Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014142.1 Kokia drynarioides strain JFW-HI SEQ_129175, 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: 139558
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 67 characters in sequence are not A, C, G, or T
Found at i:1042 original size:22 final size:22
Alignment explanation
Indices: 1017--1064 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
1007 TGTAAACCTA
1017 AAACCATGAAAAGCC-AAT-ACCC
1 AAACCAT-AAAA-CCAAATCACCC
*
1039 AAACCCTAAAACCAAATCACCC
1 AAACCATAAAACCAAATCACCC
1061 AAAC
1 AAAC
1065 TCTAGACCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 2 0.09
21 7 0.30
22 14 0.61
ACGTcount: A:0.52, C:0.35, G:0.04, T:0.08
Consensus pattern (22 bp):
AAACCATAAAACCAAATCACCC
Found at i:4544 original size:31 final size:31
Alignment explanation
Indices: 4486--4545 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
4476 AAATTTAAAA
* *
4486 AATTTAAATTTTAATGAAAGAACAATTATTT
1 AATTCAAATTTTAATGAAAAAACAATTATTT
*
4517 AATTCAAATTTTAAT-ATAAAAATAATTAT
1 AATTCAAATTTTAATGA-AAAAACAATTAT
4546 CAAATTTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 1 0.04
31 24 0.96
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (31 bp):
AATTCAAATTTTAATGAAAAAACAATTATTT
Found at i:6749 original size:59 final size:59
Alignment explanation
Indices: 6673--6893 Score: 259
Period size: 59 Copynumber: 3.7 Consensus size: 59
6663 AATTTTTTGC
** *
6673 ATGGCCGACACCCCTAATTATCTGATAAAAAAATCAAATTTTTCGGTATTGGTCATGCA
1 ATGGCCGACACCCCTAATTATCTGATAAAAAAATCAAATTTTTTTGTGTTGGTCATGCA
* *
6732 ATGGTCGACACCCCTAATTATTTGATAAAAAAATCAAATTTTTTTGTGTTGGTCATGCA
1 ATGGCCGACACCCCTAATTATCTGATAAAAAAATCAAATTTTTTTGTGTTGGTCATGCA
* * * * * *
6791 ATGGTCGACACCCCCT-TTTCTCAGATAAAAAATTCAAAATTTTTTTGTGTTGGCCATTGC-
1 ATGGCCGACA-CCCCTAATTATCTGATAAAAAAATC-AAATTTTTTTGTGTTGGTCA-TGCA
* **
6851 ATGGCCGACATCCCTTTTTATCTGA-ATAAAAAATCAAATTTTT
1 ATGGCCGACACCCCTAATTATCTGATA-AAAAAATCAAATTTTT
6894 GGTCGACACC
Statistics
Matches: 141, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
59 91 0.65
60 47 0.33
61 3 0.02
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (59 bp):
ATGGCCGACACCCCTAATTATCTGATAAAAAAATCAAATTTTTTTGTGTTGGTCATGCA
Found at i:10717 original size:17 final size:16
Alignment explanation
Indices: 10695--10745 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
10685 GTGTAAAAAC
10695 TAATTTAAAAATTAATT
1 TAATTT-AAAATTAATT
10712 TAATTTGAAAATTAATT
1 TAATTT-AAAATTAATT
* *
10729 TAAGTTGAAATTAATT
1 TAATTTAAAATTAATT
10745 T
1 T
10746 GAAAATTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
16 10 0.32
17 21 0.68
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (16 bp):
TAATTTAAAATTAATT
Found at i:10741 original size:16 final size:17
Alignment explanation
Indices: 10702--10745 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
10692 AACTAATTTA
*
10702 AAAATTAATTTAATTTG
1 AAAATTAATTTAAGTTG
10719 AAAATTAATTTAAGTTG
1 AAAATTAATTTAAGTTG
10736 -AAATTAATTT
1 AAAATTAATTT
10746 GAAAATTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 10 0.38
17 16 0.62
