Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 142 of 187
Found at i:42490979 original size:30 final size:30
Alignment explanation
Indices: 42490922--42490983 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 30
42490912 AATAACAATA
*
42490922 TCCAAAACCAAAATCAAATCCAAAAACTTAG
1 TCCAAAAACAAAA-CAAATCCAAAAACTTAG
42490953 TCCAAAAACAAAA-AAATCCAAAAAACTTAG
1 TCCAAAAACAAAACAAATCC-AAAAACTTAG
42490983 T
1 T
42490984 TAAAAATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 6 0.21
30 11 0.38
31 12 0.41
ACGTcount: A:0.58, C:0.23, G:0.03, T:0.16
Consensus pattern (30 bp):
TCCAAAAACAAAACAAATCCAAAAACTTAG
Found at i:42491254 original size:34 final size:34
Alignment explanation
Indices: 42491216--42491280 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
42491206 GTCGCATCAC
* *
42491216 CAGAAACATATATTAGACCAGAATGTCATATTTT
1 CAGAAACATATATCAGACCAAAATGTCATATTTT
* *
42491250 CAGAAGCATATATCATACCAAAATGTCATAT
1 CAGAAACATATATCAGACCAAAATGTCATAT
42491281 CATATCAGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (34 bp):
CAGAAACATATATCAGACCAAAATGTCATATTTT
Found at i:42491874 original size:31 final size:31
Alignment explanation
Indices: 42491831--42491905 Score: 141
Period size: 31 Copynumber: 2.4 Consensus size: 31
42491821 TTGGAAAATG
42491831 GGCCCACACGGCCCAACTAGCTAGCTCGTGT
1 GGCCCACACGGCCCAACTAGCTAGCTCGTGT
*
42491862 GGCCTACACGGCCCAACTAGCTAGCTCGTGT
1 GGCCCACACGGCCCAACTAGCTAGCTCGTGT
42491893 GGCCCACACGGCC
1 GGCCCACACGGCC
42491906 TCACACACGC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.19, C:0.40, G:0.27, T:0.15
Consensus pattern (31 bp):
GGCCCACACGGCCCAACTAGCTAGCTCGTGT
Found at i:42492308 original size:26 final size:26
Alignment explanation
Indices: 42492281--42492343 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
42492271 GTTAAAGGGA
*
42492281 AAAGAAAGAAACTCAA-AGA-AAAAAG
1 AAAGAAAGAAAAT-AAGAGAGAAAAAG
* *
42492306 AAAGGAAGAAAATAAGAGAGAACAAG
1 AAAGAAAGAAAATAAGAGAGAAAAAG
42492332 AAAGAAAGAAAA
1 AAAGAAAGAAAA
42492344 GAAAATATGA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
24 2 0.06
25 14 0.44
26 16 0.50
ACGTcount: A:0.71, C:0.05, G:0.21, T:0.03
Consensus pattern (26 bp):
AAAGAAAGAAAATAAGAGAGAAAAAG
Found at i:42492336 original size:14 final size:13
Alignment explanation
Indices: 42492301--42492347 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
42492291 ACTCAAAGAA
*
42492301 AAAAGAAAGGAAG
1 AAAAGAAAGAAAG
* *
42492314 AAAA-TAAGAGAG
1 AAAAGAAAGAAAG
42492326 AACAAGAAAGAAAG
1 AA-AAGAAAGAAAG
42492340 AAAAGAAA
1 AAAAGAAA
42492348 ATATGATAGA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
12 7 0.26
13 12 0.44
14 8 0.30
ACGTcount: A:0.72, C:0.02, G:0.23, T:0.02
Consensus pattern (13 bp):
AAAAGAAAGAAAG
Found at i:42501488 original size:61 final size:61
Alignment explanation
Indices: 42501393--42501516 Score: 248
Period size: 61 Copynumber: 2.0 Consensus size: 61
42501383 GATAAGTATA
42501393 ATAAGTATTGGGCGTGAAGGAAACAAGATCAACATGCTAGTTTACTTGGCAGTTATATTTG
1 ATAAGTATTGGGCGTGAAGGAAACAAGATCAACATGCTAGTTTACTTGGCAGTTATATTTG
42501454 ATAAGTATTGGGCGTGAAGGAAACAAGATCAACATGCTAGTTTACTTGGCAGTTATATTTG
1 ATAAGTATTGGGCGTGAAGGAAACAAGATCAACATGCTAGTTTACTTGGCAGTTATATTTG
42501515 AT
1 AT
42501517 CCACGATGTA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.31
Consensus pattern (61 bp):
ATAAGTATTGGGCGTGAAGGAAACAAGATCAACATGCTAGTTTACTTGGCAGTTATATTTG
Found at i:42502572 original size:58 final size:58
Alignment explanation
Indices: 42502510--42502632 Score: 176
Period size: 58 Copynumber: 2.1 Consensus size: 58
42502500 CTACTGTATT
* * * *
42502510 TTGGACTTTTACTTATGT-TTTTTTATTTTAATCTTGTTGTGTTGTTGTTGTTGTTTAC
1 TTGGACTTTTACTTAT-TCTTTTTAATTATAATCTTGTTGTATTGTAGTTGTTGTTTAC
* *
42502568 TTGGACTTTTGCTTCTTCTTTTTAATTATAATCTTGTTGTATTGTAGTTGTTGTTTAC
1 TTGGACTTTTACTTATTCTTTTTAATTATAATCTTGTTGTATTGTAGTTGTTGTTTAC
42502626 TTGGACT
1 TTGGACT
42502633 CATGTTGTTT
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
57 1 0.02
58 57 0.98
ACGTcount: A:0.14, C:0.09, G:0.17, T:0.60
Consensus pattern (58 bp):
TTGGACTTTTACTTATTCTTTTTAATTATAATCTTGTTGTATTGTAGTTGTTGTTTAC
Found at i:42502640 original size:19 final size:19
Alignment explanation
Indices: 42502616--42502659 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
42502606 GTATTGTAGT
*
42502616 TGTTGTTTACTTGGACTCA
1 TGTTGTTTACTTGGACTAA
* *
42502635 TGTTGTTTATTTGGGCTAA
1 TGTTGTTTACTTGGACTAA
42502654 TGTTGT
1 TGTTGT
42502660 GTTGCTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.14, C:0.09, G:0.25, T:0.52
Consensus pattern (19 bp):
TGTTGTTTACTTGGACTAA
Found at i:42505627 original size:30 final size:31
Alignment explanation
Indices: 42505592--42505655 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
42505582 ATAATTACGC
42505592 TTTAATGTAAATTTATA-A-AT-AAATTTTTAT
1 TTTAAT-TAAA-TTATACATATAAAATTTTTAT
*
42505622 TTTAATTTAATTATACATATAAAATTTTTAT
1 TTTAATTAAATTATACATATAAAATTTTTAT
42505653 TTT
1 TTT
42505656 TATTTAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 5 0.17
29 4 0.13
30 8 0.27
31 13 0.43
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (31 bp):
TTTAATTAAATTATACATATAAAATTTTTAT
Found at i:42506016 original size:9 final size:9
Alignment explanation
Indices: 42506002--42506028 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
42505992 TTACTAATTT
42506002 AAATTTAAA
1 AAATTTAAA
42506011 AAATTTAAA
1 AAATTTAAA
42506020 AAATTTAAA
1 AAATTTAAA
42506029 TAAAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
AAATTTAAA
Found at i:42506739 original size:59 final size:59
Alignment explanation
Indices: 42506674--42506793 Score: 231
Period size: 59 Copynumber: 2.0 Consensus size: 59
42506664 TATAATCTTT
*
42506674 TTCCTAGGGAATGGTTTAGGAAGCTTCTTTTGATAAGATAATTTCTTATTTCTTACTTC
1 TTCCTAGGGAATGGTTTAGGAAGCTTCTTTTGATAAGATAATTTCTTACTTCTTACTTC
42506733 TTCCTAGGGAATGGTTTAGGAAGCTTCTTTTGATAAGATAATTTCTTACTTCTTACTTC
1 TTCCTAGGGAATGGTTTAGGAAGCTTCTTTTGATAAGATAATTTCTTACTTCTTACTTC
42506792 TT
1 TT
42506794 ACTCTTCCAT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.23, C:0.14, G:0.17, T:0.46
Consensus pattern (59 bp):
TTCCTAGGGAATGGTTTAGGAAGCTTCTTTTGATAAGATAATTTCTTACTTCTTACTTC
Found at i:42513881 original size:23 final size:24
Alignment explanation
Indices: 42513847--42513891 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
42513837 CTCCCCTCAA
42513847 TTTTTCTGTCTTCCTT-TTCTTTT
1 TTTTTCTGTCTTCCTTCTTCTTTT
*
42513870 TTTTTCCT-TCTTTCTTCTTCTT
1 TTTTT-CTGTCTTCCTTCTTCTT
42513892 CCCTCAACCC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.73
Consensus pattern (24 bp):
TTTTTCTGTCTTCCTTCTTCTTTT
Found at i:42516943 original size:30 final size:30
Alignment explanation
Indices: 42516855--42516943 Score: 106
Period size: 30 Copynumber: 3.0 Consensus size: 30
42516845 TTTGATCAAC
*
42516855 AGATAGCCACAAAGGCAACCATACATCATT
1 AGATAGCCACAAAGGCATCCATACATCATT
* * * *
42516885 AGATAGCCATAAAGGCGTCGATATATCATT
1 AGATAGCCACAAAGGCATCCATACATCATT
* * *
42516915 AGATAGCTACAAAGGCATCTAGACATCAT
1 AGATAGCCACAAAGGCATCCATACATCAT
42516944 ACACTAAACT
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.21
Consensus pattern (30 bp):
AGATAGCCACAAAGGCATCCATACATCATT
Found at i:42517504 original size:16 final size:16
Alignment explanation
Indices: 42517483--42517519 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
42517473 CCTCATGTGG
*
42517483 AGACTTATTGATGCAA
1 AGACTTATTCATGCAA
42517499 AGACTTATTCATGCAA
1 AGACTTATTCATGCAA
42517515 AGACT
1 AGACT
42517520 CCATCGTGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (16 bp):
AGACTTATTCATGCAA
Found at i:42521709 original size:18 final size:17
Alignment explanation
Indices: 42521676--42521711 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
42521666 ATGAAAATTG
42521676 ATATGAACTTATAAAAA
1 ATATGAACTTATAAAAA
42521693 ATATGAAAC-TATAAAAA
1 ATATG-AACTTATAAAAA
42521710 AT
1 AT
42521712 CTAATAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 15 0.83
18 3 0.17
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.28
Consensus pattern (17 bp):
ATATGAACTTATAAAAA
Found at i:42521823 original size:18 final size:19
Alignment explanation
Indices: 42521793--42521835 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
42521783 TTAAAATTCT
*
42521793 ATAAAAATCATAATAAATA
1 ATAAAAATCATAAAAAATA
42521812 ATAAAAAT-ATAAAAAATA
1 ATAAAAATCATAAAAAATA
*
42521830 TTAAAA
1 ATAAAA
42521836 TTTAGATAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (19 bp):
ATAAAAATCATAAAAAATA
Found at i:42521864 original size:9 final size:9
Alignment explanation
Indices: 42521600--42521872 Score: 51
Period size: 9 Copynumber: 28.7 Consensus size: 9
42521590 TTAAAAAAGC
42521600 TTATAAAAAA
1 TTAT-AAAAA
* *
42521610 TCATAGAAA
1 TTATAAAAA
*
42521619 TTATCAAAA
1 TTATAAAAA
42521628 -TATAAAAA
1 TTATAAAAA
* * *
42521636 GTATTAGATA
1 TTA-TAAAAA
42521646 TTA-AAAAA
1 TTATAAAAA
*
42521654 TATTTAAAAA
1 T-TATAAAAA
* *
42521664 ATATGAAAA
1 TTATAAAAA
* *
42521673 TTGATATGAAC
1 TT-ATA-AAAA
42521684 TTATAAAAA
1 TTATAAAAA
* *
42521693 ATAT-GAAA
1 TTATAAAAA
*
42521701 CTATAAAAAA
1 TTAT-AAAAA
42521711 TCTA-ATAAAA
1 T-TATA-AAAA
42521721 TT-TAATAAA
1 TTATAA-AAA
42521730 TTATAAAAA
1 TTATAAAAA
*
42521739 -AATATAAAA
1 TTATA-AAAA
42521748 TTA-ACAAATCA
1 TTATA-AAA--A
* *
42521759 TATTTAAAATT
1 T-TATAAAA-A
42521770 TTATAAAAA
1 TTATAAAAA
* *
42521779 CGTATTAAAAT
1 -TTA-TAAAAA
42521790 TCTATAAAAA
