Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000177.1 Kokia drynarioides strain JFW-HI SEQ_110851, 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: 82758
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:741 original size:2 final size:2
Alignment explanation
Indices: 722--760 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
712 AAAGACCAGG
* *
722 GA GA GG GA GA GG GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
761 CAAGCTTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (2 bp):
GA
Found at i:989 original size:2 final size:2
Alignment explanation
Indices: 984--1010 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
974 ATATATATAT
984 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1011 TGATATTATT
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1561 original size:18 final size:19
Alignment explanation
Indices: 1534--1570 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
1524 CTATTAAATC
*
1534 TATCATATCA-ATAAATAG
1 TATCACATCATATAAATAG
1552 TATCACATCATATAAATAG
1 TATCACATCATATAAATAG
1571 ACAATTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.49, C:0.14, G:0.05, T:0.32
Consensus pattern (19 bp):
TATCACATCATATAAATAG
Found at i:1922 original size:23 final size:24
Alignment explanation
Indices: 1878--1922 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
1868 TCACACGTAA
* *
1878 ACCCAATTACAATATTTAAACCCG
1 ACCCAACTACAATATATAAACCCG
*
1902 ACCCAACTA-AATATATGAACC
1 ACCCAACTACAATATATAAACC
1923 TCTAGCAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 10 0.56
24 8 0.44
ACGTcount: A:0.44, C:0.29, G:0.04, T:0.22
Consensus pattern (24 bp):
ACCCAACTACAATATATAAACCCG
Found at i:2404 original size:6 final size:6
Alignment explanation
Indices: 2394--2423 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
2384 TGTGGGCTAC
*
2394 AGCCTC AGCCTT AGCCTT AGCCTT AGCCTT
1 AGCCTT AGCCTT AGCCTT AGCCTT AGCCTT
2424 TAGGCTACAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.37, G:0.17, T:0.30
Consensus pattern (6 bp):
AGCCTT
Found at i:3282 original size:45 final size:45
Alignment explanation
Indices: 3191--3279 Score: 162
Period size: 44 Copynumber: 2.0 Consensus size: 45
3181 TCCTAATTTA
3191 GTATCTATATATTTTTTTATCCAATTTGACACTTAAAAACTTTTT
1 GTATCTATATATTTTTTTATCCAATTTGACACTTAAAAACTTTTT
*
3236 GTATCTATAT-TTTTTTTATCTAATTTGACACTTAAAAACTTTTT
1 GTATCTATATATTTTTTTATCCAATTTGACACTTAAAAACTTTTT
3280 TGTCTTCAGT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 33 0.77
45 10 0.23
ACGTcount: A:0.30, C:0.12, G:0.04, T:0.53
Consensus pattern (45 bp):
GTATCTATATATTTTTTTATCCAATTTGACACTTAAAAACTTTTT
Found at i:10546 original size:67 final size:63
Alignment explanation
Indices: 10462--10607 Score: 229
Period size: 67 Copynumber: 2.2 Consensus size: 63
10452 TTTTATAAAT
10462 ATAAATAAATATAAAATAATATTAATTTTATTTTATTATTTATTTATTTATTATTGTATGAATAT
1 ATAAATAAATATAAAATAATATTAATTTTATTTTATTATTTATTTA-TTA-T-TT-TATGAATAT
10527 AA
62 AA
* *
10529 ATAAATAAATGTAAAATAATATTAATTTTGTTTTATTATTTATTTATTATTTTATGAATATAA
1 ATAAATAAATATAAAATAATATTAATTTTATTTTATTATTTATTTATTATTTTATGAATATAA
10592 ATAAATAAATAATAAA
1 ATAAATAAAT-ATAAA
10608 CCCAAAGTCA
Statistics
Matches: 75, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
63 21 0.28
64 6 0.08
65 1 0.01
66 3 0.04
67 44 0.59
