Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold180
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: 544442
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.32
Warning! 40629 characters in sequence are not A, C, G, or T
File 4 of 4
Found at i:513676 original size:16 final size:16
Alignment explanation
Indices: 513648--513709 Score: 70
Period size: 17 Copynumber: 3.8 Consensus size: 16
513638 AAAAAATTTT
513648 AATAATTTAAAATAAAA
1 AATAATTT-AAATAAAA
* *
513665 AATAATTGAAATTTAAA
1 AATAATTTAAA-TAAAA
*
513682 AATAATTTAAATATAA
1 AATAATTTAAATAAAA
*
513698 ATTAATTTAAAT
1 AATAATTTAAAT
513710 TTTAAAAAAC
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
16 17 0.45
17 21 0.55
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (16 bp):
AATAATTTAAATAAAA
Found at i:513686 original size:34 final size:34
Alignment explanation
Indices: 513648--513725 Score: 97
Period size: 33 Copynumber: 2.4 Consensus size: 34
513638 AAAAAATTTT
513648 AATAATTTAAAATAAAAAATAATTGAAATTTAAA
1 AATAATTTAAAATAAAAAATAATTGAAATTTAAA
* * * *
513682 AATAATTT-AAATATAAATTAATTTAAATTTTAA
1 AATAATTTAAAATAAAAAATAATTGAAATTTAAA
*
513715 AA-AACTTAAAA
1 AATAATTTAAAA
513726 CCAAATATCA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
32 4 0.11
33 26 0.68
34 8 0.21
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (34 bp):
AATAATTTAAAATAAAAAATAATTGAAATTTAAA
Found at i:513704 original size:33 final size:35
Alignment explanation
Indices: 513648--513717 Score: 99
Period size: 33 Copynumber: 2.1 Consensus size: 35
513638 AAAAAATTTT
513648 AATAATTTAAAATAAAAAATAATTGAAA-TTTAAA
1 AATAATTTAAAATAAAAAATAATTGAAATTTTAAA
* * *
513682 AATAATTT-AAATATAAATTAATTTAAATTTTAAA
1 AATAATTTAAAATAAAAAATAATTGAAATTTTAAA
513716 AA
1 AA
513718 ACTTAAAACC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 16 0.50
34 16 0.50
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (35 bp):
AATAATTTAAAATAAAAAATAATTGAAATTTTAAA
Found at i:513715 original size:17 final size:17
Alignment explanation
Indices: 513648--513716 Score: 68
Period size: 17 Copynumber: 4.1 Consensus size: 17
513638 AAAAAATTTT
* **
513648 AATAATTTAAAATAAAA
1 AATAATTTAAATTTTAA
* *
513665 AATAATTGAAATTTAAA
1 AATAATTTAAATTTTAA
*
513682 AATAATTTAAA-TATAA
1 AATAATTTAAATTTTAA
*
513698 ATTAATTTAAATTTTAA
1 AATAATTTAAATTTTAA
513715 AA
1 AA
513717 AACTTAAAAC
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
16 13 0.31
17 29 0.69
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (17 bp):
AATAATTTAAATTTTAA
Found at i:514599 original size:16 final size:15
Alignment explanation
Indices: 514584--514616 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
514574 TGATGATTAT
*
514584 TTTAGATGATTTTTA
1 TTTAAATGATTTTTA
514599 TTTAAATGATTTTT-
1 TTTAAATGATTTTTA
514613 TTTA
1 TTTA
514617 GAAAATCAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (15 bp):
TTTAAATGATTTTTA
Found at i:515519 original size:16 final size:16
Alignment explanation
Indices: 515495--515671 Score: 76
Period size: 16 Copynumber: 10.9 Consensus size: 16
515485 CGGAAAGTTT
515495 AAATAATTTAAATTTA
1 AAATAATTTAAATTTA
*
515511 AAATGATTTAAATTT-
