Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1373
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: 199800
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
File 2 of 2
Found at i:153443 original size:33 final size:33
Alignment explanation
Indices: 153406--153472 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
153396 TTCAACGATT
153406 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
153439 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
153472 T
1 T
153473 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:153444 original size:13 final size:13
Alignment explanation
Indices: 153426--153450 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
153416 CATAAAATGT
153426 TGTATCGATACAA
1 TGTATCGATACAA
153439 TGTATCGATACA
1 TGTATCGATACA
153451 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:153537 original size:13 final size:13
Alignment explanation
Indices: 153519--153545 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
153509 ATTACTCACA
153519 TGTATCGATACAT
1 TGTATCGATACAT
153532 TGTATCGATACAT
1 TGTATCGATACAT
153545 T
1 T
153546 TTATAATGTA
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:158917 original size:16 final size:18
Alignment explanation
Indices: 158892--158935 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 18
158882 TGATAATTTG
158892 TTTGAATGATTTTGT-ATT
1 TTTG-ATGATTTTGTGATT
158910 TTTG-TGA-TTTGTGATT
1 TTTGATGATTTTGTGATT
158926 TTTGATGATT
1 TTTGATGATT
158936 GTGTTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 5 0.22
16 10 0.43
17 3 0.13
18 5 0.22
ACGTcount: A:0.18, C:0.00, G:0.20, T:0.61
Consensus pattern (18 bp):
TTTGATGATTTTGTGATT
Found at i:158946 original size:17 final size:16
Alignment explanation
Indices: 158892--158951 Score: 50
Period size: 16 Copynumber: 3.6 Consensus size: 16
158882 TGATAATTTG
*
158892 TTTGAATGATTTTGTATT
1 TTTG-ATGATTGTGT-TT
*
158910 TTTG-TGATTTGTGATT
1 TTTGATGA-TTGTGTTT
158926 TTTGATGATTGTGTTT
1 TTTGATGATTGTGTTT
*
158942 ATTTGTTGAT
1 -TTTGATGAT
158952 AAATTTGATG
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
16 16 0.46
17 15 0.43
18 4 0.11
ACGTcount: A:0.17, C:0.00, G:0.22, T:0.62
Consensus pattern (16 bp):
TTTGATGATTGTGTTT
Found at i:160814 original size:16 final size:16
Alignment explanation
Indices: 160790--160829 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
160780 ACTTTTGTTC
**
160790 CTTTCCTTGTTTTTAA
1 CTTTCCTTGTACTTAA
*
160806 CTTTGCTTGTACTTAA
1 CTTTCCTTGTACTTAA
160822 CTTTCCTT
1 CTTTCCTT
160830 AATGAATGAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.12, C:0.23, G:0.07, T:0.57
Consensus pattern (16 bp):
CTTTCCTTGTACTTAA
Found at i:161057 original size:18 final size:18
Alignment explanation
Indices: 161036--161070 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
161026 TTGAGAAATT
*
161036 AACTTGTTTTATAAAAAG
1 AACTTGTTATATAAAAAG
161054 AACTTGTTATATAAAAA
1 AACTTGTTATATAAAAA
161071 AGGTGAGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.37
Consensus pattern (18 bp):
AACTTGTTATATAAAAAG
Found at i:161827 original size:13 final size:13
Alignment explanation
Indices: 161809--161833 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
161799 CATATTGTTT
161809 TGTATCGATACAG
1 TGTATCGATACAG
161822 TGTATCGATACA
1 TGTATCGATACA
161834 TGATCTTGGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:163715 original size:31 final size:31
Alignment explanation
Indices: 163674--163734 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
163664 CCTAAGGAAA
*
163674 TGTATTGATACATG-GGATAATGTATCGATAT
1 TGTATCGATACATGAGGA-AATGTATCGATAT
*
163705 TGTATCGATACATGAGGAATTGTATCGATA
1 TGTATCGATACATGAGGAAATGTATCGATA
163735 CATCATGTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 24 0.89
32 3 0.11
ACGTcount: A:0.33, C:0.08, G:0.23, T:0.36
Consensus pattern (31 bp):
TGTATCGATACATGAGGAAATGTATCGATAT
Found at i:168779 original size:18 final size:19
Alignment explanation
Indices: 168756--168796 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
168746 TTTGATGTTC
* *
168756 AATTGTGTTGTTTTAT-TG
1 AATTGTATTGTTTGATATG
168774 AATTGTATTGTTTGATATG
1 AATTGTATTGTTTGATATG
168793 AATT
1 AATT
