Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 176 of 427
Found at i:48954487 original size:10 final size:10
Alignment explanation
Indices: 48954472--48954498 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
48954462 TAAGTTGAAG
48954472 TTGAGCTGAT
1 TTGAGCTGAT
48954482 TTGAGCTGAT
1 TTGAGCTGAT
48954492 TTGAGCT
1 TTGAGCT
48954499 TGAAGGAGAA
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:0.19, C:0.11, G:0.30, T:0.41
Consensus pattern (10 bp):
TTGAGCTGAT
Found at i:48956465 original size:13 final size:13
Alignment explanation
Indices: 48956447--48956471 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48956437 GTATTGATCA
48956447 TGTGTTCACACCT
1 TGTGTTCACACCT
48956460 TGTGTTCACACC
1 TGTGTTCACACC
48956472 ATGATGACCA
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:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTGTTCACACCT
Found at i:48962365 original size:30 final size:30
Alignment explanation
Indices: 48962271--48962367 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
48962261 TAAACTAAAA
* * * *
48962271 TGAGCTAAGCTTTAGCTCGTGAGCTAAAAT
1 TGAGCTAAGGTTTAGCTCGTAAGCTGAAAG
* * * * *
48962301 TGAGCTGAGGCTAAACTCCTAAGCTG-AAG
1 TGAGCTAAGGTTTAGCTCGTAAGCTGAAAG
*
48962330 TTGAGCTAAGGTTTAGCTCGTAAGTTGAAAG
1 -TGAGCTAAGGTTTAGCTCGTAAGCTGAAAG
48962361 TGAGCTA
1 TGAGCTA
48962368 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 15, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
29 2 0.04
30 45 0.90
31 3 0.06
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTAAGCTGAAAG
Found at i:48968767 original size:11 final size:11
Alignment explanation
Indices: 48968743--48968783 Score: 57
Period size: 12 Copynumber: 3.7 Consensus size: 11
48968733 CATAAATCAC
*
48968743 TTTTTTTTC-T
1 TTTTTTTTCAA
48968753 TTTTTTTTCAA
1 TTTTTTTTCAA
48968764 TTTTTTTTCAAA
1 TTTTTTTTC-AA
48968776 TTTTTTTT
1 TTTTTTTT
48968784 AAACTTGTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
10 9 0.32
11 9 0.32
12 10 0.36
ACGTcount: A:0.12, C:0.07, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:48968767 original size:12 final size:12
Alignment explanation
Indices: 48968743--48968783 Score: 52
Period size: 10 Copynumber: 3.6 Consensus size: 12
48968733 CATAAATCAC
48968743 TTTTTTTTC--T
1 TTTTTTTTCAAT
48968753 TTTTTTTTCAA-
1 TTTTTTTTCAAT
48968764 TTTTTTTTCAAAT
1 TTTTTTTTC-AAT
48968777 TTTTTTT
1 TTTTTTT
48968784 AAACTTGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 9 0.33
11 9 0.33
12 2 0.07
13 7 0.26
ACGTcount: A:0.12, C:0.07, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTTTTTCAAT
Found at i:48972950 original size:14 final size:14
Alignment explanation
Indices: 48972931--48972975 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
48972921 AACTCATCTT
*
48972931 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
48972945 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
48972958 AATTTAATTTAATG
1 AGTTTAATTTAATG
48972972 AGTT
1 AGTT
48972976 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:48973726 original size:29 final size:29
Alignment explanation
Indices: 48973693--48973752 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
48973683 ATAACCAAAC
* *
48973693 CTACAAAAACTTTATATCCATAAATCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
48973722 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
48973751 CT
1 CT
48973753 TTGAATCCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:48973745 original size:15 final size:15
Alignment explanation
Indices: 48973699--48973746 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
48973689 AAACCTACAA
*
48973699 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
48973714 AAA-TCCATCTACAT
1 AAACTTCATATCCAT
48973728 AAACTTCATATCCAT
1 AAACTTCATATCCAT
48973743 AAAC
1 AAAC
48973747 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:0.25, G:0.00, T:0.31
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:48973990 original size:20 final size:21
Alignment explanation
Indices: 48973965--48974017 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
48973955 TCAAGTAAGT
48973965 TTCAAAAAAAATG-AAAAAAA
1 TTCAAAAAAAATGAAAAAAAA
*
48973985 TTCAAAAACAA-GAAAAAAAA
1 TTCAAAAAAAATGAAAAAAAA
48974005 TTCAAACAAAAAT
1 TTCAAA-AAAAAT
48974018 TCTGAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 1 0.04
20 23 0.82
21 4 0.14
ACGTcount: A:0.72, C:0.09, G:0.04, T:0.15
Consensus pattern (21 bp):
TTCAAAAAAAATGAAAAAAAA
Found at i:48975108 original size:18 final size:19
Alignment explanation
Indices: 48975065--48975110 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
48975055 CGAGAGAAGC
*
48975065 GAAAAAG-AGAAAGAATGT
1 GAAAAAGAAAAAAGAATGT
* *
48975083 GAACAAGAAAAAAGAGTG-
1 GAAAAAGAAAAAAGAATGT
48975101 GAAAAAGAAA
1 GAAAAAGAAA
48975111 TTGAGATAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.65, C:0.02, G:0.26, T:0.07
Consensus pattern (19 bp):
GAAAAAGAAAAAAGAATGT
Found at i:48977540 original size:14 final size:14
Alignment explanation
Indices: 48977521--48977565 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
48977511 AACTCATCTT
*
48977521 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
48977535 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
48977548 AATTTAATTTAATG
1 AGTTTAATTTAATG
48977562 AGTT
1 AGTT
48977566 GCTTTAATTA
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:48978310 original size:29 final size:29
Alignment explanation
Indices: 48978277--48978336 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
48978267 ATAACCAAAC
* *
48978277 CTACAAAAACTTTATATCCATAAATCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
48978306 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
48978335 CT
1 CT
48978337 TTGAATCCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:48978329 original size:15 final size:15
Alignment explanation
Indices: 48978283--48978330 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
48978273 AAACCTACAA
*
48978283 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
48978298 AAA-TCCATCTACAT
1 AAACTTCATATCCAT
48978312 AAACTTCATATCCAT
1 AAACTTCATATCCAT
48978327 AAAC
1 AAAC
48978331 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:0.25, G:0.00, T:0.31
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:48978792 original size:30 final size:30
Alignment explanation
Indices: 48978758--48978860 Score: 93
Period size: 30 Copynumber: 3.5 Consensus size: 30
48978748 AGCTCACTCC
48978758 TAGCTCATATTTAGCTCACGAGCTAAACCT
1 TAGCTCATATTTAGCTCACGAGCTAAACCT
** * * * * * *
48978788 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTTAGCTCACGAGCTAAACCT
* *
48978818 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
48978848 TAGCTCAT-TTTAG
1 TAGCTCATATTTAG
48978861 ATTAACTCGA
Statistics
Matches: 54, Mismatches: 17, Indels: 5
0.71 0.22 0.07
Matches are distributed among these distances:
29 5 0.09
30 49 0.91
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (30 bp):
TAGCTCATATTTAGCTCACGAGCTAAACCT
Found at i:48980397 original size:19 final size:19
Alignment explanation
Indices: 48980373--48980411 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
48980363 AGCTCCCATG
48980373 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
48980392 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
48980411 T
1 T
48980412 GATGCTCACG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:48982424 original size:20 final size:20
Alignment explanation
Indices: 48982401--48982511 Score: 58
Period size: 20 Copynumber: 5.5 Consensus size: 20
48982391 CTCACATTCT
48982401 TTTTCTTTTTCATCTTTTTC
1 TTTTCTTTTTCATCTTTTTC
**
48982421 TTTTCTTATTT--TCCTTTCAC
1 TTTTCTT-TTTCAT-CTTTTTC
48982441 TTTAT-TTTATT-A--TTTTTC
1 TTT-TCTTT-TTCATCTTTTTC
* *
48982459 CTCTCTTTTTC-TCATTTTTC
1 TTTTCTTTTTCATC-TTTTTC
48982479 TTTTCTTTTTACAT-TTTCATTC
1 TTTTCTTTTT-CATCTTT--TTC
48982501 TTTTCTTTTTC
1 TTTTCTTTTTC
48982512 TCTCATTTGA
Statistics
Matches: 69, Mismatches: 8, Indels: 27