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (17 bp):
AAAATTAATTTAAGTTG
Found at i:10952 original size:84 final size:82
Alignment explanation
Indices: 10840--11097 Score: 297
Period size: 83 Copynumber: 3.1 Consensus size: 82
10830 ACTGTTTAAA
* *
10840 TAAA-AAAAGATTATTATTATATTTCAATTTATATCAAATATTATGTTCATTTGACAATACATTA
1 TAAATAAAA-ATTATTATTATATTACAATTTATATCAAATA-TATGTTAATTTGACAATACATTA
** **
10904 TTTA-TCACTTTTTCATATT
64 TTTACT-AAATTTAAATATT
* * * *
10923 TAAATTACAAATTATTATTATGTTACAATTTTTATCAAATAATGTGTTAATTTGACAATACATTA
1 TAAA-TAAAAATTATTATTATATTACAATTTATATCAAAT-ATATGTTAATTTGACAATACATTA
10988 TTTACTAAATTTAAATATT
64 TTTACTAAATTTAAATATT
* * * * *
11007 TAAATAAAAAATAATATTATATTAAAATTTCA-ATCAAATGATATGTTGATTTGATAATACATTA
1 TAAATAAAAATTATTATTATATTACAATTT-ATATCAAAT-ATATGTTAATTTGACAATACATTA
11071 TTTACTAAATTTAAATATT
64 TTTACTAAATTTAAATATT
11090 TAAATAAA
1 TAAATAAA
11098 TTGGACTCAT
Statistics
Matches: 150, Mismatches: 20, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
83 80 0.53
84 65 0.43
85 5 0.03
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (82 bp):
TAAATAAAAATTATTATTATATTACAATTTATATCAAATATATGTTAATTTGACAATACATTATT
TACTAAATTTAAATATT
Found at i:11935 original size:30 final size:29
Alignment explanation
Indices: 11873--11983 Score: 114
Period size: 30 Copynumber: 3.7 Consensus size: 29
11863 TCAGTTTACT
* * *
11873 TTTTAAATTCAATTTGTAATTTCGATTTTA
1 TTTTAAATTTAATTTCTAATTTC-ATTATA
*
11903 TTTTAAATTTAATTTCTAATTTCCTGTATA
1 TTTTAAATTTAATTTCTAATTTCAT-TATA
* * * *
11933 TTTTTATTTTAATTTCTAATTTCGTTTATC
1 TTTTAAATTTAATTTCTAATTTC-ATTATA
*
11963 TTTTAAATTTCATTTCTAATT
1 TTTTAAATTTAATTTCTAATT
11984 ATTATTTTTC
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
29 1 0.01
30 66 0.97
31 1 0.01
ACGTcount: A:0.27, C:0.09, G:0.04, T:0.60
Consensus pattern (29 bp):
TTTTAAATTTAATTTCTAATTTCATTATA
Found at i:12925 original size:116 final size:114
Alignment explanation
Indices: 12786--13012 Score: 253
Period size: 116 Copynumber: 2.0 Consensus size: 114
12776 TTGGTGTCGA
*
12786 TCATTGCATGACCAACATAAAAAAAAATTAATTTTTTG-CCAAAAAAAAAAAAAGGTGTCGACCA
1 TCATTGCATGACCAAC--ACAAAAAAATTAATTTTTTGACCAAAAAAAAAAAAAGGTGTCGACCA
* * *
12850 TGGCATGGCCAACTTAAAAAAAAATT-AAATTTTTTATTTGACAAAAAGGGGG
64 TGACATGACCAAC--AAAAAAAAATTCAAATTTTTTATCTGACAAAAAGGGGG
* *** * * *
12902 TCATTGCAT-AGCCAACACAAAAAAATTTATTTTTTGTACTTGATAAAAAAGAAGGTGTCGATCA
1 TCATTGCATGA-CCAACACAAAAAAATTAATTTTTTG-ACCAAAAAAAAAAAAAGGTGTCGACCA
* * *
12966 TGACATGACCAACACAAAAAAATTCGAATTTTTTATCTGATAAAAAG
64 TGACATGACCAACAAAAAAAAATTCAAATTTTTTATCTGACAAAAAG
13013 AGAGCGTTGG
Statistics
Matches: 93, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
114 28 0.30
115 20 0.22
116 45 0.48
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.28
Consensus pattern (114 bp):
TCATTGCATGACCAACACAAAAAAATTAATTTTTTGACCAAAAAAAAAAAAAGGTGTCGACCATG
ACATGACCAACAAAAAAAAATTCAAATTTTTTATCTGACAAAAAGGGGG
Found at i:41637 original size:31 final size:31
Alignment explanation
Indices: 41585--41643 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
41575 TGACCATATT
*
41585 TTTAAAATTATTATATTATTTTAATTTAATA
