Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010108.1 Kokia drynarioides strain JFW-HI SEQ_124894, 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: 41302
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:567 original size:38 final size:38
Alignment explanation
Indices: 472--590 Score: 193
Period size: 38 Copynumber: 3.0 Consensus size: 38
462 GGTTGATTTT
472 TCCAAAATCAACCAAATTAGATCATCCAAAAACAAGTG
1 TCCAAAATCAACCAAATTAGATCATCCAAAAACAAGTG
*
510 TCCAAACAAAATCAACCAAATTACATCATCCAAAAACAAGTG
1 T-C---CAAAATCAACCAAATTAGATCATCCAAAAACAAGTG
552 TCCAAAATCAACCAAATTAGATCATCCAAAAACAAGTG
1 TCCAAAATCAACCAAATTAGATCATCCAAAAACAAGTG
590 T
1 T
591 ATTTTTCATA
Statistics
Matches: 75, Mismatches: 2, Indels: 8
0.88 0.02 0.09
Matches are distributed among these distances:
38 37 0.49
39 1 0.01
41 1 0.01
42 36 0.48
ACGTcount: A:0.50, C:0.24, G:0.07, T:0.18
Consensus pattern (38 bp):
TCCAAAATCAACCAAATTAGATCATCCAAAAACAAGTG
Found at i:953 original size:55 final size:55
Alignment explanation
Indices: 854--974 Score: 145
Period size: 55 Copynumber: 2.2 Consensus size: 55
844 ATCGATTATT
* * * * *
854 ATGTTGAAATATTACTTCTTTTTAATCGATTATTTTTATGTTTAAAT-AGATTGTC
1 ATGTTGAAATATTACTTCTTTTGAATCAATTATTTATATATTTAAATCA-ACTGTC
* * * *
909 ATGTTGGAATATTGCTTCTTTTGAATTAATTGTTTATATATTTAAATCAACTGTC
1 ATGTTGAAATATTACTTCTTTTGAATCAATTATTTATATATTTAAATCAACTGTC
964 ATGTTGAAATA
1 ATGTTGAAATA
975 CTTTTATGAC
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
55 54 0.98
56 1 0.02
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (55 bp):
ATGTTGAAATATTACTTCTTTTGAATCAATTATTTATATATTTAAATCAACTGTC
Found at i:4199 original size:21 final size:22
Alignment explanation
Indices: 4163--4205 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
4153 CAGCAAATGA
*
4163 TTTTAAAATTATTAAAATTATT
1 TTTTAAAATTAATAAAATTATT
4185 TTTTAAAA-TAATAAAATTATT
1 TTTTAAAATTAATAAAATTATT
4206 AAATAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTTAAAATTAATAAAATTATT
Found at i:4920 original size:3 final size:3
Alignment explanation
Indices: 4912--4950 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
4902 GGGGAACGAG
* *
4912 GAT GAT GAT GAT GAT GAT GAG GAAT GGT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT G-AT GAT GAT GAT GAT GA
4951 CTTTAAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 29 0.94
4 2 0.06
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.28
Consensus pattern (3 bp):
GAT
Found at i:10682 original size:29 final size:30
Alignment explanation
Indices: 10620--10686 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
10610 TTAGTTTTAT
*
10620 TTTATTTTATTTCTGTTTCTAATTTGTACC
1 TTTAATTTATTTCTGTTTCTAATTTGTACC
10650 TTTAATTTATTTAC-GTTTC-AATTTAGT-CC
1 TTTAATTTATTT-CTGTTTCTAATTT-GTACC
10679 TTT-ATTTA
1 TTTAATTTA
10687 ATTTTGCCTC
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