0.66 0.08 0.26
Matches are distributed among these distances:
17 3 0.04
18 8 0.12
19 2 0.03
20 36 0.52
21 6 0.09
22 14 0.20
ACGTcount: A:0.09, C:0.20, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTCTTTTTCATCTTTTTC
Found at i:48984350 original size:30 final size:31
Alignment explanation
Indices: 48984316--48984412 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
48984306 AGCTCACTCC
*
48984316 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
48984346 TAGCTCAAC-TTCAGCTTAGGAGTTTAATCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
48984376 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
48984406 TAGCTCA
1 TAGCTCA
48984413 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
30 48 0.92
31 4 0.08
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:48988021 original size:30 final size:30
Alignment explanation
Indices: 48987936--48988032 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
48987926 TAAACTAAAA
* *
48987936 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
* ** * *
48987966 TGAGCTAAGATTAAAATCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
*
48987996 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
48988025 ATGAGCTA
1 -TGAGCTA
48988033 GGAGTGAGCT
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
Found at i:48990275 original size:30 final size:30
Alignment explanation
Indices: 48990204--48990286 Score: 82
Period size: 30 Copynumber: 2.7 Consensus size: 30
48990194 CTTTTGTTTC
*
48990204 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCACTCTCA
48990235 AATTTC-TTTTCGTTCTCTTTTTCGA-TCTC-
1 AATTTCTTTTTC-TTCTCTTTTTC-ACTCTCA
* *
48990264 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
48990287 GCTTTTCAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
29 5 0.11
30 31 0.69
31 9 0.20
ACGTcount: A:0.12, C:0.22, G:0.02, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCACTCTCA
Found at i:48990293 original size:12 final size:12
Alignment explanation
Indices: 48990262--48990286 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
48990252 TTTTTCGATC
48990262 TCATTTTCTTTT
1 TCATTTTCTTTT
48990274 TCATTTTCTTTT
1 TCATTTTCTTTT
48990286 T
1 T
48990287 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:48990365 original size:5 final size:5
Alignment explanation
Indices: 48990355--48990411 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
48990345 CTCTTGCCTC
*
48990355 TCTTT TCTTT T-TATT TCGTTT TCTTT T-TCT TCTTT TACTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
48990402 TCTTT TCTTT
1 TCTTT TCTTT
48990412 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:48990395 original size:15 final size:14
Alignment explanation
Indices: 48990355--48990411 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
48990345 CTCTTGCCTC
*
48990355 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
48990370 TCGTTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
48990385 TCTTTTACTTTTTCTTT
1 TCTTTT-CTTTTTC--T
48990402 TCTTTTCTTT
1 TCTTTTCTTT
48990412 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:48990421 original size:21 final size:20
Alignment explanation
Indices: 48990353--48990422 Score: 63
Period size: 20 Copynumber: 3.4 Consensus size: 20
48990343 GCCTCTTGCC
48990353 TCTCTTTTCTTTTTATTTCGTTT
1 TCTCTTTTC-TTTT-TTT-GTTT
**
48990376 TCT-TTTTCTTCTTTTACTTT
1 TCTCTTTTCTT-TTTTTGTTT
48990396 T-TCTTTTCTTTTCTTTGTTT
1 TCTCTTTTCTTTT-TTTGTTT
48990416 TCTCTTT
1 TCTCTTT
48990423 ACAAGAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
19 3 0.08
20 17 0.44
21 9 0.23
22 7 0.18
23 3 0.08
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.76
Consensus pattern (20 bp):
TCTCTTTTCTTTTTTTGTTT
Found at i:48991742 original size:14 final size:14
Alignment explanation
Indices: 48991708--48991755 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
48991698 GTACGAATGG
*
48991708 AATGGTAGGAACGA
1 AATGGTAGGAACAA
**
48991722 AGGGGTAGGAACAA
1 AATGGTAGGAACAA
*
48991736 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
48991750 ATTGGT
1 AATGGT
48991756 CGGTTAGGTT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.42, C:0.06, G:0.33, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:48992999 original size:19 final size:19
Alignment explanation
Indices: 48992975--48993011 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
48992965 TAAACTAAAA
* *
48992975 TGAGCTAAGGTTTAGCTCG
1 TGAGCTAAAGTTGAGCTCG
48992994 TGAGCTAAAGTTGAGCTC
1 TGAGCTAAAGTTGAGCTC
48993012 AGATTAAACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (19 bp):
TGAGCTAAAGTTGAGCTCG
Found at i:48993060 original size:30 final size:30
Alignment explanation
Indices: 48992975--48993071 Score: 115
Period size: 30 Copynumber: 3.2 Consensus size: 30
48992965 TAAACTAAAA
*
48992975 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
* * * * * *
48993005 TGAGCTCAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
48993035 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
48993064 ATGAGCTA
1 -TGAGCTA
48993072 GGAGTGAGCT
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Found at i:48993789 original size:13 final size:13
Alignment explanation
Indices: 48993771--48993795 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48993761 GTATTGATCA
48993771 TGTGTTCACACCT
1 TGTGTTCACACCT
48993784 TGTGTTCACACC
1 TGTGTTCACACC
48993796 ATGATGACCA
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:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTGTTCACACCT
Found at i:49000743 original size:30 final size:30
Alignment explanation
Indices: 49000672--49000754 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
49000662 CTTTTGTTTC
* *
49000672 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
49000703 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
49000732 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
49000755 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:0.13, C:0.22, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:49000754 original size:18 final size:18
Alignment explanation
Indices: 49000705--49000760 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
49000695 CACTCTCAAA
* *
49000705 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
49000722 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
49000740 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
49000759 TT
1 TT
49000761 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:49000761 original size:12 final size:12
Alignment explanation
Indices: 49000730--49000754 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
49000720 TTTTTCAATC
49000730 TCATTTTCTTTT
1 TCATTTTCTTTT
49000742 TCATTTTCTTTT
1 TCATTTTCTTTT
49000754 T
1 T
49000755 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:49000783 original size:11 final size:12
Alignment explanation
Indices: 49000757--49000787 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
49000747 TTCTTTTTGC
49000757 TTTTCAAAGGCT
1 TTTTCAAAGGCT
*
49000769 TTTTCAAAGGTT
1 TTTTCAAAGGCT
49000781 TTTTCAA
1 TTTTCAA
49000788 GTTCTCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:49000844 original size:5 final size:5
Alignment explanation
Indices: 49000834--49000890 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
49000824 CCTTTGCCTC
*
49000834 TCTTT TCTTT T-TATT TCGTTT TCTTT T-TCT TCTTT TGCCTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T--CTTT TCTTT
49000881 TCTTT TCTTT
1 TCTTT TCTTT
49000891 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 30 0.68
6 4 0.09
7 6 0.14
ACGTcount: A:0.02, C:0.19, G:0.04, T:0.75
Consensus pattern (5 bp):
TCTTT
Found at i:49000890 original size:15 final size:14
Alignment explanation
Indices: 49000834--49000897 Score: 65
Period size: 16 Copynumber: 4.2 Consensus size: 14
49000824 CCTTTGCCTC
49000834 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-TT
*
49000849 TCGTTTTCTTTTTCT
1 TC-TTTTCTTTTTTT
49000864 TCTTTTGCCTTTTCTTT