1 T-TATAAAAA
*
42521800 TCATAATAAA
1 TTATAA-AAA
*
42521810 TAATAAAAA
1 TTATAAAAA
42521819 -TATAAAAA
1 TTATAAAAA
* *
42521827 ATATTAAAA
1 TTATAAAAA
*
42521836 TT-TAGATAAGC
1 TTATA-A-AA-A
42521847 TTATAAAAA
1 TTATAAAAA
42521856 TTATTAAAAAA
1 TTA-T-AAAAA
42521867 TTATAA
1 TTATAA
42521873 TAACTTGAAT
Statistics
Matches: 187, Mismatches: 46, Indels: 61
0.64 0.16 0.21
Matches are distributed among these distances:
8 29 0.16
9 65 0.35
10 59 0.32
11 27 0.14
12 6 0.03
13 1 0.01
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (9 bp):
TTATAAAAA
Found at i:42522304 original size:9 final size:9
Alignment explanation
Indices: 42522287--42522510 Score: 81
Period size: 9 Copynumber: 24.6 Consensus size: 9
42522277 TTTATGATTT
42522287 TTTTATATAA
1 TTTT-TATAA
42522297 TTTTTATAA
1 TTTTTATAA
*
42522306 GTTTGTATCAA
1 -TTTTTAT-AA
**
42522317 TTTCAATATA
1 TTTTTATA-A
*
42522327 TTTTTATAT
1 TTTTTATAA
*
42522336 TTTTTACAA
1 TTTTTATAA
*
42522345 TTTATTATTA
1 TTT-TTATAA
*
42522355 TTTTTAAGAA
1 TTTTT-ATAA
* *
42522365 TTCTAATACA
1 TTTTTATA-A
42522375 TTTTT-TAA
1 TTTTTATAA
*
42522383 TTTTGA-ATA
1 TTTTTATA-A
*
42522392 TTTTAATAA
1 TTTTTATAA
**
42522401 GCTTTATTAA
1 TTTTTA-TAA
42522411 -TTTTATAA
1 TTTTTATAA
* *
42522419 TTTATTAGAT
1 TTT-TTATAA
42522429 TTTTTAT-A
1 TTTTTATAA
42522437 TTTTT-TAA
1 TTTTTATAA
*
42522445 TATTTATAA
1 TTTTTATAA
**
42522454 GTTTAAATAA
1 -TTTTTATAA
*
42522464 -ATTT-TAA
1 TTTTTATAA
42522471 TATTTTATAA
1 T-TTTTATAA
*
42522481 TATTTA-ATA
1 TTTTTATA-A
42522490 TTTTTAT--
1 TTTTTATAA
42522497 TTTTTATAA
1 TTTTTATAA
42522506 TTTTT
1 TTTTT
42522511 TCTTATTTTT
Statistics
Matches: 155, Mismatches: 37, Indels: 45
0.65 0.16 0.19
Matches are distributed among these distances:
7 11 0.07
8 21 0.14
9 62 0.40
10 59 0.38
11 2 0.01
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (9 bp):
TTTTTATAA
Found at i:42522698 original size:3 final size:3
Alignment explanation
Indices: 42522685--42522724 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
42522675 TATAGTGGCT
*
42522685 TAA TTA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
42522725 TTTATATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:42522992 original size:28 final size:27
Alignment explanation
Indices: 42522961--42523014 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
42522951 ATAAAATTGC
*
42522961 ATTTTAAC-CTTCAAAATTTAAAAATTTA
1 ATTTTAACTCTCCAAAA--TAAAAATTTA
*
42522989 ATTTTGACTCTCCAAAATAAAAATTT
1 ATTTTAACTCTCCAAAATAAAAATTT
42523015 TTAATTAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 9 0.39
28 7 0.30
29 7 0.30
ACGTcount: A:0.44, C:0.13, G:0.02, T:0.41
Consensus pattern (27 bp):
ATTTTAACTCTCCAAAATAAAAATTTA
Found at i:42524733 original size:24 final size:24
Alignment explanation
Indices: 42524701--42524748 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
42524691 GGTCATGTAG
*
42524701 TTTGAAAATAAAATCTGCAGTTGA
1 TTTGAAAATAAAATCTACAGTTGA
42524725 TTTGAAAATAAAATCTACAGTTGA
1 TTTGAAAATAAAATCTACAGTTGA
42524749 CTCTATCAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (24 bp):
TTTGAAAATAAAATCTACAGTTGA
Found at i:42526933 original size:39 final size:39
Alignment explanation
Indices: 42526890--42526967 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 39
42526880 GAGCTTTGAC
*
42526890 TACATACACTATTCCGTCAAACATTACCGTCTCCTTTAT
1 TACATACACTATTCCGTCAAACATTACCATCTCCTTTAT
* *
42526929 TACATCCACTATTCCGTCAAACATTATCATCTCCTTTAT
1 TACATACACTATTCCGTCAAACATTACCATCTCCTTTAT
42526968 GATACTTTGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.28, C:0.31, G:0.04, T:0.37
Consensus pattern (39 bp):
TACATACACTATTCCGTCAAACATTACCATCTCCTTTAT
Found at i:42533345 original size:20 final size:20
Alignment explanation
Indices: 42533300--42533345 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
42533290 ATCATGGTCT
42533300 TTGCTT-CTTCTTTACTTAC
1 TTGCTTACTTCTTTACTTAC
*
42533319 TCT-CTTACTTGTTTACTTAC
1 T-TGCTTACTTCTTTACTTAC
42533339 TTGCTTA
1 TTGCTTA
42533346 TTTAAATAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.13, C:0.24, G:0.07, T:0.57
Consensus pattern (20 bp):
TTGCTTACTTCTTTACTTAC
Found at i:42533733 original size:50 final size:50
Alignment explanation
Indices: 42533594--42533739 Score: 157
Period size: 50 Copynumber: 2.9 Consensus size: 50
42533584 TTTCCTGTAT
* * ** *
42533594 TGCCAATGCCATATCCTAGATATGGTCTTACATGAGATTTCTCAAATCGA
1 TGCCAATGCCATGTCCTAGACATGGTCTTACATGAGACCTCTCATATCGA
* * ** * * *
42533644 TGCCCATGCCATGTCCTAGACATGGTTTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCTAGACATGGTCTTACATGAGACCTCTCATATCGA
* * *
42533694 TGCCAACGCCATGTCCCAGACATGGTCTTGCATGAGACCTCTCATA
1 TGCCAATGCCATGTCCTAGACATGGTCTTACATGAGACCTCTCATA
42533740 ACCTCAATAA
Statistics
Matches: 75, Mismatches: 21, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
50 75 1.00
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCTAGACATGGTCTTACATGAGACCTCTCATATCGA
Found at i:42535675 original size:79 final size:78
Alignment explanation
Indices: 42535525--42535675 Score: 180
Period size: 79 Copynumber: 1.9 Consensus size: 78
42535515 TAGAAGGTAA
* ** * * **
42535525 AAGGGAGAAATAAAAATTTTAGGGGGATTTTGATTTTTGGGAGTAAAATGGGGAGGGCAAGTAAA
1 AAGGGAGAAATAAAAATTTTAGGGGGATTTTAAAGTTGGGGAGTAAAAAGGGGAGGAAAAGTAAA
42535590 AATTTTTTAGGGT
66 AATTTTTTAGGGT
* *
42535603 AAGGGGGAAAT-AAAATATTTATGGGGGATTTTAAAGTTGGGGGGTAAAAGAGGGGAGGAAAAGT
1 AAGGGAGAAATAAAAAT-TTTA-GGGGGATTTTAAAGTTGGGGAGTAAAA-AGGGGAGGAAAAGT
42535667 -AAAATTTTT
63 AAAAATTTTT
42535676 GAAGAGATGG
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
77 5 0.08
78 14 0.23
79 31 0.51
80 11 0.18
ACGTcount: A:0.38, C:0.01, G:0.33, T:0.28
Consensus pattern (78 bp):
AAGGGAGAAATAAAAATTTTAGGGGGATTTTAAAGTTGGGGAGTAAAAAGGGGAGGAAAAGTAAA
AATTTTTTAGGGT
Found at i:42536238 original size:26 final size:26
Alignment explanation
Indices: 42536182--42536242 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
42536172 ATTTTACCTA
*
42536182 GTAAAATTTTGACATTTTTACACTCG
1 GTAAAATTTTGACATTTTAACACTCG
* *
42536208 ATAAAATTTTGACAATTTTAACCCT-G
1 GTAAAATTTTGAC-ATTTTAACACTCG
42536234 GTAAAATTT
1 GTAAAATTT
42536243 CGGGAAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 21 0.70
27 9 0.30
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (26 bp):
GTAAAATTTTGACATTTTAACACTCG
Found at i:42539173 original size:94 final size:94
Alignment explanation
Indices: 42539009--42539424 Score: 399
Period size: 94 Copynumber: 4.4 Consensus size: 94
42538999 CCTTAAAAGA
* * * *
42539009 GGTTACAAGTGTAAGACCATAGCTT-GACTATGGAAACATGGAGAGTCCGTTGGGACAGTAAACA
1 GGTTACATGTGTAAGACCATAG-TTCGACTATGGCAACATGGGGAGTCCGTCGGGACAGTAAACA
* * *
42539073 CAGGGTAATTAACTAGGACATTAAACATGG
65 TAGGGTAGTCAACTAGGACATTAAACATGG
* * ** *
42539103 GGTTACATGTGTAAGACCATATTTCGACTATGGCAACACGGGGAGTTTGTCGGGACAATAAACA-
1 GGTTACATGTGTAAGACCATAGTTCGACTATGGCAACATGGGGAGTCCGTCGGGACAGTAAACAT
* *
42539167 ATGGGTAGTCTA-TCAGGACATTAAATATGG
66 A-GGGTAGTCAACT-AGGACATTAAACATGG
* * * * * * * *
42539197 GGTTGCATGTGTAAGACCATA-TCCTAGCAATGACAACATGGGGAGTCCGCCGAGATAGTAAACA
1 GGTTACATGTGTAAGACCATAGTTCGA-CTATGGCAACATGGGGAGTCCGTCGGGACAGTAAACA
* * *
42539261 TAGGGTAGTCCACTAGGAAATTAAACATGT
65 TAGGGTAGTCAACTAGGACATTAAACATGG
* * * ** * * *
42539291 GGTTACATGCGTAAGACTATAGCTCGACTATGATAGCATAGGGAGTCTGTCGGGACAGTAAACAT
1 GGTTACATGTGTAAGACCATAGTTCGACTATGGCAACATGGGGAGTCCGTCGGGACAGTAAACAT
* * * **
42539356 GGGGTAGTCCACCAAAACATTAAACATGG
66 AGGGTAGTCAACTAGGACATTAAACATGG
* * *
42539385 GGTTACATGTGTAAGACCATAGCTCGACTACGGCAGCATG
1 GGTTACATGTGTAAGACCATAGTTCGACTATGGCAACATG
42539425 TGATGTTCAT
Statistics
Matches: 260, Mismatches: 55, Indels: 14
0.79 0.17 0.04
Matches are distributed among these distances:
93 7 0.03
94 249 0.96
95 4 0.02
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.23
Consensus pattern (94 bp):
GGTTACATGTGTAAGACCATAGTTCGACTATGGCAACATGGGGAGTCCGTCGGGACAGTAAACAT
AGGGTAGTCAACTAGGACATTAAACATGG
Found at i:42539344 original size:188 final size:188
Alignment explanation
Indices: 42539065--42539405 Score: 459
Period size: 188 Copynumber: 1.8 Consensus size: 188
42539055 CCGTTGGGAC
* * * **
42539065 AGTAAACACAGGGTAATTAACTAGGACATTAAACATGGGGTTACATGTGTAAGACCATATTTCGA
1 AGTAAACACAGGGTAATCAACTAGGAAATTAAACATGGGGTTACATGCGTAAGACCATAGCTCGA
* * * * * ** *
42539130 CTATGGCAACACGGGGAGTTTGTCGGGACAATAAACAAT-GGGTAGTCTATCAGGACATTAAATA
66 CTATGACAACACAGGGAGTCTGTCGGGACAATAAAC-ATGGGGTAGTCCACCAAAACATTAAACA
*
42539194 TGGGGTTGCATGTGTAAGACCATATCCTAGCAATGACAACATGGGGAGTCCGCCGAGAT
130 TGGGGTTACATGTGTAAGACCATATCCTAGCAATGACAACATGGGGAGTCCGCCGAGAT
* * * * *
42539253 AGTAAACATAGGGTAGTCCACTAGGAAATTAAACATGTGGTTACATGCGTAAGACTATAGCTCGA
1 AGTAAACACAGGGTAATCAACTAGGAAATTAAACATGGGGTTACATGCGTAAGACCATAGCTCGA
* * * *
42539318 CTATGATAGCATAGGGAGTCTGTCGGGACAGTAAACATGGGGTAGTCCACCAAAACATTAAACAT
66 CTATGACAACACAGGGAGTCTGTCGGGACAATAAACATGGGGTAGTCCACCAAAACATTAAACAT
42539383 GGGGTTACATGTGTAAGACCATA
131 GGGGTTACATGTGTAAGACCATA
42539406 GCTCGACTAC
Statistics
Matches: 129, Mismatches: 23, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
187 2 0.02
188 127 0.98
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (188 bp):
AGTAAACACAGGGTAATCAACTAGGAAATTAAACATGGGGTTACATGCGTAAGACCATAGCTCGA
CTATGACAACACAGGGAGTCTGTCGGGACAATAAACATGGGGTAGTCCACCAAAACATTAAACAT
GGGGTTACATGTGTAAGACCATATCCTAGCAATGACAACATGGGGAGTCCGCCGAGAT
Found at i:42546246 original size:19 final size:18
