Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1641
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: 141022
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:2019 original size:15 final size:15
Alignment explanation
Indices: 1999--2029 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1989 TAAAAATGTC
*
1999 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
2014 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
2029 C
1 C
2030 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:4120 original size:13 final size:13
Alignment explanation
Indices: 4102--4139 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
4092 CATTTTTCTT
4102 TGTATCGATACAA
1 TGTATCGATACAA
*
4115 TGTATCGATACAC
1 TGTATCGATACAA
4128 TGTATCGATACA
1 TGTATCGATACA
4140 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:6705 original size:13 final size:13
Alignment explanation
Indices: 6687--6712 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6677 TACACCAAGT
6687 ATGTATCGATACA
1 ATGTATCGATACA
6700 ATGTATCGATACA
1 ATGTATCGATACA
6713 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:6710 original size:32 final size:33
Alignment explanation
Indices: 6669--6732 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
6659 TAGCCAAACT
* **
6669 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
6701 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
6733 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:7879 original size:22 final size:23
Alignment explanation
Indices: 7851--7895 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
7841 ATAAAAAAAA
7851 AATTTCT-CCCTTTGTCAAATGT
1 AATTTCTCCCCTTTGTCAAATGT
7873 AATTTCTCCCCCTTTGTCAAATG
1 AATTTCT-CCCCTTTGTCAAATG
7896 CCAAATTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.33
24 14 0.67
ACGTcount: A:0.22, C:0.27, G:0.09, T:0.42
Consensus pattern (23 bp):
AATTTCTCCCCTTTGTCAAATGT
Found at i:15149 original size:20 final size:20
Alignment explanation
Indices: 15124--15286 Score: 98
Period size: 20 Copynumber: 7.6 Consensus size: 20
15114 GTAAAAAGAT
*
15124 AGAATGTATCGGTACATTGA
1 AGAATGTATCGATACATTGA
*
15144 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
*
15164 TA-CATGTATCGATACATTGA
1 -AGAATGTATCGATACATTGA
* *
15184 AAAATGTATCAATACATCTGGATAAAAAGA
1 AGAATGTATCGATACA--T---T-----GA
*
15214 CAGAATGTATCAATACATTGA
1 -AGAATGTATCGATACATTGA
*
15235 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
* *
15255 TA-CATTTATCGATACATTGA
1 -AGAATGTATCGATACATTGA
15275 A-AATTGTATCGA
1 AGAA-TGTATCGA
15287 CATATCTGGG
Statistics
Matches: 114, Mismatches: 14, Indels: 30
0.72 0.09 0.19
Matches are distributed among these distances:
19 3 0.03
20 86 0.75
21 4 0.04
22 1 0.01
25 1 0.01
26 1 0.01
29 1 0.01
30 2 0.02
31 15 0.13
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:15152 original size:51 final size:50
Alignment explanation
Indices: 15076--15251 Score: 183
Period size: 51 Copynumber: 3.7 Consensus size: 50
15066 TTTTAACTAG
* *
15076 ATGTATCGATACATTGAATAATGTATTGATACATCTGGGTAAAAAGATAGA
1 ATGTATCGATACATTGAAGAATGTATCGATACATCT-GGTAAAAAGATAGA
* * *
15127 ATGTATCGGTACATTGAAGAATGTATCGATACA--T--T-----CATA-C
1 ATGTATCGATACATTGAAGAATGTATCGATACATCTGGTAAAAAGATAGA
* * *
15167 ATGTATCGATACATTGAAAAATGTATCAATACATCTGGATAAAAAGACAGA
1 ATGTATCGATACATTGAAGAATGTATCGATACATCTGG-TAAAAAGATAGA
*
15218 ATGTATCAATACATTGAAGAATGTATCGATACAT
1 ATGTATCGATACATTGAAGAATGTATCGATACAT
15252 TCATACATTT
Statistics
Matches: 100, Mismatches: 14, Indels: 22
0.74 0.10 0.16
Matches are distributed among these distances:
40 30 0.30
41 3 0.03
42 1 0.01
45 1 0.01
46 1 0.01
49 1 0.01
50 2 0.02
51 61 0.61
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.30
Consensus pattern (50 bp):
ATGTATCGATACATTGAAGAATGTATCGATACATCTGGTAAAAAGATAGA
Found at i:15231 original size:91 final size:91
Alignment explanation
Indices: 15076--15302 Score: 355
Period size: 91 Copynumber: 2.5 Consensus size: 91
15066 TTTTAACTAG
* * * **
15076 ATGTATCGATACATTGAATAATGTATTGATACATCTGGGTAAAAAGATAGAATGTATCGGTACAT
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGACAGAATGTATCAATACAT
15141 TGAAGAATGTATCGATACATTCATAC
66 TGAAGAATGTATCGATACATTCATAC
* *
15167 ATGTATCGATACATTGAAAAATGTATCAATACATCTGGATAAAAAGACAGAATGTATCAATACAT
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGACAGAATGTATCAATACAT
15232 TGAAGAATGTATCGATACATTCATAC
66 TGAAGAATGTATCGATACATTCATAC
* * * *
15258 ATTTATCGATACATTGAAAATTGTATCGACATATCTGGGTAAAAA
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAA
15303 TGTGATTTTT
Statistics
Matches: 123, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
91 123 1.00
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (91 bp):
ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGACAGAATGTATCAATACAT
TGAAGAATGTATCGATACATTCATAC
Found at i:16610 original size:29 final size:30
Alignment explanation
Indices: 16395--16785 Score: 277
Period size: 28 Copynumber: 13.2 Consensus size: 30
16385 AAAGTAGTGA
* ** *
16395 TTTGAAAAGGGTTGCCACCGACTTGCGTGGGT
1 TTTGAAAAGAGTTGCCACTAACTT--GTGGGC
* * * *
16427 TTTAAAAAAAGGTGCCACCAACTTGTGTGGCC
1 TTTGAAAAGAGTTGCCACTAACTTGTG-GG-C
* * **
16459 TTTGAAAAAAGTT-CTCACCGATTTGTGTGGGC
1 TTTGAAAAGAGTTGC-CA-CTAACT-TGTGGGC
* *
16491 TTTGAAAAGAGTTACCACTGACTTGTGGGC
1 TTTGAAAAGAGTTGCCACTAACTTGTGGGC
* * *
16521 TTTGAAAAAAGTTACCACTGACTTGTGGGC
1 TTTGAAAAGAGTTGCCACTAACTTGTGGGC
* * *
16551 TTTGAAAAGAGTTACCACTAGCTTGTAGGC
1 TTTGAAAAGAGTTGCCACTAACTTGTGGGC
*
16581 TTTGAAAAGAG-TGCCACTAACTTATGGGC
1 TTTGAAAAGAGTTGCCACTAACTTGTGGGC
* *
16610 TTTG-AAAG-GATGCCATTAACTTGTGGGC
1 TTTGAAAAGAGTTGCCACTAACTTGTGGGC
* * * *
16638 TTTG-AAAG-GGTGCAATTGACTTGTGGGC
1 TTTGAAAAGAGTTGCCACTAACTTGTGGGC
* * * * *
16666 TTTGAGAAG-GATGCCATTGACTTGTTGGC
1 TTTGAAAAGAGTTGCCACTAACTTGTGGGC
**
16695 TTTGAAAAG-G-TGCCACTAACTTGTGGTTT
1 TTTGAAAAGAGTTGCCACTAACTTGTGG-GC
*
16724 TTTG--AAGAGATGCCACTAACTTGTGGGC
1 TTTGAAAAGAGTTGCCACTAACTTGTGGGC
* * *
16752 TTT-AAAAG-GATGCCATTGACTTGTGGGC
1 TTTGAAAAGAGTTGCCACTAACTTGTGGGC
16780 TTTGAA
1 TTTGAA
16786 GAGATGAACG
Statistics
Matches: 301, Mismatches: 44, Indels: 31
0.80 0.12 0.08
Matches are distributed among these distances:
27 4 0.01
28 87 0.29
29 72 0.24
30 76 0.25
31 5 0.02
32 47 0.16
33 6 0.02
34 4 0.01
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (30 bp):
TTTGAAAAGAGTTGCCACTAACTTGTGGGC
Found at i:16676 original size:57 final size:58
Alignment explanation
Indices: 16484--16791 Score: 286
Period size: 57 Copynumber: 5.4 Consensus size: 58
16474 CACCGATTTG
* * * * * * *
16484 TGTGGGCTTTGAAAAGAGTTACCACTGACTTGTGGGCTTTGAAAAAAGTTACCACTGACT
1 TGTGGGCTTTGAGAAGAGATGCCACTAACTTGTGGGCTTTG--AAAGGGTGCCACTGACT
* * * * * * *
16544 TGTGGGCTTTGAAAAGAGTTACCACTAGCTTGTAGGCTTTGAAAAGAGTGCCACTAACT
1 TGTGGGCTTTGAGAAGAGATGCCACTAACTTGTGGGCTTTG-AAAGGGTGCCACTGACT
* * * *
16603 TATGGGCTTTGA-AAG-GATGCCATTAACTTGTGGGCTTTGAAAGGGTGCAATTGACT
1 TGTGGGCTTTGAGAAGAGATGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * *
16659 TGTGGGCTTTGAGAAG-GATGCCATTGACTTGTTGGCTTTGAAAAGGTGCCACTAACT
1 TGTGGGCTTTGAGAAGAGATGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTGACT
* ** * * *
16716 TGT-GGTTTTTTGAAGAGATGCCACTAACTTGTGGGCTTTAAAAGGATGCCATTGACT
1 TGTGGGCTTTGAGAAGAGATGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTGACT
16773 TGTGGGCTTT--GAAGAGATG
1 TGTGGGCTTTGAGAAGAGATG
16792 AACGTTCTAG
Statistics
Matches: 208, Mismatches: 37, Indels: 10
0.82 0.15 0.04
Matches are distributed among these distances:
56 42 0.20
57 96 0.46
58 8 0.04
59 24 0.12
60 38 0.18
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (58 bp):
TGTGGGCTTTGAGAAGAGATGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTGACT
Found at i:16681 original size:85 final size:84
Alignment explanation
Indices: 16484--16785 Score: 259
Period size: 85 Copynumber: 3.5 Consensus size: 84
16474 CACCGATTTG
* * * * * *
16484 TGTGGGCTTTGAAAAGAGTTACCACTGACTTGTGGGCTTTGAAAAAAGTTACCACTGACTTGTGG
1 TGTGGGCTTTG-AAAG-GATGCCATTGACTTGTGGGCTTTG---AAAGGTGCCACTAACTTGTGG
* * * *
16549 -GCTTTGAAAAGAGTTACCACTAGCT
61 TGCTTTG--AAGAGATGCAACTAACT
* * * * * *
16574 TGTAGGCTTTGAAAAGAGTGCCACTAACTTATGGGCTTTGAAAGGATGCCATTAACTTGTGG-GC
1 TGTGGGCTTTGAAAGGA-TGCCATTGACTTGTGGGCTTTGAAAGG-TGCCACTAACTTGTGGTGC
* * *
16638 TTTGAA-AGGGTGCAATTGACT
64 TTTGAAGA-GATGCAACTAACT
