Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014089.1 Kokia drynarioides strain JFW-HI SEQ_129120, 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: 76794
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 113 characters in sequence are not A, C, G, or T
Found at i:140 original size:13 final size:13
Alignment explanation
Indices: 85--162 Score: 77
Period size: 13 Copynumber: 5.9 Consensus size: 13
75 AACACATTAC
85 CTTTCTTTCCTTCTT
1 CTTTCTTT-CTT-TT
* * *
100 CTTTCGTTCCTCT
1 CTTTCTTTCTTTT
* *
113 CCTTC-TTCCTTT
1 CTTTCTTTCTTTT
*
125 CTTTTTTTCTTTT
1 CTTTCTTTCTTTT
138 CTTTCTTTCTTTT
1 CTTTCTTTCTTTT
151 CTTTCTTTCTTT
1 CTTTCTTTCTTT
163 CCCGTTTATT
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
12 9 0.17
13 35 0.66
14 2 0.04
15 7 0.13
ACGTcount: A:0.00, C:0.29, G:0.01, T:0.69
Consensus pattern (13 bp):
CTTTCTTTCTTTT
Found at i:142 original size:4 final size:4
Alignment explanation
Indices: 85--163 Score: 70
Period size: 4 Copynumber: 19.2 Consensus size: 4
75 AACACATTAC
* * * * * *
85 CTTT CTTT CCTT C-TT CTTT CGTTC CTCT CCTT CTTC CTTT CTTT TTTT
1 CTTT CTTT CTTT CTTT CTTT C-TTT CTTT CTTT CTTT CTTT CTTT CTTT
133 CTTTT CTTT CTTT CTTTT CTTT CTTT CTTT C
1 C-TTT CTTT CTTT C-TTT CTTT CTTT CTTT C
164 CCGTTTATTT
Statistics
Matches: 60, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
3 3 0.05
4 46 0.77
5 11 0.18
ACGTcount: A:0.00, C:0.30, G:0.01, T:0.68
Consensus pattern (4 bp):
CTTT
Found at i:143 original size:17 final size:17
Alignment explanation
Indices: 115--163 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
105 GTTCCTCTCC
*
115 TTCTTCCTTTCTTT-TT
1 TTCTTTCTTTCTTTCTT
131 TTCTTTTCTTTCTTTCTT
1 TTC-TTTCTTTCTTTCTT
149 TTCTTTCTTTCTTTC
1 TTCTTTCTTTCTTTC
164 CCGTTTATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 3 0.10
17 22 0.73
18 5 0.17
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (17 bp):
TTCTTTCTTTCTTTCTT
Found at i:2223 original size:24 final size:24
Alignment explanation
Indices: 2196--2243 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
2186 AAATCTAGAT
2196 ACATATAAGCATGTGAAGTGATAA
1 ACATATAAGCATGTGAAGTGATAA
*
2220 ACATATAAGCATGTGATGTGATAA
1 ACATATAAGCATGTGAAGTGATAA
2244 GTAAATTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.44, C:0.08, G:0.21, T:0.27
Consensus pattern (24 bp):
ACATATAAGCATGTGAAGTGATAA
Found at i:6273 original size:23 final size:23
Alignment explanation
Indices: 6213--6371 Score: 135
Period size: 23 Copynumber: 6.9 Consensus size: 23
6203 CAAAAAGTAC
*
6213 CAAAGTACT-AACAGAGAGCACA
1 CAAAGTGCTAAACAGAGAGCACA
* *
6235 -TAAGTGCTGGGCAACAGAGAGCACA
1 CAAAGTGCT---AAACAGAGAGCACA
* *
6260 CACAGTGCTAAACAGAGAGTACA
1 CAAAGTGCTAAACAGAGAGCACA
* * *
6283 CAAAGTACTAATCAGTGAGCACA
1 CAAAGTGCTAAACAGAGAGCACA
*
6306 CAAAGTGCTAATCAGAGAGCACA
1 CAAAGTGCTAAACAGAGAGCACA
* **
6329 CACAGTGCTAATTAGAGAGCACGA
1 CAAAGTGCTAAACAGAGAGCAC-A
* *
6353 -GATGTGCTAAACAGAGAGC
1 CAAAGTGCTAAACAGAGAGC
6372 GCGCTAGTGT
Statistics
Matches: 111, Mismatches: 20, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
21 6 0.05
23 85 0.77
24 1 0.01
25 13 0.12
26 6 0.05
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.14
Consensus pattern (23 bp):
CAAAGTGCTAAACAGAGAGCACA
Found at i:6347 original size:69 final size:66
Alignment explanation
Indices: 6208--6339 Score: 176
Period size: 69 Copynumber: 1.9 Consensus size: 66
6198 AAAAACAAAA
*
