Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014656.1 Kokia drynarioides strain JFW-HI SEQ_129695, 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: 72202
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Warning! 51 characters in sequence are not A, C, G, or T
Found at i:665 original size:3 final size:3
Alignment explanation
Indices: 657--694 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
647 ATAAAATGCA
657 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
695 AATGCCATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1081 original size:36 final size:35
Alignment explanation
Indices: 1034--1106 Score: 85
Period size: 36 Copynumber: 2.1 Consensus size: 35
1024 GTAAAGCAAT
* *
1034 TAAAATTAAAAGGA-AAAATTAAAATAAATAAATAAA
1 TAAAA-TAAAAAGACAAAATTAAAACAAATAAA-AAA
* *
1070 TAAAATAAAAAGACTAAATTAAAACAAATTAAAAA
1 TAAAATAAAAAGACAAAATTAAAACAAATAAAAAA
1105 TA
1 TA
1107 CAACAGGACC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
35 12 0.38
36 20 0.62
ACGTcount: A:0.71, C:0.03, G:0.04, T:0.22
Consensus pattern (35 bp):
TAAAATAAAAAGACAAAATTAAAACAAATAAAAAA
Found at i:10664 original size:15 final size:15
Alignment explanation
Indices: 10646--10687 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
10636 TGACATTTAA
*
10646 TTTATTGATTTTTTG
1 TTTATTTATTTTTTG
10661 TTTATTTATTTATTTG
1 TTTATTTATTT-TTTG
10677 -TTATTTATTTT
1 TTTATTTATTTT
10688 CATGTCTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 1 0.04
15 20 0.80
16 4 0.16
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (15 bp):
TTTATTTATTTTTTG
Found at i:10669 original size:19 final size:19
Alignment explanation
Indices: 10640--10686 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
10630 TTATTTTGAC
*
10640 ATTTAATTTATTGATTTTTT
1 ATTT-ATTTATTGATTTGTT
* *
10660 GTTTATTTATTTATTTGTT
1 ATTTATTTATTGATTTGTT
10679 ATTTATTT
1 ATTTATTT
10687 TCATGTCTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 20 0.87
20 3 0.13
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.72
Consensus pattern (19 bp):
ATTTATTTATTGATTTGTT
Found at i:10721 original size:13 final size:13
Alignment explanation
Indices: 10703--10770 Score: 52
Period size: 13 Copynumber: 5.3 Consensus size: 13
10693 CTAATCCCAA
10703 TTATATTTATTAT
1 TTATATTTATTAT
* *
10716 TTATATTTGTTCGT
1 TTATATTTATT-AT
**
10730 TTAT-TTTAGCAT
1 TTATATTTATTAT
10742 TTA-ATTT-TTAT
1 TTATATTTATTAT
*
10753 TTTTATTTATTTAT
1 TTATATTTA-TTAT
10767 TTAT
1 TTAT
10771 TTATTTATTT
Statistics
Matches: 40, Mismatches: 10, Indels: 9
0.68 0.17 0.15
Matches are distributed among these distances:
11 4 0.10
12 11 0.28
13 13 0.32
14 12 0.30
ACGTcount: A:0.24, C:0.03, G:0.04, T:0.69
Consensus pattern (13 bp):
TTATATTTATTAT
Found at i:10795 original size:4 final size:4
Alignment explanation
Indices: 10754--10780 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
10744 AATTTTTATT
