Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr8
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: 56894857
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1173888 characters in sequence are not A, C, G, or T
File 21 of 185
Found at i:5926009 original size:15 final size:16
Alignment explanation
Indices: 5925989--5926026 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
5925979 TATGGTAGCT
5925989 ATAAAATAGTCT-AAA
1 ATAAAATAGTCTAAAA
*
5926004 ATAAAATATTCTAAAA
1 ATAAAATAGTCTAAAA
5926020 ATAAAAT
1 ATAAAAT
5926027 TAGTAATCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.29
Consensus pattern (16 bp):
ATAAAATAGTCTAAAA
Found at i:5927777 original size:58 final size:58
Alignment explanation
Indices: 5927683--5927827 Score: 191
Period size: 58 Copynumber: 2.5 Consensus size: 58
5927673 ATAACCGACA
*
5927683 ACCATAGCATCTTTCATCTATGGTCTTACACCGTATACCTTAGACATTTTACCTTGCC
1 ACCATTGCATCTTTCATCTATGGTCTTACACCGTATACCTTAGACATTTTACCTTGCC
** * * * **
5927741 ACCATTGCATCTTTCATCTATGGTCTTACATTGTATATCTTATACCTTTTACCTTGTT
1 ACCATTGCATCTTTCATCTATGGTCTTACACCGTATACCTTAGACATTTTACCTTGCC
* * *
5927799 GCCATTGCGTCTTTCATCCATGGTCTTAC
1 ACCATTGCATCTTTCATCTATGGTCTTAC
5927828 TCCATTACCA
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
58 76 1.00
ACGTcount: A:0.21, C:0.27, G:0.11, T:0.41
Consensus pattern (58 bp):
ACCATTGCATCTTTCATCTATGGTCTTACACCGTATACCTTAGACATTTTACCTTGCC
Found at i:5943443 original size:50 final size:50
Alignment explanation
Indices: 5943375--5943486 Score: 125
Period size: 50 Copynumber: 2.2 Consensus size: 50
5943365 AGATATTTAG
* * * *
5943375 TCTTATCGCCTTGACATTGCAATGGAAAAGATTGAAGCCACAACGGCGAA
1 TCTTATCTCCCTGGCATTGCAACGGAAAAGATTGAAGCCACAACGGCGAA
* * * ** * *
5943425 TCTTATTTCCCTGGCATTGTAGCGGAGCAGATTGAAGTCACGACGGCGAA
1 TCTTATCTCCCTGGCATTGCAACGGAAAAGATTGAAGCCACAACGGCGAA
5943475 TCTTATCTCCCT
1 TCTTATCTCCCT
5943487 AGCGTTAAGG
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (50 bp):
TCTTATCTCCCTGGCATTGCAACGGAAAAGATTGAAGCCACAACGGCGAA
Found at i:5943893 original size:267 final size:267
Alignment explanation
Indices: 5943388--5943929 Score: 769
Period size: 267 Copynumber: 2.0 Consensus size: 267
5943378 TATCGCCTTG
* * * *
5943388 ACATTGCAATGGAAAAGATTGAAGCCACAACGGCGAATCTTATTTCCCTGGCATTGTAGCGGAGC
1 ACATTGCAATGGAAAAGACTGAAGCCACAACGGCGAATCTTACTTCCCTGGCATTGTAACAGAGC
* * *
5943453 AGATTGAAGTCACGACGGCGAATCTTATCTCCCTAGCGTTAAGGCTTGGATTAGCTGAAGTGGAG
66 AAATTGAAGCCACGACGGCGAATCTTATCTCCCTAGCGTTAAGGCTTGGATTAGCTAAAGTGGAG
*
5943518 CGAATTAAGGCTGTGGGCAGCAAATCCTATCTCTTTAGCATTACAGTCGAACAGATTGAAACCAC
131 CGAATTAAAGCTGTGGGCAGCAAATCCTATCTCTTTAGCATTACAGTCGAACAGATTGAAACCAC
* * * * * *
5943583 GACGGTGAATATTACTCCCCTGATGGTGTAGTGGAATAGATTGAAGCTACGATAGCGAATCTTGT
196 AACGGTGAATATTACTCCCCTGACGGTGTAGCGGAACAGATTGAAGCCACGACAGCGAATCTTGT
*
5943648 TTCCTCA
261 TTCCCCA
** * * * *
5943655 ACATTGCAATTTAAAAGACTGAAGCCGCGACGGCGAGTCTTACTTCCCTGGCGTTGTAACAGAGC
1 ACATTGCAATGGAAAAGACTGAAGCCACAACGGCGAATCTTACTTCCCTGGCATTGTAACAGAGC
*
5943720 AAATTGAAGCCACGACGGCGAATCTTATCTCCCTAGTGTTAAGGCTTGGATTAGCTAAAGTGGAG
66 AAATTGAAGCCACGACGGCGAATCTTATCTCCCTAGCGTTAAGGCTTGGATTAGCTAAAGTGGAG
* * * * *
5943785 CGGATTAAAGCTGTGGGCAGCGAATTCTATCTCTTTAGCATTACAGTGGAGCAGATTGAAACCAC
131 CGAATTAAAGCTGTGGGCAGCAAATCCTATCTCTTTAGCATTACAGTCGAACAGATTGAAACCAC
* * * * * * *
5943850 AACGGTGAATCTTACTTCCCTGGCGTTGTAGCGGAGCAGATTGAAGCCACGACGGTGAATCTTGT
196 AACGGTGAATATTACTCCCCTGACGGTGTAGCGGAACAGATTGAAGCCACGACAGCGAATCTTGT
*
5943915 TTCCCCG
261 TTCCCCA
5943922 ACATTGCA
1 ACATTGCA
5943930 GATGACAAAT
Statistics
Matches: 240, Mismatches: 35, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
267 240 1.00
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (267 bp):
ACATTGCAATGGAAAAGACTGAAGCCACAACGGCGAATCTTACTTCCCTGGCATTGTAACAGAGC
AAATTGAAGCCACGACGGCGAATCTTATCTCCCTAGCGTTAAGGCTTGGATTAGCTAAAGTGGAG
CGAATTAAAGCTGTGGGCAGCAAATCCTATCTCTTTAGCATTACAGTCGAACAGATTGAAACCAC
AACGGTGAATATTACTCCCCTGACGGTGTAGCGGAACAGATTGAAGCCACGACAGCGAATCTTGT
TTCCCCA
Found at i:5945604 original size:30 final size:28
Alignment explanation
Indices: 5945568--5945634 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 28
5945558 TACATATGTA
* *
5945568 TATATTTATATTTTTTTATGAATATTTTT
1 TATATTTAT-TTTTTTAATAAATATTTTT
5945597 CTATATTTCATTTTTTTAATAAATATTTTT
1 -TATATTT-ATTTTTTTAATAAATATTTTT
5945627 T-TATTTAT
1 TATATTTAT
5945635 CCGTATATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
27 2 0.06
28 5 0.15
29 1 0.03
30 24 0.71
31 2 0.06
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.67
Consensus pattern (28 bp):
TATATTTATTTTTTTAATAAATATTTTT
Found at i:5945624 original size:15 final size:14
Alignment explanation
Indices: 5945575--5945630 Score: 58
Period size: 15 Copynumber: 3.9 Consensus size: 14
5945565 GTATATATTT
*
5945575 ATATTTTTTTATGA
1 ATATTTTTTTATAA
* *
5945589 ATATTTTTCTATAT
1 ATATTTTTTTATAA
*
5945603 TTCATTTTTTTAATAA
1 AT-ATTTTTTT-ATAA
5945619 ATATTTTTTTAT
1 ATATTTTTTTAT
5945631 TTATCCGTAT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
14 14 0.42
15 15 0.45
16 4 0.12
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.66
Consensus pattern (14 bp):
ATATTTTTTTATAA
Found at i:5950383 original size:62 final size:62
Alignment explanation
Indices: 5950286--5950410 Score: 196
Period size: 62 Copynumber: 2.0 Consensus size: 62
5950276 TTCGCCGTTC
* * *
5950286 TATCTTTGCTCTTAAAGTTTTTGCATAAAGACATTAGGTTAATAGTTTAGTTTAAGAAATTT
1 TATCTTTGCTCTTAAAGTTTTTGCATAAAGACATTAGATTAATAGTTAAATTTAAGAAATTT
* * *
5950348 TATCTTTGGTTTTAATGTTTTTGCATAAAGACATTAGATTAATAGTTAAATTTAAGAAATTT
1 TATCTTTGCTCTTAAAGTTTTTGCATAAAGACATTAGATTAATAGTTAAATTTAAGAAATTT
5950410 T
1 T
5950411 CTATGATATT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
62 57 1.00
ACGTcount: A:0.34, C:0.06, G:0.14, T:0.46
Consensus pattern (62 bp):
TATCTTTGCTCTTAAAGTTTTTGCATAAAGACATTAGATTAATAGTTAAATTTAAGAAATTT
Found at i:5953585 original size:25 final size:26
Alignment explanation
Indices: 5953538--5953586 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
5953528 TTTTTCTTTT
*
5953538 CTTTTCATTTTAAGATTAGATTTTCC
1 CTTTTCATTTTAAGAATAGATTTTCC
* *
5953564 CTTTTC-TTTTTAGAATATATTTT
1 CTTTTCATTTTAAGAATAGATTTT
5953587 ATTTTTGTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.22, C:0.12, G:0.06, T:0.59
Consensus pattern (26 bp):
CTTTTCATTTTAAGAATAGATTTTCC
Found at i:5955566 original size:5 final size:5
Alignment explanation
Indices: 5955555--5955590 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
5955545 TATTTAAATT
* *
5955555 AAAAG AAGAG AAAAG AAATG AAAAG AAAAG AAAAG A
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG A
5955591 GAGAAAACAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (5 bp):
AAAAG
Found at i:5955570 original size:10 final size:10
Alignment explanation
Indices: 5955555--5955597 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
5955545 TATTTAAATT
5955555 AAAAGAAGAG
1 AAAAGAAGAG
5955565 AAAAGAA-ATG
1 AAAAGAAGA-G
*
5955575 AAAAGAAAAG
1 AAAAGAAGAG
5955585 AAAAG-AGAG
1 AAAAGAAGAG
5955594 AAAA
1 AAAA
5955598 CAAAGAAAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
9 8 0.27
10 21 0.70
11 1 0.03
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.02
Consensus pattern (10 bp):
AAAAGAAGAG
Found at i:5955578 original size:20 final size:20
Alignment explanation
Indices: 5955550--5955590 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
5955540 TTAATTATTT
* *
5955550 AAATTAAAAGAAGAGAAAAG
1 AAATGAAAAGAAAAGAAAAG
5955570 AAATGAAAAGAAAAGAAAAG
1 AAATGAAAAGAAAAGAAAAG
5955590 A
1 A
5955591 GAGAAAACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (20 bp):
AAATGAAAAGAAAAGAAAAG
Found at i:5956311 original size:5 final size:5
Alignment explanation
Indices: 5956301--5956326 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
5956291 TGAGCATTCG
5956301 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
5956327 AATTTTTGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:5957366 original size:9 final size:9
Alignment explanation
Indices: 5957352--5957388 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
5957342 TATAGTTTGA
5957352 TATTCGAAT
1 TATTCGAAT
5957361 TATTCGAAT
1 TATTCGAAT
*
5957370 TATTCGAGT
1 TATTCGAAT
*
5957379 TATTTGAAT
1 TATTCGAAT
5957388 T
1 T
5957389 CGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:5957918 original size:11 final size:11
Alignment explanation
Indices: 5957904--5957939 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
5957894 GATAATCACT
5957904 TTAATAGTAAA
1 TTAATAGTAAA
5957915 TTAATA--AAA
1 TTAATAGTAAA
5957924 -TAATAGTAAA
1 TTAATAGTAAA
5957934 TTAATA
1 TTAATA
5957940 AAATATTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
8 5 0.23
9 3 0.14
10 3 0.14
11 11 0.50
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (11 bp):
TTAATAGTAAA
Found at i:5957919 original size:20 final size:20
Alignment explanation
Indices: 5957870--5957938 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
5957860 CAACTATAAT
*
5957870 TAAACTTAATCACTTTAATAT
1 TAAA-TTAATCACTTTAATAG
5957891 TAAGA-TAATCACTTTAATAG
1 TAA-ATTAATCACTTTAATAG
***
5957911 TAAATTAAT-AAAATAATAG
1 TAAATTAATCACTTTAATAG
5957930 TAAATTAAT
1 TAAATTAAT
5957939 AAAATATTGT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
19 17 0.40
20 21 0.50
21 3 0.07
22 1 0.02
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38
Consensus pattern (20 bp):
TAAATTAATCACTTTAATAG
Found at i:5957929 original size:19 final size:19
Alignment explanation
Indices: 5957905--5957944 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
5957895 ATAATCACTT
5957905 TAATAGTAAATTAATAAAA
1 TAATAGTAAATTAATAAAA
5957924 TAATAGTAAATTAATAAAA
1 TAATAGTAAATTAATAAAA
5957943 TA
1 TA
5957945 TTGTTAAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (19 bp):
