98
129 4 0.02
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (128 bp):
AATTTTTTTACGCAAATTGAGATGACAAGCCAAACACCTCAACCCGGTTACTCAATTTGAAAAGT
CTTTAGCTTATTTTTCAAGGTAGCTCGGTTAGTGGAATGTTACAAGCTTCGATTCATCACTCG
Found at i:65045 original size:6 final size:6
Alignment explanation
Indices: 65034--65072 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
65024 TGATCAAAAT
* * *
65034 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
65073 TATGAATTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:68754 original size:6 final size:6
Alignment explanation
Indices: 68743--68781 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
68733 TGATCAAAAT
* * *
68743 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
68782 TATGAATTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:74451 original size:18 final size:18
Alignment explanation
Indices: 74406--74441 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
74396 TACCTTTCAA
74406 AACATCTCTAAAATTTCT
1 AACATCTCTAAAATTTCT
74424 AACATCTCTAAAATTTCT
1 AACATCTCTAAAATTTCT
74442 TTCTCTTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.22, G:0.00, T:0.39
Consensus pattern (18 bp):
AACATCTCTAAAATTTCT
Found at i:81820 original size:32 final size:31
Alignment explanation
Indices: 81765--81825 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 31
81755 TAAAGTGTAA
81765 TAAAAAATATTTCAGATATTTTAATATAATT
1 TAAAAAATATTTCAGATATTTTAATATAATT
*
81796 TAAAAAATCTTTCA-ATATAATTTAATATAA
1 TAAAAAATATTTCAGATAT--TTTAATATAA
81826 AAATAATTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 4 0.15
31 13 0.48
32 10 0.37
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.43
Consensus pattern (31 bp):
TAAAAAATATTTCAGATATTTTAATATAATT
Found at i:82084 original size:16 final size:16
Alignment explanation
Indices: 82063--82113 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
82053 TGAATTACTG
* *
82063 ATTACAATTCTATTTC
1 ATTACAACTCTATTCC
82079 ATTACAACTCTATTCC
1 ATTACAACTCTATTCC
*
82095 ATTATAAC-CTTATTCC
1 ATTACAACTC-TATTCC
82111 ATT
1 ATT
82114 CCAATGAACC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
15 1 0.03
16 30 0.97
ACGTcount: A:0.31, C:0.24, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTACAACTCTATTCC
Found at i:88805 original size:16 final size:18
Alignment explanation
Indices: 88778--88813 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
88768 TGTCTTTATT
88778 TTTTTTATTTTTA-ATAA
1 TTTTTTATTTTTAGATAA
88795 TTTTTTA-TTTTAGATAA
1 TTTTTTATTTTTAGATAA
88812 TT
1 TT
88814 AATGTAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (18 bp):
TTTTTTATTTTTAGATAA
Found at i:89880 original size:26 final size:23
Alignment explanation
Indices: 89847--89898 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 23
89837 AATTGTACGG
89847 TTAAAATGTTATTATAATAATTATA
1 TTAAAATGTTATTA-AATAA-TATA
*
89872 TTAAGAATGTTATTAAATTATATA
1 TTAA-AATGTTATTAAATAATATA
89896 TTA
1 TTA
89899 TTTATTAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 7 0.28
25 8 0.32
26 10 0.40
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (23 bp):
TTAAAATGTTATTAAATAATATA
Found at i:89960 original size:57 final size:59
Alignment explanation
Indices: 89860--89997 Score: 178
Period size: 57 Copynumber: 2.4 Consensus size: 59
89850 AAATGTTATT
* * * *
89860 ATAATAATTATATTAAGA-AT-GTTATTAAATTATATATTATTTATTAATTTATGTTTA
1 ATAATAATTATATTAAAATATAATTATTAAATTATATATTATTTATTAAATTATATTTA
89917 ATAATAATTATATTAAAATATAATTAATT-AATTAT-TATT-TTTATTAAATTATATTTA
1 ATAATAATTATATTAAAATATAATT-ATTAAATTATATATTATTTATTAAATTATATTTA