* **
16659 TGTGGGCTTTGAGAAGGATGCCATTGACTTGTTGGCTTTGAAAAGGTGCCACTAACTTGTGGTTT
1 TGTGGGCTTTGA-AAGGATGCCATTGACTTGTGGGCTTTG-AAAGGTGCCACTAACTTGTGGTGC
*
16724 TTTGAAGAGATGCCACTAACT
64 TTTGAAGAGATGCAACTAACT
*
16745 TGTGGGCTTTAAAAGGATGCCATTGACTTGTGGGCTTTGAA
1 TGTGGGCTTTGAAAGGATGCCATTGACTTGTGGGCTTTGAA
16786 GAGATGAACG
Statistics
Matches: 174, Mismatches: 31, Indels: 20
0.77 0.14 0.09
Matches are distributed among these distances:
84 3 0.02
85 79 0.45
86 39 0.22
87 20 0.11
88 1 0.01
89 22 0.13
90 10 0.06
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.32
Consensus pattern (84 bp):
TGTGGGCTTTGAAAGGATGCCATTGACTTGTGGGCTTTGAAAGGTGCCACTAACTTGTGGTGCTT
TGAAGAGATGCAACTAACT
Found at i:18034 original size:10 final size:10
Alignment explanation
Indices: 18019--18045 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
18009 ATTTGTTTGT
18019 TTTTTTTTAA
1 TTTTTTTTAA
18029 TTTTTTTTAA
1 TTTTTTTTAA
18039 TTTTTTT
1 TTTTTTT
18046 GTTTTTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTTTAA
Found at i:22268 original size:21 final size:21
Alignment explanation
Indices: 22235--22275 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
22225 CTAAGTAAAA
22235 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
22256 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
22276 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:22341 original size:21 final size:20
Alignment explanation
Indices: 22312--22368 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
22302 AAAACCCTGA
**
22312 AAAGTATCGATACACATTTT
1 AAAGTATCGATACACATTGC
*
22332 AAATGTATCGATACAGATTGC
1 AAA-GTATCGATACACATTGC
*
22353 ATAGTATCGATACACA
1 AAAGTATCGATACACA
22369 CAAATATGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (20 bp):
AAAGTATCGATACACATTGC
Found at i:22439 original size:53 final size:53
Alignment explanation
Indices: 22356--22492 Score: 229
Period size: 53 Copynumber: 2.6 Consensus size: 53
22346 AGATTGCATA
* *
22356 GTATCGATACACACAAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
1 GTATCGATACACAC-AATATGTATCGATACAGGACACTGGCAGTAGCAAAATTT
*
22410 GTATCGATACACACAATATGTATCGATACAGGTCACTGGCAGTAGCAAAATTT
1 GTATCGATACACACAATATGTATCGATACAGGACACTGGCAGTAGCAAAATTT
*
22463 GTATCGATACACAAAATATGTATCGATACA
1 GTATCGATACACACAATATGTATCGATACA
22493 TTGGTAGTAG
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
53 65 0.82
54 14 0.18
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (53 bp):
GTATCGATACACACAATATGTATCGATACAGGACACTGGCAGTAGCAAAATTT
Found at i:22479 original size:19 final size:19
Alignment explanation
Indices: 22455--22492 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
22445 CTGGCAGTAG
*
22455 CAAAATTTGTATCGATACA
1 CAAAATATGTATCGATACA
22474 CAAAATATGTATCGATACA
1 CAAAATATGTATCGATACA
22493 TTGGTAGTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.29
Consensus pattern (19 bp):
CAAAATATGTATCGATACA
Found at i:22613 original size:47 final size:47
Alignment explanation
Indices: 22547--22643 Score: 160
Period size: 47 Copynumber: 2.1 Consensus size: 47
22537 GTATCGATAC
*
22547 ATCACTTTCATGTATCGTTAAAAATCACTGTTCA-CACTATTCACGT
1 ATCACTTTCATGTACCGTTAAAAATCACTGTTCATCACTATTCACGT
*
22593 ATCACTATTCATGTACCGTTAAAAATCACTGTTCATCACTATTCATGT
1 ATCACT-TTCATGTACCGTTAAAAATCACTGTTCATCACTATTCACGT
22641 ATC
1 ATC
22644 GATACATCAT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
46 6 0.13
47 27 0.57
48 14 0.30
ACGTcount: A:0.31, C:0.24, G:0.08, T:0.37
Consensus pattern (47 bp):
ATCACTTTCATGTACCGTTAAAAATCACTGTTCATCACTATTCACGT
Found at i:23919 original size:47 final size:47
Alignment explanation
Indices: 23865--23960 Score: 192
Period size: 47 Copynumber: 2.0 Consensus size: 47
23855 ATCCATGGCC
23865 TCTTTAATAGAAAGTTATAAGATGGATTGATATCCATTACTTGAAAG
1 TCTTTAATAGAAAGTTATAAGATGGATTGATATCCATTACTTGAAAG
23912 TCTTTAATAGAAAGTTATAAGATGGATTGATATCCATTACTTGAAAG
1 TCTTTAATAGAAAGTTATAAGATGGATTGATATCCATTACTTGAAAG
23959 TC
1 TC
23961 AACTCCATAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (47 bp):
TCTTTAATAGAAAGTTATAAGATGGATTGATATCCATTACTTGAAAG
Found at i:33346 original size:51 final size:49
Alignment explanation
Indices: 33286--33462 Score: 192
Period size: 51 Copynumber: 3.7 Consensus size: 49
33276 TTTTAACTAC
* *
33286 ATGTATCGATACATTGAATAATGTATTGATACATCTGAGTAAAAAGATAGA
1 ATGTATCGATACATTGAAGAATGTATCGATACAT-T-AGTAAAAAGATAGA
* *
33337 ATGTATCGATACATTGAAGAATGTATCGATACA-T--T-----CATA-C
1 ATGTATCGATACATTGAAGAATGTATCGATACATTAGTAAAAAGATAGA
* * *
33377 ATGTATCGATACATTGAAAAATGTATCCATACATATAGGTAAAAAGACAGA
1 ATGTATCGATACATTGAAGAATGTATCGATACAT-TA-GTAAAAAGATAGA
33428 ATGTATCGATACATTGAAGAATGTATCGATACATT
1 ATGTATCGATACATTGAAGAATGTATCGATACATT
33463 CATACATGTA
Statistics
Matches: 104, Mismatches: 11, Indels: 23
0.75 0.08 0.17
Matches are distributed among these distances:
40 31 0.30
41 3 0.03
42 1 0.01
45 1 0.01
46 1 0.01
49 1 0.01
50 3 0.03
51 63 0.61
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.31
Consensus pattern (49 bp):
ATGTATCGATACATTGAAGAATGTATCGATACATTAGTAAAAAGATAGA
Found at i:33359 original size:20 final size:20
Alignment explanation
Indices: 33334--33501 Score: 133
Period size: 20 Copynumber: 7.8 Consensus size: 20
33324 GTAAAAAGAT
33334 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
*
33354 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
*
33374 TA-CATGTATCGATACATTGA
1 -AGAATGTATCGATACATTGA
* *
33394 AAAATGTATCCATACATATAGGTAAAAAGA
1 AGAATGTATCGATAC--AT---T-----GA
33424 CAGAATGTATCGATACATTGA
1 -AGAATGTATCGATACATTGA
*
33445 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
*
33465 TA-CATGTATCGATACATTGA
1 -AGAATGTATCGATACATTGA
* *
33485 AAAATGGATCGATACAT
1 AGAATGTATCGATACAT
33502 CTGGGTAAAA
Statistics
Matches: 121, Mismatches: 12, Indels: 30
0.74 0.07 0.18
Matches are distributed among these distances:
19 2 0.02
20 94 0.78
21 4 0.03
22 2 0.02
25 1 0.01
26 1 0.01
29 2 0.02
30 2 0.02
31 13 0.11
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:33438 original size:91 final size:90
Alignment explanation
Indices: 33283--33512 Score: 379
Period size: 91 Copynumber: 2.5 Consensus size: 90
33273 TAATTTTAAC
* * *
33283 TACATGTATCGATACATTGAATAATGTATTGATACATCTGAGTAAAAAGATAGAATGTATCGATA
1 TACATGTATCGATACATTGAAAAATGTATCGATACATCTG-GTAAAAAGACAGAATGTATCGATA
33348 CATTGAAGAATGTATCGATACATTCA
65 CATTGAAGAATGTATCGATACATTCA
* *
33374 TACATGTATCGATACATTGAAAAATGTATCCATACATATAGGTAAAAAGACAGAATGTATCGATA
1 TACATGTATCGATACATTGAAAAATGTATCGATACATCT-GGTAAAAAGACAGAATGTATCGATA
33439 CATTGAAGAATGTATCGATACATTCA
65 CATTGAAGAATGTATCGATACATTCA
*
33465 TACATGTATCGATACATTGAAAAATGGATCGATACATCTGGGTAAAAA
1 TACATGTATCGATACATTGAAAAATGTATCGATACATCT-GGTAAAAA
33513 TGTAATTTTT
Statistics
Matches: 129, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
91 128 0.99
92 1 0.01
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.30
Consensus pattern (90 bp):
TACATGTATCGATACATTGAAAAATGTATCGATACATCTGGTAAAAAGACAGAATGTATCGATAC
ATTGAAGAATGTATCGATACATTCA
Found at i:35937 original size:37 final size:37
Alignment explanation
Indices: 35896--35969 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
35886 TTTTGATGTG
35896 ACATATAAAACATAATGAATGATTCATGCAAATTTTT
1 ACATATAAAACATAATGAATGATTCATGCAAATTTTT
*
35933 ACATATAAAACATAGTGAATGATTCATGCAAATTTTT
1 ACATATAAAACATAATGAATGATTCATGCAAATTTTT
35970 GTTTTTCTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.35
Consensus pattern (37 bp):
ACATATAAAACATAATGAATGATTCATGCAAATTTTT
Found at i:36616 original size:3 final size:3
Alignment explanation
Indices: 36602--36642 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
36592 TCAGTCAACT
* * *
36602 TCA TCA TTA TCA TCA TCA TCA TCT TCA TCA TCT TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
36643 TTTGACAGTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.27, C:0.32, G:0.00, T:0.41
Consensus pattern (3 bp):
TCA
Found at i:36616 original size:9 final size:9
Alignment explanation
Indices: 36610--36644 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
36600 CTTCATCATT
*
36610 ATCATCATC
1 ATCATCTTC
36619 ATCATCTTC
1 ATCATCTTC
36628 ATCATCTTC
1 ATCATCTTC
36637 ATCATCTT
1 ATCATCTT
36645 TGACAGTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.26, C:0.31, G:0.00, T:0.43
Consensus pattern (9 bp):
ATCATCTTC
