Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2251
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: 66343
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:5102 original size:16 final size:16
Alignment explanation
Indices: 5068--5100 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
5058 ATGAAGATCT
5068 AACATTGAAAAAATCA
1 AACATTGAAAAAATCA
*
5084 AACA-TGAAACAATCA
1 AACATTGAAAAAATCA
5099 AA
1 AA
5101 ACCCCAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.64, C:0.15, G:0.06, T:0.15
Consensus pattern (16 bp):
AACATTGAAAAAATCA
Found at i:7240 original size:18 final size:19
Alignment explanation
Indices: 7201--7242 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
7191 TTATGATTAT
7201 TTTAAA-ATTAAATTAAAA
1 TTTAAATATTAAATTAAAA
*
7219 -TTAAATATTATA-TAAAA
1 TTTAAATATTAAATTAAAA
7236 TTTAAAT
1 TTTAAAT
7243 TGATTTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TTTAAATATTAAATTAAAA
Found at i:9148 original size:12 final size:13
Alignment explanation
Indices: 9131--9159 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
9121 ATGTGAGAAT
9131 ATTA-TTAAAAAA
1 ATTATTTAAAAAA
9143 ATTATTTAAAAAA
1 ATTATTTAAAAAA
9156 ATTA
1 ATTA
9160 CCAAAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.25
13 12 0.75
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATTATTTAAAAAA
Found at i:10504 original size:20 final size:20
Alignment explanation
Indices: 10463--10502 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
10453 AAATTTTGTG
*
10463 TTAATTAAATTAATTTTAAA
1 TTAATTAAATTAAATTTAAA
*
10483 TTAATTCAATTAAAATTTAA
1 TTAATTAAATT-AAATTTAA
10503 TTTTTTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (20 bp):
TTAATTAAATTAAATTTAAA
Found at i:10554 original size:44 final size:43
Alignment explanation
Indices: 10470--10560 Score: 103
Period size: 44 Copynumber: 2.1 Consensus size: 43
10460 GTGTTAATTA
* * * *
10470 AATTAATTTTAAATTAATTCAATTAAAATTTAATTTTTTATATT
1 AATTAATTTTAAATCAATGCAATTAAAATTGAATTCTTTATA-T
* *
10514 AATTCATTTTAAATCAGTGCAATTAAAATATGAA-TCTTTATAT
1 AATTAATTTTAAATCAATGCAATTAAAAT-TGAATTCTTTATAT
10557 AATT
1 AATT
10561 TCAAATCAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
43 5 0.12
44 32 0.80
45 3 0.08
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.48
Consensus pattern (43 bp):
AATTAATTTTAAATCAATGCAATTAAAATTGAATTCTTTATAT
Found at i:11453 original size:24 final size:27
Alignment explanation
Indices: 11412--11462 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
11402 TCATAAAATA
11412 TTTAATTTTT-TTACTTT-TTTTCTCTT
1 TTTAATTTTTCTTA-TTTGTTTTCTCTT
11438 TTTAATTTTTCTT-TTTGTTTTCTCT
1 TTTAATTTTTCTTATTTGTTTTCTCT
11463 ATTAATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 3 0.13
26 18 0.78
27 2 0.09
ACGTcount: A:0.10, C:0.12, G:0.02, T:0.76
Consensus pattern (27 bp):
TTTAATTTTTCTTATTTGTTTTCTCTT
Found at i:11467 original size:25 final size:25
Alignment explanation
Indices: 11413--11468 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
11403 CATAAAATAT
*
11413 TTAATTTTTTTACTTTTTTTCTCTTT
1 TTAATTTTTTTA-TTTTTTTCTCTTA
11439 TTAATTTTTCTT-TTTGTTTTCTC-TA
1 TTAATTTTT-TTATTT-TTTTCTCTTA
11464 TTAAT
1 TTAAT
11469 AAATAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 9 0.33
26 16 0.59
27 2 0.07
ACGTcount: A:0.14, C:0.11, G:0.02, T:0.73
Consensus pattern (25 bp):
TTAATTTTTTTATTTTTTTCTCTTA
Found at i:11743 original size:17 final size:16
Alignment explanation