1 AAATAATTTAAATTTA
* *
515526 AAATAATTT-GATTTT
1 AAATAATTTAAATTTA
* * * *
515541 GAGTAATTAAAATGTCAAATC
1 AAATAATTTAAAT-T----TA
*
515562 AAATTATTTAAATTTA
1 AAATAATTTAAATTTA
* ***
515578 GAATAATACGAATTTA
1 AAATAATTTAAATTTA
* *
515594 AAATGAA-CTAAATATA
1 AAAT-AATTTAAATTTA
* * *
515610 AGATATTTTTAATTTA
1 AAATAATTTAAATTTA
* *
515626 TAATGATTTAAATTTA
1 AAATAATTTAAATTTA
*
515642 AAATAA-TTAAA-TAA
1 AAATAATTTAAATTTA
515656 TAAATAATTTAAATTT
1 -AAATAATTTAAATTT
515672 CTCGTGATTG
Statistics
Matches: 112, Mismatches: 37, Indels: 23
0.65 0.22 0.13
Matches are distributed among these distances:
14 6 0.05
15 26 0.23
16 65 0.58
17 4 0.04
20 1 0.01
21 10 0.09
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (16 bp):
AAATAATTTAAATTTA
Found at i:516014 original size:2 final size:2
Alignment explanation
Indices: 516007--516032 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
515997 TCTGCAAGTT
516007 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
516033 AAAGTCCCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:516251 original size:17 final size:16
Alignment explanation
Indices: 516229--516262 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
516219 ATTGATATTT
516229 ATATGATATAAAATATA
1 ATATGATATAAAA-ATA
516246 ATATGATATAAAAATA
1 ATATGATATAAAAATA
516262 A
1 A
516263 AAATATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (16 bp):
ATATGATATAAAAATA
Found at i:516310 original size:14 final size:14
Alignment explanation
Indices: 516293--516359 Score: 50
Period size: 14 Copynumber: 4.6 Consensus size: 14
516283 GATATTTTTA
516293 AAATTATATAATAT
1 AAATTATATAATAT
516307 AAATTAT-TAATAAAT
1 AAATTATATAAT--AT
516322 AAATATTATATAATAT
1 -AA-ATTATATAATAT
*
516338 ATAA-TATTTTAATAT
1 A-AATTA-TATAATAT
516353 -AATTATA
1 AAATTATA
516360 ATATTTAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 17
0.69 0.03 0.27
Matches are distributed among these distances:
13 7 0.16
14 11 0.26
15 11 0.26
16 5 0.12
17 5 0.12
18 4 0.09
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
AAATTATATAATAT
Found at i:516350 original size:15 final size:16
Alignment explanation
Indices: 516303--516353 Score: 61
Period size: 17 Copynumber: 3.2 Consensus size: 16
516293 AAATTATATA
516303 ATATAA-ATTATTAAT
1 ATATAATATTATTAAT
*
516318 AAATAAATATTATATAAT
1 ATAT-AATATTAT-TAAT
516336 ATATAATATT-TTAAT
1 ATATAATATTATTAAT
516351 ATA
1 ATA
516354 ATTATAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
15 10 0.32
16 3 0.10
17 11 0.35
18 7 0.23
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATATAATATTATTAAT
Found at i:517426 original size:29 final size:30
Alignment explanation
Indices: 517387--517453 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
517377 TATATTTATT
* *
517387 ATAATTATAAATATAAATATT-AATTA-TAA
1 ATAATAATAAAAATAAAT-TTAAATTATTAA
*
517416 ATAATAATAAAAATATATTTAAATTATTAA
1 ATAATAATAAAAATAAATTTAAATTATTAA
517446 ATAATAAT
1 ATAATAAT
517454 CATAAAATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 2 0.06
29 20 0.61
30 11 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (30 bp):
ATAATAATAAAAATAAATTTAAATTATTAA
