Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3585
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: 44219
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:64 original size:19 final size:19
Alignment explanation
Indices: 42--92 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
32 TTACTTATTA
*
42 TTTTTTTTTTTTAGTATAT
1 TTTTTTTTTTTTAGTAAAT
* *
61 TTTTATTTTTTAAGTAAAT
1 TTTTTTTTTTTTAGTAAAT
*
80 TTTTTATTTTTTA
1 TTTTTTTTTTTTA
93 ATTATATTAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.75
Consensus pattern (19 bp):
TTTTTTTTTTTTAGTAAAT
Found at i:83 original size:20 final size:20
Alignment explanation
Indices: 41--93 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
31 TTTACTTATT
*
41 ATTTTTT-TTTTTT-AGTAT
1 ATTTTTTATTTTTTAAGTAA
59 A-TTTTTATTTTTTAAGTAA
1 ATTTTTTATTTTTTAAGTAA
78 ATTTTTTATTTTTTAA
1 ATTTTTTATTTTTTAA
94 TTATATTAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 5 0.16
18 7 0.23
19 5 0.16
20 14 0.45
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.72
Consensus pattern (20 bp):
ATTTTTTATTTTTTAAGTAA
Found at i:217 original size:18 final size:19
Alignment explanation
Indices: 202--238 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
192 AAATTTATTA
202 TTATTATTTTATTTATAAT
1 TTATTATTTTATTTATAAT
*
221 TTTTTATTTT-TTTATAAT
1 TTATTATTTTATTTATAAT
239 AATTTCTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (19 bp):
TTATTATTTTATTTATAAT
Found at i:233 original size:22 final size:22
Alignment explanation
Indices: 202--253 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
192 AAATTTATTA
*
202 TTATTATTTTATTTATAATTT-T
1 TTATTATTTTA-TAATAATTTCT
*
224 TTATTTTTTTATAATAATTTCT
1 TTATTATTTTATAATAATTTCT
246 TTA-TATTT
1 TTATTATTT
254 CTCATCTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 12 0.46
22 14 0.54
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (22 bp):
TTATTATTTTATAATAATTTCT
Found at i:310 original size:24 final size:23
Alignment explanation
Indices: 279--331 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
269 AATTAAATTA
*
279 TATTTAATA-ATATTCATTTTTTTT
1 TATTTAATATATA-T-ATATTTTTT
*
303 TATTTAATCTATATATATTTTTT
1 TATTTAATATATATATATTTTTT
326 TATTTA
1 TATTTA
332 TATTAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 14 0.54
24 9 0.35
25 3 0.12
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (23 bp):
TATTTAATATATATATATTTTTT
Found at i:345 original size:23 final size:23
Alignment explanation
Indices: 297--368 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 23
287 AATATTCATT
*
297 TTTTTTTATTTA-ATCTATATATA
1 TTTTTTTATTTATAT-TAAATATA
320 TTTTTTTATTTATATTAAAT-TAA
1 TTTTTTTATTTATATTAAATAT-A
*
343 TTTTTATT-TTTCTATT-AATATA
1 TTTTT-TTATTTATATTAAATATA
365 TTTT
1 TTTT
369 GTTAAATTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
22 9 0.21
23 30 0.70
24 4 0.09
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (23 bp):
TTTTTTTATTTATATTAAATATA
Found at i:569 original size:10 final size:10
Alignment explanation
Indices: 509--729 Score: 68
Period size: 10 Copynumber: 22.0 Consensus size: 10
499 CTATTATTAA
509 TATTTCTTT-T
1 TATTT-TTTAT
*
519 TATTTTTGAT
1 TATTTTTTAT
529 ATATTTTCTTAT
1 -TATTTT-TTAT
*
541 TAATATTTTA-
1 T-ATTTTTTAT
*
551 TATTCTTTAT
1 TATTTTTTAT
*
561 TATTTTTTAA
1 TATTTTTTAT
* *
571 TATTTATCACT
1 TATTTTTTA-T
*
582 AATTTTTT-T
1 TATTTTTTAT
591 T-TTTTATT-T
1 TATTTT-TTAT
600 TATTTTTT-T
1 TATTTTTTAT
609 T-TTTTTT-T
1 TATTTTTTAT
* *
617 TTTTTTTTTT
1 TATTTTTTAT
* *
627 TTTTTTTTGTT
1 TATTTTTT-AT
*
638 TAATATTTTAT
1 T-ATTTTTTAT
649 T-TTTATTTAT
1 TATTT-TTTAT
* *
659 TATTTATAAT
1 TATTTTTTAT
*
669 TA-ATTTTAT
1 TATTTTTTAT
678 ATATTCTTTTAAT
1 -TATT-TTTT-AT
*
691 TAATTTTTA-
1 TATTTTTTAT
* *
700 TATTATTAAT
1 TATTTTTTAT
*
710 TATTTTCTAT
1 TATTTTTTAT
* *
720 AATATTTTAT
1 TATTTTTTAT
730 AAATTGCTAA
Statistics
Matches: 158, Mismatches: 34, Indels: 38
0.69 0.15 0.17
Matches are distributed among these distances:
