Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1680
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: 33205
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Found at i:2566 original size:21 final size:21
Alignment explanation
Indices: 2542--2618 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
2532 AATATTTTCA
2542 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
2563 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
* * *
2584 AATGTATCAATACA-TTCTACA
1 AATGTATCGATACATTTGTA-G
2605 AATGTATCGATACA
1 AATGTATCGATACA
2619 GGGTCCCAAC
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 4 0.08
21 47 0.92
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:2678 original size:19 final size:19
Alignment explanation
Indices: 2654--2721 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
2644 AATTCAACAA
2654 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
2673 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
2688 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
2705 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
2722 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:2693 original size:13 final size:13
Alignment explanation
Indices: 2675--2699 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2665 ACATAAGTTT
2675 TGTATCGATACAA
1 TGTATCGATACAA
2688 TGTATCGATACA
1 TGTATCGATACA
2700 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2697 original size:32 final size:32
Alignment explanation
Indices: 2656--2718 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2646 TTCAACAATT
*
2656 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
2688 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
2719 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:2785 original size:33 final size:33
Alignment explanation
Indices: 2743--2807 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
2733 CAAGGAAATG
***
2743 TATCGATACATTTTTCTGTGTATCGATACATTA
1 TATCGATACATGGATCTGTGTATCGATACATTA
*
2776 TATCGATACATGGATCTTTGTATCGATACATT
1 TATCGATACATGGATCTGTGTATCGATACATT
2808 TGGAAATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (33 bp):
TATCGATACATGGATCTGTGTATCGATACATTA
Found at i:5239 original size:51 final size:48
Alignment explanation
Indices: 5140--5256 Score: 125
Period size: 51 Copynumber: 2.4 Consensus size: 48
5130 CAATTCTCCG
* *
5140 CAATCGGGGATA-TCCCAACTCTGATTTCATTTTTAAAACACTAATTTT
1 CAATCGGGGATACT-CCAACTCCGATTTCATTTCTAAAACACTAATTTT
*
5188 CTATAATCGGGGATACTCCAACTCCGATTTTATTTCT-AAACA-TCAATTTTT
1 C---AATCGGGGATACTCCAACTCCGATTTCATTTCTAAAACACT-AA-TTTT
5239 C-ATCGGGGATACTCCAAC
1 CAATCGGGGATACTCCAAC
5257 CCCGTTAATC
Statistics
Matches: 60, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
47 17 0.28
48 1 0.02
49 1 0.02
50 7 0.12
51 33 0.55
52 1 0.02
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (48 bp):
CAATCGGGGATACTCCAACTCCGATTTCATTTCTAAAACACTAATTTT
Found at i:5276 original size:27 final size:27
Alignment explanation
Indices: 5238--5314 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 27
5228 CATCAATTTT
5238 TCATCGGGGATACTCCAACCCCGTTAA
1 TCATCGGGGATACTCCAACCCCGTTAA
* *
5265 TCATCGGGGATACTCCAACCTCGTTAT
1 TCATCGGGGATACTCCAACCCCGTTAA
** *
5292 TTTTGAGGGGATACTCCAACCCC
1 TCAT-CGGGGATACTCCAACCCC
5315 CGGCTTTATT
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 27 0.63
28 16 0.37
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.26
Consensus pattern (27 bp):
TCATCGGGGATACTCCAACCCCGTTAA
Found at i:5443 original size:79 final size:80
Alignment explanation
Indices: 5267--5446 Score: 240
Period size: 80 Copynumber: 2.3 Consensus size: 80
5257 CCCGTTAATC
* * **
5267 ATCGGGGATACTCCAACCTCGTTATTTTTGAGGGGATACTCCAACCCCCGGCTTTATTTCTAAAA
1 ATCGGGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCCCCGGCTTTATTTCTAAAA
* *
5332 TATTAATTTCTCATA
66 TATGAATTTCTCACA
* *
5347 ATCGGGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAA-CCCCGGTTTTATTTC-CAAA
1 ATCGGGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCCCCGGCTTTATTTCTAAAA
*
5410 TCATCGATTTTC-CACA
66 T-AT-GAATTTCTCACA