TAATAGTAAATTAATAAAA
Found at i:5959616 original size:15 final size:15
Alignment explanation
Indices: 5959596--5959625 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5959586 TATGCATGCA
5959596 AAATATAAAAGACAT
1 AAATATAAAAGACAT
5959611 AAATATAAAAGACAT
1 AAATATAAAAGACAT
5959626 TATAGTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.07, G:0.07, T:0.20
Consensus pattern (15 bp):
AAATATAAAAGACAT
Found at i:5961150 original size:16 final size:17
Alignment explanation
Indices: 5961124--5961156 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
5961114 CATGCGCATG
5961124 AATATAAAAATAATAAT
1 AATATAAAAATAATAAT
5961141 AATA-AAAAATAATAAT
1 AATATAAAAATAATAAT
5961157 GATACAAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AATATAAAAATAATAAT
Found at i:5961676 original size:229 final size:229
Alignment explanation
Indices: 5961404--5961860 Score: 905
Period size: 229 Copynumber: 2.0 Consensus size: 229
5961394 ATCAATAAAT
5961404 AAATTATACACAAATCAACAAAATAAGAACGCAAGAGAGAGAGAAATTTGAGTAAATACTCTTAA
1 AAATTATACACAAATCAACAAAATAAGAACGCAAGAGAGAGAGAAATTTGAGTAAATACTCTTAA
5961469 GAATTATTATTACTCCCCACTTCCGTCCTTTACAATGAAGGGAGAGGCATCTATTTATAGTTGAG
66 GAATTATTATTACTCCCCACTTCCGTCCTTTACAATGAAGGGAGAGGCATCTATTTATAGTTGAG
*
5961534 CCTCCCAAAATCCAACGGTACAGATTAATTACATCAACGGCTAAGATTAAAAGGTATCTACAAAT
131 CATCCCAAAATCCAACGGTACAGATTAATTACATCAACGGCTAAGATTAAAAGGTATCTACAAAT
5961599 TAAATCTCTAAGATCATATCTTCTAAGATTGTAA
196 TAAATCTCTAAGATCATATCTTCTAAGATTGTAA
5961633 AAATTATACACAAATCAACAAAATAAGAACGCAAGAGAGAGAGAAATTTGAGTAAATACTCTTAA
1 AAATTATACACAAATCAACAAAATAAGAACGCAAGAGAGAGAGAAATTTGAGTAAATACTCTTAA
5961698 GAATTATTATTACTCCCCACTTCCGTCCTTTACAATGAAGGGAGAGGCATCTATTTATAGTTGAG
66 GAATTATTATTACTCCCCACTTCCGTCCTTTACAATGAAGGGAGAGGCATCTATTTATAGTTGAG
5961763 CATCCCAAAATCCAACGGTACAGATTAATTACATCAACGGCTAAGATTAAAAGGTATCTACAAAT
131 CATCCCAAAATCCAACGGTACAGATTAATTACATCAACGGCTAAGATTAAAAGGTATCTACAAAT
5961828 TAAATCTCTAAGATCATATCTTCTAAGATTGTA
196 TAAATCTCTAAGATCATATCTTCTAAGATTGTA
5961861 TATCATATCT
Statistics
Matches: 227, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
229 227 1.00
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.28
Consensus pattern (229 bp):
AAATTATACACAAATCAACAAAATAAGAACGCAAGAGAGAGAGAAATTTGAGTAAATACTCTTAA
GAATTATTATTACTCCCCACTTCCGTCCTTTACAATGAAGGGAGAGGCATCTATTTATAGTTGAG
CATCCCAAAATCCAACGGTACAGATTAATTACATCAACGGCTAAGATTAAAAGGTATCTACAAAT
TAAATCTCTAAGATCATATCTTCTAAGATTGTAA
Found at i:5961873 original size:19 final size:19
Alignment explanation
Indices: 5961834--5961902 Score: 83
Period size: 19 Copynumber: 3.8 Consensus size: 19
5961824 AAATTAAATC
5961834 TCTAAGA-T-CATATC-T-
1 TCTAAGATTGCATATCATA
*
5961849 TCTAAGATTGTATATCATA
1 TCTAAGATTGCATATCATA
*
5961868 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
*
5961887 TTTAAGATTGCATATC
1 TCTAAGATTGCATATC
5961903 CTTGAAGATT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
15 7 0.16
16 1 0.02
17 5 0.11
18 1 0.02
19 31 0.69
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:5962020 original size:13 final size:14
Alignment explanation
Indices: 5962002--5962033 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
5961992 ATAATTTTGG
5962002 ATTTTG-TTTTATT
1 ATTTTGTTTTTATT
5962015 ATTTTGTTTTTATT
1 ATTTTGTTTTTATT
5962029 ATTTT
1 ATTTT
5962034 TTTATGAGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.16, C:0.00, G:0.06, T:0.78
Consensus pattern (14 bp):
ATTTTGTTTTTATT
Found at i:5967347 original size:27 final size:27
Alignment explanation
Indices: 5967317--5967494 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
5967307 ATATTGAGTC
* * * *
5967317 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
5967344 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
5967371 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
5967399 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
5967426 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
5967453 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
5967480 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
5967495 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:5967456 original size:82 final size:81
Alignment explanation
Indices: 5967338--5967493 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
5967328 TGCTATATAA
* *
5967338 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
5967403 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
5967420 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
5967484 CACTTAGTGC
65 CACTTAGTGC
5967494 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:5974572 original size:51 final size:50
Alignment explanation
Indices: 5974470--5974660 Score: 213
Period size: 51 Copynumber: 3.7 Consensus size: 50
5974460 TGTGAAAATA
* ** * ** *
5974470 AGGTATAAGACCATGTAAGAGAGGCACCATGACATATACAGATATCG-TATG
1 AGGTATAAGACCATGTGAGAGAGG-TTCATGGCATCCACATATAT-GATATG
5974521 AGGTATAAGACCATGTGAGAGAGGTTGCATGGCATCCACATATATGATATG
1 AGGTATAAGACCATGTGAGAGAGGTT-CATGGCATCCACATATATGATATG
* **
5974572 AGGTATAAGACCATGTGAGAGAGGCTTCATGTCATTTACATATATGATATG
1 AGGTATAAGACCATGTGAGAGAGG-TTCATGGCATCCACATATATGATATG
* * *
5974623 AGGTGTAAGACCATGTGAGAAATGTTCAATGGCATCCA
1 AGGTATAAGACCATGTGAGAGAGGTTC-ATGGCATCCA
5974661 TTGTGTTAGT
Statistics
Matches: 120, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
50 4 0.03
51 114 0.95
52 2 0.02
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.26
Consensus pattern (50 bp):
AGGTATAAGACCATGTGAGAGAGGTTCATGGCATCCACATATATGATATG
Found at i:5974655 original size:102 final size:102
Alignment explanation
Indices: 5974470--5974660 Score: 269
Period size: 102 Copynumber: 1.9 Consensus size: 102
5974460 TGTGAAAATA
5974470 AGGTATAAGACCATGTAAGAGAGGCACCATGACATATACAGATATCGTATGAGGTATAAGACCAT
1 AGGTATAAGACCATGTAAGAGAGGCACCATGACATATACAGATATCGTATGAGGTATAAGACCAT
*
5974535 GTGAGAGAGGTTGCATGGCATCCACATATATGATATG
66 GTGAGAAAGGTTGCATGGCATCCACATATATGATATG
* ** * * * *
5974572 AGGTATAAGACCATGTGAGAGAGGCTTCATGTCATTTACATATAT-GATATGAGGTGTAAGACCA
1 AGGTATAAGACCATGTAAGAGAGGCACCATGACATATACAGATATCG-TATGAGGTATAAGACCA
*
5974636 TGTGAGAAATGTT-CAATGGCATCCA
65 TGTGAGAAAGGTTGC-ATGGCATCCA
5974661 TTGTGTTAGT
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
101 2 0.03
102 76 0.97
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.26
Consensus pattern (102 bp):
AGGTATAAGACCATGTAAGAGAGGCACCATGACATATACAGATATCGTATGAGGTATAAGACCAT
GTGAGAAAGGTTGCATGGCATCCACATATATGATATG
Found at i:5976006 original size:30 final size:30
Alignment explanation
Indices: 5975965--5976032 Score: 100
Period size: 30 Copynumber: 2.3 Consensus size: 30
5975955 TGAGACTAAG
* * *
5975965 AGGAGATCTATATGCCTAGGTAAAATCGAA
1 AGGAGAACTATATGCCTAGGTAAAACCAAA
*
5975995 AGGAGAACTATATGCCTAGGTGAAACCAAA
1 AGGAGAACTATATGCCTAGGTAAAACCAAA
5976025 AGGAGAAC
1 AGGAGAAC
5976033 CTACATGGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.43, C:0.15, G:0.25, T:0.18
Consensus pattern (30 bp):
AGGAGAACTATATGCCTAGGTAAAACCAAA
Found at i:5978468 original size:14 final size:13
Alignment explanation
Indices: 5978440--5978469 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
5978430 TACTTTTGAG
5978440 AAATGCTTTAAAA
1 AAATGCTTTAAAA
*
5978453 AAATGCTTTGAAA
1 AAATGCTTTAAAA
5978466 AAAT
1 AAAT
5978470 AATTTTGAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.53, C:0.07, G:0.10, T:0.30
Consensus pattern (13 bp):
AAATGCTTTAAAA
Found at i:5980513 original size:92 final size:92
Alignment explanation
Indices: 5980341--5980530 Score: 256
Period size: 92 Copynumber: 2.1 Consensus size: 92
5980331 GTTGCATTTA
* * * * *
5980341 GTACTTGTACTTTAATAAAATATTCAATGTAGTACATGTACTTTGAAAATGTCCAATGTGGTATC
1 GTACCTGTACTTTAATAAAATATCCAATGTAGTACATATACTTTGAAAATGTCCAATATGGTACC
* *
5980406 TGAACCATCAGTATGTGTTTTCTTATG
66 TGAACCATCAATATGTGTTTTATTATG
* * *
5980433 GTACCTGTGCTTTCATAAAATATCCAATGT-GATACCTATACTTTGAAAATGTCCAATATGGTAC
1 GTACCTGTACTTTAATAAAATATCCAATGTAG-TACATATACTTTGAAAATGTCCAATATGGTAC
*
5980497 CTGAACTATCAATATGTGTTTTATTATG
65 CTGAACCATCAATATGTGTTTTATTATG
*
5980525 ATACCT
1 GTACCT
5980531 AGTATTATCA
Statistics
Matches: 85, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
91 1 0.01
92 84 0.99
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (92 bp):
GTACCTGTACTTTAATAAAATATCCAATGTAGTACATATACTTTGAAAATGTCCAATATGGTACC
TGAACCATCAATATGTGTTTTATTATG
Found at i:5986991 original size:19 final size:18
Alignment explanation
Indices: 5986954--5987034 Score: 60
Period size: 18 Copynumber: 4.4 Consensus size: 18
5986944 ATAAAACATG
5986954 AAAATATAAATATCATAA
1 AAAATATAAATATCATAA
* *
5986972 AAAATATGAATGTACATAA
1 AAAATATAAATAT-CATAA
*
5986991 AATATATAAACTAT-A-AA
1 AAAATATAAA-TATCATAA
* *
5987008 AATAATAT-GATATGATAA
1 AA-AATATAAATATCATAA
5987026 TAAAATATA
1 -AAAATATA
5987035 TACGTACTAC
Statistics
Matches: 49, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
16 3 0.06
17 6 0.12
18 23 0.47
19 15 0.31
20 2 0.04
ACGTcount: A:0.62, C:0.04, G:0.05, T:0.30
Consensus pattern (18 bp):
AAAATATAAATATCATAA
Found at i:5987168 original size:12 final size:15
Alignment explanation
Indices: 5987133--5987165 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
5987123 AATAATATAC
5987133 AATATAATAATAATT
1 AATATAATAATAATT
5987148 AATATAATAA-AATT
1 AATATAATAATAATT
5987162 AATA
1 AATA
5987166 ATATATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
AATATAATAATAATT
Found at i:5988742 original size:10 final size:11
Alignment explanation
Indices: 5988667--5988738 Score: 65
Period size: 11 Copynumber: 6.1 Consensus size: 11
5988657 AATTATAAAA
*
5988667 TAATTAAATTA
1 TAATTAAATTT
5988678 TAATTAAATTAT
1 TAATTAAATT-T
5988690 TAACATGTCAAATTT
1 T-A-AT-T-AAATTT
5988705 TAATTAAATTT
1 TAATTAAATTT
5988716 ATAATTAAATTT
1 -TAATTAAATTT
*
5988728 TGATT-AATTT
1 TAATTAAATTT
5988738 T
1 T
