Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A08
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: 119882356
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2655529 characters in sequence are not A, C, G, or T
File 152 of 362
Found at i:50170727 original size:14 final size:14
Alignment explanation
Indices: 50170685--50170729 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
50170675 TTAAAGAAGC
50170685 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
50170699 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
50170712 AACTCATTTAATTA
1 AACTCATTAAATTA
50170726 AACT
1 AACT
50170730 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:50179476 original size:18 final size:18
Alignment explanation
Indices: 50179455--50179489 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
50179445 TTTTTCTTTT
50179455 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
50179473 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
50179490 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:50182509 original size:12 final size:12
Alignment explanation
Indices: 50182483--50182526 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
50182473 CAGATTTTGT
*
50182483 TTTTTTTTCAAAA
1 TTTTTTTTC-GAA
*
50182496 TTTTTTTTTGAA
1 TTTTTTTTCGAA
50182508 TTTTTTTTCG-A
1 TTTTTTTTCGAA
50182519 TTTTTTTT
1 TTTTTTTT
50182527 GAAACTTACT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 9 0.32
12 11 0.39
13 8 0.29
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.75
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:50182511 original size:11 final size:11
Alignment explanation
Indices: 50182497--50182529 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
50182487 TTTTCAAAAT
50182497 TTTTTTTTGAA
1 TTTTTTTTGAA
50182508 TTTTTTTTCG-A
1 TTTTTTTT-GAA
50182519 TTTTTTTTGAA
1 TTTTTTTTGAA
50182530 ACTTACTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 1 0.05
11 18 0.90
12 1 0.05
ACGTcount: A:0.15, C:0.03, G:0.09, T:0.73
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:50182811 original size:29 final size:29
Alignment explanation
Indices: 50182745--50182801 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
50182735 GATTCAAAGA
*
50182745 TGGGTTTATGGAAATGAAGTTTATGTAGT
1 TGGGTTTATGGAAATAAAGTTTATGTAGT
* *
50182774 TGGGTTTATGGATATAAAGTTTTTGTAG
1 TGGGTTTATGGAAATAAAGTTTATGTAG
50182802 GTTTGGTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.26, C:0.00, G:0.30, T:0.44
Consensus pattern (29 bp):
TGGGTTTATGGAAATAAAGTTTATGTAGT
Found at i:50183821 original size:14 final size:14
Alignment explanation
Indices: 50183779--50183823 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
50183769 TTAAAGAAGC
50183779 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
50183793 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
50183806 AACTCATTTAATTA
1 AACTCATTAAATTA
50183820 AACT
1 AACT
50183824 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:50185293 original size:19 final size:20
Alignment explanation
Indices: 50185269--50185309 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
50185259 TTGTTCACTT
50185269 TCTTTTCTTTGTTT-TTCTC
1 TCTTTTCTTTGTTTCTTCTC
50185288 TCTTTTCTTTGTTTCTTCTC
1 TCTTTTCTTTGTTTCTTCTC
50185308 TC
1 TC
50185310 GATTTCATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.00, C:0.24, G:0.05, T:0.71
Consensus pattern (20 bp):
TCTTTTCTTTGTTTCTTCTC
Found at i:50187721 original size:21 final size:20
Alignment explanation
Indices: 50187695--50187735 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
50187685 AATAGCTGAC
50187695 ACGAGCTAAATTCGAACTCAA
1 ACGAGCTAAATT-GAACTCAA
* *
50187716 ACGAGCTGAATTGAGCTCAA
1 ACGAGCTAAATTGAACTCAA
50187736 GTGAGCTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.20
Consensus pattern (20 bp):
ACGAGCTAAATTGAACTCAA
Found at i:50193869 original size:20 final size:20
Alignment explanation
Indices: 50193846--50193892 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
50193836 GGGTTAAGAT
*
50193846 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
50193866 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
50193886 TGAGCTG
1 TGAGCTG
50193893 GAAACAAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:50194123 original size:30 final size:30
Alignment explanation
Indices: 50194067--50194123 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
50194057 TGGGCTCAAA
* **
50194067 TCAAGAAAATCAAGATTCACTTTCTTGTTT
1 TCAAGAAAATCAAGAATCACAATCTTGTTT
50194097 TCAAGAAAATCAAGAAATCA-AATCTTG
1 TCAAGAAAATCAAG-AATCACAATCTTG
50194124 GCCCAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 19 0.83
31 4 0.17
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.32
Consensus pattern (30 bp):
TCAAGAAAATCAAGAATCACAATCTTGTTT
Found at i:50196112 original size:19 final size:19
Alignment explanation
Indices: 50196088--50196127 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
50196078 AGCTCCCATG
50196088 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
50196107 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
50196126 TA
1 TA
50196128 TCAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:50203747 original size:14 final size:14
Alignment explanation
Indices: 50203728--50203772 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
50203718 AACTCATCTT
*
50203728 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
50203742 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
50203755 AATTTAATTTAATG
1 AGTTTAATTTAATG
50203769 AGTT
1 AGTT
50203773 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:50204781 original size:29 final size:29
Alignment explanation
Indices: 50204749--50204808 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
50204739 ATAACCAAAC
*
50204749 CTACAAAAACTTTATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
50204778 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
50204807 CT
1 CT
50204809 TTGAATCCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.30, G:0.00, T:0.28
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:50204801 original size:15 final size:15
Alignment explanation
Indices: 50204755--50204802 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
50204745 AAACCTACAA
*
50204755 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
50204770 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
50204784 AAACTTCATATCCAT
1 AAACTTCATATCCAT
50204799 AAAC
1 AAAC
50204803 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:50207519 original size:20 final size:20
Alignment explanation
Indices: 50207496--50207542 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
50207486 GGGTTAAGAT
*
50207496 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
50207516 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
50207536 TGAGCTG
1 TGAGCTG
50207543 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:50209268 original size:48 final size:48
Alignment explanation
Indices: 50209213--50209318 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
50209203 TTGTCTTTTC
*
50209213 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
50209261 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
50209309 TTTCTTTTTC
1 TTTCTTTTTC
50209319 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:50210370 original size:10 final size:11