6208 AGTACCAAAGTACTAACAGAGAGCACATAAGTGCTGGGCAACAGAGAGCACACACAGTGCTAAAC
1 AGTACCAAAGTACTAACAGAGAGCACAAAAGTGCT--G-AACAGAGAGCACACACAGTGCTAAAC
6273 AGAG
63 AGAG
*
6277 AGTACACAAAGTACTAATCAGTGAGCACACAAAGTGCT-AATCAGAGAGCACACACAGTGCTAA
1 AGTAC-CAAAGTACTAA-CAGAGAGCACA-AAAGTGCTGAA-CAGAGAGCACACACAGTGCTAA
6340 TTAGAGAGCA
Statistics
Matches: 57, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
68 2 0.04
69 27 0.47
70 11 0.19
71 10 0.18
72 7 0.12
ACGTcount: A:0.42, C:0.22, G:0.22, T:0.14
Consensus pattern (66 bp):
AGTACCAAAGTACTAACAGAGAGCACAAAAGTGCTGAACAGAGAGCACACACAGTGCTAAACAGA
G
Found at i:13427 original size:21 final size:22
Alignment explanation
Indices: 13401--13493 Score: 89
Period size: 22 Copynumber: 4.1 Consensus size: 22
13391 ATACGGAACA
*
13401 AACAGAGAGTAC-CAAAGTACT
1 AACAGAGAGCACACAAAGTACT
*
13422 AACAGAGAGCACACAAAGTGCT
1 AACAGAGAGCACACAAAGTACT
* *
13444 AATCAGAGAGCACACACAGTGCTAAT
1 AA-CAGAGAGCACACA-A-AG-TACT
* *
13470 AACAGAGAGCACACACAGTGCT
1 AACAGAGAGCACACAAAGTACT
13492 AA
1 AA
13494 TAACAGAGAG
Statistics
Matches: 58, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
21 11 0.19
22 14 0.24
23 14 0.24
24 1 0.02
25 14 0.24
26 4 0.07
ACGTcount: A:0.45, C:0.23, G:0.20, T:0.12
Consensus pattern (22 bp):
AACAGAGAGCACACAAAGTACT
Found at i:13450 original size:23 final size:24
Alignment explanation
Indices: 13402--13506 Score: 128
Period size: 25 Copynumber: 4.5 Consensus size: 24
13392 TACGGAACAA
* *
13402 ACAGAGAGTAC-CAAAGTACT-A-
1 ACAGAGAGCACACAAAGTGCTAAT
13423 ACAGAGAGCACACAAAGTGCTAAT
1 ACAGAGAGCACACAAAGTGCTAAT
*
13447 -CAGAGAGCACACACAGTGCTAAT
1 ACAGAGAGCACACAAAGTGCTAAT
*
13470 AACAGAGAGCACACACAGTGCTAAT
1 -ACAGAGAGCACACAAAGTGCTAAT
13495 AACAGAGAGCAC
1 -ACAGAGAGCAC
13507 GAGATGTGCT
Statistics
Matches: 76, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
21 10 0.13
22 8 0.11
23 23 0.30
25 35 0.46
ACGTcount: A:0.45, C:0.23, G:0.21, T:0.11
Consensus pattern (24 bp):
ACAGAGAGCACACAAAGTGCTAAT
Found at i:13518 original size:25 final size:25
Alignment explanation
Indices: 13421--13506 Score: 149
Period size: 25 Copynumber: 3.5 Consensus size: 25
13411 ACCAAAGTAC
*
13421 TAACAGAGAGCACACAAAGTGCTAA
1 TAACAGAGAGCACACACAGTGCTAA
13446 T--CAGAGAGCACACACAGTGCTAA
1 TAACAGAGAGCACACACAGTGCTAA
13469 TAACAGAGAGCACACACAGTGCTAA
1 TAACAGAGAGCACACACAGTGCTAA
13494 TAACAGAGAGCAC
1 TAACAGAGAGCAC
13507 GAGATGTGCT
Statistics
Matches: 58, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
23 22 0.38
25 36 0.62
ACGTcount: A:0.44, C:0.23, G:0.21, T:0.12
Consensus pattern (25 bp):
TAACAGAGAGCACACACAGTGCTAA
Found at i:25831 original size:20 final size:20
Alignment explanation
Indices: 25806--25851 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
25796 TTCCAAGTTT
25806 TTGATTCGGCCTCACTTTTA
1 TTGATTCGGCCTCACTTTTA
25826 TTGATTCGGCCTCACTTTTA
1 TTGATTCGGCCTCACTTTTA
25846 TTGATT
1 TTGATT
25852 GTGCTACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.15, C:0.22, G:0.15, T:0.48
Consensus pattern (20 bp):
TTGATTCGGCCTCACTTTTA
Found at i:26050 original size:40 final size:40
Alignment explanation
Indices: 25995--26158 Score: 175
Period size: 40 Copynumber: 4.0 Consensus size: 40
25985 TTTGGATAGA
* *
25995 AAACGCCGTAAAAGGTGAAGCAATAGTGGCGTTTTTCCAT
1 AAACGCCGCAAAAGGTAAAGCAATAGTGGCGTTTTTCCAT
*
26035 AAACGCCGCAAAAGGTAAAGCAATAGCGGCGTTTTTCCAT
1 AAACGCCGCAAAAGGTAAAGCAATAGTGGCGTTTTTCCAT
* * * *** *