168797 AGGATTGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.24, C:0.00, G:0.20, T:0.56
Consensus pattern (19 bp):
AATTGTATTGTTTGATATG
Found at i:171423 original size:20 final size:19
Alignment explanation
Indices: 171400--171450 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
171390 TATCCAGATT
*
171400 TATCGATACATCATGCTTTG
1 TATCGATACAT-ATGCATTG
* *
171420 TATCGATACATGTTCATTG
1 TATCGATACATATGCATTG
171439 TATCGATACATA
1 TATCGATACATA
171451 CTCAATTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (19 bp):
TATCGATACATATGCATTG
Found at i:171542 original size:33 final size:33
Alignment explanation
Indices: 171499--171561 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
171489 CTAAGTGAAA
*
171499 TGTATTGATACATG-GGACAATGTATCGATAGAT
1 TGTATCGATACATGAGGA-AATGTATCGATAGAT
*
171532 TGTATCGATACATGAGGAATTGTATCGATA
1 TGTATCGATACATGAGGAAATGTATCGATA
171562 TATCATGTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 24 0.89
34 3 0.11
ACGTcount: A:0.33, C:0.10, G:0.24, T:0.33
Consensus pattern (33 bp):
TGTATCGATACATGAGGAAATGTATCGATAGAT
Found at i:176102 original size:48 final size:48
Alignment explanation
Indices: 175881--176629 Score: 627
Period size: 48 Copynumber: 15.8 Consensus size: 48
175871 TAAAGAATGT
* * *
175881 CAATGTGCTGATTCACA-GTCAGTGACATTAGACTTAAAGATGAGAAGAATGC
1 CAATGTGCTGATTCA-AGGCCAGCGACATTGGACTTAAAGATGAG--G--TGC
* **
175933 CAATGTGCTGATTCAAGGCCAACGACATTGGGTTTTAAAGATGACGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATT-GGACTTAAAGAT---G-AGGTGC
* *
175986 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG-AGGTGC
*
176035 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGGTGC
* * * *
176083 CAATATGCTGATTCAAGGCCAGTGATATTGGGCTTAAAGATGGTTGAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGA----TGAGGTGC
* * * *
176135 CGATGTGCTGATTCAAGGCCAACGACATCGGTCTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG-AGGTGC
*
176184 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTAC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG-AGGTGC
* *
176233 CAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATGACGAAGGTAC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT---G-AGGTGC
* * * *
176285 CAATATGCTGATTCAAGGCTAGCGATATTGGGC-T-----T---GTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGGTGC
* * ** *
176324 CAATGTGTTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGT
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGGTGC
* * *
176372 CAATATGCTGATTCAAGGCCAGCGATATTGGGC-T-----T-A--TGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGGTGC
* * ** *
176411 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAGAGACAACGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGGTGC
* * * * ** *
176459 CAATATGCTGATTCAAGGCCAGCGACATTGGTCTCAGAGACAACGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGGTGC
* * * *
176507 CAATATGCTGATTCAAGGCTAGCGATATTGGGC-T-----T-A--TGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGGTGC
* * **
176546 CAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAGACAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGGTGC
* *
176594 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTA
176630 GAAAAAGGCA
Statistics
Matches: 584, Mismatches: 72, Indels: 86
0.79 0.10 0.12
Matches are distributed among these distances:
39 94 0.16
40 3 0.01
41 2 0.00
46 3 0.01
47 1 0.00
48 189 0.32
49 138 0.24
51 2 0.00
52 110 0.19
53 38 0.07
55 1 0.00
56 1 0.00
57 2 0.00
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (48 bp):
CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGGTGC
Found at i:176404 original size:87 final size:87
Alignment explanation
Indices: 176232--176489 Score: 390
Period size: 87 Copynumber: 2.9 Consensus size: 87
176222 GATGAAGGTA
* * *
176232 CCAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATGACGAAGGTACCAATATGCTGAT
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT-AA-A-GAC-AAGGTGCCAATATGCTGAT
* *
176297 TCAAGGCTAGCGATATTGGGCTTGTG
62 TCAAGGCCAGCGATATTGGGCTTATG
* *
176323 CCAATGTGTTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGTCAATATGCTGATTCAA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
176388 GGCCAGCGATATTGGGCTTATG
66 GGCCAGCGATATTGGGCTTATG
* *