1 TCTTTT--CTTTT-TTT
*
49000881 TCTTTTCTTTGTTT
1 TCTTTTCTTTTTTT
49000895 TCT
1 TCT
49000898 CTTTACAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
14 10 0.24
15 9 0.21
16 15 0.36
17 8 0.19
ACGTcount: A:0.02, C:0.19, G:0.05, T:0.75
Consensus pattern (14 bp):
TCTTTTCTTTTTTT
Found at i:49000900 original size:21 final size:20
Alignment explanation
Indices: 49000832--49000901 Score: 63
Period size: 20 Copynumber: 3.4 Consensus size: 20
49000822 TGCCTTTGCC
49000832 TCTCTTTTCTTTTTATTTCGTTT
1 TCTCTTTTC-TTTT-TTT-GTTT
* *
49000855 TCT-TTTTCTTCTTTTGCCTT
1 TCTCTTTTCTTTTTTTG-TTT
49000875 T-TCTTTTCTTTTCTTTGTTT
1 TCTCTTTTCTTTT-TTTGTTT
49000895 TCTCTTT
1 TCTCTTT
49000902 ACAAAAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
19 2 0.05
20 17 0.44
21 12 0.31
22 5 0.13
23 3 0.08
ACGTcount: A:0.01, C:0.20, G:0.04, T:0.74
Consensus pattern (20 bp):
TCTCTTTTCTTTTTTTGTTT
Found at i:49000901 original size:42 final size:44
Alignment explanation
Indices: 49000808--49000901 Score: 108
Period size: 41 Copynumber: 2.2 Consensus size: 44
49000798 GATTCGCTCA
*
49000808 TTTTCTCTCTTACTTGCCTTTGCCTCTCTTTTCTTTTTATTTCG
1 TTTTCTCTTTTACTTGCCTTTGCCTCTCTTTTCTTTTTATTTCG
* * *
49000852 TTTTCT-TTTT-CTT-CTTTTGCCTTTTCTTTTC-TTTTCTTT-G
1 TTTTCTCTTTTACTTGCCTTTGCC-TCTCTTTTCTTTTTATTTCG
49000892 TTTTCTCTTT
1 TTTTCTCTTT
49000902 ACAAAAATGT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
40 7 0.16
41 17 0.39
42 11 0.25
43 3 0.07
44 6 0.14
ACGTcount: A:0.02, C:0.23, G:0.05, T:0.69
Consensus pattern (44 bp):
TTTTCTCTTTTACTTGCCTTTGCCTCTCTTTTCTTTTTATTTCG
Found at i:49003517 original size:30 final size:30
Alignment explanation
Indices: 49003483--49003579 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
49003473 TAAACTAAAA
* *
49003483 TGAGCTAAGCTTTAGCTTGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
* * * * * *
49003513 TGAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
* *
49003543 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGATTTAGCTCGTGAGCT-AAAGT
49003573 TGAGCTA
1 TGAGCTA
49003580 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
30 47 0.94
31 3 0.06
ACGTcount: A:0.29, C:0.13, G:0.28, T:0.30
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
Found at i:49003585 original size:11 final size:11
Alignment explanation
Indices: 49003571--49003600 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
49003561 GTGAGTTGAA
49003571 AGTGAGCTAGG
1 AGTGAGCTAGG
49003582 AGTGAGCTAGG
1 AGTGAGCTAGG
49003593 AGTGAGCT
1 AGTGAGCT
49003601 CGGTTTAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.27, C:0.10, G:0.43, T:0.20
Consensus pattern (11 bp):
AGTGAGCTAGG
Found at i:49004485 original size:14 final size:15
Alignment explanation
Indices: 49004466--49004500 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
49004456 TAAAGATAAC
49004466 AAGAAAACC-GAATA
1 AAGAAAACCAGAATA
*
49004480 AAGAAATCCAGAATA
1 AAGAAAACCAGAATA
49004495 AAGAAA
1 AAGAAA
49004501 CCCAAGATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.66, C:0.11, G:0.14, T:0.09
Consensus pattern (15 bp):
AAGAAAACCAGAATA
Found at i:49008143 original size:14 final size:14
Alignment explanation
Indices: 49008124--49008150 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
49008114 ATCTTTGCAA
49008124 GTGAAAAAAAATTC
1 GTGAAAAAAAATTC
49008138 GTGAAAAAAAATT
1 GTGAAAAAAAATT
49008151 GTTTAAGTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.04, G:0.15, T:0.22
Consensus pattern (14 bp):
GTGAAAAAAAATTC
Found at i:49010931 original size:42 final size:42
Alignment explanation
Indices: 49010862--49011037 Score: 151
Period size: 42 Copynumber: 4.0 Consensus size: 42
49010852 CTTCATTTTC
** * * *
49010862 TCGATGCCATAGTTCAAGTATGGTCTTAGACATCTTCACATAA
1 TCGATGCCATAGCCCAACTATGGTCTTACACATATTCACAT-A
* * *
49010905 T-GATGTCATAGCCCAGCTATGATCTTACACATATTCACATA
1 TCGATGCCATAGCCCAACTATGGTCTTACACATATTCACATA
*
49010946 TCGATGCCATGGCCCAACTATGGTCTTACACGTAATCACATATCACATA
1 TCGATGCCATAGCCCAACTATGGTCTTACAC---AT---AT-TCACATA
* *
49010995 TCGATGCCATAGCCCAGCTATGGCCTTACACGA-A-TCACATA
1 TCGATGCCATAGCCCAACTATGGTCTTACAC-ATATTCACATA
49011036 TC
1 TC
49011038 TCACTGATGT
Statistics
Matches: 109, Mismatches: 16, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
41 11 0.10
42 56 0.51
43 2 0.02
45 2 0.02
47 1 0.01
48 2 0.02
49 35 0.32
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (42 bp):
TCGATGCCATAGCCCAACTATGGTCTTACACATATTCACATA
Found at i:49011010 original size:49 final size:49
Alignment explanation
Indices: 49010932--49011189 Score: 224
Period size: 47 Copynumber: 5.2 Consensus size: 49
49010922 TATGATCTTA
* *
49010932 CACATATTCACATATCGATGCCATGGCCCAACTATGGTCTTACACGTAAT
1 CACATA-TCACATATCGATGCCATAGCCCAACTATGGTCTTATACGTAAT
* * *
49010982 CACATATCACATATCGATGCCATAGCCCAGCTATGGCCTTACACG-AAT
1 CACATATCACATATCGATGCCATAGCCCAACTATGGTCTTATACGTAAT
* * * * *
49011030 CACATATCTCA-CT-GATGTCATATCCCAGA-TATGGTCTTATACAGT-AG
1 CACATATCACATATCGATGCCATAGCCCA-ACTATGGTCTTATAC-GTAAT
* * * * * *
49011077 CATATATCAC--ACCGATGCCATATCCCAAATATGGTCTTATACGGAAG
1 CACATATCACATATCGATGCCATAGCCCAACTATGGTCTTATACGTAAT
* * *
49011124 CACATAATCACATCTCTCCGATGCTATAGCCCAACTATGGTCTTATACGGAAAT
1 CACAT-ATCACA--TAT-CGATGCCATAGCCCAACTATGGTCTTATAC-GTAAT
49011178 CACATATCACAT
1 CACATATCACAT
49011190 GTTGCCATGG
Statistics
Matches: 170, Mismatches: 25, Indels: 25
0.77 0.11 0.11
Matches are distributed among these distances:
46 25 0.15
47 43 0.25
48 18 0.11
49 36 0.21
50 6 0.04
51 1 0.01
53 33 0.19
54 8 0.05
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.27
Consensus pattern (49 bp):
CACATATCACATATCGATGCCATAGCCCAACTATGGTCTTATACGTAAT
Found at i:49011157 original size:53 final size:53
Alignment explanation
Indices: 49011088--49011189 Score: 152
Period size: 53 Copynumber: 1.9 Consensus size: 53
49011078 ATATATCACA
*
49011088 CCGATGCCATATCCCAAATATGGTCTTATACGG-AAGCACATAATCACATCTCT
1 CCGATGCCATAGCCCAAATATGGTCTTATACGGAAAGCACAT-ATCACATCTCT
* * *
49011141 CCGATGCTATAGCCCAACTATGGTCTTATACGGAAATCACATATCACAT
1 CCGATGCCATAGCCCAAATATGGTCTTATACGGAAAGCACATATCACAT
49011190 GTTGCCATGG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
53 37 0.84
54 7 0.16
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.26
Consensus pattern (53 bp):
CCGATGCCATAGCCCAAATATGGTCTTATACGGAAAGCACATATCACATCTCT
Found at i:49015395 original size:42 final size:42
Alignment explanation
Indices: 49015334--49015495 Score: 182
Period size: 42 Copynumber: 3.7 Consensus size: 42
49015324 TTGTTTTCTG
**
49015334 GATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAAT-
1 GATGCCATAGCCCAACTATGGTCTTACACATCTTCACAT-ATC
* * *
49015376 GATGCCATAGCCCAGCTATGATCTTACACATATTCACATATC
1 GATGCCATAGCCCAACTATGGTCTTACACATCTTCACATATC
*
49015418 GATGCCATGGCCCAACTATGGTCTTACACGTAATCACATATCACATATC
1 GATGCCATAGCCCAACTATGGTCTTACAC---AT--C-T-TCACATATC
*
49015467 GATGCCATAGCCCAGCTATGGTCTTACAC
1 GATGCCATAGCCCAACTATGGTCTTACAC
49015496 GAATCACGTA
Statistics
Matches: 101, Mismatches: 11, Indels: 9
0.83 0.09 0.07
Matches are distributed among these distances:
41 2 0.02
42 60 0.59
45 2 0.02
48 1 0.01
49 36 0.36
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (42 bp):
GATGCCATAGCCCAACTATGGTCTTACACATCTTCACATATC
Found at i:49015533 original size:46 final size:46
Alignment explanation
Indices: 49015375--49015665 Score: 177
Period size: 46 Copynumber: 6.2 Consensus size: 46
49015365 CTTCACATAA
* * * * * *
49015375 TGATGCCATAGCCCAGCTATGATCTTACACATATTCAC-AT-A-TC
1 TGATGCCATATCCCAGATATGGTCTTACACGTAATCACTATCACAC
** *
49015418 -GATGCCATGGCCCA-ACTATGGTCTTACACGTAATCACATATCACATA
1 TGATGCCATATCCCAGA-TATGGTCTTACACGTAATCAC-TATCACA-C
* * *
49015465 TCGATGCCATAGCCCAGCTATGGTCTTACACG-AATCACGTATCTCAC
1 T-GATGCCATATCCCAGATATGGTCTTACACGTAATCAC-TATCACAC
* *
49015512 TGATGCCATATCCCAGATATGGTCTTATATAGTAGAT-A-TATCACAC
1 TGATGCCATATCCCAGATATGGTCTTACA-CGTA-ATCACTATCACAC
* * *
49015558 TGATGCCATATCCCAGATATGGTCTTATACGGAAGCACATAATCACATCTC