Alignment explanation
Indices: 50210343--50210371 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
50210333 CTTTTCACTT
50210343 TTTTTTTGTTC
1 TTTTTTTGTTC
50210354 TTTTTTT-TTC
1 TTTTTTTGTTC
50210364 TTTTTTTG
1 TTTTTTTG
50210372 CTCATTTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.86
Consensus pattern (11 bp):
TTTTTTTGTTC
Found at i:50210383 original size:22 final size:20
Alignment explanation
Indices: 50210341--50210389 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
50210331 GACTTTTCAC
* *
50210341 TTTTTTTTTGTTCTTTTTTT
1 TTTTTTTTTGCTCTTTCTTT
50210361 TTCTTTTTTTGCTCATTTCTTT
1 TT-TTTTTTTGCTC-TTTCTTT
50210383 TTTTTTT
1 TTTTTTT
50210390 GAATTTCGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 15 0.60
22 8 0.32
ACGTcount: A:0.02, C:0.10, G:0.04, T:0.84
Consensus pattern (20 bp):
TTTTTTTTTGCTCTTTCTTT
Found at i:50211935 original size:20 final size:20
Alignment explanation
Indices: 50211912--50211958 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
50211902 GGGTTAAGAT
*
50211912 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
50211932 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
50211952 TGAGCTG
1 TGAGCTG
50211959 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:50212211 original size:12 final size:12
Alignment explanation
Indices: 50212179--50212212 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
50212169 TATTGACTTT
50212179 TTAATTAATAAG
1 TTAATTAATAAG
50212191 TTCAA-TAATAAG
1 TT-AATTAATAAG
50212203 TTAATTAATA
1 TTAATTAATA
50212213 TCCTACATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 2 0.10
12 16 0.80
13 2 0.10
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (12 bp):
TTAATTAATAAG
Found at i:50214327 original size:21 final size:22
Alignment explanation
Indices: 50214301--50214344 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
50214291 AAATGAGCTC
50214301 GTTGAGCTAAGTTGAG-TTGAA
1 GTTGAGCTAAGTTGAGCTTGAA
* *
50214322 GTTGAGCTGATTTGAGCTTGAA
1 GTTGAGCTAAGTTGAGCTTGAA
50214344 G
1 G
50214345 GAGTATGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.25, C:0.07, G:0.34, T:0.34
Consensus pattern (22 bp):
GTTGAGCTAAGTTGAGCTTGAA
Found at i:50214945 original size:14 final size:14
Alignment explanation
Indices: 50214926--50214969 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
50214916 TTTTTCATAT
50214926 CCTTTCATTCCTAC
1 CCTTTCATTCCTAC
50214940 CCTTTCATTCCTAC
1 CCTTTCATTCCTAC
* * *
50214954 CATTCCATTCGTAC
1 CCTTTCATTCCTAC
50214968 CC
1 CC
50214970 CTCTTTCTCC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.16, C:0.43, G:0.02, T:0.39
Consensus pattern (14 bp):
CCTTTCATTCCTAC
Found at i:50215284 original size:30 final size:30
Alignment explanation
Indices: 50215250--50215346 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
50215240 TAAACTAAAA
*
50215250 TGAGCTAAGCTTTAGCTTGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
50215280 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
50215310 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
50215340 TGAGCTA
1 TGAGCTA
50215347 GGAGTGAGCT
Statistics
Matches: 49, Mismatches: 15, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
29 2 0.04
30 41 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:50217496 original size:28 final size:28
Alignment explanation
Indices: 50217442--50217494 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
50217432 CTTTTTCATC
*
50217442 TTCTTTTTCACTCTCAAATTTCTTTTCG
1 TTCTTTTTCAATCTCAAATTTCTTTTCG
*
50217470 TTCTTTTTCAATCTC-ATTTTCTTTT
1 TTCTTTTTCAATCTCAAATTTCTTTT
50217495 TCTTTTTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.13, C:0.23, G:0.02, T:0.62
Consensus pattern (28 bp):
TTCTTTTTCAATCTCAAATTTCTTTTCG
Found at i:50217585 original size:5 final size:5
Alignment explanation
Indices: 50217575--50217631 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
50217565 CTCTTGCCTC
*
50217575 TCTTT TCTTT T-TATT TCATTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
50217622 TCTTT TCTTT
1 TCTTT TCTTT
50217632 GTTTTCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:50217615 original size:15 final size:14
Alignment explanation
Indices: 50217575--50217631 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
50217565 CTCTTGCCTC
*
50217575 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
50217590 TCATTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
50217605 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
50217622 TCTTTTCTTT
1 TCTTTTCTTT
50217632 GTTTTCTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:50217632 original size:21 final size:21
Alignment explanation
Indices: 50217575--50217642 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
50217565 CTCTTGCCTC
* *
50217575 TCTTTTCTTTT-TATTTCATTT
1 TCTTTTCTTTTCT-TTGCTTTT
*
50217596 TCTTTT-TCTTCTTTTGCTTTT
1 TCTTTTCTTTTC-TTTGCTTTT
50217617 TCTTTTCTTTTCTTTG-TTTT
1 TCTTTTCTTTTCTTTGCTTTT
50217637 CTCTTT
1 -TCTTT
50217643 ACAAGAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 7 0.18
21 27 0.69
22 5 0.13
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (21 bp):
TCTTTTCTTTTCTTTGCTTTT
Found at i:50218601 original size:12 final size:13
Alignment explanation
Indices: 50218567--50218599 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
50218557 TTTTCGAAAA
50218567 TTTTTTTTGAATT
1 TTTTTTTTGAATT
50218580 TTTTTTTTGAATT
1 TTTTTTTTGAATT
50218593 TTTTTTT
1 TTTTTTT
50218600 GACTTGTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (13 bp):
TTTTTTTTGAATT
Found at i:50220313 original size:30 final size:30
Alignment explanation
Indices: 50220279--50220375 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
50220269 TAAACTAAAA
50220279 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
50220309 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
50220339 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
50220369 TGAGCTA
1 TGAGCTA
50220376 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:50223033 original size:13 final size:12
Alignment explanation
Indices: 50223017--50223059 Score: 54
Period size: 11 Copynumber: 3.7 Consensus size: 12
50223007 TTCAGATTTT
50223017 TTTTCTTTTCGAA
1 TTTT-TTTTCGAA
*
50223030 TTTTTTTTTGAA
1 TTTTTTTTCGAA
50223042 -TTTTTTT-GAA
1 TTTTTTTTCGAA
50223052 TTTTTTTT
1 TTTTTTTT
50223060 AACTTGAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 3 0.11
11 14 0.50
12 7 0.25
13 4 0.14
ACGTcount: A:0.14, C:0.05, G:0.07, T:0.74
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:50223037 original size:12 final size:11
Alignment explanation
Indices: 50223017--50223059 Score: 52
Period size: 10 Copynumber: 3.7 Consensus size: 11
50223007 TTCAGATTTT
50223017 TTTTCTTTTCGAA
1 TTTT-TTTT-GAA
50223030 TTTTTTTTTGAA
1 -TTTTTTTTGAA
50223042 -TTTTTTTGAA
1 TTTTTTTTGAA
50223052 TTTTTTTT
1 TTTTTTTT
50223060 AACTTGAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 10 0.36
11 7 0.25
12 3 0.11
13 4 0.14
14 4 0.14
ACGTcount: A:0.14, C:0.05, G:0.07, T:0.74
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:50223045 original size:9 final size:10
Alignment explanation
Indices: 50223032--50223058 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
50223022 TTTTCGAATT
50223032 TTTTTTTGAA
1 TTTTTTTGAA
50223042 TTTTTTTGAA
1 TTTTTTTGAA