Found at i:519506 original size:16 final size:16
Alignment explanation
Indices: 519467--519513 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
519457 ATAAAAAATT
519467 AATATAAAATAATTTA
1 AATATAAAATAATTTA
* * *
519483 AATTTAAATTAATTTG
1 AATATAAAATAATTTA
*
519499 AATATAAAATTATTT
1 AATATAAAATAATTT
519514 CAACTCAAGA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (16 bp):
AATATAAAATAATTTA
Found at i:520204 original size:42 final size:41
Alignment explanation
Indices: 520157--520238 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 41
520147 ACAAGTTTTA
* *
520157 TAATATAAATCATTAAAATAAGTTAATGTTTTGAAATTCAAG
1 TAATATAAATCATTAAAACAAATTAATGTTTT-AAATTCAAG
* **
520199 TAATATAAATTATTAAAACAAATTTGTGTTTTAAATTCAA
1 TAATATAAATCATTAAAACAAATTAATGTTTTAAATTCAA
520239 AAAGGATAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
41 8 0.23
42 27 0.77
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.40
Consensus pattern (41 bp):
TAATATAAATCATTAAAACAAATTAATGTTTTAAATTCAAG
Found at i:521337 original size:12 final size:12
Alignment explanation
Indices: 521322--521346 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
521312 TAAAATTTTA
521322 TAATAAATTAAT
1 TAATAAATTAAT
521334 TAATAAATTAAT
1 TAATAAATTAAT
521346 T
1 T
521347 TTATATAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAATAAATTAAT
Found at i:521602 original size:31 final size:31
Alignment explanation
Indices: 521550--521639 Score: 108
Period size: 31 Copynumber: 2.9 Consensus size: 31
521540 AAATCTAAAG
* * *
521550 TTGAATTGAAAATACTTTAAATTTAAAATTAC
1 TTGAATTCAAAA-AATTTAAATTTAAAATAAC
* *
521582 TTGAATTCAAAAAATTTAAATCTAATATAAC
1 TTGAATTCAAAAAATTTAAATTTAAAATAAC
**
521613 TAAAATTCAAAAAATTTAAATTTAAAA
1 TTGAATTCAAAAAATTTAAATTTAAAA
521640 GACATAATTC
Statistics
Matches: 49, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 38 0.78
32 11 0.22
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.37
Consensus pattern (31 bp):
TTGAATTCAAAAAATTTAAATTTAAAATAAC
Found at i:524272 original size:104 final size:104
Alignment explanation
Indices: 524081--524281 Score: 287
Period size: 104 Copynumber: 1.9 Consensus size: 104
524071 GAAAGATCAA
* * *
524081 CTTAATTTGAGAATTCAAGATGAAAATGCATCTTTTAATGACTTCAGAGCAATGAAAGCACCTGA
1 CTTAATTTGAGAATTCAAGATGAAAATGCATCTTTCAATGACTTCAAAGCAATGAAAGCACCTAA
*
524146 GTGATGGGGAAAACTGTTTGCATGCTGATACAATCAAAT
66 GTGATGGGGAAAACTGTATGCATGCTGATACAATCAAAT
* * * *
524185 CTTATTTTGAGAGTTCGAAGATGAAAATGTATCTTTCAATGTCTTCAAAGCAATG-AAGCACCTA
1 CTTAATTTGAGAATTC-AAGATGAAAATGCATCTTTCAATGACTTCAAAGCAATGAAAGCACCTA
** *
524249 AGTGATGGGGAAAGTTGTATGCATGTTGATACA
65 AGTGATGGGGAAAACTGTATGCATGCTGATACA
524282 GTTTATTTTT
Statistics
Matches: 85, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
104 51 0.60
105 34 0.40
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.30
Consensus pattern (104 bp):
CTTAATTTGAGAATTCAAGATGAAAATGCATCTTTCAATGACTTCAAAGCAATGAAAGCACCTAA
GTGATGGGGAAAACTGTATGCATGCTGATACAATCAAAT
Found at i:524466 original size:16 final size:16
Alignment explanation
Indices: 524445--524477 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
524435 GCTTGGAGAA
524445 TAAACATCTAGGACAC