5988739 GATTTATTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
10 6 0.11
11 20 0.38
12 13 0.25
13 3 0.06
14 3 0.06
15 3 0.06
16 5 0.09
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (11 bp):
TAATTAAATTT
Found at i:5995402 original size:48 final size:48
Alignment explanation
Indices: 5995331--5995435 Score: 165
Period size: 48 Copynumber: 2.2 Consensus size: 48
5995321 ACGGGAAGTC
*
5995331 CGATGTCGCAACATAGAGAACATAATAAAGAAAGTACGAAACTACCTT
1 CGATGTCGCAACATAGAGAACATAATAAAGAAAGTACAAAACTACCTT
* ** *
5995379 CGATGTTGCAACATAGAGAACATAATGGAGAAAGTACAAAACTGCCTT
1 CGATGTCGCAACATAGAGAACATAATAAAGAAAGTACAAAACTACCTT
5995427 CGATGTCGC
1 CGATGTCGC
5995436 GACACTGAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.41, C:0.19, G:0.20, T:0.20
Consensus pattern (48 bp):
CGATGTCGCAACATAGAGAACATAATAAAGAAAGTACAAAACTACCTT
Found at i:5999846 original size:13 final size:12
Alignment explanation
Indices: 5999797--5999852 Score: 58
Period size: 13 Copynumber: 4.4 Consensus size: 12
5999787 TGTTAATAGG
*
5999797 GGAAAATGAAAT
1 GGAAAATAAAAT
5999809 GGAAAAATAAAAT
1 GG-AAAATAAAAT
5999822 GGAAAGATAAAAT
1 GGAAA-ATAAAAT
*
5999835 TGAAAATGAAAAT
1 GGAAAAT-AAAAT
*
5999848 AGAAA
1 GGAAA
5999853 CCAAAATTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
12 7 0.18
13 31 0.82
ACGTcount: A:0.64, C:0.00, G:0.20, T:0.16
Consensus pattern (12 bp):
GGAAAATAAAAT
Found at i:6015908 original size:26 final size:26
Alignment explanation
Indices: 6015874--6015946 Score: 87
Period size: 26 Copynumber: 2.9 Consensus size: 26
6015864 TGGCTATTCA
6015874 GAGC-TCCTGATTAAAGGCTCTTCGT
1 GAGCTTCCTGATTAAAGGCTCTTCGT
* *
6015899 GAGCTTCCTGATTAAAGGTTCTTTGT
1 GAGCTTCCTGATTAAAGGCTCTTCGT
* * *
6015925 AAACTTCCTGATT-ATGGCTCTT
1 GAGCTTCCTGATTAAAGGCTCTT
6015947 ATGAGTTTCC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
25 11 0.27
26 30 0.73
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (26 bp):
GAGCTTCCTGATTAAAGGCTCTTCGT
Found at i:6028901 original size:20 final size:20
Alignment explanation
Indices: 6028876--6028916 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
6028866 TCATATTAGA
6028876 ATACTAGATTTCCTTACACT
1 ATACTAGATTTCCTTACACT
6028896 ATACTAGATTTCCTTACACT
1 ATACTAGATTTCCTTACACT
6028916 A
1 A
6028917 GGTTCTTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (20 bp):
ATACTAGATTTCCTTACACT
Found at i:6032435 original size:27 final size:27
Alignment explanation
Indices: 6032389--6032518 Score: 138
Period size: 27 Copynumber: 4.8 Consensus size: 27
6032379 CGAAGACATT
* *
6032389 CATTTCCATAGATCGCCACAAAGGC-TC
1 CATTT-CACAGATTGCCACAAAGGCTTC
*
6032416 CTATTTCACAGATTGCCACAAAGCCTTC
1 C-ATTTCACAGATTGCCACAAAGGCTTC
* * *
6032444 CATTTCACAGATTTCCATAAAGCCTTC
1 CATTTCACAGATTGCCACAAAGGCTTC
* *
6032471 CATTTCATCA-ATTTCCATAAAGGCTTC
1 CATTTCA-CAGATTGCCACAAAGGCTTC
*
6032498 CATTTCATAGATTGCCACAAA
1 CATTTCACAGATTGCCACAAA
6032519 AGCTCCTTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
26 1 0.01
27 80 0.89
28 9 0.10
ACGTcount: A:0.31, C:0.29, G:0.10, T:0.30
Consensus pattern (27 bp):
CATTTCACAGATTGCCACAAAGGCTTC
Found at i:6040919 original size:3 final size:3
Alignment explanation
Indices: 6040913--6040939 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
6040903 TTATTAATAC
6040913 CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT
6040940 TATTATTATT
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:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:6045280 original size:17 final size:18
Alignment explanation
Indices: 6045258--6045291 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
6045248 CGACCGCGAC
6045258 AAACGCGA-CGCGACCGA
1 AAACGCGACCGCGACCGA
6045275 AAACGCGACCGCGACCG
1 AAACGCGACCGCGACCG
6045292 CAATTTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.32, C:0.38, G:0.29, T:0.00
Consensus pattern (18 bp):
AAACGCGACCGCGACCGA
Found at i:6047799 original size:59 final size:60
Alignment explanation
Indices: 6047736--6047858 Score: 230
Period size: 60 Copynumber: 2.1 Consensus size: 60
6047726 CCTGCAAAAT
6047736 AAAATTGATAAATTTTTTTTG-AAAATATAATCTAATAGATTATGAAAAAATGAATACAA
1 AAAATTGATAAATTTTTTTTGAAAAATATAATCTAATAGATTATGAAAAAATGAATACAA
*
6047795 AAAATTGGTAAATTTTTTTTGAAAAATATAATCTAATAGATTATGAAAAAATGAATACAA
1 AAAATTGATAAATTTTTTTTGAAAAATATAATCTAATAGATTATGAAAAAATGAATACAA
6047855 AAAA
1 AAAA
6047859 AAAAAATAGA
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
59 20 0.32
60 42 0.68
ACGTcount: A:0.54, C:0.03, G:0.09, T:0.34
Consensus pattern (60 bp):
AAAATTGATAAATTTTTTTTGAAAAATATAATCTAATAGATTATGAAAAAATGAATACAA
Found at i:6066079 original size:339 final size:339
Alignment explanation
Indices: 6065459--6066135 Score: 1318
Period size: 339 Copynumber: 2.0 Consensus size: 339
6065449 AGAAGAACCA
6065459 GTCAAGCTAAGTGTTGAACCTGAATATACAACTATCATGTCGACTTCTGCAAGTGCTTCAAAGAA
1 GTCAAGCTAAGTGTTGAACCTGAATATACAACTATCATGTCGACTTCTGCAAGTGCTTCAAAGAA
6065524 ATCAGAGTTGTCAATTTTGATGGATATGTGCAAGTTCATGCACAATCAACAACAAACTTACTGGA
66 ATCAGAGTTGTCAATTTTGATGGATATGTGCAAGTTCATGCACAATCAACAACAAACTTACTGGA
6065589 AATATGAAAAAATTAGAGATGACTCAATTCAAAATACTTTTAAGAATATATCTAATACTTTTGTT
131 AATATGAAAAAATTAGAGATGACTCAATTCAAAATACTTTTAAGAATATATCTAATACTTTTGTT
6065654 CCTGAGTTCCCAGATGCTATCTTTGAGACATGGACGGAAGATACTGACAATGCAAGCGGAGATGG
196 CCTGAGTTCCCAGATGCTATCTTTGAGACATGGACGGAAGATACTGACAATGCAAGCGGAGATGG
6065719 ACCTAAAGAAGACAAGGGGAATAAGTCAAAAAAATAAAAGGGGGAATTCTTGTCCTATTATTTAT
261 ACCTAAAGAAGACAAGGGGAATAAGTCAAAAAAATAAAAGGGGGAATTCTTGTCCTATTATTTAT
6065784 TTAATTATTTTTAG
326 TTAATTATTTTTAG
*
6065798 GTCAAGCTAAGTGTTGAACCTGAATATACAACTGTCATGTCGACTTCTGCAAGTGCTTCAAAGAA
1 GTCAAGCTAAGTGTTGAACCTGAATATACAACTATCATGTCGACTTCTGCAAGTGCTTCAAAGAA
6065863 ATCAGAGTTGTCAATTTTGATGGATATGTGCAAGTTCATGCACAATCAACAACAAACTTACTGGA
66 ATCAGAGTTGTCAATTTTGATGGATATGTGCAAGTTCATGCACAATCAACAACAAACTTACTGGA
* *
6065928 AATATGCAAAAATTAGAGATGACTCAATTCGAAATACTTTTAAGAATATATCTAATACTTTTGTT
131 AATATGAAAAAATTAGAGATGACTCAATTCAAAATACTTTTAAGAATATATCTAATACTTTTGTT
6065993 CCTGAGTTCCCAGATGCTATCTTTGAGACATGGACGGAAGATACTGACAATGCAAGCGGAGATGG
196 CCTGAGTTCCCAGATGCTATCTTTGAGACATGGACGGAAGATACTGACAATGCAAGCGGAGATGG
*
6066058 ACCTAAAGAAGACAAGGGGAATAAGTCAAAAAAATAAAAGGGGGAATTCTTGTCCTGTTATTTAT
261 ACCTAAAGAAGACAAGGGGAATAAGTCAAAAAAATAAAAGGGGGAATTCTTGTCCTATTATTTAT
6066123 TTAATTATTTTTA
326 TTAATTATTTTTA
6066136 AGTCTTTAGG
Statistics
Matches: 334, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
339 334 1.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (339 bp):
GTCAAGCTAAGTGTTGAACCTGAATATACAACTATCATGTCGACTTCTGCAAGTGCTTCAAAGAA
ATCAGAGTTGTCAATTTTGATGGATATGTGCAAGTTCATGCACAATCAACAACAAACTTACTGGA
AATATGAAAAAATTAGAGATGACTCAATTCAAAATACTTTTAAGAATATATCTAATACTTTTGTT
CCTGAGTTCCCAGATGCTATCTTTGAGACATGGACGGAAGATACTGACAATGCAAGCGGAGATGG
ACCTAAAGAAGACAAGGGGAATAAGTCAAAAAAATAAAAGGGGGAATTCTTGTCCTATTATTTAT
TTAATTATTTTTAG
Found at i:6071715 original size:25 final size:25
Alignment explanation
Indices: 6071620--6071726 Score: 108
Period size: 25 Copynumber: 4.3 Consensus size: 25
6071610 AGCTCCCCTA
** *
6071620 AGCTGAATAACAGTAAAATCCT-CTG
1 AGCTGAATAACAGTAAGCTCATAC-G
* *
6071645 AGCTGAATAACAGTAAGCTCCTTCG
1 AGCTGAATAACAGTAAGCTCATACG
*
6071670 AGCTGAATAACGGTAAGCTCATACG
1 AGCTGAATAACAGTAAGCTCATACG
* * * *
6071695 AGCTGAGTATCAGTATGCTCATAAG
1 AGCTGAATAACAGTAAGCTCATACG
6071720 AGCTGAA
1 AGCTGAA
6071727 ATCGATAACC
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
25 69 0.99
26 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (25 bp):
AGCTGAATAACAGTAAGCTCATACG
Found at i:6071850 original size:45 final size:45
Alignment explanation
Indices: 6071786--6071876 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 45
6071776 TCAAATGGGG
* * *
6071786 CTCGGTAATCGTCGTACGTCGTTCGACAAGCAATCGATATTCATT
1 CTCGGTAATCATCATACGTCGTTAGACAAGCAATCGATATTCATT
* *
6071831 CTCGGTAGTCATCATACGTCGTTAGATAAGCAATCGATATTCATT
1 CTCGGTAATCATCATACGTCGTTAGACAAGCAATCGATATTCATT
6071876 C
1 C
6071877 ATGGCAATTA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (45 bp):
CTCGGTAATCATCATACGTCGTTAGACAAGCAATCGATATTCATT
Found at i:6073182 original size:316 final size:316
Alignment explanation
Indices: 6072609--6073307 Score: 1344
Period size: 316 Copynumber: 2.2 Consensus size: 316
6072599 TTTTTAATTG
6072609 GGTAAAATTTCTCAACAAAATTTTTATACGATAATACTATCATGCTACAGATCATAAATTATTAT
1 GGTAAAATTTCTCAACAAAATTTTTATACGATAATACTATCATGCTACAGATCATAAATTATTAT
6072674 TATTAACTAAATTACAAATTTTTTTTAACTTATTATATCATTATTAACTAAATTACAAAATTAAC
66 TATTAACTAAATTACAAATTTTTTTTAACTTATTATATCATTATTAACTAAATTACAAAATTAAC
6072739 CTTTATAAACATTATTTATTACACAAAATGCCAAGTCATCATAATCCACTATCTCTTTAATGGGC
131 CTTTATAAACATTATTTATTACACAAAATGCCAAGTCATCATAATCCACTATCTCTTTAATGGGC
6072804 TATTTACCATATAAGAACCTCCAATTTAAATTTCTATAGCTATTAGACACCTTTAGCTATTAGAA
196 TATTTACCATATAAGAACCTCCAATTTAAATTTCTATAGCTATTAGACACCTTTAGCTATTAGAA
*
6072869 CACAACTTTCGCACTTTATGTGATTTAGTCCTTTTTATCAAATTGAGCATGTAATC
261 CACAACTTTCGCACTTTACGTGATTTAGTCCTTTTTATCAAATTGAGCATGTAATC
*
6072925 GGTAAAATTTCTTAACAAAATTTTTATACGATAATACTATCATGCTACAGATCATAAATTATTAT
1 GGTAAAATTTCTCAACAAAATTTTTATACGATAATACTATCATGCTACAGATCATAAATTATTAT
6072990 TATTAACTAAATTACAAATTTTTTTTAACTTATTATATCATTATTAACTAAATTACAAAATTAAC
66 TATTAACTAAATTACAAATTTTTTTTAACTTATTATATCATTATTAACTAAATTACAAAATTAAC
6073055 CTTTATAAACATTATTTATTACACAAAATGCCAAGTCATCATAATCCACTATCTCTTTAATGGGC
131 CTTTATAAACATTATTTATTACACAAAATGCCAAGTCATCATAATCCACTATCTCTTTAATGGGC
*
6073120 TATTTACCATATAAGAACCTCCAATTTAAATTTCTATAGCTATTAGACACCTTTATCTATTAGAA
196 TATTTACCATATAAGAACCTCCAATTTAAATTTCTATAGCTATTAGACACCTTTAGCTATTAGAA
*
6073185 CACAACTTTTGCACTTTACGTGATTTAGTCCTTTTTATCAAATTGAGCATGTAATC
261 CACAACTTTCGCACTTTACGTGATTTAGTCCTTTTTATCAAATTGAGCATGTAATC
* *
6073241 GGTAAAATTTCTCAACAAAATTTTTATACGATAATACTATCATGCTACAGATCATAAAATAATAT
1 GGTAAAATTTCTCAACAAAATTTTTATACGATAATACTATCATGCTACAGATCATAAATTATTAT