Alignment explanation
Indices: 42546211--42546249 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
42546201 ATTTTGATTT
42546211 AATTATTTGATTCTAATC
1 AATTATTTGATTCTAATC
* *
42546229 AATTCATTTTATTTTAATC
1 AATT-ATTTGATTCTAATC
42546248 AA
1 AA
42546250 ATTGATTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.36, C:0.10, G:0.03, T:0.51
Consensus pattern (18 bp):
AATTATTTGATTCTAATC
Found at i:42548691 original size:36 final size:36
Alignment explanation
Indices: 42548646--42548720 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 36
42548636 TTAGGGATGT
* *
42548646 AAATGTGCCAGATTGT-AAGTCTATGGACATTTAGAA
1 AAATATGCCAGA-TGTCAAGTCTATGCACATTTAGAA
* *
42548682 AAATATGCCATATGTCACGTCTATGCACATTTAGAA
1 AAATATGCCAGATGTCAAGTCTATGCACATTTAGAA
42548718 AAA
1 AAA
42548721 AAAAGTACCA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 3 0.09
36 31 0.91
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (36 bp):
AAATATGCCAGATGTCAAGTCTATGCACATTTAGAA
Found at i:42555266 original size:8 final size:9
Alignment explanation
Indices: 42555252--42555277 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
42555242 TTAAAAAATT
42555252 ATAAAAAAC
1 ATAAAAAAC
42555261 ATAAAAAAC
1 ATAAAAAAC
42555270 ATAAAAAA
1 ATAAAAAA
42555278 GATGATAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.81, C:0.08, G:0.00, T:0.12
Consensus pattern (9 bp):
ATAAAAAAC
Found at i:42562754 original size:21 final size:21
Alignment explanation
Indices: 42562724--42562780 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
42562714 ACTGTTGGTG
42562724 AGAAGAAAGTTGCTGCTGCAA-A
1 AGAAG-AAGTTGCTGCTG-AAGA
* *
42562746 AGAGGAAGTTGTTGCTGAAGA
1 AGAAGAAGTTGCTGCTGAAGA
42562767 AGAAGAAGTTGCTG
1 AGAAGAAGTTGCTG
42562781 AAAATGAGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 2 0.07
21 24 0.80
22 4 0.13
ACGTcount: A:0.37, C:0.09, G:0.33, T:0.21
Consensus pattern (21 bp):
AGAAGAAGTTGCTGCTGAAGA
Found at i:42568023 original size:3 final size:3
Alignment explanation
Indices: 42568015--42568090 Score: 136
Period size: 3 Copynumber: 25.3 Consensus size: 3
42568005 ATCATTGTCC
42568015 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
42568063 TCA TCA TCA TCA TCA TCA TTCA -CA TCA T
1 TCA TCA TCA TCA TCA TCA -TCA TCA TCA T
42568091 TCTCGCAATC
Statistics
Matches: 71, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.03
3 66 0.93
4 3 0.04
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:42573593 original size:28 final size:28
Alignment explanation
Indices: 42573529--42573638 Score: 69
Period size: 32 Copynumber: 3.7 Consensus size: 28
42573519 TCTAAATAGG
* * *
42573529 TATATATAATACATATTTTTGCGTCTCGATA
1 TATATATAAT--ATATTTGTG-GTCTTGTTA
*
42573560 AATATATAATATATTTGTGGTCTTGTTA
1 TATATATAATATATTTGTGGTCTTGTTA
* *
42573588 TATATAATATATATATGCCTCTGGT-TCTGTTA
1 TATAT-ATA-ATATAT--TTGTGGTCT-TGTTA
* *
42573620 TATATATACTATATATGTG
1 TATATATAATATATTTGTG
42573639 TCTAGGGATT
Statistics
Matches: 64, Mismatches: 10, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
28 14 0.22
29 11 0.17
30 11 0.17
31 13 0.20
32 15 0.23
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.47
Consensus pattern (28 bp):
TATATATAATATATTTGTGGTCTTGTTA
Found at i:42576869 original size:18 final size:18
Alignment explanation
Indices: 42576842--42576876 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42576832 GAATTTCGGT
*
42576842 GTTTTAGTTGTTTAATTG
1 GTTTTAGTTGGTTAATTG
*
42576860 GTTTTGGTTGGTTAATT
1 GTTTTAGTTGGTTAATT
42576877 TAGGCTTCAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.00, G:0.26, T:0.60
Consensus pattern (18 bp):
GTTTTAGTTGGTTAATTG
Found at i:42581014 original size:35 final size:35
Alignment explanation
Indices: 42580968--42581277 Score: 186
Period size: 35 Copynumber: 8.8 Consensus size: 35
42580958 TCACTAATTA
*
42580968 TTCGTCGGTTTATCCGACTAGCGCTAGGCACAACT
1 TTCGTCAGTTTATCCGACTAGCGCTAGGCACAACT
* * *
42581003 TTCGTCAGTTTATCTGACTAGTGCT-GAGCAC-ACA
1 TTCGTCAGTTTATCCGACTAGCGCTAG-GCACAACT
* *
42581037 TTCGTCAGTTTATCCGACTAGTGCTGGGCACAACT
1 TTCGTCAGTTTATCCGACTAGCGCTAGGCACAACT
* * * * *
42581072 TTCATCATTTTATCTGACTAGTGCTGGGCAC-A-T
1 TTCGTCAGTTTATCCGACTAGCGCTAGGCACAACT
* * *
42581105 ATTCGTCGGTTTATCC-AGCTAGCGCTAGGCGCAAAT
1 -TTCGTCAGTTTATCCGA-CTAGCGCTAGGCACAACT
* * * * * * * *
42581141 ATT-GTCGGTTTATGCAACAAGAGTTGGGCTCACTAATT
1 -TTCGTCAGTTTATCCGACTAGCGCTAGG--CAC-AACT
* ** *
42581179 ATTCGTCGGTTTATCCGACTAGCGCTAGGCGTAACC
1 -TTCGTCAGTTTATCCGACTAGCGCTAGGCACAACT
* ** * * *
42581215 TTCGTCATTTTATCTTACTAGTGCTGGGCAC-ACAA
1 TTCGTCAGTTTATCCGACTAGCGCTAGGCACAAC-T
*
42581250 TT-GTCAGTTTATCCGACTAGCACTAGGC
1 TTCGTCAGTTTATCCGACTAGCGCTAGGC
42581278 GCAAACTCTT
Statistics
Matches: 214, Mismatches: 48, Indels: 27
0.74 0.17 0.09
Matches are distributed among these distances:
33 2 0.01
34 76 0.36
35 101 0.47
36 7 0.03
37 3 0.01
38 6 0.03
39 19 0.09
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.32
Consensus pattern (35 bp):
TTCGTCAGTTTATCCGACTAGCGCTAGGCACAACT
Found at i:42581054 original size:69 final size:69
Alignment explanation
Indices: 42580967--42581277 Score: 315
Period size: 69 Copynumber: 4.4 Consensus size: 69
42580957 CTCACTAATT
*
42580967 ATTCGTCGGTTTATCCGACTAGCGCTAGGCACAACTTTCGTCAGTTTATCTGACTAGTGCTGAGC
1 ATTCGTCGGTTTATCCGACTAGCGCTAGGCACAACTTTCGTCAGTTTATCTGACTAGTGCTGGGC
42581032 ACAC
66 ACAC
* * * * *
42581036 ATTCGTCAGTTTATCCGACTAGTGCTGGGCACAACTTTCATCATTTTATCTGACTAGTGCTGGGC
1 ATTCGTCGGTTTATCCGACTAGCGCTAGGCACAACTTTCGTCAGTTTATCTGACTAGTGCTGGGC
*
42581101 ACAT
66 ACAC
* * * * * * *
42581105 ATTCGTCGGTTTATCC-AGCTAGCGCTAGGCGCAAATATT-GTCGGTTTATGC-AACAAGAGTTG
1 ATTCGTCGGTTTATCCGA-CTAGCGCTAGGCACAACT-TTCGTCAGTTTAT-CTGACTAGTGCTG
*
42581167 GGCTCACTAATT
63 GG--CAC--A-C
** * * *
42581179 ATTCGTCGGTTTATCCGACTAGCGCTAGGCGTAACCTTCGTCATTTTATCTTACTAGTGCTGGGC
1 ATTCGTCGGTTTATCCGACTAGCGCTAGGCACAACTTTCGTCAGTTTATCTGACTAGTGCTGGGC
42581244 ACAC
66 ACAC
* *
42581248 AATT-GTCAGTTTATCCGACTAGCACTAGGC
1 -ATTCGTCGGTTTATCCGACTAGCGCTAGGC
42581278 GCAAACTCTT
Statistics
Matches: 199, Mismatches: 31, Indels: 24
0.78 0.12 0.09
Matches are distributed among these distances:
68 1 0.01
69 131 0.66
70 7 0.04
71 3 0.02
72 3 0.02
73 4 0.02
74 49 0.25
75 1 0.01
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.32
Consensus pattern (69 bp):
ATTCGTCGGTTTATCCGACTAGCGCTAGGCACAACTTTCGTCAGTTTATCTGACTAGTGCTGGGC
ACAC
Found at i:42588029 original size:16 final size:17
Alignment explanation
Indices: 42587995--42588037 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
42587985 AATTTAAATT
* *
42587995 TTTTTCTTTTATTCTTA
1 TTTTTCTTTTATCCGTA
42588012 TTTTTCTTTT-TCCGTA
1 TTTTTCTTTTATCCGTA
42588028 TTTTTCTTTT
1 TTTTTCTTTT
42588038 CTTTCCTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.07, C:0.14, G:0.02, T:0.77
Consensus pattern (17 bp):
TTTTTCTTTTATCCGTA
Found at i:42590045 original size:22 final size:22
Alignment explanation
Indices: 42590017--42590060 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
42590007 GTGAACAACT
42590017 CACCCTTGTATTTATACTAGGG
1 CACCCTTGTATTTATACTAGGG
42590039 CACCCTTGTATTTATACTAGGG
1 CACCCTTGTATTTATACTAGGG
42590061 TTGCCACCCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (22 bp):
CACCCTTGTATTTATACTAGGG
Found at i:42601099 original size:31 final size:31
Alignment explanation
Indices: 42601063--42601167 Score: 115
Period size: 31 Copynumber: 3.4 Consensus size: 31
42601053 TATATTAAAT
* * *
42601063 TTAATTTAATATTTATCTAAACAGTAATTTA
1 TTAATTTAATATTTATCTAGATAATAATTTA
* * * *
42601094 TTAATTTAATATTAATATGAGATATTAA-AT-
1 TTAATTTAATATTTATCT-AGATAATAATTTA
*
42601124 TTAATTTAATATTTATCTAGATAATATTTTA
1 TTAATTTAATATTTATCTAGATAATAATTTA
42601155 TTAATTTAATATT
1 TTAATTTAATATT
42601168 AATATGGTTA
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
29 7 0.12
30 17 0.28
31 30 0.50
32 6 0.10
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (31 bp):
TTAATTTAATATTTATCTAGATAATAATTTA
Found at i:42601112 original size:61 final size:61
Alignment explanation
Indices: 42601041--42601173 Score: 221
Period size: 61 Copynumber: 2.2 Consensus size: 61
42601031 ATTTATCTTG
* *
42601041 ATATTAATATGATATATTAAATTTAATTTAATATTTATCTAAACAGTAATTTATTAATTTA
1 ATATTAATATGAGATATTAAATTTAATTTAATATTTATCTAAACAATAATTTATTAATTTA
* * *
42601102 ATATTAATATGAGATATTAAATTTAATTTAATATTTATCTAGATAATATTTTATTAATTTA
1 ATATTAATATGAGATATTAAATTTAATTTAATATTTATCTAAACAATAATTTATTAATTTA
42601163 ATATTAATATG
1 ATATTAATATG
42601174 GTTAATTCTA
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 67 1.00
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.50
Consensus pattern (61 bp):
ATATTAATATGAGATATTAAATTTAATTTAATATTTATCTAAACAATAATTTATTAATTTA
Found at i:42602096 original size:9 final size:9
Alignment explanation
Indices: 42602082--42602111 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
42602072 ACACTAATAT
*
42602082 ATTATTTGA
1 ATTATTCGA
42602091 ATTATTCGA
1 ATTATTCGA
42602100 ATTATTCGA
1 ATTATTCGA
42602109 ATT
1 ATT
42602112 GTAAAATTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (9 bp):
ATTATTCGA
Found at i:42608515 original size:46 final size:44
Alignment explanation
Indices: 42608423--42608515 Score: 141
Period size: 44 Copynumber: 2.1 Consensus size: 44
42608413 TTACAACTCT
* *
42608423 ATTCCATTCAACCAAACACAAGAATACCATTACGCCTCTATTCC
1 ATTCCATTCAACCAAACAAAAGAATACCATTACGCATCTATTCC
*