176410 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAGAGACAACGTGCCAATATGCTGATTCAA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
*
176475 GGCCAGCGACATTGG
66 GGCCAGCGATATTGG
176490 TCTCAGAGAC
Statistics
Matches: 155, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
87 116 0.75
88 3 0.02
89 1 0.01
90 2 0.01
91 33 0.21
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.25
Consensus pattern (87 bp):
CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
GGCCAGCGATATTGGGCTTATG
Found at i:176489 original size:135 final size:135
Alignment explanation
Indices: 176320--176629 Score: 512
Period size: 135 Copynumber: 2.3 Consensus size: 135
176310 TATTGGGCTT
* * * *
176320 GTGCCAATGTGTTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGTCAATATGCTGATT
1 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAACGTGCCAATATGCTGATT
* *
176385 CAAGGCCAGCGATATTGGGCTTATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAGAG
66 CAAGGCCAGCGATATTGGGCTTATGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAG
176450 ACAAC
131 ACAAC
* *
176455 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTCAGAGACAACGTGCCAATATGCTGATT
1 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAACGTGCCAATATGCTGATT
*
176520 CAAGGCTAGCGATATTGGGCTTATGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAG
66 CAAGGCCAGCGATATTGGGCTTATGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAG
*
176585 ACAAG
131 ACAAC
* *
176590 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA
1 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTA
176630 GAAAAAGGCA
Statistics
Matches: 162, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
135 162 1.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (135 bp):
GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAACGTGCCAATATGCTGATT
CAAGGCCAGCGATATTGGGCTTATGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAG
ACAAC
Found at i:176547 original size:87 final size:87
Alignment explanation
Indices: 176456--176629 Score: 285
Period size: 87 Copynumber: 2.0 Consensus size: 87
176446 AGAGACAACG
* *
176456 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTCAGAGACAACGTGCCAATATGCTGATTC
1 TGCCAATATGCTGATTCAAGGCCAACGACATTGGTCTCAAAGACAACGTGCCAATATGCTGATTC
* *
176521 AAGGCTAGCGATATTGGGCTTA
66 AAGGCCAGCGATATTGGACTTA
* * *
176543 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTC
1 TGCCAATATGCTGATTCAAGGCCAACGACATTGGTCTCAAAGACAACGTGCCAATATGCTGATTC
176608 AAGGCCAGCGATATTGGACTTA
66 AAGGCCAGCGATATTGGACTTA
176630 GAAAAAGGCA
Statistics
Matches: 80, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 80 1.00
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (87 bp):
TGCCAATATGCTGATTCAAGGCCAACGACATTGGTCTCAAAGACAACGTGCCAATATGCTGATTC
AAGGCCAGCGATATTGGACTTA
Found at i:176751 original size:30 final size:29
Alignment explanation
Indices: 176651--176775 Score: 148
Period size: 29 Copynumber: 4.3 Consensus size: 29
176641 CACCAATTTG
*
176651 TGTGGGCTTTTGAAAGGGTTG-CACCAACT
1 TGTGGGCTTTTGAAAGGG-TGCCACTAACT
* * *
176680 TGTGTGCTTTTG-AAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAGGGTGCCACTAACT
* *
176708 TGTGGGC-TTTGAAAGAGGTGCCATTGACT
1 TGTGGGCTTTTGAAAG-GGTGCCACTAACT
176737 TGTGGGCTTTTGAAAAGGGTGCCACTAACT
1 TGTGGGCTTTTG-AAAGGGTGCCACTAACT
176767 TGTGGGCTT
1 TGTGGGCTT
176776 AAAAGGAGAA
Statistics
Matches: 82, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
27 6 0.07
28 19 0.23
29 29 0.35
30 24 0.29
31 4 0.05
ACGTcount: A:0.18, C:0.16, G:0.32, T:0.34
Consensus pattern (29 bp):
TGTGGGCTTTTGAAAGGGTGCCACTAACT
Found at i:176853 original size:27 final size:27
Alignment explanation
Indices: 176789--177439 Score: 492
Period size: 27 Copynumber: 21.7 Consensus size: 27
176779 AGGAGAAAGA
176789 TGCCACGGAGTTGTGGACTTAAAAAGAACAAGG
1 TGCCACGGAGTTGTGGACTT-AAAAG-----GG
* *
176822 CGCCATGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
176849 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAG
1 TGCCACGGAGTTGTGGACTTAAAAGG-----G
*
176881 AATGCCACGGAGTTGTGGGCTTAAAAGGG
1 --TGCCACGGAGTTGTGGACTTAAAAGGG
*
176910 TGCCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
176937 TGCCACGAAGTTATGGACTTAAAAGGAAAAAGAG
1 TGCCACGGAGTTGTGGACTTAAAA-G-----G-G
