Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014469.1 Kokia drynarioides strain JFW-HI SEQ_129508, 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: 110382
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Warning! 129 characters in sequence are not A, C, G, or T
Found at i:8354 original size:2 final size:2
Alignment explanation
Indices: 8347--8379 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
8337 GTACACCCAG
8347 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
8380 AAAGATCGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8431 original size:18 final size:17
Alignment explanation
Indices: 8403--8449 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 17
8393 GTATTGCTTT
8403 TAAAAAGTATTTTTGGAAA
1 TAAAAA-TATTTTT-GAAA
8422 -AAAAATTATTTTTGAAA
1 TAAAAA-TATTTTTGAAA
8439 TAAAAATATTT
1 TAAAAATATTT
8450 CTAAACAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 9 0.35
18 17 0.65
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (17 bp):
TAAAAATATTTTTGAAA
Found at i:8433 original size:17 final size:17
Alignment explanation
Indices: 8403--8449 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 17
8393 GTATTGCTTT
8403 TAAAAAGTATTTTTGGAAA
1 TAAAAA-TA-TTTTGGAAA
*
8422 -AAAAATTATTTTTGAAA
1 TAAAAA-TATTTTGGAAA
8439 TAAAAATATTT
1 TAAAAATATTT
8450 CTAAACAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (17 bp):
TAAAAATATTTTGGAAA
Found at i:9126 original size:3 final size:3
Alignment explanation
Indices: 9118--9162 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
9108 ATATATACCT
*
9118 TAA TAA TAA TAA TAA TAA TAA TAA TAA CAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
9163 AAGAATGCAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:9563 original size:15 final size:17
Alignment explanation
Indices: 9543--9582 Score: 57
Period size: 15 Copynumber: 2.5 Consensus size: 17
9533 AACTATTTAC
9543 AAATTATAAAAAT-AT-
1 AAATTATAAAAATGATA
*
9558 AAATTATTAAAATGATA
1 AAATTATAAAAATGATA
9575 AAATTATA
1 AAATTATA
9583 TTTTTACTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (17 bp):
AAATTATAAAAATGATA
Found at i:12553 original size:21 final size:19
Alignment explanation
Indices: 12527--12579 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 19
12517 GAAGTTTTTG
12527 GTATCGGTAGATGCATGACTT
1 GTATCGGTAGAT-CAT-ACTT
12548 GTATCGGTAGAAATCATACTT
1 GTATCGGTAG--ATCATACTT
12569 GTATCGGTAGA
1 GTATCGGTAGA
12580 GCTAGCACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
19 1 0.03
21 24 0.80
22 3 0.10
23 2 0.07
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.32
Consensus pattern (19 bp):
GTATCGGTAGATCATACTT
Found at i:13001 original size:19 final size:17
Alignment explanation
Indices: 12959--13002 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 17
12949 TATTTATATT