Found at i:38334 original size:19 final size:19
Alignment explanation
Indices: 38291--38339 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
38281 TTTCATGTAG
* *
38291 CGATACAATTGAGTATGTAT
1 CGATACAA-TGAGCATGCAT
*
38311 TGATACAATGAGCATGCAT
1 CGATACAATGAGCATGCAT
38330 CGATACAATG
1 CGATACAATG
38340 TATCGATACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (19 bp):
CGATACAATGAGCATGCAT
Found at i:38605 original size:21 final size:20
Alignment explanation
Indices: 38581--38620 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
38571 TTTAAAAGAA
38581 TAAAACTTGTTTACGATTTTT
1 TAAAACTT-TTTACGATTTTT
* *
38602 TAAATCTTTTTTCGATTTT
1 TAAAACTTTTTACGATTTT
38621 ATTCATACTT
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:0.25, C:0.10, G:0.07, T:0.57
Consensus pattern (20 bp):
TAAAACTTTTTACGATTTTT
Found at i:38873 original size:21 final size:21
Alignment explanation
Indices: 38840--38880 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
38830 CTAAGTAAAA
38840 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
38861 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
38881 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:38946 original size:21 final size:20
Alignment explanation
Indices: 38919--38991 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
38909 AACCCTGAGA
38919 AGTATCGATACACATTTTGAAT
1 AGTATCGATACACA--TTGAAT
* *
38941 -GTATCGATACAGATTGCAT
1 AGTATCGATACACATTGAAT
**
38960 AGTATCGATACACA-CAAAT
1 AGTATCGATACACATTGAAT
38979 ATGTATCGATACA
1 A-GTATCGATACA
38992 GGACATTGGC
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 8 0.19
20 23 0.53
21 12 0.28
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.30
Consensus pattern (20 bp):
AGTATCGATACACATTGAAT
Found at i:39044 original size:53 final size:53
Alignment explanation
Indices: 38961--39097 Score: 229
Period size: 53 Copynumber: 2.6 Consensus size: 53
38951 AGATTGCATA
* *
38961 GTATCGATACACACAAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
1 GTATCGATACACAC-AATATGTATCGATACAGGACACTAGCAGTAGCCAAATTT
*
39015 GTATCGATACACACAATATGTATCGATACAGGTCACTAGCAGTAGCCAAATTT
1 GTATCGATACACACAATATGTATCGATACAGGACACTAGCAGTAGCCAAATTT
*
39068 GTATCGATACACAAAATATGTATCGATACA
1 GTATCGATACACACAATATGTATCGATACA
39098 TTGGTAGTAG
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
53 65 0.82
54 14 0.18
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (53 bp):
GTATCGATACACACAATATGTATCGATACAGGACACTAGCAGTAGCCAAATTT
Found at i:39140 original size:10 final size:10
Alignment explanation
Indices: 39121--39151 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
39111 AATCTCATTT
39121 TCACTGTTCA
1 TCACTGTTCA
*
39131 TCACTATTCA
1 TCACTGTTCA
39141 TCACTGTTCA
1 TCACTGTTCA
39151 T
1 T
39152 ATATCGATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.23, C:0.29, G:0.06, T:0.42
Consensus pattern (10 bp):
TCACTGTTCA
Found at i:39708 original size:34 final size:35
Alignment explanation
Indices: 39645--39711 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
39635 CTAAGTGATT
39645 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
39681 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
39712 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:40859 original size:28 final size:28
Alignment explanation
Indices: 40819--40920 Score: 134
Period size: 28 Copynumber: 3.6 Consensus size: 28
40809 ATTTTCATCT
*
40819 AGGGGATACTCCAACCCCGTTA-TTTCTG
1 AGGGGATACTCCAACCCCATTATTTTC-G
**
40847 AGGGGATACTCCAACCTTATTATTTTCG
1 AGGGGATACTCCAACCCCATTATTTTCG
* *
40875 AGGGGATACTCCAACCCTATCATTTTCG
1 AGGGGATACTCCAACCCCATTATTTTCG
*
40903 AGGGGATACTCGAACCCC
1 AGGGGATACTCCAACCCC
40921 GTTTTCACTT
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
28 62 0.94
29 4 0.06
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (28 bp):
AGGGGATACTCCAACCCCATTATTTTCG
Found at i:42952 original size:31 final size:31
Alignment explanation
Indices: 42917--42992 Score: 152
Period size: 31 Copynumber: 2.5 Consensus size: 31
42907 TACATGGAAG
42917 AATGTATCGATACATTTGGGCCAAAACCCAA
1 AATGTATCGATACATTTGGGCCAAAACCCAA
42948 AATGTATCGATACATTTGGGCCAAAACCCAA
1 AATGTATCGATACATTTGGGCCAAAACCCAA
42979 AATGTATCGATACA
1 AATGTATCGATACA
42993 ATAAATAATT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.24
Consensus pattern (31 bp):
AATGTATCGATACATTTGGGCCAAAACCCAA
Found at i:43010 original size:51 final size:50
Alignment explanation
Indices: 42946--43066 Score: 134
Period size: 51 Copynumber: 2.4 Consensus size: 50
42936 GCCAAAACCC
* * * *
42946 AAAATGTATCGATACATTTGGGCCAAAACCCAAAATGTATCGATACAATA
1 AAAATGTATCGATACATTTAGGCAAAAACCCAAAATATATCAATACAATA
* * ** *
42996 AATAATTTATCGATACATGTCAGTTAAAAACCCAGAATATATCAATACAATA
1 AA-AATGTATCGATACAT-TTAGGCAAAAACCCAAAATATATCAATACAATA
*
43048 GAAATGTATCGATACATTT
1 AAAATGTATCGATACATTT
43067 TCCTTCAAAA
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
50 3 0.05
51 28 0.49
52 26 0.46
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.28
Consensus pattern (50 bp):
AAAATGTATCGATACATTTAGGCAAAAACCCAAAATATATCAATACAATA
Found at i:43588 original size:51 final size:51
Alignment explanation
Indices: 43532--43646 Score: 151
Period size: 51 Copynumber: 2.3 Consensus size: 51
43522 GCCTTCTTAC
* * * * *
43532 TAGGTGCCAACTTATGTGGACTTGGATTTTATAGGGTTTAACCT-TCTCATA
1 TAGGTGCCAACTAATGTGAACTTGGACTTTATAGGGCTTAACCTCCCT-ATA
*
43583 TAGGTGCCAGCTAATGTGAACTTGGACTTTATAGGGCTTAACCTCCCTATA
1 TAGGTGCCAACTAATGTGAACTTGGACTTTATAGGGCTTAACCTCCCTATA
*
43634 TAAGTGCCAACTA
1 TAGGTGCCAACTA
43647 GGATGGATGT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
51 53 0.96
52 2 0.04
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (51 bp):
TAGGTGCCAACTAATGTGAACTTGGACTTTATAGGGCTTAACCTCCCTATA
Found at i:43875 original size:52 final size:52
Alignment explanation
Indices: 43696--43950 Score: 176
Period size: 51 Copynumber: 5.0 Consensus size: 52
43686 ACGTACTAGC
* * * * * *
43696 TAGACTTTGACTTTATAA-GCTTAACCTCCCTATATAGGTGCCAGCTAATTG
1 TAGACTTAGATTTTATAAGGCTTGACCTCCCTATACAGGTGCTAACTAATTG
* * * * * * * * * * *
43747 TGGATTTAGATTCTGTAAGGGTAGACCTCTCTATACAGGTG-TCAGTTAGTG
1 TAGACTTAGATTTTATAAGGCTTGACCTCCCTATACAGGTGCTAACTAATTG
* * *
43798 TGGACTTAGATTTTATAGGGCTTGACCTCCCTATATAGGTGCTAACTAATTG
1 TAGACTTAGATTTTATAAGGCTTGACCTCCCTATACAGGTGCTAACTAATTG
* * * * *
43850 TAGACTTAGATTTTATAAGGTTTGACCTCCTTATACAAGTGCTAGC-AAATG
1 TAGACTTAGATTTTATAAGGCTTGACCTCCCTATACAGGTGCTAACTAATTG
* * * * * * * *
43901 T-GAACATAGGTTCTATAAAGTTTGACCACACTATACAGGTGCCAACTAAT
1 TAG-ACTTAGATTTTATAAGGCTTGACCTCCCTATACAGGTGCTAACTAAT
43951 GTGGATTTTG
Statistics
Matches: 152, Mismatches: 48, Indels: 7
0.73 0.23 0.03
Matches are distributed among these distances:
50 1 0.01
51 87 0.57
52 64 0.42
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.34
Consensus pattern (52 bp):
TAGACTTAGATTTTATAAGGCTTGACCTCCCTATACAGGTGCTAACTAATTG
Found at i:43967 original size:51 final size:49
Alignment explanation
Indices: 43723--44079 Score: 169
Period size: 51 Copynumber: 7.0 Consensus size: 49
43713 AGCTTAACCT
* * * * * *
43723 CCCTATATAGGTGCCAGCTAATTGTGGATTTAGATTCTGTAAGGGTAGAC
1 CCCTATATAGGTGCCAACTAA-TGTGGATTTTGACTCTATAAGGTTTGAC
* * ** * * * * * * *
43773 CTCTCTATACAGGTGTCAGTTAGTGTGGACTTAGATTTTATAGGGCTTGACC
1 C-C-CTATATAGGTGCCAACTAATGTGGATTTTGACTCTATAAGGTTTGA-C
* * * * * *
43825 TCCCTATATAGGTGCTAACTAATTGTAGACTTAGATTTTATAAGGTTTGAC
1 -CCCTATATAGGTGCCAACTAA-TGTGGATTTTGACTCTATAAGGTTTGAC
* * * * * * ** * ** *
43876 CTCCTTATACAAGTGCTAGCAAATGTGAACATAGGTTCTATAAAGTTTGAC
1 C-CC-TATATAGGTGCCAACTAATGTGGATTTTGACTCTATAAGGTTTGAC
* *
43927 CACACTATACAGGTGCCAACTAATGTGGATTTTGACTCTATTAGGATTT-ATC
1 C-C-CTATATAGGTGCCAACTAATGTGGATTTTGACTCTATAAGG-TTTGA-C
* * * * *
43979 CCCTTATATAGATGGCAGCTAATGTGGATTTTAACTCTATAAGGCTTGAC
1 CCC-TATATAGGTGCCAACTAATGTGGATTTTGACTCTATAAGGTTTGAC
*
44029 CTCTCTATATAGGTGCCAATTAATGTGGATTTTGACTCTAT-AGGATTTGAC
1 C-C-CTATATAGGTGCCAACTAATGTGGATTTTGACTCTATAAGG-TTTGAC
44080 TTCTCTAAAT
Statistics
Matches: 237, Mismatches: 55, Indels: 29
0.74 0.17 0.09
Matches are distributed among these distances:
50 10 0.04
51 164 0.69
52 62 0.26
53 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.35
Consensus pattern (49 bp):
CCCTATATAGGTGCCAACTAATGTGGATTTTGACTCTATAAGGTTTGAC
Found at i:44085 original size:51 final size:51
