Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold932
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: 54414
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Found at i:142 original size:68 final size:67
Alignment explanation
Indices: 1--143 Score: 171
Period size: 67 Copynumber: 2.1 Consensus size: 67
* * * * *
1 CATGATGGTGATTAGACTTGTGAAGTCTCGAGTTGATGGAAAGACTTGGCATCACTAAATGTGAT
1 CATGGTGGTGATCAGACTTATGAAGTCTCAAGTTAATGGAAAGACTTGGCATCACTAAATGTGAT
*
66 GC
66 AC
* * *
68 CATGGTGGTGATCAGACTTATGAAGTC-CTAATTTAATGGAAATGACTTGGCATCAGTGAATGTG
1 CATGGTGGTGATCAGACTTATGAAGTCTC-AAGTTAATGGAAA-GACTTGGCATCACTAAATGTG
*
132 ATAT
64 ATAC
136 CATGGTGG
1 CATGGTGG
144 CAATTAGACA
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
66 1 0.02
67 34 0.53
68 29 0.45
ACGTcount: A:0.29, C:0.13, G:0.28, T:0.31
Consensus pattern (67 bp):
CATGGTGGTGATCAGACTTATGAAGTCTCAAGTTAATGGAAAGACTTGGCATCACTAAATGTGAT
AC
Found at i:162 original size:68 final size:68
Alignment explanation
Indices: 36--185 Score: 167
Period size: 68 Copynumber: 2.2 Consensus size: 68
26 TCTCGAGTTG
* ** * *
36 ATGGAAA-GACTTGGCATCACTAAATGTGATGCCATGGTGGTGATCAGACTTATGAAGTCCTAAT
1 ATGGAAATGACTTGGCATCACTAAATGTGATACCATGGTGGCAATCAGACATATAAAGTCCTAAT
*
100 TTA
66 ATA
* * * * * *
103 ATGGAAATGACTTGGCATCAGTGAATGTGATATCATGGTGGCAATTAGACATGTAAAGTCTTAAT
1 ATGGAAATGACTTGGCATCACTAAATGTGATACCATGGTGGCAATCAGACATATAAAGTCCTAAT
*
168 ATG
66 ATA
*
171 ATGGAAGTGACTTGG
1 ATGGAAATGACTTGG
186 TGTCACTGAG
Statistics
Matches: 68, Mismatches: 14, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
67 7 0.10
68 61 0.90
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (68 bp):
ATGGAAATGACTTGGCATCACTAAATGTGATACCATGGTGGCAATCAGACATATAAAGTCCTAAT
ATA
Found at i:7030 original size:21 final size:21
Alignment explanation
Indices: 7006--7056 Score: 84
Period size: 22 Copynumber: 2.4 Consensus size: 21
6996 AATCAATCAA
*
7006 ATAAAGAGCAGGAGAAATTTG
1 ATAAAAAGCAGGAGAAATTTG
7027 ATAAAAAAGCAGGAGAAATTTG
1 AT-AAAAAGCAGGAGAAATTTG
7049 ATAAAAAG
1 ATAAAAAG
7057 ATGAGAGTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 8 0.29
22 20 0.71
ACGTcount: A:0.55, C:0.04, G:0.24, T:0.18
Consensus pattern (21 bp):
ATAAAAAGCAGGAGAAATTTG
Found at i:7038 original size:22 final size:22
Alignment explanation
Indices: 7012--7055 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
7002 TCAAATAAAG
7012 AGCAGGAGAAATTTGATAAAAA
1 AGCAGGAGAAATTTGATAAAAA
7034 AGCAGGAGAAATTTGATAAAAA
1 AGCAGGAGAAATTTGATAAAAA
7056 GATGAGAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.55, C:0.05, G:0.23, T:0.18
Consensus pattern (22 bp):
AGCAGGAGAAATTTGATAAAAA
Found at i:7393 original size:12 final size:12
Alignment explanation
Indices: 7378--7433 Score: 58
Period size: 12 Copynumber: 4.4 Consensus size: 12
7368 GAATTTAAAA
7378 ATATATTTTAAT
1 ATATATTTTAAT
*
7390 ATATATATTTAAAAA
1 ATATAT-TTT--AAT
7405 ATATATTTTAAT
1 ATATATTTTAAT
**
7417 ATATATTAAAAT
1 ATATATTTTAAT
7429 ATATA
1 ATATA
7434 AATATAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
12 23 0.62
13 3 0.08
14 3 0.08
15 8 0.22
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATATATTTTAAT
Found at i:7397 original size:14 final size:14
Alignment explanation
Indices: 7378--7422 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
7368 GAATTTAAAA
7378 ATATATTTTAATAT
1 ATATATTTTAATAT
* *
7392 ATATA-TTTAAAAA
1 ATATATTTTAATAT
7405 ATATATTTTAATAT
1 ATATATTTTAATAT
7419 ATAT
1 ATAT
7423 TAAAATATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
13 11 0.42
14 15 0.58