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.49
Consensus pattern (63 bp):
ATAAATAAATATAAAATAATATTAATTTTATTTTATTATTTATTTATTATTTTATGAATATAA
Found at i:15625 original size:6 final size:6
Alignment explanation
Indices: 15609--15652 Score: 52
Period size: 6 Copynumber: 6.8 Consensus size: 6
15599 AAAAAAGAGA
*
15609 AAAAGAG AAAAAG AAAAGG AAAAAG AAGAAAAG AAAAAG AAAAA
1 AAAA-AG AAAAAG AAAAAG AAAAAG -A-AAAAG AAAAAG AAAAA
15653 TGGGAGGTCG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
6 22 0.67
7 6 0.18
8 5 0.15
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:15632 original size:21 final size:20
Alignment explanation
Indices: 15601--15652 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 20
15591 AAAAAAGGAA
15601 AAAAGAGAAAAAG-AGAAAAAG
1 AAAA-AGAAAAAGAAG-AAAAG
*
15622 AAAAGGAAAAAGAAGAAAAG
1 AAAAAGAAAAAGAAGAAAAG
15642 AAAAAGAAAAA
1 AAAAAGAAAAA
15653 TGGGAGGTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 22 0.79
21 6 0.21
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (20 bp):
AAAAAGAAAAAGAAGAAAAG
Found at i:16751 original size:50 final size:50
Alignment explanation
Indices: 16559--16750 Score: 231
Period size: 50 Copynumber: 3.8 Consensus size: 50
16549 CGATAGAACA
** * *
16559 ACAAATCTTTTACCCCTAAAAGCTGTGGAGGTGCAGATTGAAACTGCAATG
1 ACAAATCTCATACACCT-AAAGCTGTAGAGGTGCAGATTGAAACTGCAATG
* * * *
16610 GCAAATCTCATACACCTAAAGCTGTGGAGGTGCAGATTGAAACCGTAATG
1 ACAAATCTCATACACCTAAAGCTGTAGAGGTGCAGATTGAAACTGCAATG
* * * * *
16660 ACAAATCTCATACACTTAAAGCTGTAGTGGGGCAGAATGAAGCTGCAATG
1 ACAAATCTCATACACCTAAAGCTGTAGAGGTGCAGATTGAAACTGCAATG
* * *
16710 ACAAATCTCATTCACCTAAAGCTGTAGAGGAGAAGATTGAA
1 ACAAATCTCATACACCTAAAGCTGTAGAGGTGCAGATTGAA
16751 GTCACAAGTA
Statistics
Matches: 120, Mismatches: 21, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
50 107 0.89
51 13 0.11
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (50 bp):
ACAAATCTCATACACCTAAAGCTGTAGAGGTGCAGATTGAAACTGCAATG
Found at i:16946 original size:80 final size:80
Alignment explanation
Indices: 16808--17459 Score: 1003
Period size: 80 Copynumber: 8.2 Consensus size: 80
16798 TACAACCTCC
* * *
16808 AATCTTTTACCCTAACTAGAGGGCAAGATTGAAGACTATCCGATCTTTTACCCTGATCATGGGGC
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
*
16873 AAATTGAAGAAATCT
66 AGATTGAAGAAATCT
* *
16888 AATCTTTTACCCTAACCAGAGGGCAAGATTAAAAACCATCCGATCTTTTACCCCGATCATGGGGC
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
16953 AGATTGAAGAAATCCT
66 AGATTGAAGAAAT-CT
* *
16969 -ATCTTTTACCCTAATCAGAGGGCAAGATTGAAGACTATCCGATCTTTTACCCCGATCATGGGGC
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
17033 AGATTGAAGAAAT-T
66 AGATTGAAGAAATCT
* *
17047 CAATCTTTTATCCC-AACTAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATAGG
1 -AATCTTTTA-CCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGG
*
17111 GTAGATTGAAGAAA-CTT
64 GCAGATTGAAGAAATC-T
17128 AATCTTTTATCCC-AACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGG
1 AATCTTTTA-CCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGG
*
17192 CA-ATT-AAGGAAATCC
65 CAGATTGAA-GAAATCT
* * *
17207 AATCATTTACCTTAATCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
*
17272 AGATTGAAGAAATCC
66 AGATTGAAGAAATCT
*
17287 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGATCATCCGATCTTTTACCCCGATCATGGGGC