Alignment explanation
Indices: 43931--44116 Score: 180
Period size: 51 Copynumber: 3.6 Consensus size: 51
43921 TTTGACCACA
* * *
43931 CTATACAGGTGCCAACTAATGTGGATTTTGACTCTATTAGGATTT-A-TCCC
1 CTATATAGGTGCCAACTAATGTGGATTTTGACTCTA-TAGGATTTGACTTCT
* * * * * *
43981 CTTATATAGATGGCAGCTAATGTGGATTTTAACTCTATAAGG-CTTGACCTCT
1 C-TATATAGGTGCCAACTAATGTGGATTTTGACTCTAT-AGGATTTGACTTCT
*
44033 CTATATAGGTGCCAATTAATGTGGATTTTGACTCTATAGGATTTGACTTCT
1 CTATATAGGTGCCAACTAATGTGGATTTTGACTCTATAGGATTTGACTTCT
* * ** * *
44084 CTAAATAAGTGCCAGTTAATATGGACTTTGACT
1 CTATATAGGTGCCAACTAATGTGGATTTTGACT
44117 TTGTAGACTT
Statistics
Matches: 110, Mismatches: 21, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
50 7 0.06
51 101 0.92
52 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (51 bp):
CTATATAGGTGCCAACTAATGTGGATTTTGACTCTATAGGATTTGACTTCT
Found at i:45600 original size:11 final size:11
Alignment explanation
Indices: 45584--45617 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
45574 CAAATGAATG
45584 AAAAAGAGAAA
1 AAAAAGAGAAA
45595 AAAAAGAGAAA
1 AAAAAGAGAAA
45606 AAAAAGA-AAA
1 AAAAAGAGAAA
45616 AA
1 AA
45618 GAAAAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 5 0.22
11 18 0.78
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAAGAGAAA
Found at i:45606 original size:9 final size:9
Alignment explanation
Indices: 45583--45624 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
45573 GCAAATGAAT
45583 GAAAAAGAGA
1 GAAAAA-AGA
*
45593 AAAAAAAGA
1 GAAAAAAGA
*
45602 GAAAAAAAA
1 GAAAAAAGA
45611 GAAAAAAGA
1 GAAAAAAGA
45620 -AAAAA
1 GAAAAA
45625 TAAACTAAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
8 5 0.18
9 18 0.64
10 5 0.18
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (9 bp):
GAAAAAAGA
Found at i:49024 original size:13 final size:13
Alignment explanation
Indices: 49006--49031 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
48996 ATATTTTTTG
49006 TGTATCGATACAT
1 TGTATCGATACAT
49019 TGTATCGATACAT
1 TGTATCGATACAT
49032 ATTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:49042 original size:32 final size:33
Alignment explanation
Indices: 48985--49049 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
48975 TACAAGCCAA
48985 TGTATCGATACATATTTTTTGTGTATCGATACAT
1 TGTATCGATACATA-TTTTTGTGTATCGATACAT
49019 TGTATCGATACATA-TTTTGTGTATCGATACA
1 TGTATCGATACATATTTTTGTGTATCGATACA
49050 AGTTTGGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 17 0.55
34 14 0.45
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATATTTTTGTGTATCGATACAT
Found at i:49043 original size:19 final size:19
Alignment explanation
Indices: 48985--49049 Score: 70
Period size: 19 Copynumber: 3.6 Consensus size: 19
48975 TACAAGCCAA
48985 TGTATCGATACATATTTTTTG
1 TGTATCGATACATA--TTTTG
49006 TGTATCGATAC--A---T-
1 TGTATCGATACATATTTTG
49019 TGTATCGATACATATTTTG
1 TGTATCGATACATATTTTG
49038 TGTATCGATACA
1 TGTATCGATACA
49050 AGTTTGGCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
15 1 0.03
18 1 0.03
19 13 0.34
21 11 0.29
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (19 bp):
TGTATCGATACATATTTTG
Found at i:49830 original size:33 final size:32
Alignment explanation
Indices: 49788--49855 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
49778 CGTTACAAGC
*
49788 CAATGTATCGATACATTTTGTGATGGATCGATA
1 CAATGTATCGATACATATTGTG-TGGATCGATA
*
49821 CAATGTATCGATACATATTGTGTGTATCGATA
1 CAATGTATCGATACATATTGTGTGGATCGATA
49853 CAA
1 CAA
49856 ATTTAGCTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 12 0.36
33 21 0.64
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATATTGTGTGGATCGATA
Found at i:49913 original size:20 final size:20
Alignment explanation
Indices: 49888--49940 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
49878 CCAATGACTT
*
49888 GTATCGATACATTCT-TTCAA
1 GTATCGATACATT-TAGTCAA
*
49908 GTATCGATACATTTAGTCAT
1 GTATCGATACATTTAGTCAA
49928 GTATCGATACATT
1 GTATCGATACATT
49941 ATATCGATAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (20 bp):
GTATCGATACATTTAGTCAA
Found at i:50552 original size:28 final size:28
Alignment explanation
Indices: 50512--50568 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
50502 TTTTCTCTCC
50512 CCCTTAATAAAATAATTTAACAATTTCG
1 CCCTTAATAAAATAATTTAACAATTTCG
50540 CCCTTAATAAAATAATTTAACAATTTCG
1 CCCTTAATAAAATAATTTAACAATTTCG
50568 C
1 C
50569 ACATTAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.42, C:0.19, G:0.04, T:0.35
Consensus pattern (28 bp):
CCCTTAATAAAATAATTTAACAATTTCG
Found at i:50579 original size:28 final size:28
Alignment explanation
Indices: 50515--50585 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
50505 TCTCTCCCCC
*
50515 TTAATAAAATAATTTAACAATTTCGCCC
1 TTAATAAAATAATTTAACAATTTCGCCA
50543 TTAATAAAATAATTTAACAATTTCGCACA
1 TTAATAAAATAATTTAACAATTTCGC-CA
* *
50572 TTAAAAAAAAAATT
1 TTAATAAAATAATT
50586 CTTTCTCCCC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 26 0.67
29 13 0.33
ACGTcount: A:0.51, C:0.13, G:0.03, T:0.34
Consensus pattern (28 bp):
TTAATAAAATAATTTAACAATTTCGCCA
Found at i:52681 original size:8 final size:8
Alignment explanation
Indices: 52668--52693 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
52658 AACATCATTC
52668 ATCACAAA
1 ATCACAAA
52676 ATCACAAA
1 ATCACAAA
52684 ATCACAAA
1 ATCACAAA
52692 AT
1 AT
52694 TGAATCCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.23, G:0.00, T:0.15
Consensus pattern (8 bp):
ATCACAAA
Found at i:58730 original size:20 final size:20
Alignment explanation
Indices: 58705--58757 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
58695 CCAATGACTT
**
58705 GTATCGATACATTTTTTCAA
1 GTATCGATACATTTAGTCAA
*
58725 GTATCGATACATTTAGTCAT
1 GTATCGATACATTTAGTCAA
58745 GTATCGATACATT
1 GTATCGATACATT
58758 GTATCGATAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (20 bp):
GTATCGATACATTTAGTCAA
Found at i:60083 original size:13 final size:13
Alignment explanation
Indices: 60065--60090 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
60055 CAATTTTTTG
60065 ATGTATCGATACA
1 ATGTATCGATACA
60078 ATGTATCGATACA
1 ATGTATCGATACA
60091 TACATGGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:62682 original size:20 final size:20
Alignment explanation
Indices: 62657--62734 Score: 66
Period size: 20 Copynumber: 3.6 Consensus size: 20
62647 ATAATCCCCC
62657 TGTATCGATACAAAGAAAGA
1 TGTATCGATACAAAGAAAGA
**
62677 TGTATCGATACATTGAATTTTCCAGA
1 TGTATCGATACAAAGAA------AGA
* *
62703 TGTATCGATACACAGAAACA
1 TGTATCGATACAAAGAAAGA
62723 TGTATCGATACA
1 TGTATCGATACA
62735 TTTTGGAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
20 29 0.62
26 18 0.38
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (20 bp):
TGTATCGATACAAAGAAAGA
Found at i:66626 original size:22 final size:20
Alignment explanation
Indices: 66577--66628 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
66567 ATCATGCAAG
66577 TTTTTATTTTTCTTAGCTAAT
1 TTTTTA-TTTTCTTAGCTAAT
**
66598 TCATTATTTTCATTAGCTAAAT
1 TTTTTATTTTC-TTAGCT-AAT
66620 TTTTTATTT
1 TTTTTATTT
66629 CAACTTGCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 5 0.20
21 10 0.40
22 10 0.40
ACGTcount: A:0.23, C:0.10, G:0.04, T:0.63
Consensus pattern (20 bp):
TTTTTATTTTCTTAGCTAAT
Found at i:72740 original size:34 final size:35
Alignment explanation
Indices: 72702--72768 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
72692 CCTTACAACA
72702 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
72736 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
72769 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:73245 original size:13 final size:13
Alignment explanation
Indices: 73227--73252 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
73217 ACAATTTTTG
73227 TGTATCGATACAT
1 TGTATCGATACAT
73240 TGTATCGATACAT
1 TGTATCGATACAT
73253 ACTTTCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:73249 original size:32 final size:32
Alignment explanation
Indices: 73208--73270 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
73198 TACAAGCCAA
* *
73208 TGTATCGATACA-ATTTTTGTGTATCGATACAT
1 TGTATCGATACATA-CTTTCTGTATCGATACAT
73240 TGTATCGATACATACTTTCTGTATCGATACA
1 TGTATCGATACATACTTTCTGTATCGATACA
73271 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 27 0.96
33 1 0.04
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (32 bp):