10754 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
10781 TGTTGTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:11256 original size:31 final size:29
Alignment explanation
Indices: 11175--11263 Score: 97
Period size: 31 Copynumber: 3.0 Consensus size: 29
11165 AATTTACAAT
* * *
11175 AATTGGATCAAATCAAAATTTCATGTATAA
1 AATTGCATAAAATC-AAAGTTCATGTATAA
*
11205 AATTGCATAAAATCAAAGTTCATGTATAC
1 AATTGCATAAAATCAAAGTTCATGTATAA
* *
11234 AATTGCACATTAAATCATAGTTCATGTATA
1 AATTG--CATAAAATCAAAGTTCATGTATA
11264 GTTTTGATAT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
29 18 0.35
30 12 0.24
31 21 0.41
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (29 bp):
AATTGCATAAAATCAAAGTTCATGTATAA
Found at i:15179 original size:13 final size:14
Alignment explanation
Indices: 15161--15200 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
15151 TTTCATATAT
*
15161 ATATAATAAA-AAA
1 ATATAAAAAATAAA
15174 ATATAAAAAAT-AA
1 ATATAAAAAATAAA
15187 A-ATAAAAAATAAA
1 ATATAAAAAATAAA
15200 A
1 A
15201 ATTCTCACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 9 0.38
13 15 0.62
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (14 bp):
ATATAAAAAATAAA
Found at i:15191 original size:12 final size:12
Alignment explanation
Indices: 15163--15200 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
15153 TCATATATAT
15163 ATAATAAAA-AAA
1 ATAA-AAAATAAA
15175 TATAAAAAATAAA
1 -ATAAAAAATAAA
15188 ATAAAAAATAAA
1 ATAAAAAATAAA
15200 A
1 A
15201 ATTCTCACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 17 0.71
13 7 0.29
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (12 bp):
ATAAAAAATAAA
Found at i:16869 original size:52 final size:51
Alignment explanation
Indices: 16790--17022 Score: 259
Period size: 52 Copynumber: 4.5 Consensus size: 51
16780 TTCGCATTTG
* * * *
16790 ATACTCACGATGACACAAAGTCATTGGACCTTTAATCCGCAATGGATTTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTAATCCACAAAGGA-TTCAT
* * * * * **
16842 ATACTTACGATGACACTTAGTCTTTGGATCTTTTAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGA-CCTTTAATCCACAAAGGATTCAT
* * * *
16894 ATACTCACGATGACACATAGCCACCGGACCTTATAATCCACAAGGGATTCGT
1 ATACTCACGATGACACATAGTCATCGGACCTT-TAATCCACAAAGGATTCAT
* * *
16946 ATACTCACGATGACACAGAGTCATCGGACCTCTTAATCCATAAAAGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCT-TTAATCCACAAAGGATTCAT
*
16998 ATACTCACGATGACACTTAGTCATC
1 ATACTCACGATGACACATAGTCATC
17023 AAACCTTTTT
Statistics
Matches: 151, Mismatches: 27, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
51 3 0.02
52 132 0.87
53 16 0.11
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (51 bp):
ATACTCACGATGACACATAGTCATCGGACCTTTAATCCACAAAGGATTCAT
Found at i:17029 original size:104 final size:104
Alignment explanation
Indices: 16790--17022 Score: 297
Period size: 104 Copynumber: 2.2 Consensus size: 104
16780 TTCGCATTTG
* * * * *