1 TTTAAAATTATTATATAATTTTAATTTAATA
* *
41616 TTTAATAATT-TTATGTAATTTTTATTTA
1 TTTAA-AATTATTATATAATTTTAATTTA
41644 TTAAAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 20 0.83
32 4 0.17
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (31 bp):
TTTAAAATTATTATATAATTTTAATTTAATA
Found at i:46753 original size:16 final size:16
Alignment explanation
Indices: 46732--46764 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
46722 GCAAGTAATG
46732 ATTTTTGGAAATTTCT
1 ATTTTTGGAAATTTCT
46748 ATTTTTGGAAATTTCT
1 ATTTTTGGAAATTTCT
46764 A
1 A
46765 CTGTAATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.27, C:0.06, G:0.12, T:0.55
Consensus pattern (16 bp):
ATTTTTGGAAATTTCT
Found at i:47238 original size:15 final size:15
Alignment explanation
Indices: 47218--47263 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
47208 TCATTTAATG
47218 TAATTAATAATTTTA
1 TAATTAATAATTTTA
47233 TAATTAAT-ATTTTCA
1 TAATTAATAATTTT-A
* *
47248 T-ATAAATATTTTTA
1 TAATTAATAATTTTA
47262 TA
1 TA
47264 TGCAATTGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (15 bp):
TAATTAATAATTTTA
Found at i:68815 original size:2 final size:2
Alignment explanation
Indices: 68810--68855 Score: 74
Period size: 2 Copynumber: 22.0 Consensus size: 2
68800 ACACACGCAC
68810 AT AT AT AT AT GAGT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT -A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
68854 AT
1 AT
68856 TTGCAGAAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 39 0.93
3 2 0.05
4 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:83339 original size:52 final size:52
Alignment explanation
Indices: 83255--83353 Score: 162
Period size: 52 Copynumber: 1.9 Consensus size: 52
83245 GTACAAATAG
* * *
83255 TAAGAAAATATTATTAAATTATTTAATTTTAATTAATTAATTATTATGTGGT
1 TAAGAAAATATTATTAAATTATATAATATTAATTAATTAAATATTATGTGGT
*
83307 TAAGAAAATATTATTAAATTATATAATATTAATTAGTTAAATATTAT
1 TAAGAAAATATTATTAAATTATATAATATTAATTAATTAAATATTAT
83354 TAATTTTTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.47
Consensus pattern (52 bp):
TAAGAAAATATTATTAAATTATATAATATTAATTAATTAAATATTATGTGGT
Found at i:83354 original size:18 final size:17
Alignment explanation
Indices: 83312--83358 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
83302 GTGGTTAAGA
83312 AAATATTATTAA--ATT
1 AAATATTATTAATTATT
* *
83327 ATATAATATTAATTAGTT
1 AAATATTATTAATTA-TT
83345 AAATATTATTAATT
1 AAATATTATTAATT
83359 TTTTATGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
15 10 0.40
17 1 0.04
18 14 0.56
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (17 bp):
AAATATTATTAATTATT
Found at i:92155 original size:25 final size:25
Alignment explanation
Indices: 92127--92177 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
92117 AGAGGGATAT
92127 ACGATTATAATTTTCTACTTTTGTG
1 ACGATTATAATTTTCTACTTTTGTG
92152 ACGATTATAATTTTCTACTTTTGTG
1 ACGATTATAATTTTCTACTTTTGTG
92177 A
1 A
92178 GGGAATGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.25, C:0.12, G:0.12, T:0.51
Consensus pattern (25 bp):
ACGATTATAATTTTCTACTTTTGTG
Found at i:101256 original size:32 final size:30