42608467 ATTCCATTCAACCAAACAAAAGATTTACCTATTACGCATCTATTCC
1 ATTCCATTCAACCAAACAAAAGA-ATACC-ATTACGCATCTATTCC
42608513 ATT
1 ATT
42608516 ACACCTCTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 22 0.50
45 4 0.09
46 18 0.41
ACGTcount: A:0.37, C:0.30, G:0.04, T:0.29
Consensus pattern (44 bp):
ATTCCATTCAACCAAACAAAAGAATACCATTACGCATCTATTCC
Found at i:42611389 original size:3 final size:3
Alignment explanation
Indices: 42611383--42611437 Score: 101
Period size: 3 Copynumber: 18.3 Consensus size: 3
42611373 TTTCCTAATC
*
42611383 TCA TCA TCA TCA ACA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
42611431 TCA TCA T
1 TCA TCA T
42611438 TACCTTCTTC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.35, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:42612219 original size:20 final size:21
Alignment explanation
Indices: 42612182--42612225 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
42612172 GCTTTTTTAG
*
42612182 AGAAGAAGAATAAGGAAACAA
1 AGAAGAAGAATAAGGAAAAAA
42612203 AGAA-AAGAGATAA-GAAAAAA
1 AGAAGAAGA-ATAAGGAAAAAA
42612223 AGA
1 AGA
42612226 GAAAAGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.70, C:0.02, G:0.23, T:0.05
Consensus pattern (21 bp):
AGAAGAAGAATAAGGAAAAAA
Found at i:42612231 original size:22 final size:21
Alignment explanation
Indices: 42612180--42612233 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
42612170 GGGCTTTTTT
* *
42612180 AGAGAAGAAGAATAAGGAAACA
1 AGAGAA-AAGAATAAGAAAAAA
42612202 A-AGAAAAGAGATAAGAAAAAA
1 AGAGAAAAGA-ATAAGAAAAAA
42612223 AGAGAAAAGAA
1 AGAGAAAAGAA
42612234 AAAAAGAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
20 4 0.14
21 15 0.54
22 9 0.32
ACGTcount: A:0.70, C:0.02, G:0.24, T:0.04
Consensus pattern (21 bp):
AGAGAAAAGAATAAGAAAAAA
Found at i:42612245 original size:14 final size:14
Alignment explanation
Indices: 42612205--42612246 Score: 66
Period size: 15 Copynumber: 2.9 Consensus size: 14
42612195 GGAAACAAAG
42612205 AAAAGAGATAAGAAA
1 AAAAGAGA-AAGAAA
42612220 AAAAGAGAAAAGAAA
1 AAAAGAG-AAAGAAA
42612235 AAAAGAGAAAGA
1 AAAAGAGAAAGA
42612247 CGATAAAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.19
15 20 0.77
16 1 0.04
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.02
Consensus pattern (14 bp):
AAAAGAGAAAGAAA
Found at i:42612586 original size:19 final size:18
Alignment explanation
Indices: 42612564--42612617 Score: 72
Period size: 19 Copynumber: 2.9 Consensus size: 18
42612554 AGGTTGAGTT
42612564 TTTTTTATATTTTTTTAAG
1 TTTTTTATATTTTTTT-AG
**
42612583 TTTTTTATATATTCATTAG
1 TTTTTTATAT-TTTTTTAG
42612602 TTTTTTATATTTTTTT
1 TTTTTTATATTTTTTT
42612618 TGAAATGTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 4 0.13
19 22 0.73
20 4 0.13
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.74
Consensus pattern (18 bp):
TTTTTTATATTTTTTTAG
Found at i:42623107 original size:20 final size:20
Alignment explanation
Indices: 42623082--42623120 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
42623072 AGACTTTTCA
42623082 AACACTTTTACATGATTTAT
1 AACACTTTTACATGATTTAT
42623102 AACACTTTTACATGATTTA
1 AACACTTTTACATGATTTA
42623121 ACTTTAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.15, G:0.05, T:0.44
Consensus pattern (20 bp):
AACACTTTTACATGATTTAT
Found at i:42624044 original size:3 final size:3
Alignment explanation
Indices: 42624036--42624089 Score: 62
Period size: 3 Copynumber: 19.0 Consensus size: 3
42624026 CCTAGGCAGT
*
42624036 AGA AGA AGA AG- AGA AAA AGA AGA AGA AG- AGA AGA A-A TAG- AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA -AGA AGA
42624078 AGA AGA AGA AGA
1 AGA AGA AGA AGA
42624090 TAAAATTGAA
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
2 7 0.16
3 37 0.84
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (3 bp):
AGA
Found at i:42624057 original size:14 final size:14
Alignment explanation
Indices: 42624038--42624094 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
42624028 TAGGCAGTAG
42624038 AAGAAGAAGAGAAA
1 AAGAAGAAGAGAAA
*
42624052 AAGAAGAAGA-AGAG
1 AAGAAGAAGAGA-AA
*
42624066 AAGAA-ATAGAGAAG
1 AAGAAGA-AGAGAAA
*
42624080 AAGAAGAAGATAAA
1 AAGAAGAAGAGAAA
42624094 A
1 A
42624095 TTGAATGAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
13 2 0.06
14 32 0.89
15 2 0.06
ACGTcount: A:0.68, C:0.00, G:0.28, T:0.04
Consensus pattern (14 bp):
AAGAAGAAGAGAAA
Found at i:42624067 original size:11 final size:11
Alignment explanation
Indices: 42624036--42624086 Score: 56
Period size: 11 Copynumber: 4.8 Consensus size: 11
42624026 CCTAGGCAGT
42624036 AGAAGAAGA-A
1 AGAAGAAGAGA
42624046 GAGAA-AA-AGA
1 -AGAAGAAGAGA
42624056 AGAAGAAGAGA
1 AGAAGAAGAGA
42624067 AGAA-ATAGAGA
1 AGAAGA-AGAGA
42624078 AGAAGAAGA
1 AGAAGAAGA
42624087 AGATAAAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
9 5 0.14
10 6 0.17
11 23 0.66
12 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (11 bp):
AGAAGAAGAGA
Found at i:42624084 original size:17 final size:18
Alignment explanation
Indices: 42624036--42624094 Score: 66
Period size: 20 Copynumber: 3.1 Consensus size: 18
42624026 CCTAGGCAGT
42624036 AGAAGAAGAAG-AGAAAA
1 AGAAGAAGAAGAAGAAAA
42624053 AGAAGAAGAAGAGAAGAAATA
1 AGAAGAAG-A-AGAAGAAA-A
42624074 GAGAAGAAGAAGAAGATAAA
1 -AGAAGAAGAAGAAGA-AAA
42624094 A
1 A
42624095 TTGAATGAGC
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
17 8 0.22
18 1 0.03
19 3 0.08
20 12 0.33
21 4 0.11
22 8 0.22
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (18 bp):
AGAAGAAGAAGAAGAAAA
Found at i:42625661 original size:18 final size:18
Alignment explanation
Indices: 42625638--42625683 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
42625628 CATGTGGTCT
*
42625638 ACCCGTGTGGACCGACAC
1 ACCCGTGTGGACCCACAC
*
42625656 ACCCGTGTGGACCCACCC
1 ACCCGTGTGGACCCACAC
*
42625674 GCCCGTGTGG
1 ACCCGTGTGG
42625684 CTCACTTGGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.15, C:0.41, G:0.30, T:0.13
Consensus pattern (18 bp):
ACCCGTGTGGACCCACAC
Found at i:42630672 original size:105 final size:105
Alignment explanation
Indices: 42630477--42630673 Score: 243
Period size: 105 Copynumber: 1.9 Consensus size: 105
42630467 AATGTTTAAA
* ** **
42630477 TGTAAAACCATAGCTGGGCTATGGCATTTTAATGAAAAGACCATAACTGGGTTATAGCACCTTGA
1 TGTAAAACCATAGCTGGGCTATGGCATTCTAATGAAAAGACCATAACTAAGTTATAGCACCTCAA
** *
42630542 ACGTAAGACCATGGTTGGACTATGGCAGTATAGATACATG
66 ACGTAAGACCATGGCAGGACCATGGCAGTATAGATACATG
* * * * *
42630582 TGTAAGACCATGGCTGGGCTATGGCATTCTGATGATAAGACCATAACTAAGTTATGGCA-CTACA
1 TGTAAAACCATAGCTGGGCTATGGCATTCTAATGAAAAGACCATAACTAAGTTATAGCACCT-CA
* *
42630646 AATGTAAGACCATGGCAGGGCCATGGCA
65 AACGTAAGACCATGGCAGGACCATGGCA
42630674 ATGCATGTGT
Statistics
Matches: 76, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
104 2 0.03
105 74 0.97
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (105 bp):
TGTAAAACCATAGCTGGGCTATGGCATTCTAATGAAAAGACCATAACTAAGTTATAGCACCTCAA
ACGTAAGACCATGGCAGGACCATGGCAGTATAGATACATG
Found at i:42633175 original size:16 final size:16
Alignment explanation
Indices: 42633135--42633180 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
42633125 CCCTTATAAA
*
42633135 AAATGTTATAAATTAT
1 AAATGTTATATATTAT
*
42633151 AAAAGTTATATATTAT
1 AAATGTTATATATTAT
42633167 AAAT-TT-TATATTAT
1 AAATGTTATATATTAT
42633181 TTAGACCTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
14 8 0.30
15 2 0.07
16 17 0.63
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (16 bp):
AAATGTTATATATTAT
Found at i:42634195 original size:13 final size:13
Alignment explanation
Indices: 42634177--42634201 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42634167 ATTTTTTTAA
42634177 TTTTAATTAATAT
1 TTTTAATTAATAT
42634190 TTTTAATTAATA
1 TTTTAATTAATA
42634202 ACTCATTTAT
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTTAATTAATAT
Found at i:42640663 original size:13 final size:13
Alignment explanation
Indices: 42640645--42640669 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42640635 AATAATTTAT
42640645 TATTTAAAATATA
1 TATTTAAAATATA
42640658 TATTTAAAATAT
1 TATTTAAAATAT
42640670 CACAATATTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TATTTAAAATATA
Found at i:42640932 original size:23 final size:23
Alignment explanation
Indices: 42640906--42640961 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 23
42640896 ATAATATTAA
*
42640906 TTATTTAATAAATTATTTTTATT
1 TTATTTAAAAAATTATTTTTATT
*
42640929 TTATTGAAAAAAATTATTTTTATT
1 TTATT-TAAAAAATTATTTTTATT
42640953 TTAATTTAA
1 TT-ATTTAA
42640962 CTTTGGTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 5 0.18
24 20 0.71
25 3 0.11
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (23 bp):
TTATTTAAAAAATTATTTTTATT
Found at i:42645144 original size:26 final size:26
Alignment explanation
Indices: 42645115--42645165 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
42645105 AAAATAATCA
*
42645115 TTAACGTATCAAATAATTATTTTTAT
1 TTAACATATCAAATAATTATTTTTAT
*
42645141 TTAATATATCAAATAATTATTTTTA
1 TTAACATATCAAATAATTATTTTTA
42645166 GAAAGGGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.51
Consensus pattern (26 bp):
TTAACATATCAAATAATTATTTTTAT
Found at i:42646123 original size:21 final size:22
Alignment explanation
Indices: 42646098--42646141 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
42646088 TAAAAAAACC
42646098 CTAATATTTTTCCA-TGTTTTG
1 CTAATATTTTTCCACTGTTTTG
* *
42646119 CTAATGTTTTTCCACTTTTTTG