TGTATCGATACATACTTTCTGTATCGATACAT
Found at i:73317 original size:21 final size:21
Alignment explanation
Indices: 73291--73366 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
73281 CTGCCAAGAA
*
73291 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
73312 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
73332 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
73353 ATGTATCGATACAT
1 ATGTATCGATACAT
73367 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:73337 original size:20 final size:20
Alignment explanation
Indices: 73312--73384 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
73302 CATCTTTTTT
73312 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
73332 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
73353 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
73373 ATGTATCGATAC
1 ATGTATCGATAC
73385 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:73348 original size:41 final size:41
Alignment explanation
Indices: 73291--73384 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
73281 CTGCCAAGAA
*
73291 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
73332 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
73373 ATGTATCGATAC
1 ATGTATCGATAC
73385 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:75028 original size:13 final size:13
Alignment explanation
Indices: 75010--75034 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
75000 ACTGAAGCAA
75010 TGTATCGATACAT
1 TGTATCGATACAT
75023 TGTATCGATACA
1 TGTATCGATACA
75035 ATCTGGAAAA
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:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:78075 original size:34 final size:35
Alignment explanation
Indices: 78037--78103 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
78027 CCTTACAACA
78037 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
78071 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
78104 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:78580 original size:13 final size:13
Alignment explanation
Indices: 78562--78587 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
78552 ACAATTTTTG
78562 TGTATCGATACAT
1 TGTATCGATACAT
78575 TGTATCGATACAT
1 TGTATCGATACAT
78588 ACTTTCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:78584 original size:32 final size:32
Alignment explanation
Indices: 78543--78605 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
78533 TACAAGCCAA
* *
78543 TGTATCGATACA-ATTTTTGTGTATCGATACAT
1 TGTATCGATACATA-CTTTCTGTATCGATACAT
78575 TGTATCGATACATACTTTCTGTATCGATACA
1 TGTATCGATACATACTTTCTGTATCGATACA
78606 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 27 0.96
33 1 0.04
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (32 bp):
TGTATCGATACATACTTTCTGTATCGATACAT
Found at i:78652 original size:21 final size:21
Alignment explanation
Indices: 78626--78701 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
78616 CTGCCAAGAA
*
78626 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
78647 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
78667 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
78688 ATGTATCGATACAT
1 ATGTATCGATACAT
78702 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:78672 original size:20 final size:20
Alignment explanation
Indices: 78647--78719 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
78637 CATCTTTTTT
78647 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
78667 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
78688 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
78708 ATGTATCGATAC
1 ATGTATCGATAC
78720 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:78683 original size:41 final size:41
Alignment explanation
Indices: 78626--78719 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
78616 CTGCCAAGAA
*
78626 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
78667 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
78708 ATGTATCGATAC
1 ATGTATCGATAC
78720 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:82332 original size:3 final size:3
Alignment explanation
Indices: 82326--82352 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
82316 TGCTACTTGC
82326 TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG
82353 CTGCTGTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:82469 original size:32 final size:29
Alignment explanation
Indices: 82420--82520 Score: 89
Period size: 30 Copynumber: 3.3 Consensus size: 29
82410 GCAAAGTAAC
82420 TTTTCTTTTTTTCTTGTTGTTTCGTC-TTTT
1 TTTTCTTTTTTTCTTGTTGTTT--TCATTTT
82450 TTTTCTTTTTTTCTATTGTTGTTTTCATTTT
1 TTTTCTTTTTTTC--TTGTTGTTTTCATTTT
* * * *
82481 TGTTCTTTTGTTGTTTTTGTTTTTC-TTTT
1 TTTTCTTTTTTTCTTGTTG-TTTTCATTTT
82510 ATTCTTCTTTT
1 -TT-TTCTTTT
82521 GCTATAGCTG
Statistics
Matches: 60, Mismatches: 5, Indels: 11
0.79 0.07 0.14
Matches are distributed among these distances:
29 9 0.15
30 21 0.35
31 21 0.35
32 9 0.15
ACGTcount: A:0.03, C:0.11, G:0.09, T:0.77
Consensus pattern (29 bp):
TTTTCTTTTTTTCTTGTTGTTTTCATTTT
Found at i:82503 original size:23 final size:22
Alignment explanation
Indices: 82449--82504 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
82439 TTTCGTCTTT
*
82449 TTTTTCTTTTTTTCTATTGTTG
1 TTTTTATTTTTTTCTATTGTTG
* *
82471 TTTTCATTTTTGTTCTTTTGTTG
1 TTTTTATTTTT-TTCTATTGTTG
*
82494 TTTTTGTTTTT
1 TTTTTATTTTT
82505 CTTTTATTCT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 9 0.32
23 19 0.68
ACGTcount: A:0.04, C:0.07, G:0.11, T:0.79
Consensus pattern (22 bp):
TTTTTATTTTTTTCTATTGTTG
Found at i:82867 original size:3 final size:3
Alignment explanation
Indices: 82861--82898 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
82851 TTTTTAATTA
* *
82861 ATT ATT ATT ATT ATT ATT -TA ATT ATG ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
82899 TTTTATTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
2 1 0.03
3 29 0.97
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:82883 original size:20 final size:20
Alignment explanation
Indices: 82858--82899 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
82848 TTTTTTTTAA
*
82858 TTAATTATTATTATTATTAT
1 TTAATTATGATTATTATTAT
82878 TTAATTATGATTATTATTAT
1 TTAATTATGATTATTATTAT
82898 TT
1 TT
82900 TTTATTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
TTAATTATGATTATTATTAT
Found at i:93082 original size:19 final size:19
Alignment explanation
Indices: 93039--93094 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
93029 CTGCTAATTT
*
93039 CATGTATCGATATAATTGAG
1 CATGTATCGATACAA-TGAG
*
93059 TATGTATCGATACAATGAG
1 CATGTATCGATACAATGAG
*
93078 CATGTATCAATACAATG
1 CATGTATCGATACAATG
93095 TATCGATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 19 0.59
20 13 0.41
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAG
Found at i:93116 original size:20 final size:20
Alignment explanation
Indices: 93091--93190 Score: 93
Period size: 20 Copynumber: 5.7 Consensus size: 20
93081 GTATCAATAC
93091 AATGTATCGATACAAAGCAT
1 AATGTATCGATACAAAGCAT
93111 AATGTATCGAT----A-CAT
1 AATGTATCGATACAAAGCAT
93126 --TGTATCGATACAAAGCAT
1 AATGTATCGATACAAAGCAT
93144 AATGTATCGAT----A-CAT
1 AATGTATCGATACAAAGCAT
93159 --TGTATCGATACAAAGCAT
1 AATGTATCGATACAAAGCAT
*
93177 AATGTATTGATACA
1 AATGTATCGATACA
93191 TATGGATGTG
Statistics
Matches: 65, Mismatches: 1, Indels: 28
0.69 0.01 0.30
Matches are distributed among these distances:
13 18 0.28
15 6 0.09
16 2 0.03
17 2 0.03
18 6 0.09
20 31 0.48
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (20 bp):
AATGTATCGATACAAAGCAT
Found at i:93124 original size:33 final size:33
Alignment explanation
Indices: 93060--93190 Score: 192
Period size: 33 Copynumber: 4.0 Consensus size: 33
93050 ATAATTGAGT
* ** *
93060 ATGTATCGATACAATG-AGCATGTATCAATACA
1 ATGTATCGATACAAAGCATAATGTATCGATACA
93092 ATGTATCGATACAAAGCATAATGTATCGATACA
1 ATGTATCGATACAAAGCATAATGTATCGATACA
*
93125 TTGTATCGATACAAAGCATAATGTATCGATACA
1 ATGTATCGATACAAAGCATAATGTATCGATACA
* *
93158 TTGTATCGATACAAAGCATAATGTATTGATACA
1 ATGTATCGATACAAAGCATAATGTATCGATACA
93191 TATGGATGTG
Statistics
Matches: 92, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 15 0.16
33 77 0.84
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (33 bp):
ATGTATCGATACAAAGCATAATGTATCGATACA
Found at i:93131 original size:13 final size:12