Alignment explanation
Indices: 101187--101260 Score: 85
Period size: 32 Copynumber: 2.4 Consensus size: 30
101177 TTGAATAATT
* * *
101187 TATATTTTTATAATTTTTAAAGGATTAAAT
1 TATATTTTTATTATTTTTAAAGAATTAAAA
*
101217 TAAATTTTTATTATTTTTAAAAAGAATTAAAA
1 TATATTTTTATTATTTTT--AAAGAATTAAAA
*
101249 TGTATTTTTATT
1 TATATTTTTATT
101261 TTTACTAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
30 16 0.44
32 20 0.56
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (30 bp):
TATATTTTTATTATTTTTAAAGAATTAAAA
Found at i:102002 original size:19 final size:19
Alignment explanation
Indices: 101975--102017 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
101965 TTTAACTTTA
*
101975 GAAAAAGTAAACATTTATC
1 GAAATAGTAAACATTTATC
101994 GAAATAGTAAACATTTATC
1 GAAATAGTAAACATTTATC
102013 GAAAT
1 GAAAT
102018 GACGTAGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.51, C:0.09, G:0.12, T:0.28
Consensus pattern (19 bp):
GAAATAGTAAACATTTATC
Found at i:102823 original size:20 final size:20
Alignment explanation
Indices: 102788--102853 Score: 82
Period size: 20 Copynumber: 3.2 Consensus size: 20
102778 ATCTTTCCCA
102788 AAAAATATTACAAAATAATTTT
1 AAAAA-ATT-CAAAATAATTTT
102810 AAAAAATTCAAAATAATTTT
1 AAAAAATTCAAAATAATTTT
*
102830 -AAAAATTCAATAT-ATTTAT
1 AAAAAATTCAAAATAATTT-T
102849 AAAAA
1 AAAAA
102854 TCCCAAAATT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
18 4 0.10
19 13 0.32
20 16 0.39
21 3 0.07
22 5 0.12
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAAAATTCAAAATAATTTT
Found at i:102847 original size:17 final size:19
Alignment explanation
Indices: 102798--102854 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
102788 AAAAATATTA
102798 CAAAATAATTTTAAAAAATT
1 CAAAATAATTTT-AAAAATT
102818 CAAAATAATTTTAAAAATT
1 CAAAATAATTTTAAAAATT
*
102837 CAATAT-ATTTATAAAAAT
1 CAAAATAATTT-TAAAAAT
102855 CCCAAAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
18 4 0.11
19 19 0.54
20 12 0.34
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
CAAAATAATTTTAAAAATT
Found at i:114918 original size:15 final size:16
Alignment explanation
Indices: 114900--114933 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
114890 TTTATTTTAG
114900 AAAATAAATAAAA-TT
1 AAAATAAATAAAAGTT
*
114915 AAAATAACTAAAAGTT
1 AAAATAAATAAAAGTT
114931 AAA
1 AAA
114934 TGTAATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (16 bp):
AAAATAAATAAAAGTT
Found at i:118399 original size:8 final size:8
Alignment explanation
Indices: 118388--118417 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
118378 TTTATATTTT
118388 TATTAAAA
1 TATTAAAA
118396 TATTAAAA
1 TATTAAAA
118404 TATTAAAA
1 TATTAAAA
118412 TATTAA
1 TATTAA
118418 TTAATTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
TATTAAAA
Found at i:130849 original size:24 final size:23
Alignment explanation
Indices: 130821--130872 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
130811 AATTTAGAAT
130821 TTATTAGCATAATATATTTATTA
1 TTATTAGCATAATATATTTATTA
** * *
130844 TCTATTATTATAATTTTTTTATTA
1 T-TATTAGCATAATATATTTATTA
130868 TTATT
1 TTATT