Indices: 11721--11762 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
11711 ATTTATAAAT
*
11721 ATAAAAAAGCAAAAAAG
1 ATAAAAAA-CAAAAAAA
*
11738 ATAAAAAATAAAAAAA
1 ATAAAAAACAAAAAAA
11754 ATAAAAAAC
1 ATAAAAAAC
11763 TGAAAATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.81, C:0.05, G:0.05, T:0.10
Consensus pattern (16 bp):
ATAAAAAACAAAAAAA
Found at i:12694 original size:22 final size:20
Alignment explanation
Indices: 12655--12704 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 20
12645 ATTTATCTTT
12655 ATTAATATAAAAAATATT-A
1 ATTAATATAAAAAATATTAA
12674 ATATAATATAAAAAAATTATTAA
1 AT-TAATAT-AAAAAA-TATTAA
12697 ATTAATAT
1 ATTAATAT
12705 CACGAGTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 2 0.07
20 6 0.22
21 6 0.22
22 10 0.37
23 3 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
ATTAATATAAAAAATATTAA
Found at i:15136 original size:3 final size:3
Alignment explanation
Indices: 15130--15158 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
15120 ATCATCATTG
15130 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
15159 TATAGAAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:16973 original size:21 final size:20
Alignment explanation
Indices: 16944--16991 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
16934 ATATTAAAAA
*
16944 ATATATTATTAAATTAAATAT
1 ATATTTTATT-AATTAAATAT
*
16965 ATATTTTATTAAGTAAATATT
1 ATATTTTATTAATTAAATA-T
16986 ATATTT
1 ATATTT
16992 AATATTTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
ATATTTTATTAATTAAATAT
Found at i:16975 original size:16 final size:16
Alignment explanation
Indices: 16942--16996 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
16932 ATATATTAAA
*
16942 AAATATATTATTAAATT
1 AAATATA-TATTATATT
*
16959 AAATATATATTTTATT
1 AAATATATATTATATT
* *
16975 AAGTAAATATTATATT
1 AAATATATATTATATT
*
16991 TAATAT
1 AAATAT
16997 TTATATAAAA
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
16 23 0.77
17 7 0.23
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
AAATATATATTATATT
Found at i:18826 original size:2 final size:2
Alignment explanation
Indices: 18819--18850 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
18809 GAAAGGAAGA
18819 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
18851 GTAGGTATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20108 original size:20 final size:20
Alignment explanation
Indices: 20074--20119 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
20064 AAGAATTGAA
*
20074 GAGGGATACAAGAGAAGGAT
1 GAGGGATACAAGAGAAGGAG
** *
20094 GAGGGATACTTGAGATGGAG
1 GAGGGATACAAGAGAAGGAG
20114 GAGGGA
1 GAGGGA
20120 GCCTCTATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.04, G:0.46, T:0.13
Consensus pattern (20 bp):
GAGGGATACAAGAGAAGGAG
Found at i:25679 original size:30 final size:30
Alignment explanation
Indices: 25643--25703 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
25633 TTCATTTTGA
25643 AAACTGAATATTTCGTATCAGGCACTGGAG
1 AAACTGAATATTTCGTATCAGGCACTGGAG
25673 AAACTGAATATTTCGTATCAGGCACTGGAG
1 AAACTGAATATTTCGTATCAGGCACTGGAG
25703 A
1 A
25704 GATACCGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.26
Consensus pattern (30 bp):
AAACTGAATATTTCGTATCAGGCACTGGAG
Found at i:27730 original size:12 final size:13
Alignment explanation
Indices: 27713--27747 Score: 54
Period size: 12 Copynumber: 2.7 Consensus size: 13
27703 CCATTTCATA
27713 TTTTTTCTTTTT-
1 TTTTTTCTTTTTC
27725 TTTTTTCTTTTTC
1 TTTTTTCTTTTTC
27738 TTTCTTTCTT
1 TTT-TTTCTT