Alignment explanation
Indices: 93112--93170 Score: 54
Period size: 13 Copynumber: 5.1 Consensus size: 12
93102 ACAAAGCATA
93112 ATGTATCGATAC
1 ATGTATCGATAC
93124 ATTGTATCGATAC
1 A-TGTATCGATAC
* *
93137 A--AAGC-ATA-
1 ATGTATCGATAC
93145 ATGTATCGATAC
1 ATGTATCGATAC
93157 ATTGTATCGATAC
1 A-TGTATCGATAC
93170 A
1 A
93171 AAGCATAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 11
0.71 0.08 0.21
Matches are distributed among these distances:
8 1 0.03
9 3 0.08
10 4 0.11
11 3 0.08
12 2 0.05
13 24 0.65
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.32
Consensus pattern (12 bp):
ATGTATCGATAC
Found at i:102598 original size:33 final size:33
Alignment explanation
Indices: 102561--102627 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
102551 AGTAGCTTAA
102561 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
102594 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
102627 A
1 A
102628 AATAGTTGAA
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:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:102601 original size:13 final size:13
Alignment explanation
Indices: 102583--102607 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
102573 CAAAAAAATA
102583 TGTATCGATACAT
1 TGTATCGATACAT
102596 TGTATCGATACA
1 TGTATCGATACA
102608 ACACTTTATG
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:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:103778 original size:12 final size:12
Alignment explanation
Indices: 103747--103779 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
103737 TCTAAGTCAA
103747 CTTCATCATTAT
1 CTTCATCATTAT
103759 CATT-ATCATTAT
1 C-TTCATCATTAT
103771 CTTCATCAT
1 CTTCATCAT
103780 CTTTGATGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 2 0.11
12 15 0.79
13 2 0.11
ACGTcount: A:0.27, C:0.24, G:0.00, T:0.48
Consensus pattern (12 bp):
CTTCATCATTAT
Found at i:105495 original size:19 final size:19
Alignment explanation
Indices: 105452--105507 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
105442 TTGTTAATTT
105452 CATGTATCGATACAATTGAG
1 CATGTATCGATACAA-TGAG
* *
105472 TATGTATTGATACAATGAG
1 CATGTATCGATACAATGAG
105491 CATGTATCGATACAATG
1 CATGTATCGATACAATG
105508 TATCGATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 19 0.59
20 13 0.41
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAG
Found at i:105510 original size:13 final size:13
Alignment explanation
Indices: 105492--105518 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
105482 TACAATGAGC
105492 ATGTATCGATACA
1 ATGTATCGATACA
105505 ATGTATCGATACA
1 ATGTATCGATACA
105518 A
1 A
105519 AGCATAATAT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:105533 original size:20 final size:20
Alignment explanation
Indices: 105508--105577 Score: 113
Period size: 20 Copynumber: 3.5 Consensus size: 20
105498 CGATACAATG
105508 TATCGATACAAAGCATAATA
1 TATCGATACAAAGCATAATA
*
105528 TATCGATACAAAGCATAATG
1 TATCGATACAAAGCATAATA
*
105548 GATCGATACAAAGCATAATA
1 TATCGATACAAAGCATAATA
*
105568 TATCTATACA
1 TATCGATACA
105578 TCTGGATGTG
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.26
Consensus pattern (20 bp):
TATCGATACAAAGCATAATA
Found at i:107273 original size:63 final size:64
Alignment explanation
Indices: 107205--107327 Score: 187
Period size: 64 Copynumber: 1.9 Consensus size: 64
107195 TTTGGTTCTC
* *
107205 CATTAAGGTATGAAATGAATTTTCATAA-AATTAAAAACTAAA-TAAATTTTATTATCTTATCTT
1 CATTAACGTACGAAATGAATTTTCATAAGAATTAAAAACTAAATTAAA-TTTATTATCTTATCTT
**
107268 CATTAACGTACGAAATGAATTTTTTTAAGAATTAAAAACTAAATTAAATTTATTATCTTA
1 CATTAACGTACGAAATGAATTTTCATAAGAATTAAAAACTAAATTAAATTTATTATCTTA
107328 ATTTTTCAAG
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
63 24 0.44
64 26 0.48
65 4 0.07
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.41
Consensus pattern (64 bp):
CATTAACGTACGAAATGAATTTTCATAAGAATTAAAAACTAAATTAAATTTATTATCTTATCTT
Found at i:107548 original size:133 final size:135
Alignment explanation
Indices: 107307--107566 Score: 305
Period size: 133 Copynumber: 1.9 Consensus size: 135
107297 AATTAAAAAC
* * * * *
107307 TAAATTAAATTTATTATCTTAATTTTTCAAGATTTCTAATATTCCCATGGTTCTCTGTAGGGTTA
1 TAAATAAAAATTATTATCTTAATTCTTCAAGATTTCTAATATTCCCAAGGTTCTCTGTAGGGGTA
* **
107372 TAGAATTCTTCAAAACTTTTTGCATATTTTCAATTCTCCATTAAGGTACA-AAATGA-ATTTTTT
66 TAGAAATCTTCAAAAAATTTTGCATATTTTCAATTCTCCATTAAGGTA-AGAAATGAGATTTTTT
107435 GGAAAT
130 GGAAAT
* *
107441 TAAATAAAAATTATTGTCTTAATTCTTCAAGATTTCT-ATA-TCCCTAAGGTT-TTTCGTAGGGG
1 TAAATAAAAATTATTATCTTAATTCTTCAAGATTTCTAATATTCCC-AAGGTTCTCT-GTAGGGG
* * *** **
107503 TATAGAAATCTTCAAAAAATTTTGTATCTTTTTTGTTCTTTATTAAGGTAAGAAATGAGATTTT
64 TATAGAAATCTTCAAAAAATTTTGCATATTTTCAATTCTCCATTAAGGTAAGAAATGAGATTTT
107567 CGAAATTTAC
Statistics
Matches: 105, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
132 7 0.07
133 60 0.57
134 38 0.36
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (135 bp):
TAAATAAAAATTATTATCTTAATTCTTCAAGATTTCTAATATTCCCAAGGTTCTCTGTAGGGGTA
TAGAAATCTTCAAAAAATTTTGCATATTTTCAATTCTCCATTAAGGTAAGAAATGAGATTTTTTG
GAAAT
Found at i:107943 original size:156 final size:157
Alignment explanation
Indices: 107693--108036 Score: 430
Period size: 156 Copynumber: 2.2 Consensus size: 157
107683 AGGTACTTCT
* * * * * *
107693 ATGTCGAAAGTAT-CCTCTAGGGGCATTTTCATAATTTTTCTAGAACCGAGTCCTAGGTTGTTAT
1 ATGTTGAAAGTATACCTCTAAGGGCATTTTCATAATTTTTCTAGAACCAAATCCTAGGTTGTCAC
*
107757 CGGGTCTACTTTTATGCTGAAGATGGGTATTTAACATAGGTTCATCCCATCTATAATCTTTTTAA
66 CGGGTCTACTTTTATGCCGAAGATGGGTATTTAACATAGGTTCATCCCATCTATAATCTTTTTAA
* * *
107822 GTCTTTTAGGGTTACCGA-GATGCTTTC
131 GTCCTTTAAGGTTA-CGAGGATACTTTC
* * *
107849 ATGTTGAAAGTATATCTCTAAGGGCATTTTTATAATTTTT-TAGAACTAAATCCTAGGTTGTCAC
1 ATGTTGAAAGTATACCTCTAAGGGCATTTTCATAATTTTTCTAGAACCAAATCCTAGGTTGTCAC
* * **
107913 CGAGT-TCGCTTTTATGCCGAA-AGTGGGTATTTAGGATAGGTTCATCCCATCTATAATCTTTTT
66 CGGGTCT-ACTTTTATGCCGAAGA-TGGGTATTTAACATAGGTTCATCCCATCTATAATCTTTTT
*
107976 AAGTCCTTTAAGGTTACTAGGATACTTTC
129 AAGTCCTTTAAGGTTACGAGGATACTTTC
* *
108005 ATGTTGAAGGTATACC-CATAGGGGCATTTTCA
1 ATGTTGAAAGTATACCTC-TAAGGGCATTTTCA
108037 ATTTTTTTCA
Statistics
Matches: 161, Mismatches: 22, Indels: 10
0.83 0.11 0.05
Matches are distributed among these distances:
155 5 0.03
156 133 0.83
157 23 0.14
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (157 bp):
ATGTTGAAAGTATACCTCTAAGGGCATTTTCATAATTTTTCTAGAACCAAATCCTAGGTTGTCAC
CGGGTCTACTTTTATGCCGAAGATGGGTATTTAACATAGGTTCATCCCATCTATAATCTTTTTAA
GTCCTTTAAGGTTACGAGGATACTTTC
Found at i:108080 original size:156 final size:157
Alignment explanation
Indices: 107759--108082 Score: 363
Period size: 156 Copynumber: 2.1 Consensus size: 157
107749 GTTGTTATCG
* *
107759 GGTCTACTTTTATGCTGAAGATGGGTATTTAACATAGGTTCATCCCATCTATAATCTTTTTAAGT
1 GGTCTGCTTTTATGCCGAAGATGGGTATTTAACATAGGTTCATCCCATCTATAATCTTTTTAAGT
* * * * * *
107824 CTTTTAGGGTTACCGAGATGCTTTCATGTTGAAAGTATATCTCTAAGGGCATTTTTATAATTTTT
66 CCTTTAAGGTTACAGAGATACTTTCATGTTGAAAGTATATCCCTAAGGGCATTTTCATAATTTTT
* *****
107889 TAGAACTAAATCCTAGGTTGTCACCGA
131 TAAAACTAAATCCTACAAAATCACCGA
* **
107916 GTTC-GCTTTTATGCCGAA-AGTGGGTATTTAGGATAGGTTCATCCCATCTATAATCTTTTTAAG
1 GGTCTGCTTTTATGCCGAAGA-TGGGTATTTAACATAGGTTCATCCCATCTATAATCTTTTTAAG
* * *
107979 TCCTTTAAGGTTACTAG-GATACTTTCATGTTGAAGGTATA-CCCATAGGGGCATTTTCA-ATTT
65 TCCTTTAAGGTTAC-AGAGATACTTTCATGTTGAAAGTATATCCC-TAAGGGCATTTTCATAATT
* * *
108041 TTTTCAAAACTTAGTCCTACAAAATTACC-A
128 TTTT-AAAACTAAATCCTACAAAATCACCGA
108071 GGTCTGCTTTTA
1 GGTCTGCTTTTA
108083 CACCGAAGGT
Statistics
Matches: 138, Mismatches: 24, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
155 14 0.10
156 120 0.87
157 4 0.03
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.40
Consensus pattern (157 bp):
GGTCTGCTTTTATGCCGAAGATGGGTATTTAACATAGGTTCATCCCATCTATAATCTTTTTAAGT
CCTTTAAGGTTACAGAGATACTTTCATGTTGAAAGTATATCCCTAAGGGCATTTTCATAATTTTT
TAAAACTAAATCCTACAAAATCACCGA
Found at i:109347 original size:44 final size:44
Alignment explanation
Indices: 109298--109812 Score: 354
Period size: 44 Copynumber: 11.7 Consensus size: 44
109288 CCTTATATTT
* * *
109298 GTTTGACATGATGGTTCTACCCTAGTCAAA-TGCGTTTCACTTTC
1 GTTTGACATGATGGTTATACCCTGGTCAAACT-CCTTTCACTTTC
* ** * *
109342 GTTTGACGTGAAAGTTATGCCCTGATCAAACTCCATTT-ACTTTC
1 GTTTGACATGATGGTTATACCCTGGTCAAACTCC-TTTCACTTTC
* * *