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
17352 AGATTGAAGAAATCT
66 AGATTGAAGAAATCT
* * * *
17367 AATCTTTTACCCTAACTAAAGGGCAAGATTGAAGACCATCCAATCTTTTACCCCGATCATGGGAC
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
*
17432 AGATTGAAGAAATCC
66 AGATTGAAGAAATCT
17447 AATCTTTTACCCT
1 AATCTTTTACCCT
17460 GACTATGGCG
Statistics
Matches: 528, Mismatches: 33, Indels: 22
0.91 0.06 0.04
Matches are distributed among these distances:
78 5 0.01
79 67 0.13
80 448 0.85
81 8 0.02
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (80 bp):
AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
AGATTGAAGAAATCT
Found at i:17392 original size:319 final size:320
Alignment explanation
Indices: 16808--17459 Score: 1050
Period size: 319 Copynumber: 2.0 Consensus size: 320
16798 TACAACCTCC
* * *
16808 AATCTTTTACCCTAACTAGAGGGCAAGATTGAAGACTATCCGATCTTTTACCCTGATCATGGGGC
1 AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
* *
16873 AAATTGAAGAAATCTAATCTTTTACCCTAACCAGAGGGCAAGATTAAAAACCATCCGATCTTTTA
66 AAATTGAAGAAATCCAATCATTTACCCTAACCAGAGGGCAAGATTAAAAACCATCCGATCTTTTA
* *
16938 CCCCGATCATGGGGCAGATTGAAGAAATCCTATCTTTTACCCTAATCAGAGGGCAAGATTGAAGA
131 CCCCGATCATGGGGCAGATTGAAGAAATCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGA
*
17003 CTATCCGATCTTTTACCCCGATCATGGGGCAGATTGAAGAAATTCAATCTTTTATCCCAACTAGA
196 CTATCCGATCTTTTACCCCGATCATGGGGCAGATTGAAGAAATTCAATCTTTTATCCCAACTAAA
* *
17068 GGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATAGGG-TAGATTGAAGAAACTT
261 GGGCAAGATTGAAGACCATCCAATCTTTTACCCCGATCAT-GGGACAGATTGAAGAAACTT
17128 AATCTTTTATCCC-AACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGG
1 AATCTTTTA-CCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGG
* * * *
17192 C-AATT-AAGGAAATCCAATCATTTACCTTAATCAGAGGGCAAGATTGAAGACCATCCGATCTTT
65 CAAATTGAA-GAAATCCAATCATTTACCCTAACCAGAGGGCAAGATTAAAAACCATCCGATCTTT
17255 TACCCCGATCATGGGGCAGATTGAAGAAATCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAA
129 TACCCCGATCATGGGGCAGATTGAAGAAATCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAA
17320 GA-TCATCCGATCTTTTACCCCGATCATGGGGCAGATTGAAGAAA-TCTAATCTTTTA-CCCTAA
194 GACT-ATCCGATCTTTTACCCCGATCATGGGGCAGATTGAAGAAATTC-AATCTTTTATCCC-AA
17382 CTAAAGGGCAAGATTGAAGACCATCCAATCTTTTACCCCGATCATGGGACAGATTGAAGAAA-TC
256 CTAAAGGGCAAGATTGAAGACCATCCAATCTTTTACCCCGATCATGGGACAGATTGAAGAAACT-
*
17446 C
320 T
17447 AATCTTTTACCCT
1 AATCTTTTACCCT
17460 GACTATGGCG
Statistics
Matches: 309, Mismatches: 15, Indels: 17
0.91 0.04 0.05
Matches are distributed among these distances:
318 15 0.05
319 233 0.75
320 58 0.19
321 3 0.01
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (320 bp):
AATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGGGGC
AAATTGAAGAAATCCAATCATTTACCCTAACCAGAGGGCAAGATTAAAAACCATCCGATCTTTTA
CCCCGATCATGGGGCAGATTGAAGAAATCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGA
CTATCCGATCTTTTACCCCGATCATGGGGCAGATTGAAGAAATTCAATCTTTTATCCCAACTAAA
GGGCAAGATTGAAGACCATCCAATCTTTTACCCCGATCATGGGACAGATTGAAGAAACTT
Found at i:17575 original size:39 final size:39
Alignment explanation
Indices: 16805--17577 Score: 523
Period size: 39 Copynumber: 19.4 Consensus size: 39
16795 AGTTACAACC
** * *
16805 TCCAATCTTTTACCCTAACTA-GAGGGCAAGATTGAAGACTA
1 TCCAATCTTTTACCCCGACCATG-GGGC-AGATTGAAGA-AA
* * * *
16846 TCCGATCTTTTACCCTGATCATGGGGCAAATTGAAGAAA