*
12959 ATTGAATTATTTAATAAT
1 ATTGAA-TATTTAATAAA
12977 ATTGAATATTTATATTAAA
1 ATTGAATATTTA-A-TAAA
12996 ATTGAAT
1 ATTGAAT
13003 TATTAATGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 6 0.26
18 7 0.30
19 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (17 bp):
ATTGAATATTTAATAAA
Found at i:23139 original size:45 final size:45
Alignment explanation
Indices: 23075--23165 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 45
23065 ATTCGTTGAA
23075 TCACCCAATCAGATAACCATAGGTAAAAAAACTCAAGATTGCAAG
1 TCACCCAATCAGATAACCATAGGTAAAAAAACTCAAGATTGCAAG
* *
23120 TCACCCAATCAGATAACCATAGGTGAAAAAGCTCAAGATTGCAAG
1 TCACCCAATCAGATAACCATAGGTAAAAAAACTCAAGATTGCAAG
23165 T
1 T
23166 TCCTTCGAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.44, C:0.22, G:0.15, T:0.19
Consensus pattern (45 bp):
TCACCCAATCAGATAACCATAGGTAAAAAAACTCAAGATTGCAAG
Found at i:35995 original size:33 final size:31
Alignment explanation
Indices: 35896--35995 Score: 87
Period size: 33 Copynumber: 3.1 Consensus size: 31
35886 TATATGAAAT
*
35896 ATTAATTTTAAATATTTTTAAGTAATTAATATT-A
1 ATTAATTTTAAATA--TTTAAAT-A-TAATATTAA
* * *
35930 ATTAATTATAAA-ATTTAATTAAAATATATAA
1 ATTAATTTTAAATATTTAAATATAATAT-TAA
35961 ATTATATTTTAAATATTTAAATATAATCATTAA
1 ATTA-ATTTTAAATATTTAAATATAAT-ATTAA
35994 AT
1 AT
35996 GGAGGCTAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
29 5 0.09
30 2 0.04
31 11 0.20
32 7 0.13
33 17 0.31
34 13 0.24
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (31 bp):
ATTAATTTTAAATATTTAAATATAATATTAA
Found at i:42448 original size:25 final size:23
Alignment explanation
Indices: 42403--42454 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 23
42393 GCATTTATAT
42403 ATAATTTATGTAAATATGAATACC
1 ATAATTTATGTAAATATGAATA-C
42427 ATAATTTATTTGT-AATATGAATAC
1 ATAATTTA--TGTAAATATGAATAC
42451 ATAA
1 ATAA
42455 GGTGGCCAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
24 13 0.50
25 10 0.38
26 3 0.12
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.40
Consensus pattern (23 bp):
ATAATTTATGTAAATATGAATAC
Found at i:45630 original size:78 final size:78
Alignment explanation
Indices: 45510--45666 Score: 314
Period size: 78 Copynumber: 2.0 Consensus size: 78
45500 GATTAAAGAT
45510 AATTAATAGTGAAGAAAAATAGATAGATGAAGAAGAAATGGTTGATTGAGAAGAAATAAATGGAA
1 AATTAATAGTGAAGAAAAATAGATAGATGAAGAAGAAATGGTTGATTGAGAAGAAATAAATGGAA
45575 GGACAAAGACGTA
66 GGACAAAGACGTA
45588 AATTAATAGTGAAGAAAAATAGATAGATGAAGAAGAAATGGTTGATTGAGAAGAAATAAATGGAA
1 AATTAATAGTGAAGAAAAATAGATAGATGAAGAAGAAATGGTTGATTGAGAAGAAATAAATGGAA
45653 GGACAAAGACGTA
66 GGACAAAGACGTA
45666 A
1 A
45667 GATGTGATGA
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 79 1.00
ACGTcount: A:0.53, C:0.03, G:0.25, T:0.19
Consensus pattern (78 bp):
AATTAATAGTGAAGAAAAATAGATAGATGAAGAAGAAATGGTTGATTGAGAAGAAATAAATGGAA