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
ATATATTTTAATAT
Found at i:7404 original size:27 final size:26
Alignment explanation
Indices: 7370--7422 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 26
7360 TTTTACTTGA
7370 ATTTAAAAATATATTTTAATATATAT
1 ATTTAAAAATATATTTTAATATATAT
7396 ATTTAAAAAATATATTTTAATATATAT
1 ATTT-AAAAATATATTTTAATATATAT
7423 TAAAATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 4 0.15
27 22 0.85
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
ATTTAAAAATATATTTTAATATATAT
Found at i:10298 original size:26 final size:27
Alignment explanation
Indices: 10269--10320 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
10259 ATTTTAAAAA
*
10269 AATTTAAAAAAT-TTAATTATTTATTT
1 AATTTAAAAAATATTAAATATTTATTT
*
10295 AATTTAAAAATTATTAAATATTTATT
1 AATTTAAAAAATATTAAATATTTATT
10321 AAAAAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
AATTTAAAAAATATTAAATATTTATTT
Found at i:13364 original size:16 final size:16
Alignment explanation
Indices: 13321--13378 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
13311 AAATTTACAT
*
13321 ATAATTTTTGTTCAAA
1 ATAATTTTTATTCAAA
* * *
13337 ACAACTTATATTCAAA
1 ATAATTTTTATTCAAA
* *
13353 ATAATTTTTATTTATA
1 ATAATTTTTATTCAAA
13369 ATAATTTTTA
1 ATAATTTTTA
13379 CAAAAAAAAA
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (16 bp):
ATAATTTTTATTCAAA
Found at i:22454 original size:2 final size:2
Alignment explanation
Indices: 22447--22488 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
22437 CTGCCGCTGC
22447 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22489 GTAGTATTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22558 original size:1 final size:1
Alignment explanation
Indices: 22552--22586 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
22542 CGTTACCCGA
22552 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
22587 TACCCCAGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:22808 original size:2 final size:2
Alignment explanation
Indices: 22788--22840 Score: 79
Period size: 2 Copynumber: 26.5 Consensus size: 2
22778 CCTCTCCCTT
* * *
22788 TC TC TC TG TC TA TC CC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
22830 TC TC TC TC TC T
1 TC TC TC TC TC T
22841 TTCATCCGAC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.02, C:0.47, G:0.02, T:0.49
Consensus pattern (2 bp):
TC
Found at i:25540 original size:17 final size:17
Alignment explanation
Indices: 25518--25555 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
25508 AAAAAATCAT
*
25518 AAAAAAATAC-ATTTTA
1 AAAAAAATACTATTCTA
25534 AAAAAAATACTATTCTA
1 AAAAAAATACTATTCTA
25551 AAAAA
1 AAAAA
25556 GCTATTTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAAAAATACTATTCTA
Found at i:25584 original size:3 final size:3
Alignment explanation
Indices: 25576--25601 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
25566 AAATTAAAAA
25576 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
25602 AAAAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:26022 original size:20 final size:20
Alignment explanation
Indices: 25999--26037 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
25989 TTAGTTTAAT
25999 TATAAAAATATTAATATTTG
1 TATAAAAATATTAATATTTG
* *
26019 TATAAAATTTTTAATATTT
1 TATAAAAATATTAATATTT
26038 TTTAAATAGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (20 bp):
TATAAAAATATTAATATTTG
Found at i:30479 original size:13 final size:13
Alignment explanation
Indices: 30461--30501 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
30451 TACAAAACTT