1 CTAATATTTTTCCACTGTTTTG
42646141 C
1 C
42646142 CACTATTGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.16, C:0.18, G:0.09, T:0.57
Consensus pattern (22 bp):
CTAATATTTTTCCACTGTTTTG
Found at i:42653026 original size:13 final size:13
Alignment explanation
Indices: 42652991--42653028 Score: 67
Period size: 14 Copynumber: 2.8 Consensus size: 13
42652981 GATATATTTG
42652991 TAATTTGAAAACT
1 TAATTTGAAAACT
42653004 TAAGTTTGAAAACT
1 TAA-TTTGAAAACT
42653018 TAATTTGAAAA
1 TAATTTGAAAA
42653029 TTTGGAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.47, C:0.05, G:0.11, T:0.37
Consensus pattern (13 bp):
TAATTTGAAAACT
Found at i:42653357 original size:34 final size:34
Alignment explanation
Indices: 42653266--42653458 Score: 152
Period size: 34 Copynumber: 5.6 Consensus size: 34
42653256 TCACTTGTCT
* *
42653266 TTTCTTGCAGGGAATATTTCTTGTTCACGCATTA
1 TTTCTTGCAGGGAATATTTCATGTTCACGCATCA
* * * * **
42653300 TTTTGTTGTAGGGAATCTCTCATGTTCACATATCA
1 -TTTCTTGCAGGGAATATTTCATGTTCACGCATCA
*
42653335 TTTCTTGCAGGGAATTTTTCATGTTCACGCATCA
1 TTTCTTGCAGGGAATATTTCATGTTCACGCATCA
*** * * *
42653369 TTTCTTGCAGGGAGCCTTTCCTGTCCACGCATTA
1 TTTCTTGCAGGGAATATTTCATGTTCACGCATCA
* * * * * *
42653403 TTTTGTTGCAGGGAGTCTCTCCTGTTCACACATCA
1 -TTTCTTGCAGGGAATATTTCATGTTCACGCATCA
* *
42653438 TTTTTTACAGGGAATCATTTC
1 TTTCTTGCAGGGAAT-ATTTC
42653459 TGGTATTATT
Statistics
Matches: 125, Mismatches: 31, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
34 68 0.54
35 57 0.46
ACGTcount: A:0.20, C:0.21, G:0.18, T:0.41
Consensus pattern (34 bp):
TTTCTTGCAGGGAATATTTCATGTTCACGCATCA
Found at i:42653438 original size:103 final size:103
Alignment explanation
Indices: 42653266--42653452 Score: 275
Period size: 103 Copynumber: 1.8 Consensus size: 103
42653256 TCACTTGTCT
* * * * *
42653266 TTTCTTGCAGGGAATATTTCTTGTTCACGCATTATTTTGTTGTAGGGAATCTCTCATGTTCACAT
1 TTTCTTGCAGGGAACATTTCCTGTCCACGCATTATTTTGTTGCAGGGAATCTCTCATGTTCACAC
*
42653331 ATCATTTCTTGCAGGGAATTTTTCATGTTCACGCATCA
66 ATCATTTCTTACAGGGAATTTTTCATGTTCACGCATCA
* * * *
42653369 TTTCTTGCAGGGAGCCTTTCCTGTCCACGCATTATTTTGTTGCAGGGAGTCTCTCCTGTTCACAC
1 TTTCTTGCAGGGAACATTTCCTGTCCACGCATTATTTTGTTGCAGGGAATCTCTCATGTTCACAC
*
42653434 ATCATTTTTTACAGGGAAT
66 ATCATTTCTTACAGGGAAT
42653453 CATTTCTGGT
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
103 73 1.00
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.41
Consensus pattern (103 bp):
TTTCTTGCAGGGAACATTTCCTGTCCACGCATTATTTTGTTGCAGGGAATCTCTCATGTTCACAC
ATCATTTCTTACAGGGAATTTTTCATGTTCACGCATCA
Found at i:42656160 original size:21 final size:23
Alignment explanation
Indices: 42656136--42656178 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
42656126 TTAATTTTTT
*
42656136 AAAACATATTT-CTTCT-TTTAG
1 AAAACAGATTTGCTTCTGTTTAG
42656157 AAAACAGATTTGCTTCTGTTTA
1 AAAACAGATTTGCTTCTGTTTA
42656179 TAATTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 10 0.53
22 5 0.26
23 4 0.21
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (23 bp):
AAAACAGATTTGCTTCTGTTTAG
Found at i:42660775 original size:15 final size:15
Alignment explanation
Indices: 42660755--42660788 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
42660745 TAAGCACAGA
42660755 GTTTAAAATGTCACC
1 GTTTAAAATGTCACC
42660770 GTTTAAAATGTCACC
1 GTTTAAAATGTCACC
42660785 GTTT
1 GTTT
42660789 GTTGCTAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (15 bp):
GTTTAAAATGTCACC
Found at i:42663786 original size:29 final size:30
Alignment explanation
Indices: 42663727--42663784 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
42663717 TCCGAGCCTT
*
42663727 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
42663757 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
42663785 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:42664015 original size:13 final size:13
Alignment explanation
Indices: 42663997--42664027 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
42663987 TTCCAGCAAC
42663997 TATGAATTTATTT
1 TATGAATTTATTT
42664010 TATGAATTTATTT
1 TATGAATTTATTT
*
42664023 GATGA
1 TATGA
42664028 TGATCTAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (13 bp):
TATGAATTTATTT
Found at i:42664236 original size:50 final size:50
Alignment explanation
Indices: 42664122--42664363 Score: 286
Period size: 50 Copynumber: 4.7 Consensus size: 50
42664112 ATTTGGGTAA
* * *
42664122 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--AAGA-C--G
* *
42664178 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
* * * *
42664228 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
* * * *
42664278 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
**
42664328 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
42664364 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
50 92 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
Found at i:42664314 original size:100 final size:103
Alignment explanation
Indices: 42664122--42664371 Score: 353
Period size: 100 Copynumber: 2.4 Consensus size: 103
42664112 ATTTGGGTAA
42664122 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATAAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATAAGAGGTCCC
* * *
42664187 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACCAACACG
* * * *
42664228 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATAAGAGGTCCCCTA
*
42664290 TAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCAACACG
* *
42664328 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
42664372 GTTATTATCA
Statistics
Matches: 131, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
100 50 0.38
101 39 0.30
105 2 0.02
106 40 0.31
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATAAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCAACACG
Found at i:42665765 original size:21 final size:21
Alignment explanation
Indices: 42665740--42665891 Score: 114
Period size: 21 Copynumber: 7.3 Consensus size: 21
42665730 GTGTTTTACT
*
42665740 TTTTGTTTAGCTCTTATGAGC
1 TTTTGTTCAGCTCTTATGAGC
* * *
42665761 TTTTGTTTAACTCATATGAG-
1 TTTTGTTCAGCTCTTATGAGC
*
42665781 TTTCTGTTCAGCTCTTACGAGC
1 TTT-TGTTCAGCTCTTATGAGC
* * * *
42665803 TTCTATTAAACTCTTATGAG-
1 TTTTGTTCAGCTCTTATGAGC
*
42665823 TTTCTGTTCAGCTCTTACGAGC
1 TTT-TGTTCAGCTCTTATGAGC
* * * *
42665845 TTCTATTCAACTCTTACGAGC
1 TTTTGTTCAGCTCTTATGAGC
*
42665866 TTTTATTCAGCT-TT-TGAGC
1 TTTTGTTCAGCTCTTATGAGC
*
42665885 TTCTGTT
1 TTTTGTT
42665892 AACGATGTAC
Statistics
Matches: 103, Mismatches: 24, Indels: 10
0.75 0.18 0.07
Matches are distributed among these distances:
19 9 0.09
20 7 0.07
21 83 0.81
22 4 0.04
ACGTcount: A:0.18, C:0.20, G:0.15, T:0.47
Consensus pattern (21 bp):
TTTTGTTCAGCTCTTATGAGC
Found at i:42665858 original size:42 final size:42
Alignment explanation
Indices: 42665743--42665893 Score: 173
Period size: 42 Copynumber: 3.6 Consensus size: 42
42665733 TTTTACTTTT
* * * * * *
42665743 TGTTTAGCTCTTATGAGCTTTTGTTTAACTCATATGAGTTTC
1 TGTTCAGCTCTTACGAGCTTCTATTAAACTCTTATGAGTTTC
42665785 TGTTCAGCTCTTACGAGCTTCTATTAAACTCTTATGAGTTTC
1 TGTTCAGCTCTTACGAGCTTCTATTAAACTCTTATGAGTTTC
* *
42665827 TGTTCAGCTCTTACGAGCTTCTATTCAACTCTTACGAGCTTT-
1 TGTTCAGCTCTTACGAGCTTCTATTAAACTCTTATGAG-TTTC
* * *
42665869 TATTCAGCT-TT-TGAGCTTCTGTTAA
1 TGTTCAGCTCTTACGAGCTTCTATTAA
42665894 CGATGTACTC
Statistics
Matches: 96, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
40 11 0.11
41 2 0.02
42 80 0.83
43 3 0.03
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.45
Consensus pattern (42 bp):
TGTTCAGCTCTTACGAGCTTCTATTAAACTCTTATGAGTTTC
Found at i:42665865 original size:63 final size:63
Alignment explanation
Indices: 42665750--42665872 Score: 158
Period size: 63 Copynumber: 2.0 Consensus size: 63
42665740 TTTTGTTTAG
* * * * *
42665750 CTCTTATGAGCTTTTGTTTAACTCATATGAGTTTCTGTTCAGCTCTTACGAGCTTCTATTAAA
1 CTCTTATGAGCTTTTGTTCAACTCATACGAGCTTCTATTCAACTCTTACGAGCTTCTATTAAA
* * *
42665813 CTCTTATGAG-TTTCTGTTCAGCTCTTACGAGCTTCTATTCAACTCTTACGAGCTTTTATT
1 CTCTTATGAGCTTT-TGTTCAACTCATACGAGCTTCTATTCAACTCTTACGAGCTTCTATT
42665873 CAGCTTTTGA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
62 3 0.06
63 48 0.94
ACGTcount: A:0.20, C:0.21, G:0.14, T:0.45
Consensus pattern (63 bp):
CTCTTATGAGCTTTTGTTCAACTCATACGAGCTTCTATTCAACTCTTACGAGCTTCTATTAAA
Found at i:42677387 original size:2 final size:2
Alignment explanation
Indices: 42677317--42677367 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
42677307 TTGAGAACCT
42677317 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42677359 TA TA TA TA T
1 TA TA TA TA T
42677368 GTGTGTGCTC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:42678924 original size:2 final size:2
Alignment explanation
Indices: 42678917--42678947 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
42678907 CTCATATTTA
42678917 AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42678948 GATGTACATG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42698033 original size:2 final size:2
Alignment explanation
Indices: 42698026--42698052 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
42698016 AAGTAATTAG
42698026 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
42698053 GTGGTCCAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42699556 original size:47 final size:47
Alignment explanation
Indices: 42699433--42699803 Score: 521
Period size: 47 Copynumber: 7.9 Consensus size: 47
42699423 CAACCCTGTT
* * * * * *