GGACAAAGACGTA
Found at i:45718 original size:31 final size:31
Alignment explanation
Indices: 45681--45773 Score: 168
Period size: 31 Copynumber: 3.0 Consensus size: 31
45671 TGATGAGTTG
45681 GTTGCAAAGGCAAATCTTATTGGAATATTGA
1 GTTGCAAAGGCAAATCTTATTGGAATATTGA
45712 GTTGCAAAGGCAAATCTTATTGGAATATTGA
1 GTTGCAAAGGCAAATCTTATTGGAATATTGA
* *
45743 GTTGCAAAGGTATATCTTATTGGAATATTGA
1 GTTGCAAAGGCAAATCTTATTGGAATATTGA
45774 ATGCACAACG
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 60 1.00
ACGTcount: A:0.34, C:0.09, G:0.23, T:0.34
Consensus pattern (31 bp):
GTTGCAAAGGCAAATCTTATTGGAATATTGA
Found at i:49733 original size:59 final size:59
Alignment explanation
Indices: 49661--49778 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
49651 TAGAACAAAG
49661 TAAGAATTGTACCTTTCTTTTCACGTCGGGTGTGATATTTGCAAATTCTTTCTTAACGT
1 TAAGAATTGTACCTTTCTTTTCACGTCGGGTGTGATATTTGCAAATTCTTTCTTAACGT
49720 TAAGAATTGTACCTTTCTTTTCACGTCGGGTGTGATATTTGCAAATTCTTTCTTAACGT
1 TAAGAATTGTACCTTTCTTTTCACGTCGGGTGTGATATTTGCAAATTCTTTCTTAACGT
49779 GTCCAAACTC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (59 bp):
TAAGAATTGTACCTTTCTTTTCACGTCGGGTGTGATATTTGCAAATTCTTTCTTAACGT
Found at i:50534 original size:23 final size:23
Alignment explanation
Indices: 50488--50534 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
50478 TAGGCATGGG
* *
50488 TATGAAATTTATATTAGCAGATA
1 TATGAAATTTATATTAACAAATA
*
50511 TATGGAATTTATATTAACAAATA
1 TATGAAATTTATATTAACAAATA
50534 T
1 T
50535 TTGTTGGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.45, C:0.04, G:0.11, T:0.40
Consensus pattern (23 bp):
TATGAAATTTATATTAACAAATA
Found at i:52888 original size:22 final size:22
Alignment explanation
Indices: 52831--52909 Score: 95
Period size: 23 Copynumber: 3.5 Consensus size: 22
52821 GCTGGGGAAA
*
52831 CAGTAAGCACACACAGTGCAAT
1 CAGTAGGCACACACAGTGCAAT
52853 CCAGTAGGCACACACAGTGCAAT
1 -CAGTAGGCACACACAGTGCAAT
* * * *
52876 CAATAGGCGCACATAGGGCAAAT
1 CAGTAGGCACACACAGTGC-AAT
52899 CAGTAGGCACA
1 CAGTAGGCACA
52910 TAAAGTGCGA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
22 15 0.31
23 33 0.69
ACGTcount: A:0.38, C:0.27, G:0.23, T:0.13
Consensus pattern (22 bp):
CAGTAGGCACACACAGTGCAAT
Found at i:55106 original size:22 final size:22
Alignment explanation
Indices: 55078--55126 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
55068 CATTTTTGAG
*
55078 TTTAAATTTACTT-TAATTTAAA
1 TTTAAATTTA-TTGTAAATTAAA
55100 TTTAAATTTATTGTAAATTAAA
1 TTTAAATTTATTGTAAATTAAA
*
55122 ATTAA
1 TTTAA
55127 TTAAAAAGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 2 0.08
22 22 0.92
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (22 bp):
TTTAAATTTATTGTAAATTAAA
Found at i:55835 original size:3 final size:3
Alignment explanation
Indices: 55820--55934 Score: 70
