Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1156
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: 81754
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:316 original size:23 final size:23
Alignment explanation
Indices: 290--341 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
280 TATTTTTTAA
*
290 ATATAATAATA-TATATTAATTTT
1 ATATAATAATATTA-AATAATTTT
*
313 ATATTAT-ATATTAAATAATTTT
1 ATATAATAATATTAAATAATTTT
335 -TATAATA
1 ATATAATA
342 TAAAGAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
21 5 0.21
22 11 0.46
23 8 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
ATATAATAATATTAAATAATTTT
Found at i:345 original size:18 final size:19
Alignment explanation
Indices: 295--361 Score: 55
Period size: 19 Copynumber: 3.4 Consensus size: 19
285 TTTAAATATA
*
295 ATAATATATATTAATTTTAT
1 ATAATATA-AATAATTTTAT
315 ATTATATATTAAATAATTTT-T
1 A-TA-ATA-TAAATAATTTTAT
* **
336 ATAATATAAAGAATAATAT
1 ATAATATAAATAATTTTAT
355 ATAATAT
1 ATAATAT
362 TATATTATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
18 8 0.21
19 11 0.28
20 3 0.08
21 4 0.10
22 11 0.28
23 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (19 bp):
ATAATATAAATAATTTTAT
Found at i:401 original size:35 final size:35
Alignment explanation
Indices: 361--461 Score: 91
Period size: 38 Copynumber: 2.8 Consensus size: 35
351 ATATATAATA
361 TTATATTATAAATATTAAAAATTATTTTAAATTAT
1 TTATATTATAAATATTAAAAATTATTTTAAATTAT
*
396 TTATATTTTAAAATTTAATTAAAAA--ATTATTAAATTAT
1 TTATATTAT-AAA--T-ATTAAAAATTATT-TTAAATTAT
* * *
434 TGATGATTA-AATTTTTAAAAATTATTTT
1 TTAT-ATTATAAATATTAAAAATTATTTT
462 TATATTATGA
Statistics
Matches: 53, Mismatches: 5, Indels: 16
0.72 0.07 0.22
Matches are distributed among these distances:
34 7 0.13
35 11 0.21
36 6 0.11
37 5 0.09
38 13 0.25
39 11 0.21
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (35 bp):
TTATATTATAAATATTAAAAATTATTTTAAATTAT
Found at i:3834 original size:20 final size:20
Alignment explanation
Indices: 3787--3861 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
3777 AAAAAGACAT
*
3787 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
3806 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
3827 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
3847 AATGTATCGATACAT
1 AATGTATCGATACAT
3862 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:3855 original size:40 final size:39
Alignment explanation
Indices: 3784--3861 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
3774 GGTAAAAAGA
* *
3784 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
3823 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
3862 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:4439 original size:32 final size:32
Alignment explanation
Indices: 4390--6332 Score: 2831
Period size: 32 Copynumber: 62.2 Consensus size: 32
4380 AATATGGTGA
* * **
4390 TTTGAAAAGGGTTGCCACTGACTTGCATGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
4422 TTTTAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
4454 TTTGAAATGAGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
4486 TTTGGAATGGGTTGCCACCGATTTGTGTGGGT
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
4518 TTTGAAATGGGTTACCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
4550 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
4582 TTTGAAATGGGTTGCCACCGACTTGTATGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
4614 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
4646 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
4678 TTTGGAATGGGTTGCCACCGACTTGTGTGGGT
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
4710 TTTGAAATGGGTTGCCACCGACTTGTGTGGGT
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
4742 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
4774 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
4806 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
4838 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
4870 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
4902 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
4934 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
4966 TTTGGAATGGGTTGCCACCGACTTGTGTGGGT
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
4998 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
5030 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
5062 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
5094 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
5126 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