1 TAAACATCTAGGACAC
524461 TAAACATCTAGGACAC
1 TAAACATCTAGGACAC
524477 T
1 T
524478 CCCATTGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.24, G:0.12, T:0.21
Consensus pattern (16 bp):
TAAACATCTAGGACAC
Found at i:526476 original size:4 final size:4
Alignment explanation
Indices: 526467--526494 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
526457 GTAAAAGAGA
526467 AAAC AAAC AAAC AAAC AAAC AAAC AAAC
1 AAAC AAAC AAAC AAAC AAAC AAAC AAAC
526495 GCTGGAGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.25, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:527976 original size:36 final size:36
Alignment explanation
Indices: 527917--528003 Score: 88
Period size: 36 Copynumber: 2.4 Consensus size: 36
527907 GATTATACTG
*
527917 ATTAAATTATCATTTAATTTAATTAAATTAAATTAT
1 ATTAAATTATCATTTAATGTAATTAAATTAAATTAT
* **
527953 ATTAAATTA-CATTTGATAGTAATTATTTTAAATTGAT
1 ATTAAATTATCATTTAAT-GTAATTAAATTAAATT-AT
* *
527990 -TTAATTTATTATTT
1 ATTAAATTATCATTT
528004 TTAATAAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
35 7 0.17
36 29 0.69
37 6 0.14
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.53
Consensus pattern (36 bp):
ATTAAATTATCATTTAATGTAATTAAATTAAATTAT
Found at i:535594 original size:3 final size:3
Alignment explanation
Indices: 535586--535626 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
535576 AAATCGAGAG
*
535586 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
535627 TTAGAAAAGG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:536290 original size:27 final size:27
Alignment explanation
Indices: 536215--536297 Score: 82
Period size: 27 Copynumber: 3.1 Consensus size: 27
536205 AAATAGTCAC
*
536215 AACAAATTTTAAACTAAGATAAGTTAAA
1 AACAAATTGTAAACTAAGATAAGTT-AA
* *
536243 AAAAAAGTTTGTAAA-T-A-ATAAGTTAC
1 AACAAA--TTGTAAACTAAGATAAGTTAA
*
536269 ATCAAATTGTAAACTAAGATAAGTTAA
1 AACAAATTGTAAACTAAGATAAGTTAA
536296 AA
1 AA
536298 AAAGTTTGTT
Statistics
Matches: 43, Mismatches: 7, Indels: 11
0.70 0.11 0.18
Matches are distributed among these distances:
24 7 0.16
25 1 0.02
26 6 0.14
27 16 0.37
28 6 0.14
29 1 0.02
30 6 0.14
ACGTcount: A:0.55, C:0.06, G:0.10, T:0.29
Consensus pattern (27 bp):
AACAAATTGTAAACTAAGATAAGTTAA
Found at i:537003 original size:28 final size:28
Alignment explanation
Indices: 536963--537017 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
536953 AAATGAGTTG
536963 TATGTTATTGTGATAAAAGGCATACTTT
1 TATGTTATTGTGATAAAAGGCATACTTT
*
536991 TATGTTATTGTGATATAAGGCATACTT
1 TATGTTATTGTGATAAAAGGCATACTT
537018 GGTGCCATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.31, C:0.07, G:0.18, T:0.44
Consensus pattern (28 bp):
TATGTTATTGTGATAAAAGGCATACTTT
Found at i:539539 original size:15 final size:17
Alignment explanation
Indices: 539519--539550 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
539509 AGATACTACG
539519 AATAAA-AAAAA-AAAA
1 AATAAAGAAAAACAAAA
539534 AATAAAGAAAAACAAAA
1 AATAAAGAAAAACAAAA
539551 CCAAGTAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 5 0.33
17 4 0.27
ACGTcount: A:0.88, C:0.03, G:0.03, T:0.06
Consensus pattern (17 bp):
AATAAAGAAAAACAAAA