30461 ATGTATCGATACA
1 ATGTATCGATACA
*
30474 ATGTATCGATATA
1 ATGTATCGATACA
* *
30487 TTATATCGATACA
1 ATGTATCGATACA
30500 AT
1 AT
30502 TTGTATAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:31217 original size:13 final size:13
Alignment explanation
Indices: 31199--31225 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
31189 TTAATTTTAG
31199 ATATGATATAATT
1 ATATGATATAATT
31212 ATATGATATAATT
1 ATATGATATAATT
31225 A
1 A
31226 CATAATAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (13 bp):
ATATGATATAATT
Found at i:31853 original size:14 final size:14
Alignment explanation
Indices: 31830--31861 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
31820 TGATAATTAA
31830 ATAT-TTTAATATT
1 ATATATTTAATATT
31843 ATATATTTAATATT
1 ATATATTTAATATT
31857 ATATA
1 ATATA
31862 AAAATATACT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
ATATATTTAATATT
Found at i:31912 original size:37 final size:35
Alignment explanation
Indices: 31828--31912 Score: 93
Period size: 35 Copynumber: 2.4 Consensus size: 35
31818 TATGATAATT
* *
31828 AAATAT-TTTAATATTATATATTTAATATTATATAA
1 AAATATATTTAA-ATTATATATTTAAAATTAAATAA
*
31863 AAATATACTTAAATTATAT-TTTAAAATATAAATATA
1 AAATATATTTAAATTATATATTTAAAAT-TAAATA-A
31899 AAATATTATTTAAA
1 AAATA-TATTTAAA
31913 ACCCTTCAGT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
34 7 0.17
35 18 0.43
36 10 0.24
37 7 0.17
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (35 bp):
AAATATATTTAAATTATATATTTAAAATTAAATAA
Found at i:34619 original size:2 final size:2
Alignment explanation
Indices: 34612--34636 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
34602 GAACTTTTTA
34612 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
34637 ATTTAAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35375 original size:20 final size:20
Alignment explanation
Indices: 35335--35453 Score: 91
Period size: 19 Copynumber: 5.8 Consensus size: 20
35325 ATAATAAATT
35335 TAATAATAT-AAATAAAAAA
1 TAATAATATAAAATAAAAAA
* *
35354 TAATAATATAAAATTAACAA
1 TAATAATATAAAATAAAAAA
35374 TAATAATAT-AAATAAAAATA
1 TAATAATATAAAATAAAAA-A
* * *
35394 TTAACATTATAATAATATAAAAT
1 -TAATAATATAA-AATA-AAAAA
* * *
35417 TAAGAATA-CAAATAAAAAT
1 TAATAATATAAAATAAAAAA
*
35436 TAATAACATTAAAATAAA
1 TAATAATA-TAAAATAAA
35454 TTTAATAAAA
Statistics
Matches: 79, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
19 27 0.34
20 22 0.28
21 15 0.19
22 7 0.09
23 4 0.05
24 4 0.05
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.29
Consensus pattern (20 bp):
TAATAATATAAAATAAAAAA
Found at i:35405 original size:29 final size:26
Alignment explanation
Indices: 35358--35414 Score: 78
Period size: 29 Copynumber: 2.1 Consensus size: 26
35348 AAAAAATAAT
*
35358 AATATAAAATTAACAATAATAATATA
1 AATAAAAAATTAACAATAATAATATA
35384 AATAAAAATATTAACATTATAATAATATA
1 AATAAAAA-ATTAACA--ATAATAATATA
35413 AA
1 AA
35415 ATTAAGAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 7 0.26
27 7 0.26
29 13 0.48
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.32
Consensus pattern (26 bp):
AATAAAAAATTAACAATAATAATATA
Found at i:35991 original size:2 final size:2
Alignment explanation
Indices: 35984--36008 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
35974 CCTTGTTTTG
35984 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
36009 GAGAGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:36013 original size:2 final size:2
Alignment explanation
Indices: 36008--36033 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
35998 ATATATATAT