1 TCCAATCTTTTACCCCGACCATGGGGCAGATTGAAGAAA
* ** *
16885 TCTAATCTTTTACCCTAACCA-GAGGGCAAGATT-AAAAACCA
1 TCCAATCTTTTACCCCGACCATG-GGGC-AGATTGAAGAA--A
* *
16926 TCCGATCTTTTACCCCGATCATGGGGCAGATTGAAGAAA
1 TCCAATCTTTTACCCCGACCATGGGGCAGATTGAAGAAA
* ** * *
16965 TCCTATCTTTTACCCTAATCA-GAGGGCAAGATTGAAGACTA
1 TCCAATCTTTTACCCCGACCATG-GGGC-AGATTGAAGA-AA
* *
17006 TCCGATCTTTTACCCCGATCATGGGGCAGATTGAAGAAA
1 TCCAATCTTTTACCCCGACCATGGGGCAGATTGAAGAAA
* * * * *
17045 TTCAATCTTTTATCCCAACTA-GAGGGCAAGATTGAAGACCA
1 TCCAATCTTTTACCCCGACCATG-GGGC-AGATTGAAGA-AA
* * * *
17086 TCCGATCTTTTACCCCGATCATAGGGTAGATTGAAGAAA
1 TCCAATCTTTTACCCCGACCATGGGGCAGATTGAAGAAA
* * * *
17125 -CTTAATCTTTTATCCCAACCA-GAGGGCAAGATTGAAGACCA
1 TC-CAATCTTTTACCCCGACCATG-GGGC-AGATTGAAGA-AA
* *
17166 TCCGATCTTTTACCCCGATCATGGGGCA-ATT-AAGGAAA
1 TCCAATCTTTTACCCCGACCATGGGGCAGATTGAA-GAAA
* *** * *
17204 TCCAATCATTTACCTTAATCA-GAGGGCAAGATTGAAGACCA
1 TCCAATCTTTTACCCCGACCATG-GGGC-AGATTGAAGA-AA
* *
17245 TCCGATCTTTTACCCCGATCATGGGGCAGATTGAAGAAA
1 TCCAATCTTTTACCCCGACCATGGGGCAGATTGAAGAAA
** *
17284 TCCAATCTTTTACCCTAACCA-GAGGGCAAGATTGAAGATCA
1 TCCAATCTTTTACCCCGACCATG-GGGC-AGATTGAAGA-AA
* *
17325 TCCGATCTTTTACCCCGATCATGGGGCAGATTGAAGAAA
1 TCCAATCTTTTACCCCGACCATGGGGCAGATTGAAGAAA
* ** * ** *
17364 TCTAATCTTTTACCCTAACTAAAGGGCAAGATTGAAGACCA
1 TCCAATCTTTTACCCCGACCATGGGGC-AGATTGAAGA-AA
* *
17405 TCCAATCTTTTACCCCGATCATGGGACAGATTGAAGAAA
1 TCCAATCTTTTACCCCGACCATGGGGCAGATTGAAGAAA
* * * * *
17444 TCCAATCTTTTACCCTGACTATGGCGTAGATTGAAGCAA
1 TCCAATCTTTTACCCCGACCATGGGGCAGATTGAAGAAA
* * * *
17483 TCCAATCTTTTA-CCCTAGC-TAGAGGGCAGATTAAAGACCA
1 TCCAATCTTTTACCCCGACCAT-G-GGGCAGATTGAAGA-AA
* * * *
17523 T-TAGATCTCTTACCCCGACCATGGAGCAGATTTAA-ATAA
1 TCCA-ATCTTTTACCCCGACCATGGGGCAGATTGAAGA-AA
17562 TCCAATCTTTTACCCC
1 TCCAATCTTTTACCCC
17578 TAAAACTATA
Statistics
Matches: 569, Mismatches: 122, Indels: 84
0.73 0.16 0.11
Matches are distributed among these distances:
37 2 0.00
38 32 0.06
39 205 0.36
40 144 0.25
41 178 0.31
42 8 0.01
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (39 bp):
TCCAATCTTTTACCCCGACCATGGGGCAGATTGAAGAAA
Found at i:18199 original size:59 final size:60
Alignment explanation
Indices: 18099--18271 Score: 235
Period size: 63 Copynumber: 2.9 Consensus size: 60
18089 TCATTTTTCT
* * *
18099 TATTATTTTTA-TTTATTTATTTA-TTATGATTTTCATAAATATAAATAAATAT-AAAATAA
1 TATTAATTTTATTTTA-TTATTTATTTATTATTTT-ATGAATATAAATAAATATAAAAATAA
*
18158 TATTAATTTTATTTTATTATTTATTTATTATTGTATGAATATAAATAAATGAATGAAAAATAA
1 TATTAATTTTATTTTATTATTTATTTATTATTTTATGAATATAAATAAAT--AT-AAAAATAA
*
18221 TATTAATTTTGTTTTATTATTTATTTATTATTTTATGAATATAAATAAATA
1 TATTAATTTTATTTTATTATTTATTTATTATTTTATGAATATAAATAAATA
18272 AATAACAAAC
Statistics
Matches: 102, Mismatches: 6, Indels: 10
0.86 0.05 0.08
Matches are distributed among these distances:
59 32 0.31
60 12 0.12
61 3 0.03
63 55 0.54
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (60 bp):
TATTAATTTTATTTTATTATTTATTTATTATTTTATGAATATAAATAAATATAAAAATAA
Found at i:23355 original size:17 final size:17
Alignment explanation
Indices: 23313--23357 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
23303 TTTATTTAAT
*
23313 AATATTTTTATCTCAAA
1 AATATTTTTGTCTCAAA
* *
23330 AATACTTTTTGTTTCTAA
1 AATA-TTTTTGTCTCAAA
23348 AATATTTTTG
1 AATATTTTTG