Period size: 3 Copynumber: 37.3 Consensus size: 3
55810 TTAATGACAT
* * ** **
55820 TAA TAA TAT TAA TAA TAA TAA CTACT TCT TAA TAA TAA TAA TAA TGT
1 TAA TAA TAA TAA TAA TAA TAA -TA-A TAA TAA TAA TAA TAA TAA TAA
* * * * *
55867 TAG TAA TAA TAA TAA TAA TAA TAA -ACA TCA TAA TAA TGA TAG TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
* *
55912 TAA TTAA TAT TAA TAT TAA TAA T
1 TAA -TAA TAA TAA TAA TAA TAA T
55935 CAAAAAAGAA
Statistics
Matches: 85, Mismatches: 22, Indels: 10
0.73 0.19 0.09
Matches are distributed among these distances:
2 1 0.01
3 78 0.92
4 6 0.07
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:57031 original size:29 final size:29
Alignment explanation
Indices: 56996--57138 Score: 98
Period size: 29 Copynumber: 4.9 Consensus size: 29
56986 TAGAAATTAT
56996 ATTTTGACCCCCGAACTTCCAAAAATT-CC
1 ATTTT-ACCCCCGAACTTCCAAAAATTACC
** *
57025 ATTTTGACCCCAAAACTTTCAAAAATTACC
1 ATTTT-ACCCCCGAACTTCCAAAAATTACC
* **
57055 ATTTTACCCTCG-A-TGTCCAAAAGCT-CC
1 ATTTTACCCCCGAACT-TCCAAAAATTACC
** * *
57082 ATTTTTTTTCCCCGAAACTTTCAAAAGTTACC
1 A--TTTTACCCCCG-AACTTCCAAAAATTACC
57114 ATTTTACCCCCGAA-TGTCCAAAAAT
1 ATTTTACCCCCGAACT-TCCAAAAAT
57139 GCTATTTTTG
Statistics
Matches: 87, Mismatches: 18, Indels: 18
0.71 0.15 0.15
Matches are distributed among these distances:
27 4 0.05
28 9 0.10
29 45 0.52
30 16 0.18
31 9 0.10
32 4 0.05
ACGTcount: A:0.32, C:0.29, G:0.07, T:0.31
Consensus pattern (29 bp):
ATTTTACCCCCGAACTTCCAAAAATTACC
Found at i:57147 original size:59 final size:59
Alignment explanation
Indices: 56996--57241 Score: 184
Period size: 59 Copynumber: 4.2 Consensus size: 59
56986 TAGAAATTAT
* *
56996 ATTTTGACCCCCGAACT-TCCAAAAATTCCA-TTTTGACCCCAAAACTTTCAAAAATTACC
1 ATTTT-ACCCCCGAA-TGTCCAAAAATGCTATTTTTGACCCCAAAACTTTCAAAAATTACC
* ** * *
57055 ATTTTACCCTCG-ATGTCC-AAAA-GCTCCATTTTTTTTCCCCGAAACTTTCAAAAGTTACC
1 ATTTTACCCCCGAATGTCCAAAAATGCT--A-TTTTTGACCCCAAAACTTTCAAAAATTACC
* * ** *
57114 ATTTTACCCCCGAATGTCCAAAAATGCTATTTTTGATCCC-GATTTTTCTAAAAATTACT
1 ATTTTACCCCCGAATGTCCAAAAATGCTATTTTTGACCCCAAAACTTTC-AAAAATTACC
* * * * * * * * *
57173 GTTTTACCCCTGAATATCTAAAATTTC-ATTTTTCACCTCAAAA-TTTCCCAAAATTACC
1 ATTTTACCCCCGAATGTCCAAAAATGCTATTTTTGACCCCAAAACTTT-CAAAAATTACC
57231 ATTTTACCCCC
1 ATTTTACCCCC
57242 CGAGAGTTCA
Statistics
Matches: 145, Mismatches: 31, Indels: 23
0.73 0.16 0.12
Matches are distributed among these distances:
55 1 0.01
56 5 0.03
57 5 0.03
58 40 0.28
59 80 0.55
60 7 0.05
61 4 0.03
62 3 0.02
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (59 bp):
ATTTTACCCCCGAATGTCCAAAAATGCTATTTTTGACCCCAAAACTTTCAAAAATTACC
Found at i:63137 original size:21 final size:21
Alignment explanation
Indices: 63111--63154 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
63101 TTCAAGCAAG
63111 CTTTCGAACCTTGAAGAATAA
1 CTTTCGAACCTTGAAGAATAA