50223052 TTTTTTT
1 TTTTTTT
50223059 TAACTTGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (10 bp):
TTTTTTTGAA
Found at i:50224134 original size:11 final size:12
Alignment explanation
Indices: 50224118--50224150 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
50224108 AGTTGTAAAG
50224118 TTTTATTT-TTA
1 TTTTATTTATTA
50224129 TTTTATTTATTA
1 TTTTATTTATTA
50224141 -TTTATTTATT
1 TTTTATTTATT
50224151 TACTTAGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 18 0.86
12 3 0.14
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTATTTATTA
Found at i:50224139 original size:15 final size:15
Alignment explanation
Indices: 50224119--50224152 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
50224109 GTTGTAAAGT
50224119 TTTATT-TTTATTTTA
1 TTTATTATTTA-TTTA
50224134 TTTATTATTTATTTA
1 TTTATTATTTATTTA
50224149 TTTA
1 TTTA
50224153 CTTAGTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTATTATTTATTTA
Found at i:50229549 original size:30 final size:30
Alignment explanation
Indices: 50229515--50229611 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
50229505 TAAACTAAAA
50229515 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
50229545 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
50229575 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
50229605 TGAGCTA
1 TGAGCTA
50229612 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:50232250 original size:12 final size:12
Alignment explanation
Indices: 50232223--50232265 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
50232213 AACACTCTCA
*
50232223 TTTTTTTTATAAT
1 TTTTTTTTCT-AT
50232236 TTTTTGTTTCT-T
1 TTTTT-TTTCTAT
50232248 TTTTTTTTCTAT
1 TTTTTTTTCTAT
50232260 TTTTTT
1 TTTTTT
50232266 CTCTTTCTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 5 0.19
12 13 0.48
13 5 0.19
14 4 0.15
ACGTcount: A:0.09, C:0.05, G:0.02, T:0.84
Consensus pattern (12 bp):
TTTTTTTTCTAT
Found at i:50238157 original size:29 final size:29
Alignment explanation
Indices: 50238124--50238179 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
50238114 ATAACCAAAC
*
50238124 CTACAAAAACTTTATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
50238153 CTACATAAACTTCATATCCATAAACCC
1 CTACAAAAACTTCATATCCATAAACCC
50238180 TGATACGAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.43, C:0.30, G:0.00, T:0.27
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:50238176 original size:15 final size:15
Alignment explanation
Indices: 50238130--50238177 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
50238120 AAACCTACAA
*
50238130 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
50238145 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
50238159 AAACTTCATATCCAT
1 AAACTTCATATCCAT
50238174 AAAC
1 AAAC
50238178 CCTGATACGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:50250211 original size:30 final size:30
Alignment explanation
Indices: 50250177--50250274 Score: 81
Period size: 30 Copynumber: 3.3 Consensus size: 30
50250167 AGCTCACTCC
50250177 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
50250207 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * *
50250237 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
*
50250267 TAGTTCAT
1 TAGCTCAT
50250275 TTTAGTTTAA
Statistics
Matches: 49, Mismatches: 17, Indels: 3
0.71 0.25 0.04
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.31
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:50252915 original size:9 final size:10
Alignment explanation
Indices: 50252908--50252972 Score: 62
Period size: 11 Copynumber: 6.2 Consensus size: 10
50252898 AAGAGAAAAT
50252908 AAAGAAAAGA
1 AAAGAAAAGA
50252918 AAAGAAAAAGTA
1 AAAG-AAAAG-A
*
50252930 AAAGAAGA-A
1 AAAGAAAAGA
50252939 AAAGAAAAAGA
1 AAAG-AAAAGA
50252950 AAATGAAATA-A
1 AAA-GAAA-AGA
50252961 AAAGAAAAGA
1 AAAGAAAAGA
50252971 AA
1 AA
50252973 GGCAAGAGGC
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
9 6 0.13
10 14 0.30
11 19 0.41
12 7 0.15
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:50252931 original size:21 final size:21
Alignment explanation
Indices: 50252897--50252968 Score: 69
Period size: 21 Copynumber: 3.4 Consensus size: 21
50252887 ACATTCTTGT
50252897 AAAGAGAAAA-TAAAGAAAAGA
1 AAAGA-AAAAGTAAAGAAAAGA
*
50252918 AAAGAAAAAGTAAA-AGAAGAA
1 AAAGAAAAAGTAAAGAAAAG-A
*
50252939 AAAGAAAAAGAAAATGAAATA-A
1 AAAGAAAAAGTAAA-GAAA-AGA
50252961 AAAGAAAA
1 AAAGAAAA
50252969 GAAAGGCAAG
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
20 8 0.19
21 23 0.53
22 9 0.21
23 2 0.05
24 1 0.02
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.06
Consensus pattern (21 bp):
AAAGAAAAAGTAAAGAAAAGA
Found at i:50252932 original size:6 final size:5
Alignment explanation
Indices: 50252908--50252972 Score: 62
Period size: 5 Copynumber: 12.4 Consensus size: 5
50252898 AAGAGAAAAT
*
50252908 AAAGA AAAGA AAAGAA AAAGTA AAAGA AGA-A AAAGAA AAAGA AAATGA
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAG-A AAAGA AAA-GA
50252956 AATA-A AAAGA AAAGA AA
1 AA-AGA AAAGA AAAGA AA
50252973 GGCAAGAGGC
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.08
5 27 0.53
6 19 0.37
7 1 0.02
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (5 bp):
AAAGA
Found at i:50253081 original size:24 final size:25
Alignment explanation
Indices: 50253029--50253101 Score: 69
Period size: 24 Copynumber: 3.0 Consensus size: 25
50253019 TGAAAAAGCC
*
50253029 TTTGAAAAAGAAAAAGAAAATGAGA
1 TTTGAAAAAGAAAAAGAAAATGAAA
* *
50253054 -TTGAAAAAGAGAATGAAAA-GAAA
1 TTTGAAAAAGAAAAAGAAAATGAAA
* ** *
50253077 TTTGAGAGTGAAAAAGAAGATGAAA
1 TTTGAAAAAGAAAAAGAAAATGAAA
50253102 AAGAAATTGA
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
23 3 0.08
24 30 0.81
25 4 0.11
ACGTcount: A:0.60, C:0.00, G:0.23, T:0.16
Consensus pattern (25 bp):
TTTGAAAAAGAAAAAGAAAATGAAA
Found at i:50253083 original size:30 final size:31
Alignment explanation
Indices: 50253038--50253109 Score: 96
Period size: 30 Copynumber: 2.4 Consensus size: 31
50253028 CTTTGAAAAA
* *
50253038 GAAAAAGAAA-ATGAGATTGAAAAAG-AGAAT
1 GAAAAAGAAATTTGAGAGTGAAAAAGAAG-AT
50253068 G-AAAAGAAATTTGAGAGTGAAAAAGAAGAT
1 GAAAAAGAAATTTGAGAGTGAAAAAGAAGAT
50253098 GAAAAAGAAATT
1 GAAAAAGAAATT
50253110 GAAACAAAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
29 8 0.22
30 17 0.46
31 12 0.32
ACGTcount: A:0.61, C:0.00, G:0.24, T:0.15
Consensus pattern (31 bp):
GAAAAAGAAATTTGAGAGTGAAAAAGAAGAT
Found at i:50255293 original size:30 final size:30
Alignment explanation
Indices: 50255259--50255356 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
50255249 AGCTCACTTC
50255259 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
50255289 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * *
50255319 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
50255349 TAGCTCAT
1 TAGCTCAT
50255357 TTTAGTTTAA
Statistics
Matches: 50, Mismatches: 16, Indels: 3
0.72 0.23 0.04
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:50258932 original size:19 final size:19
Alignment explanation
Indices: 50258910--50258952 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
50258900 AAGATCCTTG
50258910 AAATCCCGAAAGATTTCAC
1 AAATCCCGAAAGATTTCAC
50258929 AAATCCCGAAAGATTTCAC
1 AAATCCCGAAAGATTTCAC
50258948 AAATC
1 AAATC
50258953 TCTTCAAACG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.44, C:0.26, G:0.09, T:0.21