23358 AGAAACAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.33, C:0.09, G:0.04, T:0.53
Consensus pattern (17 bp):
AATATTTTTGTCTCAAA
Found at i:29008 original size:23 final size:23
Alignment explanation
Indices: 28982--29028 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
28972 TTTTGGAAGT
28982 TTAATTAAAAATTT-AAAAAAAAA
1 TTAA-TAAAAATTTCAAAAAAAAA
*
29005 TTAATGAAAATTTCCAAAAAAAAA
1 TTAATAAAAATTT-CAAAAAAAAA
29029 ATTGTAAGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 8 0.38
23 4 0.19
24 9 0.43
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (23 bp):
TTAATAAAAATTTCAAAAAAAAA
Found at i:32330 original size:77 final size:77
Alignment explanation
Indices: 32176--32323 Score: 287
Period size: 77 Copynumber: 1.9 Consensus size: 77
32166 GCCACAATGG
32176 ACTGCTTCTTTAAACTCCGACTAAAAACACCTAACCCTAGAGTGAAAAGATAACCAGAGGTACTC
1 ACTGCTTCTTTAAACTCCGACTAAAAACACCTAACCCTAGAGTGAAAAGATAACCAGAGGTACTC
32241 TTCATACAATCA
66 TTCATACAATCA
*
32253 ACTGCTTCTTTAAACTCCGACTAAAAACACCTGACCCTAGAGTGAAAAGATAACCAGAGGTACTC
1 ACTGCTTCTTTAAACTCCGACTAAAAACACCTAACCCTAGAGTGAAAAGATAACCAGAGGTACTC
32318 TTCATA
66 TTCATA
32324 TCATCAATGG
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 70 1.00
ACGTcount: A:0.38, C:0.26, G:0.13, T:0.24
Consensus pattern (77 bp):
ACTGCTTCTTTAAACTCCGACTAAAAACACCTAACCCTAGAGTGAAAAGATAACCAGAGGTACTC
TTCATACAATCA
Found at i:48915 original size:22 final size:22
Alignment explanation
Indices: 48876--48923 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
48866 ATGTTTTATT
*
48876 TTTTTTTATCAAAAAAAGTATG
1 TTTTTTCATCAAAAAAAGTATG
48898 TTTTTTCA-CAAAATAAAGTATG
1 TTTTTTCATCAAAA-AAAGTATG
48920 TTTT
1 TTTT
48924 CGTTATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.48
Consensus pattern (22 bp):
TTTTTTCATCAAAAAAAGTATG
Found at i:49062 original size:14 final size:14
Alignment explanation
Indices: 49043--49075 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
49033 ATACATATTA
49043 AAAAATATAAAA-AT
1 AAAAATA-AAAATAT
49057 AAAAATAAAAATAT
1 AAAAATAAAAATAT
49071 AAAAA
1 AAAAA
49076 ATTAGAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (14 bp):
AAAAATAAAAATAT
Found at i:52111 original size:39 final size:40
Alignment explanation
Indices: 52048--52157 Score: 109
Period size: 39 Copynumber: 2.8 Consensus size: 40
52038 TTTTACTTAT
* * *
52048 ATTCTTATTAGAAATTCAATTTTGTATCAAAATACTC-AA
1 ATTCTTATTAGAAACTCAACTTTGTAACAAAATACTCAAA
* * *
52087 ATTCTTTTTGGAAACTCAACTTTGTAACTAAATACTCAAA
1 ATTCTTATTAGAAACTCAACTTTGTAACAAAATACTCAAA
* * *
52127 ATTC-TACT-GAAAACACAAATTTGTAACAAAA
1 ATTCTTATTAG-AAACTCAACTTTGTAACAAAA
52158 AAAACTTATA
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
38 1 0.02
39 51 0.88
40 6 0.10
ACGTcount: A:0.43, C:0.15, G:0.06, T:0.35
Consensus pattern (40 bp):
ATTCTTATTAGAAACTCAACTTTGTAACAAAATACTCAAA
Found at i:52359 original size:37 final size:38
Alignment explanation
Indices: 52307--52393 Score: 95
Period size: 38 Copynumber: 2.3 Consensus size: 38
52297 TATGTAAGCC
* *
52307 TAAAATATAAAAATTA-AAGAATGAACTTAAAACTTAA
1 TAAATTATACAAATTATAAGAATGAACTTAAAACTTAA
* * ** *
52344 TAAATTATACAAATTATTATAATGAGTTTAAAATTTAA
1 TAAATTATACAAATTATAAGAATGAACTTAAAACTTAA
52382 TAAATTTATACA
1 TAAA-TTATACA
52394 TATTTAAATT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
37 14 0.34