26075 AAACACTGCAAAAGGTAAAGCAATAGTGGCATTTATAGAAA
1 AAACGCCGCAAAAGGTAAAGCAATAGTGGCGTTT-TTCCAT
* * * * *
26116 AAACGCCGCTAAAGGTCAGAGCATTAGTAGCGTTTTCCCAT
1 AAACGCCGCAAAAGGT-AAAGCAATAGTGGCGTTTTTCCAT
26157 AA
1 AA
26159 GCATCGCTAA
Statistics
Matches: 100, Mismatches: 22, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
40 67 0.67
41 19 0.19
42 14 0.14
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (40 bp):
AAACGCCGCAAAAGGTAAAGCAATAGTGGCGTTTTTCCAT
Found at i:26260 original size:41 final size:41
Alignment explanation
Indices: 26085--26334 Score: 193
Period size: 41 Copynumber: 6.1 Consensus size: 41
26075 AAACACTGCA
* * * *
26085 AAAGGT-AAAGCAATAGTGGCATTTATAGAAAAAACGCCGCT
1 AAAGGTCAGAGCAATAGTGGCGTTTAT-GGAAAAGCGCCGCT
* * ** * **
26126 AAAGGTCAGAGCATTAGTAGCGTTT-TCCCATAAGCATCGCT
1 AAAGGTCAGAGCAATAGTGGCGTTTAT-GGAAAAGCGCCGCT
* * * *
26167 AAAGGTCAGAGCATTAGCGACGTTTATGGAAAAGCGTCGCT
1 AAAGGTCAGAGCAATAGTGGCGTTTATGGAAAAGCGCCGCT
* *
26208 AAAGGTCAGAGTAATAGTGGCGTTTATGGGAAAGCGCCGCT
1 AAAGGTCAGAGCAATAGTGGCGTTTATGGAAAAGCGCCGCT
* * * **
26249 AAAGGTCAGAGTAATAGCGGCGTTTATAAGAAAA-CGCCATT
1 AAAGGTCAGAGCAATAGTGGCGTTTAT-GGAAAAGCGCCGCT
* * **
26290 AAATGTCAGAGCATTAGCT-GCGTTTATGTGAAAAATGCCGCT
1 AAAGGTCAGAGCAATAG-TGGCGTTTATG-GAAAAGCGCCGCT
26332 AAA
1 AAA
26335 AATTAAGCAA
Statistics
Matches: 166, Mismatches: 37, Indels: 11
0.78 0.17 0.05
Matches are distributed among these distances:
41 140 0.84
42 26 0.16
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.23
Consensus pattern (41 bp):
AAAGGTCAGAGCAATAGTGGCGTTTATGGAAAAGCGCCGCT
Found at i:27244 original size:56 final size:57
Alignment explanation
Indices: 27130--27244 Score: 137
Period size: 56 Copynumber: 2.0 Consensus size: 57
27120 AATTAGTTAT
* * * * *
27130 TTGACTCGAATCTCCTTATATAGTAATAATGTATATTAATCAATATTTAATAGTTAA
1 TTGACTCGAATCTCCTTATATACTAATAATATATATTAATCAATATTCAAGAGGTAA
*
27187 TTGACTC-AATCTCCTCT-TATACTAAT-ATATATATTAATGTAATATTCAAGAGGTAA
1 TTGACTCGAATCTCCT-TATATACTAATAATATATATTAAT-CAATATTCAAGAGGTAA
27243 TT
1 TT
27245 CACTAAAACT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
55 11 0.22
56 31 0.62
57 8 0.16
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.42
Consensus pattern (57 bp):
TTGACTCGAATCTCCTTATATACTAATAATATATATTAATCAATATTCAAGAGGTAA
Found at i:28570 original size:41 final size:40
Alignment explanation
Indices: 28461--28579 Score: 112
Period size: 41 Copynumber: 2.9 Consensus size: 40
28451 AATATGAGAA
* * ** *
28461 AGAGCATTAGTGACGCTTTTGAGAAAGCGTAGCTAAATGTC
1 AGAGCATTAGCGACGCTTATGA-AAAGCGCCGCTAAAGGTC
* * * *
28502 AAAGCAATAACGACGCTTATAGGAAAGCGCCGCTAAAGGTC
1 AGAGCATTAGCGACGCTTAT-GAAAAGCGCCGCTAAAGGTC
* *
28543 AGAGCATTAGCGACGCTTATGTAAAAGCACCACTAAA
1 AGAGCATTAGCGACGCTTATG-AAAAGCGCCGCTAAA
28580 AATTAGTGCA
Statistics
Matches: 61, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
40 1 0.02
41 59 0.97
42 1 0.02
ACGTcount: A:0.37, C:0.19, G:0.24, T:0.20
Consensus pattern (40 bp):
AGAGCATTAGCGACGCTTATGAAAAGCGCCGCTAAAGGTC
Found at i:28735 original size:10 final size:10
Alignment explanation
Indices: 28721--28756 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
28711 TATATAAACT
28721 AAAAATTTTC
1 AAAAATTTTC
*
28731 TAAAATTTT-
1 AAAAATTTTC
28740 AAAAATTTTC
1 AAAAATTTTC
28750 AAAAATT
1 AAAAATT
28757 ATGAAACTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (10 bp):
AAAAATTTTC
Found at i:28744 original size:19 final size:19
Alignment explanation