28 5 0.15
29 10 0.29
30 18 0.53
31 1 0.03
ACGTcount: A:0.21, C:0.12, G:0.06, T:0.61
Consensus pattern (30 bp):
TTTAATTTATTTCTGTTTCTAATTTGTACC
Found at i:10764 original size:4 final size:4
Alignment explanation
Indices: 10757--10897 Score: 101
Period size: 4 Copynumber: 34.0 Consensus size: 4
10747 ATTTGGTCCC
**
10757 ATTT ATTT -TTT ATATT ATTT ATATT ATTTT ATTT A-GA ATTT ATTT ATTT
1 ATTT ATTT ATTT AT-TT ATTT AT-TT A-TTT ATTT ATTT ATTT ATTT ATTT
* * * * *
10806 ATTT ACTT -GTT ATTT ATTT -TTT ATGTT GTTT ATATT ATTGC CTTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT AT-TT ATTT AT-TT ATT-T ATTT ATTT
*
10855 AGTCTT ATTT ATTT ATTT ATTT ATGT ATTTT ATTT ATTT ATTT
1 A-T-TT ATTT ATTT ATTT ATTT ATTT A-TTT ATTT ATTT ATTT
10898 TATGCCATTT
Statistics
Matches: 109, Mismatches: 15, Indels: 26
0.73 0.10 0.17
Matches are distributed among these distances:
3 9 0.08
4 72 0.66
5 24 0.22
6 4 0.04
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (4 bp):
ATTT
Found at i:10844 original size:44 final size:43
Alignment explanation
Indices: 10757--10897 Score: 121
Period size: 44 Copynumber: 3.3 Consensus size: 43
10747 ATTTGGTCCC
* *
10757 ATTTATTT-TTTA-TATTATTTATATTATTTTATTTA-GAAT-TT
1 ATTTATTTATTTAGTCTTATTTAT-TTA-TTTATTTATGTATATT
* * * *
10798 ATTTATTTATTTACTTGTTATTTATTT-TTTATGTTGTTTATATT
1 ATTTATTTATTTA-GTCTTATTTATTTATTTAT-TTATGTATATT
** *
10842 ATTGCCTTTATTTAGTCTTATTTATTTATTTATTTATGTATTTT
1 ATT-TATTTATTTAGTCTTATTTATTTATTTATTTATGTATATT
10886 ATTTATTTATTT
1 ATTTATTTATTT
10898 TATGCCATTT
Statistics
Matches: 79, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
41 13 0.16
42 6 0.08
43 11 0.14
44 36 0.46
45 13 0.16
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (43 bp):
ATTTATTTATTTAGTCTTATTTATTTATTTATTTATGTATATT
Found at i:10884 original size:60 final size:58
Alignment explanation
Indices: 10760--10900 Score: 141
Period size: 60 Copynumber: 2.4 Consensus size: 58
10750 TGGTCCCATT
*
10760 TATTTTTTATATTATTTATATTATTTTATTTAGAATTTATTTATTTATTTACTTGTTATT
1 TATTTTTTATATTATTTATATTATTTTATTTAG-ATTTATTTATTTATTTAC-TGTTATG
* *
10820 TATTTTTTATGTTGTTTATATTATTGCCTTTATTTAG-TCTTATTTATTTATTTA-T-TTATG
1 TATTTTTTATATTATTTATATTA-T---TTTATTTAGAT-TTATTTATTTATTTACTGTTATG
*
10880 TA--TTTTAT-TTATTTATTTTAT
1 TATTTTTTATATTATTTATATTAT
10901 GCCATTTATA
Statistics
Matches: 71, Mismatches: 5, Indels: 14
0.79 0.06 0.16
Matches are distributed among these distances:
56 1 0.01
57 10 0.14
58 6 0.08
60 27 0.38
61 2 0.03
62 1 0.01
63 15 0.21
64 9 0.13
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (58 bp):
TATTTTTTATATTATTTATATTATTTTATTTAGATTTATTTATTTATTTACTGTTATG
Found at i:10931 original size:24 final size:24
Alignment explanation
Indices: 10895--10940 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
10885 TATTTATTTA
* *
10895 TTTTATGCCATTTATATTTTTTCC
1 TTTTATGCAATTTATAATTTTTCC