* *
89974 ATAATAATTTTATTAAAATTTAAT
1 ATAATAATTATATTAAAATATAAT
89998 AACAATAACA
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
57 55 0.76
58 6 0.08
59 8 0.11
60 3 0.04
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (59 bp):
ATAATAATTATATTAAAATATAATTATTAAATTATATATTATTTATTAAATTATATTTA
Found at i:89982 original size:16 final size:16
Alignment explanation
Indices: 89908--89987 Score: 50
Period size: 16 Copynumber: 5.4 Consensus size: 16
89898 ATTTATTAAT
*
89908 TTATGTTTAATAATAA
1 TTATATTTAATAATAA
89924 TTATA-TTAA-AAT-A
1 TTATATTTAATAATAA
*
89937 -TA-A-TTAATTAATTA
1 TTATATTTAA-TAATAA
* *
89951 TTAT-TTTTATTA-AA
1 TTATATTTAATAATAA
89965 TTATATTTAATAATAA
1 TTATATTTAATAATAA
*
89981 TTTTATT
1 TTATATT
89988 AAAATTTAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
11 5 0.10
12 2 0.04
13 4 0.08
14 9 0.18
15 14 0.29
16 15 0.31
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (16 bp):
TTATATTTAATAATAA
Found at i:91358 original size:28 final size:28
Alignment explanation
Indices: 91327--91386 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
91317 AATTAATCGA
* *
91327 TTAAATTAATTGAAAAAATTCAATTCCG
1 TTAAATTAATTAAAAAAATTCAATTCAG
* ** *
91355 TTAATTTTTTTAAAAAAATTCGATTCAG
1 TTAAATTAATTAAAAAAATTCAATTCAG
91383 TTAA
1 TTAA
91387 CGATTAATAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.42
Consensus pattern (28 bp):
TTAAATTAATTAAAAAAATTCAATTCAG
Found at i:91954 original size:23 final size:23
Alignment explanation
Indices: 91910--91954 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
91900 ACTATTATTT
* *
91910 TTTAACATATTTATGAAAAATAC
1 TTTAAAATATTTATAAAAAATAC
91933 TTTAAAAT-TTTATAAAATAATA
1 TTTAAAATATTTATAAAA-AATA
91955 TTCAAAAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.42
Consensus pattern (23 bp):
TTTAAAATATTTATAAAAAATAC
Found at i:91961 original size:22 final size:22
Alignment explanation
Indices: 91919--91961 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
91909 TTTTAACATA
* *
91919 TTTATGAAAAATACTTTAAAAT
1 TTTATAAAAAATACTTCAAAAT
91941 TTTATAAAATAATA-TTCAAAA
1 TTTATAAAA-AATACTTCAAAA
91962 GTAATAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (22 bp):
TTTATAAAAAATACTTCAAAAT
Found at i:95470 original size:100 final size:100
Alignment explanation
Indices: 95291--95510 Score: 359
Period size: 100 Copynumber: 2.2 Consensus size: 100
95281 ACTACGAGTT
95291 GATGAGGCACTGGGTGCCAAGTTACTTCAGTTTAACTGATGAGACACTAGGTGTCAATTTATTTA
1 GATGAGGCACTGGGTGCCAAGTTACTTCAGTTTAACTGATGAGACACTAGGTGTCAATTTATTTA
*
95356 TAGCGCTGGGCACGATTTTTACTTCGAATTTATCC
66 TAGCGCTGGACACGATTTTTACTTCGAATTTATCC
* * ** *
95391 GATGAGACACTGGGTACCAAGTTACTTTGGTTTAACTGATGAGACATTAGGTGTCAATTTATTTA
1 GATGAGGCACTGGGTGCCAAGTTACTTCAGTTTAACTGATGAGACACTAGGTGTCAATTTATTTA
* *
95456 TAGCGTTGGACACGATTTTTACTTCGGATTTATCC
66 TAGCGCTGGACACGATTTTTACTTCGAATTTATCC
*
95491 GATGAGGCATTGGGTGCCAA
1 GATGAGGCACTGGGTGCCAA
95511 ACCGGTGTGT
Statistics
Matches: 109, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
100 109 1.00
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.34
Consensus pattern (100 bp):
GATGAGGCACTGGGTGCCAAGTTACTTCAGTTTAACTGATGAGACACTAGGTGTCAATTTATTTA
TAGCGCTGGACACGATTTTTACTTCGAATTTATCC
Found at i:96421 original size:21 final size:21
Alignment explanation
Indices: 96397--96436 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
96387 TTGGTAGTAA
96397 AGAGTGTAGGGTTGTATCGGT
1 AGAGTGTAGGGTTGTATCGGT
96418 AGAGTGTAGGGTTGTATCG
1 AGAGTGTAGGGTTGTATCG