16790 ATACTCACGATGACACAAAGTCATTGGACCTTTAATCCGCAATGGATTTCATATACTTACGATGA
1 ATACTCACGATGACACATAGTCATCGGACCTTTAATCCACAAGGGATTTCATATACTCACGATGA
** * * * * * *
16855 CACTTAGTCTTTGGATCTTTTAATCCGTAAAGGATTCAT
66 CACAGAGTCATCGGACCTCTTAATCCATAAAAGATTCAT
* * *
16894 ATACTCACGATGACACATAGCCACCGGACCTTATAATCCACAAGGGA-TTCGTATACTCACGATG
1 ATACTCACGATGACACATAGTCATCGGACCTT-TAATCCACAAGGGATTTCATATACTCACGATG
16958 ACACAGAGTCATCGGACCTCTTAATCCATAAAAGATTCAT
65 ACACAGAGTCATCGGACCTCTTAATCCATAAAAGATTCAT
*
16998 ATACTCACGATGACACTTAGTCATC
1 ATACTCACGATGACACATAGTCATC
17023 AAACCTTTTT
Statistics
Matches: 109, Mismatches: 19, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
104 97 0.89
105 12 0.11
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (104 bp):
ATACTCACGATGACACATAGTCATCGGACCTTTAATCCACAAGGGATTTCATATACTCACGATGA
CACAGAGTCATCGGACCTCTTAATCCATAAAAGATTCAT
Found at i:22867 original size:21 final size:21
Alignment explanation
Indices: 22820--22897 Score: 95
Period size: 21 Copynumber: 3.7 Consensus size: 21
22810 AATGGTGCAG
* *
22820 ATTTCTATCGATACCTA-TATT
1 ATTTCTATCGATA-CAAGTATA
* *
22841 AGTTCTATCGATATAAGTATA
1 ATTTCTATCGATACAAGTATA
*
22862 ATTTCTACCGATACAAGTATA
1 ATTTCTATCGATACAAGTATA
22883 ATTTCTATCGATACA
1 ATTTCTATCGATACA
22898 TGTCATGCAT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
20 1 0.02
21 47 0.98
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.40
Consensus pattern (21 bp):
ATTTCTATCGATACAAGTATA
Found at i:23619 original size:52 final size:50
Alignment explanation
Indices: 23557--23849 Score: 309
Period size: 52 Copynumber: 5.7 Consensus size: 50
23547 TTCGCATTTG
* ** **
23557 ATACTCACGATGACACAAAGTCATTAGACCTTTAATCCACAATAGATTTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTTTAATCCGTAA-AGA-TTCAT
* *
23609 ATACTCACGATGACACTTAGTCATTGGACCTTTTAATCCGTAAAGAATTCAT
1 ATACTCACGATGACACATAGTCATCGGACC-TTTAATCCGTAAAG-ATTCAT
* * * *
23661 ATACTCACGATGACACATAGCCACCGGACCTTATAATCC-AAAAGGGATTCGT
1 ATACTCACGATGACACATAGTCATCGGACCTT-TAATCCGTAAA--GATTCAT
*
23713 ATACTCACGATGACACAAAGTCATCGGACCTCTTAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCT-TTAATCCGTAAA-GATTCAT
* * *
23765 ATACTCACGATGACACTTAGTCATCAGACGTTTTAATCCGTAAAGAATTCAT
1 ATACTCACGATGACACATAGTCATCGGAC-CTTTAATCCGTAAAG-ATTCAT
* * * *
23817 ATACTAAGGATGACACTTAGTCGTCGGACCTTT
1 ATACTCACGATGACACATAGTCATCGGACCTTT
23850 TTATCTATGG
Statistics
Matches: 207, Mismatches: 25, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
51 9 0.04
52 181 0.87
53 17 0.08
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (50 bp):
ATACTCACGATGACACATAGTCATCGGACCTTTAATCCGTAAAGATTCAT
Found at i:27004 original size:12 final size:12
Alignment explanation
Indices: 26987--27044 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 12
26977 AAACTAGCAA
26987 AAAAAGAAGAAG
1 AAAAAGAAGAAG
26999 AAAAAGATAG-A-
1 AAAAAGA-AGAAG
27010 AAAAAGAA-AA-
1 AAAAAGAAGAAG
27020 AAAAA-AAGAAG
1 AAAAAGAAGAAG