36008 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
36034 GGAGGTCCCT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:36624 original size:2 final size:2
Alignment explanation
Indices: 36617--36658 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
36607 TGGAACTAGA
* *
36617 AT AT AT AT AT AT AT AT AA AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36659 TTTCGAAACC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:37068 original size:2 final size:2
Alignment explanation
Indices: 37063--37101 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
37053 AATGTGTGTG
37063 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
37102 TAAACACTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:37803 original size:17 final size:17
Alignment explanation
Indices: 37771--37821 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
37761 AAAAATAATT
37771 AAAATATAATATTATATAA
1 AAAATATAA-A-TATATAA
37790 AAAATATAAATATA-AA
1 AAAATATAAATATATAA
* *
37806 ATGAATATAAAAATAT
1 A-AAATATAAATATAT
37822 TTTAAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
16 3 0.11
17 15 0.54
18 1 0.04
19 9 0.32
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (17 bp):
AAAATATAAATATATAA
Found at i:37804 original size:15 final size:16
Alignment explanation
Indices: 37784--37816 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
37774 ATATAATATT
37784 ATATAAAA-AATATAA
1 ATATAAAAGAATATAA
37799 ATATAAAATGAATATAA
1 ATATAAAA-GAATATAA
37816 A
1 A
37817 AATATTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
17 8 0.50
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (16 bp):
ATATAAAAGAATATAA
Found at i:38528 original size:2 final size:2
Alignment explanation
Indices: 38521--38556 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
38511 ATAGCTCCAT
38521 TA TA TA TA TA 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 TA TA TA TA TA
38557 AATACGTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39594 original size:19 final size:19
Alignment explanation
Indices: 39567--39604 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
39557 TATATAGTAA
39567 TTTTATTAAAAAATTATTT
1 TTTTATTAAAAAATTATTT
* *
39586 TTTTCTTAAATAATTATTT
1 TTTTATTAAAAAATTATTT
39605 ACTTTTCCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTTATTAAAAAATTATTT
Found at i:42866 original size:2 final size:2
Alignment explanation
Indices: 42859--42901 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
42849 GAAAGCTATT
42859 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
42901 T
1 T
42902 GTTTGTCTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:44395 original size:39 final size:39
Alignment explanation
Indices: 44352--44426 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
44342 TGAACAATCA
* *
44352 TAGGAAGATTCAAGCTCGTTATTAGAAGTATCCATGGCT
1 TAGGAAGATTCAAGCTCATTATCAGAAGTATCCATGGCT
*
44391 TAGGAAGATTCAAGCTCATTATCAGATGTATCCATG
1 TAGGAAGATTCAAGCTCATTATCAGAAGTATCCATG
44427 ATCTAAGCCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (39 bp):
TAGGAAGATTCAAGCTCATTATCAGAAGTATCCATGGCT
Found at i:50586 original size:2 final size:2
Alignment explanation
Indices: 50579--50608 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
50569 CTAAGAGGAG
50579 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
50609 GCAGTAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52772 original size:18 final size:18
Alignment explanation
Indices: 52751--52793 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
52741 TTTTTTAGTT
*
52751 TTTTTAATTATTTTATAG
1 TTTTTAATTATTTTAAAG