27748 CTTCATCTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.57
13 3 0.14
14 6 0.29
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTTCTTTTTC
Found at i:29037 original size:32 final size:32
Alignment explanation
Indices: 28988--29334 Score: 543
Period size: 32 Copynumber: 10.8 Consensus size: 32
28978 AAAATGGTGA
* * *
28988 TTTGAAAAGGGTTGCCACTGACTTGCGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
29020 TTTTAAATGGGTTGCCACCGACTTGCGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
29052 TTTTAAATGGGTTGCCACCAACTTGTGGGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
**
29084 TTTGAAAAAGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
29116 TTTGAAATGGGTTGCCACCTACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
29148 TTT-AGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGA-AATGGGTTGCCACCGACTTGTGTGGGC
29180 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
29212 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
29244 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
29276 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
29308 TTTGGAATGGGTTGCCACCGATTTGTG
1 TTTGAAATGGGTTGCCACCGACTTGTG
29335 AATTTAAAAG
Statistics
Matches: 296, Mismatches: 17, Indels: 4
0.93 0.05 0.01
Matches are distributed among these distances:
31 1 0.00
32 294 0.99
33 1 0.00
ACGTcount: A:0.16, C:0.19, G:0.34, T:0.31
Consensus pattern (32 bp):
TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
Found at i:29386 original size:27 final size:27
Alignment explanation
Indices: 29320--30158 Score: 1241
Period size: 27 Copynumber: 30.7 Consensus size: 27
29310 TGGAATGGGT
* * * *
29320 TGCCACCGATTTGTGAATTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
29347 ATGCCACGGAGTTGTGGACTTAAAAGGG
1 -TGCCACGGAGTTGTGGACTTAAAAGGG
*
29375 TGCCACGGAGTTGTGGACTTAAGAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
29402 ATGCCACGGAGTTGTGGACTTAAAAGGG
1 -TGCCACGGAGTTGTGGACTTAAAAGGG
29430 ATGCCACGGAGTTGTGGACTTAAAAGGG
1 -TGCCACGGAGTTGTGGACTTAAAAGGG
* *
29458 TGCCACAGAGTTGTGGACTAAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
29485 TGCCATGGAGTTGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGG
* * *
29513 TGCCACAGAGTTGTGGACTTAAAAAAGA
1 TGCCACGGAGTTGTGGACTT-AAAAGGG
* *
29541 TGCCACAGAGTTATGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
29568 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
29595 TGCTACGGAGTTGTGGTCTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
29622 TGTCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* * *
29649 ATGCCATGGAGTTATGGACTTAAAAGAG
1 -TGCCACGGAGTTGTGGACTTAAAAGGG
29677 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
29704 TGCCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
29731 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* * *
29758 ATGCCATGGAGTTATGGACTTAAAAGAG
1 -TGCCACGGAGTTGTGGACTTAAAAGGG
29786 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
29813 TGCCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
29840 TGCCACGGAGTTGTGGTA-TTAAAAGGAA
1 TGCCACGGAGTTGTGG-ACTTAAAAGG-G
*
29868 TGCCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
29895 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
29922 TGCCACGGAGTTGTGGACTTAAAAGGAA
1 TGCCACGGAGTTGTGGACTTAAAAGG-G
** *
29950 TGCCATAGAGTTGTGGACTTAAAAAGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
29977 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