63132 CTTTCGAACCTTGAAGAATAA
1 CTTTCGAACCTTGAAGAATAA
63153 CT
1 CT
63155 CAGCCCATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (21 bp):
CTTTCGAACCTTGAAGAATAA
Found at i:63704 original size:17 final size:17
Alignment explanation
Indices: 63682--63722 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
63672 AAGTATAACA
*
63682 TATTTGAGTAACTATTG
1 TATTTGAGTAACCATTG
63699 TATTTGAGTAACCATTG
1 TATTTGAGTAACCATTG
*
63716 TAATTGA
1 TATTTGA
63723 TGGTGTCGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.32, C:0.07, G:0.17, T:0.44
Consensus pattern (17 bp):
TATTTGAGTAACCATTG
Found at i:64923 original size:22 final size:22
Alignment explanation
Indices: 64895--64943 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
64885 CATTTTTGAG
*
64895 TTTAAATTTACTT-TAATTTAAA
1 TTTAAATTTA-TTGTAAATTAAA
64917 TTTAAATTTATTGTAAATTAAA
1 TTTAAATTTATTGTAAATTAAA
*
64939 ATTAA
1 TTTAA
64944 TTAAAAAGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 2 0.08
22 22 0.92
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (22 bp):
TTTAAATTTATTGTAAATTAAA
Found at i:65652 original size:3 final size:3
Alignment explanation
Indices: 65637--65751 Score: 70
Period size: 3 Copynumber: 37.3 Consensus size: 3
65627 TTAATGACAT
* * ** **
65637 TAA TAA TAT TAA TAA TAA TAA CTACT TCT TAA TAA TAA TAA TAA TGT
1 TAA TAA TAA TAA TAA TAA TAA -TA-A TAA TAA TAA TAA TAA TAA TAA
* * * * *
65684 TAG TAA TAA TAA TAA TAA TAA TAA -ACA TCA TAA TAA TGA TAG TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
* *
65729 TAA TTAA TAT TAA TAT TAA TAA T
1 TAA -TAA TAA TAA TAA TAA TAA T
65752 CAAAAAAGAA
Statistics
Matches: 85, Mismatches: 22, Indels: 10
0.73 0.19 0.09
Matches are distributed among these distances:
2 1 0.01
3 78 0.92
4 6 0.07
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:66848 original size:29 final size:29
Alignment explanation
Indices: 66813--66955 Score: 98
Period size: 29 Copynumber: 4.9 Consensus size: 29
66803 TAGAAATTAT
66813 ATTTTGACCCCCGAACTTCCAAAAATT-CC
1 ATTTT-ACCCCCGAACTTCCAAAAATTACC
** *
66842 ATTTTGACCCCAAAACTTTCAAAAATTACC
1 ATTTT-ACCCCCGAACTTCCAAAAATTACC
* **
66872 ATTTTACCCTCG-A-TGTCCAAAAGCT-CC
1 ATTTTACCCCCGAACT-TCCAAAAATTACC
** * *
66899 ATTTTTTTTCCCCGAAACTTTCAAAAGTTACC
1 A--TTTTACCCCCG-AACTTCCAAAAATTACC
66931 ATTTTACCCCCGAA-TGTCCAAAAAT
1 ATTTTACCCCCGAACT-TCCAAAAAT
66956 GCTATTTTTG
Statistics
Matches: 87, Mismatches: 18, Indels: 18
0.71 0.15 0.15
Matches are distributed among these distances:
27 4 0.05
28 9 0.10
29 45 0.52
30 16 0.18
31 9 0.10
32 4 0.05
ACGTcount: A:0.32, C:0.29, G:0.07, T:0.31
Consensus pattern (29 bp):
ATTTTACCCCCGAACTTCCAAAAATTACC
Found at i:66964 original size:59 final size:59
Alignment explanation
Indices: 66813--67058 Score: 184
Period size: 59 Copynumber: 4.2 Consensus size: 59
