Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005666.1 Kokia drynarioides strain JFW-HI SEQ_119840, 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: 91252
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:3644 original size:12 final size:14
Alignment explanation
Indices: 3627--3658 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3617 TAAAAATCAT
3627 AAAATAA-T-TATA
1 AAAATAAGTATATA
3639 AAAATAAGTATATA
1 AAAATAAGTATATA
3653 AAAATA
1 AAAATA
3659 TTAAATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.39
13 1 0.06
14 10 0.56
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (14 bp):
AAAATAAGTATATA
Found at i:3700 original size:29 final size:30
Alignment explanation
Indices: 3632--3700 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 30
3622 ATCATAAAAT
3632 AATTATAAAAATAAGTATATAAAAATATTA
1 AATTATAAAAATAAGTATATAAAAATATTA
* * **
3662 AA-TATTAAAAT-TG-ATATAAACTTATTAA
1 AATTATAAAAATAAGTATATAAAAATATT-A
3690 AATTATAAAAA
1 AATTATAAAAA
3701 GTATAAAGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
27 11 0.34
28 4 0.12
29 15 0.47
30 2 0.06
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (30 bp):
AATTATAAAAATAAGTATATAAAAATATTA
Found at i:3760 original size:26 final size:26
Alignment explanation
Indices: 3731--3783 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
3721 ATTTGTAAAT
*
3731 ATTATCAAAATATA-AAAATCTAATAA
1 ATTATAAAAATATATAAAATC-AATAA
*
3757 ATTATAAAAATATATAGAATCAATAA
1 ATTATAAAAATATATAAAATCAATAA
3783 A
1 A
3784 ACTTATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 19 0.79
27 5 0.21
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.30
Consensus pattern (26 bp):
ATTATAAAAATATATAAAATCAATAA
Found at i:4385 original size:8 final size:8
Alignment explanation
Indices: 4364--4467 Score: 72
Period size: 9 Copynumber: 12.6 Consensus size: 8
4354 AATTAAATAT
4364 ATTTTATGA
1 ATTTTAT-A
4373 ATTTTATA
1 ATTTTATA
4381 ATTTTTATA
1 A-TTTTATA
*
4390 TTTTTATAA
1 ATTTTAT-A
4399 TATTTTATA
1 -ATTTTATA
4408 ATTTTTATA
1 A-TTTTATA
*
4417 A-CTTAT-
1 ATTTTATA
*
4423 ATTTCAT-
1 ATTTTATA
4430 ATTTT-TA
1 ATTTTATA
*
4437 ATATTAATA
1 AT-TTTATA
4446 ATTTTATA
1 ATTTTATA
*
4454 TTTTTGATA
1 ATTTT-ATA
4463 ATTTT
1 ATTTT
4468 TTATGATTGT
Statistics
Matches: 76, Mismatches: 10, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
6 2 0.03
7 13 0.17
8 20 0.26
9 35 0.46
10 6 0.08
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (8 bp):
ATTTTATA
Found at i:7221 original size:26 final size:26
Alignment explanation
Indices: 7180--7234 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
7170 TCATCATTCA
*
7180 TCTAATCCAAACTATCAGACATGTTT
1 TCTAATCAAAACTATCAGACATGTTT
*
7206 TCTAATCAAAAGTATCAGACATGTTT
1 TCTAATCAAAACTATCAGACATGTTT
7232 TCT
1 TCT
7235 GTTTTGTCGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.35, C:0.20, G:0.09, T:0.36
Consensus pattern (26 bp):
TCTAATCAAAACTATCAGACATGTTT
Found at i:9571 original size:14 final size:12
Alignment explanation
Indices: 9560--9601 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
9550 AAAATAATAC
9560 TATATCAATAAT
1 TATATCAATAAT
*
9572 TATATTAATAAT
1 TATATCAATAAT
9584 T-TAT-AATAAT
1 TATATCAATAAT
*
9594 TAAATCAA
1 TATATCAA
9602 ATCAAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
10 7 0.27
11 5 0.19
12 14 0.54
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (12 bp):
TATATCAATAAT
Found at i:10155 original size:31 final size:31
Alignment explanation
Indices: 10117--10179 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
10107 GATCAAACCC
*
10117 AAACCATGGTAGGGACTAAATTATCATTTTT
1 AAACCATGGTAGGGACTAAATTATCAGTTTT