Indices: 28720--28756 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
28710 TTATATAAAC
*
28720 TAAAAATTTTCTAAAATTT
1 TAAAAATTTTCAAAAATTT
28739 TAAAAATTTTCAAAAATT
1 TAAAAATTTTCAAAAATT
28757 ATGAAACTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.43
Consensus pattern (19 bp):
TAAAAATTTTCAAAAATTT
Found at i:31758 original size:4 final size:4
Alignment explanation
Indices: 31749--31791 Score: 50
Period size: 4 Copynumber: 10.5 Consensus size: 4
31739 TTGTATAATA
* * *
31749 TTAT TTAT TTAT TTAT TTAT TTAT ATTAT ATAT ATAT ATAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT -TTAT TTAT TTAT TTAT TT
31792 CTTTCGTGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
4 32 0.89
5 4 0.11
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (4 bp):
TTAT
Found at i:32004 original size:42 final size:43
Alignment explanation
Indices: 31914--32081 Score: 189
Period size: 43 Copynumber: 3.9 Consensus size: 43
31904 ACCTGTTAAT
* * *
31914 TTTAGCGACGTTTGT-GGGAAAAGCGCCGCTAAAGACCATGTAC
1 TTTAGCGGCGTTTGTAGGG-AAAGCGCTGCTAAAGACCATGTTC
* * *
31957 ATTAGCGGCGTTTGT-GGGAAAGTGCTGCTAAAGATCATGTTC
1 TTTAGCGGCGTTTGTAGGGAAAGCGCTGCTAAAGACCATGTTC
* * *
31999 TTTAGCGGCGTTTATAGGGAAAGCG-TCGTTAAAGACCATATTC
1 TTTAGCGGCGTTTGTAGGGAAAGCGCT-GCTAAAGACCATGTTC
* * *
32042 TTTAACGGCGTTTGTAGGGAAAGCACTGCTAAAGAACATG
1 TTTAGCGGCGTTTGTAGGGAAAGCGCTGCTAAAGACCATG
32082 GGAAAAGCGT
Statistics
Matches: 104, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
42 34 0.33
43 69 0.66
44 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.27
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTAGGGAAAGCGCTGCTAAAGACCATGTTC
Found at i:42631 original size:22 final size:22
Alignment explanation
Indices: 42574--42620 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
42564 CGATCTGAGG
* * *
42574 AAAAATAAAAGAAACAGAATTA
1 AAAAAAAAAAAAAATAGAATTA
42596 AAAAAAAAAAAAAATAGAATTA
1 AAAAAAAAAAAAAATAGAATTA
42618 AAA
1 AAA
42621 GAAATAGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.79, C:0.02, G:0.06, T:0.13
Consensus pattern (22 bp):
AAAAAAAAAAAAAATAGAATTA
Found at i:47771 original size:15 final size:16
Alignment explanation
Indices: 47746--47775 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
47736 GAATTAAAAA
47746 TAAAAGAAAATAGAAT
1 TAAAAGAAAATAGAAT
47762 TAAAAG-AAATAGAA
1 TAAAAGAAAATAGAA
47776 AATAGAGGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (16 bp):
TAAAAGAAAATAGAAT
Found at i:47775 original size:22 final size:22
Alignment explanation
Indices: 47719--47781 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
47709 CGATCTGAGG
* *
47719 AAAAATAAAAAAAAACAGAATT
1 AAAAATAAAAGAAAATAGAATT
47741 AAAAATAAAAGAAAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
*
47763 AAAAGA-AATAGAAAATAGA
1 AAAA-ATAAAAGAAAATAGA
47782 GGTGTCAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
22 36 0.97
23 1 0.03
ACGTcount: A:0.75, C:0.02, G:0.10, T:0.14
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:49663 original size:24 final size:23
Alignment explanation
Indices: 49619--49664 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
49609 ATAATTAAAA
**
49619 TATTTCTATAAATAATTAAAATT
1 TATTTCTATAAATAAAAAAAATT
*
49642 TATTATCTTTAAATAAAAAAAAT
1 TATT-TCTATAAATAAAAAAAAT
49665 CAATAATTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (23 bp):
TATTTCTATAAATAAAAAAAATT
Found at i:52091 original size:68 final size:67