5158 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
5190 TTTGGAATGGGTTGCCACCGACTTGTGTGGGT
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
5222 TTTGAAATGGGTTGCCACCGACTTGTGTGGGG
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
5254 TTTGAAATGGGTTGCCACCGACTTGTGTGGGG
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
5286 TTTGAAATGAGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
5318 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
5350 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
5382 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
5414 TTTGAAATGGGTTGCCACCGACTTGTGTGGGG
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
5446 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
5478 TTTGAAATGAGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
5510 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
5542 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
5574 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
5606 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
5638 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
5670 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
5702 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
5734 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
5766 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
5798 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
5830 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
5862 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
5894 TTTGAAATGGGTTGCCACCGAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* **
5924 TCTGAAA-GGG-TGCCACTAAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * * * *
5952 TCTGAAAAGAG-TGCCACTGGC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
5981 TTTGAAA-GGAG-TGCCACTGAC-T-TGTGGGC
1 TTTGAAATGG-GTTGCCACCGACTTGTGTGGGC
* ** *
6010 TTTGAAA--GGATGCCAATGA-GT-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
6038 TTTGAAA-GGG-TGCCACTGAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
6066 TTTGAAAAGAG-TGCCACTGA-TT-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
6095 TTTGAAA-GGAG-TGCCACTGAC-T-TGTGGGC
1 TTTGAAATGG-GTTGCCACCGACTTGTGTGGGC
*
6124 TTTGAAA-GGAG-TGCCACTGAC-T-TGTGGGC
1 TTTGAAATGG-GTTGCCACCGACTTGTGTGGGC
* * * *
6153 TTTAAAAAGAG-TGCCACTGA-TT-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * ** *
6182 TTTGAAAAGAG-TGCCACTAAC-T-TGTAGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
6211 TTTGAAA-GGAG-TGCCACTGAC-T-TGTGGGC
1 TTTGAAATGG-GTTGCCACCGACTTGTGTGGGC
*
6240 TTTGAAA-GGG-TGCCACTGAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
6268 TTTGAAAAGAG-TGCCACTGA-TT-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
6297 TTTGAAA-GGAG-TGCCACTGAC-T-TGTGGGC
1 TTTGAAATGG-GTTGCCACCGACTTGTGTGGGC
6326 TTTGAAA
1 TTTGAAA
6333 GGGATGAACA
Statistics
Matches: 1823, Mismatches: 70, Indels: 39
0.94 0.04 0.02
Matches are distributed among these distances:
27 1 0.00
28 100 0.05
29 260 0.14
30 14 0.01
31 1 0.00
32 1447 0.79
ACGTcount: A:0.17, C:0.18, G:0.35, T:0.31
Consensus pattern (32 bp):
TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
Found at i:7578 original size:14 final size:13
Alignment explanation
Indices: 7559--7595 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
7549 GACCCTTCTA
7559 TTTTTTGCTTTTTT
1 TTTTTTG-TTTTTT
7573 TTTTTTGTTTTTT
1 TTTTTTGTTTTTT
7586 TTTTTT-TTTT
1 TTTTTTGTTTT
7596 GGGTGTAACG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 4 0.17
13 12 0.52
14 7 0.30
ACGTcount: A:0.00, C:0.03, G:0.05, T:0.92
Consensus pattern (13 bp):
TTTTTTGTTTTTT
Found at i:22548 original size:20 final size:20
Alignment explanation
Indices: 22501--22575 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
22491 AAAAAGACAT
*
22501 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
22520 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
22541 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
22561 AATGTATCGATACAT
1 AATGTATCGATACAT
22576 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:22569 original size:40 final size:39
Alignment explanation
Indices: 22498--22575 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
22488 GGTAAAAAGA
* *
22498 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
22537 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
22576 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:24695 original size:16 final size:16
Alignment explanation