* *
27031 AAACAGAAAAAG
1 AAAAAGAAGAAG
27043 AA
1 AA
27045 GGGACCGAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
9 2 0.05
10 9 0.23
11 11 0.28
12 15 0.38
13 2 0.05
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (12 bp):
AAAAAGAAGAAG
Found at i:27010 original size:13 final size:11
Alignment explanation
Indices: 26985--27033 Score: 55
Period size: 12 Copynumber: 4.3 Consensus size: 11
26975 TCAAACTAGC
26985 AAAAAAAGAAG
1 AAAAAAAGAAG
26996 AAGAAAAAGATAG
1 AA-AAAAAGA-AG
*
27009 -AAAAAAGAAAA
1 AAAAAAAG-AAG
27020 AAAAAAAGAAG
1 AAAAAAAGAAG
27031 AAA
1 AAA
27034 CAGAAAAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
11 14 0.44
12 16 0.50
13 2 0.06
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (11 bp):
AAAAAAAGAAG
Found at i:27012 original size:23 final size:22
Alignment explanation
Indices: 26986--27041 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
26976 CAAACTAGCA
* *
26986 AAAAAAGAAGAAGAAAAAGATAG
1 AAAAAAGAAAAAAAAAAAGA-AG
27009 AAAAAAGAAAAAAAAAAAGAAG
1 AAAAAAGAAAAAAAAAAAGAAG
*
27031 -AAACAGAAAAA
1 AAAAAAGAAAAA
27042 GAAGGGACCG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 10 0.33
22 2 0.07
23 18 0.60
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (22 bp):
AAAAAAGAAAAAAAAAAAGAAG
Found at i:28147 original size:49 final size:49
Alignment explanation
Indices: 28075--28477 Score: 239
Period size: 49 Copynumber: 8.2 Consensus size: 49
28065 ATCCTAGAGT
* *
28075 TGAAGAGGGAAAGATTAAAGCCGCATCGGCAGATCTTACACTTTAAAAC
1 TGAAGAGGGAAAGATTAAAGCCGCAACGACAGATCTTACACTTTAAAAC
* * * * * *
28124 TGAAGAGGGATAGGTTAAAGCCGCAACGACAGACCTAACACTCTAAAAT
1 TGAAGAGGGAAAGATTAAAGCCGCAACGACAGATCTTACACTTTAAAAC
* * * * * *
28173 TGAAGAGGGAAAGATTAAAGCCGTAACGATAAATTTTACACCTTGAAAC
1 TGAAGAGGGAAAGATTAAAGCCGCAACGACAGATCTTACACTTTAAAAC
* * * ** **
28222 TGAAGAGGGATAGATTAAAGCCTCAATGATGGATC-TAGCACCCTAAAAGC
1 TGAAGAGGGAAAGATTAAAGCCGCAACGACAGATCTTA-CACTTTAAAA-C
* * * ** *
28272 -GAAAAGGGAAAGATTGAAGCCGCAACGGC-GAATCTTACACCATGAAA-
1 TGAAGAGGGAAAGATTAAAGCCGCAACGACAG-ATCTTACACTTTAAAAC
* * * * * * **
28319 TCAA-AGAGGAATAAATTAAAGCCACAATGACGGATCTAACACCCTAAAAC
1 TGAAGAG-GGAA-AGATTAAAGCCGCAACGACAGATCTTACACTTTAAAAC
* ** * * * * *
28369 TGAAGAGGGATAA-ATTAAAGTCATAAGGGC-GAATCTAACA-TCCTAAAAT
1 TGAAGAGGGA-AAGATTAAAGCCGCAACGACAG-ATCTTACACT-TTAAAAC
* * **
28418 TGAAGAGGGAAAGATTAAAGCCGCAATGACAAATCTTACACCCTAAAA-
1 TGAAGAGGGAAAGATTAAAGCCGCAACGACAGATCTTACACTTTAAAAC
28466 TAGAAGAGGGAA
1 T-GAAGAGGGAA
28478 GTATTGAACC
Statistics
Matches: 275, Mismatches: 62, Indels: 34
0.74 0.17 0.09
Matches are distributed among these distances:
47 2 0.01
48 13 0.05
49 246 0.89
50 11 0.04
51 3 0.01
ACGTcount: A:0.43, C:0.17, G:0.22, T:0.18
Consensus pattern (49 bp):
TGAAGAGGGAAAGATTAAAGCCGCAACGACAGATCTTACACTTTAAAAC
Found at i:28243 original size:98 final size:98
Alignment explanation
Indices: 28074--28514 Score: 426