* *
176971 TGCCACAGAGTTGTGGGCTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
*
176999 TGCCACGGAGTTGTGGACTTAAAAAGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
177026 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAG
1 TGCCACGGAGTTGTGGACTTAAAA-G-----G-G
* *
177060 TGCCACAGAGTTGTGGGCTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
177088 TGCCACGGAGTTGTGGACTTAAAAGGAACAAGG
1 TGCCACGGAGTTGTGGACTTAAAA-G-----GG
* *
177121 TGTCACGGAGTTGTGGACTTAAAAGAAAAAAGAA
1 TGCCACGGAGTTGTGGACTTAAAAG------G-G
177155 TGCCACGGAGTTGTGGACTTAAAAGGAATAAGG
1 TGCCACGGAGTTGTGGACTTAAAA-G-----GG
*
177188 TGCCACGGAGTTGTGGACTTAAAAGGA
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
177215 TACCACGGAGTTGTGGGCTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
* *
177243 TGCCACGGAGTTGTGGGCTTTAAAAGAG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
*
177271 TGCCACGAAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
177298 TGCCACAGAGTTGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
* *
177326 TGCCACAGAGTTGTCGACTTAAAAGGAACAAGG
1 TGCCACGGAGTTGTGGACTTAAAA-G-----GG
* *
177359 TGCCACGAAATTGTGGACTTAAAAGGAAAAAG
1 TGCCACGGAGTTGTGGACTTAAAAGG-----G
177391 AATGCCACGGAGTTGTGGACTTAAAAGGG
1 --TGCCACGGAGTTGTGGACTTAAAAGGG
**
177420 TGCCACGGAGTCATGGACTT
1 TGCCACGGAGTTGTGGACTT
177440 TGAGAAGATA
Statistics
Matches: 523, Mismatches: 48, Indels: 100
0.78 0.07 0.15
Matches are distributed among these distances:
27 176 0.34
28 113 0.22
29 4 0.01
32 10 0.02
33 96 0.18
34 111 0.21
35 13 0.02
ACGTcount: A:0.32, C:0.14, G:0.32, T:0.21
Consensus pattern (27 bp):
TGCCACGGAGTTGTGGACTTAAAAGGG
Found at i:177004 original size:28 final size:27
Alignment explanation
Indices: 176964--177439 Score: 367
Period size: 28 Copynumber: 16.0 Consensus size: 27
176954 CTTAAAAGGA
* * *
176964 AAAAGAGTGCCACAGAGTTGTGGGCTTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT
176992 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
*
177019 AAAAAGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* *
177046 AAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTT
1 AAAA-G-----G-GTGCCACGGAGTTGTGGAC-TT
177081 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
*
177108 AAAAGGAACAAGGTGTCACGGAGTTGTGGACTT
1 AAAA-G-----GGTGCCACGGAGTTGTGGACTT
*
177141 AAAAGAAAAAAGAATGCCACGGAGTTGTGGACTT
1 AAAAG------G-GTGCCACGGAGTTGTGGACTT
177175 AAAAGGAATAAGGTGCCACGGAGTTGTGGACTT
1 AAAA-G-----GGTGCCACGGAGTTGTGGACTT
* * *
177208 AAAAGGATACCACGGAGTTGTGGGCTTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT
*
177236 AAAAGGGTGCCACGGAGTTGTGGGCTTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT
* *
177264 AAAAGAGTGCCACGAAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
*
177291 AAAAGGGTGCCACAGAGTTGTGGACTTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT
* *
177319 AAAAGGGTGCCACAGAGTTGTCGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* *
177346 AAAAGGAACAAGGTGCCACGAAATTGTGGACTT
1 AAAA-G-----GGTGCCACGGAGTTGTGGACTT
177379 AAAAGGAAAAAGAATGCCACGGAGTTGTGGACTT
1 AAAAGG-----G--TGCCACGGAGTTGTGGACTT
**
177413 AAAAGGGTGCCACGGAGTCATGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
177440 TGAGAAGATA
Statistics
Matches: 381, Mismatches: 35, Indels: 65
0.79 0.07 0.14
Matches are distributed among these distances:
27 104 0.27
28 117 0.31
29 2 0.01
32 4 0.01
33 77 0.20
34 70 0.18
35 7 0.02
ACGTcount: A:0.32, C:0.14, G:0.32, T:0.21
Consensus pattern (27 bp):
AAAAGGGTGCCACGGAGTTGTGGACTT
Found at i:177031 original size:89 final size:89
Alignment explanation
Indices: 176697--177324 Score: 682
Period size: 89 Copynumber: 6.9 Consensus size: 89
176687 TTTTGAAGGT
* * * ** * *
176697 TGCCACTGACTTGTGGGCTTTGAAAGAGGTGCCATTGACTTGTGGGCTTTTGAAAAGGGTGCCAC
1 TGCCACGGAGTTGTGGGCTTTAAAAG-GGTGCCACGGAGTTGTGGAC--TT-AAAAGGGTGCCAC
** * * *
176762 TAACTTGTGGGCTTAAAAGGAGAAAGA-
62 GGAGTTGTGGACTTAAAAGGAAAAAGAG
* * * *
176789 TGCCACGGAGTTGTGGACTTAAAAAGAACAAGGCGCCATGGAGTTGTGGACTTAAAAGGGTGCCA
1 TGCCACGGAGTTGTGGGCTTTAAAAG-----GGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCA
*
176854 CGGAGTTGTGGACTTAAAAGGAAAAAGAA
61 CGGAGTTGTGGACTTAAAAGGAAAAAGAG
* *