66803 TAGAAATTAT
* *
66813 ATTTTGACCCCCGAACT-TCCAAAAATTCCA-TTTTGACCCCAAAACTTTCAAAAATTACC
1 ATTTT-ACCCCCGAA-TGTCCAAAAATGCTATTTTTGACCCCAAAACTTTCAAAAATTACC
* ** * *
66872 ATTTTACCCTCG-ATGTCC-AAAA-GCTCCATTTTTTTTCCCCGAAACTTTCAAAAGTTACC
1 ATTTTACCCCCGAATGTCCAAAAATGCT--A-TTTTTGACCCCAAAACTTTCAAAAATTACC
* * ** *
66931 ATTTTACCCCCGAATGTCCAAAAATGCTATTTTTGATCCC-GATTTTTCTAAAAATTACT
1 ATTTTACCCCCGAATGTCCAAAAATGCTATTTTTGACCCCAAAACTTTC-AAAAATTACC
* * * * * * * * *
66990 GTTTTACCCCTGAATATCTAAAATTTC-ATTTTTCACCTCAAAA-TTTCCCAAAATTACC
1 ATTTTACCCCCGAATGTCCAAAAATGCTATTTTTGACCCCAAAACTTT-CAAAAATTACC
67048 ATTTTACCCCC
1 ATTTTACCCCC
67059 CGAGAGTTCA
Statistics
Matches: 145, Mismatches: 31, Indels: 23
0.73 0.16 0.12
Matches are distributed among these distances:
55 1 0.01
56 5 0.03
57 5 0.03
58 40 0.28
59 80 0.55
60 7 0.05
61 4 0.03
62 3 0.02
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (59 bp):
ATTTTACCCCCGAATGTCCAAAAATGCTATTTTTGACCCCAAAACTTTCAAAAATTACC
Found at i:72954 original size:21 final size:21
Alignment explanation
Indices: 72928--72971 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
72918 TTCAAGCAAG
72928 CTTTCGAACCTTGAAGAATAA
1 CTTTCGAACCTTGAAGAATAA
72949 CTTTCGAACCTTGAAGAATAA
1 CTTTCGAACCTTGAAGAATAA
72970 CT
1 CT
72972 CAGCCCATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (21 bp):
CTTTCGAACCTTGAAGAATAA
Found at i:73521 original size:17 final size:17
Alignment explanation
Indices: 73499--73539 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
73489 AAGTATAACA
*
73499 TATTTGAGTAACTATTG
1 TATTTGAGTAACCATTG
73516 TATTTGAGTAACCATTG
1 TATTTGAGTAACCATTG
*
73533 TAATTGA
1 TATTTGA
73540 TGGTGTCGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.32, C:0.07, G:0.17, T:0.44
Consensus pattern (17 bp):
TATTTGAGTAACCATTG
Found at i:80379 original size:23 final size:24
Alignment explanation
Indices: 80345--80472 Score: 122
Period size: 23 Copynumber: 5.4 Consensus size: 24
80335 ACATTAGCGC
*
80345 GCTTACTG-TTCAGCACTGTGTGT
1 GCTTACTGATTCAGCACTGTATGT
80368 GCTTACT-ATTCAGCACTGTATGT
1 GCTTACTGATTCAGCACTGTATGT
*
80391 GCTTACTGATTC-GCACTATATGT
1 GCTTACTGATTCAGCACTGTATGT
* * * *
80414 GCTTACTGATT-TGCATTCTGTGT
1 GCTTACTGATTCAGCACTGTATGT
*
80437 GCTTACTGTTTCCCTAGCACT-TATGT
1 GCTTACTGATT--C-AGCACTGTATGT
*
80463 GCTCACTGAT
1 GCTTACTGAT
80473 AGTACTTCGG
Statistics
Matches: 87, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
23 67 0.77
24 4 0.05
26 12 0.14
27 4 0.05
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (24 bp):
GCTTACTGATTCAGCACTGTATGT
Found at i:81371 original size:44 final size:44
Alignment explanation
Indices: 81319--81426 Score: 207
Period size: 44 Copynumber: 2.5 Consensus size: 44
81309 GTAATTTAGT
*
81319 TGTTTGGTTGAATGAAATGAAATAAAACTGTAATAGTATTCTTG
1 TGTTTGGTTGAATGGAATGAAATAAAACTGTAATAGTATTCTTG