8 12 0.08
9 35 0.22
10 63 0.40
11 27 0.17
12 19 0.12
13 2 0.01
ACGTcount: A:0.24, C:0.03, G:0.01, T:0.72
Consensus pattern (10 bp):
TATTTTTTAT
Found at i:646 original size:18 final size:18
Alignment explanation
Indices: 625--663 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
615 TTTTTTTTTT
* *
625 TTTTTTTTTTGTTTAATA
1 TTTTATTTTTATTTAATA
*
643 TTTTATTTTTATTTATTA
1 TTTTATTTTTATTTAATA
661 TTT
1 TTT
664 ATAATTAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (18 bp):
TTTTATTTTTATTTAATA
Found at i:652 original size:1 final size:1
Alignment explanation
Indices: 584--634 Score: 84
Period size: 1 Copynumber: 51.0 Consensus size: 1
574 TTATCACTAA
* *
584 TTTTTTTTTTTTATTTTATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
635 GTTTAATATT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.04, C:0.00, G:0.00, T:0.96
Consensus pattern (1 bp):
T
Found at i:677 original size:23 final size:24
Alignment explanation
Indices: 647--712 Score: 82
Period size: 23 Copynumber: 2.8 Consensus size: 24
637 TTAATATTTT
647 ATTTTTATTTATTATTTATAATTA
1 ATTTTTATTTATTATTTATAATTA
* *
671 A-TTTTATATATTCTTT-TAATTA
1 ATTTTTATTTATTATTTATAATTA
*
693 ATTTTTATATTATTAATTAT
1 ATTTTTAT-TTATTATTTAT
713 TTTCTATAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
22 7 0.21
23 19 0.56
24 7 0.21
25 1 0.03
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (24 bp):
ATTTTTATTTATTATTTATAATTA
Found at i:710 original size:19 final size:20
Alignment explanation
Indices: 665--725 Score: 63
Period size: 19 Copynumber: 3.0 Consensus size: 20
655 TTATTATTTA
*
665 TAATTAATTTTATATATTCTTT
1 TAATTAATTTTATATA-T-TAT
687 TAATTAATTTT-TATATTAT
1 TAATTAATTTTATATATTAT
* *
706 TAATT-ATTTTCTATAATAT
1 TAATTAATTTTATATATTAT
725 T
1 T
726 TTATAAATTG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
18 5 0.14
19 15 0.42
20 1 0.03
21 4 0.11
22 11 0.31
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
TAATTAATTTTATATATTAT
Found at i:728 original size:40 final size:41
Alignment explanation
Indices: 638--730 Score: 102
Period size: 40 Copynumber: 2.3 Consensus size: 41
628 TTTTTTTGTT
* *
638 TAATATTTTATTTTTATTTATTATTTATAATTAATTTTATA
1 TAATATTTTATATTAATTTATTATTTATAATTAATTTTATA
* * *
679 TATTCTTTTA-ATTAATTT-TTATATTATTAATT-ATTTTCTA
1 TAATATTTTATATTAATTTATTAT-TTA-TAATTAATTTTATA
719 TAATATTTTATA
1 TAATATTTTATA
731 AATTGCTAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
39 4 0.10
40 24 0.57
41 14 0.33
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (41 bp):
TAATATTTTATATTAATTTATTATTTATAATTAATTTTATA
Found at i:744 original size:54 final size:53
Alignment explanation
Indices: 637--745 Score: 118
Period size: 54 Copynumber: 2.0 Consensus size: 53
627 TTTTTTTTGT
* * *
637 TTAATATTTTATTTTTATTTATTATTTATAATTAATTTTATATATTCTTTTAA
1 TTAATATTTTATTTTTAATTATTATTTATAATTAATTTTATAAATTCTATTAA
690 TTAAT-TTTTATATTATTAATTATT-TTCTATAA-T-ATTTTATAAATTGCTAATTAA
1 TTAATATTTTAT-TT-TTAATTATTATT-TATAATTAATTTTATAAATT-CT-ATTAA
744 TT
1 TT
746 TATTCAGGTG
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
52 17 0.35
53 12 0.25
54 19 0.40
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (53 bp):
TTAATATTTTATTTTTAATTATTATTTATAATTAATTTTATAAATTCTATTAA
Found at i:3558 original size:40 final size:40
Alignment explanation
Indices: 3503--3729 Score: 402
Period size: 40 Copynumber: 5.7 Consensus size: 40
3493 GAGCATTGGA
3503 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
3543 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
3583 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
3623 ATATATCCGGGCTATGA-CCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
3662 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
3702 ATATGTCCGGGTTAAGACCCGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
3730 ATGTGTTTGC
Statistics
Matches: 179, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
39 37 0.21
40 142 0.79