42699433 TTGGACAGCAATTATTCATCAAATTGGACAACAAT-AATATGCTCTAAA
1 TTGGACAGC-ATTATACATTAAAATGGACAGC-ATCAATATACTCAAAA
* * * * * ** *
42699481 -TAGATAGCATTATACATCAAATTAGACAGTTTAAATATACTCAAAA
1 TTGGACAGCATTATACATTAAAATGGACAGCATCAATATACTCAAAA
*
42699527 TTGGACAGCATTATACATTAAAATGGACAGCATCAATATACTTAAAA
1 TTGGACAGCATTATACATTAAAATGGACAGCATCAATATACTCAAAA
*
42699574 TTGGACAGCATTATACATTAAAATGGACAGTATCAATATACTCAAAA
1 TTGGACAGCATTATACATTAAAATGGACAGCATCAATATACTCAAAA
*
42699621 TTGGATAGCATTATACATTAAAATGGACAGCATCAATATACTCAAAA
1 TTGGACAGCATTATACATTAAAATGGACAGCATCAATATACTCAAAA
* *
42699668 TTGGACAGCATTATACATTAAAATGGACAGCATCAATGTACTTAAAA
1 TTGGACAGCATTATACATTAAAATGGACAGCATCAATATACTCAAAA
* *
42699715 TTGGACAGCATTATACATTAAAATGGATAGCATCAATATACTTAAAA
1 TTGGACAGCATTATACATTAAAATGGACAGCATCAATATACTCAAAA
42699762 TTGGACAGCATTATACATTAAAATGGACAGCATCAATATACT
1 TTGGACAGCATTATACATTAAAATGGACAGCATCAATATACT
42699804 ATAAATTTAT
Statistics
Matches: 293, Mismatches: 28, Indels: 5
0.90 0.09 0.02
Matches are distributed among these distances:
45 1 0.00
46 29 0.10
47 263 0.90
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.29
Consensus pattern (47 bp):
TTGGACAGCATTATACATTAAAATGGACAGCATCAATATACTCAAAA
Found at i:42700778 original size:28 final size:27
Alignment explanation
Indices: 42700746--42700844 Score: 112
Period size: 28 Copynumber: 3.6 Consensus size: 27
42700736 TTAATAAGTA
*
42700746 CGCACACTTAGTGCTTAATAATCAAACT
1 CGCACACTTAGTGCTT-ATAATTAAACT
* *
42700774 CGCACACTTAGTGCTT-TACCCTTATACT
1 CGCACACTTAGTGCTTATA--ATTAAACT
42700802 CGCACACTTAGTGCATT-TCAATTAAACT
1 CGCACACTTAGTGC-TTAT-AATTAAACT
42700830 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
42700845 AATCTCATTA
Statistics
Matches: 62, Mismatches: 5, Indels: 9
0.82 0.07 0.12
Matches are distributed among these distances:
26 2 0.03
27 1 0.02
28 55 0.89
29 3 0.05
30 1 0.02
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.31
Consensus pattern (27 bp):
CGCACACTTAGTGCTTATAATTAAACT
Found at i:42706558 original size:65 final size:62
Alignment explanation
Indices: 42706435--42706564 Score: 145
Period size: 64 Copynumber: 2.0 Consensus size: 62
42706425 AATTCATTTC
* * * * *
42706435 TCATTTTCATTTCCTTTTTGAGAAAATCACATTTATTTCCAAATGATTCCATTTTCTCCAATT
1 TCATTTTCATTTCATTTTGGAGAAAACCACAATCATTTCCAAATGATTCCATTTTCTCC-ATT
* * *
42706498 TCATTTTCATTTTCATTTTGGAGAAAACCATAATCATTTCCTAAATGTTTTC-TATTTCTCCATT
1 TCATTTTCA-TTTCATTTTGGAGAAAACCACAATCATTTCC-AAATGATTCCAT-TTTCTCCATT
42706562 TCA
1 TCA
42706565 CCATTTCGAT
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
63 9 0.16
64 32 0.57
65 15 0.27
ACGTcount: A:0.27, C:0.20, G:0.05, T:0.48
Consensus pattern (62 bp):
TCATTTTCATTTCATTTTGGAGAAAACCACAATCATTTCCAAATGATTCCATTTTCTCCATT
Found at i:42713288 original size:13 final size:15
Alignment explanation
Indices: 42713258--42713306 Score: 52
Period size: 14 Copynumber: 3.4 Consensus size: 15
42713248 AGCTCATTGC
42713258 ACATAAGAAAAACAA
1 ACATAAGAAAAACAA
42713273 ACAT-AGAAAAAC-A
1 ACATAAGAAAAACAA
42713286 ACA-AA-AATAAACCAA
1 ACATAAGAA-AAA-CAA
42713301 ACATAA
1 ACATAA
42713307 AATAATAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
12 2 0.07
13 8 0.28
14 9 0.31
15 8 0.28
16 2 0.07
ACGTcount: A:0.71, C:0.16, G:0.04, T:0.08
Consensus pattern (15 bp):
ACATAAGAAAAACAA
Found at i:42716554 original size:3 final size:3
Alignment explanation
Indices: 42716546--42716576 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
42716536 CTTTGGGCTC
*
42716546 GGT GGT GGT GGT GGT GGT GGT GGT AGT GGT G
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT G
42716577 AAACGGTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.03, C:0.00, G:0.65, T:0.32
Consensus pattern (3 bp):
GGT
Found at i:42722722 original size:15 final size:15
Alignment explanation
Indices: 42722675--42722723 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
42722665 TCAAGCTATC
42722675 CCCTCATTTCATCAT
1 CCCTCATTTCATCAT
* *
42722690 CCCTC-CTTCA-C-C
1 CCCTCATTTCATCAT
42722702 CCCTCATTTCATCAT
1 CCCTCATTTCATCAT
42722717 CCCTCAT
1 CCCTCAT
42722724 CCCTTATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
12 5 0.19
13 5 0.19
14 5 0.19
15 12 0.44
ACGTcount: A:0.16, C:0.49, G:0.00, T:0.35
Consensus pattern (15 bp):
CCCTCATTTCATCAT
Found at i:42724336 original size:20 final size:21
Alignment explanation
Indices: 42724311--42724356 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
42724301 TAACATGTTG
42724311 AATTTT-AATTAATTTTCACA
1 AATTTTGAATTAATTTTCACA
* *
42724331 AATTTTGAATTATTTTTGACA
1 AATTTTGAATTAATTTTCACA
42724352 AATTT
1 AATTT
42724357 GCACAAATGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.37, C:0.07, G:0.04, T:0.52
Consensus pattern (21 bp):
AATTTTGAATTAATTTTCACA
Found at i:42727124 original size:21 final size:21
Alignment explanation
Indices: 42727100--42727154 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
42727090 GACGACTGCA
*
42727100 GTGTCGCAACACTGAGAAGTG
1 GTGTCGCAACACCGAGAAGTG
42727121 GTGTCGCAACACCGAGAAGTG
1 GTGTCGCAACACCGAGAAGTG
*
42727142 GTATCGCAACACC
1 GTGTCGCAACACC
42727155 AGACTTCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.29, C:0.25, G:0.29, T:0.16
Consensus pattern (21 bp):
GTGTCGCAACACCGAGAAGTG
Found at i:42736471 original size:15 final size:15
Alignment explanation
Indices: 42736451--42736481 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
42736441 GATGAAGAAT
42736451 ATTATTACGATGATG
1 ATTATTACGATGATG
*
42736466 ATTATTATGATGATG
1 ATTATTACGATGATG
42736481 A
1 A
42736482 AGACGACGAC
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:0.35, C:0.03, G:0.19, T:0.42
Consensus pattern (15 bp):
ATTATTACGATGATG
Found at i:42736480 original size:18 final size:18
Alignment explanation
Indices: 42736436--42736484 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
42736426 GGTGATGACG
42736436 ATGATGATGAAGAATATT
1 ATGATGATGAAGAATATT
* * * *
42736454 ATTACGATGATGATTATT
1 ATGATGATGAAGAATATT
42736472 ATGATGATGAAGA
1 ATGATGATGAAGA
42736485 CGACGACGAC
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.41, C:0.02, G:0.22, T:0.35
Consensus pattern (18 bp):
ATGATGATGAAGAATATT
Found at i:42736547 original size:18 final size:18
Alignment explanation
Indices: 42736526--42736560 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
42736516 GAATATAATG
*
42736526 ATGAGAAAGATAAGAAAA
1 ATGAGAAAGAAAAGAAAA
42736544 ATGAGAAAGAAAAGAAA
1 ATGAGAAAGAAAAGAAA
42736561 TAAAATTGTT
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:0.69, C:0.00, G:0.23, T:0.09
Consensus pattern (18 bp):
ATGAGAAAGAAAAGAAAA
Found at i:42737621 original size:16 final size:16
Alignment explanation
Indices: 42737583--42737624 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
42737573 ACACACAACG
42737583 TAATTTTAATATATCA
1 TAATTTTAATATATCA
*
42737599 TTA-TTTAATATAAT-A
1 TAATTTTAATAT-ATCA
42737614 TAATTTTAATA
1 TAATTTTAATA
42737625 AAAATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (16 bp):
TAATTTTAATATATCA
Found at i:42739449 original size:21 final size:21
Alignment explanation
Indices: 42739415--42739454 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
42739405 CTTGAACAAC
*
42739415 TTTTAGATTATTTGTTTTACT
1 TTTTAGATTATTTGATTTACT
42739436 TTTTA-ATTATTTTGATTTA
1 TTTTAGATTA-TTTGATTTA
42739455 AAAAATGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.23, C:0.03, G:0.07, T:0.68
Consensus pattern (21 bp):
TTTTAGATTATTTGATTTACT
Found at i:42739561 original size:11 final size:11
Alignment explanation
Indices: 42739526--42739564 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
42739516 GTAAATCATC
42739526 TAATAAATATAT
1 TAAT-AATATAT
42739538 TAGATAATATAT
1 TA-ATAATATAT
*
42739550 TAATAATTTAT
1 TAATAATATAT
42739561 TAAT
1 TAAT
42739565 TTATATTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 12 0.48
12 11 0.44
13 2 0.08
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (11 bp):
TAATAATATAT
Found at i:42745196 original size:72 final size:71
Alignment explanation
Indices: 42744958--42745294 Score: 381
Period size: 72 Copynumber: 4.7 Consensus size: 71
42744948 TCACCTGTGA
** * * **
42744958 ATAAATTTTATATCC-AAAATCATATATAAACAACTATTGATAAAACTA-ATTTAGTATAAATAA
1 ATAAATTCAATATCCAAAAACCAAATATAAACAACTATTGATAAAACTAGA-TTAACATAAATAA
42745021 GTAGAAC
65 GTAGAAC
* * * * **
42745028 ATAAATTTAACATCCAAAAATCAAATATAAACAATTATTGATAAAACTAGCCCTAAGCATAAATA
1 ATAAATTCAATATCCAAAAACCAAATATAAACAACTATTGATAAAACTAG-ATTAA-CATAAATA
* *
42745093 ATTAGACC
64 AGTAGAAC
* *
42745101 ATAAATTCAATATCCAAAGACCAAATATAAACAAATATTGATAAAACTAGATTACACATAAATAA
1 ATAAATTCAATATCCAAAAACCAAATATAAACAACTATTGATAAAACTAGATTA-ACATAAATAA
**
42745166 ACAGAAC
65 GTAGAAC
* * * * *
42745173 ATAAATTCAATATCCAAAAACCAAACATAAATAGCCATTGATAAAACTAGATTACACAAAAATAA
1 ATAAATTCAATATCCAAAAACCAAATATAAACAACTATTGATAAAACTAGATTA-ACATAAATAA
*
42745238 GTAGCAC
65 GTAGAAC
* *
42745245 ATAAATTCAATATCCAAAAACCAAACATAAATAACTATTGATAAAACTAG
1 ATAAATTCAATATCCAAAAACCAAATATAAACAACTATTGATAAAACTAG
42745295 TTTAGCATTG
Statistics
Matches: 230, Mismatches: 32, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
70 13 0.06
71 31 0.13
72 127 0.55
73 59 0.26
ACGTcount: A:0.54, C:0.15, G:0.06, T:0.25
Consensus pattern (71 bp):
ATAAATTCAATATCCAAAAACCAAATATAAACAACTATTGATAAAACTAGATTAACATAAATAAG
TAGAAC
Found at i:42746611 original size:20 final size:20
Alignment explanation