Consensus pattern (19 bp):
AAATCCCGAAAGATTTCAC
Found at i:50262561 original size:23 final size:23
Alignment explanation
Indices: 50262535--50262578 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
50262525 TTTCTTTTGT
50262535 TTCTTT-TTCTAATTCATTTTCTC
1 TTCTTTCTTC-AATTCATTTTCTC
*
50262558 TTCTTTCTTCAATTCTTTTTC
1 TTCTTTCTTCAATTCATTTTC
50262579 ACTCTCATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.11, C:0.23, G:0.00, T:0.66
Consensus pattern (23 bp):
TTCTTTCTTCAATTCATTTTCTC
Found at i:50267581 original size:13 final size:14
Alignment explanation
Indices: 50267539--50267585 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
50267529 ACCTAAACCG
* *
50267539 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
50267553 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
*
50267567 ACCCTTTTG-TCCT
1 ACCATTTTGTTCCT
50267580 ACCATT
1 ACCATT
50267586 CCATTCGTAC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
13 9 0.31
14 20 0.69
ACGTcount: A:0.19, C:0.30, G:0.06, T:0.45
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:50269237 original size:15 final size:16
Alignment explanation
Indices: 50269217--50269286 Score: 74
Period size: 15 Copynumber: 4.5 Consensus size: 16
50269207 ACATTCTTGT
*
50269217 AAAAGAGAA-ACAAAG
1 AAAAGAGAAGAAAAAG
*
50269232 AAAAGAAAAGAAAAAG
1 AAAAGAGAAGAAAAAG
*
50269248 CAAA-AGAAGAAAAAG
1 AAAAGAGAAGAAAAAG
*
50269263 AAAA-AGAAATAAAAAG
1 AAAAGAG-AAGAAAAAG
50269279 AAAAGAGA
1 AAAAGAGA
50269287 GGCAAGAGGC
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
15 23 0.50
16 21 0.46
17 2 0.04
ACGTcount: A:0.77, C:0.03, G:0.19, T:0.01
Consensus pattern (16 bp):
AAAAGAGAAGAAAAAG
Found at i:50269252 original size:6 final size:5
Alignment explanation
Indices: 50269228--50269284 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
50269218 AAAGAGAAAC
*
50269228 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGAA AAAGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAG-A AAAGA AA-AGA
50269275 AAAGA AAAGA
1 AAAGA AAAGA
50269285 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 24 0.55
6 16 0.36
ACGTcount: A:0.79, C:0.02, G:0.18, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:50269277 original size:25 final size:25
Alignment explanation
Indices: 50269232--50269280 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
50269222 AGAAACAAAG
50269232 AAAAGAAAAGAAAAAGCAAAAGAAGA
1 AAAAGAAAAGAAAAA-CAAAAGAAGA
*
50269258 AAAAGAAAAAGAAATA-AAAAGAA
1 AAAAG-AAAAGAAAAACAAAAGAA
50269281 AAGAGAGGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 5 0.24
27 9 0.43
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (25 bp):
AAAAGAAAAGAAAAACAAAAGAAGA
Found at i:50269901 original size:24 final size:24
Alignment explanation
Indices: 50269869--50269914 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
50269859 TGATGTGTTT
50269869 TGATGTGAGCTTGCCTACGAACAA
1 TGATGTGAGCTTGCCTACGAACAA
50269893 TGATGTGAGCTTGCCTACGAAC
1 TGATGTGAGCTTGCCTACGAAC
50269915 CAAATGGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (24 bp):
TGATGTGAGCTTGCCTACGAACAA
Found at i:50271437 original size:13 final size:13
Alignment explanation
Indices: 50271421--50271468 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 13
50271411 AAAAAAATCG
50271421 AAAAAAAATTTGA
1 AAAAAAAATTTGA
*
50271434 AAAAAAAA-TTAA
1 AAAAAAAATTTGA
50271446 AAAAACAAATTTTTGA
1 AAAAA-AAA--TTTGA
50271462 AAAAAAA
1 AAAAAAA
50271469 TTGCATACGG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 8 0.28
13 11 0.38
15 2 0.07
16 8 0.28
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.21
Consensus pattern (13 bp):
AAAAAAAATTTGA
Found at i:50271448 original size:12 final size:12
Alignment explanation
Indices: 50271411--50271456 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
50271401 ATTGTAGATT
*
50271411 AAAAAAATCGAA
1 AAAAAAATTGAA
*
50271423 AAAAAATTTGAA
1 AAAAAAATTGAA
*
50271435 AAAAAAATTAAA
1 AAAAAAATTGAA
50271447 AAAACAAATT
1 AAAA-AAATT
50271457 TTTGAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
12 24 0.83
13 5 0.17
ACGTcount: A:0.74, C:0.04, G:0.04, T:0.17
Consensus pattern (12 bp):
AAAAAAATTGAA
Found at i:50280417 original size:30 final size:30
Alignment explanation
Indices: 50280383--50280479 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
50280373 TAAACTAAAA
50280383 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
50280413 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
50280443 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
50280473 TGAGCTA
1 TGAGCTA
50280480 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:50283389 original size:13 final size:13
Alignment explanation
Indices: 50283371--50283395 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
50283361 TAACCTACAA
50283371 AATTAAATAACAT
1 AATTAAATAACAT
50283384 AATTAAATAACA
1 AATTAAATAACA
50283396 CACAACTATT
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:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (13 bp):
AATTAAATAACAT
Found at i:50283643 original size:21 final size:21
Alignment explanation
Indices: 50283619--50283658 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
50283609 GAAAAAGGAA
*
50283619 TGAGCTGAAACGAGCTAAATT
1 TGAGCTCAAACGAGCTAAATT
50283640 TGAGCTCAAACGAGCTAAA
1 TGAGCTCAAACGAGCTAAA
50283659 ACGAGCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.20
Consensus pattern (21 bp):
TGAGCTCAAACGAGCTAAATT
Found at i:50285152 original size:14 final size:14
Alignment explanation
Indices: 50285110--50285154 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
50285100 TTAAAGAAGC
50285110 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
50285124 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
50285137 AACTCATTTAATTA
1 AACTCATTAAATTA
50285151 AACT
1 AACT
50285155 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:50289653 original size:12 final size:12
Alignment explanation
Indices: 50289631--50289680 Score: 68
Period size: 11 Copynumber: 4.2 Consensus size: 12
50289621 TATGTTCAAA
50289631 TTTTCAGATTTTT
1 TTTTCA-ATTTTT
50289644 TTTTCAA-TTTT
1 TTTTCAATTTTT
50289655 TTTT-AATTTTT
1 TTTTCAATTTTT
*
50289666 TTTTCGATTTTT
1 TTTTCAATTTTT
50289678 TTT
1 TTT
50289681 GAAACTTACT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
10 2 0.06
11 16 0.47
12 10 0.29
13 6 0.18
ACGTcount: A:0.14, C:0.06, G:0.04, T:0.76
Consensus pattern (12 bp):
TTTTCAATTTTT
Found at i:50289663 original size:22 final size:22
Alignment explanation
Indices: 50289638--50289680 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
50289628 AAATTTTCAG
50289638 ATTTTTTTTTCAATTTTTTTTA
1 ATTTTTTTTTCAATTTTTTTTA
*
50289660 ATTTTTTTTTCGATTTTTTTT
1 ATTTTTTTTTCAATTTTTTTT
50289681 GAAACTTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.14, C:0.05, G:0.02, T:0.79
Consensus pattern (22 bp):
ATTTTTTTTTCAATTTTTTTTA
Found at i:50289922 original size:15 final size:15
Alignment explanation
Indices: 50289902--50289949 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
50289892 TCAAAGATGG
50289902 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
50289917 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
50289931 GTTTATGGATATAAA
1 GTTTATGGATATGAA
50289946 GTTT
1 GTTT