10148 AAACCATGGTAGGGACTAAATTATCAGTTTT
1 AAACCATGGTAGGGACTAAATTATCAGTTTT
10179 A
1 A
10180 CTCCCACAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (31 bp):
AAACCATGGTAGGGACTAAATTATCAGTTTT
Found at i:13424 original size:117 final size:117
Alignment explanation
Indices: 13218--13451 Score: 459
Period size: 117 Copynumber: 2.0 Consensus size: 117
13208 TACCAAGCTT
*
13218 AGAAAATATGGTATTAAATAAACACAACAATGCTGCCACTGCAAGGAAAGATCTTGTTGTTGTTT
1 AGAAAATATGGTATTAAATAAACACAACAATGCTGCCACTGAAAGGAAAGATCTTGTTGTTGTTT
13283 TAATGATATAATTATGCAATCCATATCTTGAAGACTAAGGCAATTTATCATC
66 TAATGATATAATTATGCAATCCATATCTTGAAGACTAAGGCAATTTATCATC
13335 AGAAAATATGGTATTAAATAAACACAACAATGCTGCCACTGAAAGGAAAGATCTTGTTGTTGTTT
1 AGAAAATATGGTATTAAATAAACACAACAATGCTGCCACTGAAAGGAAAGATCTTGTTGTTGTTT
13400 TAATGATATAATTATGCAATCCATATCTTGAAGACTAAGGCAATTTATCATC
66 TAATGATATAATTATGCAATCCATATCTTGAAGACTAAGGCAATTTATCATC
13452 CCGTCTTCTC
Statistics
Matches: 116, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
117 116 1.00
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (117 bp):
AGAAAATATGGTATTAAATAAACACAACAATGCTGCCACTGAAAGGAAAGATCTTGTTGTTGTTT
TAATGATATAATTATGCAATCCATATCTTGAAGACTAAGGCAATTTATCATC
Found at i:20206 original size:34 final size:34
Alignment explanation
Indices: 20163--20231 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
20153 TAAGTTAATG
20163 TTAGTTTTGTTTGATTCTTTGCAATTAATGGGTT
1 TTAGTTTTGTTTGATTCTTTGCAATTAATGGGTT
*
20197 TTAGTTTTGTTTGATTCTTTGCAGTTAATGGGTT
1 TTAGTTTTGTTTGATTCTTTGCAATTAATGGGTT
20231 T
1 T
20232 AAATACAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.16, C:0.06, G:0.22, T:0.57
Consensus pattern (34 bp):
TTAGTTTTGTTTGATTCTTTGCAATTAATGGGTT
Found at i:22663 original size:19 final size:19
Alignment explanation
Indices: 22641--22684 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
22631 ACTCTAAAAG
22641 ATAAATACAAAT-TTAAATA
1 ATAAATA-AAATCTTAAATA
*
22660 ATAAATAATATCTTAAATA
1 ATAAATAAAATCTTAAATA
*
22679 TTAAAT
1 ATAAAT
22685 CATAATATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (19 bp):
ATAAATAAAATCTTAAATA
Found at i:24113 original size:41 final size:41
Alignment explanation
Indices: 24066--24148 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
24056 CTATATCCGA
24066 CTAGTTAATAAGGATTTTCAATTTACAATTAATATCACTTT
1 CTAGTTAATAAGGATTTTCAATTTACAATTAATATCACTTT
24107 CTAGTTAATAAGGATTTTCAATTTACAATTAATATCACTTT
1 CTAGTTAATAAGGATTTTCAATTTACAATTAATATCACTTT
24148 C
1 C
24149 AATTTCAATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.43
Consensus pattern (41 bp):
CTAGTTAATAAGGATTTTCAATTTACAATTAATATCACTTT
Found at i:24156 original size:6 final size:6
Alignment explanation
Indices: 24122--24189 Score: 68
Period size: 6 Copynumber: 11.5 Consensus size: 6
24112 TAATAAGGAT
* * *
24122 TTTCAA TTTACAA -TT-AA TATCAC TTTCAA TTTCAA TTTCAA TTTCAC
1 TTTCAA TTT-CAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA
* *
24169 TTTCAC TTTCAC TTTCAA TTT
1 TTTCAA TTTCAA TTTCAA TTT
24190 TGATCACAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
4 2 0.04
5 1 0.02
6 47 0.89
7 3 0.06
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (6 bp):
TTTCAA
Found at i:24162 original size:12 final size:12
Alignment explanation
Indices: 24141--24189 Score: 80
Period size: 12 Copynumber: 4.1 Consensus size: 12
24131 ACAATTAATA
24141 TCACTTTCAATT
1 TCACTTTCAATT
*
24153 TCAATTTCAATT
1 TCACTTTCAATT
*
24165 TCACTTTCACTT
1 TCACTTTCAATT
24177 TCACTTTCAATT
1 TCACTTTCAATT
24189 T
1 T
24190 TGATCACAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.51
Consensus pattern (12 bp):
TCACTTTCAATT
Found at i:24173 original size:24 final size:24