6073306 TA
66 TA
6073308 AAATAATTTT
Statistics
Matches: 376, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
316 376 1.00
ACGTcount: A:0.38, C:0.16, G:0.07, T:0.39
Consensus pattern (316 bp):
GGTAAAATTTCTCAACAAAATTTTTATACGATAATACTATCATGCTACAGATCATAAATTATTAT
TATTAACTAAATTACAAATTTTTTTTAACTTATTATATCATTATTAACTAAATTACAAAATTAAC
CTTTATAAACATTATTTATTACACAAAATGCCAAGTCATCATAATCCACTATCTCTTTAATGGGC
TATTTACCATATAAGAACCTCCAATTTAAATTTCTATAGCTATTAGACACCTTTAGCTATTAGAA
CACAACTTTCGCACTTTACGTGATTTAGTCCTTTTTATCAAATTGAGCATGTAATC
Found at i:6076308 original size:18 final size:18
Alignment explanation
Indices: 6076282--6076316 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
6076272 TCCCATGTTC
6076282 AAGGATTTATGCGAGTTT
1 AAGGATTTATGCGAGTTT
*
6076300 AAGGCTTTATGCGAGTT
1 AAGGATTTATGCGAGTT
6076317 GGGAGCTAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.09, G:0.29, T:0.37
Consensus pattern (18 bp):
AAGGATTTATGCGAGTTT
Found at i:6079309 original size:18 final size:18
Alignment explanation
Indices: 6079286--6079332 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
6079276 TCTTGTCAAA
*
6079286 AAAATAATTAATTTTTAC
1 AAAATAATTAATATTTAC
6079304 AAAATAATTAATATTTAC
1 AAAATAATTAATATTTAC
6079322 AAAATAATTAA
1 AAAATAATTAA
6079333 AGTGCACTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAATAATTAATATTTAC
Found at i:6083376 original size:28 final size:28
Alignment explanation
Indices: 6083344--6083399 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
6083334 CGTATTGGTA
6083344 CGTGTAGACAAATTTATCTTTCCTGCTG
1 CGTGTAGACAAATTTATCTTTCCTGCTG
*
6083372 CGTGTAGACAAATTTATTTTTCCTGCTG
1 CGTGTAGACAAATTTATCTTTCCTGCTG
6083400 ACTTGTGATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.21, C:0.20, G:0.18, T:0.41
Consensus pattern (28 bp):
CGTGTAGACAAATTTATCTTTCCTGCTG
Found at i:6085903 original size:27 final size:28
Alignment explanation
Indices: 6085819--6085916 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
6085809 CATGAGATTG
* * * *
6085819 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
6085848 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
6085876 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
6085903 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
6085917 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:6085927 original size:27 final size:27
Alignment explanation
Indices: 6085847--6085929 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
6085837 TAAATTGTAC
* *
6085847 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
6085875 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
6085902 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
6085929 A
1 A
6085930 TTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:6085930 original size:29 final size:27
Alignment explanation
Indices: 6085819--6085930 Score: 98
Period size: 28 Copynumber: 4.0 Consensus size: 27
6085809 CATGAGATTG
** * *
6085819 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGC-GACTT-AATTATATA
* *
6085848 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* *
6085876 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
*
6085903 GCACTGAGTGTGCGGACTTAATATATAT
1 GCACTAAGTGTGC-GACTTAAT-TATAT
6085931 TTTTGAATCA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
27 23 0.32
28 28 0.39
29 21 0.29
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTAATTATATA
Found at i:6091029 original size:25 final size:25
Alignment explanation
Indices: 6090971--6091026 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
6090961 CTAAATTTTA
*
6090971 AATTAATTATTTAATTTTTTCAATT
1 AATTAATTATTTAATATTTTCAATT
*
6090996 TATTGAATTA-TTAATATTTT-ATATT
1 AATT-AATTATTTAATATTTTCA-ATT
6091021 AATTAA
1 AATTAA
6091027 ATTTTTGAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
24 3 0.12
25 18 0.69
26 5 0.19
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (25 bp):
AATTAATTATTTAATATTTTCAATT
Found at i:6100776 original size:20 final size:20
Alignment explanation
Indices: 6100751--6100790 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
6100741 AGTTTGATTT
6100751 GTTAAAAGAC-TTTTAACTTG
1 GTTAAAA-ACATTTTAACTTG
*
6100771 GTTAAAATCATTTTAACTTG
1 GTTAAAAACATTTTAACTTG
6100791 ATTTTAAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.42
Consensus pattern (20 bp):
GTTAAAAACATTTTAACTTG
Found at i:6106743 original size:21 final size:21
Alignment explanation
Indices: 6106717--6106792 Score: 120
Period size: 21 Copynumber: 3.7 Consensus size: 21
6106707 AATCATATCT
6106717 TCTAAGATTGTATATATCATA
1 TCTAAGATTGTATATATCATA
*
6106738 TCTAAGATTGCATATATCATA
1 TCTAAGATTGTATATATCATA
*
6106759 TCTAAGATTG--CATATCATA
1 TCTAAGATTGTATATATCATA
6106778 TCTAAGATTGTATAT
1 TCTAAGATTGTATAT
6106793 CCTAGAAAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 18 0.36
21 32 0.64
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.41
Consensus pattern (21 bp):
TCTAAGATTGTATATATCATA
Found at i:6106752 original size:19 final size:19
Alignment explanation
Indices: 6106730--6106793 Score: 101
Period size: 19 Copynumber: 3.3 Consensus size: 19
6106720 AAGATTGTAT
6106730 ATATCATATCTAAGATTGC
1 ATATCATATCTAAGATTGC
6106749 ATATATCATATCTAAGATTGC
1 --ATATCATATCTAAGATTGC
*
6106770 ATATCATATCTAAGATTGT
1 ATATCATATCTAAGATTGC
6106789 ATATC
1 ATATC
6106794 CTAGAAAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
19 23 0.55
21 19 0.45
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (19 bp):
ATATCATATCTAAGATTGC
Found at i:6126131 original size:24 final size:24
Alignment explanation
Indices: 6126099--6126147 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
6126089 GAACTAAGGA
6126099 TGTGAAAAGGATAGTCAGTTCAGG
1 TGTGAAAAGGATAGTCAGTTCAGG
6126123 TGTGAAAAGGATAGTCAGTTCAGG
1 TGTGAAAAGGATAGTCAGTTCAGG
6126147 T
1 T
6126148 TTATCCTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.08, G:0.33, T:0.27
Consensus pattern (24 bp):
TGTGAAAAGGATAGTCAGTTCAGG
Found at i:6126597 original size:15 final size:16
Alignment explanation
Indices: 6126570--6126606 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
6126560 CCTAATCTCT
6126570 ATAGA-ATCTTTCTTC
1 ATAGATATCTTTCTTC
6126585 ATAGATATC-TTCTTC
1 ATAGATATCTTTCTTC
6126600 ATA-ATAT
1 ATAGATAT
6126607 AAGTCTTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 4 0.19
15 14 0.67
16 3 0.14
ACGTcount: A:0.32, C:0.16, G:0.05, T:0.46
Consensus pattern (16 bp):
ATAGATATCTTTCTTC
Found at i:6130979 original size:13 final size:13
Alignment explanation
Indices: 6130961--6130986 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6130951 TTTTTATGAT
6130961 TCGTTAGAACATC
1 TCGTTAGAACATC
6130974 TCGTTAGAACATC
1 TCGTTAGAACATC
6130987 CTAGTGTCAC
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:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
TCGTTAGAACATC
Found at i:6132606 original size:13 final size:13
Alignment explanation
Indices: 6132588--6132625 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
6132578 ATGGGTTGGG
6132588 CGGCCCGGCCCGA
1 CGGCCCGGCCCGA
6132601 CGGCCCGGCCCGA
1 CGGCCCGGCCCGA
*
6132614 CAGCCC-GCCCGA
1 CGGCCCGGCCCGA
6132626 AATATGGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 6 0.25
13 18 0.75
ACGTcount: A:0.11, C:0.55, G:0.34, T:0.00
Consensus pattern (13 bp):
CGGCCCGGCCCGA
Found at i:6132879 original size:14 final size:14
Alignment explanation
Indices: 6132860--6132892 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
6132850 AATCAACCTT
6132860 CACCTCCACCAATC
1 CACCTCCACCAATC
*
6132874 CACCTCCACCGATC
1 CACCTCCACCAATC
6132888 CACCT
1 CACCT
6132893 TCGGTCCTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.58, G:0.03, T:0.15
Consensus pattern (14 bp):
CACCTCCACCAATC
Found at i:6134746 original size:102 final size:102
Alignment explanation
Indices: 6134608--6134943 Score: 663
Period size: 102 Copynumber: 3.3 Consensus size: 102
6134598 TGAGTTAAAC
6134608 ATAACTAGTTTATTATCTCGTGCAATATATTATATTTATGAAAAACAGCAGACACGTGCAATATA
1 ATAACTAGTTTATTATCTCGTGCAATATATTATATTTATGAAAAACAGCAGACACGTGCAATATA
*
6134673 TATTACCAAACTTGTATCACAAGGCTAGCATAGTTAA
66 TATTATCAAACTTGTATCACAAGGCTAGCATAGTTAA
6134710 ATAACTAGTTTATTATCTCGTGCAATATATTATATTTATGAAAAACAGCAGACACGTGCAATATA
1 ATAACTAGTTTATTATCTCGTGCAATATATTATATTTATGAAAAACAGCAGACACGTGCAATATA
6134775 TATTATCAAACTTGTATCACAAGGCTAGCATAGTTAA
66 TATTATCAAACTTGTATCACAAGGCTAGCATAGTTAA
6134812 ATAACTAGTTTATTATCTCGTGCAATATATTATATTTATGAAAAACAGCAGACACGTGCAATATA
1 ATAACTAGTTTATTATCTCGTGCAATATATTATATTTATGAAAAACAGCAGACACGTGCAATATA
6134877 TATTATCAAACTTGTATCACAAGGCTAGCATAGTTAA
66 TATTATCAAACTTGTATCACAAGGCTAGCATAGTTAA
6134914 ATAACTAGTTTATTATCTCGTGCAATATAT
1 ATAACTAGTTTATTATCTCGTGCAATATAT
6134944 GAGTTTGGTA
Statistics
Matches: 233, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
102 233 1.00
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (102 bp):
ATAACTAGTTTATTATCTCGTGCAATATATTATATTTATGAAAAACAGCAGACACGTGCAATATA
TATTATCAAACTTGTATCACAAGGCTAGCATAGTTAA
Found at i:6135387 original size:19 final size:18
Alignment explanation
Indices: 6135336--6135402 Score: 66
Period size: 19 Copynumber: 3.7 Consensus size: 18
6135326 ACCCCAAACA
*
6135336 TATTTTTTGTTTTATCTT
1 TATTTTTTGTTTTATTTT
* * *
6135354 T-TTTCTT-TATCATTTT
1 TATTTTTTGTTTTATTTT
6135370 CTATTTTTTGTTTTATTTT
1 -TATTTTTTGTTTTATTTT
6135389 TAATTTTTTGTTTT
1 T-ATTTTTTGTTTT
6135403 TGACATTCTT
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
16 6 0.16
17 6 0.16
18 7 0.18
19 19 0.50
ACGTcount: A:0.12, C:0.06, G:0.04, T:0.78
Consensus pattern (18 bp):
TATTTTTTGTTTTATTTT
Found at i:6144825 original size:17 final size:17
Alignment explanation
Indices: 6144783--6144827 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
6144773 AATTCAATTT
6144783 TAATATAAAT-ATTCAA
1 TAATATAAATAATTCAA