Indices: 24669--24722 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
24659 GTTATTTTAC
24669 TAAAA-AATTTTAATT
1 TAAAATAATTTTAATT
*
24684 TAAAATAATTTTTATT
1 TAAAATAATTTTAATT
*
24700 TAAAATAA-TTAATATT
1 TAAAATAATTTTA-ATT
24716 TAAAATA
1 TAAAATA
24723 TTAATAGATA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
15 7 0.21
16 27 0.79
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TAAAATAATTTTAATT
Found at i:24727 original size:15 final size:16
Alignment explanation
Indices: 24681--24728 Score: 71
Period size: 16 Copynumber: 3.1 Consensus size: 16
24671 AAAAATTTTA
**
24681 ATTTAAAATAATTTTT
1 ATTTAAAATAATTAAT
24697 ATTTAAAATAATTAAT
1 ATTTAAAATAATTAAT
24713 ATTTAAAAT-ATTAAT
1 ATTTAAAATAATTAAT
24728 A
1 A
24729 GATATCTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
15 7 0.23
16 23 0.77
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTTAAAATAATTAAT
Found at i:28643 original size:3 final size:3
Alignment explanation
Indices: 28635--28665 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
28625 TTCCTTGTTC
28635 GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA G
1 GTA GTA GTA GTA GTA GTA GTA GTA GTA GTA G
28666 AAGAAGAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (3 bp):
GTA
Found at i:30280 original size:265 final size:265
Alignment explanation
Indices: 29806--30337 Score: 931
Period size: 265 Copynumber: 2.0 Consensus size: 265
29796 GTATAAAAAT
29806 AAGTGGATAGAATGGAAGAGGAGGCCAAAAGGTATCTTTGATGAATTGTTGGCTCAAAAAGACCA
1 AAGTGGATAGAATGGAAGAGGAGGCCAAAAGGTATCTTTGATGAATTGTTGGCTCAAAAAGACCA
29871 CATGTGGTGTGGTAGGCAATGATGACGACAACAGCCAATCACCAAATTCTGAAAATTTGACTAGT
66 CATGTGGTGTGGTAGGCAATGATGACGACAACAGCCAATCACCAAATTCTGAAAATTTGACTAGT
* *
29936 TTTTGTGTAAGGGCCTAGCCTAATGATCCTACGTACCCTTGCAAAGGCAATAGGTATCACCAGTG
131 TTTTGTGCAAGGGCCTAGCCTAATGATCCTACATACCCTTGCAAAGGCAATAGGTATCACCAGTG
* * * * *
30001 ATCCTACCTACTCCCACAAGAGCACTTAGTATAACATTGCATCCAAGGTATTGTATTCTCTCAGC
196 ATCCTACCTACTCCCACAAAAGCAATTAGTATAACATTGCATCCAAGGCATTGTACTCTCTAAGC
30066 CCATA
261 CCATA
*
30071 AAGTGGATAGGATGGAAGAGGAGGCCGAAAAGG-ATCTTTGATGAATTGTTGGCTCAAAAAGACC
1 AAGTGGATAGAATGGAAGAGGAGGCC-AAAAGGTATCTTTGATGAATTGTTGGCTCAAAAAGACC
30135 ACATGTGGTGTGGTAGGCAATGATGACGACAACAGCCAATCACCAAATTCTGAAAATTTGACTAG
65 ACATGTGGTGTGGTAGGCAATGATGACGACAACAGCCAATCACCAAATTCTGAAAATTTGACTAG
*
30200 TTTTTGTGCAAGGGCCTAGCCTAATGATCCTACATACCCTTGCAAAGGCACTAGGTATCACCAGT
130 TTTTTGTGCAAGGGCCTAGCCTAATGATCCTACATACCCTTGCAAAGGCAATAGGTATCACCAGT
** * *
30265 GATCCTATTTACTCCCACAAAAGCAATTAGTGTAACATTGCATCCAAGGCATTGTACTCTTTAAG
195 GATCCTACCTACTCCCACAAAAGCAATTAGTATAACATTGCATCCAAGGCATTGTACTCTCTAAG
30330 CCCATA
260 CCCATA
30336 AA
1 AA
30338 CCTTAAGGTT
Statistics
Matches: 253, Mismatches: 13, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
265 247 0.98
266 6 0.02
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (265 bp):
AAGTGGATAGAATGGAAGAGGAGGCCAAAAGGTATCTTTGATGAATTGTTGGCTCAAAAAGACCA
CATGTGGTGTGGTAGGCAATGATGACGACAACAGCCAATCACCAAATTCTGAAAATTTGACTAGT
TTTTGTGCAAGGGCCTAGCCTAATGATCCTACATACCCTTGCAAAGGCAATAGGTATCACCAGTG
ATCCTACCTACTCCCACAAAAGCAATTAGTATAACATTGCATCCAAGGCATTGTACTCTCTAAGC
CCATA
Found at i:33873 original size:21 final size:20
Alignment explanation
Indices: 33843--33881 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
33833 GAGAAAGAAA
33843 AAATTTATTAAGGGGGAGAT
1 AAATTTATTAAGGGGGAGAT
33863 AAATTCTATTAAGGGGGAG
1 AAATT-TATTAAGGGGGAG
33882 TTATATATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.38, C:0.03, G:0.31, T:0.28
Consensus pattern (20 bp):
AAATTTATTAAGGGGGAGAT
Found at i:34396 original size:21 final size:21
Alignment explanation
Indices: 34372--34432 Score: 113
Period size: 21 Copynumber: 2.9 Consensus size: 21
34362 CGGGAAAGAA
*
34372 AAATTTTATTAAGGGGGAGAT
1 AAATTCTATTAAGGGGGAGAT
34393 AAATTCTATTAAGGGGGAGAT
1 AAATTCTATTAAGGGGGAGAT
34414 AAATTCTATTAAGGGGGAG
1 AAATTCTATTAAGGGGGAG
34433 TTACATATTG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.38, C:0.03, G:0.30, T:0.30
Consensus pattern (21 bp):
AAATTCTATTAAGGGGGAGAT
Found at i:35239 original size:13 final size:13
Alignment explanation
Indices: 35218--35252 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
35208 AACTCATTCA
35218 GTATTGATACAGT
1 GTATTGATACAGT
* *
35231 GTATCGATACATT
1 GTATTGATACAGT
35244 GTATTGATA
1 GTATTGATA
35253 TATGGTGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (13 bp):
GTATTGATACAGT
Found at i:38038 original size:66 final size:67
Alignment explanation
Indices: 37896--38063 Score: 175
Period size: 66 Copynumber: 2.5 Consensus size: 67