* *
10919 TTTTATTCAATTTTTAATTTTT
1 TTTTATGCAATTTATAATTTTT
10941 AATTTTTATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.20, C:0.11, G:0.02, T:0.67
Consensus pattern (24 bp):
TTTTATGCAATTTATAATTTTTCC
Found at i:12323 original size:55 final size:55
Alignment explanation
Indices: 12206--12324 Score: 143
Period size: 55 Copynumber: 2.2 Consensus size: 55
12196 ATTGTTATAC
* * * * *
12206 TGAAATATTACTTCTTTTGAATCGATTGTTTTTATGTTTAAATCGATTGTCATGT
1 TGAAATACTACTTCTTTTGAATCGATTGTTTATATATTGAAATCAATTGTCATGT
* *
12261 T-AGAATACTGCTTCTTTTGAAT-GAGTTGTTTATATATTGAAATCAATTGTCATTT
1 TGA-AATACTACTTCTTTTGAATCGA-TTGTTTATATATTGAAATCAATTGTCATGT
12316 TGAAATACT
1 TGAAATACT
12325 TTTTATGCAG
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
54 3 0.06
55 50 0.93
56 1 0.02
ACGTcount: A:0.29, C:0.09, G:0.14, T:0.48
Consensus pattern (55 bp):
TGAAATACTACTTCTTTTGAATCGATTGTTTATATATTGAAATCAATTGTCATGT
Found at i:12530 original size:29 final size:30
Alignment explanation
Indices: 12486--12564 Score: 99
Period size: 31 Copynumber: 2.6 Consensus size: 30
12476 CTTCCATAAA
*
12486 CAAGTTTAGGTACCAACTTA-AAAAAGTGT
1 CAAGTTTAGGTACCAAATTAGAAAAAGTGT
* *
12515 CCAGTTTAGGTACCAAATTAGGAAAATGTGT
1 CAAGTTTAGGTACCAAATTA-GAAAAAGTGT
12546 CAAGTTT-GAGTACCAAATT
1 CAAGTTTAG-GTACCAAATT
12565 GGACAAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
29 18 0.42
30 1 0.02
31 24 0.56
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (30 bp):
CAAGTTTAGGTACCAAATTAGAAAAAGTGT
Found at i:14237 original size:22 final size:22
Alignment explanation
Indices: 14209--14264 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
14199 ATTCTTTATA
14209 ATTTATAAAATTTTAAATGAGT
1 ATTTATAAAATTTTAAATGAGT
14231 ATTTATAAAATTTTAAATGAGT
1 ATTTATAAAATTTTAAATGAGT
* *
14253 AATTGTAAAATT
1 ATTTATAAAATT
14265 ATACTTTGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.45
Consensus pattern (22 bp):
ATTTATAAAATTTTAAATGAGT
Found at i:14589 original size:29 final size:29
Alignment explanation
Indices: 14542--14614 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
14532 GTTAGCAAAT
* *
14542 AATT-TTAAACTTATTAAAATTATTTTTTAA
1 AATTATTAAAATTATTAAAATTA--ATTTAA
14572 AA-TA-TAAAATTATTAAAATTAATTTAA
1 AATTATTAAAATTATTAAAATTAATTTAA
14599 AATTATTAAAATTATT
1 AATTATTAAAATTATT
14615 TTTTTAAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
27 7 0.18
28 2 0.05
29 27 0.71
30 2 0.05
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (29 bp):
AATTATTAAAATTATTAAAATTAATTTAA
Found at i:14647 original size:49 final size:49
Alignment explanation
Indices: 14538--14647 Score: 161
Period size: 49 Copynumber: 2.2 Consensus size: 49
14528 CCACGTTAGC
*
14538 AAATAATTTTAAACTTATTAAAATTATTTTTTAAAATATAAAATTATTA
1 AAATAATTTTAAAATTATTAAAATTATTTTTTAAAATATAAAATTATTA
* *
14587 AAATTAA-TTTAAAATTATTAAAATTATTTTTTTAAATAATAAAATTGTT-