50289950 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:50289936 original size:14 final size:14
Alignment explanation
Indices: 50289896--50289939 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
50289886 AAGGATTCAA
50289896 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
50289910 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
50289925 AGATGGGTTTATGG
1 AGATGGGTTTATGG
50289939 A
1 A
50289940 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:50289965 original size:29 final size:29
Alignment explanation
Indices: 50289896--50289955 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
50289886 AAGGATTCAA
*
50289896 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
50289925 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
50289954 AG
1 AG
50289956 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:50290971 original size:14 final size:14
Alignment explanation
Indices: 50290929--50290973 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
50290919 TTAAAGAAGC
50290929 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
50290943 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
50290956 AACTCATTTAATTA
1 AACTCATTAAATTA
50290970 AACT
1 AACT
50290974 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:50291384 original size:10 final size:10
Alignment explanation
Indices: 50291371--50291405 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
50291361 GAGCTCCGTC
*
50291371 CAGCTCAATT
1 CAGCTCATTT
50291381 CAGCTCATTT
1 CAGCTCATTT
*
50291391 GAGCTCATTT
1 CAGCTCATTT
50291401 CAGCT
1 CAGCT
50291406 TGTTTGAGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.23, C:0.29, G:0.14, T:0.34
Consensus pattern (10 bp):
CAGCTCATTT
Found at i:50291395 original size:20 final size:20
Alignment explanation
Indices: 50291372--50291418 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
50291362 AGCTCCGTCC
50291372 AGCTCAATTCAGCTCATTTG
1 AGCTCAATTCAGCTCATTTG
* **
50291392 AGCTCATTTCAGCTTGTTTG
1 AGCTCAATTCAGCTCATTTG
50291412 AGCTCAA
1 AGCTCAA
50291419 CCGAGCTTAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.36
Consensus pattern (20 bp):
AGCTCAATTCAGCTCATTTG
Found at i:50297146 original size:30 final size:30
Alignment explanation
Indices: 50297112--50297208 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
50297102 TAAACTAAAA
*
50297112 TGAGCTAAGCTTTAGCTCATGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCATGAGCTAAAGT
* * * * * *
50297142 TGAGCTGAGGTTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCATGAGCTAAAGT
* *
50297172 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGGTTTAGCTCATGAGCT-AAAGT
50297202 TGAGCTA
1 TGAGCTA
50297209 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
30 49 0.94
31 3 0.06
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCATGAGCTAAAGT
Found at i:50303251 original size:22 final size:22
Alignment explanation
Indices: 50303200--50303265 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
50303190 AGTATTTGGG
* *
50303200 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
50303221 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
50303243 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
50303266 TCAAAGAGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.49
22 15 0.38
23 5 0.13
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:50305876 original size:12 final size:12
Alignment explanation
Indices: 50305859--50305909 Score: 77
Period size: 12 Copynumber: 4.2 Consensus size: 12
50305849 AAATCGTATG
50305859 CAATTTTTTTTT
1 CAATTTTTTTTT
50305871 CAATTTTTTTTTT
1 CAA-TTTTTTTTT
50305884 CAATTTTTTTTT
1 CAATTTTTTTTT
*
50305896 C-TTTTTTTTTT
1 CAATTTTTTTTT
50305907 CAA
1 CAA
50305910 ACTCCTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
11 10 0.29
12 13 0.37
13 12 0.34
ACGTcount: A:0.16, C:0.10, G:0.00, T:0.75
Consensus pattern (12 bp):
CAATTTTTTTTT
Found at i:50305880 original size:13 final size:13
Alignment explanation
Indices: 50305862--50305909 Score: 75
Period size: 13 Copynumber: 3.9 Consensus size: 13
50305852 TCGTATGCAA
50305862 TTTTTTTTTCAAT
1 TTTTTTTTTCAAT
50305875 TTTTTTTTTCAA-
1 TTTTTTTTTCAAT
50305887 TTTTTTTTTC--T
1 TTTTTTTTTCAAT
50305898 TTTTTTTTTCAA
1 TTTTTTTTTCAA
50305910 ACTCCTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
11 10 0.31
12 10 0.31
13 12 0.38
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTTTTTTCAAT
Found at i:50305888 original size:25 final size:23
Alignment explanation
Indices: 50305859--50305909 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 23
50305849 AAATCGTATG
50305859 CAATTTTTTTTTCAATTTTTTTTTT
1 CAATTTTTTTTTC--TTTTTTTTTT
50305884 CAATTTTTTTTTCTTTTTTTTTT
1 CAATTTTTTTTTCTTTTTTTTTT
50305907 CAA
1 CAA
50305910 ACTCCTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 13 0.50
25 13 0.50
ACGTcount: A:0.16, C:0.10, G:0.00, T:0.75
Consensus pattern (23 bp):
CAATTTTTTTTTCTTTTTTTTTT
Found at i:50305918 original size:23 final size:22
Alignment explanation
Indices: 50305874--50305922 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 22
50305864 TTTTTTTCAA
** **
50305874 TTTTTTTTTTCAATTTTTTTTT
1 TTTTTTTTTTCAAACTCCTTTT
50305896 CTTTTTTTTTTCAAACTCCTTTT
1 -TTTTTTTTTTCAAACTCCTTTT
50305919 TTTT
1 TTTT
50305923 ACGTACCTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTTTTTTTTCAAACTCCTTTT
Found at i:50306246 original size:21 final size:21
Alignment explanation
Indices: 50306220--50306282 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
50306210 TTGGTATTTG
50306220 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
50306241 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
50306262 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
50306283 ACGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:50312314 original size:17 final size:17
Alignment explanation
Indices: 50312274--50312316 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
50312264 TGCACTTAAG
50312274 CCATTCATGCATTCTAT
1 CCATTCATGCATTCTAT
50312291 -CATTTCATGCATT-TGAT
1 CCA-TTCATGCATTCT-AT
50312308 CCATTCATG
1 CCATTCATG
50312317 GACTAGCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 3 0.13
17 18 0.78
18 2 0.09
ACGTcount: A:0.23, C:0.26, G:0.09, T:0.42
Consensus pattern (17 bp):
CCATTCATGCATTCTAT
Found at i:50312800 original size:30 final size:30
Alignment explanation
Indices: 50312713--50312809 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
50312703 TAAACTAAAA
* * *
50312713 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCATGAGCTGAAGT
* * * * * * *
50312743 TGAGCTGAGGCTAAACTCCTAATCTGAAGT
1 TGAGCTAAGGTTTAGCTCATGAGCTGAAGT
50312773 TGAGCTAAGGTTTAGCTCATGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCATGAGCTGAAGT
50312802 ATGAGCTA
1 -TGAGCTA
50312810 GGATTGAGCT
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
29 1 0.02
30 49 0.98
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCATGAGCTGAAGT
Found at i:50313127 original size:12 final size:12
Alignment explanation
Indices: 50313112--50313146 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
50313102 ATAATTCACT
50313112 TTTTTTTTCAAA
1 TTTTTTTTCAAA
*
50313124 -TTTTTTTCGAA
1 TTTTTTTTCAAA
50313135 TTTTTTTTCAAA
1 TTTTTTTTCAAA
50313147 CTTGTATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.23, C:0.09, G:0.03, T:0.66
