Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014200.1 Kokia drynarioides strain JFW-HI SEQ_129233, 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: 16651
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Warning! 20 characters in sequence are not A, C, G, or T
Found at i:4784 original size:21 final size:19
Alignment explanation
Indices: 4755--4793 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
4745 ATTGGATAAT
4755 TAGCCGGTTGCGATGTGCCCG
1 TAGCCGGTTGC--TGTGCCCG
*
4776 TAGCTGGTTGCTGTGCCC
1 TAGCCGGTTGCTGTGCCC
4794 TTACAGTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
21 10 0.59
ACGTcount: A:0.08, C:0.28, G:0.36, T:0.28
Consensus pattern (19 bp):
TAGCCGGTTGCTGTGCCCG
Found at i:9087 original size:29 final size:29
Alignment explanation
Indices: 9009--9454 Score: 278
Period size: 29 Copynumber: 15.2 Consensus size: 29
8999 TTCGGACATC
*
9009 CGGGAGTAAAATGGTAATTTTTGGAAGTGT
1 CGGGGGTAAAATGGTAATTTTTGGAAGT-T
* * *
9039 -TGAGGTCAAAAATGAT-ATTTTTGGAAGTT
1 CGGGGGT--AAAATGGTAATTTTTGGAAGTT
*
9068 CGGGGGTAAAATGGTAATTTTAGGAAGTT
1 CGGGGGTAAAATGGTAATTTTTGGAAGTT
9097 CGGGGGT-AAATGGTAATTTTTGGAAGTTT
1 CGGGGGTAAAATGGTAATTTTTGGAAG-TT
** * * *
9126 TAGGGTTAAAAATGG-GACTTTTGGAAGTT
1 CGGGGGT-AAAATGGTAATTTTTGGAAGTT
* *
9155 CGAGGGTAAAATGATAATTTTTGGAAGTT
1 CGGGGGTAAAATGGTAATTTTTGGAAGTT
** ** *
9184 TTGGCATCAAAAATGG-GATTTTTGGAAGTT
1 CGGGGGT--AAAATGGTAATTTTTGGAAGTT
*
9214 CGGGGGTAAAAAT-G-AATTTTT-TATTAGTT
1 CGGGGGT-AAAATGGTAATTTTTGGA--AGTT
** *
9243 TAGGGGTAAAATGGTAATTTTTGAAAGTT
1 CGGGGGTAAAATGGTAATTTTTGGAAGTT
** *
9272 TTGGGGTCAAAAAT-G-AGATTTTTGGGAGTT
1 CGGGGGT--AAAATGGTA-ATTTTTGGAAGTT
**
9302 -TAGGGTAAAATGGTAATTTTTGGAAGTTT
1 CGGGGGTAAAATGGTAATTTTTGGAAG-TT
* * *
9331 C-GGGGTCAAAAATGG-GATTTTCGAAAGTT
1 CGGGGGT--AAAATGGTAATTTTTGGAAGTT
*
9360 CGAGGGTAAAATGG-AATTTTTTGGAAGTT
1 CGGGGGTAAAATGGTAA-TTTTTGGAAGTT
* * *
9389 CGAGGGTAAAAAT-GAAATTTTTTTAGAAGTT
1 CGGGGGT-AAAATGGTAA--TTTTTGGAAGTT
9420 -GGAGGGTAAAATGGTAATTTTTAGG-AGTT
1 CGG-GGGTAAAATGGTAATTTTT-GGAAGTT
9449 CGGGGG
1 CGGGGG
9455 ACCTCCGGGA
Statistics
Matches: 329, Mismatches: 54, Indels: 67
0.73 0.12 0.15
Matches are distributed among these distances:
27 6 0.02
28 62 0.19
29 120 0.36
30 90 0.27
31 51 0.16
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.35
Consensus pattern (29 bp):
CGGGGGTAAAATGGTAATTTTTGGAAGTT
Found at i:9138 original size:59 final size:56
Alignment explanation
Indices: 9015--9454 Score: 299
Period size: 59 Copynumber: 7.5 Consensus size: 56
9005 CATCCGGGAG
* * ** *
9015 TAAAATGGTAATTTTTGGAAGTGT-TGAGGTCAAAAATGATATTTTTGGAAGTTCGGGGG
1 TAAAATGGTAATTTTTGGAAGT-TCGGGGGT--AAAATGA-ATTTTTGGAAGTTTAGGGT