38 20 0.49
39 7 0.17
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.36
Consensus pattern (38 bp):
TAAATTATACAAATTATAAGAATGAACTTAAAACTTAA
Found at i:54021 original size:22 final size:21
Alignment explanation
Indices: 53944--54017 Score: 80
Period size: 22 Copynumber: 3.5 Consensus size: 21
53934 TTTTCAGAAA
*
53944 TTTT-TAATTTTTTTTATCAT
1 TTTTATAATTTTTTTTATAAT
53964 TTTTATCAATTTTTTTGTA-AAT
1 TTTTAT-AATTTTTTT-TATAAT
* *
53986 TTTTAAAATAATTTTTTATAAT
1 TTTTATAAT-TTTTTTTATAAT
54008 TTTTATAATT
1 TTTTATAATT
54018 ATTTAAGAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
20 4 0.09
21 6 0.14
22 32 0.73
23 2 0.05
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (21 bp):
TTTTATAATTTTTTTTATAAT
Found at i:54140 original size:10 final size:10
Alignment explanation
Indices: 54120--54171 Score: 51
Period size: 9 Copynumber: 5.7 Consensus size: 10
54110 CTGGTTTTTC
54120 TTAAT-ATTT
1 TTAATAATTT
*
54129 TTATTAATTT
1 TTAATAATTT
54139 TTAATAA-TT
1 TTAATAATTT
54148 TT-A-AATTT
1 TTAATAATTT
*
54156 TT-ATAATTC
1 TTAATAATTT
54165 TTAATAA
1 TTAATAA
54172 ACTTTAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
7 2 0.06
8 6 0.17
9 14 0.39
10 14 0.39
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (10 bp):
TTAATAATTT
Found at i:54144 original size:19 final size:17
Alignment explanation
Indices: 54120--54168 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
54110 CTGGTTTTTC
*
54120 TTAATATTTTTATTAATTT
1 TTAATAATTTTA--AATTT
54139 TTAATAATTTTAAATTT
1 TTAATAATTTTAAATTT
54156 TT-ATAATTCTTAA
1 TTAATAATT-TTAA
54169 TAAACTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 6 0.21
17 11 0.39
19 11 0.39
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (17 bp):
TTAATAATTTTAAATTT
Found at i:54163 original size:26 final size:28
Alignment explanation
Indices: 54120--54171 Score: 81
Period size: 26 Copynumber: 1.9 Consensus size: 28
54110 CTGGTTTTTC
*
54120 TTAATATTTTTATTAATTTTTAATAATT
1 TTAATATTTTTATTAATTCTTAATAATT
54148 TTAA-ATTTTTA-TAATTCTTAATAA
1 TTAATATTTTTATTAATTCTTAATAA
54172 ACTTTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 12 0.52
27 7 0.30
28 4 0.17
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (28 bp):
TTAATATTTTTATTAATTCTTAATAATT
Found at i:54459 original size:17 final size:17
Alignment explanation
Indices: 54371--54464 Score: 93
Period size: 17 Copynumber: 5.5 Consensus size: 17
54361 TCAAACTCAT
*
54371 TTTAAATTTATTTTAAGA
1 TTTAAAATTATTTTAA-A
* *
54389 -TTAAATTTGTTTTAAAA
1 TTTAAAATTATTTT-AAA
*
54406 TTT-AAATTATTTTAAG
1 TTTAAAATTATTTTAAA
*
54422 TTTAAATTTATTTTCAAA
1 TTTAAAATTATTTT-AAA
*
54440 TTTAAAATTATTATAAA
1 TTTAAAATTATTTTAAA
54457 TTTAAAAT
1 TTTAAAAT
54465 AAATAAAGTT
Statistics
Matches: 64, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
16 5 0.08
17 41 0.64
18 18 0.28
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTAAAATTATTTTAAA
Found at i:54461 original size:35 final size:35
Alignment explanation
Indices: 54371--54462 Score: 123
Period size: 34 Copynumber: 2.7 Consensus size: 35
54361 TCAAACTCAT
* * *
54371 TTTAAATTTATTTTAAGATTAAATTTGTTTTAAAA
1 TTTAAAATTATTTTAAGTTTAAATTTATTTTAAAA
*
54406 TTT-AAATTATTTTAAGTTTAAATTTATTTTCAAA
1 TTTAAAATTATTTTAAGTTTAAATTTATTTTAAAA
* *
54440 TTTAAAATTATTATAAATTTAAA
1 TTTAAAATTATTTTAAGTTTAAA
54463 ATAAATAAAG