Consensus pattern (12 bp):
TTTTTTTTCAAA
Found at i:50318876 original size:30 final size:30
Alignment explanation
Indices: 50318842--50318937 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
50318832 TAAACTAAAA
50318842 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * *
50318872 TGAGCTGAGGC--TAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
50318901 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
50318931 TGAGCTA
1 TGAGCTA
50318938 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 12, Indels: 8
0.71 0.17 0.11
Matches are distributed among these distances:
28 2 0.04
29 20 0.40
30 22 0.44
31 6 0.12
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:50321108 original size:30 final size:30
Alignment explanation
Indices: 50321074--50321170 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
50321064 TAAACTAAAA
*
50321074 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
50321104 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
50321134 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
50321163 ATGAGCTA
1 -TGAGCTA
50321171 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:50321687 original size:30 final size:31
Alignment explanation
Indices: 50321651--50321747 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
50321641 AGGTCACTTC
*
50321651 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
50321681 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
50321711 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
50321741 TAGCTCA
1 TAGCTCA
50321748 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:50324683 original size:30 final size:30
Alignment explanation
Indices: 50324612--50324694 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
50324602 CTTTTGTTTC
*
50324612 AATTTCATTTTCA-TCTTCTTTTTCACTCTCA
1 AATTTC-TTTTCATTC-TCTTTTTCAATCTCA
*
50324643 AATTTCTTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTCATTCTCTTTTTCAATCTCA
* *
50324672 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTC-TTTTCATTCTCTTTTT
50324695 GCTTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 32 0.71
31 8 0.18
ACGTcount: A:0.14, C:0.22, G:0.01, T:0.63
Consensus pattern (30 bp):
AATTTCTTTTCATTCTCTTTTTCAATCTCA
Found at i:50324694 original size:18 final size:18
Alignment explanation
Indices: 50324645--50324700 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
50324635 CACTCTCAAA
* *
50324645 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
50324662 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
50324680 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
50324699 TT
1 TT
50324701 CAAAGGCTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:50324701 original size:12 final size:12
Alignment explanation
Indices: 50324670--50324694 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
50324660 TTTTTCAATC
50324670 TCATTTTCTTTT
1 TCATTTTCTTTT
50324682 TCATTTTCTTTT
1 TCATTTTCTTTT
50324694 T
1 T
50324695 GCTTTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:50324712 original size:12 final size:12
Alignment explanation
Indices: 50324697--50324727 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
50324687 TTCTTTTTGC
50324697 TTTTCAAAGGCT
1 TTTTCAAAGGCT
50324709 TTTTCAAAGGCT
1 TTTTCAAAGGCT
50324721 TTTTCAA
1 TTTTCAA
50324728 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:50324798 original size:16 final size:16
Alignment explanation
Indices: 50324777--50324816 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
50324767 CTTGCCTCTC
50324777 TTTTCTTTTTATTTCA
1 TTTTCTTTTTATTTCA
* **
50324793 TTTTCTTTTTCTTTTG
1 TTTTCTTTTTATTTCA
50324809 TTTTCTTT
1 TTTTCTTT
50324817 GTTTTCTCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.05, C:0.12, G:0.03, T:0.80
Consensus pattern (16 bp):
TTTTCTTTTTATTTCA
Found at i:50325755 original size:17 final size:17
Alignment explanation
Indices: 50325730--50325768 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
50325720 CATTAAACAC
*
50325730 TTTTTTTTTC-AGATTT
1 TTTTTTTTTCGAAATTT
50325746 TTTTTCTTTTCGAAATTT
1 TTTTT-TTTTCGAAATTT
50325764 TTTTT
1 TTTTT
50325769 GATTTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 5 0.25
18 10 0.50
ACGTcount: A:0.13, C:0.08, G:0.05, T:0.74
Consensus pattern (17 bp):
TTTTTTTTTCGAAATTT
Found at i:50325779 original size:24 final size:24
Alignment explanation
Indices: 50325746--50325791 Score: 76
Period size: 23 Copynumber: 1.9 Consensus size: 24
50325736 TTTCAGATTT
50325746 TTTTTCTTTTCGAAATTTTTTTTGA
1 TTTTTCTTTTCG-AATTTTTTTTGA
50325771 TTTTT-TTTTCGAATTTTTTTT
1 TTTTTCTTTTCGAATTTTTTTT
50325792 ACTTGTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 10 0.48
24 6 0.29
25 5 0.24
ACGTcount: A:0.13, C:0.07, G:0.07, T:0.74
Consensus pattern (24 bp):
TTTTTCTTTTCGAATTTTTTTTGA
Found at i:50325791 original size:12 final size:12
Alignment explanation
Indices: 50325747--50325791 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
50325737 TTCAGATTTT
50325747 TTTTCTTTTCGAAA
1 TTTT-TTTTCG-AA
*
50325761 TTTTTTTT-GAT
1 TTTTTTTTCGAA
50325772 TTTTTTTTCGAA
1 TTTTTTTTCGAA
50325784 TTTTTTTT
1 TTTTTTTT
50325792 ACTTGTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 9 0.32
12 11 0.39
13 4 0.14
14 4 0.14
ACGTcount: A:0.13, C:0.07, G:0.07, T:0.73
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:50325807 original size:42 final size:41
Alignment explanation
Indices: 50325730--50325810 Score: 101
Period size: 41 Copynumber: 2.0 Consensus size: 41
50325720 CATTAAACAC
* *
50325730 TTTTTTTTTCAGATTTTTTTTCTTTTCGAAATTTTTTTTGA
1 TTTTTTTTTCAGATTTTTTTTCTTGTAGAAATTTTTTTTGA
* *
50325771 TTTTTTTTTC-GAATTTTTTTTACTTGTATAACTTTTTTTT
1 TTTTTTTTTCAG-ATTTTTTTT-CTTGTAGAAATTTTTTTT
50325811 TGTACTATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
40 1 0.03
41 19 0.56
42 14 0.41
ACGTcount: A:0.15, C:0.07, G:0.06, T:0.72
Consensus pattern (41 bp):
TTTTTTTTTCAGATTTTTTTTCTTGTAGAAATTTTTTTTGA
Found at i:50327493 original size:30 final size:30
Alignment explanation
Indices: 50327459--50327555 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
50327449 TAAACTAAAA
50327459 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * *
50327489 TGAGCTAAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCTAA-GCTTTAGCTCGTGAGCTAAAGT
* *
50327519 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
50327549 TGAGCTA
1 TGAGCTA
50327556 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
29 1 0.02
30 46 0.88
31 5 0.10
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:50329206 original size:30 final size:30
Alignment explanation
Indices: 50329172--50329271 Score: 103
Period size: 30 Copynumber: 3.3 Consensus size: 30
50329162 TAAACTAAAA
* *
50329172 TGAGCTAAGCTTTAACTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAACTCGTGAGCTGAAGT
* * * * *
50329202 TGAGCTGAGATTAAACTCCTAAGCTGAAGC
1 TGAGCTAAGATTTAACTCGTGAGCTGAAGT
* *
50329232 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGATTTAACTCGTGAGCTGAAGT
50329261 ATGAGCTAAGA
1 -TGAGCTAAGA
50329272 GTGAGCTTGG
Statistics
Matches: 54, Mismatches: 15, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
30 54 1.00
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (30 bp):
TGAGCTAAGATTTAACTCGTGAGCTGAAGT
Found at i:50332833 original size:30 final size:30