130873 TACACACTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.62
Consensus pattern (23 bp):
TTATTAGCATAATATATTTATTA
Found at i:130925 original size:21 final size:20
Alignment explanation
Indices: 130887--130926 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
130877 CACTTAAGAA
* *
130887 TTTTTTCTTGTTATAAATAT
1 TTTTTTATTGTTAAAAATAT
130907 TTTTTTATTGTTTAAAAATA
1 TTTTTTATTG-TTAAAAATA
130927 GAGTGATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (20 bp):
TTTTTTATTGTTAAAAATAT
Found at i:134318 original size:107 final size:106
Alignment explanation
Indices: 134197--134435 Score: 293
Period size: 108 Copynumber: 2.2 Consensus size: 106
134187 TTATCTGATA
134197 AAAAAATTCAAATTTTTAGGTGTCAACCAT-TGCTTTTTTCAGATAAAAAAATTTCAAAATTTTT
1 AAAAAATTCAAATTTTTAGGTGTCAACCATCTGCTTTTTTCAGATAAAAAAATTTCAAAATTTTT
*
134261 CGGTGTTGGCCATGCCATGGCCAACA-CTCCCTTTTTGTCAGAT
66 CGGTGTTGGCCATGCCATAGCCAACACCT-CC-TTTT-TCAGAT
* ** * * * *
134304 AAAAAATTCGAATTTTTTTGTGTTAGCCGTCTTCTTTTTTCAGATAAAAAAATTTCAAAATTTTT
1 AAAAAATTCAAATTTTTAGGTGTCAACCATCTGCTTTTTTCAGATAAAAAAATTTCAAAATTTTT
** * *
134369 TTGTGTTGGTCATGCCATAGCCGACACCTCCTTTTTCAGAT
66 CGGTGTTGGCCATGCCATAGCCAACACCTCCTTTTTCAGAT
*
134410 AAAAAAATTTCAAAATTTTTTGGTGT
1 -AAAAAA-TTC-AAATTTTTAGGTGT
134436 TGGTCATGCA
Statistics
Matches: 113, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
106 6 0.05
107 34 0.30
108 59 0.52
109 14 0.12
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (106 bp):
AAAAAATTCAAATTTTTAGGTGTCAACCATCTGCTTTTTTCAGATAAAAAAATTTCAAAATTTTT
CGGTGTTGGCCATGCCATAGCCAACACCTCCTTTTTCAGAT
Found at i:134476 original size:123 final size:120
Alignment explanation
Indices: 134338--134586 Score: 331
Period size: 123 Copynumber: 2.0 Consensus size: 120
134328 AGCCGTCTTC
* *
134338 TTTTTTCAGATAAAAAAATTTCAAAATTTTTTTGTGTTGGTCATGCCATAGCCGACACCTCC-TT
1 TTTTTTCAAATAAAAAAATTTCAAAATTTTTTTGTGTTAGTCATGCCATAGCCGACACC-CCTTT
* *
134402 TT-TCAGATAAAAAAATTTCAAAATTTTTTGGTGTTGGTCATGCAATGGTTGACACCCA
65 TTGTCAGAT-AAAAAA-TTC-AAATTTTTTGGTGTTGGCCATGCAATGGCTGACACCCA
* * *
134460 TTTTTTCCAAATAAAAAAATTTCAAAATTTTTTTGTGTTAGTCATGTCATGGTCGACACCCCTTT
1 TTTTTT-CAAATAAAAAAATTTCAAAATTTTTTTGTGTTAGTCATGCCATAGCCGACACCCC-TT
* * * *
134525 TTTGTCAGATAAAAAATTCGAATTTTTTTGTGTTGGCCATGTAATGGCTGACACCCC
64 TTTGTCAGATAAAAAATTCAAATTTTTTGGTGTTGGCCATGCAATGGCTGACACCCA
134582 TTTTT
1 TTTTT
134587 ATTTGGTAAA
Statistics
Matches: 112, Mismatches: 11, Indels: 8
0.85 0.08 0.06
Matches are distributed among these distances:
122 45 0.40
123 51 0.46
124 10 0.09
125 6 0.05
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (120 bp):
TTTTTTCAAATAAAAAAATTTCAAAATTTTTTTGTGTTAGTCATGCCATAGCCGACACCCCTTTT
TGTCAGATAAAAAATTCAAATTTTTTGGTGTTGGCCATGCAATGGCTGACACCCA
Found at i:134484 original size:62 final size:61
Alignment explanation
Indices: 134337--134586 Score: 303
Period size: 61 Copynumber: 4.1 Consensus size: 61
134327 TAGCCGTCTT
* *
134337 CTTTTTTCAGATAAAAAAATTTCAAAATTTTTTTGTGTTGGTCATGCCATAGCCGACACCTC
1 CTTTTTTCAGATAAAAAAATTTCAAAATTTTTTTGTGTTGGTCATGCAATGGCCGACACC-C
* **
134399 C-TTTTTCAGATAAAAAAATTTCAAAATTTTTTGGTGTTGGTCATGCAATGGTTGACACCC