176883 TGCCACGGAGTTGTGGGC-TTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGAAG
1 TGCCACGGAGTTGTGGGCTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAG
*
176947 TTATGGACTTAAAAGGAAAAAGAG
66 TTGTGGACTTAAAAGGAAAAAGAG
* *
176971 TGCCACAGAGTTGTGGGCTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAAGGTGCCACGGAG
1 TGCCACGGAGTTGTGGGCTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAG
177036 TTGTGGACTTAAAAGGAAAAAGAG
66 TTGTGGACTTAAAAGGAAAAAGAG
* *
177060 TGCCACAGAGTTGTGGGCTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAACAAGGTGTC
1 TGCCACGGAGTTGTGGGCTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA-G-----GGTGCC
* *
177125 ACGGAGTTGTGGACTTAAAAGAAAAAAGAA
60 ACGGAGTTGTGGACTTAAAAGGAAAAAGAG
* * *
177155 TGCCACGGAGTTGTGGAC-TTAAAAGGAATAAGGTGCCACGGAGTTGTGGACTTAAAAGGATACC
1 TGCCACGGAGTTGTGGGCTTTAAAA-G-----GGTGCCACGGAGTTGTGGACTTAAAAGGGTGCC
*
177219 ACGGAGTTGTGGGCTTTAAAA-G-----G-G
60 ACGGAGTTGTGGAC-TTAAAAGGAAAAAGAG
* * *
177243 TGCCACGGAGTTGTGGGCTTTAAAAGAGTGCCACGAAGTTGTGGACTTAAAAGGGTGCCACAGAG
1 TGCCACGGAGTTGTGGGCTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAG
177308 TTGTGGACTTTAAAAGG
66 TTGTGGAC-TTAAAAGG
177325 GTGCCACAGA
Statistics
Matches: 469, Mismatches: 46, Indels: 50
0.83 0.08 0.09
Matches are distributed among these distances:
83 48 0.10
84 1 0.00
88 92 0.20
89 125 0.27
92 21 0.04
93 41 0.09
94 41 0.09
95 56 0.12
96 17 0.04
99 1 0.00
100 26 0.06
ACGTcount: A:0.31, C:0.14, G:0.33, T:0.22
Consensus pattern (89 bp):
TGCCACGGAGTTGTGGGCTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAG
TTGTGGACTTAAAAGGAAAAAGAG
Found at i:177145 original size:272 final size:267
Alignment explanation
Indices: 176692--177418 Score: 752
Period size: 272 Copynumber: 2.7 Consensus size: 267
176682 TGTGCTTTTG
* * * * ** * *
176692 AAGGTTGCCACTGACTTGTGGGCTTTGAAAGAGGTGCCATTGACTTGTGGGCTTTTGAAAAGGGT
1 AAGGGTGCCACAGAGTTGTGGGCTTTAAAAG-GGTGCCACGGAGTTGTGGAC--TT-AAAAGGGT
* * * *
176757 GCCACTA-ACTTGTGGGCTTAAAAGGAGAAAGA-TGCCACGGAGTTGTGGACTTAAAAAGAACAA
62 GCCAC-AGAGTTGTGGACTTAAAAGGA-AAAGAGTGCCACAGAGTTGTGGACTTTAAAAG----A
* *
176820 GGCGCCATGGAGTTGTGGACTTAAAA-G----GGTGCCACGGAGTTGTGGACTTAAAAGGAAAAA
121 GGTGCCACGGAGTTGTGGACTTAAAAGGAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAA
* * *
176880 GAATGCCACGGAGTTGTGGGCTTAAAA-G-GGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCAC
186 GAATGCCACGGAGTTGTGGACTTAAAAGGAGGTGCCACAGAGTTGTGGACTTAAAAGGATACCAC
176943 GAAGTTATGGAC-TTAA
251 GAAGTTATGGACTTTAA
*
176959 AAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAA
1 AA-G-----G-GTGCCACAGAGTTGTGGGCTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAG
* *
177024 GGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAG-GG
59 GGTGCCACAGAGTTGTGGACTTAAAAGG-AAAAGAGTGCCACAGAGTTGTGGACTTTAAAAGAGG
* *
177088 TGCCACGGAGTTGTGGACTTAAAAGGAACAAGGTGTCACGGAGTTGTGGACTTAAAAGAAAAAAG
123 TGCCACGGAGTTGTGGACTTAAAAGGAA-AAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAG
*
177153 AATGCCACGGAGTTGTGGACTTAAAAGGAATAAGGTGCCACGGAGTTGTGGACTTAAAAGGATAC
187 AATGCCACGGAGTTGTGGACTTAAAAGG----AGGTGCCACAGAGTTGTGGACTTAAAAGGATAC
* * *
177218 CACGGAGTTGTGGGCTTTAA
248 CACGAAGTTATGGACTTTAA
* * *
177238 AAGGGTGCCACGGAGTTGTGGGCTTTAAAAGAGTGCCACGAAGTTGTGGACTTAAAAGGGTGCCA
1 AAGGGTGCCACAGAGTTGTGGGCTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCA
*
177303 CAGAGTTGTGGACTTTAAAA-G----G-GTGCCACAGAGTTGTCGAC-TTAAAAGGAACAAGGTG
66 CAGAGTTGTGGAC-TTAAAAGGAAAAGAGTGCCACAGAGTTGTGGACTTTAAAA-G----AGGTG
* * *
177361 CCACGAAATTGTGGACTTAAAAGGAAAAAGAATGCCACGGAGTTGTGGACTTAAAAGG
125 CCACGGAGTTGTGGACTTAAAAGG-AAAAG-GTGCCACGGAGTTGTGGACTTAAAAGG
177419 GTGCCACGGA
Statistics
Matches: 390, Mismatches: 38, Indels: 59
0.80 0.08 0.12
Matches are distributed among these distances:
265 6 0.02
266 42 0.11
267 4 0.01
268 1 0.00
270 33 0.08
271 55 0.14
272 153 0.39
273 25 0.06
274 23 0.06
278 42 0.11
279 6 0.02
ACGTcount: A:0.32, C:0.14, G:0.32, T:0.22
Consensus pattern (267 bp):
AAGGGTGCCACAGAGTTGTGGGCTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCA
CAGAGTTGTGGACTTAAAAGGAAAAGAGTGCCACAGAGTTGTGGACTTTAAAAGAGGTGCCACGG
AGTTGTGGACTTAAAAGGAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAATGCCACG
GAGTTGTGGACTTAAAAGGAGGTGCCACAGAGTTGTGGACTTAAAAGGATACCACGAAGTTATGG
ACTTTAA
Found at i:177293 original size:55 final size:55
Alignment explanation
Indices: 176883--177440 Score: 417
Period size: 61 Copynumber: 9.4 Consensus size: 55
176873 GGAAAAAGAA
* * *
176883 TGCCACGGAGTTGTGGGC-TTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTTAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGG
* * * * *
176937 TGCCACGAAGTTATGGACTTAAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAGGG
1 TGCCACGGAGTTGTGGACTT------TAAAAGAGTGCCACGGAGTTGTGGAC-TTAAAAGGG
*
176999 TGCCACGGAGTTGTGGACTTAAAAAG-GTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAG
1 TGCCACGGAGTTGTGGACTTTAAAAGAGTGCCACGGAGTTGTGGACTTAAAA-G-----G-G
* * *
177060 TGCCACAGAGTTGTGGGCTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAACAAGG
1 TGCCACGGAGTTGTGGACTTTAAAAGAGTGCCACGGAGTTGTGGACTTAAAA-G-----GG
*
177121 TGTCACGGAGTTGTGGAC-TTAAAAGAAAAAAGAATGCCACGGAGTTGTGGACTTAAAAGGAATA
1 TGCCACGGAGTTGTGGACTTTAAAAG-----AG--TGCCACGGAGTTGTGGACTTAAAA-G----
177185 AGG
54 -GG
* *
177188 TGCCACGGAGTTGTGGAC-TTAAAAG-GATACCACGGAGTTGTGGGCTTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTTAAAAGAG-TGCCACGGAGTTGTGGAC-TTAAAAGGG
* *
177243 TGCCACGGAGTTGTGGGCTTTAAAAGAGTGCCACGAAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTTAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGG
* * * *
177298 TGCCACAGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTCGACTTAAAAGGAACAAGG
1 TGCCACGGAGTTGTGGACTTTAAAAGAGTGCCACGGAGTTGTGGACTTAAAA-G-----GG
* *
177359 TGCCACGAAATTGTGGAC-TTAAAAGGAAAAAGAATGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTTAAAA-G----AG--TGCCACGGAGTTGTGGACTTAAAAGGG
**
177420 TGCCACGGAGTCATGGACTTT
1 TGCCACGGAGTTGTGGACTTT
177441 GAGAAGATAG
Statistics
Matches: 422, Mismatches: 42, Indels: 72
0.79 0.08 0.13
Matches are distributed among these distances:
54 21 0.05
55 93 0.22
56 29 0.07
57 1 0.00
60 32 0.08
61 104 0.25
62 61 0.14
65 2 0.00
66 1 0.00
67 78 0.18
ACGTcount: A:0.32, C:0.14, G:0.32, T:0.22
Consensus pattern (55 bp):
TGCCACGGAGTTGTGGACTTTAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGG
Found at i:177311 original size:238 final size:237
Alignment explanation
Indices: 176784--177439 Score: 784
Period size: 238 Copynumber: 2.7 Consensus size: 237
176774 TTAAAAGGAG
* * * * * **
176784 AAAGATGCCACGGAGTTGTGGACTTAAAAAGAACAAGGCGCCATGGAGTTGTGGAC-TTAAAAGG
1 AAAGGTGCCACGAAGTTGTGGACTT-AAAAGGA-GA-GTGCCACAGAGTTGTGGACTTTAAAAGG
* * *
176848 GTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAATGCCACGGAGTTGTGGGCTTAAAAG-----
63 GTGCCACGGAGTTGTGGACTTAAAAGGAACAAG-GTGCCACGGAGTTGTGGACTTAAAAGAAAAA
* *
176908 G-GTGCCACAGAGTTGTGGACTTAAAA-GGGTGCCACGAAGTTATGGACTTAAAAGGAAAAAGAG
127 GAATGCCACGGAGTTGTGGACTTAAAAGGGGTGCCACGAAGTTATGGACTTAAAAGG----AGAG
*
176971 TGCCACAGAGTTGTGGGCTTTAAAAGGGTGCCACGGAGTTGTGGACTTAA
188 TACCACAGAGTTGTGGGCTTTAAAAGGGTGCCACGGAGTTGTGGACTTAA
* *
177021 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAG
1 AAAGGTGCCACGAAGTTGTGGACTTAAAAGG----AGAGTGCCACAGAGTTGTGGACTTTAAAAG
*
177086 GGTGCCACGGAGTTGTGGACTTAAAAGGAACAAGGTGTCACGGAGTTGTGGACTTAAAAGAAAAA
62 GGTGCCACGGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGTTGTGGACTTAAAAG-AAAA
* *
177151 AGAATGCCACGGAGTTGTGGACTTAAAAGGAATAAGGTGCCACGGAGTTGTGGACTTAAAA-G-G
126 AGAATGCCACGGAGTTGTGGACTTAAAAGG-----GGTGCCACGAAGTTATGGACTTAAAAGGAG
* * *
177214 A-TACCACGGAGTTGTGGGCTTTAAAAGGGTGCCACGGAGTTGTGGGCTTTA
186 AGTACCACAGAGTTGTGGGCTTTAAAAGGGTGCCACGGAGTTGTGGACTTAA
177265 AAAGAGTGCCACGAAGTTGTGGACTTAAAA-G-G-GTGCCACAGAGTTGTGGACTTTAAAAGGGT
1 AAAG-GTGCCACGAAGTTGTGGACTTAAAAGGAGAGTGCCACAGAGTTGTGGACTTTAAAAGGGT
* * * *
177327 GCCACAGAGTTGTCGACTTAAAAGGAACAAGGTGCCACGAAATTGTGGACTTAAAAGGAAAAAGA
65 GCCACGGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGTTGTGGACTTAAAA-GAAAAAGA
* *
177392 ATGCCACGGAGTTGTGGACTTAAAA-GGGTGCCACGGAGTCATGGACTT
129 ATGCCACGGAGTTGTGGACTTAAAAGGGGTGCCACGAAGTTATGGACTT
177440 TGAGAAGATA
Statistics
Matches: 371, Mismatches: 28, Indels: 45
0.84 0.06 0.10
Matches are distributed among these distances:
232 20 0.05
236 5 0.01
237 25 0.07
238 150 0.40
239 43 0.12
240 1 0.00
244 52 0.14
245 49 0.13
246 1 0.00
250 1 0.00
251 24 0.06