Alignment explanation
Indices: 52011--52208 Score: 189
Period size: 68 Copynumber: 3.0 Consensus size: 67
52001 ATTTTAATAG
*
52011 TTTAATATTAAATTTAATTTAATACTTATTTTAATAAA-ATTTTATTAATTTAATATTAAAGTTA
1 TTTAATATTAAATTTAATTTAATATTTATTTTAATAAACATTTTATTAATTTAATATTAAAG-TA
52075 TTA
65 TTA
* * *
52078 TCTTAATATTAAATTTAATTCAATGTTTATATTGTAGATAAACATTTTATT-ATTT--TAAT-AA
1 T-TTAATATTAAATTTAATTTAATATTTAT-TT-TA-ATAAACATTTTATTAATTTAATATTAAA
52139 G----A
62 GTATTA
* * * * * *
52141 TTTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATGTTAATTTAATATTAAAGTGA
1 TTTAATATTAAATTTAATTTAATATTTATTTTAATAAACATTTTATTAATTTAATATTAAAGT-A
52206 TTA
65 TTA
52209 AGTTTAATCA
Statistics
Matches: 104, Mismatches: 13, Indels: 27
0.72 0.09 0.19
Matches are distributed among these distances:
59 11 0.11
60 5 0.05
61 1 0.01
62 28 0.27
63 5 0.05
67 1 0.01
68 29 0.28
69 5 0.05
70 2 0.02
71 9 0.09
72 8 0.08
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (67 bp):
TTTAATATTAAATTTAATTTAATATTTATTTTAATAAACATTTTATTAATTTAATATTAAAGTAT
TA
Found at i:53817 original size:24 final size:23
Alignment explanation
Indices: 53790--53841 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
53780 AGAATTAAAA
*
53790 TGATAAATATTAAATTGATTTAAT
1 TGATAAAT-TTAAATTCATTTAAT
* *
53814 TGATTCAATTTAAATTCTTTTAAT
1 TGA-TAAATTTAAATTCATTTAAT
53838 TGAT
1 TGAT
53842 TTAATGACTC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
23 1 0.04
24 19 0.79
25 4 0.17
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (23 bp):
TGATAAATTTAAATTCATTTAAT
Found at i:56709 original size:36 final size:36
Alignment explanation
Indices: 56669--56826 Score: 124
Period size: 36 Copynumber: 4.4 Consensus size: 36
56659 TGATGACCAT
* *
56669 TGTGAAAGCGAATATGTGAGTTTGCTATTCATGCCA
1 TGTGAAAGCAAATATGTGAGTATGCTATTCATGCCA
* * * *
56705 TGTGATAGTAAATATGTGGGTATGTTATTCATGCCA
1 TGTGAAAGCAAATATGTGAGTATGCTATTCATGCCA
* * *
56741 TGTGACAA-TAAATATGTAAGTACGCTATTCATG-CA
1 TGTGA-AAGCAAATATGTGAGTATGCTATTCATGCCA
* * * * *
56776 TG-AAACAGAAAATATCTGGGTATGTTATTCATGCCA
1 TGTGAA-AGCAAATATGTGAGTATGCTATTCATGCCA
* * *
56812 GGTGATAGTAAATAT
1 TGTGAAAGCAAATAT
56827 ATTGTGCTGA
Statistics
Matches: 95, Mismatches: 22, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
33 1 0.01
34 2 0.02
35 23 0.24
36 67 0.71
37 2 0.02
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.34
Consensus pattern (36 bp):
TGTGAAAGCAAATATGTGAGTATGCTATTCATGCCA
Found at i:56805 original size:35 final size:35
Alignment explanation
Indices: 56713--56809 Score: 106
Period size: 35 Copynumber: 2.7 Consensus size: 35
56703 CATGTGATAG
**
56713 TAAATATGTGGGTATGTTATTCATGCCATGTGACAA
1 TAAATATGTGGGTATGTTATTCATG-CATGAAACAA
** * *
56749 TAAATATGTAAGTACGCTATTCATGCATGAAACAGA
1 TAAATATGTGGGTATGTTATTCATGCATGAAACA-A
*
56785 -AAATATCTGGGTATGTTATTCATGC
1 TAAATATGTGGGTATGTTATTCATGC
56810 CAGGTGATAG
Statistics
Matches: 49, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
35 27 0.55
36 22 0.45
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.34
Consensus pattern (35 bp):
TAAATATGTGGGTATGTTATTCATGCATGAAACAA
Found at i:57235 original size:10 final size:10
Alignment explanation
Indices: 57220--57334 Score: 131
Period size: 10 Copynumber: 11.4 Consensus size: 10
57210 TATCATAAAC
*
57220 TGTGATTAAA
1 TGTGATTATA
*
57230 TATGATTATA
1 TGTGATTATA
* *
57240 TGTGGTTAAA
1 TGTGATTATA
57250 TGTGATTTATA
1 TGTGA-TTATA
*
57261 TGTGACTATA