Found at i:539872 original size:5 final size:5
Alignment explanation
Indices: 539864--539950 Score: 51
Period size: 5 Copynumber: 17.6 Consensus size: 5
539854 AAAAAATCAT
* * *
539864 AAATA AAATAA TAAATA AAAGA AAAT- AAA-A AAATGA AAAAA AAATG
1 AAATA AAAT-A -AAATA AAATA AAATA AAATA AAAT-A AAATA AAATA
*
539910 AAATA AAGGAT- AAATA AAAT- -AATA AAAT- AAATG AAATA AAA
1 AAATA AA--ATA AAATA AAATA AAATA AAATA AAATA AAATA AAA
539951 ACTAAGAAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 22
0.69 0.08 0.24
Matches are distributed among these distances:
3 3 0.05
4 12 0.19
5 35 0.55
6 8 0.12
7 6 0.09
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (5 bp):
AAATA
Found at i:539877 original size:12 final size:12
Alignment explanation
Indices: 539856--539940 Score: 63
Period size: 12 Copynumber: 7.2 Consensus size: 12
539846 ATAAAAGAAA
*
539856 AAAATCATAAAT
1 AAAATAATAAAT
539868 AAAATAATAAAT
1 AAAATAATAAAT
*
539880 AAAA-GA-AAAT
1 AAAATAATAAAT
*
539890 AAAAAAATGAAA-
1 AAAATAAT-AAAT
539902 AAAA-AATGAAAT
1 AAAATAAT-AAAT
**
539914 -AAAGGATAAAT
1 AAAATAATAAAT
539925 AAAATAATAAAAT
1 AAAATAAT-AAAT
539938 AAA
1 AAA
539941 TGAAATAAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
10 8 0.13
11 16 0.27
12 26 0.43
13 10 0.17
ACGTcount: A:0.75, C:0.01, G:0.06, T:0.18
Consensus pattern (12 bp):
AAAATAATAAAT
Found at i:539890 original size:58 final size:58
Alignment explanation
Indices: 539827--539951 Score: 148
Period size: 57 Copynumber: 2.2 Consensus size: 58
539817 GAGAAAACAT
* * *
539827 AAAATAGAAAAACGAATATATAAAA-GAAAAAAATCATAAATAAAATAAT-AAATAAAAG
1 AAAATAAAAAAACGAA-A-AAAAAATGAAAAAAAGCATAAATAAAATAATAAAATAAAAG
* * * *
539885 AAAATAAAAAAATGAAAAAAAAATGAAATAAAGGATAAATAAAATAATAAAATAAATG
1 AAAATAAAAAAACGAAAAAAAAATGAAAAAAAGCATAAATAAAATAATAAAATAAAAG
539943 -AAATAAAAA
1 AAAATAAAAA
539952 CTAAGAAAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
56 5 0.09
57 31 0.53
58 22 0.38
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.17
Consensus pattern (58 bp):
AAAATAAAAAAACGAAAAAAAAATGAAAAAAAGCATAAATAAAATAATAAAATAAAAG
Found at i:539941 original size:12 final size:11
Alignment explanation
Indices: 539862--539940 Score: 63
Period size: 11 Copynumber: 6.8 Consensus size: 11
539852 GAAAAAAATC
539862 ATAAATAAAATA
1 ATAAATAAAA-A
*
539874 ATAAATAAAAG
1 ATAAATAAAAA
539885 A-AAATAAAAAA
1 ATAAAT-AAAAA
539896 ATGAAA-AAAAA
1 AT-AAATAAAAA
**
539907 ATGAAATAAAGG
1 AT-AAATAAAAA
539919 ATAAATAAAATA
1 ATAAATAAAA-A
539931 ATAAAATAAA
1 AT-AAATAAA
539941 TGAAATAAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
10 4 0.07
11 24 0.44
12 17 0.31
13 10 0.18
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (11 bp):
ATAAATAAAAA
Found at i:539945 original size:33 final size:32
Alignment explanation
Indices: 539846--539950 Score: 108
Period size: 33 Copynumber: 3.2 Consensus size: 32
539836 AAACGAATAT
539846 ATAAAAGAAAA-AAATCATAAATAAAAT-AAT-AA
1 ATAAAAGAAAATAAA--A-AAATAAAATAAATGAA
*
539878 ATAAAAGAAAATAAAAAAATGAAAAAAAAATGAA
1 ATAAAAGAAAATAAAAAAAT--AAAATAAATGAA
* *
539912 ATAAAGGATAAATAAAATAATAAAATAAATGAA
1 ATAAAAGA-AAATAAAAAAATAAAATAAATGAA
539945 ATAAAA