ACGTcount: A:0.33, C:0.14, G:0.32, T:0.21
Consensus pattern (237 bp):
AAAGGTGCCACGAAGTTGTGGACTTAAAAGGAGAGTGCCACAGAGTTGTGGACTTTAAAAGGGTG
CCACGGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGTTGTGGACTTAAAAGAAAAAGAAT
GCCACGGAGTTGTGGACTTAAAAGGGGTGCCACGAAGTTATGGACTTAAAAGGAGAGTACCACAG
AGTTGTGGGCTTTAAAAGGGTGCCACGGAGTTGTGGACTTAA
Found at i:178669 original size:16 final size:15
Alignment explanation
Indices: 178644--178673 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
178634 GCACTCTCTC
178644 TTTTTTTTTTGTTTT
1 TTTTTTTTTTGTTTT
178659 TTTTGTTTTTTGTTT
1 TTTT-TTTTTTGTTT
178674 GTGTGTTTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (15 bp):
TTTTTTTTTTGTTTT
Found at i:185682 original size:19 final size:20
Alignment explanation
Indices: 185658--185710 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
185648 AGCGATACAT
185658 TGTATCGATACAACACT-TA
1 TGTATCGATACAACACTGTA
* *
185677 TGTATCGATACAGATACTGTT
1 TGTATCGATACA-ACACTGTA
185698 TGTATCGATACAA
1 TGTATCGATACAA
185711 ATTGTTGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 12 0.40
20 5 0.17
21 13 0.43
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (20 bp):
TGTATCGATACAACACTGTA
Found at i:188741 original size:27 final size:27
Alignment explanation
Indices: 188709--188760 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
188699 ATAAAAATAG
*
188709 GGTTGG-AGTATCCCCTTGAAAATAAAA
1 GGTTGGTA-TATCCCCTTAAAAATAAAA
*
188736 GGTTGGTATATCCGCTTAAAAATAA
1 GGTTGGTATATCCCCTTAAAAATAA
188761 TGGGGTTTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 21 0.95
28 1 0.05
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (27 bp):
GGTTGGTATATCCCCTTAAAAATAAAA
Found at i:188842 original size:79 final size:72
Alignment explanation
Indices: 188724--188886 Score: 184
Period size: 76 Copynumber: 2.2 Consensus size: 72
188714 GAGTATCCCC
* * *
188724 TTGAAAATAAAAGGTTGGTATATCCGCTTAAAAATAATGGGGTTTAGAGTATTCTCGAGATGAAA
1 TTGAAAATAAAAGGTTGGAATATCCGCTCAAAAATAAT-GGG-TTAGAGTA-CCTCGAGAT-AAA
188789 AA-TTTAATATT
62 AATTTTAATA-T
* * *
188800 TTGAAAATAAAATGGGGTTGGAATATTCTCTCAAAAATAATGGGTTAGAGTACCTTGAGATAAAA
1 TTGAAAATAAAA---GGTTGGAATATCCGCTCAAAAATAATGGGTTAGAGTACCTCGAGATAAAA
188865 ATTTTAATAT
63 ATTTTAATAT
*
188875 TTAAAAATAAAA
1 TTGAAAATAAAA
188887 AACGATGTTG
Statistics
Matches: 76, Mismatches: 7, Indels: 9
0.83 0.08 0.10
Matches are distributed among these distances:
75 17 0.22
76 26 0.34
77 8 0.11
78 3 0.04
79 22 0.29
ACGTcount: A:0.43, C:0.06, G:0.18, T:0.33
Consensus pattern (72 bp):
TTGAAAATAAAAGGTTGGAATATCCGCTCAAAAATAATGGGTTAGAGTACCTCGAGATAAAAATT
TTAATAT
Found at i:188944 original size:155 final size:159
Alignment explanation
Indices: 188755--189045 Score: 380
Period size: 155 Copynumber: 1.9 Consensus size: 159
188745 ATCCGCTTAA
* * * *
188755 AAATAATGGGGTTTAGAGTATTCTCGAGATGAAAAATTTAATATTTTGAAAAT-AAAA-TGGGGT
1 AAATAATAGGGTTTAGAGTATCCACGAGATG-AAAATTTAATATTTT-AAAATAAAAACGGGGGT
* * *
188818 TGGAATATTCTCTCAAAAATAA-TGGGTTAG-AGTA-CCTTGAGA-TAAAAATTTTAATATTTAA
64 TGGAATATCCTCTCAAAAATAACAGGGTT-GCAATACCCTTGAGATTAAAAATTTTAATATTTAA
188879 AAATAAAAAACGATGTTGGAGTATCACCTTGG
128 AAATAAAAAACGATGTTGGAGTATCACCTTGG
*
188911 AAATAATAGGG-TTGGAGTATCCACGAGATGAAAATTTAATATTTTAAAATAAAAACGGGGGTTG
1 AAATAATAGGGTTTAGAGTATCCACGAGATGAAAATTTAATATTTTAAAATAAAAACGGGGGTTG
* * * * **
188975 GAGTATCCTCTCGAAAATAACAGGGTTGCAATACCCTTTAGATTGAAAATTTTAATATTTTGAAA
66 GAATATCCTCTCAAAAATAACAGGGTTGCAATACCCTTGAGATTAAAAATTTTAATATTTAAAAA
189040 TAAAAA
131 TAAAAA
189046 TGAGATTGAG
Statistics
Matches: 115, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
153 5 0.04
154 19 0.17
155 41 0.36
156 18 0.16
157 7 0.06
158 25 0.22
ACGTcount: A:0.41, C:0.08, G:0.19, T:0.32
Consensus pattern (159 bp):
AAATAATAGGGTTTAGAGTATCCACGAGATGAAAATTTAATATTTTAAAATAAAAACGGGGGTTG
GAATATCCTCTCAAAAATAACAGGGTTGCAATACCCTTGAGATTAAAAATTTTAATATTTAAAAA
TAAAAAACGATGTTGGAGTATCACCTTGG
Found at i:188975 original size:78 final size:77
Alignment explanation
Indices: 188754--189045 Score: 270
Period size: 78 Copynumber: 3.7 Consensus size: 77
188744 TATCCGCTTA
* * * *
188754 AAAATAATGGGGTTTAGAGTATTCTCGAGATGAAAAATTTAATATTTTGAAAAT-AAAATGGGGT
1 AAAATAATAGGG-TTAGAGTATCCTCGAGATGAAAATTTTAATATTTT-AAAATAAAAACGGGGT