Period size: 98 Copynumber: 4.5 Consensus size: 98
28064 AATCCTAGAG
* * * * *
28074 TTGAAGAGGGAAAGATTAAAGCCGCATCGGC-AGATCTTACACTTTAAAACTGAAGAGGGATAGG
1 TTGAAGAGGGAAAGATTAAAGCCGTAACGGCGA-ATCTTACACCTTGAAACTGAAGAGGGATAGA
* * *
28138 TTAAAGCCGCAACGACAGACCTAACACTCTAAAA
65 TTAAAGCCGCAATGACAGATCTAACACCCTAAAA
*** *
28172 TTGAAGAGGGAAAGATTAAAGCCGTAACGATAAATTTTACACCTTGAAACTGAAGAGGGATAGAT
1 TTGAAGAGGGAAAGATTAAAGCCGTAACGGCGAATCTTACACCTTGAAACTGAAGAGGGATAGAT
* ** *
28237 TAAAGCCTCAATGATGGATCTAGCACCCTAAAA
66 TAAAGCCGCAATGACAGATCTAACACCCTAAAA
** * * * * * * *
28270 GCGAAAAGGGAAAGATTGAAGCCGCAACGGCGAATCTTACACCATGAAA-TCAAAGAGGAATAAA
1 TTGAAGAGGGAAAGATTAAAGCCGTAACGGCGAATCTTACACCTTGAAACT-GAAGAGGGATAGA
* *
28334 TTAAAGCCACAATGACGGATCTAACACCCTAAAA
65 TTAAAGCCGCAATGACAGATCTAACACCCTAAAA
* * * * * * * *
28368 CTGAAGAGGGATAA-ATTAAAGTCATAAGGGCGAATCTAACATCC-TAAAATTGAAGAGGGAAAG
1 TTGAAGAGGGA-AAGATTAAAGCCGTAACGGCGAATCTTACA-CCTTGAAACTGAAGAGGGATAG
* *
28431 ATTAAAGCCGCAATGACAAATCTTACACCCTAAAA
64 ATTAAAGCCGCAATGACAGATCTAACACCCTAAAA
* * *
28466 TAGAAGAGGG-AAGTATTGAA-CCGTAACGGTGAATCTTACACCTTAGAAA
1 TTGAAGAGGGAAAG-ATTAAAGCCGTAACGGCGAATCTTACACCTT-GAAA
28515 AACACTGAAG
Statistics
Matches: 276, Mismatches: 58, Indels: 18
0.78 0.16 0.05
Matches are distributed among these distances:
96 4 0.01
97 17 0.06
98 249 0.90
99 6 0.02
ACGTcount: A:0.42, C:0.17, G:0.21, T:0.19
Consensus pattern (98 bp):
TTGAAGAGGGAAAGATTAAAGCCGTAACGGCGAATCTTACACCTTGAAACTGAAGAGGGATAGAT
TAAAGCCGCAATGACAGATCTAACACCCTAAAA
Found at i:28473 original size:147 final size:146
Alignment explanation
Indices: 28118--28474 Score: 342
Period size: 147 Copynumber: 2.4 Consensus size: 146
28108 TCTTACACTT
* * * * * * *
28118 TAAAACTGAAGAGGGATAGGTTAAAGCCGCAACGACAGACCTAACACTCTAAAATTGAAGAGGGA
1 TAAAACTGAAGAGGGAAAGATTAAAGCCGCAACGACAAATCTTACACCCTAAAATAGAAGA-GGA
* ** * * * * * * *
28183 AAGATTAAAGCCGTAACGATAAATTTTACACCTTGAAACTGAAGAGGGATAGATTAAAGCCTCAA
65 AAAATTAAAGCCACAACGACAAATCTAACACCCTAAAACTGAAGAGGGATAAATTAAAGCATCAA
* * * *
28248 TGATGGATCTAGCACCC
130 GGACGAATCTAACACCC
* * * * * *
28265 TAAAAGC-GAAAAGGGAAAGATTGAAGCCGCAACGGCGAATCTTACACCATGAAATCA-AAGAGG
1 TAAAA-CTGAAGAGGGAAAGATTAAAGCCGCAACGACAAATCTTACACCCTAAAAT-AGAAGAGG
* **
28328 AATAAATTAAAGCCACAATGACGGATCTAACACCCTAAAACTGAAGAGGGATAAATTAAAGTCAT
64 AA-AAATTAAAGCCACAACGACAAATCTAACACCCTAAAACTGAAGAGGGATAAATTAAAG-CAT
* *
28393 -AAGGGCGAATCTAACATCC
127 CAAGGACGAATCTAACACCC
* *
28412 TAAAATTGAAGAGGGAAAGATTAAAGCCGCAATGACAAATCTTACACCCTAAAATAGAAGAGG
1 TAAAACTGAAGAGGGAAAGATTAAAGCCGCAACGACAAATCTTACACCCTAAAATAGAAGAGG
28475 GAAGTATTGA
Statistics
Matches: 164, Mismatches: 40, Indels: 12
0.76 0.19 0.06
Matches are distributed among these distances:
146 5 0.03
147 156 0.95
148 3 0.02
ACGTcount: A:0.44, C:0.17, G:0.21, T:0.18
Consensus pattern (146 bp):
TAAAACTGAAGAGGGAAAGATTAAAGCCGCAACGACAAATCTTACACCCTAAAATAGAAGAGGAA