1 TGTGATTATA
* *
57271 TGTGGTTAAA
1 TGTGATTATA
*
57281 TATGATTATA
1 TGTGATTATA
57291 TGTGATTATA
1 TGTGATTATA
57301 TGTGATTATA
1 TGTGATTATA
*
57311 TGTGATTCTA
1 TGTGATTATA
*
57321 TGTGATTATT
1 TGTGATTATA
57331 TGTG
1 TGTG
57335 GTTAAATGTT
Statistics
Matches: 86, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
10 77 0.90
11 9 0.10
ACGTcount: A:0.30, C:0.02, G:0.21, T:0.48
Consensus pattern (10 bp):
TGTGATTATA
Found at i:57256 original size:30 final size:30
Alignment explanation
Indices: 57215--57343 Score: 168
Period size: 30 Copynumber: 4.2 Consensus size: 30
57205 TAAACTATCA
* *
57215 TAAACTGTGATTAAATATGATTATATGTGGT
1 TAAA-TGTGATTATATGTGATTATATGTGGT
*
57246 TAAATGTGATTTATATGTGACTATATGTGGT
1 TAAATGTGA-TTATATGTGATTATATGTGGT
* *
57277 TAAATATGATTATATGTGATTATATGTGAT
1 TAAATGTGATTATATGTGATTATATGTGGT
* * *
57307 TATATGTGATTCTATGTGATTATTTGTGGT
1 TAAATGTGATTATATGTGATTATATGTGGT
57337 TAAATGT
1 TAAATGT
57344 TATTTTGGTT
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
30 55 0.65
31 30 0.35
ACGTcount: A:0.31, C:0.02, G:0.20, T:0.47
Consensus pattern (30 bp):
TAAATGTGATTATATGTGATTATATGTGGT
Found at i:57362 original size:23 final size:23
Alignment explanation
Indices: 57353--57457 Score: 131
Period size: 23 Copynumber: 4.6 Consensus size: 23
57343 TTATTTTGGT
* *
57353 TTATGCTTAAATGTTAATATGAT
1 TTATGCTTAAATGTTAATGTGAA
* *
57376 TTTTGCTTAAATATTAATGTGAA
1 TTATGCTTAAATGTTAATGTGAA
*
57399 TTATGCTTAAATATTAATGTGAA
1 TTATGCTTAAATGTTAATGTGAA
* *
57422 TTATGCTTAAATGTTAAGGTGAT
1 TTATGCTTAAATGTTAATGTGAA
57445 TTATG-TGTAAATG
1 TTATGCT-TAAATG
57458 GACCCATGAA
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
22 1 0.01
23 72 0.99
ACGTcount: A:0.34, C:0.04, G:0.16, T:0.46
Consensus pattern (23 bp):
TTATGCTTAAATGTTAATGTGAA
Found at i:60441 original size:36 final size:36
Alignment explanation
Indices: 60385--60603 Score: 296
Period size: 36 Copynumber: 6.1 Consensus size: 36
60375 GTAAAAGTGG
*
60385 ATATGTGGG-ATGTTTTTCATGCCATGTGACAGTAA
1 ATATGTGGGTATGTTATTCATGCCATGTGACAGTAA
* *
60420 ATATGTGGGTATGTTAATCATGTCATGTGACAGTAA
1 ATATGTGGGTATGTTATTCATGCCATGTGACAGTAA
* * * *
60456 ATATGTTGTTATGTTATTCATTCAATGTGACAGTAA
1 ATATGTGGGTATGTTATTCATGCCATGTGACAGTAA
*
60492 ATATGTGGGTATGTTATTCATGCCATGTGATAGTAA
1 ATATGTGGGTATGTTATTCATGCCATGTGACAGTAA
* * * * *
60528 ATATGTGAGTATGTTATTCATGCGATGAGATAGAAA
1 ATATGTGGGTATGTTATTCATGCCATGTGACAGTAA
* *
60564 ATATGTGGGTATGTTATTCATGCCATGTGATAGTGA
1 ATATGTGGGTATGTTATTCATGCCATGTGACAGTAA
60600 ATAT
1 ATAT
60604 ATTGTGCTGA
Statistics
Matches: 160, Mismatches: 23, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
35 9 0.06
36 151 0.94
ACGTcount: A:0.30, C:0.08, G:0.24, T:0.38
Consensus pattern (36 bp):
ATATGTGGGTATGTTATTCATGCCATGTGACAGTAA
Found at i:61011 original size:10 final size:10
Alignment explanation
Indices: 60993--61090 Score: 106
Period size: 10 Copynumber: 9.7 Consensus size: 10
60983 CAAACTATCA
60993 TAAACTGTGAT
1 TAAA-TGTGAT
61004 TAAATGTGAT
1 TAAATGTGAT
* *
61014 TATATGTGGT
1 TAAATGTGAT
*
61024 TAAATGTGAC
1 TAAATGTGAT
*
61034 TATATGTGAT
1 TAAATGTGAT
*
61044 TAAATATGAT
1 TAAATGTGAT
*
61054 TATATGTGAT
1 TAAATGTGAT
61064 TAAATGTGAT
1 TAAATGTGAT
** *
61074 TATTTGTGGT
1 TAAATGTGAT
61084 TAAATGT
1 TAAATGT
61091 TAGTATGATT
Statistics
Matches: 70, Mismatches: 17, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
10 66 0.94
11 4 0.06
ACGTcount: A:0.34, C:0.02, G:0.20, T:0.44