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
Found at i:3747 original size:119 final size:120
Alignment explanation
Indices: 3503--3731 Score: 379
Period size: 119 Copynumber: 1.9 Consensus size: 120
3493 GAGCATTGGA
*
3503 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATATATCCGGGCTAAGACCCGAAGG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATGATATATCCGGGCTAAGACCCGAAGG
* * **
3568 CAATTATGCGAGTTGATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
66 CAATTATGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCAAATATGCGAGCGG
*
3623 ATATATCCGGGCTATGA-CCGAAGGCAATTATGCGAGATGATATATCCGGGCTAAGACCCGAAGG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATGATATATCCGGGCTAAGACCCGAAGG
* *
3687 CAATTATGCAAGTTGATATGTCCGGGTTAAGACCCGAAGGCAAAT
66 CAATTATGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCAAAT
3732 GTGTTTGCGG
Statistics
Matches: 103, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
119 87 0.84
120 16 0.16
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (120 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATGATATATCCGGGCTAAGACCCGAAGG
CAATTATGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCAAATATGCGAGCGG
Found at i:3764 original size:79 final size:80
Alignment explanation
Indices: 3503--3729 Score: 402
Period size: 79 Copynumber: 2.9 Consensus size: 80
3493 GAGCATTGGA
3503 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATATATCCGGGCTAAGACCCGAAGG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATATATCCGGGCTAAGACCCGAAGG
*
3568 CAATTATGCGAGTTG
66 CAATTATGCGAGATG
*
3583 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATATATCCGGGCTATGA-CCGAAGG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATATATCCGGGCTAAGACCCGAAGG
3647 CAATTATGCGAGATG
66 CAATTATGCGAGATG
* * *
3662 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTGATATGTCCGGGTTAAGACCCGAAGG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATATATCCGGGCTAAGACCCGAAGG
3727 CAA
66 CAA
3730 ATGTGTTTGC
Statistics
Matches: 140, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
79 74 0.53
80 66 0.47
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (80 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGATATATCCGGGCTAAGACCCGAAGG
CAATTATGCGAGATG
Found at i:6536 original size:40 final size:40
Alignment explanation
Indices: 6504--6816 Score: 455
Period size: 40 Copynumber: 7.8 Consensus size: 40
6494 CCAGCATGAT
* * * *
6504 TGCTCTTTGGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTTGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
6544 TGCTTTTTCGGAACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTT-GGGACTTAGCCCGGATACATCACTAGCACGAA
* *
6585 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTTGGGACTTAGCCCGGATACATCACTAGCACGAA
*
6625 TGCTCTTTGGAACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTTGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
6665 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCTTTGGGACTTAGCCCGGATACATCACTAGCACGAA
*
6705 TGCTCTTTGGAACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTTGGGACTTAGCCCGGATACATCACTAGCACGAA
**
6745 TGCTCTTTGGGACTTAGCTTGGATACATCACTAGCACGAA
1 TGCTCTTTGGGACTTAGCCCGGATACATCACTAGCACGAA
* * * *
6785 TGCTCTTCGGGACTTAGCTCGGGTATATCACT
1 TGCTCTTTGGGACTTAGCCCGGATACATCACT
6817 CTCAATTCTC
Statistics
Matches: 246, Mismatches: 26, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
40 213 0.87
41 33 0.13
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
TGCTCTTTGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:8141 original size:37 final size:37
Alignment explanation
Indices: 8083--8253 Score: 281
Period size: 37 Copynumber: 4.6 Consensus size: 37
8073 GCTCAGACGA
* * * *
8083 AATCTCCACACGAAGTTATCGGGTCTTACCTGGACAA
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
8120 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
*
8157 AATCTCCACATGTAGTCATCGGGTCTTACCCGGACAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