1 CTTTTTTCAGATAAAAAAATTTCAAAATTTTTTTGTGTTGGTCATGCAATGGCCGACACCC
* * * *
134459 ATTTTTTCCAAATAAAAAAATTTCAAAATTTTTTTGTGTTAGTCATGTC-ATGGTCGACACCC
1 CTTTTTT-CAGATAAAAAAATTTCAAAATTTTTTTGTGTTGGTCATG-CAATGGCCGACACCC
* * * *
134521 CTTTTTTGTCAGAT-AAAAAA-TTC-GAATTTTTTTGTGTTGGCCATGTAATGGCTGACACCC
1 C-TTTTT-TCAGATAAAAAAATTTCAAAATTTTTTTGTGTTGGTCATGCAATGGCCGACACCC
134581 CTTTTT
1 CTTTTT
134587 ATTTGGTAAA
Statistics
Matches: 164, Mismatches: 18, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
59 5 0.03
60 32 0.20
61 61 0.37
62 55 0.34
63 10 0.06
64 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.40
Consensus pattern (61 bp):
CTTTTTTCAGATAAAAAAATTTCAAAATTTTTTTGTGTTGGTCATGCAATGGCCGACACCC
Found at i:134600 original size:59 final size:59
Alignment explanation
Indices: 134338--134619 Score: 184
Period size: 62 Copynumber: 4.6 Consensus size: 59
134328 AGCCGTCTTC
* ** * *
134338 TTTTT-TCAGATAAAAAAATTTCAAAATTTTTTTGTGTTGGTCATGCCATAGCCGACACCTCC-
1 TTTTTGTCAGAT-AAAAAA-TT--AAATTTTTTTGTGTTGGCCATGTAATGGTCGACACC-CCT
* * * * *
134400 -TTTT-TCAGATAAAAAAATTTCAAAATTTTTTGGTGTTGGTCATGCAATGGTTGACACCCAT
1 TTTTTGTCAGAT-AAAAAA-TT--AAATTTTTTTGTGTTGGCCATGTAATGGTCGACACCCCT
* * * * *
134461 TTTTT-CCAAATAAAAAAATTTCAAAATTTTTTTGTGTTAGTCATGTCATGGTCGACACCCCT
1 TTTTTGTCAGAT-AAAAAA-TT--AAATTTTTTTGTGTTGGCCATGTAATGGTCGACACCCCT
*
134523 TTTTTGTCAGATAAAAAATTCGAATTTTTTTGTGTTGGCCATGTAATGG-CTGACACCCCT
1 TTTTTGTCAGATAAAAAATT-AAATTTTTTTGTGTTGGCCATGTAATGGTC-GACACCCCT
* * *
134583 TTTTAT-T-TGGTAAAAAATTAAATTTTGTTGGTGTTGG
1 TTTT-TGTCAGATAAAAAATTAAATTTT-TTTGTGTTGG
134620 TCATCCTCAT
Statistics
Matches: 189, Mismatches: 25, Indels: 15
0.83 0.11 0.07
Matches are distributed among these distances:
58 6 0.03
59 20 0.11
60 39 0.21
61 56 0.30
62 64 0.34
63 4 0.02
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.41
Consensus pattern (59 bp):
TTTTTGTCAGATAAAAAATTAAATTTTTTTGTGTTGGCCATGTAATGGTCGACACCCCT
Found at i:134655 original size:54 final size:54
Alignment explanation
Indices: 134586--134695 Score: 202
Period size: 54 Copynumber: 2.0 Consensus size: 54
134576 CACCCCTTTT
134586 TATTTGGTAAAAAATTAAATTTTGTTGGTGTTGGTCATCCTCATTCTCTATAAA
1 TATTTGGTAAAAAATTAAATTTTGTTGGTGTTGGTCATCCTCATTCTCTATAAA
* *
134640 TATTTGGTAAAAAATTAAATTTTTTTGGTGTTGGTCATTCTCATTCTCTATAAA
1 TATTTGGTAAAAAATTAAATTTTGTTGGTGTTGGTCATCCTCATTCTCTATAAA
134694 TA
1 TA
134696 GGGTTTAGTT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.46
Consensus pattern (54 bp):
TATTTGGTAAAAAATTAAATTTTGTTGGTGTTGGTCATCCTCATTCTCTATAAA
Found at i:136297 original size:61 final size:61
Alignment explanation
Indices: 136201--136619 Score: 299
Period size: 58 Copynumber: 7.0 Consensus size: 61
136191 CCCGAGCTGG
* *
136201 ATTGCATGGCCAACACCAAAAAATTTTGTAATTTTTTTATCTAAAAAAAGGGGTGTCGATC
1 ATTGCATGACCAACACCAAAAAATTTTGAAATTTTTTTATCTAAAAAAAGGGGTGTCGATC
* ** * * **
136262 ATTGCATGGCCAACA-CAAAAAAAATTCAAA-TTTTTTATCTGACAAAAAGAGGGTGTCGGCC
1 ATTGCATGACCAACACCAAAAAATTTTGAAATTTTTTTATCT-AAAAAAAG-GGGTGTCGATC
*
136323 ATGGCATGACCAACACCAAAAAATTTTGAAATTTTTTTATCTAAAAAAAGGGGGTGTCGATC