Alignment explanation
Indices: 24122--24189 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 24
24112 TAATAAGGAT
*
24122 TTTCAATTTACAA-TT-AATATCAC
1 TTTCAATTT-CAATTTCAATTTCAC
24145 TTTCAATTTCAATTTCAATTTCAC
1 TTTCAATTTCAATTTCAATTTCAC
* *
24169 TTTCACTTTCACTTTCAATTT
1 TTTCAATTTCAATTTCAATTT
24190 TGATCACAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
22 3 0.08
23 11 0.28
24 26 0.65
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (24 bp):
TTTCAATTTCAATTTCAATTTCAC
Found at i:25205 original size:30 final size:32
Alignment explanation
Indices: 25169--25228 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 32
25159 CACACCTTAA
*
25169 CTTTCTCCTT-TT-CTTTTTCTTCAATTTGGT
1 CTTTCTCCTTCTTCCTCTTTCTTCAATTTGGT
25199 CTTTCTCCTTCTTCCCTCTTTCTTCAATTT
1 CTTTCTCCTTCTT-CCTCTTTCTTCAATTT
25229 CATACAAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 10 0.38
31 2 0.08
33 14 0.54
ACGTcount: A:0.07, C:0.30, G:0.03, T:0.60
Consensus pattern (32 bp):
CTTTCTCCTTCTTCCTCTTTCTTCAATTTGGT
Found at i:27300 original size:8 final size:9
Alignment explanation
Indices: 27286--27328 Score: 54
Period size: 8 Copynumber: 4.9 Consensus size: 9
27276 TTCCTGGACA
27286 AAAATAAAT
1 AAAATAAAT
27295 -AAATAAAT
1 AAAATAAAT
27303 AAAATAAGAT
1 AAAATAA-AT
*
27313 AGAA-AAAT
1 AAAATAAAT
27321 AAAATAAA
1 AAAATAAA
27329 ATAATTGGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
8 13 0.45
9 11 0.38
10 5 0.17
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.19
Consensus pattern (9 bp):
AAAATAAAT
Found at i:27320 original size:18 final size:17
Alignment explanation
Indices: 27286--27328 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
27276 TTCCTGGACA
27286 AAAATAAATAAATAAAT
1 AAAATAAATAAATAAAT
27303 AAAATAAGATAGAA-AAAT
1 AAAATAA-ATA-AATAAAT
27321 AAAATAAA
1 AAAATAAA
27329 ATAATTGGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.33
18 14 0.58
19 2 0.08
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.19
Consensus pattern (17 bp):
AAAATAAATAAATAAAT
Found at i:29898 original size:22 final size:22
Alignment explanation
Indices: 29843--29885 Score: 79
Period size: 21 Copynumber: 2.0 Consensus size: 22
29833 CGATCTGAGG
29843 AAAAATAAAAG-AAACAGAATT
1 AAAAATAAAAGAAAACAGAATT
29864 AAAAATAAAAGAAAACAGAATT
1 AAAAATAAAAGAAAACAGAATT
29886 GAAAGAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.72, C:0.05, G:0.09, T:0.14
Consensus pattern (22 bp):
AAAAATAAAAGAAAACAGAATT
Found at i:30702 original size:19 final size:19
Alignment explanation
Indices: 30680--30723 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
30670 ACTCTAAAAG
30680 ATAAATACAAAT-TTAAATA
1 ATAAATA-AAATCTTAAATA
*
30699 ATAAATAATATCTTAAATA
1 ATAAATAAAATCTTAAATA
*
30718 TTAAAT
1 ATAAAT
30724 CCTAATATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (19 bp):
ATAAATAAAATCTTAAATA
Found at i:32552 original size:28 final size:28
Alignment explanation
Indices: 32516--32570 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
32506 AAATAAGCAT
32516 CATGACCTTTGGGTCAACAGGGAGTAAG
1 CATGACCTTTGGGTCAACAGGGAGTAAG
* *
32544 CATGACCTTTGGGTTAATAGGGAGTAA
1 CATGACCTTTGGGTCAACAGGGAGTAA
32571 ATCGAATATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.29, C:0.15, G:0.31, T:0.25
Consensus pattern (28 bp):
CATGACCTTTGGGTCAACAGGGAGTAAG
Found at i:39871 original size:18 final size:18
Alignment explanation
Indices: 39852--39884 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
39842 TTAAAATTAT
39852 ATATTTT-T-TATTTTTA
1 ATATTTTATGTATTTTTA
39868 ATATTTTATGTATTTTT
1 ATATTTTATGTATTTTT
39885 TAAATTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (18 bp):
ATATTTTATGTATTTTTA