Consensus pattern (10 bp):
TAAATGTGAT
Found at i:61026 original size:20 final size:20
Alignment explanation
Indices: 60998--61090 Score: 141
Period size: 20 Copynumber: 4.7 Consensus size: 20
60988 TATCATAAAC
60998 TGTGATTAAATGTGATTATA
1 TGTGATTAAATGTGATTATA
* *
61018 TGTGGTTAAATGTGACTATA
1 TGTGATTAAATGTGATTATA
*
61038 TGTGATTAAATATGATTATA
1 TGTGATTAAATGTGATTATA
*
61058 TGTGATTAAATGTGATTATT
1 TGTGATTAAATGTGATTATA
*
61078 TGTGGTTAAATGT
1 TGTGATTAAATGT
61091 TAGTATGATT
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 65 1.00
ACGTcount: A:0.32, C:0.01, G:0.22, T:0.45
Consensus pattern (20 bp):
TGTGATTAAATGTGATTATA
Found at i:61109 original size:23 final size:23
Alignment explanation
Indices: 61083--61204 Score: 165
Period size: 23 Copynumber: 5.3 Consensus size: 23
61073 TTATTTGTGG
*
61083 TTAAATGTTAGTATGATTTATGC
1 TTAAATGTTAATATGATTTATGC
*
61106 TTAAATGTTAATATGATTTATAC
1 TTAAATGTTAATATGATTTATGC
*
61129 TTAAATGTTAATGTGATTTATGC
1 TTAAATGTTAATATGATTTATGC
* *
61152 TTAAATATTAATGTGATTTATGC
1 TTAAATGTTAATATGATTTATGC
**
61175 TTAAATGTTAAGGTGATTTATG-
1 TTAAATGTTAATATGATTTATGC
61197 TGTAAATG
1 T-TAAATG
61205 GATCAATGAA
Statistics
Matches: 91, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
22 1 0.01
23 90 0.99
ACGTcount: A:0.34, C:0.03, G:0.16, T:0.47
Consensus pattern (23 bp):
TTAAATGTTAATATGATTTATGC
Found at i:65521 original size:5 final size:5
Alignment explanation
Indices: 65511--65536 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
65501 TGAGCCTATA
65511 TCACC TCACC TCACC TCACC TCACC T
1 TCACC TCACC TCACC TCACC TCACC T
65537 TTCCTTTGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.58, G:0.00, T:0.23
Consensus pattern (5 bp):
TCACC
Found at i:74949 original size:96 final size:96
Alignment explanation
Indices: 74783--74956 Score: 228
Period size: 96 Copynumber: 1.8 Consensus size: 96
74773 TCGATTATCC
* ** * ** *
74783 CGATTTGATGAAAGGTTGCACCTAGTAAGTTAAGGCGTAAATTTTCAGAATCGAAGATAAGGAAA
1 CGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCACAAATTTTCAGAATCGAAGATAAAGAAA
74848 CATTGCCTCGATTAAGGGTATTCAATTATTT
66 CATTGCCTCGATTAAGGGTATTCAATTATTT
74879 CGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCACAAATTTTC-GAAACTCGAA-ATAAA-A
1 CGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCACAAATTTTCAG-AA-TCGAAGATAAAGA
*
74941 GAATATTGCCTCGATT
64 -AACATTGCCTCGATT
74957 TTAAAGTTTT
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
95 2 0.03
96 60 0.90
97 5 0.07
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (96 bp):
CGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCACAAATTTTCAGAATCGAAGATAAAGAAA
CATTGCCTCGATTAAGGGTATTCAATTATTT
Found at i:75326 original size:28 final size:29
Alignment explanation
Indices: 75286--75347 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 29
75276 TAAAAAGGGT
* * * *
75286 AATTTTGAGAGTTTTAGGGGTAAAGATGG
1 AATTTAGAGAGTTTTAGGGGCAAAAATGA
*
75315 AATTTAGA-AGTTTTGGGGGCAAAAATGA
1 AATTTAGAGAGTTTTAGGGGCAAAAATGA
75343 AATTT
1 AATTT
75348 TTGGAAGTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 21 0.75
29 7 0.25
ACGTcount: A:0.35, C:0.02, G:0.29, T:0.34
Consensus pattern (29 bp):
AATTTAGAGAGTTTTAGGGGCAAAAATGA
Found at i:75399 original size:60 final size:60
Alignment explanation
Indices: 75321--75475 Score: 204
Period size: 60 Copynumber: 2.6 Consensus size: 60
75311 ATGGAATTTA
* * * *