* * *
188818 TGGAATATTCTCTCA
64 TGGAGTA-TCCCTCG
* * * **
188833 AAAATAAT-GGGTTAGAGTA-CCTTGAGATAAAAATTTTAATATTTAAAAATAAAAAACGATGTT
1 AAAATAATAGGGTTAGAGTATCCTCGAGATGAAAATTTTAATATTTTAAAAT-AAAAACGGGGTT
*
188896 GGAGTATCACCTTG
65 GGAGTATC-CCTCG
* * *
188910 GAAATAATAGGGTTGGAGTATCCACGAGATGAAAA-TTTAATATTTTAAAATAAAAACGGGGGTT
1 AAAATAATAGGGTTAGAGTATCCTCGAGATGAAAATTTTAATATTTTAAAATAAAAAC-GGGGTT
188974 GGAGTATCCTCTCG
65 GGAGTATCC-CTCG
* * * ** *
188988 AAAATAACAGGGTT-GCAATACCCTTTAGATTGAAAATTTTAATATTTTGAAATAAAAA
1 AAAATAATAGGGTTAG-AGTATCCTCGAGA-TGAAAATTTTAATATTTTAAAATAAAAA
189046 TGAGATTGAG
Statistics
Matches: 174, Mismatches: 29, Indels: 19
0.78 0.13 0.09
Matches are distributed among these distances:
75 5 0.03
76 23 0.13
77 38 0.22
78 63 0.36
79 25 0.14
80 20 0.11
ACGTcount: A:0.41, C:0.08, G:0.19, T:0.32
Consensus pattern (77 bp):
AAAATAATAGGGTTAGAGTATCCTCGAGATGAAAATTTTAATATTTTAAAATAAAAACGGGGTTG
GAGTATCCCTCG
Found at i:189088 original size:156 final size:155
Alignment explanation
Indices: 188770--189088 Score: 364
Period size: 155 Copynumber: 2.1 Consensus size: 155
188760 ATGGGGTTTA
* * * *
188770 GAGTATTCTCGAGATGAAAAATTTAATATTTTGAAAATAAAATGGGGTTGGAATATTCTCTCAAA
1 GAGTATCCACGAGATGAAAAATTTAATATTTTGAAAATAAAAGGGGGTTGGAATATCCTCTCAAA
* *
188835 AATAATGGGTTAGAGTACCTTGAGATAAAAATTTTAATATTTAAAAATAAAAAACGATGTTGGAG
66 AATAAAGGGTTAGAATACCTTGAGATAAAAATTTTAATATTTAAAAATAAAAAACGATGTTGGAG
** *
188900 TATCACCTTGGAAATAATAGGGTTG
131 TATCACCTCAGAAATAAGAGGGTTG
* *
188925 GAGTATCCACGAGATG-AAAATTTAATATTTT-AAAATAAAAACGGGGGTTGGAGTATCCTCTCG
1 GAGTATCCACGAGATGAAAAATTTAATATTTTGAAAAT-AAAA-GGGGGTTGGAATATCCTCTCA
* * ** *
188988 AAAATAACAGGGTT-GCAATACCCTTTAGATTGAAAATTTTAATATTTTGAAAT-AAAAATGA-G
64 AAAATAA-AGGGTTAG-AATA-CCTTGAGA-TAAAAATTTTAATATTTAAAAATAAAAAACGATG
*
189050 ATT-GAGTATCCCCTCAGAAATAACGA-GGTTG
125 -TTGGAGTATCACCTCAGAAATAA-GAGGGTTG
189081 GAGTATCC
1 GAGTATCC
189089 TTTCGAAAAT
Statistics
Matches: 139, Mismatches: 17, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
153 5 0.04
154 19 0.14
155 39 0.28
156 39 0.28
157 17 0.12
158 20 0.14
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (155 bp):
GAGTATCCACGAGATGAAAAATTTAATATTTTGAAAATAAAAGGGGGTTGGAATATCCTCTCAAA
AATAAAGGGTTAGAATACCTTGAGATAAAAATTTTAATATTTAAAAATAAAAAACGATGTTGGAG
TATCACCTCAGAAATAAGAGGGTTG
Found at i:189091 original size:78 final size:79
Alignment explanation
Indices: 188770--189090 Score: 266
Period size: 78 Copynumber: 4.1 Consensus size: 79
188760 ATGGGGTTTA
* * * * * * * *
188770 GAGTATTCTCGAGATGAAAAATTTAATATTTTGAAAAT-AAAATGGGGTTGGAATATTCTCTCAA
1 GAGTATCCTTGAGATGAAAATTTTAATATTTT-AAAATAAAAATGAGGTTGGAGTATCCCCTCAG
* *
188834 AAATAA--TGGGTTA
65 AAATAACGAGGGTTG
* * * * * **
188847 GAGTA-CCTTGAGATAAAAATTTTAATATTTAAAAATAAAAAACGATGTTGGAGTATCACCTTGG
1 GAGTATCCTTGAGATGAAAATTTTAATATTTTAAAAT-AAAAATGAGGTTGGAGTATCCCCTCAG
*
188911 AAATAA-TAGGGTTG
65 AAATAACGAGGGTTG
** * * *
188925 GAGTATCCACGAGATGAAAA-TTTAATATTTTAAAATAAAAACGGGGGTTGGAGTATCCTCTC-G
1 GAGTATCCTTGAGATGAAAATTTTAATATTTTAAAATAAAAA-TGAGGTTGGAGTATCCCCTCAG
188988 AAAATAAC-AGGGTTG
65 -AAATAACGAGGGTTG
* * * * * *
189003 CAATACCCTTTAGATTGAAAATTTTAATATTTTGAAATAAAAATGAGATT-GAGTATCCCCTCAG
1 GAGTATCCTTGAGA-TGAAAATTTTAATATTTTAAAATAAAAATGAGGTTGGAGTATCCCCTCAG
189067 AAATAACGA-GGTTG
65 AAATAACGAGGGTTG
189081 GAGTATCCTT
1 GAGTATCCTT
189091 TCGAAAATAA
Statistics
Matches: 192, Mismatches: 41, Indels: 21
0.76 0.16 0.08
Matches are distributed among these distances:
75 5 0.03
76 21 0.11
77 33 0.17
78 90 0.47
79 23 0.12
80 20 0.10
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (79 bp):
GAGTATCCTTGAGATGAAAATTTTAATATTTTAAAATAAAAATGAGGTTGGAGTATCCCCTCAGA
AATAACGAGGGTTG
Found at i:191644 original size:31 final size:31
Alignment explanation
Indices: 191606--191681 Score: 125
Period size: 31 Copynumber: 2.5 Consensus size: 31
191596 TACAATGAAA
* *
191606 AATGTATCAATACATTTAGGTTAAAACCCAG
1 AATGTATCGATACATTTAGGTTAAAACCAAG
*
191637 AATGTATCGATACATTTGGGTTAAAACCAAG
1 AATGTATCGATACATTTAGGTTAAAACCAAG
191668 AATGTATCGATACA
1 AATGTATCGATACA
191682 CTGATAAATG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (31 bp):
AATGTATCGATACATTTAGGTTAAAACCAAG
Done.