* * *
52769 TTTTTAGTTTTTTTAAAT
1 TTTTTAATTATTTTAAAG
52787 TTTTTAA
1 TTTTTAA
52794 GTATGTTTTT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.70
Consensus pattern (18 bp):
TTTTTAATTATTTTAAAG
Found at i:52938 original size:19 final size:19
Alignment explanation
Indices: 52914--52957 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
52904 GATCTGATAA
*
52914 TTTTTTAATTTTATTTTAT
1 TTTTTTAATTTTATATTAT
52933 TTTTTTAATTTTATATTAT
1 TTTTTTAATTTTATATTAT
52952 TTTTTT
1 TTTTTT
52958 GTTAAGTCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTTTAATTTTATATTAT
Found at i:53517 original size:16 final size:17
Alignment explanation
Indices: 53488--53527 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
53478 TACTTAACAA
53488 AAAAAATAATGTAAAAC
1 AAAAAATAATGTAAAAC
53505 TAAAAAA-AA-GTAAAAC
1 -AAAAAATAATGTAAAAC
53521 AAAAAAT
1 AAAAAAT
53528 TTATAAGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 6 0.29
16 7 0.33
17 2 0.10
18 6 0.29
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.15
Consensus pattern (17 bp):
AAAAAATAATGTAAAAC
Found at i:54165 original size:17 final size:17
Alignment explanation
Indices: 54145--54297 Score: 71
Period size: 17 Copynumber: 8.6 Consensus size: 17
54135 GAAAATTTTA
54145 AAAAATAAAAAAATTAT
1 AAAAATAAAAAAATTAT
***
54162 AAAAATTGTAAAA-TAT
1 AAAAATAAAAAAATTAT
* *
54178 AAAATTATAAAAATTAT
1 AAAAATAAAAAAATTAT
*
54195 -AAAATATAAAAATCTAT
1 AAAAATAAAAAAAT-TAT
* *
54212 AAATTATAAAAATTCAA-AAGT
1 AAA-AATAAAAA---AATTA-T
54233 AAAATTTATAAAAAAATCTAT
1 AAAA---ATAAAAAAAT-TAT
* *
54254 AAAATTAAAAAAATTTT
1 AAAAATAAAAAAATTAT
* *
54271 AAAATTATAGAAAATTAT
1 AAAAATA-AAAAAATTAT
54289 -AAAATAAAA
1 AAAAATAAAA
54298 TTCAAAAAAT
Statistics
Matches: 103, Mismatches: 19, Indels: 29
0.68 0.13 0.19
Matches are distributed among these distances:
16 26 0.25
17 30 0.29
18 19 0.18
19 6 0.06
20 3 0.03
21 9 0.09
22 3 0.03
23 7 0.07
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (17 bp):
AAAAATAAAAAAATTAT
Found at i:54182 original size:7 final size:8
Alignment explanation
Indices: 54154--54316 Score: 90
Period size: 9 Copynumber: 19.8 Consensus size: 8
54144 AAAAAATAAA
54154 AAAATTAT
1 AAAATTAT
*
54162 AAAAATTGT
1 -AAAATTAT
54171 AAAA-TAT
1 AAAATTAT
54178 AAAATTAT
1 AAAATTAT
54186 AAAAATTAT
1 -AAAATTAT
54195 AAAA-TAT
1 AAAATTAT
54202 AAAAATCTAT
1 -AAAAT-TAT
54212 -AAATTAT
1 AAAATTAT
*
54219 AAAAATT-C
1 -AAAATTAT
*
54227 AAAAGTA-
1 AAAATTAT
*
54234 AAATTTAT
1 AAAATTAT
54242 AAAAAAATCTAT
1 ---AAAAT-TAT
*
54254 AAAATTAAA
1 AAAATT-AT
*
54263 AAAATTTT
1 AAAATTAT
54271 AAAATTAT
1 AAAATTAT
54279 AGAAAATTAT
1 --AAAATTAT
54289 -AAA--AT
1 AAAATTAT
*
54294 AAAATTCAA
1 AAAATT-AT
54303 AAAATTAT
1 AAAATTAT
54311 AAAATT
1 AAAATT
54317 TTTTATTTTC
Statistics
Matches: 121, Mismatches: 13, Indels: 41
0.69 0.07 0.23
Matches are distributed among these distances:
5 2 0.02
6 3 0.02
7 25 0.21
8 34 0.28
9 39 0.32
10 11 0.09
11 4 0.03
12 3 0.02
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (8 bp):
AAAATTAT
Found at i:54186 original size:24 final size:25
Alignment explanation
Indices: 54146--54292 Score: 108
Period size: 24 Copynumber: 5.8 Consensus size: 25
54136 AAAATTTTAA
* *
54146 AAAATAAAAAAATTATAAAAATTGT
1 AAAATATAAAAATTATAAAAATTAT
54171 AAAATAT-AAAATTATAAAAATTAT
1 AAAATATAAAAATTATAAAAATTAT
54195 AAAATATAAAAATCTAT--AAATTAT
1 AAAATATAAAAAT-TATAAAAATTAT
* * *
54219 AAAA-ATTCAAAA--GTAAAATTTAT
1 AAAATA-TAAAAATTATAAAAATTAT
* * *
54242 AAAAAAATCTATAAAATTAAAAAAATTTT
1 ---AAAATATA-AAAATTATAAAAATTAT
54271 AAAATTATAGAAAATTATAAAA