1 TGATGCCATATCCCAGATATGGTCTTACACGTAATCAC-T-ATCACA---C
* * * * *
49015609 TCCGATGCCATAGCCCAGCTATGGTCTTATAGGAAATCACATATCACA-
1 T--GATGCCATATCCCAGATATGGTCTTACACGTAATCAC-TATCACAC
*
49015657 TGTTGCCAT
1 TGATGCCAT
49015666 GGTCCAACCA
Statistics
Matches: 201, Mismatches: 26, Indels: 39
0.76 0.10 0.15
Matches are distributed among these distances:
42 31 0.15
44 3 0.01
45 4 0.02
46 68 0.34
47 3 0.01
48 21 0.10
49 29 0.14
51 2 0.01
52 6 0.03
53 34 0.17
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.28
Consensus pattern (46 bp):
TGATGCCATATCCCAGATATGGTCTTACACGTAATCACTATCACAC
Found at i:49022226 original size:30 final size:30
Alignment explanation
Indices: 49022192--49022286 Score: 93
Period size: 30 Copynumber: 3.2 Consensus size: 30
49022182 AGCTCACTCC
*
49022192 TAGCTCACTTTCAACTCACGAGCTAAACCT
1 TAGCTCACTTTCAGCTCACGAGCTAAACCT
* * * * * * *
49022222 TAGCTCAATTTCAGCTTAGGAGTTTAGCTT
1 TAGCTCACTTTCAGCTCACGAGCTAAACCT
*
49022252 TAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTC-ACTTTCAGCTCACGAGCTAAACCT
49022282 TAGCT
1 TAGCT
49022287 TATTTTAGTT
Statistics
Matches: 48, Mismatches: 16, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
30 44 0.92
31 4 0.08
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (30 bp):
TAGCTCACTTTCAGCTCACGAGCTAAACCT
Found at i:49025495 original size:12 final size:12
Alignment explanation
Indices: 49025478--49025502 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
49025468 TTCCTATTTT
49025478 AATAGGAATGGG
1 AATAGGAATGGG
49025490 AATAGGAATGGG
1 AATAGGAATGGG
49025502 A
1 A
49025503 GTGGAACAAA
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:0.44, C:0.00, G:0.40, T:0.16
Consensus pattern (12 bp):
AATAGGAATGGG
Found at i:49027541 original size:30 final size:30
Alignment explanation
Indices: 49027507--49027609 Score: 93
Period size: 30 Copynumber: 3.5 Consensus size: 30
49027497 AGCTCACTCC
*
49027507 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTTAGCTCACGAGCTAAACCT
** * * * * *
49027537 TAGCTCAGCTTTAGCTTAGGAGTTTAATCT
1 TAGCTCATATTTAGCTCACGAGCTAAACCT
* *
49027567 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
49027597 TAGCTCAT-TTTAG
1 TAGCTCATATTTAG
49027610 TTTAACTCGA
Statistics
Matches: 55, Mismatches: 16, Indels: 5
0.72 0.21 0.07
Matches are distributed among these distances:
29 5 0.09
30 50 0.91
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (30 bp):
TAGCTCATATTTAGCTCACGAGCTAAACCT
Found at i:49029142 original size:14 final size:14
Alignment explanation
Indices: 49029095--49029142 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
49029085 GTACGAATGG
*
49029095 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
49029109 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
49029123 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
49029137 ATTGGT
1 AATGGT
49029143 CGGTTTAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:49036052 original size:14 final size:14
Alignment explanation
Indices: 49036005--49036052 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
49035995 GTACGAATGG
*
49036005 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
49036019 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
49036033 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
49036047 ATTGGT
1 AATGGT
49036053 CGGTTTAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:49037993 original size:17 final size:18
Alignment explanation
Indices: 49037971--49038013 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
49037961 ACATATTAAT
49037971 AACAAATATTAAT-ATAA
1 AACAAATATTAATGATAA
*
49037988 AACAAAT-TTAATGATTA
1 AACAAATATTAATGATAA
*
49038005 AATAAATAT
1 AACAAATAT
49038014 ATTCGAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 5 0.23
17 16 0.73
18 1 0.05
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (18 bp):
AACAAATATTAATGATAA
Found at i:49046016 original size:30 final size:30
Alignment explanation
Indices: 49045921--49046017 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
49045911 AGCTCATTCC
* *
49045921 TAGCTC-ACTTTCAACTCAAGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCAAGAGCTAAAGCT
* * * **
49045951 TAGCTCAACTTCAGCTTAGGAG-TTTAGCCT
1 TAGCTCAACTTTAGCTCAAGAGCTAAAG-CT
* *
49045981 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCAAGAGCTAAAGCT
49046011 TAGCTCA
1 TAGCTCA
49046018 TTTTAGTTTA
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 41 0.82
31 7 0.14
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCAAGAGCTAAAGCT
Found at i:49046066 original size:11 final size:11
Alignment explanation
Indices: 49046050--49046074 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
49046040 TCTTTAATGC
49046050 ATTAAATAAAA
1 ATTAAATAAAA
49046061 ATTAAATAAAA
1 ATTAAATAAAA
49046072 ATT
1 ATT
49046075 TGCACATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
ATTAAATAAAA
Found at i:49047081 original size:9 final size:10
Alignment explanation
Indices: 49047074--49047130 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
49047064 AAGAGAAAAC
49047074 AAAGAAAAGA
1 AAAGAAAAGA
49047084 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
49047096 AAAGAAGA-A
1 AAAGAAAAGA
49047105 AAAGAAAATGA
1 AAAGAAAA-GA
49047116 AATA-AAAAGA
1 AA-AGAAAAGA
49047126 AAAGA
1 AAAGA
49047131 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 9 0.23
10 9 0.23
11 15 0.38
12 6 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:49047097 original size:21 final size:20
Alignment explanation
Indices: 49047063--49047130 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
49047053 ACATTCTTGT
49047063 AAAGAGAAAA-CAAAGAAAAGA
1 AAAGA-AAAAGCAAA-AAAAGA
*
49047084 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAGCAAAAAAAG-A
* *
49047105 AAAGAAAATGAAATAAAAAGA
1 AAAGAAAAAGCAA-AAAAAGA
49047126 AAAGA
1 AAAGA
49047131 GAGGCAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 8 0.20
21 27 0.68
22 5 0.12
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (20 bp):
AAAGAAAAAGCAAAAAAAGA
Found at i:49047098 original size:6 final size:5
Alignment explanation
Indices: 49047074--49047130 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
49047064 AAGAGAAAAC
*
49047074 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
49047121 AAAGA AAAGA
1 AAAGA AAAGA
49047131 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 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:49047105 original size:15 final size:14
Alignment explanation
Indices: 49047074--49047130 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
49047064 AAGAGAAAAC
49047074 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
49047090 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
49047105 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
49047121 AAAGAAAAGA
1 AAAGAAAAGA
49047131 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:49047210 original size:11 final size:12
Alignment explanation
Indices: 49047178--49047208 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
49047168 TTGAGAGAAC
49047178 TTGAAAAAGCCT
1 TTGAAAAAGCCT
49047190 TTGAAAAAGCCT
1 TTGAAAAAGCCT
49047202 TTGAAAA
1 TTGAAAA
49047209 GCATAAAGAA
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:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:49047274 original size:30 final size:31
Alignment explanation
Indices: 49047213--49047281 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
49047203 TGAAAAGCAT
* *
49047213 AAAGAAA-ATGAGATTGAAAAAGAGAACG-A
1 AAAGAAATTTGAGAGTGAAAAAGAGAACGAA
*
49047242 AAAGAAATTTGAGAGTGAAAAAGA-AGATGAA
1 AAAGAAATTTGAGAGTGAAAAAGAGA-ACGAA
49047273 AAAGAAATT
1 AAAGAAATT
49047282 GAAACAAAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 8 0.24
30 16 0.47
31 10 0.29
ACGTcount: A:0.61, C:0.01, G:0.23, T:0.14
Consensus pattern (31 bp):
AAAGAAATTTGAGAGTGAAAAAGAGAACGAA
Found at i:49048195 original size:10 final size:10
Alignment explanation
Indices: 49048180--49048206 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