1 AAA-TAATTTTAAAATTATTAAAATTATTTTTTAAAAT-ATAAAATTATTA
14636 AAATAATTTTAA
1 AAATAATTTTAA
14648 TTTTCAATTT
Statistics
Matches: 55, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
48 3 0.05
49 39 0.71
50 13 0.24
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (49 bp):
AAATAATTTTAAAATTATTAAAATTATTTTTTAAAATATAAAATTATTA
Found at i:15702 original size:40 final size:38
Alignment explanation
Indices: 15658--15748 Score: 94
Period size: 39 Copynumber: 2.3 Consensus size: 38
15648 AAATTAGAAA
*
15658 TTAAAATTATTTAATAATTTATTATTTCAAATAAATAATT
1 TTAAAATTATTTAACAATTTA-TATTTCAAA-AAATAATT
** *
15698 TT-AAATTAATTTTAACAATTTATATTTTTAAAAATTATT
1 TTAAAATT-A-TTTAACAATTTATATTTCAAAAAATAATT
*
15737 TTAAAATCATTT
1 TTAAAATTATTT
15749 GATGATGTTG
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
38 3 0.07
39 15 0.35
40 14 0.33
41 11 0.26
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (38 bp):
TTAAAATTATTTAACAATTTATATTTCAAAAAATAATT
Found at i:16633 original size:11 final size:11
Alignment explanation
Indices: 16617--16641 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
16607 TCACGTCAAC
16617 AAATTATTTTA
1 AAATTATTTTA
16628 AAATTATTTTA
1 AAATTATTTTA
16639 AAA
1 AAA
16642 ATAAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
AAATTATTTTA
Found at i:17097 original size:57 final size:58
Alignment explanation
Indices: 17034--17146 Score: 183
Period size: 58 Copynumber: 2.0 Consensus size: 58
17024 TATCTCTAGA
* *
17034 TTATTTTTTAGCATTTTC-TTTTGGGTTCAGATATGGGAAAATAAAAATTTAATATGG
1 TTATTTTTTAGCATTTTCTTTTTGGATTCAGATATGAGAAAATAAAAATTTAATATGG
* *
17091 TTATTTTTTGGCATTTTCTTTTTGGATTCAGATATGAGAAAATAAAGATTTAATAT
1 TTATTTTTTAGCATTTTCTTTTTGGATTCAGATATGAGAAAATAAAAATTTAATAT
17147 CAATGGCTAT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
57 17 0.33
58 34 0.67
ACGTcount: A:0.32, C:0.05, G:0.16, T:0.47
Consensus pattern (58 bp):
TTATTTTTTAGCATTTTCTTTTTGGATTCAGATATGAGAAAATAAAAATTTAATATGG
Found at i:18916 original size:24 final size:25
Alignment explanation
Indices: 18866--18928 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
18856 TTCCAGAAAT
* * **
18866 TTAGGTCA-TACGAGCCCAGATTGG
1 TTAGCTCATTACGAGCCCAAATAAG
18890 TTAGCTC-TTACGAGCCCAAATAAG
1 TTAGCTCATTACGAGCCCAAATAAG
18914 TTAGCTCATT-CGAGC
1 TTAGCTCATTACGAGC
18929 TCGGATAGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
24 31 0.94
25 2 0.06
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (25 bp):
TTAGCTCATTACGAGCCCAAATAAG
Found at i:20847 original size:21 final size:21
Alignment explanation
Indices: 20803--20856 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
20793 CCTGTGCTAG
*
20803 TTCTATCGATACAAGTATAAC
1 TTCTACCGATACAAGTATAAC
*
20824 TTCTACCGATACAAGTCAT-GC
1 TTCTACCGATACAAGT-ATAAC
*
20845 TTCTTCCGATAC
1 TTCTACCGATAC
20857 TAAAAACTCC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 27 0.93
22 2 0.07