37886 CCCCTCTAAC
* * *
37896 TAGTTAACTTTATCAATTTTGCCCTGGTCAACTCCTTTTTTTGACTTAAATTCTGCCCTAGACTC
1 TAGTTGACTTTATCAATTTTGCCCTAGTCAAC-ACTTTTTTTGACTTAAATTCTGCCCTAGACTC
37961 TCT
65 TCT
* * * **
37964 TACTTGACTTTATCGATTTTACCCTAGTCAACACTTTTTTT-ACTTAGGTT-TAGCCCTAGTA-T
1 TAGTTGACTTTATCAATTTTGCCCTAGTCAACACTTTTTTTGACTTAAATTCT-GCCCTAG-ACT
38026 C-CTT
64 CTC-T
*
38030 TAGTTGACTTTA-CTAGTTTTGCCCTAGTCAACAC
1 TAGTTGACTTTATC-AATTTTGCCCTAGTCAACAC
38064 CTACTGGTTT
Statistics
Matches: 84, Mismatches: 12, Indels: 10
0.79 0.11 0.09
Matches are distributed among these distances:
65 3 0.04
66 45 0.54
67 9 0.11
68 27 0.32
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.43
Consensus pattern (67 bp):
TAGTTGACTTTATCAATTTTGCCCTAGTCAACACTTTTTTTGACTTAAATTCTGCCCTAGACTCT
CT
Found at i:38073 original size:25 final size:25
Alignment explanation
Indices: 38040--38090 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
38030 TAGTTGACTT
*
38040 TACTAGTTTTGCCCTAGTCAACACC
1 TACTAGTTTCGCCCTAGTCAACACC
*
38065 TACTGGTTTCGCCCTAGTCAACACC
1 TACTAGTTTCGCCCTAGTCAACACC
38090 T
1 T
38091 CTTTCAACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.22, C:0.33, G:0.14, T:0.31
Consensus pattern (25 bp):
TACTAGTTTCGCCCTAGTCAACACC
Found at i:39472 original size:19 final size:19
Alignment explanation
Indices: 39445--39488 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
39435 TATTAAACCA
39445 TTTTT-TGAAAATTCAATT
1 TTTTTATGAAAATTCAATT
** *
39463 TTTTTATGAATTTTGAATT
1 TTTTTATGAAAATTCAATT
39482 TTTTTAT
1 TTTTTAT
39489 ATATACACTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.27, C:0.02, G:0.07, T:0.64
Consensus pattern (19 bp):
TTTTTATGAAAATTCAATT
Found at i:39615 original size:6 final size:6
Alignment explanation
Indices: 39606--39668 Score: 51
Period size: 6 Copynumber: 10.7 Consensus size: 6
39596 TTTATGATTA
* * *
39606 TTAATT TTAATT TGAATT TT-CTT TTAATT TTAGATT TCTTATT TT-ATT
1 TTAATT TTAATT TTAATT TTAATT TTAATT TTA-ATT T-TAATT TTAATT
*
39654 TT-ATT TTACTT TTAA
1 TTAATT TTAATT TTAA
39669 ACTAGTTTCA
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
5 14 0.30
6 23 0.50
7 8 0.17
8 1 0.02
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.67
Consensus pattern (6 bp):
TTAATT
Found at i:39636 original size:11 final size:12
Alignment explanation
Indices: 39606--39668 Score: 51
Period size: 11 Copynumber: 5.3 Consensus size: 12
39596 TTTATGATTA
39606 TTAATTTTAATT
1 TTAATTTTAATT
* *
39618 TGAATTTT-CTT
1 TTAATTTTAATT
39629 TTAATTTTAGATT
1 TTAATTTTA-ATT
*
39642 TCTTATTTT-ATT
1 T-TAATTTTAATT
*
39654 TT-ATTTTACTT
1 TTAATTTTAATT
39665 TTAA
1 TTAA
39669 ACTAGTTTCA
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
10 5 0.12
11 14 0.35
12 12 0.30
13 3 0.08
14 6 0.15
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.67
Consensus pattern (12 bp):
TTAATTTTAATT
Found at i:41681 original size:22 final size:22
Alignment explanation
Indices: 41625--41695 Score: 88
Period size: 22 Copynumber: 3.0 Consensus size: 22
41615 ATCAATATTT
* *
41625 ATGTATCGATAAATCATTGTTC
1 ATGTATCGATACATCACTGTTC
41647 ATCACAGTATCGATACATCACTGTTC
1 AT----GTATCGATACATCACTGTTC
41673 ATGTATCGATACATCACTGTTC
1 ATGTATCGATACATCACTGTTC
41695 A
1 A
41696 CACTATTTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
22 23 0.53
26 20 0.47
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (22 bp):
ATGTATCGATACATCACTGTTC
Found at i:43266 original size:156 final size:153
Alignment explanation
Indices: 42990--43529 Score: 534
Period size: 156 Copynumber: 3.5 Consensus size: 153
42980 CCAAATACCC
* * * * * *
42990 CTAAGATATACCTTCAACGTGAAAATATCTCGATAATCCTAAAGGACTTAAAAAATGATCATAAA
1 CTAAGGTATA-CTTCGACATGAAAGTATCTTGATAACCCTAAAGGACTT-AAAAATGATCATAAA
* * * * *
43055 TGAGATGAACCTAT-CTGAAATGCACACCTTTGGCATAAATGCATCCCGGTAACAACTTAGGACT
64 TGGGATGAACCTATCCT-AAATGCACACCTTTGGCATAAAAGCATCCCGGTGACAACCTAAGACT
*
43119 CTATTCTAAAAAAATTACGAAAATACGT
128 CAATTCTAAAAAAATTAC-AAAATAC-T
* * *
43147 CTAAGGTATATCTTCGACATAAAAGTATCTTGGTAACCCTAAATGACTTAAAAATGATCATAAAT
1 CTAAGGTATA-CTTCGACATGAAAGTATCTTGATAACCCTAAAGGACTTAAAAATGATCATAAAT
* * * * * *
43212 GGGATGAGCCTATCCTAAATACACACCTTTGACATAAAAGCATCCTGATGACAACCTACGACTCA
65 GGGATGAACCTATCCTAAATGCACACCTTTGGCATAAAAGCATCCCGGTGACAACCTAAGACTCA
* ** * *
43277 ATTTTTTAAAAATTATAAAAATACC
130 ATTCTAAAAAAATTA-CAAAATACT
* ** * ** *
43302 CTTAAGGCATACCTTTAACATGAAAGCATCTTGATAACTGTAAATGACTTAAAAATGATCATAAA
1 C-TAAGGTATA-CTTCGACATGAAAGTATCTTGATAACCCTAAAGGACTTAAAAATGATCATAAA
*