Indices: 42746586--42746624 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
42746576 TACTTTCTTC
42746586 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
42746606 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
42746625 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:42751566 original size:40 final size:40
Alignment explanation
Indices: 42751521--42751601 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 40
42751511 AAAACATAAA
* * *
42751521 AATGGGTCGATCCTGGATCAATTAAAGTAATAACTCTAGT
1 AATGGGTCGATCCTAGATCAATTAAAGCAATAACACTAGT
42751561 AATGGGTCGATCCTAGATCAATTAAAGCAATAACACTAGT
1 AATGGGTCGATCCTAGATCAATTAAAGCAATAACACTAGT
42751601 A
1 A
42751602 TCATAAAGAG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (40 bp):
AATGGGTCGATCCTAGATCAATTAAAGCAATAACACTAGT
Found at i:42752360 original size:22 final size:21
Alignment explanation
Indices: 42752306--42752361 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
42752296 ACTCTTCAGT
*
42752306 GGTATCGCGACATCCTCTTTG
1 GGTATCGCGATATCCTCTTTG
*
42752327 GGTATCGTGATATCCTCTTTTG
1 GGTATCGCGATATCCTC-TTTG
*
42752349 GGTATTGCGATAT
1 GGTATCGCGATAT
42752362 AGCCTTCGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 15 0.50
22 15 0.50
ACGTcount: A:0.16, C:0.20, G:0.25, T:0.39
Consensus pattern (21 bp):
GGTATCGCGATATCCTCTTTG
Found at i:42755221 original size:28 final size:28
Alignment explanation
Indices: 42755181--42755239 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
42755171 AGCAACATCG
42755181 TGTAGCTTACATTCTGACCCACAGCTCA
1 TGTAGCTTACATTCTGACCCACAGCTCA
42755209 TGTAGCTTACATTCTGACCCACAGCTCA
1 TGTAGCTTACATTCTGACCCACAGCTCA
42755237 TGT
1 TGT
42755240 GAGCAGACAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.24, C:0.31, G:0.15, T:0.31
Consensus pattern (28 bp):
TGTAGCTTACATTCTGACCCACAGCTCA
Found at i:42755971 original size:37 final size:37
Alignment explanation
Indices: 42755924--42756010 Score: 147
Period size: 37 Copynumber: 2.4 Consensus size: 37
42755914 ATGGCTTATG
*
42755924 TGGTATGTTTTGAGGTGGTTTGAATATGGTAAAGTTA
1 TGGTATGTTTTGAGGTAGTTTGAATATGGTAAAGTTA
42755961 TGGTATGTTTTGAGGTAGTTTGAATATGGTAAAGTTA
1 TGGTATGTTTTGAGGTAGTTTGAATATGGTAAAGTTA
* *
42755998 TAGCATGTTTTGA
1 TGGTATGTTTTGA
42756011 AAGGCATTTG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 47 1.00
ACGTcount: A:0.25, C:0.01, G:0.30, T:0.44
Consensus pattern (37 bp):
TGGTATGTTTTGAGGTAGTTTGAATATGGTAAAGTTA
Found at i:42757360 original size:2 final size:2
Alignment explanation
Indices: 42757343--42757379 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
42757333 TAATGAAAGT
*
42757343 TA TA TA TG TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42757380 GTTTAAGATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:42759364 original size:14 final size:14
Alignment explanation
Indices: 42759347--42759395 Score: 66
Period size: 14 Copynumber: 3.5 Consensus size: 14
42759337 TGATTGTTTT
42759347 ATAATGTGTTTATG
1 ATAATGTGTTTATG
42759361 ATAATGATTGTTT-T-
1 ATAATG--TGTTTATG
42759375 ATAATGTGTTTATG
1 ATAATGTGTTTATG
42759389 ATAATGT
1 ATAATGT
42759396 ACGAAATGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
12 5 0.16
13 1 0.03
14 19 0.61
15 1 0.03
16 5 0.16
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (14 bp):
ATAATGTGTTTATG
Found at i:42759366 original size:28 final size:28
Alignment explanation
Indices: 42759335--42759394 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
42759325 TATGTATGTG
42759335 AATGATTGTTTTATAATGTGTTTATGAT
1 AATGATTGTTTTATAATGTGTTTATGAT
42759363 AATGATTGTTTTATAATGTGTTTATGAT
1 AATGATTGTTTTATAATGTGTTTATGAT
42759391 AATG
1 AATG
42759395 TACGAAATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.30, C:0.00, G:0.18, T:0.52
Consensus pattern (28 bp):
AATGATTGTTTTATAATGTGTTTATGAT
Found at i:42762912 original size:5 final size:5
Alignment explanation
Indices: 42762902--42762926 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
42762892 AAGTCTCATA
42762902 TATGT TATGT TATGT TATGT TATGT
1 TATGT TATGT TATGT TATGT TATGT
42762927 GCACACCCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (5 bp):
TATGT
Found at i:42779621 original size:20 final size:20
Alignment explanation
Indices: 42779584--42779622 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
42779574 TTTGAGGAAT
* * *
42779584 TATCAGAAATTATTAGGGAG
1 TATCAAAAATCATGAGGGAG
42779604 TATCAAAAATCATGAGGGA
1 TATCAAAAATCATGAGGGA
42779623 CTACCAAATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.08, G:0.23, T:0.26
Consensus pattern (20 bp):
TATCAAAAATCATGAGGGAG
Found at i:42779938 original size:6 final size:6
Alignment explanation
Indices: 42779927--42779951 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
42779917 CTTAGATTTT
42779927 GAAAAC GAAAAC GAAAAC GAAAAC G
1 GAAAAC GAAAAC GAAAAC GAAAAC G
42779952 GGAGTCGCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.64, C:0.16, G:0.20, T:0.00
Consensus pattern (6 bp):
GAAAAC
Found at i:42781166 original size:15 final size:15
Alignment explanation
Indices: 42781144--42781184 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
42781134 NNNNNNTAAA
42781144 AATAATAATAAAGTA-
1 AATAATAATAAA-TAC
*
42781159 AGTAATAATAAATAC
1 AATAATAATAAATAC
42781174 AATAATAATAA
1 AATAATAATAA
42781185 TAATTAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 2 0.09
15 21 0.91
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (15 bp):
AATAATAATAAATAC
Found at i:42781167 original size:18 final size:17
Alignment explanation
Indices: 42781144--42781188 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 17
42781134 NNNNNNTAAA
42781144 AATAATAATA-AAGTAAGT
1 AATAATAATACAA-TAA-T
42781162 AATAATAAATACAATAAT
1 AATAAT-AATACAATAAT
42781180 AATAATAAT
1 AATAATAAT
42781189 TAATTAGCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 3 0.12
18 13 0.52
19 7 0.28
20 2 0.08
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.29
Consensus pattern (17 bp):
AATAATAATACAATAAT
Found at i:42787251 original size:56 final size:55
Alignment explanation
Indices: 42787141--42787294 Score: 209
Period size: 56 Copynumber: 2.7 Consensus size: 55
42787131 ATTTGTTGAT
* * *
42787141 ATATTATTATGAGGTATTATCTTTTTAGCCATTTGATTCCTAATGGGATATTATAGG
1 ATATTATTATGAGATATTAT-ATTTTAG-CATTTGATTCCTAATAGGATATTATAGG
* *
42787198 ATATTATTATGAGATATTATATCTTAGCAGTTTGATTCCTAATAGGATGTTATAGG
1 ATATTATTATGAGATATTATATTTTAGCA-TTTGATTCCTAATAGGATATTATAGG
* *
42787254 ATATTATTATGGGATATTATGTTTTAGCAATTTGATTCCTA
1 ATATTATTATGAGATATTATATTTTAGC-ATTTGATTCCTA
42787295 TGTAACTACT
Statistics
Matches: 87, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
55 2 0.02
56 65 0.75
57 20 0.23
ACGTcount: A:0.30, C:0.08, G:0.17, T:0.45
Consensus pattern (55 bp):
ATATTATTATGAGATATTATATTTTAGCATTTGATTCCTAATAGGATATTATAGG
Found at i:42787316 original size:2 final size:2
Alignment explanation
Indices: 42787309--42787364 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
42787299 ACTACTATTT
42787309 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42787351 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
42787365 CCTTAAGTTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:42793469 original size:40 final size:41
Alignment explanation
Indices: 42793402--42793478 Score: 93
Period size: 40 Copynumber: 1.9 Consensus size: 41
42793392 CGTTTGAATA
* *
42793402 AAAAGCGCCGCTAAAGATGGAGAATTAGAGGCGCTTTCTGT
1 AAAAGCGCCACTAAAGATCGAGAATTAGAGGCGCTTTCTGT
* * * *
42793443 AAAA-CGCCACTAAAGGTCGAGCATTAGTGGCTCTTT
1 AAAAGCGCCACTAAAGATCGAGAATTAGAGGCGCTTT
42793479 ATTAAAATGC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
40 26 0.87
41 4 0.13
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.23
Consensus pattern (41 bp):
AAAAGCGCCACTAAAGATCGAGAATTAGAGGCGCTTTCTGT
Found at i:42793631 original size:41 final size:41
Alignment explanation
Indices: 42793574--42793878 Score: 504
Period size: 41 Copynumber: 7.4 Consensus size: 41
42793564 GTTTTCGGGG
* *
42793574 CTTTAGTGGCGTTTTTGAGGAAGCGCCGCTAATGCTTAGGC
1 CTTTAGCGGCGTTTTTGAGGAAGCGCCGCTAATGCTCAGGC
**
42793615 CTTTAGCGGCGTTTTTGATAAAGCGCCGCTAATGCTCAGGC
1 CTTTAGCGGCGTTTTTGAGGAAGCGCCGCTAATGCTCAGGC
42793656 CTTTAGCGGCGTTTTTGAGGAAGCGCCGCTAATGCTCAGGC
1 CTTTAGCGGCGTTTTTGAGGAAGCGCCGCTAATGCTCAGGC
* *
42793697 CTTTAGCGGCGTTTTTGAGGAAGTGCCGCTAATGCTCATGC
1 CTTTAGCGGCGTTTTTGAGGAAGCGCCGCTAATGCTCAGGC
** *
42793738 CTTTAGCGGCGTTTTTGATAAAGCGCCGCTAATGCTTAGGC
1 CTTTAGCGGCGTTTTTGAGGAAGCGCCGCTAATGCTCAGGC
*
42793779 CTTTAGCGGCGTTTGTGAGGAAGCGCCGCTAATGCTCAGGC
1 CTTTAGCGGCGTTTTTGAGGAAGCGCCGCTAATGCTCAGGC
42793820 CTTTAGCGGCGTTTTT-ATGGAAGCGCCGCTAATGCTCAGGC
1 CTTTAGCGGCGTTTTTGA-GGAAGCGCCGCTAATGCTCAGGC
42793861 CTTTAGCGGCGTTTTTGA
1 CTTTAGCGGCGTTTTTGA
42793879 AGATTTGGTT
Statistics
Matches: 244, Mismatches: 18, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
40 1 0.00
41 242 0.99
42 1 0.00
ACGTcount: A:0.17, C:0.23, G:0.30, T:0.30
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGAGGAAGCGCCGCTAATGCTCAGGC
Found at i:42794075 original size:21 final size:21
Alignment explanation
Indices: 42794050--42794136 Score: 61
Period size: 21 Copynumber: 4.1 Consensus size: 21
42794040 TAGGGATCAT
* *
42794050 GGTTTAAGGGTTGGGATTTAA
1 GGTTTAAGGGTTAGGAGTTAA
*
42794071 GGTTT-AGAGGTTAGGAGTTAG
1 GGTTTAAG-GGTTAGGAGTTAA
* ** *
42794092 GGGTTAAGGGTTAATAGTTAG
1 GGTTTAAGGGTTAGGAGTTAA
*
42794113 GGATTT-AGGGTTTAGGATTTAA