96437 ATAAAACCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.05, G:0.42, T:0.33
Consensus pattern (21 bp):
AGAGTGTAGGGTTGTATCGGT
Found at i:105166 original size:3 final size:3
Alignment explanation
Indices: 105158--105208 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
105148 TTTATCCTTT
105158 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
105205 ATA A
1 ATA A
105209 GAAAATAAGA
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 45 0.96
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:105663 original size:12 final size:11
Alignment explanation
Indices: 105625--105668 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
105615 AGATAAATGT
*
105625 TATTTAATTAA
1 TATTTTATTAA
105636 TATTTTATTAA
1 TATTTTATTAA
* *
105647 GATTTTTTGTAA
1 TATTTTAT-TAA
105659 TATTTTATTA
1 TATTTTATTA
105669 TTAAATTATT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:127742 original size:2 final size:2
Alignment explanation
Indices: 127737--127763 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
127727 TATATATATA
127737 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
127764 ATGTTTGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:131760 original size:19 final size:18
Alignment explanation
Indices: 131718--131761 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 18
131708 ATTTAAATCT
131718 TAAAAAATTTTAAAGTTA
1 TAAAAAATTTTAAAGTTA
131736 TGAAAAAATTTTACATA-TTA
1 T-AAAAAATTTTA-A-AGTTA
131756 TAAAAA
1 TAAAAA
131762 TATTATAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 1 0.04
19 16 0.70
20 5 0.22
21 1 0.04
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (18 bp):
TAAAAAATTTTAAAGTTA
Found at i:134613 original size:65 final size:65
Alignment explanation
Indices: 134543--134690 Score: 253
Period size: 65 Copynumber: 2.3 Consensus size: 65
134533 AATCTAAGTG
* * * *
134543 ATTTTTGAAAATTAATTTTGATAAAGTAAAATTTAATTAATCAATTTAATTAAAATTAATATGAT
1 ATTTTTGGAAATTAATTTTAATAAAGTAAAATTAAATTAATCAAATTAATTAAAATTAATATGAT
134608 ATTTTTGGAAATTAATTTTAATAAAGTAAAATTAAATTAATCAAATTAATTAAAATTAATATGAT
1 ATTTTTGGAAATTAATTTTAATAAAGTAAAATTAAATTAATCAAATTAATTAAAATTAATATGAT
134673 A-TTTTGGAAATTAATTTT
1 ATTTTTGGAAATTAATTTT
134691 CAAGTCACAA
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
64 17 0.22
65 62 0.78
ACGTcount: A:0.47, C:0.01, G:0.07, T:0.45
Consensus pattern (65 bp):
ATTTTTGGAAATTAATTTTAATAAAGTAAAATTAAATTAATCAAATTAATTAAAATTAATATGAT
Found at i:134684 original size:30 final size:30
Alignment explanation
Indices: 134588--134688 Score: 87
Period size: 30 Copynumber: 3.2 Consensus size: 30
134578 ATTAATCAAT
134588 TTAATTAAAATTAATATGATATTTTTGGAAA
1 TTAATTAAAATTAATATGATA-TTTTGGAAA
* * * * * *
134619 TTAATTTTAATAAAGTAAAATTAAATTAAT-CAAA
1 TTAA--TT-A-AAATTAATATGATATT-TTGGAAA
134653 TTAATTAAAATTAATATGATATTTTGGAAA
1 TTAATTAAAATTAATATGATATTTTGGAAA
134683 TTAATT
1 TTAATT
134689 TTCAAGTCAC
Statistics
Matches: 52, Mismatches: 12, Indels: 13
0.68 0.16 0.17
Matches are distributed among these distances:
29 1 0.02
30 21 0.40
31 5 0.10
32 2 0.04
33 2 0.04
34 10 0.19
35 11 0.21
ACGTcount: A:0.49, C:0.01, G:0.07, T:0.44
Consensus pattern (30 bp):
TTAATTAAAATTAATATGATATTTTGGAAA
Found at i:135036 original size:26 final size:26
Alignment explanation
Indices: 134989--135040 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
134979 AGTTGTAGAG
134989 AGAAAATTCTCTAAAGAGATTTATTTT
1 AGAAAATTCTCTAAAGAGATTT-TTTT
* *
135016 AGAAAA-TCTCTACAGATATTTTTTT
1 AGAAAATTCTCTAAAGAGATTTTTTT
135041 GATTTACAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 13 0.57