Found at i:39883 original size:23 final size:23
Alignment explanation
Indices: 39839--39883 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
39829 TTGAAACAAT
*
39839 TTTTTAAAATTATATATTTTTTA
1 TTTTTAAAATTATATATATTTTA
* * *
39862 TTTTTAATATTTTATGTATTTT
1 TTTTTAAAATTATATATATTTT
39884 TTAAATTTTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (23 bp):
TTTTTAAAATTATATATATTTTA
Found at i:40439 original size:19 final size:20
Alignment explanation
Indices: 40401--40439 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
40391 ATTAAAATAT
* *
40401 TTTTATTATTTGAAAGTTAA
1 TTTTATTATTTAAAAATTAA
40421 TTTT-TTATTTAAAAATTAA
1 TTTTATTATTTAAAAATTAA
40440 GAAAAATATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTTATTATTTAAAAATTAA
Found at i:40998 original size:18 final size:18
Alignment explanation
Indices: 40977--41015 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
40967 AGCAAGAAAC
*
40977 AAAAA-GAAAAAGGAAAAT
1 AAAAATGAAAAA-CAAAAT
40995 AAAAATGAAAAACAAAAT
1 AAAAATGAAAAACAAAAT
41013 AAA
1 AAA
41016 TAAAAAAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.79, C:0.03, G:0.10, T:0.08
Consensus pattern (18 bp):
AAAAATGAAAAACAAAAT
Found at i:53090 original size:2 final size:2
Alignment explanation
Indices: 53083--53112 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
53073 TCTGCAAGTA
53083 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
53113 TACGTGTGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:61535 original size:120 final size:120
Alignment explanation
Indices: 61376--61600 Score: 450
Period size: 120 Copynumber: 1.9 Consensus size: 120
61366 ACATATAATG
61376 TAAAATCAGTTGGGGCTTGTATGTTTTGGAGATGGATCATGTTTATGCGACCCCAAGAAAAGAAA
1 TAAAATCAGTTGGGGCTTGTATGTTTTGGAGATGGATCATGTTTATGCGACCCCAAGAAAAGAAA
61441 AATAGGTAAGGAAAAGTAGAGTAACTCCAGTATGAAGTTGAGTTGTTGATGCTTT
66 AATAGGTAAGGAAAAGTAGAGTAACTCCAGTATGAAGTTGAGTTGTTGATGCTTT
61496 TAAAATCAGTTGGGGCTTGTATGTTTTGGAGATGGATCATGTTTATGCGACCCCAAGAAAAGAAA
1 TAAAATCAGTTGGGGCTTGTATGTTTTGGAGATGGATCATGTTTATGCGACCCCAAGAAAAGAAA
61561 AATAGGTAAGGAAAAGTAGAGTAACTCCAGTATGAAGTTG
66 AATAGGTAAGGAAAAGTAGAGTAACTCCAGTATGAAGTTG
61601 TTGATGCTTT
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 105 1.00
ACGTcount: A:0.35, C:0.10, G:0.27, T:0.28
Consensus pattern (120 bp):
TAAAATCAGTTGGGGCTTGTATGTTTTGGAGATGGATCATGTTTATGCGACCCCAAGAAAAGAAA
AATAGGTAAGGAAAAGTAGAGTAACTCCAGTATGAAGTTGAGTTGTTGATGCTTT
Found at i:72876 original size:31 final size:29
Alignment explanation
Indices: 72820--72877 Score: 71
Period size: 31 Copynumber: 1.9 Consensus size: 29
72810 TAAAATAAAA
*
72820 TAAAAATTATTTAAGACTTTTAAAATTTT
1 TAAAAATTATTTAAGACTTTAAAAATTTT
**
72849 TAAAAATTTGATTTAATCCTTTAAAAATT
1 TAAAAA-TT-ATTTAAGACTTTAAAAATT
72878 ATAAAGATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 6 0.25
30 2 0.08
31 16 0.67
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (29 bp):
TAAAAATTATTTAAGACTTTAAAAATTTT
Found at i:76039 original size:2 final size:2
Alignment explanation
Indices: 76032--76064 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
76022 GGAGTAATTC
*
76032 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
76065 AAGCATACTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:84437 original size:18 final size:18
Alignment explanation
Indices: 84399--84439 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
84389 TAAAGAAGTT
*
84399 TTATTTTTTTACTATGTA
1 TTATTTTTTTACTATCTA
84417 TTATTTTTTTA-TATCTAA
1 TTATTTTTTTACTATCT-A
84435 TTATT
1 TTATT
84440 ATAATACTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.68
Consensus pattern (18 bp):
TTATTTTTTTACTATCTA
Done.