1 AAAA-TATA-AAAATTATAAAA
54293 TAAAATTCAA
Statistics
Matches: 95, Mismatches: 14, Indels: 24
0.71 0.11 0.18
Matches are distributed among these distances:
21 1 0.01
23 7 0.07
24 39 0.41
25 11 0.12
26 12 0.13
27 18 0.19
29 7 0.07
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (25 bp):
AAAATATAAAAATTATAAAAATTAT
Found at i:54195 original size:33 final size:33
Alignment explanation
Indices: 54153--54225 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 33
54143 TAAAAAATAA
*
54153 AAAAATTATAAAA-ATTGTAAAATATA-AAATTAT
1 AAAAATTATAAAATA-T-AAAAATATATAAATTAT
*
54186 AAAAATTATAAAATATAAAAATCTATAAATTAT
1 AAAAATTATAAAATATAAAAATATATAAATTAT
54219 AAAAATT
1 AAAAATT
54226 CAAAAGTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
32 7 0.19
33 28 0.78
34 1 0.03
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (33 bp):
AAAAATTATAAAATATAAAAATATATAAATTAT
Found at i:54314 original size:9 final size:9
Alignment explanation
Indices: 54136--54292 Score: 98
Period size: 9 Copynumber: 17.3 Consensus size: 9
54126 TTCAAATTTG
*
54136 AAAATTTTA
1 AAAATTATA
* *
54145 AAAAATAAA
1 AAAATTATA
54154 AAAATTATA
1 AAAATTATA
*
54163 AAAATTGT-
1 AAAATTATA
54171 AAAA-TAT-
1 AAAATTATA
54178 AAAATTATA
1 AAAATTATA
54187 AAAATTAT-
1 AAAATTATA
54195 AAAA-TATA
1 AAAATTATA
54203 AAAATCTAT-
1 AAAAT-TATA
54212 -AAATTATA
1 AAAATTATA
54220 AAAATTCAAAAGTA
1 AAAATT----A-TA
*
54234 AAATTTATAAA
1 AAAATTAT--A
54245 AAAATCTAT-
1 AAAAT-TATA
*
54254 AAAATTAAA
1 AAAATTATA
*
54263 AAAATT-TT
1 AAAATTATA
54271 AAAATTATA
1 AAAATTATA
54280 GAAAATTATA
1 -AAAATTATA
54290 AAA
1 AAA
54293 TAAAATTCAA
Statistics
Matches: 117, Mismatches: 13, Indels: 36
0.70 0.08 0.22
Matches are distributed among these distances:
7 12 0.10
8 27 0.23
9 49 0.42
10 13 0.11
11 5 0.04
12 3 0.03
13 1 0.01
14 7 0.06
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (9 bp):
AAAATTATA
Found at i:54334 original size:16 final size:15
Alignment explanation
Indices: 54313--54374 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 15
54303 AAAATTATAA
54313 AATTTTTTATTTTCTT
1 AATTTTTTATTTTC-T
* *
54329 AATTTTATACATTTTAT
1 AATTTT-T-TATTTTCT
*
54346 AATTTTTTAATTTTCA
1 AATTTTTT-ATTTTCT
54362 AACTTTTTTATTT
1 AA-TTTTTTATTT
54375 ATATTTTTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
16 18 0.49
17 14 0.38
18 5 0.14
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.66
Consensus pattern (15 bp):
AATTTTTTATTTTCT
Found at i:54356 original size:8 final size:8
Alignment explanation
Indices: 54313--54359 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
54303 AAAATTATAA
54313 AATTTTTT
1 AATTTTTT
54321 -ATTTTCTT
1 AATTTT-TT
*
54329 AATTTTAT
1 AATTTTTT
*
54337 ACATTTTAT
1 A-ATTTTTT
54346 AATTTTTT
1 AATTTTTT
54354 AATTTT
1 AATTTT
54360 CAAACTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
7 5 0.15
8 16 0.47
9 13 0.38
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (8 bp):
AATTTTTT
Found at i:54377 original size:40 final size:39
Alignment explanation
Indices: 54332--54413 Score: 105
Period size: 41 Copynumber: 2.1 Consensus size: 39
54322 TTTTCTTAAT
54332 TTTATACATTTT-ATAATTTTTT-AATTTTCAAACTTTTTTA
1 TTTATACATTTTAATAATTTTTTGAA-TTTCAAA--TTTTTA
**
54372 TTTATATTTTTTAATAATTTTTTGAATTTCAAATTTTTA
1 TTTATACATTTTAATAATTTTTTGAATTTCAAATTTTTA
54411 TTT
1 TTT
54414 T
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
39 9 0.24
40 10 0.26
41 17 0.45
42 2 0.05
ACGTcount: A:0.29, C:0.05, G:0.01, T:0.65
Consensus pattern (39 bp):
TTTATACATTTTAATAATTTTTTGAATTTCAAATTTTTA
Done.