49048170 TACTCCTTCA
49048180 AGCTCAAATC
1 AGCTCAAATC
49048190 AGCTCAAATC
1 AGCTCAAATC
49048200 AGCTCAA
1 AGCTCAA
49048207 CTTCAACTTA
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:0.41, C:0.30, G:0.11, T:0.19
Consensus pattern (10 bp):
AGCTCAAATC
Found at i:49055019 original size:10 final size:10
Alignment explanation
Indices: 49055004--49055030 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
49054994 TACTCCTTCA
49055004 AGCTCAAATC
1 AGCTCAAATC
49055014 AGCTCAAATC
1 AGCTCAAATC
49055024 AGCTCAA
1 AGCTCAA
49055031 CTTCAACTTA
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:0.41, C:0.30, G:0.11, T:0.19
Consensus pattern (10 bp):
AGCTCAAATC
Found at i:49057917 original size:30 final size:30
Alignment explanation
Indices: 49057822--49057918 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
49057812 AGCTCATTCC
* * *
49057822 TAGCTC-ACTTTCAACTCACAAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAAGCT
* * * **
49057852 TAGCTCAACTTCAGCTTAGGAG-TTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAG-CT
*
49057882 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAGCT
49057912 TAGCTCA
1 TAGCTCA
49057919 TTTTAGTTTA
Statistics
Matches: 49, Mismatches: 15, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
29 2 0.04
30 40 0.82
31 7 0.14
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAAGCT
Found at i:49064571 original size:6 final size:6
Alignment explanation
Indices: 49064562--49064605 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
49064552 AAGTGAAATT
** * *
49064562 GAAAAA GAAAGT GAAAAA GAAAAA GAGAAG GAAAAA GAAAAA GA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GA
49064606 GATCGAGAGT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (6 bp):
GAAAAA
Found at i:49064606 original size:18 final size:19
Alignment explanation
Indices: 49064545--49064607 Score: 85
Period size: 18 Copynumber: 3.4 Consensus size: 19
49064535 AGAGAATGAG
* **
49064545 AAAAGAAAAGTGAAATTGA
1 AAAAGAGAAGTGAAAAAGA
49064564 AAAAGA-AAGTGAAAAAGA
1 AAAAGAGAAGTGAAAAAGA
49064582 AAAAGAGAAG-GAAAAAGA
1 AAAAGAGAAGTGAAAAAGA
49064600 AAAAGAGA
1 AAAAGAGA
49064608 TCGAGAGTGA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
18 32 0.78
19 9 0.22
ACGTcount: A:0.70, C:0.00, G:0.24, T:0.06
Consensus pattern (19 bp):
AAAAGAGAAGTGAAAAAGA
Found at i:49071147 original size:30 final size:30
Alignment explanation
Indices: 49071062--49071158 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
49071052 TAAACTAAAA
* *
49071062 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
* * * * * *
49071092 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
49071122 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
49071151 ATGAGCTA
1 -TGAGCTA
49071159 GGAGTGAGCT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
Found at i:49075250 original size:19 final size:19
Alignment explanation
Indices: 49075226--49075263 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
49075216 ATAACTAAAC
49075226 AATTTA-AAAGCAATAATTA
1 AATTTAGAAA-CAATAATTA
*
49075245 AATTTAGAAATAATAATTA
1 AATTTAGAAACAATAATTA
49075264 TAAGTCAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (19 bp):
AATTTAGAAACAATAATTA
Found at i:49084646 original size:30 final size:31
Alignment explanation
Indices: 49084575--49084648 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 31
49084565 CTTTTGTTTC
*
49084575 AATTTCTTTTTCATCTTCTTCTTCACTCTCA
1 AATTTCTTTTTCATCTTCTTCTTCAATCTCA
* *
49084606 AATTTC-TTTTCGT-TCTCTTTTTCAATCTC-
1 AATTTCTTTTTCATCT-TCTTCTTCAATCTCA
*
49084635 ATTTTCTTTTTCAT
1 AATTTCTTTTTCAT
49084649 TTTCCTTTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
29 6 0.17
30 24 0.67
31 6 0.17
ACGTcount: A:0.15, C:0.24, G:0.01, T:0.59
Consensus pattern (31 bp):
AATTTCTTTTTCATCTTCTTCTTCAATCTCA
Found at i:49084657 original size:18 final size:18
Alignment explanation
Indices: 49084608--49084663 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
49084598 CACTCTCAAA
* *
49084608 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
49084625 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
49084643 TTTCATTTTCCTTTTACTT
1 TTTCATTTTCATTTT-CTT
49084662 TT
1 TT
49084664 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:0.09, C:0.21, G:0.02, T:0.68
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:49084736 original size:5 final size:5
Alignment explanation
Indices: 49084726--49084782 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
49084716 CTCTTGCCTC
*
49084726 TCTTT TCTTT T-TATT TCATTT TCTTT T-TCT TCTTTT TCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TC-TTT TC-TTT TCTTT
49084773 TCTTT TCTTT
1 TCTTT TCTTT
49084783 ATTTTCTCTT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
4 4 0.09
5 26 0.58
6 14 0.31
7 1 0.02
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.79
Consensus pattern (5 bp):
TCTTT
Found at i:49087277 original size:30 final size:30
Alignment explanation
Indices: 49087243--49087338 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
49087233 TAAACTAAAA
49087243 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* ** * * *
49087273 TGAGCTGAGGC--TAAATCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
49087302 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
49087332 TGAGCTA
1 TGAGCTA
49087339 GGAGTGAGCT
Statistics
Matches: 48, Mismatches: 14, Indels: 8
0.69 0.20 0.11
Matches are distributed among these distances:
28 2 0.04
29 19 0.40
30 21 0.44
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:49089224 original size:42 final size:42
Alignment explanation
Indices: 49089176--49089272 Score: 176
Period size: 42 Copynumber: 2.3 Consensus size: 42
49089166 AGCCTCTTAG
49089176 AATAAATGAGTTGCTGATCATTAATACAACTCATCTTAGTTT
1 AATAAATGAGTTGCTGATCATTAATACAACTCATCTTAGTTT
*
49089218 AATAAATGAGTTGCTGGTCATTAATACAACTCATCTTAGTTT
1 AATAAATGAGTTGCTGATCATTAATACAACTCATCTTAGTTT
49089260 AATTAAATGAGTT
1 AA-TAAATGAGTT
49089273 TATTTAATGA
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
42 43 0.81
43 10 0.19
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.38
Consensus pattern (42 bp):
AATAAATGAGTTGCTGATCATTAATACAACTCATCTTAGTTT
Found at i:49089274 original size:14 final size:14
Alignment explanation
Indices: 49089255--49089299 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
49089245 AACTCATCTT
*
49089255 AGTTTAATTAAATG
1 AGTTTAATTTAATG
49089269 AGTTT-ATTTAATG
1 AGTTTAATTTAATG
*
49089282 AATTTAATTTAATG
1 AGTTTAATTTAATG
49089296 AGTT
1 AGTT
49089300 GCTTCTTGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:49090973 original size:25 final size:25
Alignment explanation
Indices: 49090943--49090991 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
49090933 GTAGGGCTTG
49090943 GTAAAGTGCTATTAAAGGGCTAATA
1 GTAAAGTGCTATTAAAGGGCTAATA
49090968 GTAAAGTGCTATTAAAGGGCTAAT
1 GTAAAGTGCTATTAAAGGGCTAAT
49090992 TTGATACGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.08, G:0.24, T:0.29
Consensus pattern (25 bp):
GTAAAGTGCTATTAAAGGGCTAATA
Found at i:49091194 original size:30 final size:30
Alignment explanation
Indices: 49091160--49091257 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
49091150 AGCTCACTCC
49091160 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
49091190 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * *
49091220 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
49091250 TAGCTCAT
1 TAGCTCAT
49091258 TTTAATTTAA
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:49092953 original size:16 final size:13
Alignment explanation
Indices: 49092908--49092969 Score: 70
Period size: 14 Copynumber: 4.5 Consensus size: 13
49092898 TATACAAGTT
49092908 AAAAAAAATCAAA
1 AAAAAAAATCAAA
* *
49092921 AAAAAAATTCCACA
1 AAAAAAAAT-CAAA
*
49092935 AAAAAAATTCGAAA
1 AAAAAAAATC-AAA
49092949 TAAAAAAAATCAAA
1 -AAAAAAAATCAAA
49092963 AAAAAAA
1 AAAAAAA
49092970 GGAAAAGAGT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