1 ATTGCATGACCAACACCAAAAAATTTTGAAATTTTTTTATCTAAAAAAA-GGGGTGTCGATC
* ** *
136385 ATTGCATGACCAACACCTAAAAA-TTTG--ATTTTTTTAATC-AAATAAATAGGAATGTCG-GC
1 ATTGCATGACCAACACCAAAAAATTTTGAAATTTTTTT-ATCTAAA-AAA-AGGGGTGTCGATC
* * * * *
136444 TATTACATG-CCAACACCAAAAAA--TTG--ATTTTTTTTTTTACAAAAAGAGGGTGTCGACC
1 -ATTGCATGACCAACACCAAAAAATTTTGAAATTTTTTTATCTAAAAAAAG-GGGTGTCGATC
* * * * * * * *
136502 ATTACATGGCTAACACCCAAAAA-TTTG--A-TTTTTTATC-AGATGAATAGGGGTATCGACC
1 ATTGCATGACCAACACCAAAAAATTTTGAAATTTTTTTATCTA-A-AAAAAGGGGTGTCGATC
* *
136560 ATTGTAT-AGCCAACACGAAAAAA--TTG-AATTTTTTT-T-TGACAAAAAAGGGGTGTCGATC
1 ATTGCATGA-CCAACACCAAAAAATTTTGAAATTTTTTTATCT-A-AAAAAAGGGGTGTCGATC
136618 AT
1 AT
136620 GTAAAAATTT
Statistics
Matches: 290, Mismatches: 47, Indels: 45
0.76 0.12 0.12
Matches are distributed among these distances:
56 2 0.01
57 22 0.08
58 76 0.26
59 51 0.18
60 38 0.13
61 42 0.14
62 48 0.17
63 11 0.04
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (61 bp):
ATTGCATGACCAACACCAAAAAATTTTGAAATTTTTTTATCTAAAAAAAGGGGTGTCGATC
Found at i:136345 original size:62 final size:60
Alignment explanation
Indices: 136201--136410 Score: 260
Period size: 62 Copynumber: 3.4 Consensus size: 60
136191 CCCGAGCTGG
* * *
136201 ATTGCATGGCCAACACCAAAAAATTTTGTAATTTTTTTATCTAAAAAAAGGGGTGTCGATC
1 ATTGCATGACCAACACCAAAAAATTTT-CAAATTTTTTATCTAAAAAAAGGGGTGTCGATC
* ** * **
136262 ATTGCATGGCCAACA-CAAAAAAAATTCAAATTTTTTATCTGACAAAAAGAGGGTGTCGGCC
1 ATTGCATGACCAACACCAAAAAATTTTCAAATTTTTTATCT-AAAAAAAG-GGGTGTCGATC
* *
136323 ATGGCATGACCAACACCAAAAAATTTTGAAATTTTTTTATCTAAAAAAAGGGGGTGTCGATC
1 ATTGCATGACCAACACCAAAAAATTTTCAAA-TTTTTTATCTAAAAAAA-GGGGTGTCGATC
*
136385 ATTGCATGACCAACACCTAAAAATTT
1 ATTGCATGACCAACACCAAAAAATTT
136411 GATTTTTTTA
Statistics
Matches: 127, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
59 12 0.09
60 16 0.13
61 37 0.29
62 51 0.40
63 11 0.09
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.29
Consensus pattern (60 bp):
ATTGCATGACCAACACCAAAAAATTTTCAAATTTTTTATCTAAAAAAAGGGGTGTCGATC
Found at i:136441 original size:122 final size:119
Alignment explanation
Indices: 136204--136619 Score: 372
Period size: 122 Copynumber: 3.5 Consensus size: 119
136194 GAGCTGGATT
136204 GCATGGCCAACACCAAAAAATTTTGTAATTTTTTTATCTAAAAAAA-GGGGTGTCGATCATTGCA
1 GCAT-GCCAACACCAAAAAATTTTG-AATTTTTTTATCTAAAAAAAGGGGGTGTCGATCATTGCA
* ** * *
136268 TGGCCAACACAAAAAAAATTCAAATTTTTTATCTGACAAAAAGAGGGTGTCGGCCATG
64 TGGCCAACAC-CAAAAAATTTGATTTTTTTATC-GACAAAAAGAGGATGTCGGCCATG
136326 GCATGACCAACACCAAAAAATTTTGAAATTTTTTTATCTAAAAAAAGGGGGTGTCGATCATTGCA
1 GCATG-CCAACACCAAAAAATTTTG-AATTTTTTTATCTAAAAAAAGGGGGTGTCGATCATTGCA
* * * * *
136391 TGACCAACACCTAAAAATTTGATTTTTTTAATC-A-AATAAATAGGAATGTCGGCTATT
64 TGGCCAACACCAAAAAATTTGATTTTTTT-ATCGACAA-AAAGAGG-ATGTCGGCCATG
* * * * * * *
136448 ACATGCCAACACCAAAAAA--TTG-ATTTTTTTTTTTACAAAAAGAGGGTGTCGACCATTACATG
1 GCATGCCAACACCAAAAAATTTTGAATTTTTTTATCTAAAAAAAGGGGGTGTCGATCATTGCATG
* * ** * * * * *
136510 GCTAACACCCAAAAATTTGA-TTTTTTATCAGATGAATAG-GGGTATCGACCATT
66 GCCAACACCAAAAAATTTGATTTTTTTATC-GACAAAAAGAGGATGTCGGCCATG
* *
136563 GTATAGCCAACACGAAAAAA--TTGAATTTTTTT-T-TGACAAAAAA-GGGGTGTCGATCAT