*
9074 TAAAATGGTAATTTTAGGAAGTTCGGGGGT-AAATGGTAATTTTTGGAAGTTTTAGGGT
1 TAAAATGGTAATTTTTGGAAGTTCGGGGGTAAAAT-G-AATTTTTGGAAG-TTTAGGGT
* * * * *
9132 TAAAAATGG-GACTTTTGGAAGTTCGAGGGTAAAATGATAATTTTTGGAAGTTTTGGCAT
1 T-AAAATGGTAATTTTTGGAAGTTCGGGGGTAAAATG--AATTTTTGGAAGTTTAGG-GT
* * * *
9191 CAAAAATGG-GATTTTTGGAAGTTCGGGGGTAAAAATGAATTTTT-TATTAGTTTAGGGG
1 -TAAAATGGTAATTTTTGGAAGTTCGGGGGT-AAAATGAATTTTTGGA--AGTTTAGGGT
* ** *
9249 TAAAATGGTAATTTTTGAAAGTTTTGGGGTCAAAAATGAGATTTTTGGGAGTTTAGGG-
1 TAAAATGGTAATTTTTGGAAGTTCGGGGGT--AAAATGA-ATTTTTGGAAGTTTAGGGT
* * * *
9307 TAAAATGGTAATTTTTGGAAGTTTC-GGGGTCAAAAATGGGATTTTCGAAAGTTCGAGGG-
1 TAAAATGGTAATTTTTGGAAG-TTCGGGGGT--AAAAT-GAATTTTTGGAAGTT-TAGGGT
* * *
9366 TAAAATGG-AATTTTTTGGAAGTTCGAGGGTAAAAATGAAATTTTTTTAGAAGTTGGAGGG-
1 TAAAATGGTAA-TTTTTGGAAGTTCGGGGGT-AAAATG-AA--TTTTTGGAAGTT-TAGGGT
9426 TAAAATGGTAATTTTTAGG-AGTTCGGGGG
1 TAAAATGGTAATTTTT-GGAAGTTCGGGGG
9455 ACCTCCGGGA
Statistics
Matches: 315, Mismatches: 40, Indels: 51
0.78 0.10 0.13
Matches are distributed among these distances:
56 4 0.01
57 21 0.07
58 109 0.35
59 129 0.41
60 48 0.15
61 4 0.01
ACGTcount: A:0.31, C:0.03, G:0.30, T:0.36
Consensus pattern (56 bp):
TAAAATGGTAATTTTTGGAAGTTCGGGGGTAAAATGAATTTTTGGAAGTTTAGGGT
Found at i:9150 original size:30 final size:30
Alignment explanation
Indices: 9112--9402 Score: 151
Period size: 30 Copynumber: 9.9 Consensus size: 30
9102 GTAAATGGTA
9112 ATTTTTGGAAGTTTTAGGGTTAAAAATGGG
1 ATTTTTGGAAGTTTTAGGGTTAAAAATGGG
* ** **
9142 ACTTTTGGAAGTTCGAGGG-T-AAAATGATA
1 ATTTTTGGAAGTTTTAGGGTTAAAAATG-GG
* *
9171 ATTTTTGGAAGTTTT-GGCATCAAAAATGGG
1 ATTTTTGGAAGTTTTAGG-GTTAAAAATGGG
** * *
9201 ATTTTTGGAAG-TTCGGGGGTAAAAAT-GA
1 ATTTTTGGAAGTTTTAGGGTTAAAAATGGG
* * *
9229 ATTTTT-TATTAG-TTTAGGGGT-AAAATGGTA
1 ATTTTTGGA--AGTTTTAGGGTTAAAAATGG-G
* * * *
9259 ATTTTTGAAAGTTTTGGGGTCAAAAATGAG
1 ATTTTTGGAAGTTTTAGGGTTAAAAATGGG
* *
9289 ATTTTTGGGAG-TTTAGGG-T-AAAATGGTA
1 ATTTTTGGAAGTTTTAGGGTTAAAAATGG-G
** *
9317 ATTTTTGGAAGTTTCGGGGTCAAAAATGGG
1 ATTTTTGGAAGTTTTAGGGTTAAAAATGGG
* * ** *
9347 ATTTTCGAAAGTTCGAGGG-T-AAAATGGA
1 ATTTTTGGAAGTTTTAGGGTTAAAAATGGG
**
9375 ATTTTTTGGAAGTTCGAGGG-TAAAAATG
1 A-TTTTTGGAAGTTTTAGGGTTAAAAATG
9403 AAATTTTTTT
Statistics
Matches: 197, Mismatches: 46, Indels: 36
0.71 0.16 0.13
Matches are distributed among these distances:
27 7 0.04
28 38 0.19
29 61 0.31
30 71 0.36
31 20 0.10
ACGTcount: A:0.31, C:0.04, G:0.29, T:0.36
Consensus pattern (30 bp):
ATTTTTGGAAGTTTTAGGGTTAAAAATGGG
Found at i:9351 original size:88 final size:86
Alignment explanation
Indices: 9112--9359 Score: 243
Period size: 88 Copynumber: 2.8 Consensus size: 86
9102 GTAAATGGTA
* * *