43367 TGGGACT-AACCTATCCTAAATGCACACCTTTGGCATCAAAGCATCCCGGTGACAACCTAAGACT
64 TGGGA-TGAACCTATCCTAAATGCACACCTTTGGCATAAAAGCATCCCGGTGACAACCTAAGACT
* *
43431 CGA-TC-AAAGAGAATTACAAGAATTAC-
128 CAATTCTAAA-AAAATTACAA-AA-TACT
* * **
43457 CTTAGGGTATACTTTCGACATGAAAGTAT-TCTGATAACCTTAAAGGACTTAAAAATGATTGTAA
1 C-TAAGGTATAC-TTCGACATGAAAGTATCT-TGATAACCCTAAAGGACTTAAAAATGATCATAA
43521 ATGGGATGA
63 ATGGGATGA
43530 CTTTTACCCA
Statistics
Matches: 315, Mismatches: 58, Indels: 22
0.80 0.15 0.06
Matches are distributed among these distances:
154 6 0.02
155 67 0.21
156 200 0.63
157 42 0.13
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (153 bp):
CTAAGGTATACTTCGACATGAAAGTATCTTGATAACCCTAAAGGACTTAAAAATGATCATAAATG
GGATGAACCTATCCTAAATGCACACCTTTGGCATAAAAGCATCCCGGTGACAACCTAAGACTCAA
TTCTAAAAAAATTACAAAATACT
Found at i:46288 original size:154 final size:151
Alignment explanation
Indices: 46038--46432 Score: 402
Period size: 154 Copynumber: 2.6 Consensus size: 151
46028 ATTAAAAAAA
* * * *
46038 TTAAGAACTCATAAAATAAATTAGACTTTTCAAAAACTGATTTAACATTAATTTAATAATAATAT
1 TTAA-AACTCATAAAATAAATTA-ATTTTTC-AAAACTGATTTAATATAAATTAAATAATAATAT
** * * ** *
46103 TTGATGAATTTT-AAATATTTTGATCTGAGAAAAATT-TAACAAAAAAATTTATTGAGTAGAAAA
63 TT-AAAAATTTTGAAA-ATTATAAAATGAGAAAAATTCTAAC-AAAAAATTTATGGAGTAGAAAA
* * *
46166 -TCTCGTCTATCGAAAACA-AGAAAATTT
125 CT-TCATATATCGAAAACAGA-AAAAATT
* *
46193 TTAAAACTCATAAAATAAATTGAATTTTTCAAAACTGATTTAATATCAATTAAATAAAAATATTT
1 TTAAAACTCATAAAATAAATT-AATTTTTCAAAACTGATTTAATATAAATTAAATAATAATATTT
* ** * *
46258 AACAAATTTTTGAAAATTATAAAATTAGAAAAATTCTTTCGAAAAATTTATGGAGTATAAAACTT
65 AA-AAA-TTTTGAAAATTATAAAATGAGAAAAATTCTAACAAAAAATTTATGGAGTAGAAAACTT
* *
46323 TATATATCGATAACAGAAAAAATT
128 CATATATCGAAAACAGAAAAAATT
* * * *
46347 TTAAAAGTCATAGAATAAATTAAATTTTTTAAAACTGATTTAATATAAAATAAATAATAATATTT
1 TTAAAACTCATAAAATAAATT-AATTTTTCAAAACTGATTTAATATAAATTAAATAATAATATTT
46412 AAATAATTTTGAAAATTATAA
65 AAA-AATTTTGAAAATTATAA
46433 CTTAAAAAAT
Statistics
Matches: 203, Mismatches: 29, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
152 1 0.00
153 49 0.24
154 141 0.69
155 12 0.06
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (151 bp):
TTAAAACTCATAAAATAAATTAATTTTTCAAAACTGATTTAATATAAATTAAATAATAATATTTA
AAAATTTTGAAAATTATAAAATGAGAAAAATTCTAACAAAAAATTTATGGAGTAGAAAACTTCAT
ATATCGAAAACAGAAAAAATT
Found at i:47826 original size:66 final size:66
Alignment explanation
Indices: 47614--47853 Score: 195
Period size: 66 Copynumber: 3.7 Consensus size: 66
47604 GGTTGACTAC
* * * * ** * *
47614 GATGAAACCTAAG-TAAAAAAAAGTTGA-CTAGGGCAAAACCATCACATCAA-TAAAGGGTGACC
1 GATGAAACCTAAGTTGAAAAGAGGTTGATC-AAGGCAAAACCATCATGTCAACTAAAAGATGACC
47676 AA
65 AA
* * * * * ** *
47678 GGTG-AACTTAAGTCGAAAGGAGGTTGATTAAGGTGAAACCATCATGTCAACTAAAAGATGA-CT
1 GATGAAACCTAAGTTGAAAAGAGGTTGATCAAGGCAAAACCATCATGTCAACTAAAAGATGACCA
47741 A
66 A
* * * *
47742 GA-GCAAAACTTAAATTGAAAAGAGATTGATCAAGGCAAAACCATCTTGTCAACTAAAAGATGAC
1 GATG--AAACCTAAGTTGAAAAGAGGTTGATCAAGGCAAAACCATCATGTCAACTAAAAGATGAC
47806 CAA
64 CAA
* * * *
47809 GATGAAACCTAAGTTGAAAGGAGGTTGACCAGGGCGAAACCATCA
1 GATGAAACCTAAGTTGAAAAGAGGTTGATCAAGGCAAAACCATCA
47854 CATCAACAAA
Statistics
Matches: 134, Mismatches: 34, Indels: 14
0.74 0.19 0.08
Matches are distributed among these distances:
63 8 0.06
64 31 0.23
65 8 0.06
66 82 0.61
67 4 0.03
68 1 0.01
ACGTcount: A:0.44, C:0.16, G:0.22, T:0.19
Consensus pattern (66 bp):
GATGAAACCTAAGTTGAAAAGAGGTTGATCAAGGCAAAACCATCATGTCAACTAAAAGATGACCA
A
Found at i:48614 original size:73 final size:75
Alignment explanation
Indices: 48493--48715 Score: 202
Period size: 73 Copynumber: 3.0 Consensus size: 75
48483 TGGTAACAGT
* ** * ** * *
48493 CTGAAGAAGAAGAACATGATGGGGAATATGTCATCTCCAAAATTTTTATTAACAACCAAAACAAA
1 CTGAA-AAGAAGAACATGATAGGGAATATGTTGTTTTTACAATTTTTATCAACAACCAAAACAAA
* * *
48558 CTGATAA-CAG
65 CTGAAAATAAA
** * * **
48568 CTTG-AAA-AAGAACATGATAGGTTATATGTTGTTTTTATAATTTTTATCAACGACTGAAACAAA
1 C-TGAAAAGAAGAACATGATAGGGAATATGTTGTTTTTACAATTTTTATCAACAACCAAAACAAA
*
48631 CTAAAAATAAA
65 CTGAAAATAAA
* * *
48642 CTGAAAAAGAAGAACATTATAGGGAATATGTTGTTTTTACAA-TTTTATCAATAAACAAAACAAA
1 CTG-AAAAGAAGAACATGATAGGGAATATGTTGTTTTTACAATTTTTATCAACAACCAAAACAAA
48706 CTGAAAATAA
65 CTGAAAATAA
48716 GCTGGAGGAT
Statistics
Matches: 116, Mismatches: 27, Indels: 10
0.76 0.18 0.07
Matches are distributed among these distances:
73 50 0.43
74 4 0.03
75 31 0.27
76 31 0.27
ACGTcount: A:0.47, C:0.12, G:0.13, T:0.28
Consensus pattern (75 bp):
CTGAAAAGAAGAACATGATAGGGAATATGTTGTTTTTACAATTTTTATCAACAACCAAAACAAAC
TGAAAATAAA