1 ATAAAA
539951 ACTAAGAAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
30 4 0.06
31 1 0.02
32 15 0.24
33 22 0.35
34 9 0.15
35 11 0.18
ACGTcount: A:0.75, C:0.01, G:0.07, T:0.17
Consensus pattern (32 bp):
ATAAAAGAAAATAAAAAAATAAAATAAATGAA
Found at i:540002 original size:1 final size:1
Alignment explanation
Indices: 539996--540213 Score: 76
Period size: 1 Copynumber: 218.0 Consensus size: 1
539986 AAGAACTACC
* * * * * * * * * *
539996 AAAAAAAAAAAAAATAAAAAGAAAAAATAAAACAATAAGACAAAAAAATACAAAAAAAAAAAATA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
** * * * * * * * ** * * * * *
540061 AAAATTAACACAACAACACAAAAAAACAAAAAAAAAGAACGAATAAAACAAAAAACACAAATAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * * * * * *
540126 ACAAAAATACAAACAAAAAACAAAAAAAAATAAAAAACAAAACAAAAAAATAAAAAAAAATAAAG
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
540191 CAAAATAAAAAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAA
540214 CAAGAAACCC
Statistics
Matches: 141, Mismatches: 76, Indels: 0
0.65 0.35 0.00
Matches are distributed among these distances:
1 141 1.00
ACGTcount: A:0.82, C:0.09, G:0.03, T:0.06
Consensus pattern (1 bp):
A
Found at i:540040 original size:41 final size:38
Alignment explanation
Indices: 539995--540220 Score: 161
Period size: 39 Copynumber: 5.6 Consensus size: 38
539985 AAAGAACTAC
539995 CAAAAAAAAAAAAAATAAAAAGAAAAAATAAAACAATAAGA
1 CAAAAAAAAAAAAAA-AAAAAGAAAAAATAAAACAA-AA-A
* *
540036 CAAAAAAATACAAAAAAAAAAA-ATAAAAATTAACACAACAA
1 CAAAAAAA-A-AAAAAAAAAAAGA-AAAAA-TAAAACAAAAA
* * **
540077 CACAAAAAAACAAAAAAAAAGAACGAATAAAACAAAAAA
1 CAAAAAAAAAAAAAAAAAAAGAAAAAATAAAAC-AAAAA
* * * *
540116 CACAAATAAAACAAAAATACAAACAAAAAACAAAA-AAAAA
1 CA-AAA-AAAA-AAAAAAAAAAAGAAAAAATAAAACAAAAA
* * *
540156 TAAAAAACAAAACAAAAAAATAAAAAAAAATAAAGCAAAATA
1 CAAAAAA-AAAA-AAAAAAA-AAGAAAAAATAAAACAAAA-A
* *
540198 -AAAAAAAAAGAAAAAACAAGAAA
1 CAAAAAAAAAAAAAAAAAAAGAAA
540221 CCCCCCCCCC
Statistics
Matches: 146, Mismatches: 25, Indels: 31
0.72 0.12 0.15
Matches are distributed among these distances:
38 14 0.10
39 35 0.24
40 24 0.16
41 31 0.21
42 29 0.20
43 13 0.09
ACGTcount: A:0.81, C:0.10, G:0.03, T:0.06
Consensus pattern (38 bp):
CAAAAAAAAAAAAAAAAAAAGAAAAAATAAAACAAAAA
Found at i:540112 original size:30 final size:27
Alignment explanation
Indices: 539997--540205 Score: 110
Period size: 28 Copynumber: 7.5 Consensus size: 27
539987 AGAACTACCA
*
539997 AAAAAAAAAAAAATAAAA-AGAAAAAAT
1 AAAAAAAAAAAAATAAAACA-AAAAAAC
540024 AAAACAATAAGACAAAA-AAATAC-AAAAAA-
1 AAAA-AA-AA-A-AAAATAAA-ACAAAAAAAC
* * * * *
540053 AAAAAATAAAAATTAACACAACAACAC
1 AAAAAAAAAAAAATAAAACAAAAAAAC
* *
540080 AAAAAAACAAAAAAAAAGAACGAATAAAAC
1 AAAAAAA-AAAAAATAA-AAC-AAAAAAAC
* * *
540110 -AAAAAACACAAATAAAACAAAAATAC
1 AAAAAAAAAAAAATAAAACAAAAAAAC
540136 AAACAAAAAACAAAA-AAAA-ATAAAAAAC
1 AAA-AAAAAA-AAAATAAAACA-AAAAAAC
* *
540164 -AAAACAAAAAAATAAAAAAAAATAAAGC
1 AAAAAAAAAAAAATAAAACAAAA-AAA-C
540192 AAAATAAAAAAAAA
1 AAAA-AAAAAAAAA
540206 AGAAAAAACA
Statistics
Matches: 139, Mismatches: 21, Indels: 41
0.69 0.10 0.20
Matches are distributed among these distances:
25 9 0.06
26 25 0.18
27 23 0.17