30004 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
30031 TGCCACAGAGTTGTGGACTT-AAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
* *
30057 TGCCACAGAGTTGTGGACTAAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
30084 TGCCACGGAGTTGTGGATTTTAAAAGGG
1 TGCCACGGAGTTGTGGA-CTTAAAAGGG
*
30112 TGCCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
30139 TACCACGGAGTTGTGGACTT
1 TGCCACGGAGTTGTGGACTT
30159 TGAAAAGGTC
Statistics
Matches: 737, Mismatches: 63, Indels: 23
0.90 0.08 0.03
Matches are distributed among these distances:
26 25 0.03
27 469 0.64
28 243 0.33
ACGTcount: A:0.29, C:0.14, G:0.34, T:0.23
Consensus pattern (27 bp):
TGCCACGGAGTTGTGGACTTAAAAGGG
Found at i:29592 original size:82 final size:81
Alignment explanation
Indices: 29320--30158 Score: 1277
Period size: 82 Copynumber: 10.2 Consensus size: 81
29310 TGGAATGGGT
* * * * *
29320 TGCCACCGATTTGTGAATTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAG
1 TGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAG
*
29385 TTGTGGACTTAAGAGGG
65 TTGTGGACTTAAAAGGG
29402 ATGCCACGGAGTTGTGGACTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGA
1 -TGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGA
*
29467 GTTGTGGACTAAAAAGGG
64 GTTGTGGACTTAAAAGGG
* * * *
29485 TGCCATGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAAAGATGCCACAGA
1 TGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTT-AAAAGGGTGCCACAGA
*
29550 GTTATGGACTTAAAAGGG
64 GTTGTGGACTTAAAAGGG
* * * *
29568 TGCCACGGAGTTGTGGACTTAAAAGGGTGCTACGGAGTTGTGGTCTTAAAAGGGTGTCACGGAGT
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGT
29633 TGTGGACTTAAAAGGG
66 TGTGGACTTAAAAGGG
* * *
29649 ATGCCATGGAGTTATGGACTTAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAG
1 -TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAG
29714 TTGTGGACTTAAAAGGG
65 TTGTGGACTTAAAAGGG
* * * *
29731 TGCCACGGAGTTGTGGACTTAAAAGGGATGCCATGGAGTTATGGACTTAAAAGAGTGCCACGGAG
1 TGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAG
29796 TTGTGGACTTAAAAGGG
65 TTGTGGACTTAAAAGGG
* *
29813 TGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGTA-TTAAAAGGAATGCCACAGA
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGG-ACTTAAAAGG-GTGCCACAGA
29877 GTTGTGGACTTAAAAGGG
64 GTTGTGGACTTAAAAGGG
* *
29895 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAATGCCATAGAG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGG-GTGCCACAGAG
*
29960 TTGTGGACTTAAAAAGG
65 TTGTGGACTTAAAAGGG
29977 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGT
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGT
30042 TGTGGACTT-AAAGGG
66 TGTGGACTTAAAAGGG
* * *
30057 TGCCACAGAGTTGTGGACTAAAAAGGGTGCCACGGAGTTGTGGATTTTAAAAGGGTGCCACAGAG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGA-CTTAAAAGGGTGCCACAGAG
30122 TTGTGGACTTAAAAGGG
65 TTGTGGACTTAAAAGGG
*
30139 TACCACGGAGTTGTGGACTT
1 TGCCACGGAGTTGTGGACTT
30159 TGAAAAGGTC
Statistics
Matches: 693, Mismatches: 54, Indels: 19
0.90 0.07 0.02
Matches are distributed among these distances:
80 47 0.07
81 123 0.18
82 392 0.57
83 131 0.19
ACGTcount: A:0.29, C:0.14, G:0.34, T:0.23
Consensus pattern (81 bp):
TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGT
TGTGGACTTAAAAGGG
Found at i:29673 original size:109 final size:109
Alignment explanation
Indices: 29320--30158 Score: 1272
Period size: 109 Copynumber: 7.7 Consensus size: 109
29310 TGGAATGGGT
* * * *
29320 TGCCACCGATTTGTGAATTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAG
1 TGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAG
*
29385 TTGTGGACTTAAGAGGGATGCCACGGAGTTGTGGACTTAAAAGGGA
65 TTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGGA
* * *
29431 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTAAAAAGGGTGCCATGGAGT
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
* **
29496 TGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAAAGA
66 TGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGA
* * *
29541 TGCCACAGAGTTATGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCTACGGAGT
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
* *
29606 TGTGGTCTTAAAAGGGTGTCACGGAGTTGTGGACTTAAAAGGGA
66 TGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGA
* * * *
29650 TGCCATGGAGTTATGGACTTAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGT
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
29715 TGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGA
66 TGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGA
* * * *
29759 TGCCATGGAGTTATGGACTTAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGT
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
*
29824 TGTGGACTTAAAAGGGTGCCACGGAGTTGTGGTA-TTAAAAGGAA
66 TGTGGACTTAAAAGGGTGCCACGGAGTTGTGG-ACTTAAAAGGGA
*
29868 TGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
* ** *
29933 TGTGGACTTAAAAGGAATGCCATAGAGTTGTGGACTTAAAAAGG-
66 TGTGGACTTAAAAGG-GTGCCACGGAGTTGTGGACTTAAAAGGGA
*
29977 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGT
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
* *
30042 TGTGGACTT-AAAGGGTGCCACAGAGTTGTGGACTAAAAAGGG-
66 TGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGA
* * *
30084 TGCCACGGAGTTGTGGATTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTACCACGGAG
1 TGCCACGGAGTTGTGGA-CTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAG
30149 TTGTGGACTT
65 TTGTGGACTT
30159 TGAAAAGGTC
Statistics
Matches: 673, Mismatches: 50, Indels: 13
0.91 0.07 0.02
Matches are distributed among these distances:
107 41 0.06
108 58 0.09
109 389 0.58
110 154 0.23
111 31 0.05
ACGTcount: A:0.29, C:0.14, G:0.34, T:0.23
Consensus pattern (109 bp):
TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
TGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGA
Found at i:37986 original size:17 final size:17
Alignment explanation
Indices: 37964--37999 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
37954 CATTTCATAT
* *
37964 TTTTTCTTTTTTTTTTC
1 TTTTTCTTTCTTTCTTC
37981 TTTTTCTTTCTTTCTTC
1 TTTTTCTTTCTTTCTTC
37998 TT
1 TT
38000 CATCTTCCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTCTTTCTTTCTTC
Found at i:38935 original size:18 final size:18
Alignment explanation
Indices: 38914--38949 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
38904 TAATTAATCC
38914 TGAAACTCAAATTTATAT
1 TGAAACTCAAATTTATAT
38932 TGAAACTCAAATTTATAT
1 TGAAACTCAAATTTATAT
38950 AGATACATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.06, T:0.39
Consensus pattern (18 bp):
TGAAACTCAAATTTATAT
Found at i:40302 original size:22 final size:22
Alignment explanation
Indices: 40268--40354 Score: 79
Period size: 22 Copynumber: 4.0 Consensus size: 22
40258 CATAATACTC
* *
40268 TAAATAATAAATAATATAGTAA
1 TAAATGATTAATAATATAGTAA
* *
40290 TAAATGATTAATAACATTGTAA
1 TAAATGATTAATAATATAGTAA
* *
40312 T-GAT-ATTAATAATATTGTAA
1 TAAATGATTAATAATATAGTAA
** *
40332 TAAATGATGGATAAAATAGTAA
1 TAAATGATTAATAATATAGTAA