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (21 bp):
TTCTACCGATACAAGTATAAC
Found at i:26819 original size:29 final size:29
Alignment explanation
Indices: 26787--26941 Score: 102
Period size: 29 Copynumber: 5.2 Consensus size: 29
26777 AAATAGATGT
* *
26787 TAAAAATGGAATTTTGGAAAGTTCAAGAG
1 TAAAAATGGAATTTTGAAAAGTTCAAGGG
* **
26816 T-AAAATGGTAATTTTTAAAAAAATC-AGGG
1 TAAAAATGG-AA-TTTTGAAAAGTTCAAGGG
* **
26845 TCAAAAATGGAATTTTTAAAAGTTCGGGGG
1 T-AAAAATGGAATTTTGAAAAGTTCAAGGG
* *
26875 TAAAAATGTAATTTTTTGGAAAA-ATCAA-GG
1 TAAAAATGGAA--TTTT-GAAAAGTTCAAGGG
* * *
26905 TAAAAAATGGGATTTTGTAAAGTTTAAGGG
1 T-AAAAATGGAATTTTGAAAAGTTCAAGGG
26935 TAAAAAT
1 TAAAAAT
26942 ATAATTTTTG
Statistics
Matches: 96, Mismatches: 19, Indels: 22
0.70 0.14 0.16
Matches are distributed among these distances:
28 11 0.11
29 39 0.41
30 21 0.22
31 21 0.22
32 4 0.04
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.31
Consensus pattern (29 bp):
TAAAAATGGAATTTTGAAAAGTTCAAGGG
Found at i:26911 original size:60 final size:59
Alignment explanation
Indices: 26718--26950 Score: 229
Period size: 59 Copynumber: 3.9 Consensus size: 59
26708 CCTTGATTTT
* * * *
26718 AAATCGAGGTCAAAAATGGAATTTTGGAAAGTTC-GGGTGTGAAAATATAATTTTCTGAA
1 AAATCAAGGTCAAAAATGGAATTTTGGAAAGTTCAAGG-GTAAAAATATAATTTTTTGAA
* * * * **
26777 AAAT-AGATGTTAAAAATGGAATTTTGGAAAGTTCAAGAGT-AAAATGGTAATTTTTAAAA
1 AAATCA-AGGTCAAAAATGGAATTTTGGAAAGTTCAAGGGTAAAAAT-ATAATTTTTTGAA
* ** ** *
26836 AAATCAGGGTCAAAAATGGAATTTTTAAAAGTTCGGGGGTAAAAATGTAATTTTTTGGAA
1 AAATCAAGGTCAAAAATGGAATTTTGGAAAGTTCAAGGGTAAAAATATAATTTTTT-GAA
* * * *
26896 AAATCAAGGTAAAAAATGGGATTTTGTAAAGTTTAAGGGTAAAAATATAATTTTT
1 AAATCAAGGTCAAAAATGGAATTTTGGAAAGTTCAAGGGTAAAAATATAATTTTT
26951 GGATAGTTTA
Statistics
Matches: 140, Mismatches: 28, Indels: 11
0.78 0.16 0.06
Matches are distributed among these distances:
58 5 0.04
59 80 0.57
60 55 0.39
ACGTcount: A:0.43, C:0.04, G:0.21, T:0.32
Consensus pattern (59 bp):
AAATCAAGGTCAAAAATGGAATTTTGGAAAGTTCAAGGGTAAAAATATAATTTTTTGAA
Found at i:28064 original size:12 final size:12
Alignment explanation
Indices: 28023--28126 Score: 74
Period size: 12 Copynumber: 8.8 Consensus size: 12
28013 TCTCCTTTTT
*
28023 TTATTAA-AATA
1 TTATTAATATTA
28034 TTATTTAATATTAA
1 TTA-TTAATATT-A
28048 TTATTAATATTA
1 TTATTAATATTA
*
28060 TTATTAAT-TAA
1 TTATTAATATTA
*
28071 TGTCATTAGTATTA
1 T-T-ATTAATATTA
*
28085 -TATT--CATTA
1 TTATTAATATTA
*
28094 TTATTATTATTA
1 TTATTAATATTA
**
28106 TTATTAATGCTA
1 TTATTAATATTA
28118 TTATTAATA
1 TTATTAATA
28127 ATAGAATTAA
Statistics
Matches: 74, Mismatches: 10, Indels: 17
0.73 0.10 0.17
Matches are distributed among these distances:
9 4 0.05
10 4 0.05
11 9 0.12
12 36 0.49
13 15 0.20
14 6 0.08
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (12 bp):
TTATTAATATTA
Found at i:28119 original size:15 final size:14
Alignment explanation