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
34 30 0.60
35 20 0.40
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.53
Consensus pattern (35 bp):
TTTAAAATTATTTTAAGTTTAAATTTATTTTAAAA
Found at i:54474 original size:51 final size:51
Alignment explanation
Indices: 54371--54474 Score: 113
Period size: 51 Copynumber: 2.0 Consensus size: 51
54361 TCAAACTCAT
* * * * ** *
54371 TTTAAATTTATTTTAAGATTAAATTTGTTTTAAAATTTAAATTATTTTAAG
1 TTTAAATTTATTTTAAGATTAAAATTATTATAAAATTTAAAATAAATAAAG
54422 TTTAAATTTATTTTCAA-ATTTAAAATTATTAT-AAATTTAAAATAAATAAAG
1 TTTAAATTTATTTT-AAGA-TTAAAATTATTATAAAATTTAAAATAAATAAAG
54473 TT
1 TT
54475 CAATTACAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
51 32 0.73
52 12 0.27
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (51 bp):
TTTAAATTTATTTTAAGATTAAAATTATTATAAAATTTAAAATAAATAAAG
Found at i:54927 original size:57 final size:58
Alignment explanation
Indices: 54829--55106 Score: 402
Period size: 57 Copynumber: 4.8 Consensus size: 58
54819 TGAGCTTCCG
* * *
54829 AAAATTCCATTTTTAACCTCAAAACTTCCAAAAATT-AAATTTTGCCCCAAACTTCTA
1 AAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTCCAATTTTACCCCAAACTTCTA
54886 AAAATTCCA-TTTTAACCCCAAAACTTCCAAAAATTCCAATTTTACCCCCAAACTTCTA
1 AAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTCCAATTTTA-CCCCAAACTTCTA
* * * * *
54944 AAAATTCCATTTTTTACCCTAAAACTTCTAAAAATTCCATTTTTACCCCAAACTTCCA
1 AAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTCCAATTTTACCCCAAACTTCTA
* * *
55002 AAAATTCCA-TTTTGACCCCCAAACTTCTAAAAATTCC-ATTTTACCCCAAACTTCTA
1 AAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTCCAATTTTACCCCAAACTTCTA
* *
55058 AAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCC
1 AAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTCCAATTTTACCCC
55107 TGAACATCCA
Statistics
Matches: 200, Mismatches: 16, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
56 51 0.25
57 66 0.33
58 52 0.26
59 31 0.16
ACGTcount: A:0.37, C:0.29, G:0.01, T:0.33
Consensus pattern (58 bp):
AAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTCCAATTTTACCCCAAACTTCTA
Found at i:55119 original size:29 final size:28
Alignment explanation
Indices: 54823--55106 Score: 347
Period size: 29 Copynumber: 9.9 Consensus size: 28
54813 TACCATTGAG
* *
54823 CTTCCGAAAATTCCATTTTTAACCTCAAAA
1 CTTCCAAAAATTCCATTTTT-ACC-CCAAA
* * *
54853 CTTCCAAAAATT-AAATTTTGCCCCAAA
1 CTTCCAAAAATTCCATTTTTACCCCAAA
* *
54880 CTTCTAAAAATTCCATTTTAACCCCAAAA
1 CTTCCAAAAATTCCATTTTTACCCC-AAA
*
54909 CTTCCAAAAATTCCAATTTTACCCCCAAA
1 CTTCCAAAAATTCCATTTTTA-CCCCAAA
* *
54938 CTTCTAAAAATTCCATTTTTTACCCTAAAA
1 CTTCCAAAAATTCCA-TTTTTACCC-CAAA
*
54968 CTTCTAAAAATTCCATTTTTACCCCAAA
1 CTTCCAAAAATTCCATTTTTACCCCAAA
*
54996 CTTCCAAAAATTCCATTTTGACCCCCAAA
1 CTTCCAAAAATTCCATTTTTA-CCCCAAA
*
55025 CTTCTAAAAATTCCA-TTTTACCCCAAA
1 CTTCCAAAAATTCCATTTTTACCCCAAA
*
55052 CTTCTAAAAATTCCATTTTTGACCCCAAAA
1 CTTCCAAAAATTCCATTTTT-ACCCC-AAA
55082 CTTCCAAAAATTCCATTTTTACCCC
1 CTTCCAAAAATTCCATTTTTACCCC
55107 TGAACATCCA
Statistics
Matches: 223, Mismatches: 22, Indels: 19
0.84 0.08 0.07
Matches are distributed among these distances:
27 37 0.17
28 40 0.18
29 86 0.39
30 60 0.27
ACGTcount: A:0.37, C:0.29, G:0.01, T:0.33
Consensus pattern (28 bp):
CTTCCAAAAATTCCATTTTTACCCCAAA
Found at i:63866 original size:18 final size:17