109386 GTTTGACGTGATGGTT-TAGCACTGGTCAAACTCTTTTCA-TTCTC
1 GTTTGACATGATGGTTATA-CCCTGGTCAAACTCCTTTCACTT-TC
* * *
109430 GTTTGACATGATGGTTATACCTTGCTCAAACTCCGTTCACTTTC
1 GTTTGACATGATGGTTATACCCTGGTCAAACTCCTTTCACTTTC
* ** * * *
109474 ATTTTTCATGATGGTT-TAGCCCTGGTCCAACT-TTTTCA-TCCTC
1 GTTTGACATGATGGTTATA-CCCTGGTCAAACTCCTTTCACT-TTC
* * *
109517 GTTTGACATGATGGTTCTACCTTGGTCAAACT-CTTTCCACTTTT
1 GTTTGACATGATGGTTATACCCTGGTCAAACTCCTTT-CACTTTC
** * * *
109561 GTTTGATGTGATGGTTATGCCCTAGTCAAAC-CCTTTTTAC-TTC
1 GTTTGACATGATGGTTATACCCTGGTCAAACTCC-TTTCACTTTC
** * * *
109604 TGTTTGATGTGCTGGTTCTACCATGGTCAAACTCCTTTCACTTTC
1 -GTTTGACATGATGGTTATACCCTGGTCAAACTCCTTTCACTTTC
* * * * * * *
109649 ATTTGACTTAATGGTTTTGCCCTGGTCAAACCCCTTTCACTATC
1 GTTTGACATGATGGTTATACCCTGGTCAAACTCCTTTCACTTTC
* * * *
109693 GTTTGACATGATGGTTTTACTCGGGTCAAACTCCATTCACTTTC
1 GTTTGACATGATGGTTATACCCTGGTCAAACTCCTTTCACTTTC
* * * * **
109737 ATTTGACGTGATGGTT-TAGCCATGGTTAAACTTTTTTCA-TCTTC
1 GTTTGACATGATGGTTATA-CCCTGGTCAAACTCCTTTCACT-TTC
** *
109781 GTTTGATGTGATGGTTCA-GCCCTGGTCAAACT
1 GTTTGACATGATGGTT-ATACCCTGGTCAAACT
109813 TGTTACATTT
Statistics
Matches: 366, Mismatches: 84, Indels: 42
0.74 0.17 0.09
Matches are distributed among these distances:
42 1 0.00
43 46 0.13
44 302 0.83
45 17 0.05
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.40
Consensus pattern (44 bp):
GTTTGACATGATGGTTATACCCTGGTCAAACTCCTTTCACTTTC
Found at i:109447 original size:88 final size:87
Alignment explanation
Indices: 109299--109812 Score: 416
Period size: 88 Copynumber: 5.9 Consensus size: 87
109289 CTTATATTTG
* * * * ** *
109299 TTTGACATGATGGTTCTA-CCCTAGTCAAA-TGCGTTTCACTT-TCGTTTGACGTGAAAGTTATG
1 TTTGACGTGATGGTT-TAGCCCTGGTCAAACT-CTTTTCA-TTCTCGTTTGACATGATGGTTATA
* *
109361 CCCTGATCAAACTCCATTTACTTTCG
63 CCCTGGTCAAACTCC-TTTACTTTCA
* *
109387 TTTGACGTGATGGTTTAGCACTGGTCAAACTCTTTTCATTCTCGTTTGACATGATGGTTATACCT
1 TTTGACGTGATGGTTTAGCCCTGGTCAAACTCTTTTCATTCTCGTTTGACATGATGGTTATACCC
* *
109452 TGCTCAAACTCCGTTCACTTTCA
66 TGGTCAAACTCC-TTTACTTTCA
** * * * * *
109475 TTTTTCATGATGGTTTAGCCCTGGTCCAACT-TTTTCATCCTCGTTTGACATGATGGTTCTACCT
1 TTTGACGTGATGGTTTAGCCCTGGTCAAACTCTTTTCATTCTCGTTTGACATGATGGTTATACCC
**
109539 TGGTCAAACT-CTTTCCACTTTTG
66 TGGTCAAACTCCTTT--ACTTTCA
* * * * ** * *
109562 TTTGATGTGATGG-TTATGCCCTAGTCAAACCCTTTTTACTTCT-GTTTGATGTGCTGGTTCTAC
1 TTTGACGTGATGGTTTA-GCCCTGGTCAAACTCTTTTCA-TTCTCGTTTGACATGATGGTTATAC
*
109625 CATGGTCAAACTCCTTTCACTTTCA
64 CCTGGTCAAACTCCTTT-ACTTTCA
* * * * * * * * *
109650 TTTGACTTAATGGTTTTGCCCTGGTCAAACCCCTTTCACTATCGTTTGACATGATGGTTTTACTC
1 TTTGACGTGATGGTTTAGCCCTGGTCAAACTCTTTTCATTCTCGTTTGACATGATGGTTATACCC
* *
109715 GGGTCAAACTCCATTCACTTTCA
66 TGGTCAAACTCC-TTTACTTTCA
* * * ** *
109738 TTTGACGTGATGGTTTAGCCATGGTTAAACTTTTTTCA-TCTTCGTTTGATGTGATGGTTCA-GC
1 TTTGACGTGATGGTTTAGCCCTGGTCAAACTCTTTTCATTC-TCGTTTGACATGATGGTT-ATAC
109801 CCTGGTCAAACT
64 CCTGGTCAAACT
109813 TGTTACATTT
Statistics
Matches: 341, Mismatches: 71, Indels: 28
0.77 0.16 0.06
Matches are distributed among these distances:
85 2 0.01
86 4 0.01
87 72 0.21
88 251 0.74
89 12 0.04
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.40
Consensus pattern (87 bp):
TTTGACGTGATGGTTTAGCCCTGGTCAAACTCTTTTCATTCTCGTTTGACATGATGGTTATACCC
TGGTCAAACTCCTTTACTTTCA
Found at i:109707 original size:219 final size:219
Alignment explanation
Indices: 109298--109709 Score: 496
Period size: 219 Copynumber: 1.9 Consensus size: 219
109288 CCTTATATTT
109298 GTTTGACATGATGGTTCTACCCTAGTCAAATGCGTTTCACTTTCGTTTGACGTGAAAGTTATGCC
1 GTTTGACATGATGGTTCTACCCTAGTCAAATGCGTTTCACTTTCGTTTGACGTGAAAGTTATGCC
* *
109363 CTGATCAAACTCCATTTACTTTCGTTTGACGTGATGGTTTAGCACTGGTCAAACTCTTTTCATTC
66 CTGATCAAACTCCATTTACTTTCGTTTGACGTGATGGTTTACCACTGGTCAAACTCCTTTCATTC
* * * * * **
109428 TCGTTTGACATGATGGTTATACCTTGCTCAAACTCCGTTCACTTTCATTTTTCATGATGGTTTAG
131 TCATTTGACATAATGGTTATACCCTGCTCAAACCCCGTTCACTATCATTTGACATGATGGTTTAG
109493 CCCTGGTCCAACTTTTTCATCCTC
196 CCCTGGTCCAACTTTTTCATCCTC
* * * * **
109517 GTTTGACATGATGGTTCTACCTTGGTCAAACT-C-TTTCCACTTTTGTTTGATGTGATGGTTATG
1 GTTTGACATGATGGTTCTACCCTAGTCAAA-TGCGTTT-CACTTTCGTTTGACGTGAAAGTTATG
* * *
109580 CCCT-AGTCAAAC-CCTTTTTAC-TTCTGTTTGATGTGCTGGTTCTACCA-TGGTCAAACTCCTT
64 CCCTGA-TCAAACTCC-ATTTACTTTC-GTTTGACGTGATGGTT-TACCACTGGTCAAACTCCTT
* * * * * *
109641 TCACTT-TCATTTGACTTAATGGTTTTGCCCTGGTCAAACCCCTTTCACTATCGTTTGACATGAT
125 TCA-TTCTCATTTGACATAATGGTTATACCCTGCTCAAACCCCGTTCACTATCATTTGACATGAT
109705 GGTTT
189 GGTTT
109710 TACTCGGGTC
Statistics
Matches: 162, Mismatches: 24, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
218 9 0.06
219 146 0.90
220 7 0.04
ACGTcount: A:0.19, C:0.23, G:0.17, T:0.41
Consensus pattern (219 bp):
GTTTGACATGATGGTTCTACCCTAGTCAAATGCGTTTCACTTTCGTTTGACGTGAAAGTTATGCC
CTGATCAAACTCCATTTACTTTCGTTTGACGTGATGGTTTACCACTGGTCAAACTCCTTTCATTC
TCATTTGACATAATGGTTATACCCTGCTCAAACCCCGTTCACTATCATTTGACATGATGGTTTAG
CCCTGGTCCAACTTTTTCATCCTC
Found at i:109752 original size:132 final size:132
Alignment explanation
Indices: 109298--109811 Score: 406
Period size: 132 Copynumber: 3.9 Consensus size: 132
109288 CCTTATATTT
* * * **
109298 GTTTGACATGATGGTTCTACCCTAGTCAAA-TGCGTTTCACTTTCGTTTGACGTGAAAG-TTATG
1 GTTTGACATGATGGTTATACCCTAGTCAAACT-CCTTTCACTTTCATTTGACGTGATGGTTTA-G
* * * * * * *
109361 CCCTGATCAAACTCCATTT-A-CTTTCGTTTGACGTGATGGTTTAGCACTGGTCAAACTCTTTTC
64 CCATGGTCAAACTCC-TTTCATC-TTCGTTTGACTTGATGGTTCAGCCCTGGTCAAACCCCTTTC
* *
109424 ATTCTC
127 ACTATC
* * ** *
109430 GTTTGACATGATGGTTATA-CCTTGCTCAAACTCCGTTCACTTTCATTTTTCATGATGGTTTAGC
1 GTTTGACATGATGGTTATACCCTAG-TCAAACTCCTTTCACTTTCATTTGACGTGATGGTTTAGC
* * * * * * *
109494 CCTGGTCCAACT-TTTTCATCCTCGTTTGACATGATGGTTCTA-CCTTGGTCAAA-CTCTTTCCA
65 CATGGTCAAACTCCTTTCATCTTCGTTTGACTTGATGGTTC-AGCCCTGGTCAAACCCCTTT-CA
* *
109556 CTTTT
128 CTATC
** * * * * *
109561 GTTTGATGTGATGGTTATGCCCTAGTCAAAC-CCTTTTTAC-TTCTGTTTGATGTGCTGGTTCTA
1 GTTTGACATGATGGTTATACCCTAGTCAAACTCC-TTTCACTTTC-ATTTGACGTGATGGTT-TA
* * **
109624 -CCATGGTCAAACTCCTTTCA-CTTTCATTTGACTTAATGGTTTTGCCCTGGTCAAACCCCTTTC
63 GCCATGGTCAAACTCCTTTCATC-TTCGTTTGACTTGATGGTTCAGCCCTGGTCAAACCCCTTTC
109687 ACTATC
127 ACTATC
* * ** *
109693 GTTTGACATGATGGTTTTACTCGGGTCAAACTCCATTCACTTTCATTTGACGTGATGGTTTAGCC
1 GTTTGACATGATGGTTATACCCTAGTCAAACTCCTTTCACTTTCATTTGACGTGATGGTTTAGCC
* **
109758 ATGGTTAAACTTTTTTCATCTTCGTTTGA-TGTGATGGTTCAGCCCTGGTCAAAC
66 ATGGTCAAACTCCTTTCATCTTCGTTTGACT-TGATGGTTCAGCCCTGGTCAAAC
109812 TTGTTACATT
Statistics
Matches: 294, Mismatches: 68, Indels: 40
0.73 0.17 0.10
Matches are distributed among these distances:
130 11 0.04
131 86 0.29
132 182 0.62
133 15 0.05
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.40
Consensus pattern (132 bp):
GTTTGACATGATGGTTATACCCTAGTCAAACTCCTTTCACTTTCATTTGACGTGATGGTTTAGCC
ATGGTCAAACTCCTTTCATCTTCGTTTGACTTGATGGTTCAGCCCTGGTCAAACCCCTTTCACTA
TC
Found at i:116454 original size:3 final size:3
Alignment explanation
Indices: 116446--116501 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
116436 TTCAAAAATA
116446 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
116494 AAT AAT AA
1 AAT AAT AA
116502 ATACAAATAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:116677 original size:16 final size:17
Alignment explanation
Indices: 116655--116696 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 17
116645 GATATTTAAT
116655 AAAATAAAATAAAAAT-
1 AAAATAAAATAAAAATC
* *
116671 TAAAT-AAATAATAATC
1 AAAATAAAATAAAAATC
116687 AAAATAAAAT
1 AAAATAAAAT
116697 GAATAAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
15 9 0.43
16 8 0.38
17 4 0.19
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAATAAAATAAAAATC
Found at i:116694 original size:20 final size:20
Alignment explanation
Indices: 116656--116708 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
116646 ATATTTAATA
116656 AAATAAAATAAAAATTAAAT
1 AAATAAAATAAAAATTAAAT
* *
116676 AAATAATAATCAAAATAAAAT
1 AAATAA-AATAAAAATTAAAT
*
116697 GAATAAATATAA
1 AAATAAA-ATAA
116709 CCTTTTAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 7 0.26
21 20 0.74
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.25
Consensus pattern (20 bp):
AAATAAAATAAAAATTAAAT
Found at i:117430 original size:16 final size:16
Alignment explanation
Indices: 117384--117435 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
117374 GCAAGTTCAG
*