9112 ATTTTTGGAAGTTTTAGGGTTAAAAATGGGACTTTTGGAAG-TTCGAGGGTAAAATGATAATTTT
1 ATTTTTGGAAG-TTTAGGG-TAAAAATGGAATTTTTGGAAGTTTCG-GGGTAAAATG-GAATTTT
* *
9176 TGGAAGTTTTGGCATCAAAAATGGG
62 TGAAAGTTTTGGCATCAAAAATGAG
** * *
9201 ATTTTTGGAAGTTCGGGGGTAAAAAT-GAATTTTT-TATTAGTTTAGGGGTAAAATGGTAATTTT
1 ATTTTTGGAAGTT-TAGGGTAAAAATGGAATTTTTGGA--AGTTTCGGGGTAAAATGG-AATTTT
**
9264 TGAAAGTTTTGGGGTCAAAAATGAG
62 TGAAAGTTTTGGCATCAAAAATGAG
* * *
9289 ATTTTTGGGAGTTTAGGGT-AAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTC
1 ATTTTTGGAAGTTTAGGGTAAAAATGG-AATTTTTGGAAGTTTCGGGGT--AAAATGGAATTTTT
9353 GAAAGTT
63 GAAAGTT
9360 CGAGGGTAAA
Statistics
Matches: 131, Mismatches: 18, Indels: 21
0.77 0.11 0.12
Matches are distributed among these distances:
86 6 0.05
87 21 0.16
88 79 0.60
89 25 0.19
ACGTcount: A:0.31, C:0.04, G:0.28, T:0.38
Consensus pattern (86 bp):
ATTTTTGGAAGTTTAGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTAAAATGGAATTTTTGAA
AGTTTTGGCATCAAAAATGAG
Found at i:9410 original size:146 final size:146
Alignment explanation
Indices: 9014--9399 Score: 485
Period size: 146 Copynumber: 2.6 Consensus size: 146
9004 ACATCCGGGA
* **
9014 GTAAAATGGTAATTTTTGGAAGTGTTGAGGTCAAAAATGATATTTTTGGAAGTTCGGGGGTAAAA
1 GTAAAATGGTAATTTTTGGAAGT-TTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAA
* * * * *
9079 TGGTAA-TTTTAGGAAGTTCGGGGGT-AAATGGTAATTTTTGGAAGTTTTAGGGTTAAAAATGGG
65 TGG-AATTTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGAAAGTTTTAGGGTCAAAAATGAG
9142 ACTTTTGGAAGTTCGAGG
129 ACTTTTGGAAGTTCGAGG
* **
9160 GTAAAATGATAATTTTTGGAAGTTTTGGCATCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAA
1 GTAAAATGGTAATTTTTGGAAG-TTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT-AAA
*** * *
9225 AT-GAATTTTTTATTAGTT-TAGGGGTAAAATGGTAATTTTTGAAAGTTTTGGGGTCAAAAATGA
64 ATGGAATTTTTTGGAAGTTCGA-GGGTAAAATGGTAATTTTTGAAAGTTTTAGGGTCAAAAATGA
* * *
9288 GATTTTTGGGAGTT-TAGG
128 GACTTTTGGAAGTTCGAGG
* * *
9306 GTAAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTCGAAAGTTCGAGGGTAAAA
1 GTAAAATGGTAATTTTTGGAAGTTT-GGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAA
9371 TGGAATTTTTTGGAAGTTCGAGGGTAAAA
65 TGGAATTTTTTGGAAGTTCGAGGGTAAAA
9400 ATGAAATTTT
Statistics
Matches: 203, Mismatches: 29, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
145 10 0.05
146 141 0.69
147 52 0.26
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.35
Consensus pattern (146 bp):
GTAAAATGGTAATTTTTGGAAGTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAT
GGAATTTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGAAAGTTTTAGGGTCAAAAATGAGAC
TTTTGGAAGTTCGAGG
Found at i:9439 original size:31 final size:30
Alignment explanation