*
8194 AATCTCCACATGTAGTCATCGGGTCTTACCCGGACAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
8231 AATCT-CACACGTAGTCATCGGGT
1 AATCTCCACACGTAGTCATCGGGT
8254 TACCGGAATA
Statistics
Matches: 128, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
36 17 0.13
37 111 0.87
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (37 bp):
AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
Found at i:8473 original size:47 final size:47
Alignment explanation
Indices: 8422--8746 Score: 528
Period size: 47 Copynumber: 7.0 Consensus size: 47
8412 TTTCACACTA
* * *
8422 GCCATTCGGCTTTACCACATATATGCATGTTCATATTCATCACATTG
1 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
* *
8469 GCCATTCGG-CTT-TCACACATATGCATGCTCACATTCATCACATTG
1 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
8514 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
1 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
* *
8561 GCCATTCGGCCTTATCACACATATGCATGCTCACATTCATCACATTG
1 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
8608 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
1 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
8655 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
1 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
* * ** *
8702 GCCATTCGGCCTTATCTCATATATACACATTCGCATTCATCACAT
1 GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACAT
8747 AAAATATCAA
Statistics
Matches: 260, Mismatches: 16, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
45 38 0.15
46 5 0.02
47 217 0.83
ACGTcount: A:0.26, C:0.29, G:0.12, T:0.33
Consensus pattern (47 bp):
GCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTG
Found at i:18014 original size:74 final size:75
Alignment explanation
Indices: 17925--18078 Score: 274
Period size: 74 Copynumber: 2.1 Consensus size: 75
17915 ACGTATGATA
17925 ATTCAATTATAGAAATGCTATTAGTTTTCACACAATCACATGAAAAA-AAATCAATAAAACATAG
1 ATTCAATTATAGAAATGCTATTAGTTTTCACACAATCACATGAAAAACAAATCAATAAAACATAG
17989 TTTGTATTTT
66 TTTGTATTTT
* * *
17999 ATTCAATTATAGAAATGCTATTAGTTTTCACACAATCACATGAAAAACACATCAATTAAACATGG
1 ATTCAATTATAGAAATGCTATTAGTTTTCACACAATCACATGAAAAACAAATCAATAAAACATAG
18064 TTTGTATTTT
66 TTTGTATTTT
18074 ATTCA
1 ATTCA
18079 TTTTAGTCAT
Statistics
Matches: 76, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
74 47 0.62
75 29 0.38
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.36
Consensus pattern (75 bp):
ATTCAATTATAGAAATGCTATTAGTTTTCACACAATCACATGAAAAACAAATCAATAAAACATAG
TTTGTATTTT
Found at i:18415 original size:55 final size:53
Alignment explanation
Indices: 18328--18561 Score: 237
Period size: 55 Copynumber: 4.4 Consensus size: 53
18318 ATTAGGGTTT
* *
18328 AAGGATACCATGTAAGACCATGCCAAGGCATGGATATTGGTAAGGTTTCTAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGG-CATTGGTAA-GTTTCTAAGGC
* * * *
18383 AAGGATATCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTT--TCTAAGGC
* * * * *
18438 AAAGG-TCCCATGTAAGACCATGCCAAGGCATAGCATTGGTGAG-TTCATAAAGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTTC-TAAGGC
* ** *
18491 AAGGATACCATGTAAGACCATGTCGGGACATGGCAATGGTAAGTTTC-AA---
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTTCTAAGGC
18540 AAGGATACCATGTAAGACCATG
1 AAGGATACCATGTAAGACCATG
18562 ATAAGTGTAA
Statistics
Matches: 150, Mismatches: 23, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
49 22 0.15
52 7 0.05
53 38 0.25
54 11 0.07
55 68 0.45
56 4 0.03
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTTCTAAGGC
Found at i:18534 original size:108 final size:110
Alignment explanation
Indices: 18335--18535 Score: 291
Period size: 108 Copynumber: 1.8 Consensus size: 110
18325 TTTAAGGATA
* * * *
18335 CCATGTAAGACCATGCCAAGGCATGGATATTGGTAAGGTTTCTAAGGCAAGGATATCATGTAAGA
1 CCATGTAAGACCATGCCAAGGCATAGACATTGGTAAGGTTTCTAAAGCAAGGATACCATGTAAGA
*
18400 CCATGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTC
66 CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC
*
18445 CCATGTAAGACCATGCCAAGGCATAG-CATTGGTGA-G-TTCATAAAGCAAGGATACCATGTAAG
1 CCATGTAAGACCATGCCAAGGCATAGACATTGGTAAGGTTTC-TAAAGCAAGGATACCATGTAAG
** *
18507 ACCATGTCGGGACATGGCAATGGTAAGTT
65 ACCATGTCAAGACATGGCAATGATAAGTT
18536 TCAAAAGGAT
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
107 3 0.04
108 46 0.57
109 7 0.09
110 25 0.31
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.23
Consensus pattern (110 bp):
CCATGTAAGACCATGCCAAGGCATAGACATTGGTAAGGTTTCTAAAGCAAGGATACCATGTAAGA
CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC
Found at i:19139 original size:33 final size:34
Alignment explanation
Indices: 19097--19168 Score: 119
Period size: 34 Copynumber: 2.1 Consensus size: 34
19087 GTGAATAACA
19097 CAGTATCAGTACAGTCT-GGCCAAAGCCCTTTTT
1 CAGTATCAGTACAGTCTGGGCCAAAGCCCTTTTT
**
19130 CAGTATCAGTACAGTCTGGGCCTTAGCCCTTTTT
1 CAGTATCAGTACAGTCTGGGCCAAAGCCCTTTTT
19164 CAGTA
1 CAGTA
19169 GCAATGTGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
33 17 0.47
34 19 0.53
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.32
Consensus pattern (34 bp):
CAGTATCAGTACAGTCTGGGCCAAAGCCCTTTTT
Found at i:22915 original size:19 final size:19
Alignment explanation
Indices: 22893--22940 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
22883 GAATGCTTGC
*
22893 ACACATAGTGTATAATGGA
1 ACACATAGTGCATAATGGA
* * *
22912 ACACATAATGCATATTGGC
1 ACACATAGTGCATAATGGA
22931 ACACATAGTG
1 ACACATAGTG
22941 AATCATTGGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.25
Consensus pattern (19 bp):
ACACATAGTGCATAATGGA
Found at i:27288 original size:43 final size:43
Alignment explanation
Indices: 27241--27361 Score: 129
Period size: 42 Copynumber: 2.8 Consensus size: 43
27231 CCTCGATTGA
* *
27241 GATTTACGTATAAGACCATTTCTGGGACATCGGCATCG-TATCT
1 GATTTACGTGTAAGACCATGTCTGGGACATCGGCATCGATAT-T
* **
27284 GATTT-CGTGTAAGACCCTGTCTGGGACAGAGGCATCGATATT
1 GATTTACGTGTAAGACCATGTCTGGGACATCGGCATCGATATT
* * * * *
27326 GAGTTACATGTAAGACCACGTCCGGGACGTCGGCAT
1 GATTTACGTGTAAGACCATGTCTGGGACATCGGCAT
27362 TGTACTTGTT
Statistics
Matches: 63, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
42 32 0.51
43 31 0.49
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.27
Consensus pattern (43 bp):
GATTTACGTGTAAGACCATGTCTGGGACATCGGCATCGATATT
Found at i:27307 original size:42 final size:42
Alignment explanation
Indices: 27241--27361 Score: 111
Period size: 43 Copynumber: 2.8 Consensus size: 42
27231 CCTCGATTGA
* * *
27241 GATTTACGTATAAGACCATTTCTGGGACATCGGCATCG-TATCT
1 GATTT-CGTGTAAGACCCTGTCTGGGACATCGGCATCGATAT-T
**
27284 GATTTCGTGTAAGACCCTGTCTGGGACAGAGGCATCGATATT
1 GATTTCGTGTAAGACCCTGTCTGGGACATCGGCATCGATATT
* * * *
27326 GAGTTACATGTAAGACCAC-GTCCGGGACGTCGGCAT
1 GA-TTTCGTGTAAGACC-CTGTCTGGGACATCGGCAT
27362 TGTACTTGTT
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
42 30 0.47
43 33 0.52
44 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.27
Consensus pattern (42 bp):
GATTTCGTGTAAGACCCTGTCTGGGACATCGGCATCGATATT
Found at i:29057 original size:33 final size:34
Alignment explanation
Indices: 29015--29087 Score: 105
Period size: 34 Copynumber: 2.2 Consensus size: 34
29005 GTATGCATCT
29015 CTGATACTG-TACTG-AATTGGGCTAAGGCCCACA
1 CTGATACTGTTACTGTAA-TGGGCTAAGGCCCACA
**
29048 CTGATACTGTTACTGTAATGGGCTAAGGCCTGCA
1 CTGATACTGTTACTGTAATGGGCTAAGGCCCACA
29082 CTGATA
1 CTGATA
29088 TTGCCACTGA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
33 9 0.25
34 25 0.69
35 2 0.06
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.27
Consensus pattern (34 bp):
CTGATACTGTTACTGTAATGGGCTAAGGCCCACA
Found at i:29103 original size:34 final size:34
Alignment explanation
Indices: 29015--29118 Score: 97
Period size: 34 Copynumber: 3.1 Consensus size: 34
29005 GTATGCATCT
* *
29015 CTGATACTG-TACTG-AATTGGGCTAAGGCCCACA
1 CTGATACTGCCACTGTAA-TGGGCTAAGGCCTACA
** *
29048 CTGATACTGTTACTGTAATGGGCTAAGGCCTGCA