40354 T
1 T
40355 TAACAATTGA
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
20 16 0.31
21 4 0.08
22 32 0.62
ACGTcount: A:0.53, C:0.01, G:0.10, T:0.36
Consensus pattern (22 bp):
TAAATGATTAATAATATAGTAA
Found at i:40526 original size:22 final size:22
Alignment explanation
Indices: 40498--40546 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
40488 GGTAGTATGC
40498 TAGGTGAGCATATTAAGTGTGT
1 TAGGTGAGCATATTAAGTGTGT
*
40520 TAGGTGAGCATATTAGGTGTGT
1 TAGGTGAGCATATTAAGTGTGT
40542 TAGGT
1 TAGGT
40547 AACGTATTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.24, C:0.04, G:0.35, T:0.37
Consensus pattern (22 bp):
TAGGTGAGCATATTAAGTGTGT
Found at i:45374 original size:34 final size:34
Alignment explanation
Indices: 45296--45379 Score: 107
Period size: 34 Copynumber: 2.5 Consensus size: 34
45286 CTTTATTAAG
* ** **
45296 TGTGTTAGGTAAATATATTAGATGTGTTAGGTGT
1 TGTGTTAGGTGAGCATATTAGATGTGTTAGGTAA
45330 TGTGTTAGGTGAGCATATTA-AGTGTGTTAGGTAA
1 TGTGTTAGGTGAGCATATTAGA-TGTGTTAGGTAA
45364 TGTGTTAGGTGAGCAT
1 TGTGTTAGGTGAGCAT
45380 GATATTTTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
33 1 0.02
34 43 0.98
ACGTcount: A:0.25, C:0.02, G:0.32, T:0.40
Consensus pattern (34 bp):
TGTGTTAGGTGAGCATATTAGATGTGTTAGGTAA
Found at i:46080 original size:21 final size:22
Alignment explanation
Indices: 45960--46100 Score: 78
Period size: 22 Copynumber: 6.7 Consensus size: 22
45950 TAGTGGTAAG
* * * *
45960 ATAAAATATTAGTATATAATTG
1 ATAATATAATAGTAAATAATTA
*
45982 ATAACATAATAGTAAAT--TT-
1 ATAATATAATAGTAAATAATTA
* * *
46001 ATAAT-TAAAAATAAATAA-TG
1 ATAATATAATAGTAAATAATTA
* * * *
46021 ATAAGATAATAGTATATGATAA
1 ATAATATAATAGTAAATAATTA
* ** * *
46043 ATAAAATAATAACAAATTATTG
1 ATAATATAATAGTAAATAATTA
*
46065 ATAA-ATAGTAGTAAATAATTA
1 ATAATATAATAGTAAATAATTA
46086 ATAATATAATAGTAA
1 ATAATATAATAGTAA
46101 CTAACGAAAT
Statistics
Matches: 87, Mismatches: 26, Indels: 12
0.70 0.21 0.10
Matches are distributed among these distances:
18 9 0.10
19 5 0.06
20 6 0.07
21 25 0.29
22 42 0.48
ACGTcount: A:0.57, C:0.01, G:0.08, T:0.34
Consensus pattern (22 bp):
ATAATATAATAGTAAATAATTA
Found at i:46095 original size:43 final size:42
Alignment explanation
Indices: 45978--46096 Score: 111
Period size: 43 Copynumber: 2.9 Consensus size: 42
45968 TTAGTATATA
* *
45978 ATTGATAACATAATAGTAAAT-TT-ATAAT-TAAAAATAAAT
1 ATTGATAACATAATAGTAAATATTAATAATATAATAACAAAT
* * * * *
46017 AATGATAAGATAATAGTATATGATAAATAAAATAATAACAAATT
1 ATTGATAACATAATAGTAAAT-ATTAATAATATAATAACAAA-T
*
46061 ATTGATAA-ATAGTAGTAAATAATTAATAATATAATA
1 ATTGATAACATAATAGTAAAT-ATTAATAATATAATA
46097 GTAACTAACG
Statistics
Matches: 62, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
39 18 0.29
41 1 0.02
42 4 0.06
43 31 0.50
44 8 0.13
ACGTcount: A:0.57, C:0.02, G:0.08, T:0.34
Consensus pattern (42 bp):
ATTGATAACATAATAGTAAATATTAATAATATAATAACAAAT
Found at i:47636 original size:33 final size:34
Alignment explanation
Indices: 47584--47656 Score: 105
Period size: 33 Copynumber: 2.2 Consensus size: 34
47574 TAATGTATTA
47584 TATATTTTATATAAATTTTAATATATTAATAAT-T
1 TATATTTTATATAAATTTTAATATATTAAT-ATGT
* *
47618 TATATTTT-TATAACTTTTAATATATTCATATGT
1 TATATTTTATATAAATTTTAATATATTAATATGT
47651 TATATT
1 TATATT
47657 ATATTTTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
32 2 0.06
33 26 0.72
34 8 0.22
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (34 bp):
TATATTTTATATAAATTTTAATATATTAATATGT
Found at i:48390 original size:2 final size:2