1 GCAT-GCCAACACCAAAAAATTTTGAATTTTTTTATCT-A-AAAAAAGGGGGTGTCGATCAT
136620 GTAAAAATTT
Statistics
Matches: 248, Mismatches: 34, Indels: 30
0.79 0.11 0.10
Matches are distributed among these distances:
115 14 0.06
116 39 0.16
117 67 0.27
118 1 0.00
119 3 0.01
120 2 0.01
121 22 0.09
122 70 0.28
123 30 0.12
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.30
Consensus pattern (119 bp):
GCATGCCAACACCAAAAAATTTTGAATTTTTTTATCTAAAAAAAGGGGGTGTCGATCATTGCATG
GCCAACACCAAAAAATTTGATTTTTTTATCGACAAAAAGAGGATGTCGGCCATG
Found at i:136466 original size:59 final size:58
Alignment explanation
Indices: 136209--136535 Score: 216
Period size: 59 Copynumber: 5.4 Consensus size: 58
136199 GGATTGCATG
* * * *
136209 GCCAACACCAAAAAATTTTGTAATTTTTTT-ATCTAAAAAAAG-GGGTGTCGATCATTGCAT
1 GCCAACACCAAAAAA-TTTG--ATTTTTTTAATC-ACAAAAAGAGGATGTCGACCATTACAT
* ** * * * **
136269 GGCCAACACAAAAAAAATTCAAATTTTTT-ATCTGACAAAAAGAGGGTGTCGGCCATGGCAT
1 -GCCAACAC-CAAAAAATTTGATTTTTTTAATC--ACAAAAAGAGGATGTCGACCATTACAT
* * * * *
136330 GACCAACACCAAAAAATTTTGAAATTTTTTT-ATCTAAAAAAAGGGGGTGTCGATCATTGCAT
1 G-CCAACACCAAAAAA-TTTG--ATTTTTTTAATC-ACAAAAAGAGGATGTCGACCATTACAT
* * * *
136392 GACCAACACCTAAAAATTTGATTTTTTTAATCA-AATAAATAGGAATGTCGGCTATTACAT
1 G-CCAACACCAAAAAATTTGATTTTTTTAATCACAA-AAAGAGG-ATGTCGACCATTACAT
** * *
136452 GCCAACACCAAAAAA-TTGATTTTTTTTTTTACAAAAAGAGGGTGTCGACCATTACAT
1 GCCAACACCAAAAAATTTGATTTTTTTAATCACAAAAAGAGGATGTCGACCATTACAT
* *
136509 GGCTAACACCCAAAAATTTGATTTTTT
1 -GCCAACACCAAAAAATTTGATTTTTT
136536 ATCAGATGAA
Statistics
Matches: 216, Mismatches: 37, Indels: 28
0.77 0.13 0.10
Matches are distributed among these distances:
57 13 0.06
58 34 0.16
59 49 0.23
60 29 0.13
61 38 0.18
62 43 0.20
63 10 0.05
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (58 bp):
GCCAACACCAAAAAATTTGATTTTTTTAATCACAAAAAGAGGATGTCGACCATTACAT
Found at i:136524 original size:117 final size:115
Alignment explanation
Indices: 136327--136615 Score: 301
Period size: 117 Copynumber: 2.4 Consensus size: 115
136317 TCGGCCATGG
* * * * * *
136327 CATGACCAACACCAAAAAATTTTGAAATTTTTTTATCTAAAAAAAGGGGGTGTCGATCATTGCAT
1 CATG-CCAACACCAAAAAA--TTG--ATTTTTTTTTTTACAAAAAGAGGGTGTCGACCATTACAT
* * * *
136392 GACCAACACCTAAAAATTTGATTTTTTTAATCAAATAAATAGGAATGTCGGCTATTA
61 GACCAACACCCAAAAATTTGA-TTTTTT-ATCAAATAAATAGGAATATCGACCATTA
* *
136449 CATGCCAACACCAAAAAATTGATTTTTTTTTTTACAAAAAGAGGGTGTCGACCATTACATGGCTA
1 CATGCCAACACCAAAAAATTGATTTTTTTTTTTACAAAAAGAGGGTGTCGACCATTACATGACCA
* * ** *
136514 ACACCCAAAAATTTGATTTTTTATCAGATGAATAGGGGTATCGACCATTG
66 ACACCCAAAAATTTGATTTTTTATCAAATAAATAGGAATATCGACCATTA
* * * *
136564 TATAGCCAACACGAAAAAATTGAATTTTTTTTTGACAAAAA-AGGGGTGTCGA
1 CAT-GCCAACACCAAAAAATTGATTTTTTTTTTTACAAAAAGA-GGGTGTCGA
136616 TCATGTAAAA
Statistics
Matches: 144, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
115 23 0.16
116 49 0.34
117 51 0.35
119 3 0.02
121 14 0.10
122 4 0.03
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (115 bp):
CATGCCAACACCAAAAAATTGATTTTTTTTTTTACAAAAAGAGGGTGTCGACCATTACATGACCA
ACACCCAAAAATTTGATTTTTTATCAAATAAATAGGAATATCGACCATTA
Done.