Found at i:49549 original size:88 final size:88
Alignment explanation
Indices: 49419--49750 Score: 396
Period size: 88 Copynumber: 3.8 Consensus size: 88
49409 GCACATGAGG
* * * *
49419 CGATGTAAATGTAAGCATCAATAAAGTGG-AAATGCGTATGAAATGATGCAAATACTAATGTCAT
1 CGATGCAAATGCAAGCATCAATAAAGTGGCAAATGCATATGAAATGATGCAAATACCAATGTCAT
* *
49483 CCAAAGTGCACATATGCATGAAA
66 CTAAAGTGCACATGTGCATGAAA
* * * ** * * *
49506 CAATACAAATGCTAGCATCAATAAAAAGGCAAATGCATATGAAATAATGTAAATACCAATGTTAT
1 CGATGCAAATGCAAGCATCAATAAAGTGGCAAATGCATATGAAATGATGCAAATACCAATGTCAT
* * *
49571 CTAAAATGCACATGTCCGTGAAA
66 CTAAAGTGCACATGTGCATGAAA
* * *
49594 CGATGCAAATGCAAGTATCAATAAAGTGACAAATGCATATGAAATGATGCAAATACCAATGTTAT
1 CGATGCAAATGCAAGCATCAATAAAGTGGCAAATGCATATGAAATGATGCAAATACCAATGTCAT
* *
49659 CTAAAGTGTAGATGTGCATGAAA
66 CTAAAGTGCACATGTGCATGAAA
* * * * * * *
49682 CGATGCAATTGCAAGCATAAATAAAGGGGTAAATGTATGTGAAATGATGCAAATGCCAATGTCAT
1 CGATGCAAATGCAAGCATCAATAAAGTGGCAAATGCATATGAAATGATGCAAATACCAATGTCAT
49747 CTAA
66 CTAA
49751 TCCCAATTTG
Statistics
Matches: 203, Mismatches: 41, Indels: 1
0.83 0.17 0.00
Matches are distributed among these distances:
87 22 0.11
88 181 0.89
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.24
Consensus pattern (88 bp):
CGATGCAAATGCAAGCATCAATAAAGTGGCAAATGCATATGAAATGATGCAAATACCAATGTCAT
CTAAAGTGCACATGTGCATGAAA
Found at i:49680 original size:44 final size:43
Alignment explanation
Indices: 49556--49689 Score: 121
Period size: 44 Copynumber: 3.0 Consensus size: 43
49546 GAAATAATGT
* * *
49556 AAATACCAATGTTATCTAAAATGCACATGTCCGTGAAACGATGC
1 AAATACCAATGTTATCTAAAGTG-ACATGTGCATGAAACGATGC
* ** *
49600 AAAT-GCAA-G-TATCAATAAAGTGACAAATGCATATGAAATGATGC
1 AAATACCAATGTTATC--TAAAGTGACATGTGC--ATGAAACGATGC
*
49644 AAATACCAATGTTATCTAAAGTGTAGATGTGCATGAAACGATGC
1 AAATACCAATGTTATCTAAAGTG-ACATGTGCATGAAACGATGC
49688 AA
1 AA
49690 TTGCAAGCAT
Statistics
Matches: 70, Mismatches: 12, Indels: 16
0.71 0.12 0.16
Matches are distributed among these distances:
41 4 0.06
42 6 0.09
43 9 0.13
44 31 0.44
45 10 0.14
46 6 0.09
47 4 0.06
ACGTcount: A:0.43, C:0.15, G:0.18, T:0.25
Consensus pattern (43 bp):
AAATACCAATGTTATCTAAAGTGACATGTGCATGAAACGATGC
Found at i:52993 original size:13 final size:13
Alignment explanation
Indices: 52975--53000 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
52965 TACAGCAAGT
52975 ATGTATCGATACA
1 ATGTATCGATACA
52988 ATGTATCGATACA
1 ATGTATCGATACA
53001 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:55828 original size:160 final size:156
Alignment explanation
Indices: 55597--56106 Score: 557
Period size: 155 Copynumber: 3.2 Consensus size: 156
55587 AATGTCTTAA
* * *
55597 TAACCCTAAAAGACTTAAAAAATGATCATAAATGGGGTGAACC-ATCCTAAATGCACCCCTTTGG
1 TAACCCTAAAGGACTT-AAAAATGATCATAAATGGGATGAACCTATCCTAAATGCACACCTTTGG
* * *
55661 CATAAAAGCATCCCAATGACAACCTAGGACTCGGTTCTAAAAAAATTATGAAAATATCTCTAAGG
65 CATAAAAGCATCCCAGTGACAACCTAGGACTCGGTTCTAGAAAAATTA-GAAAAT-CCTCTAAGG
* *
55726 TAGGTATACCTTCGACATGAAAGTATCTTGG
128 T--GTATACCTTCGATATGAAAGTATCTCGG
* * * * **
55757 TAACCCTAAATGG-CTTAAAAATTATCATAAATGGGATGAACCTATTCTAAATACATATTTTTGG
1 TAACCCTAAA-GGACTTAAAAATGATCATAAATGGGATGAACCTATCCTAAATGCACACCTTTGG
* * * * *
55821 TATAAAAGCATCCCGGTGACAACCTAGGACTCGATTCTAGAAAAATTACAAAATGCCTTTAA-GT
65 CATAAAAGCATCCCAGTGACAACCTAGGACTCGGTTCTAGAAAAATTAGAAAAT-CCTCTAAGGT
* * *
55885 -TATACCTTTGATATGAAAATATCTCGA
129 GTATACCTTCGATATGAAAGTATCTCGG
* * * *
55912 TAACCCTAAAGGACTTCAAAATGATTATAAATGGGACGAACCTATCCTAAATGTACACCTTTGGC
1 TAACCCTAAAGGACTTAAAAATGATCATAAATGGGATGAACCTATCCTAAATGCACACCTTTGGC
* * * * *
55977 ATAAAAGCATCCCAGTGAAAACCTAGGACAT-AGTTCTGGGAAAATTACGAAAATGCTCATAAGG
66 ATAAAAGCATCCCAGTGACAACCTAGGAC-TCGGTTCTAGAAAAATTA-GAAAATCCTC-TAAGG
* *
56041 TG--TACTTTCGATATGAAAGTATCTCAG
128 TGTATACCTTCGATATGAAAGTATCTCGG
* * *
56068 TAACCTTAAAGGACTTAAAAATAATCGTAAATGGGATGA
1 TAACCCTAAAGGACTTAAAAATGATCATAAATGGGATGA
56107 CTTTTACCCT
Statistics
Matches: 288, Mismatches: 54, Indels: 20
0.80 0.15 0.06
Matches are distributed among these distances:
154 2 0.01
155 114 0.40
156 62 0.22
157 2 0.01
158 2 0.01
159 34 0.12
160 71 0.25
161 1 0.00
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (156 bp):
TAACCCTAAAGGACTTAAAAATGATCATAAATGGGATGAACCTATCCTAAATGCACACCTTTGGC
ATAAAAGCATCCCAGTGACAACCTAGGACTCGGTTCTAGAAAAATTAGAAAATCCTCTAAGGTGT
ATACCTTCGATATGAAAGTATCTCGG
Found at i:58644 original size:14 final size:15
Alignment explanation
Indices: 58620--58648 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
58610 AAATTTTGAA
58620 TTGAGAAAAATTTAT