6144799 T-ATGACTAAATAATTCAA
1 TAAT-A-TAAATAATTCAA
6144817 TAATATAAATA
1 TAATATAAATA
6144828 GTAGATATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
15 2 0.08
16 2 0.08
17 11 0.44
18 8 0.32
19 2 0.08
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.36
Consensus pattern (17 bp):
TAATATAAATAATTCAA
Found at i:6145091 original size:30 final size:31
Alignment explanation
Indices: 6145052--6145111 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
6145042 AGAGGTGGGA
*
6145052 TGGGAAGGGAATAAAAGTTTT-AGGGCAAAAG
1 TGGGAAGGGAATAAAAATTTTGAGGG-AAAAG
*
6145083 TGGG-AGGGAGTAAAAATTTTGAGGGAAAA
1 TGGGAAGGGAATAAAAATTTTGAGGGAAAA
6145112 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.42, C:0.02, G:0.37, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTGAGGGAAAAG
Found at i:6145339 original size:9 final size:9
Alignment explanation
Indices: 6145325--6145361 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
6145315 TATAGTTTGA
6145325 TATTCGAAT
1 TATTCGAAT
6145334 TATTCGAAT
1 TATTCGAAT
*
6145343 TATTCGAGT
1 TATTCGAAT
6145352 TATTCGAAT
1 TATTCGAAT
6145361 T
1 T
6145362 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:6148393 original size:42 final size:42
Alignment explanation
Indices: 6148298--6148437 Score: 147
Period size: 42 Copynumber: 3.3 Consensus size: 42
6148288 GTCTCAAATG
* * * *
6148298 TGGTCTTACATGTAATCAAATAACGATGCCACTGTTCCAGACA
1 TGGTCTTACACGTAATCATAT-ACGATGCCAATGTCCCAGACA
* * *
6148341 GGGTCTTACACGTAATCATATACGACGCCAATGTCCCAAACA
1 TGGTCTTACACGTAATCATATACGATGCCAATGTCCCAGACA
* * *
6148383 TGGTCTTACACGTAAATC-TCAAATCGATGCCAACGTCCCAGACG
1 TGGTCTTACACGT-AATCAT-ATA-CGATGCCAATGTCCCAGACA
6148427 TGGTCTTACAC
1 TGGTCTTACAC
6148438 AATATCACAT
Statistics
Matches: 81, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
42 30 0.37
43 24 0.30
44 27 0.33
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (42 bp):
TGGTCTTACACGTAATCATATACGATGCCAATGTCCCAGACA
Found at i:6150674 original size:13 final size:13
Alignment explanation
Indices: 6150658--6150694 Score: 56
Period size: 15 Copynumber: 2.7 Consensus size: 13
6150648 ATTAAGGCAG
6150658 TAAATATTTTTAT
1 TAAATATTTTTAT
6150671 TAAATATATTTTTAT
1 T-AA-ATATTTTTAT
6150686 TAAATATTT
1 TAAATATTT
6150695 ATAGAGTCGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 7 0.32
14 4 0.18
15 11 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TAAATATTTTTAT
Found at i:6150681 original size:15 final size:15
Alignment explanation
Indices: 6150661--6150692 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
6150651 AAGGCAGTAA
6150661 ATATTTTTATTAAAT
1 ATATTTTTATTAAAT
6150676 ATATTTTTATTAAAT
1 ATATTTTTATTAAAT
6150691 AT
1 AT
6150693 TTATAGAGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATATTTTTATTAAAT
Found at i:6152760 original size:48 final size:48
Alignment explanation
Indices: 6152688--6152785 Score: 160
Period size: 48 Copynumber: 2.0 Consensus size: 48
6152678 GTAATTAAGT
* *
6152688 GAAGTATGCAAGTTTAATCTTGAGTTTAAGAAAGAAATGGTAAGTTTG
1 GAAGTATGCAAGTTTAATCCTGAGTCTAAGAAAGAAATGGTAAGTTTG
* *
6152736 GAAGTATGCAAGTTTCATCCTGAGTCTAAGCAAGAAATGGTAAGTTTG
1 GAAGTATGCAAGTTTAATCCTGAGTCTAAGAAAGAAATGGTAAGTTTG
6152784 GA
1 GA
6152786 TGAGTATGGT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.36, C:0.08, G:0.26, T:0.31
Consensus pattern (48 bp):
GAAGTATGCAAGTTTAATCCTGAGTCTAAGAAAGAAATGGTAAGTTTG
Found at i:6153451 original size:54 final size:54
Alignment explanation
Indices: 6153367--6153500 Score: 198
Period size: 54 Copynumber: 2.5 Consensus size: 54
6153357 GTGTAGGTTT
* * * **
6153367 CACACGGTCTG-GCACACGGCCATGTAACCCAACATCGAATTGAATAGGGTCTAG
1 CACACGGCCTGCG-ACACGGCCATGTGACCCAACATCGAATTGAACACAGTCTAG
6153421 CACACGGCCTGCGACACGGCCATGTGACCCAACATCGAATTGAACACAGTCTAG
1 CACACGGCCTGCGACACGGCCATGTGACCCAACATCGAATTGAACACAGTCTAG
*
6153475 CATACGGCCTGCGACACGGCCATGTG
1 CACACGGCCTGCGACACGGCCATGTG
6153501 GAATTATTTC
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
54 72 0.99
55 1 0.01
ACGTcount: A:0.28, C:0.31, G:0.25, T:0.16
Consensus pattern (54 bp):
CACACGGCCTGCGACACGGCCATGTGACCCAACATCGAATTGAACACAGTCTAG
Found at i:6155986 original size:19 final size:20
Alignment explanation
Indices: 6155942--6155987 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 20
6155932 TCTTGTTGCC
*
6155942 TTTCTT-TCTCTACCCTTTG
1 TTTCTTCTCTCAACCCTTTG
*
6155961 TTCTCTTCTCTCAACTCTTT-
1 TT-TCTTCTCTCAACCCTTTG
6155981 TTTCTTC
1 TTTCTTC
6155988 AATCTTCTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 7 0.30
20 6 0.26
21 10 0.43
ACGTcount: A:0.07, C:0.33, G:0.02, T:0.59
Consensus pattern (20 bp):
TTTCTTCTCTCAACCCTTTG
Found at i:6169247 original size:79 final size:81
Alignment explanation
Indices: 6169145--6169329 Score: 222
Period size: 79 Copynumber: 2.3 Consensus size: 81
6169135 GCTCCTCGTT
* *
6169145 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCACAAATGCCTTCGGGA-CTTAACC
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCACAAATGCCTTC-GGATCTTAACC
*
6169207 CGGAT-TTAGTAAC-TCGCA
63 CGGATATT-GTAACTTAGCA
***
6169225 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTGGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAACCCGG
*
6169289 ATATTGTCACTTAGCA
66 ATATTGTAACTTAGCA
6169305 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
6169330 CATCATTCAA
Statistics
Matches: 92, Mismatches: 7, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
78 5 0.05
79 51 0.55
80 36 0.39
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATTGTAACTTAGCA
Found at i:6169329 original size:40 final size:41
Alignment explanation
Indices: 6169145--6169329 Score: 208
Period size: 40 Copynumber: 4.6 Consensus size: 41
6169135 GCTCCTCGTT
* * *
6169145 CAAATGCCTTCGGGACATAGCCCGGTTA-TAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATTAGTACTTCGCA
*
6169185 CAAATGCCTTCGGGACTTAACCCGGAT-TTAGTAAC-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATTAGT-ACTTCGCA
6169225 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTA-TCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATTAGTACT-TCGCA
* * *
6169264 CAAATGCCTTC-GGATCTTGGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATTAGT-ACTTCGCA
6169305 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
6169330 CATCATTCAA
Statistics
Matches: 124, Mismatches: 10, Indels: 22
0.79 0.06 0.14
Matches are distributed among these distances:
38 3 0.02
39 31 0.25
40 73 0.59
41 16 0.13
42 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (41 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATTAGTACTTCGCA
Found at i:6175291 original size:27 final size:28
Alignment explanation
Indices: 6175219--6175294 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 28
6175209 AGATATTACG
*
6175219 TAAACTTTTATTATATTAAGTCAAGTTT
1 TAAAGTTTTATTATATTAAGTCAAGTTT
*
6175247 TATAGTTTTATTATATTACA-T-AACGTTT
1 TAAAGTTTTATTATATTA-AGTCAA-GTTT
6175275 TAAAG-TTTATTATATTAAGT
1 TAAAGTTTTATTATATTAAGT
6175295 TTTATAGTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
26 1 0.02
27 15 0.36
28 25 0.60
29 1 0.02
ACGTcount: A:0.36, C:0.05, G:0.08, T:0.51
Consensus pattern (28 bp):
TAAAGTTTTATTATATTAAGTCAAGTTT
Found at i:6178194 original size:41 final size:41
Alignment explanation
Indices: 6178137--6178250 Score: 185
Period size: 41 Copynumber: 2.8 Consensus size: 41
6178127 AGTAAGATGA
*
6178137 TTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATGT
1 TTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAT
*
6178178 TTCAGACTTTACGTCTAGCTGGCTTAATGCCGGTGAAATAT
1 TTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAT
*
6178219 TTTAGACTTTACGTCTAGCAGGC-TAATTGCCG
1 TTCAGACTTTACGTCTAGCAGGCTTAA-TGCCG
6178251 ATGTACTGAA
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
40 3 0.04
41 65 0.96
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (41 bp):
TTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAT
Found at i:6189440 original size:34 final size:35
Alignment explanation
Indices: 6189357--6189448 Score: 107
Period size: 34 Copynumber: 2.7 Consensus size: 35
6189347 CACTAATTAT
* * *
6189357 TTCGTCGGTTTATCCGACTAGCGCTGAGTGCAACT
1 TTCGTCAGTTTATCTGACTAGCGCTGAGTGCAACA
* * *
6189392 TTCATTAGTTTATCTGACTAGTGCTG-G-GCACACA
1 TTCGTCAGTTTATCTGACTAGCGCTGAGTGCA-ACA
6189426 TTCGTCAGTTTATCTGACTAGCG
1 TTCGTCAGTTTATCTGACTAGCG
6189449 TTGGGCGCAA
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
33 3 0.06
34 23 0.49
35 21 0.45
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.35
Consensus pattern (35 bp):
TTCGTCAGTTTATCTGACTAGCGCTGAGTGCAACA
Found at i:6189534 original size:75 final size:75
Alignment explanation
Indices: 6189298--6189534 Score: 238
Period size: 75 Copynumber: 3.2 Consensus size: 75
6189288 GATTCTTTCA
* * *
6189298 ACTACCGCTGGGCGCAAATACCATTAATTTATCCAACTAGAGCTGGGCTCACTAATTATTTCGTC
1 ACTAGCGCTGGGCGCAAATACTATTAGTTTATCCAACTAGAGCTGGGCTCACTAATTATTTCGTC
*
6189363 GGTTTATCCG
66 GATTTATCCG
* * * * ** * *
6189373 ACTAGCGCTGAGTGCAACT-TTCATTAGTTTATCTGACTAGTGCTGGG--CAC--A-CA-TTCGT
1 ACTAGCGCTGGGCGCAAATACT-ATTAGTTTATCCAACTAGAGCTGGGCTCACTAATTATTTCGT
*
6189431 C-AGTTTATCTG
65 CGA-TTTATCCG
* * **
6189442 ACTAGCGTTGGGCGCAAATACTATTGGTTTATCCAACTAGAGCTGGGCTCACTAATTATTTTTTC
1 ACTAGCGCTGGGCGCAAATACTATTAGTTTATCCAACTAGAGCTGGGCTCACTAATTATTTCGTC
6189507 GATTTATCCG
66 GATTTATCCG
*
6189517 ACTAGCGCTGGGTGCAAA
1 ACTAGCGCTGGGCGCAAA
6189535 CTCTTTCGCG
Statistics
Matches: 124, Mismatches: 28, Indels: 20
0.72 0.16 0.12
Matches are distributed among these distances:
69 49 0.40
70 2 0.02
71 4 0.03
73 4 0.03
74 1 0.01
75 63 0.51
76 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.32
Consensus pattern (75 bp):
ACTAGCGCTGGGCGCAAATACTATTAGTTTATCCAACTAGAGCTGGGCTCACTAATTATTTCGTC
GATTTATCCG
Found at i:6194901 original size:17 final size:17
Alignment explanation