1 CTGATACTGCCACTGTAATGGGCTAAGGCCTACA
* * *
29082 CTGATATTGCCACTG-ATATGGGCTTAGGCCTAGA
1 CTGATACTGCCACTGTA-ATGGGCTAAGGCCTACA
29116 CTG
1 CTG
29119 CTTTGCACTG
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
33 10 0.17
34 48 0.80
35 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (34 bp):
CTGATACTGCCACTGTAATGGGCTAAGGCCTACA
Found at i:36631 original size:40 final size:39
Alignment explanation
Indices: 36547--36731 Score: 194
Period size: 40 Copynumber: 4.6 Consensus size: 39
36537 TTGAATGATG
* * * *
36547 TCCGGGCTAAGTCTCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTC-CGAAGGCATTTGTGC-GAGTTACTAAA
* * *
36587 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
* *
36627 TCCGGGCTAAGCCCGAAGGCATTTATGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
* *
36666 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
*
36707 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
36732 AACGAGTAGC
Statistics
Matches: 122, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
39 34 0.28
40 77 0.63
41 11 0.09
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:36753 original size:79 final size:79
Alignment explanation
Indices: 36600--36764 Score: 185
Period size: 79 Copynumber: 2.1 Consensus size: 79
36590 GGACTAAGAT
* * *
36600 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTATGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTATACGAGTTACTAA
*
36665 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
36679 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGA-ACGAG-TAG
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTT-ATACGAGTTA-
* * *
36741 CTATAT-CTGGTTAAATT
62 CTAAATCCGGGTTAAATC
36758 CCGAAGG
1 CCGAAGG
36765 TATGTGATTT
Statistics
Matches: 73, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
78 2 0.03
79 48 0.66
80 22 0.30
81 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTATACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:38196 original size:36 final size:37
Alignment explanation
Indices: 38124--38201 Score: 113
Period size: 36 Copynumber: 2.1 Consensus size: 37
38114 CTTATACGAA
* * *
38124 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
38161 GTCTTACCCGGA-AAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
38197 GTCTT
1 GTCTT
38202 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 25 0.68
37 12 0.32
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:38431 original size:47 final size:47
Alignment explanation
Indices: 38316--38828 Score: 867
Period size: 47 Copynumber: 10.9 Consensus size: 47
38306 GCCTTCGGGA
* * * * *
38316 CTTATCACATTTATACACTTTTCACATCCATCACGT-GGCCACTCGGC
1 CTTATCACATATATACAC-TTTCACATTCATCACATCGGCCATTAGGC
*
38363 C-TGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
38409 CTTATCACATATATACACTTTCACATTCATCACATCGGCCA-TAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
38455 CTTATCACATATATATACAC-TTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
38503 CCTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
38552 CTTATCACA-ATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
38598 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
38645 CTTATCACATATATACACTTCCACATTCATCACATCGGCCATTAGG-
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
38691 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
38738 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
38785 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTA
38829 CGCCATACTA
Statistics
Matches: 447, Mismatches: 11, Indels: 16
0.94 0.02 0.03
Matches are distributed among these distances:
45 15 0.03
46 128 0.29
47 235 0.53
48 34 0.08
49 35 0.08
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.31
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:38647 original size:93 final size:94
Alignment explanation
Indices: 38316--38828 Score: 867
Period size: 93 Copynumber: 5.5 Consensus size: 94
38306 GCCTTCGGGA