1 TTGAGAAAAATTTAT
58635 TTGA-AAAAATTTAT
1 TTGAGAAAAATTTAT
58649 GGAGTAGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.41
Consensus pattern (15 bp):
TTGAGAAAAATTTAT
Found at i:58884 original size:152 final size:150
Alignment explanation
Indices: 58526--58916 Score: 400
Period size: 152 Copynumber: 2.6 Consensus size: 150
58516 TTGATATTAA
* *
58526 AAAAATTC-AAAACTCATAAAATAAATTAGATTTTTCAAAAACTGATTTAACATAAATTTAATAA
1 AAAAATTCTAAAACTCATAAAATAAATTA-ATTTTTC-AAAACTGATTTAATAT-AATTTAAAAA
* * ** * ** *
58590 AAACATTTGATGAATTTTAAAAATTTTGAATTGAGAAAAATTTATTTGAAAAAATTTATGGAGTA
63 AAATATTTGATGAATTTT-GAAATTTCAAATTCAGAAAAATTTA-TCCAAAAAATTTACGGAGTA
58655 GAAAATCTCATATATCGAAAGTAGG
126 GAAAATCTCATATATCGAAAGTAGG
* ** * * *
58680 AAAAATTCTAAAACTTATAAAATAAATTAAAAATTTCAAAGCTGATTCAATATCATTTAAACAAA
1 AAAAATTCTAAAACTCATAAAATAAATT-AATTTTTCAAAACTGATTTAATATAATTTAAA-AAA
*
58745 AATATTTCATGAATTTTGAAATTTACAAACTTCA-AAAAATTCTA-CCAAAAAATTTACGGAGTA
64 AATATTTGATGAATTTTGAAATTT-CAAA-TTCAGAAAAATT-TATCCAAAAAATTTACGGAGTA
* *
58808 GAAAA-CTCCATATTTTGATAAG-A-G
126 GAAAATCT-CATATATCGA-AAGTAGG
* * *
58832 AAAAATTCTAAGACTCATAAATTAAATTGAATTTTTCAAAACTGATTTAATATGAA-ATAAAAAA
1 AAAAATTCTAAAACTCATAAAATAAATT-AATTTTTCAAAACTGATTTAATAT-AATTTAAAAAA
*
58896 AATATTTGATAAATTTTGAAA
64 AATATTTGATGAATTTTGAAA
58917 ATTATATACT
Statistics
Matches: 197, Mismatches: 31, Indels: 21
0.79 0.12 0.08
Matches are distributed among these distances:
151 22 0.11
152 52 0.26
153 43 0.22
154 51 0.26
155 28 0.14
156 1 0.01
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.33
Consensus pattern (150 bp):
AAAAATTCTAAAACTCATAAAATAAATTAATTTTTCAAAACTGATTTAATATAATTTAAAAAAAA
TATTTGATGAATTTTGAAATTTCAAATTCAGAAAAATTTATCCAAAAAATTTACGGAGTAGAAAA
TCTCATATATCGAAAGTAGG
Found at i:58950 original size:152 final size:152
Alignment explanation
Indices: 58638--58989 Score: 365
Period size: 152 Copynumber: 2.3 Consensus size: 152
58628 AATTTATTTG
* * * *
58638 AAAAAATTTATGGAGTAGAAAA-TCTCATATATCGA-AAGTAGGAAAAATTCTAAAACTTATAAA
1 AAAAAATTTACGGAGTAGAAAACTC-CATATTTTGATAAG-A-GAAAAATTCTAAAACTCATAAA
* ** *
58701 ATAAATTAAAAATTTCAAAGCTGATTCAATATCATTTAAACAAAAATATTTCATGAATTTTGAAA
63 ATAAATTAAAAATTTCAAAACTGATTCAATATCAAATAAACAAAAATATTTCATAAATTTTGAAA
* *
58766 TTTACAAACTTCAAAAAATTCTACC
128 ATTACAAACTTCAAAAAATACTACC
* *
58791 AAAAAATTTACGGAGTAGAAAACTCCATATTTTGATAAGAGAAAAATTCTAAGACTCATAAATTA
1 AAAAAATTTACGGAGTAGAAAACTCCATATTTTGATAAGAGAAAAATTCTAAAACTCATAAAATA
* ** * * *
58856 AATTGAATTTTTCAAAACTGATTTAATATGAAATAAA-AAAAATATTTGATAAATTTTGAAAATT
66 AATTAAAAATTTCAAAACTGATTCAATATCAAATAAACAAAAATATTTCATAAATTTTGAAAATT
* * *
58920 ATATAC-TCAGACAAATACTA-C
131 ACAAACTTCA-AAAAATACTACC
** * * *
58941 AAGAGAAATTTACAAAGTCA-AAAACTCTATATTTTGATAACAAAAAAAT
1 AA-A-AAATTTACGGAGT-AGAAAACTCCATATTTTGATAAGAGAAAAAT
58990 CTGAAAGAAA
Statistics
Matches: 167, Mismatches: 26, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
150 6 0.04
151 37 0.22
152 88 0.53
153 31 0.19
154 5 0.03
ACGTcount: A:0.50, C:0.10, G:0.09, T:0.31
Consensus pattern (152 bp):
AAAAAATTTACGGAGTAGAAAACTCCATATTTTGATAAGAGAAAAATTCTAAAACTCATAAAATA
AATTAAAAATTTCAAAACTGATTCAATATCAAATAAACAAAAATATTTCATAAATTTTGAAAATT
ACAAACTTCAAAAAATACTACC
Found at i:60458 original size:153 final size:150
Alignment explanation
Indices: 60259--60642 Score: 396
Period size: 154 Copynumber: 2.5 Consensus size: 150
60249 TTCATTATTA
* * * * *
60259 CATAATATTTTTATATCCTTTAGGGTTATTAAGAT-CTTTCACGTCGAAGTTATACTTGAAGGGC
1 CATAATATTTTTGTGTCCTTTA-GGTTA-CAAGATACTTTCATGTCGAAGATATACTTGAA-GGC
* *
60323 ATTTGGTAATTTTCCTTAGAACCGAATCTTAGATAG-CACCGGGTCACTTTTATGCCAAAGGTAT
63 ATTTGGTAATTTTCC-TAGAACCGAATCTTAGATAGTCACCGGGTCACTCTTATGCCAAAAGTAT
* *
60387 GCATTTAGGATAGGTTCATCCTTT
127 ACATTTAGGATAAGTTCATCCTTT
* * * *
60411 TATAATATTTTTGTGTCTTTTAGGTTTACCAAGATACTTTCATGTCGAAGATATACCTCAAGGCA
1 CATAATATTTTTGTGTCCTTTAGG-TTA-CAAGATACTTTCATGTCGAAGATATACTTGAAGGCA
* * * * **
60476 TTTAGGTAATTTTTCCTAGAACTGAGTCTTAGGTAGTCATCGGGTTGCTCTTATGCCAAAAGTAT
64 TTT-GGTAA-TTTTCCTAGAACCGAATCTTAGATAGTCACCGGGTCACTCTTATGCCAAAAGTAT
*
60541 ATATTTAGGATAAGTTCATCCTTT
127 ACATTTAGGATAAGTTCATCCTTT
* * * * * * *
60565 CATGATCTTTTCGTGTCCTGTAGAGTTACTAGATATTTTCATGTCGAAGGTATA-TTGAAAGGCT
1 CATAATATTTTTGTGTCCTTTAG-GTTACAAGATACTTTCATGTCGAAGATATACTTG-AAGGC-
60629 ATTTTGGTAATTTT
63 A-TTTGGTAATTTT
60643 TTAAAATCGA
Statistics
Matches: 191, Mismatches: 32, Indels: 17
0.80 0.13 0.07
Matches are distributed among these distances:
151 2 0.01
152 34 0.18
153 75 0.39
154 76 0.40
155 4 0.02