Alignment explanation
Indices: 50332799--50332881 Score: 87
Period size: 30 Copynumber: 2.8 Consensus size: 30
50332789 TAAACTAAAA
50332799 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
50332829 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
50332859 TGAGCTAAGGTTTAGCTCGTGAG
1 TGAGCTAAGCTTTAGCTCGTGAG
50332882 TTGAAAGTGA
Statistics
Matches: 39, Mismatches: 12, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
29 2 0.05
30 34 0.87
31 3 0.08
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:50337538 original size:13 final size:12
Alignment explanation
Indices: 50337511--50337542 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
50337501 GTTCTTTTTG
50337511 TTTTTCAAAGGC
1 TTTTTCAAAGGC
50337523 TTTTTCAAAGGC
1 TTTTTCAAAGGC
*
50337535 CTTTTCAA
1 TTTTTCAA
50337543 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.44
Consensus pattern (12 bp):
TTTTTCAAAGGC
Found at i:50337600 original size:5 final size:5
Alignment explanation
Indices: 50337590--50337646 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
50337580 CTTTTGCCTC
*
50337590 TCTTT TCTTT T-TATT TCATTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
50337637 TCTTT TCTTT
1 TCTTT TCTTT
50337647 GTTTTCTCGT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:50337630 original size:15 final size:14
Alignment explanation
Indices: 50337590--50337646 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
50337580 CTTTTGCCTC
*
50337590 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
50337605 TCATTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
50337620 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
50337637 TCTTTTCTTT
1 TCTTTTCTTT
50337647 GTTTTCTCGT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:50337647 original size:21 final size:21
Alignment explanation
Indices: 50337590--50337651 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
50337580 CTTTTGCCTC
* *
50337590 TCTTTTCTTTT-TATTTCATTT
1 TCTTTTCTTTTCT-TTGCTTTT
*
50337611 TCTTTT-TCTTCTTTTGCTTTT
1 TCTTTTCTTTTC-TTTGCTTTT
50337632 TCTTTTCTTTTCTTTG-TTTT
1 TCTTTTCTTTTCTTTGCTTTT
50337652 CTCGTTACAA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
20 7 0.21
21 22 0.65
22 5 0.15
ACGTcount: A:0.03, C:0.16, G:0.03, T:0.77
Consensus pattern (21 bp):
TCTTTTCTTTTCTTTGCTTTT
Found at i:50338608 original size:33 final size:32
Alignment explanation
Indices: 50338573--50338633 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
50338563 CTATAAATTT
*
50338573 TTTTTTTA--ATTTTGAATTTTTTTTCTCTTTC
1 TTTTTTTACTATTTTG-ACTTTTTTTCTCTTTC
50338604 TTTTTTTACTATTTTGACTTTTTTTCTCTT
1 TTTTTTTACTATTTTGACTTTTTTTCTCTT
50338634 CAAATAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 8 0.30
32 13 0.48
33 6 0.22
ACGTcount: A:0.11, C:0.11, G:0.03, T:0.74
Consensus pattern (32 bp):
TTTTTTTACTATTTTGACTTTTTTTCTCTTTC
Found at i:50339899 original size:34 final size:33
Alignment explanation
Indices: 50339835--50339900 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
50339825 TTAAAGATGT
* *
50339835 TGTTCTACATGCATGGAACGGCAATTAATGAGA
1 TGTTCCACATGCATGGAACGACAATTAATGAGA
*
50339868 TGTTCCACATGCAATGG-ACGACATTTAAATGAG
1 TGTTCCACATGC-ATGGAACGACAATT-AATGAG
50339901 GGAGAGTGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 18 0.64
34 10 0.36
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (33 bp):
TGTTCCACATGCATGGAACGACAATTAATGAGA
Found at i:50342011 original size:33 final size:32
Alignment explanation
Indices: 50341969--50342030 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 32
50341959 GTACGAGCGA
**
50341969 GAAAAAGAAATCGAAAGAAAAGAAAAAGAGATT
1 GAAAAAGAAAAAGAAAGAAAA-AAAAAGAGATT
*
50342002 GAAAAAGAAAAAGAAATAAAAAAAAAGAG
1 GAAAAAGAAAAAGAAAGAAAAAAAAAGAG
50342031 TGAGGTCGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 8 0.31
33 18 0.69
ACGTcount: A:0.73, C:0.02, G:0.19, T:0.06
Consensus pattern (32 bp):
GAAAAAGAAAAAGAAAGAAAAAAAAAGAGATT
Found at i:50344264 original size:34 final size:33
Alignment explanation
Indices: 50344200--50344265 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
50344190 TTAAAGATGT
* *
50344200 TGTTCTACATGCATGGAACGGCAATTAATGAGA
1 TGTTCCACATGCATGGAACGACAATTAATGAGA
*
50344233 TGTTCCACATGCAATGG-ACGACATTTAAATGAG
1 TGTTCCACATGC-ATGGAACGACAATT-AATGAG
50344266 GGAGAGTGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 18 0.64
34 10 0.36
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (33 bp):
TGTTCCACATGCATGGAACGACAATTAATGAGA
Found at i:50348145 original size:20 final size:20
Alignment explanation
Indices: 50348099--50348145 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
50348089 AGCTCGTTTC
*
50348099 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
50348119 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
50348139 CAGCTCA
1 CAGCTCA
50348146 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:50354959 original size:30 final size:30
Alignment explanation
Indices: 50354925--50355021 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
50354915 TAAACTAAAA
50354925 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
50354955 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
50354985 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
50355015 TGAGCTA
1 TGAGCTA
50355022 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:50357553 original size:20 final size:20
Alignment explanation
Indices: 50357530--50357576 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
50357520 GGGTTAAGAT
*
50357530 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
50357550 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
50357570 TGAGCTG
1 TGAGCTG
50357577 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:50359300 original size:48 final size:48
Alignment explanation
Indices: 50359245--50359350 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
50359235 TTGTCTTTTC
*
50359245 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
50359293 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
50359341 TTTCTTTTTC
1 TTTCTTTTTC
50359351 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:50360523 original size:11 final size:11
Alignment explanation
Indices: 50360508--50360542 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
50360498 TTTTTGCTCG
50360508 ATTTTTTTTCA
1 ATTTTTTTTCA
* *
50360519 CTTTTTTTTGA
1 ATTTTTTTTCA
50360530 ATTTTTTTTCA
1 ATTTTTTTTCA
50360541 AT
1 AT
50360543 CAAATTTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.17, C:0.09, G:0.03, T:0.71
Consensus pattern (11 bp):
ATTTTTTTTCA
Found at i:50360523 original size:31 final size:29
Alignment explanation
Indices: 50360464--50360527 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 29
50360454 TTAAACTTGA
*
50360464 TTTTTTTTGCTCACCTTTTTTTTTCTTTTCT
1 TTTTTTTTGCTCA-CTTTTTTTTACTTTT-T
50360495 TTTTTTTTGCTCGA-TTTTTTTTCACTTTTT
1 TTTTTTTTGCTC-ACTTTTTTTT-ACTTTTT
50360525 TTT
1 TTT
50360528 GAATTTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 12 0.40
31 17 0.57
32 1 0.03
ACGTcount: A:0.05, C:0.16, G:0.05, T:0.75
Consensus pattern (29 bp):
TTTTTTTTGCTCACTTTTTTTTACTTTTT
Found at i:50362069 original size:20 final size:20
Alignment explanation
Indices: 50362046--50362092 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
50362036 GGGTTAAGAT
*