117384 GCTTTTTCGAGTTTAA
1 GCTTTTTCGAGTTTGA
*
117400 ACTTTTTCGAGTTTGA
1 GCTTTTTCGAGTTTGA
*
117416 GTTTTTTCGAGTTTGA
1 GCTTTTTCGAGTTTGA
117432 GCTT
1 GCTT
117436 AATTGGGTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.15, C:0.12, G:0.21, T:0.52
Consensus pattern (16 bp):
GCTTTTTCGAGTTTGA
Found at i:117469 original size:16 final size:16
Alignment explanation
Indices: 117450--117480 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
117440 GGGTTTGGAC
117450 TTTTTCGGGTTCAGGT
1 TTTTTCGGGTTCAGGT
*
117466 TTTTTTGGGTTCAGG
1 TTTTTCGGGTTCAGG
117481 CTTATTCGAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.06, C:0.10, G:0.32, T:0.52
Consensus pattern (16 bp):
TTTTTCGGGTTCAGGT
Found at i:118065 original size:16 final size:16
Alignment explanation
Indices: 118043--118079 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
118033 TCATAAAGAG
118043 TTAATAAAT-TTTATT
1 TTAATAAATATTTATT
118058 TATAAT-AATATTTATT
1 T-TAATAAATATTTATT
118074 TTAATA
1 TTAATA
118080 TTAATTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTAATAAATATTTATT
Found at i:118385 original size:16 final size:15
Alignment explanation
Indices: 118358--118387 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
118348 ATGTTAACTT
118358 TATATTCTATTCTAC
1 TATATTCTATTCTAC
118373 TATATTACTATTCTA
1 TATATT-CTATTCTA
118388 AATGTAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.30, C:0.17, G:0.00, T:0.53
Consensus pattern (15 bp):
TATATTCTATTCTAC
Found at i:118960 original size:16 final size:16
Alignment explanation
Indices: 118941--118971 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
118931 AGTTCGCACT
118941 ATTTCAAGTTTGGGTA
1 ATTTCAAGTTTGGGTA
*
118957 ATTTCGAGTTTGGGT
1 ATTTCAAGTTTGGGT
118972 TTTTGACTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.06, G:0.29, T:0.45
Consensus pattern (16 bp):
ATTTCAAGTTTGGGTA
Found at i:120193 original size:13 final size:13
Alignment explanation
Indices: 120175--120200 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
120165 TACACAAAGT
120175 ATGTATCGATACA
1 ATGTATCGATACA
120188 ATGTATCGATACA
1 ATGTATCGATACA
120201 CAAAAACTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:120218 original size:33 final size:32
Alignment explanation
Indices: 120157--120220 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
120147 TAGCCAAACT
*
120157 TGTATCGATACACAAAGTATGTATCGATACAA
1 TGTATCGATACACAAACTATGTATCGATACAA
120189 TGTATCGATACACAAAAACT-TGTATCGATACA
1 TGTATCGATACAC--AAACTATGTATCGATACA
120221 TTGGCTTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 13 0.45
33 12 0.41
34 4 0.14
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACAAACTATGTATCGATACAA
Found at i:120721 original size:34 final size:35
Alignment explanation
Indices: 120658--120724 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
120648 CTAAGTGATT
120658 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
120694 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
120725 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:123029 original size:13 final size:13
Alignment explanation
Indices: 123011--123036 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
123001 CAATTTTTTG
123011 TGTATCGATACAT
1 TGTATCGATACAT
123024 TGTATCGATACAT
1 TGTATCGATACAT
123037 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:123775 original size:21 final size:21
Alignment explanation
Indices: 123734--123777 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
123724 CTCTCCTTTA
* *
123734 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
123755 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
123776 TC
1 TC
123778 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:127703 original size:15 final size:15
Alignment explanation
Indices: 127683--127713 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
127673 ATTTTGTTTG
*
127683 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
127698 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
127713 G
1 G
127714 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:129546 original size:21 final size:21
Alignment explanation
Indices: 129517--129561 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
129507 AAGTTTTCAT
*
129517 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
129537 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
129559 TTT
1 TTT
129562 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:131794 original size:13 final size:13
Alignment explanation
Indices: 131776--131801 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
131766 CAATTTTTTG
131776 TGTATCGATACAT
1 TGTATCGATACAT
131789 TGTATCGATACAT
1 TGTATCGATACAT
131802 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:133170 original size:111 final size:110
Alignment explanation
Indices: 133051--133272 Score: 354
Period size: 111 Copynumber: 2.0 Consensus size: 110
133041 ATCAAATATC
*
133051 ATCATTTAATTCACATTAAATCAATTTTGAAAATTTCTTTTTATTTCATTATTTTTTTATTTTTT
1 ATCATTTAATTCACATTAAATCAATTTTGAAAATTTCTTTTTATTTCATGATTTTTTTA-TTTTT
* * * *
133116 TTTTGAAATTCTCTAATTTTCGAAATACAAAGTTTTCTACTCTGTA
65 TCTTAAAATTCTCTAATTTTCAAAATACAAAGTTTTCTACTCCGTA
*
133162 ATCATTTAATTCACATTAAATCAATTTTGAAAATTTCTTTTTATTTCATGCTTTTTTTATTTTTT
1 ATCATTTAATTCACATTAAATCAATTTTGAAAATTTCTTTTTATTTCATGATTTTTTTATTTTTT
* **
133227 CTTAAAATTTTCTAATTTTCAAAATACGGAGTTTTCTACTCCGTA
66 CTTAAAATTCTCTAATTTTCAAAATACAAAGTTTTCTACTCCGTA
133272 A
1 A
133273 ATGTTTATGG
Statistics
Matches: 102, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
110 45 0.44
111 57 0.56
ACGTcount: A:0.30, C:0.13, G:0.05, T:0.53
Consensus pattern (110 bp):
ATCATTTAATTCACATTAAATCAATTTTGAAAATTTCTTTTTATTTCATGATTTTTTTATTTTTT
CTTAAAATTCTCTAATTTTCAAAATACAAAGTTTTCTACTCCGTA
Found at i:134993 original size:5 final size:5
Alignment explanation
Indices: 134983--135029 Score: 85
Period size: 5 Copynumber: 9.4 Consensus size: 5
134973 TTACAGATGA
*
134983 TTGTG TTGTG TTGTG TTGTG TTGTG TTGTG TTGTG TTGTG TTATG TT
1 TTGTG TTGTG TTGTG TTGTG TTGTG TTGTG TTGTG TTGTG TTGTG TT
135030 CACTCCCAAC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.02, C:0.00, G:0.36, T:0.62
Consensus pattern (5 bp):
TTGTG
Found at i:135124 original size:3 final size:3
Alignment explanation
Indices: 135109--135144 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
135099 AATTCTACAT
*
135109 ATA ATA TATA ATA ATA ATA ATA ATA ATA ATA GTA AT
1 ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
135145 TTGTTTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:137731 original size:27 final size:27
Alignment explanation
Indices: 137673--137732 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
137663 ATTGTACTTC
137673 TGTTATCTAAATAAAATTTTAATTATT
1 TGTTATCTAAATAAAATTTTAATTATT
* *
137700 AGTTATCTAAATAAATTTTTATATT-TT
1 TGTTATCTAAATAAAATTTTA-ATTATT
137727 TGTTAT
1 TGTTAT
137733 ATTTGAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 26 0.90
28 3 0.10
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (27 bp):
TGTTATCTAAATAAAATTTTAATTATT
Found at i:137763 original size:30 final size:31
Alignment explanation
Indices: 137712--137772 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
137702 TTATCTAAAT
*
137712 AAATTTTTATATTTTTGTTATA-TTTGAATA
1 AAATTTTTATATTTTTATTATACTTTGAATA
*
137742 AAATTTTTA-ATTTTTAATTATACTTTTAATA
1 AAATTTTTATATTTTT-ATTATACTTTGAATA
137773 TTTAACTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 6 0.22
30 14 0.52
31 7 0.26
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (31 bp):
AAATTTTTATATTTTTATTATACTTTGAATA
Found at i:137770 original size:19 final size:20
Alignment explanation
Indices: 137746--137783 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
137736 TGAATAAAAT
*
137746 TTTTAATTTTTAA-TTATAC
1 TTTTAATATTTAACTTATAC
137765 TTTTAATATTTAACTTATA
1 TTTTAATATTTAACTTATA
137784 TCTAAATAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTTAATATTTAACTTATAC
Found at i:138824 original size:14 final size:15
Alignment explanation
Indices: 138793--138826 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
138783 TTTATTATCT
138793 TTTTAAAGTTTATTA
1 TTTTAAAGTTTATTA
*
138808 TTTTAAA-TTTTTTA
1 TTTTAAAGTTTATTA
138822 TTTTA
1 TTTTA
138827 GTTTTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (15 bp):
TTTTAAAGTTTATTA
Done.