75321 GAAGTTTTGGGGGCAAAAATGAAATTTTTGGAAGTTTCAAGGTCAAAAATGGGATTTTTG
1 GAAGTTTCGGGGGTAAAAATGAGATTTTTGGAAGTTTCAAGGTAAAAAATGGGATTTTTG
* * ***
75381 GAAGTTTGGGGGGTAAAAATGAGATTTTTGAAAGTTTTGGGGTAAAAAATGGGATTTTTG
1 GAAGTTTCGGGGGTAAAAATGAGATTTTTGGAAGTTTCAAGGTAAAAAATGGGATTTTTG
* *
75441 GAAG-TTCGAGGGTAAAAATGGGATTTTTGGAAGTT
1 GAAGTTTCGGGGGTAAAAATGAGATTTTTGGAAGTT
75476 CGGGGATAAA
Statistics
Matches: 83, Mismatches: 12, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
59 27 0.33
60 56 0.67
ACGTcount: A:0.32, C:0.03, G:0.32, T:0.34
Consensus pattern (60 bp):
GAAGTTTCGGGGGTAAAAATGAGATTTTTGGAAGTTTCAAGGTAAAAAATGGGATTTTTG
Found at i:75438 original size:29 final size:29
Alignment explanation
Indices: 75295--75498 Score: 173
Period size: 30 Copynumber: 6.9 Consensus size: 29
75285 TAATTTTGAG
* * *
75295 AGTTTTAGGGGTAAAGAT-GGA-ATTTAGA
1 AGTTTT-GGGGTAAAAATGGGATTTTTGGA
* **
75323 AGTTTTGGGGGCAAAAATGAAATTTTTGGA
1 AGTTTT-GGGGTAAAAATGGGATTTTTGGA
***
75353 AGTTTCAAGGTCAAAAATGGGATTTTTGGA
1 AGTTTTGGGGT-AAAAATGGGATTTTTGGA
* * *
75383 AGTTTGGGGGGTAAAAATGAGATTTTTGAA
1 AGTTT-TGGGGTAAAAATGGGATTTTTGGA
75413 AGTTTTGGGGTAAAAAATGGGATTTTTGGA
1 AGTTTTGGGGT-AAAAATGGGATTTTTGGA
*
75443 AG-TTCGAGGGTAAAAATGGGATTTTTGGA
1 AGTTTTG-GGGTAAAAATGGGATTTTTGGA
* * *
75472 AG-TTCGGGGATAAAAACGAGATTTTTG
1 AGTTTTGGGG-TAAAAATGGGATTTTTG
75499 AAAAAATTAG
Statistics
Matches: 145, Mismatches: 24, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
28 18 0.12
29 50 0.34
30 74 0.51
31 3 0.02
ACGTcount: A:0.33, C:0.03, G:0.31, T:0.33
Consensus pattern (29 bp):
AGTTTTGGGGTAAAAATGGGATTTTTGGA
Found at i:76525 original size:34 final size:33
Alignment explanation
Indices: 76458--76539 Score: 92
Period size: 34 Copynumber: 2.4 Consensus size: 33
76448 TAATTATTAA
* * *
76458 TATTACTATTATTATTATTAATGAGACAGTTAT
1 TATTAATATTATTATTATTAATAACACAGTTAT
* * *
76491 TACTTATTATTATTATTATTATTAACACATTTAT
1 TA-TTAATATTATTATTATTAATAACACAGTTAT
76525 TATTAATAGTTATTA
1 TATTAATA-TTATTA
76540 AATAAATTGA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
33 7 0.17
34 34 0.83
ACGTcount: A:0.37, C:0.06, G:0.05, T:0.52
Consensus pattern (33 bp):
TATTAATATTATTATTATTAATAACACAGTTAT
Found at i:76529 original size:3 final size:3
Alignment explanation
Indices: 76441--76514 Score: 58
Period size: 3 Copynumber: 23.0 Consensus size: 3
76431 TTTCGATTTT
* * * **
76441 TTA TTA TTAA TTA TTA ATA TTA CTA TTA TTA TTA TTAA TGA GACA GTTA
1 TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA -TTA -TTA
76490 TTA CTTA TTA TTA TTA TTA TTA TTA
1 TTA -TTA TTA TTA TTA TTA TTA TTA
76515 ACACATTTAT
Statistics
Matches: 58, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
3 47 0.81
4 11 0.19
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.55
Consensus pattern (3 bp):
TTA
Found at i:76538 original size:37 final size:38
Alignment explanation
Indices: 76450--76539 Score: 98
Period size: 37 Copynumber: 2.4 Consensus size: 38
76440 TTTATTATTA
* *
76450 ATTATTAATATTACTATTATTATTATTAATGAGACAGTT
1 ATTATTAATATTATTATTATTATTATTAA-GACACAGTT
* *
76489 ATTACT--TATTATTATTATTATTATT-A-ACACATTT
1 ATTATTAATATTATTATTATTATTATTAAGACACAGTT
76523 ATTATTAATAGTTATTA
1 ATTATTAATA-TTATTA
76540 AATAAATTGA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
34 11 0.26
36 3 0.07
37 24 0.56
39 5 0.12
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.52
Consensus pattern (38 bp):
ATTATTAATATTATTATTATTATTATTAAGACACAGTT
Done.