5426 ATCGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
5447 GCTTTATTTT
Statistics
Matches: 89, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
78 4 0.04
79 40 0.45
80 45 0.51
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.29
Consensus pattern (80 bp):
ATCGGGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCCCCGGCTTTATTTCTAAAA
TATGAATTTCTCACA
Found at i:5506 original size:53 final size:51
Alignment explanation
Indices: 5380--5548 Score: 194
Period size: 51 Copynumber: 3.3 Consensus size: 51
5370 ATCTCCGAGG
* * * *
5380 GGATACTCCAACCCCGGTTTTATTTCCAAATCATCGATTTTCCACAATCGG
1 GGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTCCACAATCGA
* * **
5431 GGATACTCCAACCCCGGCTTTATTTTCAAAACACCAATTTTCCTTTTAATCGA
1 GGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTCC--ACAATCGA
* * * **
5484 GGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATTAA
1 GGATACTCCAACCCCGGTTTTATTTCC-AAAACACCAATTTTCCACAATCGA
5536 GGATACTCCAACC
1 GGATACTCCAACC
5549 TTGTTATTTC
Statistics
Matches: 97, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
51 38 0.39
52 16 0.16
53 28 0.29
54 15 0.15
ACGTcount: A:0.30, C:0.28, G:0.10, T:0.31
Consensus pattern (51 bp):
GGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTCCACAATCGA
Found at i:5657 original size:291 final size:285
Alignment explanation
Indices: 5168--5738 Score: 743
Period size: 291 Copynumber: 2.0 Consensus size: 285
5158 CTCTGATTTC
* * * * *
5168 ATTTTTAAAACACTAATTTTCTATAATCGGGGATACTCCAACTCCGATTTTATTTCTAAACATCA
1 ATTTTCAAAACACCAATTTTCTATAATCGAGGATACTCCAACTCCGATTTTATTTCAAAACACCA
** * ** **
5233 ATTTTTCATCGGGGATACTCCAACCCCGTTAATCATCGGGGATACTCCAACCTCGTTATTTTTGA
66 ATTTTTCATCAAGGATACTCCAACCCCGTTAATCATCGGGGATACTCCAACCCCGTTACCTCCGA
* * *
5298 GGGGATACTCCAACCCCCGGCTTTATTTCTAAAATATTAATTTCTCATAATCGGGGATACTCCAA
131 GGGGATACTCCAACCCCCGGCTTTATTCCCAAAATATTAATTTCTCATAATCAGGGATACTCCAA
*
5363 CCCCGTTATCTCCGAGGGGATACTCCAACCCCGGT-TTTATTTCCAAATCATCGATTT-TCCACA
196 CCCCGTTATCTCCGAGGGGATACTCCAACCCCGATATTTATTTCCAAATCATCGATTTCT-CACA
*
5426 ATCGGGGATACTCCAACCCCGGCTTT
260 ACCGGGGATACTCCAACCCCGGCTTT
*
5452 ATTTTCAAAACACCAATTTTCCTTTTAATCGAGGATACTCCAACTCCGATTTTATTTCCAAAAAC
1 ATTTTCAAAACACCAATTTT-C-TATAATCGAGGATACTCCAACTCCGATTTTATTT-C-AAAAC
* ** * *
5517 ACCAATTTTTCACAATTAAGGATACTCCAACCTTGTTATTTCATCGGGGATACTCTAACCCCGTT
62 ACCAATTTTT--C-ATCAAGGATACTCCAACCCCGTTA-ATCATCGGGGATACTCCAACCCCGTT
* *
5582 ACCTCCGAGGGGATACTCCAA-CCCCGGCTTTATTCCCAAAATATTGATTTCTCATAATTAGGGA
123 ACCTCCGAGGGGATACTCCAACCCCCGGCTTTATTCCCAAAATATTAATTTCTCATAATCAGGGA
* * * * * * *
5646 TACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCCCGATATTTTTTTTCTAATCATTGATT
188 TACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCCCGATATTTATTTCCAAATCATCGATT
*
5711 TCTCACAACCGGGGATACTCCAGCCCCG
253 TCTCACAACCGGGGATACTCCAACCCCG
5739 TCATTTTCAA
Statistics
Matches: 244, Mismatches: 33, Indels: 12
0.84 0.11 0.04
Matches are distributed among these distances:
284 18 0.07
285 1 0.00
286 32 0.13
287 1 0.00
288 13 0.05
290 1 0.00
291 96 0.39
292 81 0.33
293 1 0.00
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (285 bp):
ATTTTCAAAACACCAATTTTCTATAATCGAGGATACTCCAACTCCGATTTTATTTCAAAACACCA
ATTTTTCATCAAGGATACTCCAACCCCGTTAATCATCGGGGATACTCCAACCCCGTTACCTCCGA
GGGGATACTCCAACCCCCGGCTTTATTCCCAAAATATTAATTTCTCATAATCAGGGATACTCCAA
CCCCGTTATCTCCGAGGGGATACTCCAACCCCGATATTTATTTCCAAATCATCGATTTCTCACAA
CCGGGGATACTCCAACCCCGGCTTT
Found at i:18075 original size:1 final size:1
Alignment explanation
Indices: 18064--18123 Score: 57
Period size: 1 Copynumber: 60.0 Consensus size: 1
18054 CCTTCTCTTC
* * * * * * *
18064 AAAAAAGAAAAAAAAACAAAAAAAAACAAAAAAACAAAACAAAGAAAAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
18124 TCTGCTTAAG
Statistics
Matches: 45, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.88, C:0.07, G:0.05, T:0.00
Consensus pattern (1 bp):
A
Found at i:18087 original size:18 final size:18
Alignment explanation
Indices: 18064--18116 Score: 81
Period size: 18 Copynumber: 2.9 Consensus size: 18
18054 CCTTCTCTTC
18064 AAAAAAGAAAAAAAAACA
1 AAAAAAGAAAAAAAAACA