* * * * * *
38316 CTTATCACATTTATACACTTTTCACATCCATCACGT-GGCCACTCGGCC-TGTCACATATATACA
1 CTTATCACATATATACAC-TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
38379 CTTTCACATTCATCACATCGGCCATTAGGC
65 CTTTCACATTCATCACATCGGCCATTAGGC
38409 CTTATCACATATATACACTTTCACATTCATCACATCGGCCA-TAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
38473 AC-TTCACATTCATCACATCGGCCATTAGGC
64 ACTTTCACATTCATCACATCGGCCATTAGGC
*
38503 CCTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA-ATATAC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
38567 ACTTTCACATTCATCACATCGGCCATTAGGC
64 ACTTTCACATTCATCACATCGGCCATTAGGC
38598 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
38663 TTCCACATTCATCACATCGGCCATTAGG-
66 TTTCACATTCATCACATCGGCCATTAGGC
38691 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
38756 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
38785 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTA
38829 CGCCATACTA
Statistics
Matches: 401, Mismatches: 9, Indels: 19
0.93 0.02 0.04
Matches are distributed among these distances:
92 20 0.05
93 167 0.42
94 122 0.30
95 46 0.11
96 33 0.08
97 13 0.03
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.31
Consensus pattern (94 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGC
Found at i:38734 original size:140 final size:141
Alignment explanation
Indices: 38316--38828 Score: 867
Period size: 140 Copynumber: 3.6 Consensus size: 141
38306 GCCTTCGGGA
* * * * * *
38316 CTTATCACATTTATACACTTTTCACATCCATCACGT-GGCCACTCGGCC-TGTCACATATATACA
1 CTTATCACATATATACAC-TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA
38379 CTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACAT
65 CTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACAT
38444 CGGCCA-TAGGC
130 CGGCCATTAGGC
*
38455 CTTATCACATATATATACAC-TTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATAT
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATAT
38519 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA-ATATACACTTTCACATTCATCA
62 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
38583 CATCGGCCATTAGGC
127 CATCGGCCATTAGGC
38598 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
38663 TTCCACATTCATCACATCGGCCATTAGG-CTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
38727 GGCCATTAGGC
131 GGCCATTAGGC
38738 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
38803 TTTCACATTCATCACATCGGCCATTA
66 TTTCACATTCATCACATCGGCCATTA
38829 CGCCATACTA
Statistics
Matches: 356, Mismatches: 9, Indels: 17
0.93 0.02 0.04
Matches are distributed among these distances:
139 31 0.09
140 174 0.49
141 24 0.07
142 66 0.19
143 61 0.17
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.31
Consensus pattern (141 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
GGCCATTAGGC
Found at i:42274 original size:40 final size:39
Alignment explanation
Indices: 42225--42633 Score: 548
Period size: 40 Copynumber: 10.5 Consensus size: 39
42215 TTTCGAGACC
* * * **
42225 TAGCCCGGATATAACACCAGCACGAATGCTCTTCGAGGTT
1 TAGCCCGGATATATCACTAGCACGAATGCTCCTCG-GACT
* * *
42265 TAGCACGGATATATTACTAGCACGAATGCTCTTCGGAACT
1 TAGCCCGGATATATCACTAGCACGAATGCTCCTCGG-ACT
* *
42305 TAGCCCGGATACATCACTAGCACGAATGCTTCTCGTGACT
1 TAGCCCGGATATATCACTAGCACGAATGCTCCTCG-GACT
*
42345 TAACCCGG--ATATCACTAGCACGAATGCTTCCTCGGACT
1 TAGCCCGGATATATCACTAGCACGAATGC-TCCTCGGACT
42383 TAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGACT
1 TAGCCCGGATATATCACTAGCACGAATGCTCCTC-GGACT
42423 TAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGACT
1 TAGCCCGGATATATCACTAGCACGAATGCTCCTC-GGACT
*
42463 TAGCCCGGATATATCACTAGCACAAAATGCTCCTCGGACT
1 TAGCCCGGATATATCACTAGCAC-GAATGCTCCTCGGACT
42503 TAGCCCGGATATATCACTAGCACG-ATGCTCCTCGGGACT
1 TAGCCCGGATATATCACTAGCACGAATGCTCCTC-GGACT
42542 TAGCCCGGA-A-AT-ACTAGCACGAATGCTCCTCGGGACT
1 TAGCCCGGATATATCACTAGCACGAATGCTCCTC-GGACT
*
42579 TAGCCCGGATATAT-ACTAGC-CAAATGCT-CTCGGGACT