AAATTAAAGCCACAACGACAAATCTAACACCCTAAAACTGAAGAGGGATAAATTAAAGCATCAAG
GACGAATCTAACACCC
Found at i:29062 original size:23 final size:22
Alignment explanation
Indices: 29012--29055 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
29002 TAAACTAAAA
29012 AATGGAAAAACCTAGCAATTGC
1 AATGGAAAAACCTAGCAATTGC
29034 AATGGAAAAACCTAGCAATTGC
1 AATGGAAAAACCTAGCAATTGC
29056 CCTTGGATGC
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:0.18, G:0.18, T:0.18
Consensus pattern (22 bp):
AATGGAAAAACCTAGCAATTGC
Found at i:29458 original size:3 final size:3
Alignment explanation
Indices: 29450--29493 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
29440 GAGTTCGTCT
29450 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
29494 TAGTTGTTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:29642 original size:15 final size:15
Alignment explanation
Indices: 29622--29663 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
29612 AATTTTAATT
29622 TTTATTTATTTTTTG
1 TTTATTTATTTTTTG
*
29637 TTTATTTATCTTGTTG
1 TTTATTTAT-TTTTTG
29653 -TTATTTATTTT
1 TTTATTTATTTT
29664 CATGTCATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 2 0.08
15 17 0.71
16 5 0.21
ACGTcount: A:0.14, C:0.02, G:0.07, T:0.76
Consensus pattern (15 bp):
TTTATTTATTTTTTG
Found at i:30070 original size:29 final size:28
Alignment explanation
Indices: 29992--30070 Score: 65
Period size: 29 Copynumber: 2.7 Consensus size: 28
29982 TTAATCAATA
*
29992 TTTATTGTCATTATT-ATTATGATTATATT
1 TTTATTGT--TTATTAATTATAATTATATT
*
30021 GTTA-T-TTTATTTAATACTATAATTATATT
1 TTTATTGTTTA-TTAAT--TATAATTATATT
30050 TTTATTGTGTTATTAATTATA
1 TTTATTGT-TTATTAATTATA
30071 TTTAACTGTC
Statistics
Matches: 40, Mismatches: 3, Indels: 14
0.70 0.05 0.25
Matches are distributed among these distances:
25 3 0.08
26 2 0.05
27 3 0.08
28 1 0.03
29 21 0.52
30 1 0.03
31 6 0.15
32 3 0.08
ACGTcount: A:0.30, C:0.03, G:0.06, T:0.61
Consensus pattern (28 bp):
TTTATTGTTTATTAATTATAATTATATT
Found at i:35280 original size:25 final size:25
Alignment explanation
Indices: 35252--35300 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
35242 TTTTATTCAA
35252 AATACATAAATTGCCCCTAACTTTT
1 AATACATAAATTGCCCCTAACTTTT
* * * *
35277 AATACTTATATTGTCCCTACCTTT
1 AATACATAAATTGCCCCTAACTTT
35301 AACTTTTAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.31, C:0.24, G:0.04, T:0.41
Consensus pattern (25 bp):
AATACATAAATTGCCCCTAACTTTT
Found at i:37441 original size:21 final size:21
Alignment explanation
Indices: 37417--37459 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
37407 ATAATTTGAA
37417 TCTCAAATGATATTACAAATG
1 TCTCAAATGATATTACAAATG
* *
37438 TCTCAAATGTTATTATAAATG
1 TCTCAAATGATATTACAAATG
37459 T
1 T
37460 GTAACAATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.40
Consensus pattern (21 bp):
TCTCAAATGATATTACAAATG
Found at i:48475 original size:81 final size:81
Alignment explanation
Indices: 48335--48497 Score: 317