28 33 0.24
29 20 0.14
30 24 0.17
31 5 0.04
ACGTcount: A:0.81, C:0.10, G:0.02, T:0.07
Consensus pattern (27 bp):
AAAAAAAAAAAAATAAAACAAAAAAAC
Found at i:540212 original size:30 final size:30
Alignment explanation
Indices: 539996--540213 Score: 130
Period size: 30 Copynumber: 7.1 Consensus size: 30
539986 AAGAACTACC
*
539996 AAAAAAA-AAA-AAAATAAAAAGAAAAA-AT
1 AAAAAAATAAACAAAATAAAAA-AAAAACAA
* * *
540024 AAAACAATAAGACAAAAAAATACAAAAAAAAAA
1 AAAAAAATAA-ACAAAATAA-A-AAAAAAACAA
* * *
540057 AATAAAAATTAACACAACAACACAAAAAAACAA
1 AA-AAAAATAAACAAAATAA-A-AAAAAAACAA
* * *
540090 AAAAAAA-GAAC-GAATAAAACAAAAAACAC
1 AAAAAAATAAACAAAATAAAA-AAAAAACAA
* *
540119 AAATAAA-ACA-AAAATACAAACAAAAAACAA
1 AAAAAAATAAACAAAATA-AAA-AAAAAACAA
*
540149 AAAAAAATAAA-AAACA-AAACAAAAAAATAA
1 AAAAAAATAAACAAA-ATAAA-AAAAAAACAA
*
540179 AAAAAAATAAAGCAAAATAAAAAAAAAAGAA
1 AAAAAAATAAA-CAAAATAAAAAAAAAACAA
540210 AAAA
1 AAAA
540214 CAAGAAACCC
Statistics
Matches: 152, Mismatches: 22, Indels: 29
0.75 0.11 0.14
Matches are distributed among these distances:
28 7 0.05
29 22 0.14
30 44 0.29
31 30 0.20
32 18 0.12
33 25 0.16
34 6 0.04
ACGTcount: A:0.82, C:0.09, G:0.03, T:0.06
Consensus pattern (30 bp):
AAAAAAATAAACAAAATAAAAAAAAAACAA
Found at i:540301 original size:19 final size:19
Alignment explanation
Indices: 540260--540301 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
540250 ACAAAGAAGT
*
540260 AAAACCATAAAACAACCAC
1 AAAACCATAAAACAACCAA
*
540279 AAAACACATACAAC-ACCAA
1 AAAAC-CATAAAACAACCAA
540298 AAAA
1 AAAA
540302 AAAAAAACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.67, C:0.29, G:0.00, T:0.05
Consensus pattern (19 bp):
AAAACCATAAAACAACCAA
Found at i:540385 original size:1 final size:1
Alignment explanation
Indices: 540381--540422 Score: 66
Period size: 1 Copynumber: 42.0 Consensus size: 1
540371 CCCCCCATAA
* *
540381 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCGCCCCCACCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
540423 ACAATATATA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.02, C:0.95, G:0.02, T:0.00
Consensus pattern (1 bp):
C
Found at i:540899 original size:14 final size:13
Alignment explanation
Indices: 540859--540907 Score: 55
Period size: 13 Copynumber: 3.6 Consensus size: 13
540849 ACAAAACTTC
540859 AAAAAAAA-AAAA
1 AAAAAAAACAAAA
*
540871 TAAAAAAACAAAA
1 AAAAAAAACAAAA
540884 AAAAAAAAGCATAAA
1 AAAAAAAA-CA-AAA
540899 AAAACAAAA
1 AAAA-AAAA
540908 AACTCAAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
12 7 0.23
13 11 0.35
14 2 0.06
15 7 0.23
16 4 0.13
ACGTcount: A:0.88, C:0.06, G:0.02, T:0.04
Consensus pattern (13 bp):
AAAAAAAACAAAA
Found at i:540916 original size:24 final size:24
Alignment explanation
Indices: 540859--540909 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
540849 ACAAAACTTC
540859 AAAAAAAAAAA--ATAAAAAAACA
1 AAAAAAAAAAAGCATAAAAAAACA
540881 AAAAAAAAAAAGCATAAAAAAACA
1 AAAAAAAAAAAGCATAAAAAAACA
540905 AAAAA
1 AAAAA
540910 CTCAAAGTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 11 0.41
24 16 0.59
ACGTcount: A:0.88, C:0.06, G:0.02, T:0.04
Consensus pattern (24 bp):
AAAAAAAAAAAGCATAAAAAAACA
Done.