Indices: 9355--9441 Score: 122
Period size: 31 Copynumber: 2.9 Consensus size: 30
9345 GGATTTTCGA
*
9355 AAGTTCGAGGGTAAAATGGAA-TTTTTTGG
1 AAGTTCGAGGGTAAAATGGAATTTTTTTAG
*
9384 AAGTTCGAGGGTAAAAATGAAATTTTTTTAG
1 AAGTTCGAGGGT-AAAATGGAATTTTTTTAG
*
9415 AAGTTGGAGGGTAAAATGGTAATTTTT
1 AAGTTCGAGGGTAAAATGG-AATTTTT
9442 AGGAGTTCGG
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
29 12 0.24
30 14 0.27
31 25 0.49
ACGTcount: A:0.34, C:0.02, G:0.28, T:0.36
Consensus pattern (30 bp):
AAGTTCGAGGGTAAAATGGAATTTTTTTAG
Found at i:10984 original size:88 final size:87
Alignment explanation
Indices: 10837--11011 Score: 341
Period size: 88 Copynumber: 2.0 Consensus size: 87
10827 GAACAAAATA
10837 TGTGTAGGGATCAAAAGGCTTAAGTTTAAATGCGATTTCTTTCCTTTTCCAAAAAAAAAAAAGGG
1 TGTGTAGGGATCAAAAGGCTTAAGTTTAAATGCGATTTCTTTCCTTTTCC-AAAAAAAAAAAGGG
10902 GACTTTTACAAACGTTCAATTTG
65 GACTTTTACAAACGTTCAATTTG
10925 TGTGTAGGGATCAAAAGGCTTAAGTTTAAATGCGATTTCTTTCCTTTTCCAAAAAAAAAAAGGGG
1 TGTGTAGGGATCAAAAGGCTTAAGTTTAAATGCGATTTCTTTCCTTTTCCAAAAAAAAAAAGGGG
10990 ACTTTTACAAACGTTCAATTTG
66 ACTTTTACAAACGTTCAATTTG
11012 GCTCTTATAG
Statistics
Matches: 87, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
87 37 0.43
88 50 0.57
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (87 bp):
TGTGTAGGGATCAAAAGGCTTAAGTTTAAATGCGATTTCTTTCCTTTTCCAAAAAAAAAAAGGGG
ACTTTTACAAACGTTCAATTTG
Found at i:11351 original size:17 final size:16
Alignment explanation
Indices: 11331--11417 Score: 66
Period size: 17 Copynumber: 5.2 Consensus size: 16
11321 CTGAACATTT
11331 TTTAAATGAATTTTAAA
1 TTTAAAT-AATTTTAAA
* **
11348 TTTAAATTCATAATAAA
1 TTTAAA-TAATTTTAAA
*
11365 TTTAAATAAATTTAAA
1 TTTAAATAATTTTAAA
** *
11381 TTTAAGATAAACTTAAT
1 TTTAA-ATAATTTTAAA
*
11398 TTTAAAATAAATTTAAA
1 TTT-AAATAATTTTAAA
11415 TTT
1 TTT
11418 GTTGGGCTCA
Statistics
Matches: 56, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
16 11 0.20
17 42 0.75
18 3 0.05
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (16 bp):
TTTAAATAATTTTAAA
Found at i:11390 original size:27 final size:27
Alignment explanation
Indices: 11344--11396 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
11334 AAATGAATTT
*
11344 TAAATTTAAATTCATAATAAATTTAAA
1 TAAATTTAAATTCATAATAAACTTAAA
*
11371 TAAATTTAAATTTA-AGATAAACTTAA
1 TAAATTTAAATTCATA-ATAAACTTAA
11397 TTTTAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 1 0.04
27 22 0.96
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (27 bp):
TAAATTTAAATTCATAATAAACTTAAA
Found at i:12518 original size:18 final size:17
Alignment explanation
Indices: 12490--12523 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
12480 TGTAAAAAAA
12490 AGAAAGAAAAATTGAAT