Alignment explanation
Indices: 48383--48415 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
48373 GTACTCCCCT
48383 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
48416 TCATCTCTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:49736 original size:28 final size:28
Alignment explanation
Indices: 49677--49741 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 28
49667 CCACCCATTT
* *
49677 ATTTGTTAAAAATGGTGGTTATTTTGTG
1 ATTTGTCAAAAATGATGGTTATTTTGTG
*
49705 -TTTGTCAAAAATGATGGTTTTCTTTG-G
1 ATTTGTCAAAAATGATGGTTAT-TTTGTG
49732 ATTTGTCAAA
1 ATTTGTCAAA
49742 TATGGAGGCT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 19 0.59
28 13 0.41
ACGTcount: A:0.26, C:0.05, G:0.22, T:0.48
Consensus pattern (28 bp):
ATTTGTCAAAAATGATGGTTATTTTGTG
Found at i:50282 original size:34 final size:33
Alignment explanation
Indices: 50241--50358 Score: 166
Period size: 34 Copynumber: 3.5 Consensus size: 33
50231 GGTAAAAACT
*
50241 ACCATTTAATCAACAATGGCAACCTACCAAATC
1 ACCATTTAATCAACAATGGTAACCTACCAAATC
*
50274 TACCATTTAGTCAACAATGGTAAGCC-ACCAAATC
1 -ACCATTTAATCAACAATGGTAA-CCTACCAAATC
* *
50308 ACCCATTTAATCAATAATGGTAAACTACCAAATC
1 A-CCATTTAATCAACAATGGTAACCTACCAAATC
50342 ACCATTTAATCAACAAT
1 ACCATTTAATCAACAAT
50359 TCTCCCACTT
Statistics
Matches: 75, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
33 17 0.23
34 56 0.75
35 2 0.03
ACGTcount: A:0.42, C:0.26, G:0.07, T:0.25
Consensus pattern (33 bp):
ACCATTTAATCAACAATGGTAACCTACCAAATC
Found at i:59586 original size:2 final size:2
Alignment explanation
Indices: 59581--59607 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
59571 TATATATATA
59581 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
59608 TTAAGTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:60310 original size:21 final size:19
Alignment explanation
Indices: 60254--60312 Score: 55
Period size: 21 Copynumber: 2.9 Consensus size: 19
60244 AATAATATTT
*
60254 AAAATTAAATTAAATTTTA
1 AAAATTAATTTAAATTTTA
*
60273 AAAATATTATTTAAAATTTGATA
1 AAAAT-TAATTT-AAATTT--TA
*
60296 TAAATTAATTTAAATTT
1 AAAATTAATTTAAATTT
60313 ATTTAACTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
19 5 0.16
20 4 0.12
21 12 0.38
22 5 0.16
23 6 0.19
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (19 bp):
AAAATTAATTTAAATTTTA
Found at i:61164 original size:21 final size:23
Alignment explanation
Indices: 61138--61179 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
61128 TTATTATTGT
61138 TATTTTA-TT-TTTTTCATGTCA
1 TATTTTAGTTATTTTTCATGTCA
*
61159 TATTTTAGTTATTTTTTATGT
1 TATTTTAGTTATTTTTCATGT
61180 TATGTTGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 2 0.11
23 9 0.50
ACGTcount: A:0.19, C:0.05, G:0.07, T:0.69
Consensus pattern (23 bp):
TATTTTAGTTATTTTTCATGTCA
Found at i:61891 original size:2 final size:2
Alignment explanation
Indices: 61884--61914 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
61874 TTAGTGTATG
61884 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 T
61915 TTACCAAGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:64739 original size:4 final size:4
Alignment explanation
Indices: 64726--64755 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
64716 TATATATATA
*
64726 TATG TCTG TATG TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TATG TA
64756 CTAACAAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.23, C:0.03, G:0.23, T:0.50
Consensus pattern (4 bp):
TATG
Done.