Indices: 6194879--6194911 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
6194869 TCTGCCACTT
6194879 TTTTCTCTG-TTGTTCTC
1 TTTTCT-TGTTTGTTCTC
6194896 TTTTCTTGTTTGTTCT
1 TTTTCTTGTTTGTTCT
6194912 ATTTCCTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.00, C:0.18, G:0.12, T:0.70
Consensus pattern (17 bp):
TTTTCTTGTTTGTTCTC
Found at i:6197053 original size:56 final size:50
Alignment explanation
Indices: 6196830--6197077 Score: 232
Period size: 50 Copynumber: 4.9 Consensus size: 50
6196820 TGATAATAAA
* * * *
6196830 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGCGA--TGT-TTCTTG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTG
* * * * ** *
6196877 TACTGCCAATGTCATATCTCAGATATGGTCTTACATGGGAGTTCTCATATTG
1 -A-TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTG
* * *
6196929 GTGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTTG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTG
* * * *
6196979 GTGCGAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATAACCTCAATG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT---CT---TG
*
6197035 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
6197078 TTACCCAAAT
Statistics
Matches: 161, Mismatches: 29, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
48 1 0.01
49 31 0.19
50 81 0.50
51 2 0.01
52 4 0.02
53 2 0.01
56 40 0.25
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (50 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTG
Found at i:6204380 original size:12 final size:11
Alignment explanation
Indices: 6204364--6204394 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
6204354 AGAAAAAGAA
6204364 GAAAAAAACAG
1 GAAAAAAACAG
6204375 GAAAAAAACAG
1 GAAAAAAACAG
6204386 GAAAAAAAC
1 GAAAAAAAC
6204395 GTACAAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.74, C:0.10, G:0.16, T:0.00
Consensus pattern (11 bp):
GAAAAAAACAG
Found at i:6204564 original size:37 final size:37
Alignment explanation
Indices: 6204514--6205406 Score: 1759
Period size: 37 Copynumber: 24.1 Consensus size: 37
6204504 ATACAGAAGC
*
6204514 TTAACCATTGAACTAGCAAGCTCATTCTTGACATAGA
1 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
6204551 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
1 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
6204588 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
1 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
6204625 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
1 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
6204662 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
1 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
6204699 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
1 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
6204736 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
1 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
6204773 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
1 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
6204810 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
1 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
6204847 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
1 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
6204884 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
1 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
6204921 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
1 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
6204958 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
1 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
6204995 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
1 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
6205032 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
1 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
6205069 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
1 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
6205106 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
1 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
6205143 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
1 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
6205180 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
1 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
6205217 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
1 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
6205254 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
1 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
6205291 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
1 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
6205328 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
1 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
* *
6205365 TTAACCATTGAACTATCAAGCTCATTCTTGACATAGA
1 TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
6205402 TTAAC
1 TTAAC
6205407 TTAAGTTGAG
Statistics
Matches: 853, Mismatches: 3, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 853 1.00
ACGTcount: A:0.33, C:0.24, G:0.13, T:0.30
Consensus pattern (37 bp):
TTAACCATTGAACTAGCCAGCTCATTCTTGACATAGA
Found at i:6207601 original size:49 final size:49
Alignment explanation
Indices: 6207547--6207646 Score: 191
Period size: 49 Copynumber: 2.0 Consensus size: 49
6207537 CATGAATTTG
6207547 AATATCATTTAAATATATATTTTATTTTATAACTTATCGAAAAAAATAA
1 AATATCATTTAAATATATATTTTATTTTATAACTTATCGAAAAAAATAA
*
6207596 AATATCATTTAAATATATATTTTATTTTATAACTTATCTAAAAAAATAA
1 AATATCATTTAAATATATATTTTATTTTATAACTTATCGAAAAAAATAA
6207645 AA
1 AA
6207647 GATTATCAGA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.50, C:0.06, G:0.01, T:0.43
Consensus pattern (49 bp):
AATATCATTTAAATATATATTTTATTTTATAACTTATCGAAAAAAATAA
Found at i:6210749 original size:16 final size:16
Alignment explanation
Indices: 6210720--6210753 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
6210710 TTTGTTTCTC
6210720 TTTTCTTTTATTCTCTT
1 TTTTCTTTTATTCT-TT
6210737 TTTTCTTTT-TTCTTT
1 TTTTCTTTTATTCTTT
6210752 TT
1 TT
6210754 AGTTTAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 4 0.24
17 9 0.53
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTCTTTTATTCTTT
Found at i:6212141 original size:40 final size:40
Alignment explanation
Indices: 6212053--6212157 Score: 129
Period size: 40 Copynumber: 2.6 Consensus size: 40
6212043 ATCTCGTGCT
* * *
6212053 TAGGAGCATCATATTTTGGATGATCAGTTTAAGCTCATGCC
1 TAGGAGCATCATATTTTGG-TGAACAATTTAAGCTCATACC
* * *
6212094 TAAGAGCACCATATTTTGGTGAACAATTTAAGCTCATACG
1 TAGGAGCATCATATTTTGGTGAACAATTTAAGCTCATACC
*
6212134 TAGGAGCATCATTTTTTGGGTGAA
1 TAGGAGCATCATATTTT-GGTGAA
6212158 TGGTTAAAGC
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
40 31 0.57
41 23 0.43
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (40 bp):
TAGGAGCATCATATTTTGGTGAACAATTTAAGCTCATACC
Found at i:6212168 original size:41 final size:41
Alignment explanation
Indices: 6212053--6212171 Score: 125
Period size: 41 Copynumber: 2.9 Consensus size: 41
6212043 ATCTCGTGCT
* *
6212053 TAGGAGCATCATATTTTGGATG-ATCAGTTTAAGCTCATGCC
1 TAGGAGCATCATATTTTGGGTGAAT-AGTTTAAGCTCATACC
* * * * *
6212094 TAAGAGCACCATATTTT-GGTGAACAATTTAAGCTCATACG
1 TAGGAGCATCATATTTTGGGTGAATAGTTTAAGCTCATACC
* * *
6212134 TAGGAGCATCATTTTTTGGGTGAATGGTTAAAGCTCAT
1 TAGGAGCATCATATTTTGGGTGAATAGTTTAAGCTCAT
6212172 TGATAGCAAG
Statistics
Matches: 62, Mismatches: 14, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
40 30 0.48
41 32 0.52
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (41 bp):
TAGGAGCATCATATTTTGGGTGAATAGTTTAAGCTCATACC
Found at i:6218237 original size:11 final size:11
Alignment explanation
Indices: 6218223--6218249 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
6218213 TTTATTTGAA
6218223 AAAATATATTT
1 AAAATATATTT
6218234 AAAATATATTT
1 AAAATATATTT
6218245 AAAAT
1 AAAAT
6218250 TTAAATCTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
AAAATATATTT
Found at i:6218680 original size:22 final size:22
Alignment explanation
Indices: 6218623--6218688 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
6218613 CTGGCTCGAA
6218623 TTAT-ATATTAAATATATATTT
1 TTATGATATTAAATATATATTT
** *
6218644 TTATTTTAATCAAATATATA-TT
1 TTATGAT-ATTAAATATATATTT
6218666 TTATAGATATTAAATATATATTT
1 TTAT-GATATTAAATATATATTT
6218689 AATATGGGCC
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
21 4 0.11
22 18 0.50
23 14 0.39
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (22 bp):
TTATGATATTAAATATATATTT
Found at i:6219776 original size:23 final size:23
Alignment explanation
Indices: 6219733--6219776 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
6219723 TAACTTTGGA
* *
6219733 TTAAATTAAATTTTGATTTAAAG
1 TTAAATTAAATTTTCAATTAAAG
*
6219756 TTAAATTAAGTTTTCAATTAA
1 TTAAATTAAATTTTCAATTAA
6219777 TTTTTAATTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (23 bp):
TTAAATTAAATTTTCAATTAAAG
Found at i:6222681 original size:58 final size:57
Alignment explanation
Indices: 6222606--6222742 Score: 175
Period size: 58 Copynumber: 2.4 Consensus size: 57
6222596 TATTGTTATT
* * *
6222606 AAATTTTAATAAAATTATTATTAAAAATAATTGCATAAAAATAATAAATAATTTAACC
1 AAATTTTAATATAATTATTATTAAAAATAATTGAAT-AAAATAATAAATAATTTAACA
* * * * * *
6222664 ATATTTTAACATAATTATTATTAAATATAATTTAATAAAATAATATATAATTTAATA
1 AAATTTTAATATAATTATTATTAAAAATAATTGAATAAAATAATAAATAATTTAACA
6222721 AAATTCTTAATATAATTATTAT
1 AAATT-TTAATATAATTATTAT
6222743 ATGAATTAAA
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
57 22 0.33
58 45 0.67
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (57 bp):
AAATTTTAATATAATTATTATTAAAAATAATTGAATAAAATAATAAATAATTTAACA
Found at i:6223903 original size:30 final size:30
Alignment explanation
Indices: 6223867--6223958 Score: 116
Period size: 30 Copynumber: 3.0 Consensus size: 30