27 6 0.26
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (26 bp):
AGAAAATTCTCTAAAGAGATTTTTTT
Found at i:135414 original size:27 final size:26
Alignment explanation
Indices: 135357--135414 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
135347 ATTCAGATTA
** *
135357 CCAAAATAAAATCTACATGTCAGAGT
1 CCAAAATAAAAAATACATGTCAAAGT
* *
135383 TCAAAATAAATAAATACATTTCAAAGT
1 CCAAAATAAA-AAATACATGTCAAAGT
135410 CCAAA
1 CCAAA
135415 CAAGTCCCAG
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
26 9 0.36
27 16 0.64
ACGTcount: A:0.52, C:0.17, G:0.07, T:0.24
Consensus pattern (26 bp):
CCAAAATAAAAAATACATGTCAAAGT
Found at i:136478 original size:16 final size:16
Alignment explanation
Indices: 136457--136491 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
136447 ACAGAACTGA
*
136457 ACTTACTTTTTTAAAT
1 ACTTACATTTTTAAAT
*
136473 ACTTACATTTTTAGAT
1 ACTTACATTTTTAAAT
136489 ACT
1 ACT
136492 AAAGATGAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.31, C:0.14, G:0.03, T:0.51
Consensus pattern (16 bp):
ACTTACATTTTTAAAT
Found at i:138533 original size:20 final size:20
Alignment explanation
Indices: 138505--138584 Score: 58
Period size: 20 Copynumber: 4.0 Consensus size: 20
138495 CCACGTCATC
*
138505 AAATGATTTTAAATTTATTA
1 AAATTATTTTAAATTTATTA
*
138525 AAATTATTTTTTTAAA-ATA-TA
1 AAATTA---TTTTAAATTTATTA
*
138546 AAA-TATTTTAAATTATTTTA
1 AAATTATTTTAAATT-TATTA
* *
138566 AAATTAATTTAAAATTATT
1 AAATTATTTTAAATTTATT
138585 TTTTAAAATA
Statistics
Matches: 46, Mismatches: 7, Indels: 14
0.69 0.10 0.21
Matches are distributed among these distances:
17 7 0.15
19 1 0.02
20 15 0.33
21 14 0.30
22 2 0.04
23 7 0.15
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (20 bp):
AAATTATTTTAAATTTATTA
Found at i:138562 original size:10 final size:10
Alignment explanation
Indices: 138544--138586 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
138534 TTTTAAAATA
*
138544 TAAAATATTT
1 TAAATTATTT
138554 TAAATTATTT
1 TAAATTATTT
138564 TAAAATTAATTT
1 T-AAATT-ATTT
*
138576 AAAATTATTT
1 TAAATTATTT
138586 T
1 T
138587 TTAAAATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
10 14 0.50
11 10 0.36
12 4 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
TAAATTATTT
Found at i:138570 original size:51 final size:50
Alignment explanation
Indices: 138505--138600 Score: 149
Period size: 51 Copynumber: 1.9 Consensus size: 50
138495 CCACGTCATC
*
138505 AAATGATTTTAAATTTA-TTAAAATTATTTTTTTAAAATATAAAATATTTT
1 AAATGATTTTAAATTAATTTAAAATTA-TTTTTTAAAATATAAAATATTTT
*
138555 AAATTATTTTAAAATTAATTTAAAATTATTTTTTAAAATATAAAAT
1 AAATGATTTT-AAATTAATTTAAAATTATTTTTTAAAATATAAAAT
138601 TATTAAAATC
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
50 9 0.21
51 24 0.57
52 9 0.21
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (50 bp):
AAATGATTTTAAATTAATTTAAAATTATTTTTTAAAATATAAAATATTTT
Found at i:138571 original size:11 final size:11
Alignment explanation
Indices: 138544--138586 Score: 63
Period size: 11 Copynumber: 4.1 Consensus size: 11
138534 TTTTAAAATA
138544 TAAAA-TATTT
1 TAAAATTATTT
138554 T-AAATTATTT
1 TAAAATTATTT
*
138564 TAAAATTAATT
1 TAAAATTATTT
138575 TAAAATTATTT
1 TAAAATTATTT
138586 T
1 T
138587 TTAAAATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
9 3 0.10
10 7 0.24
11 19 0.66
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
TAAAATTATTT
Found at i:138661 original size:6 final size:6
Alignment explanation
Indices: 138644--138687 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
138634 GTTTTTTTTG
* * *