1 AGAAAGAAAAATTGAAT
12507 AGAAATGAAAAATTGAA
1 AGAAA-GAAAAATTGAA
12524 GCATATAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.65, C:0.00, G:0.18, T:0.18
Consensus pattern (17 bp):
AGAAAGAAAAATTGAAT
Found at i:12833 original size:18 final size:18
Alignment explanation
Indices: 12810--12846 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
12800 TTTGTGATCA
12810 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
12828 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
12846 A
1 A
12847 TATGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:12995 original size:40 final size:39
Alignment explanation
Indices: 12949--13047 Score: 96
Period size: 38 Copynumber: 2.5 Consensus size: 39
12939 CGACCTTGAG
** *
12949 TCGATGAGACACTGGTGTCATTATTTTACTTCGGA-TAGAT
1 TCGATGAGACACTGGTGTCACCACTTTACTTC-GACTAG-T
**
12989 TCGATGAGGTACTGG-GT-ACCACTTTACTTCGACTAGT
1 TCGATGAGACACTGGTGTCACCACTTTACTTCGACTAGT
*
13026 CCGATGAGACACTGGGTGTCAC
1 TCGATGAGACACT-GGTGTCAC
13048 TTTATTGCTT
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
37 13 0.28
38 15 0.32
39 4 0.09
40 15 0.32
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.31
Consensus pattern (39 bp):
TCGATGAGACACTGGTGTCACCACTTTACTTCGACTAGT
Found at i:13040 original size:37 final size:37
Alignment explanation
Indices: 12950--13079 Score: 102
Period size: 40 Copynumber: 3.4 Consensus size: 37
12940 GACCTTGAGT
* * *
12950 CGATGAGACACTGGTGTCATTATTTTACTTCGGA-TAGATT
1 CGATGAGACACTGG-GT-ATCACTTTACTTC-GACTAG-TC
** *
12990 CGATGAGGTACTGGGTACCACTTTACTTCGACTAGTC
1 CGATGAGACACTGGGTATCACTTTACTTCGACTAGTC
*
13027 CGATGAGACACTGGGTGTCACTTTATTGCTTCGAACTA-TC
1 CGATGAGACACTGGGTATCACTTTA---CTTCG-ACTAGTC
*
13067 CGATGAGGCACTG
1 CGATGAGACACTG
13080 AGTGCCATTC
Statistics
Matches: 74, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
37 24 0.32
38 13 0.18
39 2 0.03
40 31 0.42
41 4 0.05
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32
Consensus pattern (37 bp):
CGATGAGACACTGGGTATCACTTTACTTCGACTAGTC
Found at i:14370 original size:17 final size:16
Alignment explanation
Indices: 14350--14436 Score: 66
Period size: 17 Copynumber: 5.2 Consensus size: 16
14340 CTGAACATTT
14350 TTTAAATGAATTTTAAA
1 TTTAAAT-AATTTTAAA
* **
14367 TTTAAATTCATAATAAA
1 TTTAAA-TAATTTTAAA
*
14384 TTTAAATAAATTTAAA
1 TTTAAATAATTTTAAA
** *
14400 TTTAAGATAAACTTAAT
1 TTTAA-ATAATTTTAAA
*
14417 TTTAAAATAAATTTAAA
1 TTT-AAATAATTTTAAA
14434 TTT
1 TTT
14437 GTTGGGCTCA
Statistics
Matches: 56, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
16 11 0.20
17 42 0.75
18 3 0.05
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (16 bp):
TTTAAATAATTTTAAA