13 16 0.38
14 17 0.40
15 9 0.21
ACGTcount: A:0.77, C:0.10, G:0.02, T:0.11
Consensus pattern (13 bp):
AAAAAAAATCAAA
Found at i:49095637 original size:30 final size:30
Alignment explanation
Indices: 49095543--49095638 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
49095533 AGCTCACTCC
49095543 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * * *
49095573 T-GCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
49095602 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
49095632 TAGCTCA
1 TAGCTCA
49095639 TTTTAGTTTA
Statistics
Matches: 49, Mismatches: 15, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
29 21 0.43
30 28 0.57
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:49095991 original size:17 final size:16
Alignment explanation
Indices: 49095966--49095997 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
49095956 ATGTATTTGC
49095966 CAAAAACATGAATGCA
1 CAAAAACATGAATGCA
49095982 CAAAATACATGAATGC
1 CAAAA-ACATGAATGC
49095998 TTGGGTTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.53, C:0.19, G:0.12, T:0.16
Consensus pattern (16 bp):
CAAAAACATGAATGCA
Found at i:49096523 original size:30 final size:30
Alignment explanation
Indices: 49096489--49096572 Score: 80
Period size: 30 Copynumber: 2.8 Consensus size: 30
49096479 TAAACTAAAA
* *
49096489 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGC
* * * * * *
49096519 TGAGCTGAGATTAAACTCCTAAGCTGAAGC
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGC
*
49096549 TGAGC-AAGGTTTAGCTCGTGAGCT
1 TGAGCTAAGATTTAGCTCGTGAGCT
49096573 GAATATGAGC
Statistics
Matches: 40, Mismatches: 14, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
29 13 0.32
30 27 0.68
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.27
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTAAAGC
Found at i:49101409 original size:29 final size:29
Alignment explanation
Indices: 49101376--49101432 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
49101366 ATAACCAAAC
*
49101376 CTACAAAAACTTTATATCCATAAACCCAA
1 CTACAAAAACTTCATATCCATAAACCCAA
*
49101405 CTACATAAACTTCATATCCATAAACCCA
1 CTACAAAAACTTCATATCCATAAACCCA
49101433 TCTTTGAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.25
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAA
Found at i:49102622 original size:12 final size:12
Alignment explanation
Indices: 49102607--49102640 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
49102597 CTTGAAAGAG
* *
49102607 ATTGAGAAAGTC
1 ATTGAAAAAGCC
49102619 ATTGAAAAAGCC
1 ATTGAAAAAGCC
49102631 ATTGAAAAAG
1 ATTGAAAAAG
49102641 AAAAAGAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.50, C:0.09, G:0.21, T:0.21
Consensus pattern (12 bp):
ATTGAAAAAGCC
Found at i:49102772 original size:30 final size:28
Alignment explanation
Indices: 49102736--49102791 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
49102726 AAGCGAAAAA
* *
49102736 GAAAAAGAGTGTGTGCAAGAAAGTAAAGTT
1 GAAAAAGAGAGTGAGCAA-AAAG-AAAGTT
49102766 GAAAAAGAGAGTGAGCAAAAAGAAAG
1 GAAAAAGAGAGTGAGCAAAAAGAAAG
49102792 CGTGGAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 4 0.17
30 16 0.67
ACGTcount: A:0.54, C:0.04, G:0.30, T:0.12
Consensus pattern (28 bp):
GAAAAAGAGAGTGAGCAAAAAGAAAGTT
Found at i:49106044 original size:29 final size:29
Alignment explanation
Indices: 49106012--49106068 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
49106002 ATAACCAAAC
*
49106012 CTACAAAAACTTTATATCCATAAACCCAA
1 CTACAAAAACTTCATATCCATAAACCCAA
*
49106041 CTACATAAACTTCATATCCATAAACCCA
1 CTACAAAAACTTCATATCCATAAACCCA
49106069 TCTTTGAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.25
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAA
Found at i:49106347 original size:17 final size:19
Alignment explanation
Indices: 49106315--49106349 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
49106305 AAAAAAATTC
49106315 AAACAAAAATTCTGAAAAA
1 AAACAAAAATTCTGAAAAA
49106334 AAAC-AAAA-TCTGAAAA
1 AAACAAAAATTCTGAAAA
49106350 TTTGAACATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 4 0.25
19 4 0.25
ACGTcount: A:0.69, C:0.11, G:0.06, T:0.14
Consensus pattern (19 bp):
AAACAAAAATTCTGAAAAA
Found at i:49107622 original size:12 final size:11
Alignment explanation
Indices: 49107605--49107657 Score: 63
Period size: 11 Copynumber: 4.7 Consensus size: 11
49107595 CAAAAATCAC
49107605 TTTTTTTTCAA
1 TTTTTTTTCAA
49107616 TTTTTTTT-AGA
1 TTTTTTTTCA-A
* *
49107627 ATTTTTTTCGA
1 TTTTTTTTCAA
49107638 TTTTTTTTCGAA
1 TTTTTTTTC-AA
49107650 TTTTTTTT
1 TTTTTTTT
49107658 AACTTGTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
10 1 0.03
11 25 0.71
12 9 0.26
ACGTcount: A:0.15, C:0.06, G:0.06, T:0.74
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:49107631 original size:22 final size:22
Alignment explanation
Indices: 49107606--49107656 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
49107596 AAAAATCACT
49107606 TTTTTTTCAATTTTTTTTAGAA
1 TTTTTTTCAATTTTTTTTAGAA
* *
49107628 TTTTTTTCGATTTTTTTTCGAA
1 TTTTTTTCAATTTTTTTTAGAA
49107650 TTTTTTT
1 TTTTTTT
49107657 TAACTTGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.16, C:0.06, G:0.06, T:0.73
Consensus pattern (22 bp):
TTTTTTTCAATTTTTTTTAGAA
Found at i:49108040 original size:14 final size:14
Alignment explanation
Indices: 49108023--49108062 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
49108013 CGAATGGAGT
*
49108023 GGTAGGAACGAAAG
1 GGTAGGAACAAAAG
49108037 GGTAGGAACAAAAG
1 GGTAGGAACAAAAG
* *
49108051 GATATGAACAAA
1 GGTAGGAACAAA
49108063 TTGGTCGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.50, C:0.07, G:0.33, T:0.10
Consensus pattern (14 bp):
GGTAGGAACAAAAG
Found at i:49110902 original size:17 final size:17
Alignment explanation
Indices: 49110877--49110919 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
49110867 GAGACAGCCA
*
49110877 CCATACATGCACTTAAG
1 CCATTCATGCACTTAAG
* * *
49110894 CCATTCATGCATTTGAT
1 CCATTCATGCACTTAAG
49110911 CCATTCATG
1 CCATTCATG
49110920 GACTAGCCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.33
Consensus pattern (17 bp):
CCATTCATGCACTTAAG
Found at i:49111350 original size:30 final size:30
Alignment explanation
Indices: 49111316--49111398 Score: 78
Period size: 30 Copynumber: 2.8 Consensus size: 30
49111306 TAAACTAAAA
49111316 TGAGCTAAGCTTTAGCTCATGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCATGAGCTAAAGT
* * * * * *
49111346 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCATGAGCTAAAGT
* *
49111376 TGAGCTAAGGTTTAGCTCGTGAG
1 TGAGCTAAGCTTTAGCTCATGAG
49111399 TTGAATATGA
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:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCATGAGCTAAAGT
Found at i:49112165 original size:10 final size:10
Alignment explanation
Indices: 49112132--49112177 Score: 58
Period size: 10 Copynumber: 4.5 Consensus size: 10
49112122 AAAAAGGAAT
49112132 GAGCTGAAAC
1 GAGCTGAAAC
49112142 GAGCT-AAATTC
1 GAGCTGAAA--C
49112153 GAGCTGAAAC
1 GAGCTGAAAC
*
49112163 GAGCTAAAAC
1 GAGCTGAAAC
49112173 GAGCT
1 GAGCT
49112178 CAAGTGAGCT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
9 3 0.09
10 20 0.62
11 6 0.19
12 3 0.09
ACGTcount: A:0.39, C:0.20, G:0.26, T:0.15
Consensus pattern (10 bp):
GAGCTGAAAC
Found at i:49114116 original size:11 final size:11
Alignment explanation
Indices: 49114097--49114142 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
49114087 TCTCATGCTT
*
49114097 GGAAACTTCAA
1 GGAAGCTTCAA
49114108 GGAAGCTTCCAA
1 GGAAGCTT-CAA
*
49114120 GGACG-TTCAA
1 GGAAGCTTCAA
49114130 -GAAGCTTCAA
1 GGAAGCTTCAA
49114140 GGA
1 GGA
49114143 GGGTTCCAGC
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
9 3 0.10
10 8 0.28
11 11 0.38
12 7 0.24
ACGTcount: A:0.37, C:0.20, G:0.26, T:0.17
Consensus pattern (11 bp):
GGAAGCTTCAA
Found at i:49114148 original size:21 final size:22
Alignment explanation
Indices: 49114103--49114142 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