6223857 GGCCCATTTT
6223867 TATTTTAAAAATTTTAAAAAATTAAAAAAG
1 TATTTTAAAAATTTTAAAAAATTAAAAAAG
6223897 TATTTTAAAATTATTTT--AAAATTAAAAAAAG
1 TATTTTAAAA--ATTTTAAAAAATT-AAAAAAG
*
6223928 TATTTTAAAAATATTTAAAAATTTTAAAAAA
1 TATTTTAAAAAT-TTTAAAAA-ATTAAAAAA
6223959 ATTTAAAAAG
Statistics
Matches: 54, Mismatches: 1, Indels: 12
0.81 0.01 0.18
Matches are distributed among these distances:
29 2 0.04
30 19 0.35
31 17 0.31
32 14 0.26
33 2 0.04
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (30 bp):
TATTTTAAAAATTTTAAAAAATTAAAAAAG
Found at i:6223906 original size:11 final size:10
Alignment explanation
Indices: 6223867--6223990 Score: 67
Period size: 10 Copynumber: 12.1 Consensus size: 10
6223857 GGCCCATTTT
6223867 TATTTTAAAA
1 TATTTTAAAA
6223877 -ATTTTAAAA
1 TATTTTAAAA
* **
6223886 AATTAAAAAA
1 TATTTTAAAA
6223896 GTATTTTAAAA
1 -TATTTTAAAA
6223907 TTATTTTAAAA
1 -TATTTTAAAA
***
6223918 T-TAAAAAAA
1 TATTTTAAAA
6223927 GTATTTTAAAA
1 -TATTTTAAAA
6223938 -ATATTTAAAA
1 TAT-TTTAAAA
6223948 -ATTTTAAAAA
1 TATTTT-AAAA
* *
6223958 AATTTAAAAA
1 TATTTTAAAA
**
6223968 GTATGTAAAAAA
1 -TAT-TTTAAAA
6223980 TATTTTAAAA
1 TATTTTAAAA
6223990 T
1 T
6223991 TAAAAAAAAT
Statistics
Matches: 88, Mismatches: 17, Indels: 18
0.72 0.14 0.15
Matches are distributed among these distances:
9 19 0.22
10 32 0.36
11 31 0.35
12 6 0.07
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (10 bp):
TATTTTAAAA
Found at i:6223928 original size:31 final size:30
Alignment explanation
Indices: 6223867--6223959 Score: 109
Period size: 31 Copynumber: 3.0 Consensus size: 30
6223857 GGCCCATTTT
6223867 TATTTTAAAA-ATTTTAAAAAATT-AAAAAAG
1 TATTTTAAAATATTTT--AAAATTAAAAAAAG
6223897 TATTTTAAAATTATTTTAAAATTAAAAAAAG
1 TATTTTAAAA-TATTTTAAAATTAAAAAAAG
*
6223928 TATTTTAAAAATATTTAAAAATTTTAAAAAAA
1 TATTTT-AAAATATTTTAAAA--TTAAAAAAA
6223960 TTTAAAAAGT
Statistics
Matches: 56, Mismatches: 1, Indels: 9
0.85 0.02 0.14
Matches are distributed among these distances:
30 16 0.29
31 22 0.39
32 9 0.16
33 9 0.16
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (30 bp):
TATTTTAAAATATTTTAAAATTAAAAAAAG
Found at i:6223945 original size:41 final size:42
Alignment explanation
Indices: 6223866--6223992 Score: 129
Period size: 41 Copynumber: 3.1 Consensus size: 42
6223856 CGGCCCATTT
*
6223866 TTATTTTAAAAATTTTAAAAA--AT-TAAAAAAGTATTTTAAAA
1 TTATTTTAAAAA-TTAAAAAAGTATGTAAAAAA-TATTTTAAAA
* * *
6223907 TTATTTT-AAAATTAAAAAAAGTATTTTAAAAATATTTAAAAA
1 TTATTTTAAAAATT-AAAAAAGTATGTAAAAAATATTTTAAAA
** *
6223949 TT-TTAAAAAAATTTAAAAAGTATGTAAAAAATATTTTAAAA
1 TTATTTTAAAAATTAAAAAAGTATGTAAAAAATATTTTAAAA
6223990 TTA
1 TTA
6223993 AAAAAAATAA
Statistics
Matches: 71, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
39 2 0.03
40 9 0.13
41 35 0.49
42 19 0.27
43 6 0.08
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (42 bp):
TTATTTTAAAAATTAAAAAAGTATGTAAAAAATATTTTAAAA
Found at i:6232425 original size:20 final size:20
Alignment explanation
Indices: 6232400--6232441 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
6232390 AATTATCTGA
6232400 AAAAATAGGTATATTATATG
1 AAAAATAGGTATATTATATG
*
6232420 AAAAATATGTATATTATATG
1 AAAAATAGGTATATTATATG
6232440 AA
1 AA
6232442 CAATTTTTAA
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:0.52, C:0.00, G:0.12, T:0.36
Consensus pattern (20 bp):
AAAAATAGGTATATTATATG
Found at i:6233562 original size:30 final size:31
Alignment explanation
Indices: 6233521--6233581 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
6233511 GGGTTGGGAG
* *
6233521 GGGAGAGGAGTAAAAATTTTGGGGGGAAAGT
1 GGGAGAGGAGTAAAAATTTTGAGGGAAAAGT
*
6233552 GGGA-AGGAGTAAAAGTTTTGAGGGAAAAGT
1 GGGAGAGGAGTAAAAATTTTGAGGGAAAAGT
6233582 TAAAAGGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 23 0.85
31 4 0.15
ACGTcount: A:0.38, C:0.00, G:0.43, T:0.20
Consensus pattern (31 bp):
GGGAGAGGAGTAAAAATTTTGAGGGAAAAGT
Found at i:6233644 original size:9 final size:9
Alignment explanation
Indices: 6233630--6233666 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
6233620 TATAGTTTGA
6233630 TATTCGAAT
1 TATTCGAAT
6233639 TATTCGAAT
1 TATTCGAAT
*
6233648 TATTCGAGT
1 TATTCGAAT
*
6233657 TATTCAAAT
1 TATTCGAAT
6233666 T
1 T
6233667 CGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:6240641 original size:5 final size:5
Alignment explanation
Indices: 6240631--6240677 Score: 53
Period size: 5 Copynumber: 9.6 Consensus size: 5
6240621 TTTAGTTGAT
* *
6240631 AAATA AAATA AAATA AACA-A ATATA TAATA AAA-A AAATA AAATA AAA
1 AAATA AAATA AAATA AA-ATA AAATA AAATA AAATA AAATA AAATA AAA
6240678 AAGAATTATG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
4 5 0.14
5 29 0.83
6 1 0.03
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:6240676 original size:14 final size:14
Alignment explanation
Indices: 6240629--6240679 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
6240619 AATTTAGTTG
*
6240629 ATAAATAAAATAAA
1 ATAAAAAAAATAAA
* *
6240643 ATAAACAAATATATA
1 ATAAA-AAAAATAAA
6240658 ATAAAAAAAATAAA
1 ATAAAAAAAATAAA
6240672 ATAAAAAA
1 ATAAAAAA
6240680 GAATTATGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
14 20 0.65
15 11 0.35
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (14 bp):
ATAAAAAAAATAAA
Found at i:6250292 original size:20 final size:20
Alignment explanation
Indices: 6250255--6250292 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6250245 TCTCTTCACA
*
6250255 ATTTTTGGTCCAACTTCTCT
1 ATTTTTGGTCCAAATTCTCT
*
6250275 ATTTTTGGTTCAAATTCT
1 ATTTTTGGTCCAAATTCT
6250293 AAAGTCCCCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.18, G:0.11, T:0.53
Consensus pattern (20 bp):
ATTTTTGGTCCAAATTCTCT
Found at i:6267608 original size:27 final size:27
Alignment explanation
Indices: 6267574--6267628 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
6267564 AGCTATGGAG
*
6267574 AAGAGAAGAGAAAACTAA-AACCCTAA
1 AAGAGAAGAGAAAACTAAGAAACCTAA
*
6267600 AAGATGAAGAGAAACCTAAGAAACCTAA
1 AAGA-GAAGAGAAAACTAAGAAACCTAA
6267628 A
1 A
6267629 CTAAACTAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 4 0.16
27 13 0.52
28 8 0.32
ACGTcount: A:0.60, C:0.15, G:0.16, T:0.09
Consensus pattern (27 bp):
AAGAGAAGAGAAAACTAAGAAACCTAA
Found at i:6272030 original size:24 final size:26
Alignment explanation
Indices: 6271997--6272050 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 26
6271987 TCTTCTTAGA
*
6271997 TTTAGTCTTTA-GTTT-TTCTC-TTTT
1 TTTAGGCTTTAGGTTTATT-TCATTTT
6272021 TTTAGGCTTTAGGTTTATTTCATTTT
1 TTTAGGCTTTAGGTTTATTTCATTTT
6272047 TTTA
1 TTTA
6272051 TTTGCTTTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 10 0.38
25 6 0.23
26 10 0.38
ACGTcount: A:0.13, C:0.09, G:0.11, T:0.67
Consensus pattern (26 bp):
TTTAGGCTTTAGGTTTATTTCATTTT
Found at i:6273244 original size:19 final size:19
Alignment explanation
Indices: 6273222--6273259 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
6273212 ATCACTGTCA
6273222 CCCACCATAATCAAATTTG
1 CCCACCATAATCAAATTTG
* *
6273241 CCCATCGTAATCAAATTTG
1 CCCACCATAATCAAATTTG
6273260 TTATTAACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.08, T:0.29
Consensus pattern (19 bp):
CCCACCATAATCAAATTTG
Found at i:6273857 original size:29 final size:31
Alignment explanation
Indices: 6273819--6273880 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 31
6273809 GGGGGTAGGA
6273819 TGGGAAGGGAGCAAAAGTTATGGG-GGAAAG
1 TGGGAAGGGAGCAAAAGTTATGGGAGGAAAG
* *
6273849 TGGG-AGGGAGTAAAAGTTTTGGGAGGAAAG
1 TGGGAAGGGAGCAAAAGTTATGGGAGGAAAG
6273879 TG
1 TG
6273881 AAGAGGTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 17 0.59
30 12 0.41
ACGTcount: A:0.34, C:0.02, G:0.47, T:0.18
Consensus pattern (31 bp):
TGGGAAGGGAGCAAAAGTTATGGGAGGAAAG
Found at i:6286919 original size:88 final size:88
Alignment explanation
Indices: 6286800--6287061 Score: 515
Period size: 88 Copynumber: 3.0 Consensus size: 88
6286790 GTTTATAGTT
6286800 ATATGTATGAAACGCATATTTTGTAAATGCGATATTGGTGACAGATTTTATGAATTTAAATATCA
1 ATATGTATGAAACGCATATTTTGTAAATGCGATATTGGTGACAGATTTTATGAATTTAAATATCA
6286865 AATAATGATTTGTTTTGATTTTA
66 AATAATGATTTGTTTTGATTTTA
6286888 ATATGTATGAAACGCATATTTTGTAAATGCGATATTGGTGACAGATTTTATGAATTTAAATATCA
1 ATATGTATGAAACGCATATTTTGTAAATGCGATATTGGTGACAGATTTTATGAATTTAAATATCA
6286953 AATAATGATTTGTTTTGATTTTA
66 AATAATGATTTGTTTTGATTTTA
6286976 ATATGTATGAAACGCATATTTTGTAAATGCGATATTGGTGACAGATTTTATGAATTTAAATATCA
1 ATATGTATGAAACGCATATTTTGTAAATGCGATATTGGTGACAGATTTTATGAATTTAAATATCA
*
6287041 AAGAATGATTTGTTTTGATTT
66 AATAATGATTTGTTTTGATTT
6287062 GAACTACTAT
Statistics
Matches: 173, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 173 1.00
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.43
Consensus pattern (88 bp):
ATATGTATGAAACGCATATTTTGTAAATGCGATATTGGTGACAGATTTTATGAATTTAAATATCA
AATAATGATTTGTTTTGATTTTA
Found at i:6289641 original size:276 final size:277
Alignment explanation
Indices: 6289098--6289646 Score: 749
Period size: 276 Copynumber: 2.0 Consensus size: 277
6289088 ATTTCAATTC
*
6289098 ACATTCATCGGTTTGTCACGTTTCCATATTGGCCCCCTAGGCTTATATAACTGATTCTCAATATA
1 ACATTCATCGATTTGTCACGTTTCCATATTGGCCCCCTAGGCTTATATAACTGATTCTCAATATA
* * * * *
6289163 TATATGCATCAGCCGATCATTGTATCAAATCAATCTAAAAAATCATTTATTCCAATTACATTATA
66 TAAATGCATCAGCCAATCATTGTATCAAATCAATATAAAAAATCATGTATTCCAATTACATTACA
* * * *
6289228 CATGTCCCTATTAACCTAACTCAAACTCGAACTAATACACGAATCCAACCTACACACCAATTTGG
131 CATGTCCCTATTAACCTAACTCAAACTCAAACAAATACACGAATCCAACCAACACAACAATTTGG
* * * * *
6289293 CACCTAATGCCTGATGGATAAATTCGTAATAATGAATTGCGCACTACGCTGGCTGGTAAAACTAA
196 CACCTAATCCCTGACGGATAAATCCGTAATAATGAATTGCGCACTACACTGGCTAGTAAAACTAA
6289358 AAAATAAATGTGTGATT
261 AAAATAAATGTGTGATT
* * * * * *
6289375 ACATTTATCGATTTTTCATGTTTCCATATTGGCCCCCTGGGCTTATATAACTGATTTTCAATATG
1 ACATTCATCGATTTGTCACGTTTCCATATTGGCCCCCTAGGCTTATATAACTGATTCTCAATATA
* * *