81363 TGTTTGGTTGAATGGAATGAAATAAAACTGTAATAGTATTCTTG
1 TGTTTGGTTGAATGGAATGAAATAAAACTGTAATAGTATTCTTG
81407 TGTTTGGTTGAATGGAATGA
1 TGTTTGGTTGAATGGAATGA
81427 TGCTATAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 63 1.00
ACGTcount: A:0.33, C:0.04, G:0.24, T:0.39
Consensus pattern (44 bp):
TGTTTGGTTGAATGGAATGAAATAAAACTGTAATAGTATTCTTG
Found at i:86987 original size:26 final size:26
Alignment explanation
Indices: 86947--87008 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 26
86937 ATCCAATCAC
*
86947 ATATTAATTTTGTAAAT-AATTTTTTT
1 ATATT-ATTTTGTAAATAAATTTTTCT
86973 ATATTATTTTGGTAAATGAAATTTTTCT
1 ATATTATTTT-GTAAAT-AAATTTTTCT
87001 ATATTATT
1 ATATTATT
87009 GATGCAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 5 0.16
26 11 0.34
28 16 0.50
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.58
Consensus pattern (26 bp):
ATATTATTTTGTAAATAAATTTTTCT
Found at i:96561 original size:56 final size:56
Alignment explanation
Indices: 96453--96566 Score: 140
Period size: 56 Copynumber: 2.0 Consensus size: 56
96443 CTAGACTATG
* ***
96453 ATCCATGTTCAATGATACTATTTCGAGATTTCAAACATAAAGTGGTGGGAAAATAA
1 ATCCATGTTCAATGATACTATATCGAGATTTCAAACATAAAGTGGCACGAAAATAA
* * * *
96509 ATCCATGTTCAATTATACTGTAT-GTAGATTTCATACCTAAAGTGGCACGAAAATAA
1 ATCCATGTTCAATGATACTATATCG-AGATTTCAAACATAAAGTGGCACGAAAATAA
96565 AT
1 AT
96567 AGTGGAAATA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
55 1 0.02
56 48 0.98
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (56 bp):
ATCCATGTTCAATGATACTATATCGAGATTTCAAACATAAAGTGGCACGAAAATAA
Found at i:101685 original size:13 final size:13
Alignment explanation
Indices: 101669--101693 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
101659 ATGTTTATGT
101669 CATTTTTTTAATC
1 CATTTTTTTAATC
101682 CATTTTTTTAAT
1 CATTTTTTTAAT
101694 GATACATAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (13 bp):
CATTTTTTTAATC
Found at i:102606 original size:18 final size:18
Alignment explanation
Indices: 102583--102620 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
102573 ATAAAAGTTC
*
102583 TTAAAAAGTTT-TTATTTT
1 TTAAAAACTTTATT-TTTT
102601 TTAAAAACTTTATTTTTT
1 TTAAAAACTTTATTTTTT
102619 TT
1 TT
102621 TTGTTTTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (18 bp):
TTAAAAACTTTATTTTTT
Found at i:103745 original size:22 final size:23
Alignment explanation
Indices: 103690--103745 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
103680 AATTCAAATT
103690 ACCGTGCCATAGAAACAAACATA
1 ACCGTGCCATAGAAACAAACATA
*
103713 ACCATGCCATAGAAACAAA-ATA
1 ACCGTGCCATAGAAACAAACATA
*
103735 TCCGTGCCATA
1 ACCGTGCCATA
103746 AAAGATGACA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 12 0.40
23 18 0.60
ACGTcount: A:0.45, C:0.27, G:0.12, T:0.16
Consensus pattern (23 bp):
ACCGTGCCATAGAAACAAACATA
Done.