49114093 GCTTGGAAAC
49114103 TTCAAGGAAGCTTCCAAGGACG
1 TTCAAGGAAGCTTCCAAGGACG
49114125 TTCAA-GAAGCTT-CAAGGA
1 TTCAAGGAAGCTTCCAAGGA
49114143 GGGTTCCAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 7 0.39
22 5 0.28
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (22 bp):
TTCAAGGAAGCTTCCAAGGACG
Found at i:49114538 original size:42 final size:42
Alignment explanation
Indices: 49114479--49114584 Score: 203
Period size: 42 Copynumber: 2.5 Consensus size: 42
49114469 CATTTAAGCC
49114479 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
1 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
49114521 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
1 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
49114563 TCTTAGTTTAATTAAATGAGTT
1 TCTTAGTTTAA-TAAATGAGTT
49114585 TATTTAATGA
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 53 0.84
43 10 0.16
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (42 bp):
TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
Found at i:49114586 original size:14 final size:14
Alignment explanation
Indices: 49114567--49114611 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
49114557 AACTCATCTT
*
49114567 AGTTTAATTAAATG
1 AGTTTAATTTAATG
49114581 AGTTT-ATTTAATG
1 AGTTTAATTTAATG
*
49114594 AATTTAATTTAATG
1 AGTTTAATTTAATG
49114608 AGTT
1 AGTT
49114612 GCTTCTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:49115617 original size:29 final size:29
Alignment explanation
Indices: 49115584--49115643 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
49115574 ATAACCAAAC
* *
49115584 CTACAAAAACTTTATATCCATAAATCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
49115613 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
49115642 CT
1 CT
49115644 TTGAATCCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:49115636 original size:15 final size:15
Alignment explanation
Indices: 49115590--49115637 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
49115580 AAACCTACAA
*
49115590 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
49115605 AAA-TCCATCTACAT
1 AAACTTCATATCCAT
49115619 AAACTTCATATCCAT
1 AAACTTCATATCCAT
49115634 AAAC
1 AAAC
49115638 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:0.25, G:0.00, T:0.31
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:49115865 original size:12 final size:12
Alignment explanation
Indices: 49115848--49115893 Score: 74
Period size: 12 Copynumber: 3.8 Consensus size: 12
49115838 AGTAAGTTTC
49115848 AAAAAAAAATTG
1 AAAAAAAAATTG
*
49115860 AAAAAAAAATTC
1 AAAAAAAAATTG
49115872 AAAAAAAAATTTG
1 AAAAAAAAA-TTG
49115885 AAAAAAAAA
1 AAAAAAAAA
49115894 ACAAAATCTG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 20 0.65
13 11 0.35
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.15
Consensus pattern (12 bp):
AAAAAAAAATTG
Found at i:49115877 original size:24 final size:25
Alignment explanation
Indices: 49115845--49115893 Score: 91
Period size: 24 Copynumber: 2.0 Consensus size: 25
49115835 TCAAGTAAGT
49115845 TTCAAAAAAAAA-TTGAAAAAAAAA
1 TTCAAAAAAAAATTTGAAAAAAAAA
49115869 TTCAAAAAAAAATTTGAAAAAAAAA
1 TTCAAAAAAAAATTTGAAAAAAAAA
49115894 ACAAAATCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 12 0.50
25 12 0.50
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.18
Consensus pattern (25 bp):
TTCAAAAAAAAATTTGAAAAAAAAA
Found at i:49115898 original size:24 final size:24
Alignment explanation
Indices: 49115847--49115899 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
49115837 AAGTAAGTTT
*
49115847 CAAAAAAAAATTGAAAAAAAAATT
1 CAAAAAAAAATTGAAAAAAAAATA
49115871 CAAAAAAAAATTTGAAAAAAAAA-A
1 CAAAAAAAAA-TTGAAAAAAAAATA
49115895 CAAAA
1 CAAAA
49115900 TCTGAAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 15 0.56
25 12 0.44
ACGTcount: A:0.77, C:0.06, G:0.04, T:0.13
Consensus pattern (24 bp):
CAAAAAAAAATTGAAAAAAAAATA
Found at i:49118090 original size:21 final size:21
Alignment explanation
Indices: 49118026--49118099 Score: 50
Period size: 21 Copynumber: 3.6 Consensus size: 21
49118016 GAAAAAAATA
49118026 GAAAAAGAAAACAAAAGAG-AG
1 GAAAAAGAAAA-AAAAGAGAAG
**
49118047 TG-AAAAG-AAAATCAGTA-AA-
1 -GAAAAAGAAAAAAAAG-AGAAG
49118066 GAAAAAGAAAAAAAAGAGAAG
1 GAAAAAGAAAAAAAAGAGAAG
**
49118087 GAAATTGAAAAAA
1 GAAAAAGAAAAAA
49118100 TGAGTGTCTT
Statistics
Matches: 40, Mismatches: 6, Indels: 13
0.68 0.10 0.22
Matches are distributed among these distances:
18 1 0.03
19 9 0.22
20 13 0.32
21 16 0.40
22 1 0.03
ACGTcount: A:0.70, C:0.03, G:0.20, T:0.07
Consensus pattern (21 bp):
GAAAAAGAAAAAAAAGAGAAG
Found at i:49121181 original size:42 final size:42
Alignment explanation
Indices: 49121122--49121227 Score: 203
Period size: 42 Copynumber: 2.5 Consensus size: 42
49121112 CATTTAAGCC
49121122 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
1 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
49121164 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
1 TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
49121206 TCTTAGTTTAATTAAATGAGTT
1 TCTTAGTTTAA-TAAATGAGTT
49121228 TATTTAATGA
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 53 0.84
43 10 0.16
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (42 bp):
TCTTAGTTTAATAAATGAGTTGCTGGTCATTAATACAACTCA
Found at i:49121229 original size:14 final size:14
Alignment explanation
Indices: 49121210--49121254 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
49121200 AACTCATCTT
*
49121210 AGTTTAATTAAATG
1 AGTTTAATTTAATG
49121224 AGTTT-ATTTAATG
1 AGTTTAATTTAATG
*
49121237 AATTTAATTTAATG
1 AGTTTAATTTAATG
49121251 AGTT
1 AGTT
49121255 GCTTCTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:49122262 original size:29 final size:29
Alignment explanation
Indices: 49122229--49122288 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
49122219 ATAACCAAAC
* *
49122229 CTACAAAAACTTTATATCCATAAATCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
49122258 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
49122287 CT
1 CT
49122289 TTGAATCCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:49122281 original size:15 final size:15
Alignment explanation
Indices: 49122235--49122282 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
49122225 AAACCTACAA
*
49122235 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
49122250 AAA-TCCATCTACAT
1 AAACTTCATATCCAT
49122264 AAACTTCATATCCAT
1 AAACTTCATATCCAT
49122279 AAAC
1 AAAC
49122283 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:0.25, G:0.00, T:0.31
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:49127895 original size:24 final size:24
Alignment explanation
Indices: 49127851--49127896 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
49127841 GAAAGAGAGC
*
49127851 AAAAAGAGATCGAGATTGAAAAAG
1 AAAAAGAGATCGAGATAGAAAAAG
*
49127875 AAAAAGAG-TGCGAGCTAGAAAA
1 AAAAAGAGAT-CGAGATAGAAAA
49127897 GCATATCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 1 0.05
24 18 0.95
ACGTcount: A:0.57, C:0.07, G:0.26, T:0.11
Consensus pattern (24 bp):
AAAAAGAGATCGAGATAGAAAAAG
Found at i:49128332 original size:19 final size:20
Alignment explanation
Indices: 49128292--49128332 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
49128282 CCCATTTTTG
*
49128292 ATTTGTTGGAATAAGCATTTA
1 ATTTGCTGGAATAA-CATTTA
49128313 ATTTGCTGGAATAA-ATTTA
1 ATTTGCTGGAATAACATTTA
49128332 A
1 A
49128333 ATAATATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
21 13 0.68
ACGTcount: A:0.37, C:0.05, G:0.17, T:0.41
Consensus pattern (20 bp):
ATTTGCTGGAATAACATTTA
Found at i:49128430 original size:19 final size:19
Alignment explanation
Indices: 49128406--49128499 Score: 88
Period size: 19 Copynumber: 5.1 Consensus size: 19
49128396 AATAAATTAC
49128406 TCATCTTAGTTAATTAAGT
1 TCATCTTAGTTAATTAAGT
49128425 TCATCTTAGTTAATTAAGT
1 TCATCTTAGTTAATTAAGT
** * * *
49128444 TGC-T-GGAATAAATT-A-C
1 T-CATCTTAGTTAATTAAGT
49128460 TCATCTTAGTTAATTAAGT
1 TCATCTTAGTTAATTAAGT
* *