Indices: 28042--28128 Score: 63
Period size: 15 Copynumber: 5.9 Consensus size: 14
28032 TATTATTTAA
*
28042 TATTAATTATTAATAT
1 TATT-ATTATTAAT-G
28058 TATTATTAATTAATG
1 TATTATT-ATTAATG
*
28073 TCATTAGTATTATAT-
1 T-ATTATTATTA-ATG
28088 TCATTATTATT-AT-
1 T-ATTATTATTAATG
28101 TATTATTATTAATG
1 TATTATTATTAATG
*
28115 CTATTATTAATAAT
1 -TATTATTATTAAT
28129 AGAATTAAGA
Statistics
Matches: 61, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
12 9 0.15
13 5 0.08
15 30 0.49
16 17 0.28
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.55
Consensus pattern (14 bp):
TATTATTATTAATG
Found at i:28123 original size:3 final size:3
Alignment explanation
Indices: 28032--28111 Score: 63
Period size: 3 Copynumber: 25.7 Consensus size: 3
28022 TTTATTAAAA
* * * * * *
28032 TAT TATT TAA TAT TAAT TAT TAA TAT TAT TAT TAAT TAA TGT CAT TAG
1 TAT TA-T TAT TAT T-AT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT
28080 TAT TA- TAT TCAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TA
28112 ATGCTATTAT
Statistics
Matches: 60, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
2 2 0.03
3 46 0.77
4 12 0.20
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:29502 original size:98 final size:98
Alignment explanation
Indices: 29367--29906 Score: 674
Period size: 98 Copynumber: 5.5 Consensus size: 98
29357 TAAAAAAATT
* * ** *
29367 TTCATGCTTCTGGGGTATAAGGTTCGCCATTATGACTTAAACCCTTCCCTTTGTGTCTTTGTGGT
1 TTCATGCTTCTGAGGTACAAGGTTCGCCATTGCGACTTAAACCCTTCCCTTTGTGTCTTTGCGGT
* * * * *
29432 ATTGAATCCGTCGTCGTGGCTTAGATCTTTCCC
66 ACTGGATCCGCCGTTGCGGCTTAGATCTTTCCC
* * * * ***
29465 TTCATGCTTCTGAGGTACAAGGTTTGCCATTGCGACTTAAACCTTTTCC-TTATGTCTTCATGGT
1 TTCATGCTTCTGAGGTACAAGGTTCGCCATTGCGACTTAAACCCTTCCCTTTGTGTCTTTGCGGT
* * * * *
29529 ACTAGATCTGCCATTGCGGCCTAGATTTTTCCC
66 ACTGGATCCGCCGTTGCGGCTTAGATCTTTCCC
* * *
29562 TTCATGTTTCTGAGGTACAAGGTTCGCCGTTTCGACTTAAACCCTTCCCTTTGTGTCTTTGCGGT
1 TTCATGCTTCTGAGGTACAAGGTTCGCCATTGCGACTTAAACCCTTCCCTTTGTGTCTTTGCGGT
* *
29627 ACTGGATCCGTCGTTGCGGCTTAGATCTTTCTC
66 ACTGGATCCGCCGTTGCGGCTTAGATCTTTCCC
29660 TTCATG-TCTCTGAGGTACAAGGTTCGCCATTGCGACTTAAACCCTTCCCTTTGTGTCTTTGCGG
1 TTCATGCT-TCTGAGGTACAAGGTTCGCCATTGCGACTTAAACCCTTCCCTTTGTGTCTTTGCGG
* *
29724 TACTGGATACGCCATTGCGGCTTAGATCTTTCCC
65 TACTGGATCCGCCGTTGCGGCTTAGATCTTTCCC
* ** *
29758 TTCATG-TCTCTGAGGTACAAGGTTCGCCATTGCGACTTAAACCTTTCCCTTCATATCTTTGCGG
1 TTCATGCT-TCTGAGGTACAAGGTTCGCCATTGCGACTTAAACCCTTCCCTTTGTGTCTTTGCGG
* *
29822 TACTGGATTCACCGTTGCGGCTTAGATCTTTCCC
65 TACTGGATCCGCCGTTGCGGCTTAGATCTTTCCC
* * * *
29856 TTCATGCTTCT-AGGGTACTAGGTTCACCGTTGCGACTTAAACCTTTCCCTT
1 TTCATGCTTCTGA-GGTACAAGGTTCGCCATTGCGACTTAAACCCTTCCCTT
29907 CATATCTTCT
Statistics
Matches: 385, Mismatches: 53, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
97 80 0.21
98 304 0.79
99 1 0.00
ACGTcount: A:0.16, C:0.26, G:0.20, T:0.37