18082 AAAAAA-AACAAAAAAACA
1 AAAAAAGAA-AAAAAAACA
18100 AAACAAAGAAAAAAAAA
1 AAA-AAAGAAAAAAAAA
18117 AGAAAAATCT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
17 2 0.06
18 18 0.56
19 10 0.31
20 2 0.06
ACGTcount: A:0.89, C:0.08, G:0.04, T:0.00
Consensus pattern (18 bp):
AAAAAAGAAAAAAAAACA
Found at i:18102 original size:23 final size:21
Alignment explanation
Indices: 18064--18123 Score: 75
Period size: 23 Copynumber: 2.8 Consensus size: 21
18054 CCTTCTCTTC
*
18064 AAAAAAGAAAAAAAAACAAAA
1 AAAAAAAAAAAAAAAACAAAA
*
18085 AAAAACAAAAAAACAAAACAAAG
1 AAAAA-AAAAAAA-AAAACAAAA
*
18108 AAAAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAA
18124 TCTGCTTAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 9 0.26
22 12 0.35
23 13 0.38
ACGTcount: A:0.88, C:0.07, G:0.05, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAAAAAAAACAAAA
Found at i:18112 original size:28 final size:27
Alignment explanation
Indices: 18063--18123 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
18053 ACCTTCTCTT
*
18063 CAAAAAAGAAAAAAAAACAAAAAAAAA
1 CAAAAAACAAAAAAAAACAAAAAAAAA
*
18090 CAAAAAAACAAAACAAAGA-AAAAAAAAA
1 C-AAAAAACAAAA-AAAAACAAAAAAAAA
*
18118 GAAAAA
1 CAAAAA
18124 TCTGCTTAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 6 0.21
28 19 0.66
29 4 0.14
ACGTcount: A:0.87, C:0.08, G:0.05, T:0.00
Consensus pattern (27 bp):
CAAAAAACAAAAAAAAACAAAAAAAAA
Found at i:18123 original size:27 final size:27
Alignment explanation
Indices: 18063--18116 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
18053 ACCTTCTCTT
18063 CAAAAAAGA-AAAAAAAACAAAAAAAAA
1 CAAAAAA-ACAAAAAAAACAAAAAAAAA
* *
18090 CAAAAAAACAAAACAAAGAAAAAAAAA
1 CAAAAAAACAAAAAAAACAAAAAAAAA
18117 AGAAAAATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 1 0.04
27 23 0.96
ACGTcount: A:0.87, C:0.09, G:0.04, T:0.00
Consensus pattern (27 bp):
CAAAAAAACAAAAAAAACAAAAAAAAA
Found at i:19375 original size:55 final size:55
Alignment explanation
Indices: 19117--19620 Score: 642
Period size: 55 Copynumber: 9.0 Consensus size: 55
19107 GATGCCTTTT
* *
19117 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-CAGTCCTCAAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGACA
* * *
19171 CCTTTTAAAGCCCACACAAGTTGGTGGCAC-TTCCCGATCCTCAAAGAGCAGGACG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCCAG-TCCTCAAAGAGCAGGACA
* *
19226 CCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAGAGAGCAGGACGCCTT
1 CCTT-T-C----AAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGA------
19291 CA
54 CA
*
19293 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGACA
* *
19348 CCTCTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCCCAAAGAGCAGGAC-
1 CCTTTCAAAGCCCACACAAGTTGGTGGCA-CTTTCCAGTCCTCAAAGAGCAGGACA
* *
19402 CTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATCCTCAAAGAGCAGGACA
1 C-CTTTCAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGACA
*
19458 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGACA
* * *
19513 CCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCTTCAAAAAGCAGGACG
1 CCT-TTCAAAGCCCACACAAGTTGGTGGCA-CTTTCCAGTCCTCAAAGAGCAGGACA
* **
19568 CCTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGA
19621 TACACTTTAT
Statistics
Matches: 401, Mismatches: 26, Indels: 45
0.85 0.06 0.10
Matches are distributed among these distances:
53 2 0.00
54 42 0.10
55 253 0.63
56 10 0.02
61 83 0.21
62 4 0.01
65 1 0.00
66 1 0.00
67 5 0.01
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.22
Consensus pattern (55 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGACA
Found at i:20388 original size:21 final size:21
Alignment explanation
Indices: 20364--20440 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
20354 TATATTTTCA
20364 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
20385 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
* *
20406 AATGTATCGATACA-TTCTACA
1 AATGTATCGATACATTTGTA-G
20427 AATGTATCGATACA
1 AATGTATCGATACA
20441 GGGTCCCAAC
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 3 0.06
21 48 0.94
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:20500 original size:19 final size:19