49128479 TCATTTTAGTTAATTTAGT
1 TCATCTTAGTTAATTAAGT
49128498 TC
1 TC
49128500 CTGGAACAAC
Statistics
Matches: 58, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
15 1 0.02
16 2 0.03
17 7 0.12
18 7 0.12
19 40 0.69
20 1 0.02
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.47
Consensus pattern (19 bp):
TCATCTTAGTTAATTAAGT
Found at i:49128442 original size:54 final size:54
Alignment explanation
Indices: 49128380--49128505 Score: 225
Period size: 54 Copynumber: 2.3 Consensus size: 54
49128370 TATAGTTTAA
49128380 TTAATTAAGTTGCTGGAATAAATTACTCATCTTAGTTAATTAAGTTCATCTTAG
1 TTAATTAAGTTGCTGGAATAAATTACTCATCTTAGTTAATTAAGTTCATCTTAG
*
49128434 TTAATTAAGTTGCTGGAATAAATTACTCATCTTAGTTAATTAAGTTCATTTTAG
1 TTAATTAAGTTGCTGGAATAAATTACTCATCTTAGTTAATTAAGTTCATCTTAG
* *
49128488 TTAATTTAGTTCCTGGAA
1 TTAATTAAGTTGCTGGAA
49128506 CAACTTAGTG
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 69 1.00
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.44
Consensus pattern (54 bp):
TTAATTAAGTTGCTGGAATAAATTACTCATCTTAGTTAATTAAGTTCATCTTAG
Found at i:49128916 original size:19 final size:19
Alignment explanation
Indices: 49128892--49128931 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
49128882 AGCTCCCATG
49128892 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
49128911 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
49128930 TA
1 TA
49128932 TCAGTTCACG
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:49129188 original size:14 final size:14
Alignment explanation
Indices: 49129171--49129210 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
49129161 CGAATGGAAT
*
49129171 GGTAGGAACGAAAG
1 GGTAGGAACAAAAG
49129185 GGTAGGAACAAAAG
1 GGTAGGAACAAAAG
* *
49129199 GATATGAACAAA
1 GGTAGGAACAAA
49129211 TTGGTCAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.50, C:0.07, G:0.33, T:0.10
Consensus pattern (14 bp):
GGTAGGAACAAAAG
Found at i:49134568 original size:30 final size:30
Alignment explanation
Indices: 49134482--49134579 Score: 97
Period size: 30 Copynumber: 3.3 Consensus size: 30
49134472 TTAAACTAAA
* *
49134482 ATGAGCTAAGCTTTAGCTCGTGAGCTAAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * * * * *
49134512 TTGAGCTGAGATTAAACTCCTAAGCTGAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * *
49134542 CTGAGCTAAGGTTTAGCTCGTGAGCTGAAT
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
49134572 ATGAGCTA
1 ATGAGCTA
49134580 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
Found at i:49136862 original size:30 final size:30
Alignment explanation
Indices: 49136791--49136873 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
49136781 CTTTTGTTTC
* *
49136791 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
49136822 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
49136851 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
49136874 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:0.13, C:0.22, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:49136873 original size:18 final size:18
Alignment explanation
Indices: 49136824--49136879 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
49136814 CACTCTCAAA
* *
49136824 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
49136841 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
49136859 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
49136878 TT
1 TT
49136880 CAAAGACTTT
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:49136880 original size:12 final size:12
Alignment explanation
Indices: 49136849--49136873 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
49136839 TTTTTCAATC
49136849 TCATTTTCTTTT
1 TCATTTTCTTTT
49136861 TCATTTTCTTTT
1 TCATTTTCTTTT
49136873 T
1 T
49136874 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:49136891 original size:12 final size:12
Alignment explanation
Indices: 49136876--49136906 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
49136866 TTCTTTTTGC
49136876 TTTTCAAAGACT
1 TTTTCAAAGACT
*
49136888 TTTTCAAAGGCT
1 TTTTCAAAGACT
49136900 TTTTCAA
1 TTTTCAA
49136907 GTTCTCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.29, C:0.16, G:0.10, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGACT
Found at i:49136964 original size:5 final size:5
Alignment explanation
Indices: 49136954--49137010 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
49136944 CTCTTGCCTC
*
49136954 TCTTT TCTTT T-TATT TCGTTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
49137001 TCTTT TCTTT
1 TCTTT TCTTT
49137011 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:0.02, C:0.18, G:0.04, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:49136994 original size:15 final size:14
Alignment explanation
Indices: 49136954--49137010 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
49136944 CTCTTGCCTC
*
49136954 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
49136969 TCGTTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
49136984 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
49137001 TCTTTTCTTT
1 TCTTTTCTTT
49137011 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:0.02, C:0.18, G:0.04, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:49137011 original size:21 final size:21
Alignment explanation
Indices: 49136954--49137021 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
49136944 CTCTTGCCTC
* *
49136954 TCTTTTCTTTT-TATTTCGTTT
1 TCTTTTCTTTTCT-TTGCTTTT
*
49136975 TCTTTT-TCTTCTTTTGCTTTT
1 TCTTTTCTTTTC-TTTGCTTTT
49136996 TCTTTTCTTTTCTTTG-TTTT
1 TCTTTTCTTTTCTTTGCTTTT
49137016 CTCTTT
1 -TCTTT
49137022 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:0.01, C:0.18, G:0.04, T:0.76
Consensus pattern (21 bp):
TCTTTTCTTTTCTTTGCTTTT
Found at i:49137948 original size:11 final size:11
Alignment explanation
Indices: 49137932--49137982 Score: 77
Period size: 11 Copynumber: 4.6 Consensus size: 11
49137922 CTCTTTTTCT
49137932 TTTTTTTCGAA
1 TTTTTTTCGAA
49137943 TTTTTTTCGAA
1 TTTTTTTCGAA
49137954 TTTTTTTTCGAA
1 -TTTTTTTCGAA
*
49137966 TTTTTTTTG-A
1 TTTTTTTCGAA
49137976 TTTTTTT
1 TTTTTTT
49137983 TAACTTGTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
10 8 0.21
11 19 0.50
12 11 0.29
ACGTcount: A:0.14, C:0.06, G:0.08, T:0.73
Consensus pattern (11 bp):
TTTTTTTCGAA
Found at i:49137948 original size:12 final size:12
Alignment explanation
Indices: 49137931--49137983 Score: 85
Period size: 12 Copynumber: 4.7 Consensus size: 12
49137921 ACTCTTTTTC
49137931 TTTTTTTTCGAA
1 TTTTTTTTCGAA
49137943 -TTTTTTTCGAA
1 TTTTTTTTCGAA
49137954 TTTTTTTTCGAA
1 TTTTTTTTCGAA
49137966 TTTTTTTT-G-A
1 TTTTTTTTCGAA
49137976 TTTTTTTT
1 TTTTTTTT
49137984 AACTTGTATA
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
10 9 0.22
11 12 0.30
12 19 0.47
ACGTcount: A:0.13, C:0.06, G:0.08, T:0.74
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:49137961 original size:23 final size:22
Alignment explanation
Indices: 49137931--49137983 Score: 88
Period size: 23 Copynumber: 2.4 Consensus size: 22
49137921 ACTCTTTTTC
49137931 TTTTTTTTCGAATTTTTTTCGAA
1 TTTTTTTTCGAATTTTTTTCG-A
*
49137954 TTTTTTTTCGAATTTTTTTTGA
1 TTTTTTTTCGAATTTTTTTCGA
49137976 TTTTTTTT
1 TTTTTTTT
49137984 AACTTGTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 9 0.31
23 20 0.69
ACGTcount: A:0.13, C:0.06, G:0.08, T:0.74
Consensus pattern (22 bp):
TTTTTTTTCGAATTTTTTTCGA
Found at i:49139717 original size:30 final size:30
Alignment explanation
Indices: 49139631--49139728 Score: 97
Period size: 30 Copynumber: 3.3 Consensus size: 30
49139621 TTAAACTAAA
* *
49139631 ATGAGCTAAGCTTTAGCTCGTGAGCTAAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * * * * *
49139661 TTGAGCTGAGATTAAACTCCTAAGCTGAAG
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
* * *
49139691 CTGAGCTAAGGTTTAGCTCGTGAGCTGAAT
1 ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
49139721 ATGAGCTA
1 ATGAGCTA
49139729 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
ATGAGCTAAGATTTAGCTCGTGAGCTGAAG
Done.