1 TAGCCCGGATATATCACTAGCACGAATGCTCCTC-GGACT
42616 TAGCCCGGATATATCACT
1 TAGCCCGGATATATCACT
42634 CTCAATTCTC
Statistics
Matches: 339, Mismatches: 18, Indels: 26
0.89 0.05 0.07
Matches are distributed among these distances:
36 9 0.03
37 49 0.14
38 50 0.15
39 33 0.10
40 187 0.55
41 11 0.03
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (39 bp):
TAGCCCGGATATATCACTAGCACGAATGCTCCTCGGACT
Found at i:42453 original size:158 final size:156
Alignment explanation
Indices: 42225--42633 Score: 582
Period size: 158 Copynumber: 2.6 Consensus size: 156
42215 TTTCGAGACC
* * * * *
42225 TAGCCCGGATATAACACCAGCACGAATGCTCTTCGAGG-TTTAGCACGGATATATTACTAGCACG
1 TAGCCCGGATATATCACTAGCACGAATGCTCCTCG-GGACTTAGCCCGGATATA-TACTAGCACG
* * * *
42289 AATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCAC-GAATGCTTCTCGTGACTTAACCCGG
64 AATGCTC-TCGGGACTTAGCCCGGATATATCACTAGCACAAAATGCTCCTCG-GACTTAACCCGG
42353 -ATATCACTAGCACGAATGCTTCCTC-GGACT
127 AATATCACTAGCACG-ATGC-TCCTCGGGACT
42383 TAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGACTTAGCCCGGATATATCACTAGCACGA
1 TAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGACTTAGCCCGGATATAT-ACTAGCACGA
*
42448 ATGCTCCTCGGGACTTAGCCCGGATATATCACTAGCACAAAATGCTCCTCGGACTTAGCCCGGAT
65 ATGCT-CTCGGGACTTAGCCCGGATATATCACTAGCACAAAATGCTCCTCGGACTTAACCCGGA-
42513 ATATCACTAGCACGATGCTCCTCGGGACT
128 ATATCACTAGCACGATGCTCCTCGGGACT
*
42542 TAGCCCGGA-A-AT-ACTAGCACGAATGCTCCTCGGGACTTAGCCCGGATATATACTAGC-CAAA
1 TAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGACTTAGCCCGGATATATACTAGCACGAA
42603 TGCTCTCGGGACTTAGCCCGGATATATCACT
66 TGCTCTCGGGACTTAGCCCGGATATATCACT
42634 CTCAATTCTC
Statistics
Matches: 233, Mismatches: 11, Indels: 19
0.89 0.04 0.07
Matches are distributed among these distances:
153 27 0.12
154 7 0.03
155 6 0.03
156 39 0.17
157 5 0.02
158 106 0.45
159 29 0.12
160 14 0.06
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (156 bp):
TAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGACTTAGCCCGGATATATACTAGCACGAA
TGCTCTCGGGACTTAGCCCGGATATATCACTAGCACAAAATGCTCCTCGGACTTAACCCGGAATA
TCACTAGCACGATGCTCCTCGGGACT
Found at i:44204 original size:49 final size:47
Alignment explanation
Indices: 44033--44218 Score: 268
Period size: 47 Copynumber: 3.9 Consensus size: 47
44023 CCTTCGGACT
* * * **
44033 TATCACATTTATACACTTTTCACATCCATCACGT-GGCCA-CCGGCCC
1 TATCACATATATACAC-TTTCACATTCATCACATCGGCCATTAGGCCC
* *
44079 TGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCC
44126 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCC
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCC
44173 TATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGG
1 TATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGG
44219 G
Statistics
Matches: 127, Mismatches: 9, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
45 15 0.12
46 19 0.15
47 55 0.43
49 38 0.30
ACGTcount: A:0.28, C:0.31, G:0.10, T:0.31
Consensus pattern (47 bp):
TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCC
Found at i:44205 original size:96 final size:93
Alignment explanation
Indices: 44031--44218 Score: 279
Period size: 96 Copynumber: 2.0 Consensus size: 93
44021 GCCCTTCGGA
* * * *
44031 CTTATCACATTTATACACTTTTCACATCCATCACGTGGCCACCGGCCCTGTCACATATATACACT
1 CTTATCACATATATACACTTTTCACATCCATCACATGGCCACAGGCCCTATCACATATATACACT
44096 TTCACATTCATCACATCGGCCATTAGGC
66 TTCACATTCATCACATCGGCCATTAGGC
* *
44124 CTTATCACATATATACAC-TTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATA
1 CTTATCACATATATACACTTTTCACATCCATCACAT-GGCCA-CAGGCCCTATCAC--ATATATA
44188 CACTTTCACATTCATCACATCGGCCATTAGG
62 CACTTTCACATTCATCACATCGGCCATTAGG
44219 G
Statistics
Matches: 85, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
92 15 0.18
93 22 0.26
94 10 0.12
96 38 0.45
ACGTcount: A:0.28, C:0.31, G:0.10, T:0.31
Consensus pattern (93 bp):
CTTATCACATATATACACTTTTCACATCCATCACATGGCCACAGGCCCTATCACATATATACACT
TTCACATTCATCACATCGGCCATTAGGC
Done.