6289440 TAAATTCATCAGTCAATCATTGTATCAAATCAATAT-GAAAATCATGTATTCCAATTACATTACA
66 TAAATGCATCAGCCAATCATTGTATCAAATCAATATAAAAAATCATGTATTCCAATTACATTACA
* * * * * *
6289504 TATGTCTCTATTAACCTAACTTAGACTCAAACAAATACATGGATCCAACCAACACAACAATTTGG
131 CATGTCCCTATTAACCTAACTCAAACTCAAACAAATACACGAATCCAACCAACACAACAATTTGG
** * * * * *
6289569 CATTTAGTCCCTGACGGATAAATCCGTAATAATGAATTGTGCCCTACACTGGCTAGTAAAATTGA
196 CACCTAATCCCTGACGGATAAATCCGTAATAATGAATTGCGCACTACACTGGCTAGTAAAACTAA
*
6289634 CAAATAAATGTGT
261 AAAATAAATGTGT
6289647 CCAACACTGG
Statistics
Matches: 234, Mismatches: 38, Indels: 1
0.86 0.14 0.00
Matches are distributed among these distances:
276 145 0.62
277 89 0.38
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.32
Consensus pattern (277 bp):
ACATTCATCGATTTGTCACGTTTCCATATTGGCCCCCTAGGCTTATATAACTGATTCTCAATATA
TAAATGCATCAGCCAATCATTGTATCAAATCAATATAAAAAATCATGTATTCCAATTACATTACA
CATGTCCCTATTAACCTAACTCAAACTCAAACAAATACACGAATCCAACCAACACAACAATTTGG
CACCTAATCCCTGACGGATAAATCCGTAATAATGAATTGCGCACTACACTGGCTAGTAAAACTAA
AAAATAAATGTGTGATT
Found at i:6295581 original size:16 final size:18
Alignment explanation
Indices: 6295560--6295596 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
6295550 GCTCACATTC
6295560 TCTTTTT-A-TCTCTTCT
1 TCTTTTTCATTCTCTTCT
*
6295576 TCTTTTTCATTCTCTTTT
1 TCTTTTTCATTCTCTTCT
6295594 TCT
1 TCT
6295597 CACAACTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 1 0.06
18 10 0.56
ACGTcount: A:0.05, C:0.24, G:0.00, T:0.70
Consensus pattern (18 bp):
TCTTTTTCATTCTCTTCT
Found at i:6295605 original size:28 final size:28
Alignment explanation
Indices: 6295555--6295609 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
6295545 TTCAAGCTCA
* **
6295555 CATTCTCTTTTTATCTCTTCTTCTTTTT
1 CATTCTCTTTTTATCACAACTTCTTTTT
*
6295583 CATTCTCTTTTTCTCACAACTTCTTTT
1 CATTCTCTTTTTATCACAACTTCTTTT
6295610 CTCACACACT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.11, C:0.27, G:0.00, T:0.62
Consensus pattern (28 bp):
CATTCTCTTTTTATCACAACTTCTTTTT
Found at i:6295668 original size:20 final size:21
Alignment explanation
Indices: 6295628--6295686 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
6295618 CTCACTTTTT
6295628 ATTTCCTTTTCTTTTTCTCTC
1 ATTTCCTTTTCTTTTTCTCTC
* *
6295649 ATTTCTTTTTTTTTCTTCTCTC
1 ATTTCCTTTTCTTT-TTCTCTC
* *
6295671 AATCTCCTTTACTTTT
1 -ATTTCCTTTTCTTTT
6295687 CTTTCTTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
21 12 0.40
22 8 0.27
23 10 0.33
ACGTcount: A:0.08, C:0.25, G:0.00, T:0.66
Consensus pattern (21 bp):
ATTTCCTTTTCTTTTTCTCTC
Found at i:6295763 original size:30 final size:31
Alignment explanation
Indices: 6295722--6295784 Score: 85
Period size: 30 Copynumber: 2.0 Consensus size: 31
6295712 CTTCTCTCTT
6295722 TTCTTAATTTCTTTT-TTTTCTC-AATTTTC
1 TTCTTAATTTCTTTTATTTTCTCTAATTTTC
*
6295751 TTCTTCAATTTCTTTTAGTTTTCTCTCATTTTC
1 TTCTT-AATTTCTTTTA-TTTTCTCTAATTTTC
6295784 T
1 T
6295785 CTCATTATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 5 0.17
30 10 0.34
32 7 0.24
33 7 0.24
ACGTcount: A:0.13, C:0.19, G:0.02, T:0.67
Consensus pattern (31 bp):
TTCTTAATTTCTTTTATTTTCTCTAATTTTC
Found at i:6302357 original size:33 final size:36
Alignment explanation
Indices: 6302308--6302375 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 36
6302298 ACTTTATTTA
* *
6302308 ATGCAAAACACATAATG-T-ATGTCATAATTAAAAG
1 ATGCAAAACACATAATGATCAAGACATAATTAAAAG
*
6302342 ATGC-AAACACTTAATGATCAAGACATAATTAAAA
1 ATGCAAAACACATAATGATCAAGACATAATTAAAA
6302376 ATTGTAGAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
33 11 0.38
34 5 0.17
35 13 0.45
ACGTcount: A:0.51, C:0.13, G:0.10, T:0.25
Consensus pattern (36 bp):
ATGCAAAACACATAATGATCAAGACATAATTAAAAG
Found at i:6306870 original size:48 final size:48
Alignment explanation
Indices: 6306799--6306897 Score: 171
Period size: 48 Copynumber: 2.1 Consensus size: 48
6306789 TTAGAAATAG
*
6306799 ATAACATCTAGGCGAATTCCTAAGAGCTAATCTCCTATTTGCGGAATC
1 ATAACATCTAGGCGAATTCCTAAGAGCTAATCCCCTATTTGCGGAATC
* *
6306847 ATAACATCTAGGCGAATTTCTAAGAGCTAATCCCCTGTTTGCGGAATC
1 ATAACATCTAGGCGAATTCCTAAGAGCTAATCCCCTATTTGCGGAATC
6306895 ATA
1 ATA
6306898 CATATGAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.29
Consensus pattern (48 bp):
ATAACATCTAGGCGAATTCCTAAGAGCTAATCCCCTATTTGCGGAATC
Found at i:6307371 original size:22 final size:22
Alignment explanation
Indices: 6307253--6307380 Score: 87
Period size: 22 Copynumber: 5.9 Consensus size: 22
6307243 TCCTTTGCCA
* * *
6307253 CCCAT-AAGAGCTCTAATATGT
1 CCCATAAAGGGCTCTCATACGT
* * *
6307274 CCCATAAAGAGCTTTTATACGT
1 CCCATAAAGGGCTCTCATACGT
* * * * *
6307296 CCTAGAAAGGGTTTTCATATGT
1 CCCATAAAGGGCTCTCATACGT
* * * * *
6307318 CTCATAAAAGGCTCTTATGCAT
1 CCCATAAAGGGCTCTCATACGT
*
6307340 CCCATTAAGGGCTCTCATACGT
1 CCCATAAAGGGCTCTCATACGT
*
6307362 CCCATAAAGGGCTTTCATA
1 CCCATAAAGGGCTCTCATA
6307381 TATTGGTGTC
Statistics
Matches: 79, Mismatches: 27, Indels: 1
0.74 0.25 0.01
Matches are distributed among these distances:
21 5 0.06
22 74 0.94
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.30
Consensus pattern (22 bp):
CCCATAAAGGGCTCTCATACGT
Found at i:6309732 original size:34 final size:34
Alignment explanation
Indices: 6309683--6309747 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
6309673 TTTTAATTAA
6309683 TATAAAATTATAAAATCAATTAAATAATAATATG
1 TATAAAATTATAAAATCAATTAAATAATAATATG
* * *
6309717 TATACAATTGTAAAATTAATTAAATAATAAT
1 TATAAAATTATAAAATCAATTAAATAATAAT
6309748 TAATATGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (34 bp):
TATAAAATTATAAAATCAATTAAATAATAATATG
Found at i:6317278 original size:3 final size:3
Alignment explanation
Indices: 6317270--6317308 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
6317260 TTTCGACTCT
6317270 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
6317309 ATCATCACTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:6322322 original size:36 final size:36
Alignment explanation
Indices: 6322282--6322350 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
6322272 AAGGGTGATG
*
6322282 ATTCATTAATCTCTACATATAATCCAATTGAAGATA
1 ATTCAATAATCTCTACATATAATCCAATTGAAGATA
6322318 ATTCAATAATCTCTACATATAATCCAATTGAAG
1 ATTCAATAATCTCTACATATAATCCAATTGAAG
6322351 GTGGAGTCGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.42, C:0.17, G:0.06, T:0.35
Consensus pattern (36 bp):
ATTCAATAATCTCTACATATAATCCAATTGAAGATA
Found at i:6327474 original size:12 final size:12
Alignment explanation
Indices: 6327459--6327490 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
6327449 TAAAAAGGAA
6327459 AATAATAATAGT
1 AATAATAATAGT
6327471 AATAATAATAGT
1 AATAATAATAGT
6327483 AA-AATAAT
1 AATAATAAT
6327491 TAATTTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (12 bp):
AATAATAATAGT
Found at i:6340071 original size:27 final size:27
Alignment explanation
Indices: 6339991--6340072 Score: 83
Period size: 27 Copynumber: 3.0 Consensus size: 27
6339981 TAAAATTTTG
* * * *
6339991 AAAATAATAAGTGAAAAATAACATATT
1 AAAAAAATAAATGAAAAGTAATATATT
* *
6340018 ATAAAAAACCAAATGGAAAGTAATATATT
1 A-AAAAAA-TAAATGAAAAGTAATATATT
*
6340047 AAAAAAATAACTGAAAAGTAATATAT
1 AAAAAAATAAATGAAAAGTAATATAT
6340073 CCAAATTAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
27 17 0.39
28 11 0.25
29 16 0.36
ACGTcount: A:0.62, C:0.05, G:0.09, T:0.24
Consensus pattern (27 bp):
AAAAAAATAAATGAAAAGTAATATATT
Found at i:6341877 original size:31 final size:31
Alignment explanation
Indices: 6341839--6341902 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
6341829 GCTTGGGAAG
*
6341839 AAAAAATAAAAGGG-AAAGAAAGAAAGGGAGA
1 AAAAAATAAAAGGGAAAAGAAAAAAAGGG-GA
6341870 AAAAAATAAAAGGGAAAAGAAAAAAAGGGGA
1 AAAAAATAAAAGGGAAAAGAAAAAAAGGGGA
6341901 AA
1 AA
6341903 CCTCTCATAC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 18 0.58
32 13 0.42
ACGTcount: A:0.70, C:0.00, G:0.27, T:0.03
Consensus pattern (31 bp):
AAAAAATAAAAGGGAAAAGAAAAAAAGGGGA
Found at i:6341895 original size:15 final size:15
Alignment explanation
Indices: 6341846--6341898 Score: 63
Period size: 16 Copynumber: 3.5 Consensus size: 15
6341836 AAGAAAAAAT
6341846 AAAAGGG-AAAGAAA
1 AAAAGGGAAAAGAAA
* *
6341860 GAAAGGGAGAAAAAAA
1 AAAAGGGA-AAAGAAA
6341876 TAAAAGGGAAAAGAAA
1 -AAAAGGGAAAAGAAA
6341892 AAAAGGG
1 AAAAGGG
6341899 GAAACCTCTC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
14 6 0.19
15 7 0.22
16 12 0.38
17 7 0.22
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.02
Consensus pattern (15 bp):
AAAAGGGAAAAGAAA
Found at i:6345268 original size:29 final size:29
Alignment explanation
Indices: 6345209--6345269 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
6345199 AATATATATC
* ***
6345209 TAAAAGATTATAAACACTTTTTTTTAAAA
1 TAAAAGATTATAAACACATTTAAATAAAA
6345238 TAAAA-ATTATAAACACATTTAAATAACAA
1 TAAAAGATTATAAACACATTTAAATAA-AA
6345267 TAA
1 TAA
6345270 TACTTTGAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 17 0.63
29 10 0.37
ACGTcount: A:0.56, C:0.08, G:0.02, T:0.34
Consensus pattern (29 bp):
TAAAAGATTATAAACACATTTAAATAAAA
Found at i:6348473 original size:9 final size:9
Alignment explanation
Indices: 6348461--6348485 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
6348451 AAAAACTTCT
6348461 AAAAATATA
1 AAAAATATA
6348470 AAAAATATA
1 AAAAATATA
6348479 AAAAATA
1 AAAAATA
6348486 ATATATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAAAATATA
Found at i:6348740 original size:40 final size:40
Alignment explanation
Indices: 6348684--6348763 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
6348674 TTATTAAATA
*
6348684 AAGTATGGGCCAAACATGTGTAGATACTCTAATAATTAAT
1 AAGTATGGGCCAAACATGTATAGATACTCTAATAATTAAT
* *
6348724 AAGTATGGGTCTAACATGTATAGATACTCTAATAATTAAT
1 AAGTATGGGCCAAACATGTATAGATACTCTAATAATTAAT
6348764 TTCTAATTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.33
Consensus pattern (40 bp):
AAGTATGGGCCAAACATGTATAGATACTCTAATAATTAAT
Done.