Alignment explanation
Indices: 20476--20543 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
20466 AATTCAACAA
20476 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
20495 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
20510 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
20527 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
20544 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:20515 original size:13 final size:13
Alignment explanation
Indices: 20497--20521 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20487 ACATAAGTTT
20497 TGTATCGATACAA
1 TGTATCGATACAA
20510 TGTATCGATACA
1 TGTATCGATACA
20522 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:20519 original size:32 final size:32
Alignment explanation
Indices: 20478--20540 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
20468 TTCAACAATT
*
20478 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
20510 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
20541 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:20601 original size:13 final size:13
Alignment explanation
Indices: 20583--20608 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20573 CATTTTTCTG
20583 TGTATCGATACAT
1 TGTATCGATACAT
20596 TGTATCGATACAT
1 TGTATCGATACAT
20609 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:20605 original size:33 final size:33
Alignment explanation
Indices: 20563--20629 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
20553 GCCAAGGAAA
***
20563 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
20596 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
20629 T
1 T
20630 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:27422 original size:20 final size:20
Alignment explanation
Indices: 27326--27412 Score: 111
Period size: 20 Copynumber: 4.3 Consensus size: 20
27316 ACTATGATAA
* **
27326 ATGTATCGATGCATTTTAAGC
1 ATGTATCGATACA-TTTACTC
*
27347 ATATATCGATACATTTACTC
1 ATGTATCGATACATTTACTC
*
27367 ATGTATCGATACATTTACTT
1 ATGTATCGATACATTTACTC
*
27387 ATATATCGATACATTTACTC
1 ATGTATCGATACATTTACTC
27407 ATGTAT
1 ATGTAT
27413 TAATATATTT
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
20 46 0.81
21 11 0.19
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTACTC
Found at i:28734 original size:19 final size:18
Alignment explanation
Indices: 28708--28773 Score: 70
Period size: 19 Copynumber: 3.8 Consensus size: 18
28698 AATTTCAACG
28708 GTTTGTATCGATACATAA
1 GTTTGTATCGATACATAA
*
28726 GTGTTGTATTGATAC--AA
1 GT-TTGTATCGATACATAA
28743 ---TGTATCGATACATAA
1 GTTTGTATCGATACATAA
28758 GTTTTGTATCGATACA
1 G-TTTGTATCGATACA
28774 ATGTATCGCT
Statistics
Matches: 39, Mismatches: 2, Indels: 13
0.72 0.04 0.24
Matches are distributed among these distances:
13 10 0.26
15 2 0.05
17 2 0.05
18 2 0.05
19 23 0.59
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (18 bp):
GTTTGTATCGATACATAA
Found at i:28752 original size:32 final size:32
Alignment explanation
Indices: 28711--28781 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
28701 TTCAACGGTT
*
28711 TGTATCGATACATAAGTGTTGTATTGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
28743 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
28775 TGTATCG
1 TGTATCG
28782 CTACGAAGCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:28844 original size:13 final size:13
Alignment explanation
Indices: 28826--28850 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28816 ATTACTCAAA
28826 TGTATCGATACAT
1 TGTATCGATACAT
28839 TGTATCGATACA
1 TGTATCGATACA
28851 CTAATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:28902 original size:52 final size:52
Alignment explanation
Indices: 28859--28987 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
28849 CACTAATCTT
* *
28859 TGTATCGATACATGCAGGTAAATTTGCCCAGATGTATCGATACAATATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
*
28911 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
28963 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
28988 TCATATTTCG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Done.