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (150 bp):
CATAATATTTTTGTGTCCTTTAGGTTACAAGATACTTTCATGTCGAAGATATACTTGAAGGCATT
TGGTAATTTTCCTAGAACCGAATCTTAGATAGTCACCGGGTCACTCTTATGCCAAAAGTATACAT
TTAGGATAAGTTCATCCTTT
Found at i:61721 original size:41 final size:41
Alignment explanation
Indices: 61664--61816 Score: 105
Period size: 41 Copynumber: 3.7 Consensus size: 41
61654 GTCACCCTTT
*
61664 GTTGACTCATTTGGTTTCATCCTAGTCAACATTTCTTATTC
1 GTTGACTCATATGGTTTCATCCTAGTCAACATTTCTTATTC
* ** ** * * *
61705 GTTGACTTATATGGTTTTGTATTGGTCAACTTTTCCCT-TTC
1 GTTGACTCATATGGTTTCATCCTAGTCAACATTT-CTTATTC
** * * * *
61746 GTTGACTTGTATGGTTTCGTCCT-GATCAACCCTTT-TCATTT
1 GTTGACTCATATGGTTTCATCCTAG-TCAA-CATTTCTTATTC
* *
61787 GTTGACTCGTATGATTTCATCCTAGTCAAC
1 GTTGACTCATATGGTTTCATCCTAGTCAAC
61817 CTTTTTAACT
Statistics
Matches: 87, Mismatches: 20, Indels: 11
0.74 0.17 0.09
Matches are distributed among these distances:
40 2 0.02
41 78 0.90
42 7 0.08
ACGTcount: A:0.18, C:0.21, G:0.16, T:0.46
Consensus pattern (41 bp):
GTTGACTCATATGGTTTCATCCTAGTCAACATTTCTTATTC
Found at i:61817 original size:41 final size:41
Alignment explanation
Indices: 61746--61843 Score: 110
Period size: 41 Copynumber: 2.4 Consensus size: 41
61736 TTTCCCTTTC
* * * * *
61746 GTTGACTTGTATGGTTTCGTCCTGATCAACCCTTTTCATTT
1 GTTGACTCGTATGATTTCATCCTGATCAACCCTTTTAACTT
*
61787 GTTGACTCGTATGATTTCATCCT-AGTCAACCTTTTTAACTT
1 GTTGACTCGTATGATTTCATCCTGA-TCAACCCTTTTAACTT
*
61828 GTTG-TTCGTATGATTT
1 GTTGACTCGTATGATTT
61844 TGTCCTAGCT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
40 12 0.24
41 37 0.76
ACGTcount: A:0.17, C:0.19, G:0.16, T:0.47
Consensus pattern (41 bp):
GTTGACTCGTATGATTTCATCCTGATCAACCCTTTTAACTT
Found at i:66416 original size:13 final size:13
Alignment explanation
Indices: 66394--66430 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
66384 ATAGTACCTT
* *
66394 TGTATTGATACAG
1 TGTATCGATACAA
66407 TGTATCGATACAA
1 TGTATCGATACAA
66420 TGTATCGATAC
1 TGTATCGATAC
66431 TAAAAACATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:69860 original size:19 final size:19
Alignment explanation
Indices: 69816--69871 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
69806 CTGCTAATCT
* **
69816 CATGTAGCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
69836 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
69855 CATGTATCGATATAATG
1 CATGTATCGATACAATG
69872 TATCGATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:69878 original size:32 final size:33
Alignment explanation
Indices: 69837--69899 Score: 94
Period size: 32 Copynumber: 1.9 Consensus size: 33
69827 ACAATTGTCC
*
69837 ATGTATCGATACAATG-A-ACATGTATCGATATA
1 ATGTATCGATACAAAGCATA-ATGTATCGATATA
69869 ATGTATCGATACAAAGCATAATGTATCGATA
1 ATGTATCGATACAAAGCATAATGTATCGATA
69900 CATTTGGGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 15 0.54
33 12 0.43
34 1 0.04
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (33 bp):
ATGTATCGATACAAAGCATAATGTATCGATATA
Found at i:70469 original size:21 final size:22
Alignment explanation
Indices: 70424--70469 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
70414 AGTTTTCGTT
* *
70424 TTTCTCCCCCTTAATTAAAACA
1 TTTCTCCCCCTAAATCAAAACA
70446 TTTCTCCCCCTAAATCAAAA-A
1 TTTCTCCCCCTAAATCAAAACA
70467 TTT
1 TTT
70470 ATTTATTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTCTCCCCCTAAATCAAAACA
Found at i:78057 original size:19 final size:20
Alignment explanation
Indices: 78033--78085 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
78023 TACACCCAGA
**
78033 TGTATCGATACATGTTC-AT
1 TGTATCGATACATGGACAAT
*
78052 TGTATCAATACATGGACAAT
1 TGTATCGATACATGGACAAT
*
78072 TGTATCGATGCATG
1 TGTATCGATACATG
78086 AGATTGGCAG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATGGACAAT
Found at i:78151 original size:13 final size:13
Alignment explanation
Indices: 78130--78160 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
78120 CGATACATGG
*
78130 TACAATGTATCGA
1 TACATTGTATCGA
78143 TACATTGTATCGA
1 TACATTGTATCGA
78156 TACAT
1 TACAT
78161 GATGAATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:78177 original size:33 final size:33
Alignment explanation
Indices: 78114--78182 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
78104 CTACCACTAT
* *
78114 TTGTATCGATACATGGTACAATGTATCGATACA
1 TTGTATCGATACATGATACAATGTAACGATACA
*
78147 TTGTATCGATACATGATGA-ATTGTAACGATACA
1 TTGTATCGATACATGAT-ACAATGTAACGATACA
78180 TTG
1 TTG
78183 CTTGTAACGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (33 bp):
TTGTATCGATACATGATACAATGTAACGATACA
Done.