Consensus pattern (98 bp):
TTCATGCTTCTGAGGTACAAGGTTCGCCATTGCGACTTAAACCCTTCCCTTTGTGTCTTTGCGGT
ACTGGATCCGCCGTTGCGGCTTAGATCTTTCCC
Found at i:29610 original size:49 final size:48
Alignment explanation
Indices: 29458--29962 Score: 292
Period size: 49 Copynumber: 10.3 Consensus size: 48
29448 TGGCTTAGAT
* * *
29458 CTTTCCCTTCATGCTTCTGAGGTACAAGGTTTGCCATTGCGACTTAAAC
1 CTTTCCCTTCATGTTTCTGAGGTAC-AGGTTCGCCGTTGCGACTTAAAC
* * * * * * *
29507 CTTTTCCTT-ATGTCTTC--ATGGTACTA-GATCTGCCATTGCGGCCTAGAT
1 CTTTCCCTTCATGT-TTCTGA-GGTAC-AGGTTC-GCCGTTGCGACTTAAAC
* *
29555 TTTTCCCTTCATGTTTCTGAGGTACAAGGTTCGCCGTTTCGACTTAAAC
1 CTTTCCCTTCATGTTTCTGAGGTAC-AGGTTCGCCGTTGCGACTTAAAC
* ** * * * * * * *
29604 CCTTCCCTTTGTGTCTT-TGCGGTACTGGATCCGTCGTTGCGGCTTAGAT
1 CTTTCCCTTCATGT-TTCTGAGGTACAGG-TTCGCCGTTGCGACTTAAAC
* * *
29653 CTTTCTCTTCATGTCTCTGAGGTACAAGGTTCGCCATTGCGACTTAAAC
1 CTTTCCCTTCATGTTTCTGAGGTAC-AGGTTCGCCGTTGCGACTTAAAC
* ** * * * * * * *
29702 CCTTCCCTTTGTGTCTT-TGCGGTACTGGATACGCCATTGCGGCTTAGAT
1 CTTTCCCTTCATGT-TTCTGAGGTACAGG-TTCGCCGTTGCGACTTAAAC
* *
29751 CTTTCCCTTCATGTCTCTGAGGTACAAGGTTCGCCATTGCGACTTAAAC
1 CTTTCCCTTCATGTTTCTGAGGTAC-AGGTTCGCCGTTGCGACTTAAAC
* * * * * * *
29800 CTTTCCCTTCATATCTT-TGCGGTACTGGATTCACCGTTGCGGCTTAGAT
1 CTTTCCCTTCATGT-TTCTGAGGTACAGG-TTCGCCGTTGCGACTTAAAC
* *
29849 CTTTCCCTTCATGCTTCT-AGGGTACTAGGTTCACCGTTGCGACTTAAAC
1 CTTTCCCTTCATGTTTCTGA-GGTAC-AGGTTCGCCGTTGCGACTTAAAC
* * * ** *
29898 CTTTCCCTTCATATCTTCT-TGGTACTAGATTCGTTGTTGC-AGCTTAAAT
1 CTTTCCCTTCATGT-TTCTGAGGTAC-AGGTTCGCCGTTGCGA-CTTAAAC
*
29947 TTTTCCCTTCATGTTT
1 CTTTCCCTTCATGTTT
29963 TGTGGTATTG
Statistics
Matches: 343, Mismatches: 91, Indels: 45
0.72 0.19 0.09
Matches are distributed among these distances:
47 3 0.01
48 45 0.13
49 277 0.81
50 18 0.05
ACGTcount: A:0.16, C:0.26, G:0.19, T:0.38
Consensus pattern (48 bp):
CTTTCCCTTCATGTTTCTGAGGTACAGGTTCGCCGTTGCGACTTAAAC
Found at i:34681 original size:24 final size:25
Alignment explanation
Indices: 34654--34732 Score: 76
Period size: 24 Copynumber: 3.2 Consensus size: 25
34644 GGCTTGAATA
34654 AGCTAACTTAT-TTGGGCTCGTAAG
1 AGCTAACTTATCTTGGGCTCGTAAG
* *
34678 AGCTAACCTATCTT-GGCTCGTATG
1 AGCTAACTTATCTTGGGCTCGTAAG
* *
34702 AGCTAA-TTTTGTCTGGGCTCGTATA-
1 AGCTAACTTATCT-TGGGCTCGTA-AG
34727 AGCTAA
1 AGCTAA
34733 ATTTTTGGAA
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
23 3 0.07
24 26 0.58
25 16 0.36
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (25 bp):
AGCTAACTTATCTTGGGCTCGTAAG
Found at i:40816 original size:20 final size:21
Alignment explanation
Indices: 40791--40829 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
40781 TCCTCCTTGT
40791 TTCATTTTATTTTA-AATTGG
1 TTCATTTTATTTTAGAATTGG
*
40811 TTCATTTTCTTTTAGAATT
1 TTCATTTTATTTTAGAATT
40830 TTTTTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.62
Consensus pattern (21 bp):
TTCATTTTATTTTAGAATTGG
Done.