Period size: 81 Copynumber: 2.0 Consensus size: 81
48325 AATAAATAGT
48335 CAAAAAAAGATTACATATGGATGACATTTATAAACTCTAGTTTAACATTATTGTTTAGACACATA
1 CAAAAAAAGATTACATATGGATGACATTTATAAACTCTAGTTTAACATTATTGTTTAGACACATA
48400 ATAGGTATCTAAAGAC
66 ATAGGTATCTAAAGAC
*
48416 CAAACAAAGATTACATATGGATGACATTTATAAACTCTAGTTTAACATTATTGTTTAGACACATA
1 CAAAAAAAGATTACATATGGATGACATTTATAAACTCTAGTTTAACATTATTGTTTAGACACATA
48481 ATAGGTATCTAAAGAC
66 ATAGGTATCTAAAGAC
48497 C
1 C
48498 CTAGAGAAAA
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 81 1.00
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.32
Consensus pattern (81 bp):
CAAAAAAAGATTACATATGGATGACATTTATAAACTCTAGTTTAACATTATTGTTTAGACACATA
ATAGGTATCTAAAGAC
Found at i:56075 original size:45 final size:46
Alignment explanation
Indices: 55993--56081 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 46
55983 TTAGCTGAAG
*
55993 ATCTAGCAATAAGTTGAATTTCTATTAATGAATATACTAATACGAC
1 ATCTAGCAATAAGTTGAACTTCTATTAATGAATATACTAATACGAC
*
56039 ATCTAGCAATAAGTTGGACTT-TATTAATGAATATACTAATACG
1 ATCTAGCAATAAGTTGAACTTCTATTAATGAATATACTAATACG
56082 GCAGAAGTAG
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 22 0.54
46 19 0.46
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (46 bp):
ATCTAGCAATAAGTTGAACTTCTATTAATGAATATACTAATACGAC
Found at i:59844 original size:44 final size:44
Alignment explanation
Indices: 59785--59882 Score: 112
Period size: 43 Copynumber: 2.2 Consensus size: 44
59775 CAAGATAGAG
* * *
59785 AAAGTTACGT-GAAAAAGGCCACATT-CAAGAAACGAC-AAAGAAA
1 AAAGCTACGTGGAAAAA-ACCAC-TTCCAAGAAACGACAAAAAAAA
* *
59828 GAAGCTACGTGGAAAAAACCACTTCCAAGAAATGACAAAAAAAA
1 AAAGCTACGTGGAAAAAACCACTTCCAAGAAACGACAAAAAAAA
59872 AAAGCTACGTG
1 AAAGCTACGTG
59883 AAAGCCACCC
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
42 2 0.04
43 22 0.48
44 22 0.48
ACGTcount: A:0.52, C:0.17, G:0.18, T:0.12
Consensus pattern (44 bp):
AAAGCTACGTGGAAAAAACCACTTCCAAGAAACGACAAAAAAAA
Found at i:60607 original size:15 final size:16
Alignment explanation
Indices: 60568--60610 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
60558 TAATTTGTAG
* *
60568 TAATATATAATATTAT
1 TAATAAATAAAATTAT
*
60584 TACTAAATAAAATT-T
1 TAATAAATAAAATTAT
60599 TAATAAATAAAA
1 TAATAAATAAAA
60611 ATAATAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (16 bp):
TAATAAATAAAATTAT
Found at i:60674 original size:33 final size:33
Alignment explanation
Indices: 60627--60694 Score: 86
Period size: 33 Copynumber: 2.0 Consensus size: 33
60617 AAATTATTAA
60627 ATATTCAATATTAAA-TTAAAAAAATATAAATAT
1 ATATTCAATATTAAATTTAAAAAAA-ATAAATAT
*
60660 ATATTC-ATATTTAAATTTTTAAAAAAATAAATAT
1 ATATTCAATA-TTAAA-TTTAAAAAAAATAAATAT
60694 A
1 A
60695 AATAAACTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
32 3 0.10
33 11 0.35
34 9 0.29
35 8 0.26
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (33 bp):
ATATTCAATATTAAATTTAAAAAAAATAAATAT
Done.