Found at i:14409 original size:27 final size:27
Alignment explanation
Indices: 14363--14415 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
14353 AAATGAATTT
*
14363 TAAATTTAAATTCATAATAAATTTAAA
1 TAAATTTAAATTCATAATAAACTTAAA
*
14390 TAAATTTAAATTTA-AGATAAACTTAA
1 TAAATTTAAATTCATA-ATAAACTTAA
14416 TTTTAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 1 0.04
27 22 0.96
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (27 bp):
TAAATTTAAATTCATAATAAACTTAAA
Found at i:15537 original size:18 final size:17
Alignment explanation
Indices: 15509--15542 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
15499 TGTAAAAAAA
15509 AGAAAGAAAAATTGAAT
1 AGAAAGAAAAATTGAAT
15526 AGAAATGAAAAATTGAA
1 AGAAA-GAAAAATTGAA
15543 GCATATAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.65, C:0.00, G:0.18, T:0.18
Consensus pattern (17 bp):
AGAAAGAAAAATTGAAT
Found at i:15852 original size:18 final size:18
Alignment explanation
Indices: 15829--15865 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
15819 TTTGTGATCA
15829 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
15847 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
15865 A
1 A
15866 TATGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:16014 original size:40 final size:39
Alignment explanation
Indices: 15968--16066 Score: 96
Period size: 38 Copynumber: 2.5 Consensus size: 39
15958 CGACCTTGAG
** *
15968 TCGATGAGACACTGGTGTCATTATTTTACTTCGGA-TAGAT
1 TCGATGAGACACTGGTGTCACCACTTTACTTC-GACTAG-T
**
16008 TCGATGAGGTACTGG-GT-ACCACTTTACTTCGACTAGT
1 TCGATGAGACACTGGTGTCACCACTTTACTTCGACTAGT
*
16045 CCGATGAGACACTGGGTGTCAC
1 TCGATGAGACACT-GGTGTCAC
16067 TTTATTGCTT
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
37 13 0.28
38 15 0.32
39 4 0.09
40 15 0.32
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.31
Consensus pattern (39 bp):
TCGATGAGACACTGGTGTCACCACTTTACTTCGACTAGT
Found at i:16059 original size:37 final size:37
Alignment explanation
Indices: 15969--16098 Score: 102
Period size: 40 Copynumber: 3.4 Consensus size: 37
15959 GACCTTGAGT
* * *
15969 CGATGAGACACTGGTGTCATTATTTTACTTCGGA-TAGATT
1 CGATGAGACACTGG-GT-ATCACTTTACTTC-GACTAG-TC
** *
16009 CGATGAGGTACTGGGTACCACTTTACTTCGACTAGTC
1 CGATGAGACACTGGGTATCACTTTACTTCGACTAGTC
*
16046 CGATGAGACACTGGGTGTCACTTTATTGCTTCGAACTA-TC
1 CGATGAGACACTGGGTATCACTTTA---CTTCG-ACTAGTC
*
16086 CGATGAGGCACTG
1 CGATGAGACACTG
16099 AGTGCCATTC
Statistics
Matches: 74, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
37 24 0.32
38 13 0.18
39 2 0.03
40 31 0.42
41 4 0.05
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32
Consensus pattern (37 bp):
CGATGAGACACTGGGTATCACTTTACTTCGACTAGTC
Done.