1 GG-TTTAAGGG-TTAGGAGTTAA
42794135 GG
1 GG
42794137 GTCGGGTTAG
Statistics
Matches: 51, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
20 2 0.04
21 36 0.71
22 13 0.25
ACGTcount: A:0.25, C:0.00, G:0.39, T:0.36
Consensus pattern (21 bp):
GGTTTAAGGGTTAGGAGTTAA
Found at i:42794501 original size:46 final size:46
Alignment explanation
Indices: 42794399--42794500 Score: 125
Period size: 46 Copynumber: 2.2 Consensus size: 46
42794389 AATCTAAACC
* * * *
42794399 ATTTGATATATTTGATATGGATATTTAGGTAATTATTTTTTTAAAAG
1 ATTT-ATATAATTGATATGGATATTTAGATAATTATTATTGTAAAAG
42794446 ATTTATATAATTGATATGGATATTT-GATATATTATATAATTGTAAAAG
1 ATTTATATAATTGATATGGATATTTAGATA-ATTAT-T-ATTGTAAAAG
42794494 ATTTATA
1 ATTTATA
42794501 AAAGTTATAA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
45 3 0.06
46 25 0.52
47 5 0.10
48 15 0.31
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (46 bp):
ATTTATATAATTGATATGGATATTTAGATAATTATTATTGTAAAAG
Found at i:42794572 original size:14 final size:14
Alignment explanation
Indices: 42794553--42794580 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
42794543 TTACCAAAAT
42794553 TTTAAATAATATTA
1 TTTAAATAATATTA
42794567 TTTAAATAATATTA
1 TTTAAATAATATTA
42794581 ATAATGATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTAAATAATATTA
Found at i:42794864 original size:83 final size:82
Alignment explanation
Indices: 42794720--42794952 Score: 299
Period size: 83 Copynumber: 2.8 Consensus size: 82
42794710 AATCATTCGC
* * * *
42794720 GGCGTTTGGTA-AAAAATGCCGCAAAAAATACATTTAAAATTTAACT-AAACGACACCGTTTCAT
1 GGCGTTTTGTATAAAAACGCCGCAAAAAATA-AATTAAAATTTAA-TAAAACGGCACCGTTTCAT
42794783 TGACGAATTAAATATTAGT
64 TGACGAATTAAATATTAGT
* * * *
42794802 GGCGTTTTGTATACAAACGCCGCAAAAAATATATTAAGAATTTAATAAAACGGCGCCATTTCATT
1 GGCGTTTTGTATAAAAACGCCGCAAAAAATAAATTAA-AATTTAATAAAACGGCACCGTTTCATT
*
42794867 GATGAATTAAATATTAGT
65 GACGAATTAAATATTAGT
* * * *
42794885 GGCGTTTTCTATAAAAACGCCACAAAAAATAAATTAAAAATTTAACAAAACGGCACTGTTTCATT
1 GGCGTTTTGTATAAAAACGCCGCAAAAAATAAATT-AAAATTTAATAAAACGGCACCGTTTCATT
42794950 GAC
65 GAC
42794953 TAAATAAAGA
Statistics
Matches: 129, Mismatches: 18, Indels: 7
0.84 0.12 0.05
Matches are distributed among these distances:
82 15 0.12
83 112 0.87
84 2 0.02
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (82 bp):
GGCGTTTTGTATAAAAACGCCGCAAAAAATAAATTAAAATTTAATAAAACGGCACCGTTTCATTG
ACGAATTAAATATTAGT
Found at i:42797731 original size:13 final size:13
Alignment explanation
Indices: 42797713--42797739 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
42797703 TGTGGTGCTT
42797713 TGTCGCACAGCAC
1 TGTCGCACAGCAC
42797726 TGTCGCACAGCAC
1 TGTCGCACAGCAC
42797739 T
1 T
42797740 TGGGCTACAT
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:0.22, C:0.37, G:0.22, T:0.19
Consensus pattern (13 bp):
TGTCGCACAGCAC
Found at i:42799912 original size:43 final size:43
Alignment explanation
Indices: 42799771--42800038 Score: 292
Period size: 43 Copynumber: 6.3 Consensus size: 43
42799761 GATATGTTTT
* * *
42799771 TAGCAGCGTTTGTGTGAAAAGCGCCGCTAAAGGCCAAT--TCTA
1 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGG-TAATGGTCTA
** * * * **
42799813 TAGCGGCGTTTGT-ACGAAAAAGCATCGTTAAAAGTCATGACCTA
1 TAGCGGCGTTTGTGA-G-AAAAGCGCCGCTAAAGGTAATGGTCTA
* * * * * *
42799857 TAACGGTGTTTGTGGGAGAAGCGCCACTAAAGGTAATGGTCTT
1 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTAATGGTCTA
*
42799900 TAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTAATGGTCTA
1 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTAATGGTCTA
*
42799943 TAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTAATGGTCTA
1 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTAATGGTCTA
* *
42799986 TAGCGGCGTTTGTG-GGAAAGCGCCGCTAAAGGTCATGGTCTA
1 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTAATGGTCTA
*
42800028 TAGCAGCGTTT
1 TAGCGGCGTTT
42800039 ATTTCTAAAA
Statistics
Matches: 188, Mismatches: 33, Indels: 10
0.81 0.14 0.04
Matches are distributed among these distances:
42 50 0.27
43 123 0.65
44 15 0.08
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (43 bp):
TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTAATGGTCTA
Found at i:42799999 original size:129 final size:127
Alignment explanation
Indices: 42799769--42800038 Score: 339
Period size: 129 Copynumber: 2.1 Consensus size: 127
42799759 AAGATATGTT
42799769 TTTAGCAGCGTTTGTGTGAAAAGCGCCGCTAAAGGCCAATTCTATAGCGGCGTTTGTACGAAAAA
1 TTTAGCAGCGTTTGTGTGAAAAGCGCCGCTAAAGGCCAATTCTATAGCGGCGTTTGTA-GAAAAA
* * * *
42799834 GCATCGTTAAAAGTCATGACCTATAACGGTGTTTGTGGGAGAAGCGCCACTAAAGGTAATGGTC
65 GCACCGCTAAAAGTAATGACCTATAACGGCGTTTGTGGGA-AAGCGCCACTAAAGGTAATGGTC
* *
42799898 TTTAGCGGCGTTTGTGAT-AAAAGCGCCGCTAAAGG-TAATGGTCTATAGCGGCGTTTGT-GATA
1 TTTAGCAGCGTTTGTG-TGAAAAGCGCCGCTAAAGGCCAAT--TCTATAGCGGCGTTTGTAGA-A
* * ** * * *
42799960 AAAGCGCCGCTAAAGGTAATGGTCTATAGCGGCGTTTGTGGGAAAGCGCCGCTAAAGGTCATGGT
62 AAAGCACCGCTAAAAGTAATGACCTATAACGGCGTTTGTGGGAAAGCGCCACTAAAGGTAATGGT
42800025 C
127 C
*
42800026 TATAGCAGCGTTT
1 TTTAGCAGCGTTT
42800039 ATTTCTAAAA
Statistics
Matches: 122, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
128 37 0.30
129 67 0.55
130 18 0.15
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.26
Consensus pattern (127 bp):
TTTAGCAGCGTTTGTGTGAAAAGCGCCGCTAAAGGCCAATTCTATAGCGGCGTTTGTAGAAAAAG
CACCGCTAAAAGTAATGACCTATAACGGCGTTTGTGGGAAAGCGCCACTAAAGGTAATGGTC
Found at i:42800437 original size:23 final size:22
Alignment explanation
Indices: 42800419--42800496 Score: 70
Period size: 24 Copynumber: 3.4 Consensus size: 22
42800409 GGAAATAAGT
42800419 ATAACT-AGAAAAATAAAATAAA
1 ATAACTAAGAAAAA-AAAATAAA
*
42800441 ATAACTAAGAACAAAAAATAATA
1 ATAACTAAGAAAAAAAAATAA-A
*
42800464 GATAA-TAAACAATAAATAAAATAAA
1 -ATAACT-AAGAA-AAA-AAAATAAA
42800489 ATAACTAA
1 ATAACTAA
42800497 CACTACACCA
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
22 13 0.28
23 8 0.17
24 14 0.30
25 4 0.09
26 7 0.15
ACGTcount: A:0.71, C:0.06, G:0.04, T:0.19
Consensus pattern (22 bp):
ATAACTAAGAAAAAAAAATAAA
Found at i:42800789 original size:90 final size:90
Alignment explanation
Indices: 42800636--42800812 Score: 273
Period size: 90 Copynumber: 2.0 Consensus size: 90
42800626 AAAGCGCCGC
** *
42800636 AAAAAACCTAAGCCCAACGACGTCGTTTCCCGAGCTTTCGGGGATTTAGAGGCATTTCTAAGAAA
1 AAAAAACCTAAGCCCAACGACACCGTTTCCCAAGCTTTCGGGGATTTAGAGGCATTTCTAAGAAA
42800701 GCGCCGCTAATGCTCAGGGCTTGCA
66 GCGCCGCTAATGCTCAGGGCTTGCA
* * * * * *
42800726 AAAAAACCTAATCCCAACGACACCGTTTTCTAAGCTTTCGGGGATTTAGCGGCGTTTTTAAGAAA
1 AAAAAACCTAAGCCCAACGACACCGTTTCCCAAGCTTTCGGGGATTTAGAGGCATTTCTAAGAAA
42800791 GCGCCGCTAATGCTCAGGGCTT
66 GCGCCGCTAATGCTCAGGGCTT
42800813 TGGCGGCGTT
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
90 78 1.00
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.24
Consensus pattern (90 bp):
AAAAAACCTAAGCCCAACGACACCGTTTCCCAAGCTTTCGGGGATTTAGAGGCATTTCTAAGAAA
GCGCCGCTAATGCTCAGGGCTTGCA
Found at i:42800849 original size:114 final size:114
Alignment explanation
Indices: 42800723--42800936 Score: 338
Period size: 114 Copynumber: 1.9 Consensus size: 114
42800713 CTCAGGGCTT
**
42800723 GCAAAAAAACCTAATCCCAACGACACCGTTTTCTAAGCTTTCGGGGATTTAGCGGCGTTTTTAAG
1 GCAAAAAAACCTAAGACCAACGACACCGTTTTCTAAGCTTTCGGGGATTTAGCGGCGTTTTTAAG
* *
42800788 AAAGCGCCGCTAATGCTCAGGGCTTTGGCGGCGTTTTGGGGAAAGCGCC
66 AAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTGGGGAAAGCGCC
*** * **
42800837 GCAAAAAAACCTAAGACCAACGATGTCGTTTTCTGAGCTTTCTTGGATTTAGCGGCGTTTTTAAG
1 GCAAAAAAACCTAAGACCAACGACACCGTTTTCTAAGCTTTCGGGGATTTAGCGGCGTTTTTAAG
42800902 AAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTT
66 AAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTT
42800937 AACCTAAGCC
Statistics
Matches: 90, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
114 90 1.00
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.27
Consensus pattern (114 bp):
GCAAAAAAACCTAAGACCAACGACACCGTTTTCTAAGCTTTCGGGGATTTAGCGGCGTTTTTAAG
AAAGCGCCGCTAATGCTCAGGGATTTAGCGGCGTTTTGGGGAAAGCGCC
Found at i:42801056 original size:73 final size:73
Alignment explanation
Indices: 42800937--42801083 Score: 231
Period size: 73 Copynumber: 2.0 Consensus size: 73
42800927 TAGCGGCGTT
*
42800937 AACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTTTGGAAAAGCGC
1 AACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGAGGATTTAGCGGCGTTTTTGGAAAAGCGC
*
42801002 TGCAAAAA
66 CGCAAAAA
* * * *
42801010 AACCTAAGCCCAACGACGTCGTTTTTTTAGCTTTCGAGGATTTAGCGGCGTTTTTGGAGAAGCGC
1 AACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGAGGATTTAGCGGCGTTTTTGGAAAAGCGC
*
42801075 CGCTAAAA
66 CGCAAAAA
42801083 A
1 A
42801084 TATTTTATCT
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
73 67 1.00
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.27
Consensus pattern (73 bp):
AACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGAGGATTTAGCGGCGTTTTTGGAAAAGCGC
CGCAAAAA
Found at i:42801363 original size:14 final size:15
Alignment explanation
Indices: 42801329--42801366 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
42801319 ATTTTAAGGT
* *
42801329 TTAGGGAGTATGAGT
1 TTAGGGATTATGAGA
42801344 TTAGGGATTATG-GA
1 TTAGGGATTATGAGA
42801358 TTAGGGATT
1 TTAGGGATT
42801367 GGGATTTAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 10 0.48
15 11 0.52
ACGTcount: A:0.26, C:0.00, G:0.37, T:0.37
Consensus pattern (15 bp):
TTAGGGATTATGAGA
Done.