138644 TTCCCTT TTCCCT TTCCCT TTCCCT TCCCCT TCCCCT TCCCCT T
1 TTCCC-T TTCCCT TTCCCT TTCCCT TTCCCT TTCCCT TTCCCT T
138688 CTTCTTATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
6 31 0.86
7 5 0.14
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (6 bp):
TTCCCT
Found at i:138665 original size:12 final size:12
Alignment explanation
Indices: 138644--138687 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
138634 GTTTTTTTTG
*
138644 TTCCCTTTTCCC
1 TTCCCCTTTCCC
*
138656 TTTCCCTTTCCC
1 TTCCCCTTTCCC
*
138668 TTCCCCTTCCCC
1 TTCCCCTTTCCC
138680 TTCCCCTT
1 TTCCCCTT
138688 CTTCTTATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (12 bp):
TTCCCCTTTCCC
Found at i:138677 original size:17 final size:17
Alignment explanation
Indices: 138651--138684 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
138641 TTGTTCCCTT
* *
138651 TTCCCTTTCCCTTTCCC
1 TTCCCCTTCCCCTTCCC
138668 TTCCCCTTCCCCTTCCC
1 TTCCCCTTCCCCTTCCC
138685 CTTCTTCTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (17 bp):
TTCCCCTTCCCCTTCCC
Found at i:138688 original size:6 final size:6
Alignment explanation
Indices: 138653--138688 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
138643 GTTCCCTTTT
* *
138653 CCCTTT CCCTTT CCCTTC CCCTTC CCCTTC CCCTTC
1 CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC
138689 TTCTTATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (6 bp):
CCCTTC
Found at i:139702 original size:9 final size:9
Alignment explanation
Indices: 139690--139746 Score: 55
Period size: 9 Copynumber: 6.1 Consensus size: 9
139680 ATTAAAATTA
139690 TTTAATAAT
1 TTTAATAAT
139699 TTTAATAAT
1 TTTAATAAT
*
139708 TTT-ATATTT
1 TTTAATA-AT
139717 TTTAAAAATAAT
1 TTT---AATAAT
139729 TTTAATAAT
1 TTTAATAAT
139738 TTTAA-AAT
1 TTTAATAAT
139746 T
1 T
139747 ATTTGCTGAT
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
8 7 0.17
9 27 0.66
12 4 0.10
13 3 0.07
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TTTAATAAT
Found at i:143401 original size:16 final size:16
Alignment explanation
Indices: 143364--143402 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
143354 GTTAGATTAG
143364 TTAGTTACTACAGTTA
1 TTAGTTACTACAGTTA
** *
143380 GCAGTTTCTACAGTTA
1 TTAGTTACTACAGTTA
143396 TTAGTTA
1 TTAGTTA
143403 TTTATCAACA
Statistics
Matches: 17, Mismatches: 6, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (16 bp):
TTAGTTACTACAGTTA
Found at i:145570 original size:47 final size:48
Alignment explanation
Indices: 145462--145571 Score: 159
Period size: 48 Copynumber: 2.3 Consensus size: 48
145452 AATAATGCAA
* * * *
145462 ATAAACTGCCACATAATAAAAATTATGGACAAGCCACCAAAATCGCAT
1 ATAAATTGCCACATAATAAAAATCATGGACAAGCCACCAAAATCACAG
* *
145510 ATATATTGCCACATAATAAAAATCATGGACAAGTCACC-AAATCACAG
1 ATAAATTGCCACATAATAAAAATCATGGACAAGCCACCAAAATCACAG
145557 ATAAATTGCCACATA
1 ATAAATTGCCACATA
145572 CTTCCACCTT
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
47 21 0.38
48 34 0.62
ACGTcount: A:0.47, C:0.22, G:0.10, T:0.21
Consensus pattern (48 bp):
ATAAATTGCCACATAATAAAAATCATGGACAAGCCACCAAAATCACAG
Found at i:151045 original size:23 final size:23
Alignment explanation
Indices: 151015--151070 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
151005 ACTATCGTGT
* *
151015 TATAGAAGTATACATAATTGTGC
1 TATAGAAGTAAACATAACTGTGC
*
151038 TATAGAAGCAAACATAACTGTGC
1 TATAGAAGTAAACATAACTGTGC
* *
151061 CATAAAAGTA
1 TATAGAAGTA
151071 GACAAAGTCG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.27
Consensus pattern (23 bp):
TATAGAAGTAAACATAACTGTGC
Done.