50362046 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
50362066 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
50362086 TGAGCTG
1 TGAGCTG
50362093 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:50363183 original size:30 final size:30
Alignment explanation
Indices: 50363131--50363215 Score: 84
Period size: 30 Copynumber: 2.8 Consensus size: 30
50363121 TTCTTTTGTT
* * *
50363131 TCAATTTCTTTTTC-ATCTTCTTTTTCACTC
1 TCAATTTCATTTTCGTTC-TCTTTTTCAATC
50363161 TCAAATTTC-TTTTCGTTCTCTTTTTCAATC
1 TC-AATTTCATTTTCGTTCTCTTTTTCAATC
* * *
50363191 TCATTTTCATTTTCTTTTTCTTTTT
1 TCAATTTCATTTTCGTTCTCTTTTT
50363216 GCTTTTCAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
29 5 0.11
30 34 0.72
31 8 0.17
ACGTcount: A:0.13, C:0.22, G:0.01, T:0.64
Consensus pattern (30 bp):
TCAATTTCATTTTCGTTCTCTTTTTCAATC
Found at i:50363305 original size:6 final size:5
Alignment explanation
Indices: 50363283--50363339 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
50363273 CTCTTGCCTC
*
50363283 TCTTT TCTTT T-TATT TCATTT TCTTT T-TCT TCATTT TCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TC-TTT TC-TTT TCTTT
50363330 TCTTT TCTTT
1 TCTTT TCTTT
50363340 GTTTTCTCTT
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 26 0.59
6 13 0.30
7 1 0.02
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:50363315 original size:15 final size:15
Alignment explanation
Indices: 50363285--50363328 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
50363275 CTTGCCTCTC
*
50363285 TTTTCTTTTTATTTCA
1 TTTTCTTTTT-CTTCA
50363301 TTTTCTTTTTCTTCA
1 TTTTCTTTTTCTTCA
50363316 TTTTCTTTTTCTT
1 TTTTCTTTTTCTT
50363329 TTCTTTTCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
15 17 0.63
16 10 0.37
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTCTTTTTCTTCA
Found at i:50363349 original size:16 final size:16
Alignment explanation
Indices: 50363281--50363350 Score: 74
Period size: 16 Copynumber: 4.4 Consensus size: 16
50363271 GCCTCTTGCC
*
50363281 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
50363297 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
50363313 TC-ATTTTCTTTTTCT
1 TCTCTTTTCTTTTTCT
*
50363328 TTTCTTTTCTTTGTT-T
1 TCTCTTTTCTTT-TTCT
50363344 TCTCTTT
1 TCTCTTT
50363351 ACAAGAATGT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
15 15 0.33
16 28 0.62
17 2 0.04
ACGTcount: A:0.04, C:0.19, G:0.01, T:0.76
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:50364279 original size:18 final size:18
Alignment explanation
Indices: 50364253--50364292 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
50364243 CATTAAACAC
*
50364253 TTTTTTTTTC-AGATTTT
1 TTTTTTTTTCAAAATTTT
50364270 TTTTTCTTTTCAAAATTTT
1 TTTTT-TTTTCAAAATTTT
50364289 TTTT
1 TTTT
50364293 GATTTGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 5 0.25
18 5 0.25
19 10 0.50
ACGTcount: A:0.15, C:0.07, G:0.03, T:0.75
Consensus pattern (18 bp):
TTTTTTTTTCAAAATTTT
Found at i:50366062 original size:30 final size:30
Alignment explanation
Indices: 50366028--50366124 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
50366018 TAAACTAAAA
50366028 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
50366058 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
50366088 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
50366118 TGAGCTA
1 TGAGCTA
50366125 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:50367281 original size:32 final size:32
Alignment explanation
Indices: 50367245--50367310 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
50367235 TCTATACCTA
50367245 TTCGGACCCTAAACTTGAACCTTCAATTATTC
1 TTCGGACCCTAAACTTGAACCTTCAATTATTC
50367277 TTCGGACCCTAAACTTGAACCTTCAATTATTC
1 TTCGGACCCTAAACTTGAACCTTCAATTATTC
50367309 TT
1 TT
50367311 ACCTATTCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.27, C:0.27, G:0.09, T:0.36
Consensus pattern (32 bp):
TTCGGACCCTAAACTTGAACCTTCAATTATTC
Found at i:50369746 original size:11 final size:11
Alignment explanation
Indices: 50369722--50369755 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
50369712 TATTTATTTC
*
50369722 TTTTTTTCACAA
1 TTTTTTTTA-AA
50369734 TTTTTTTTAAA
1 TTTTTTTTAAA
50369745 TTTTTTTTAAA
1 TTTTTTTTAAA
50369756 GATACGATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 13 0.62
12 8 0.38
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTTTTTTAAA
Found at i:50372118 original size:16 final size:16
Alignment explanation
Indices: 50372097--50372139 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
50372087 ATCGGTAAAA
*
50372097 GCTGAAATGCCGAAAT
1 GCTGAAAAGCCGAAAT
*
50372113 GCTGAAAAGTCGAAAT
1 GCTGAAAAGCCGAAAT
50372129 GGC-GAAAAGCC
1 -GCTGAAAAGCC
50372140 AAAAGTTTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 21 0.91
17 2 0.09
ACGTcount: A:0.40, C:0.19, G:0.28, T:0.14
Consensus pattern (16 bp):
GCTGAAAAGCCGAAAT
Found at i:50375098 original size:17 final size:18
Alignment explanation
Indices: 50375061--50375098 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
50375051 GATTGAGAGT
* *
50375061 GAAAAGGAATGTGAAACA
1 GAAAAGAAATGTGAAAAA
50375079 GAAAAGAAAT-TGAAAAA
1 GAAAAGAAATGTGAAAAA
50375096 GAA
1 GAA
50375099 GTTGAAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.63, C:0.03, G:0.24, T:0.11
Consensus pattern (18 bp):
GAAAAGAAATGTGAAAAA
Found at i:50375111 original size:13 final size:12
Alignment explanation
Indices: 50375080--50375134 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
50375070 TGTGAAACAG
*
50375080 AAAAGAAATTGA
1 AAAAGAAGTTGA
50375092 AAAAGAAGTTGA
1 AAAAGAAGTTGA
*
50375104 AGAAAGAAG-AGA
1 A-AAAGAAGTTGA
*
50375116 AAATG-AGTTAGA
1 AAAAGAAGTT-GA
50375128 AAAAGAA
1 AAAAGAA
50375135 ACAAAAGAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
10 2 0.06
11 3 0.09
12 21 0.62
13 8 0.24
ACGTcount: A:0.64, C:0.00, G:0.24, T:0.13
Consensus pattern (12 bp):
AAAAGAAGTTGA
Found at i:50378568 original size:29 final size:29
Alignment explanation
Indices: 50378523--50378582 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
50378513 ACAACCAAAC
*
50378523 CTACAAAAACTTTATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
50378552 CTACATAAAA-TTCATATCCATAAACCCAT
1 CTACA-AAAACTTCATATCCATAAACCCAT
50378581 CT
1 CT
50378583 TTGAATCCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 25 0.86
30 4 0.14
ACGTcount: A:0.43, C:0.28, G:0.00, T:0.28
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:50378807 original size:9 final size:9
Alignment explanation
Indices: 50378793--50378827 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
50378783 AGTAAGTTTA
*
50378793 AAAAAAATG
1 AAAAAAACG
50378802 AAAAAAACG
1 AAAAAAACG
50378811 AAAAAAAACG
1 -AAAAAAACG
50378821 AAAAAAA
1 AAAAAAA
50378828 TTTCAAACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 15 0.62
10 9 0.38
ACGTcount: A:0.83, C:0.06, G:0.09, T:0.03
Consensus pattern (9 bp):
AAAAAAACG
Found at i:50378807 original size:10 final size:10
Alignment explanation
Indices: 50378792--50378827 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
50378782 AAGTAAGTTT
*
50378792 AAAAAAAATG
1 AAAAAAAACG
50378802 -AAAAAAACG
1 AAAAAAAACG
50378811 AAAAAAAACG
1 AAAAAAAACG
50378821 AAAAAAA
1 AAAAAAA
50378828 TTTCAAACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.83, C:0.06, G:0.08, T:0.03
Consensus pattern (10 bp):
AAAAAAAACG
Done.