Alignment explanation
Indices: 63845--63896 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
63835 AAACATAATT
63845 TTTTAGTATTTTTATATA
1 TTTTA-TATTTTTATATA
*
63863 TTTTTTATTTTTATAATA
1 TTTTATATTTTTAT-ATA
* *
63881 TATCATATTTTTATAT
1 TTTTATATTTTTATAT
63897 TATTATTTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 11 0.38
18 18 0.62
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (17 bp):
TTTTATATTTTTATATA
Found at i:65362 original size:21 final size:22
Alignment explanation
Indices: 65336--65381 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 22
65326 TATAAAAAAT
65336 AAAAAT-TTATAAAATTTA-TAA
1 AAAAATATT-TAAAATTTACTAA
65357 AAAAATATTTAAAATTTACTAA
1 AAAAATATTTAAAATTTACTAA
65379 AAA
1 AAA
65382 TTAGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (22 bp):
AAAAATATTTAAAATTTACTAA
Found at i:65380 original size:31 final size:30
Alignment explanation
Indices: 65337--65395 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 30
65327 ATAAAAAATA
* *
65337 AAAATTTATAAAATTTATAAAAAAATATTT
1 AAAATTTATAAAAATTAGAAAAAAATATTT
65367 AAAATTTACTAAAAATTAGAAAAAAATAT
1 AAAATTTA-TAAAAATTAGAAAAAAATAT
65396 AAAATAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 8 0.31
31 18 0.69
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.34
Consensus pattern (30 bp):
AAAATTTATAAAAATTAGAAAAAAATATTT
Found at i:67192 original size:23 final size:23
Alignment explanation
Indices: 67166--67235 Score: 88
Period size: 23 Copynumber: 3.0 Consensus size: 23
67156 TTCATTTAAT
67166 TTAATAGAACATGTTCACGAACA
1 TTAATAGAACATGTTCACGAACA
*
67189 TTAA-ACGAACATGTTCATGAACA
1 TTAATA-GAACATGTTCACGAACA
* *
67212 TATAATTGAACAGGTTCACGAACA
1 T-TAATAGAACATGTTCACGAACA
67236 ATGTTAATGA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
22 1 0.03
23 21 0.52
24 18 0.45
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (23 bp):
TTAATAGAACATGTTCACGAACA
Found at i:67233 original size:47 final size:46
Alignment explanation
Indices: 67147--67235 Score: 124
Period size: 47 Copynumber: 1.9 Consensus size: 46
67137 TTTAATGTTC
** * *
67147 ACGAACATGTTCATTTAATTTAATAGAACATGTTCACGAACATTAA
1 ACGAACATGTTCATGAAATATAATAGAACAGGTTCACGAACATTAA
*
67193 ACGAACATGTTCATGAACATATAATTGAACAGGTTCACGAACA
1 ACGAACATGTTCATGAA-ATATAATAGAACAGGTTCACGAACA
67236 ATGTTAATGA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
46 15 0.41
47 22 0.59
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.28
Consensus pattern (46 bp):
ACGAACATGTTCATGAAATATAATAGAACAGGTTCACGAACATTAA
Found at i:77280 original size:2 final size:2
Alignment explanation
Indices: 77275--77305 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
77265 AAAAAATTCC
77275 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
77306 AATTTATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:80612 original size:23 final size:23
Alignment explanation
Indices: 80586--80650 Score: 112
Period size: 23 Copynumber: 2.8 Consensus size: 23
80576 TTTAATCATT
*
80586 TAAAAATTACATTTTTACTATAG
1 TAAAAATTACATTTTAACTATAG
*
80609 TAAAAATTACATTTTAACTATCG
1 TAAAAATTACATTTTAACTATAG
80632 TAAAAATTACATTTTAACT
1 TAAAAATTACATTTTAACT
80651 TCGGCTCCCT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.45, C:0.11, G:0.03, T:0.42
Consensus pattern (23 bp):
TAAAAATTACATTTTAACTATAG
Done.