Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr14
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: 244914714
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 4503000 characters in sequence are not A, C, G, or T
File 62 of 770
Found at i:18063492 original size:20 final size:20
Alignment explanation
Indices: 18063449--18063492 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
18063439 AGCTCAACTT
**
18063449 AGCTCATTTGAGCTCGTTCC
1 AGCTCATTTGAGCTCAATCC
* *
18063469 AGCTCGTTTGAGCTCAATCG
1 AGCTCATTTGAGCTCAATCC
18063489 AGCT
1 AGCT
18063493 TACTTTCAGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.18, C:0.27, G:0.23, T:0.32
Consensus pattern (20 bp):
AGCTCATTTGAGCTCAATCC
Found at i:18067796 original size:30 final size:30
Alignment explanation
Indices: 18067725--18067807 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
18067715 CTTTTGTTTC
* *
18067725 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
18067756 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
18067785 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
18067808 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:18067807 original size:18 final size:18
Alignment explanation
Indices: 18067758--18067813 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
18067748 CACTCTCAAA
* *
18067758 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
18067775 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
18067793 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
18067812 TT
1 TT
18067814 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:18067814 original size:12 final size:12
Alignment explanation
Indices: 18067783--18067807 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18067773 TTTTTCAATC
18067783 TCATTTTCTTTT
1 TCATTTTCTTTT
18067795 TCATTTTCTTTT
1 TCATTTTCTTTT
18067807 T
1 T
18067808 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:18067825 original size:12 final size:12
Alignment explanation
Indices: 18067810--18067840 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
18067800 TTCTTTTTGC
18067810 TTTTCAAAGGCT
1 TTTTCAAAGGCT
*
18067822 TTTTGAAAGGCT
1 TTTTCAAAGGCT
18067834 TTTTCAA
1 TTTTCAA
18067841 GTTCTCTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.26, C:0.13, G:0.16, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:18067898 original size:5 final size:5
Alignment explanation
Indices: 18067888--18067951 Score: 53
Period size: 5 Copynumber: 12.6 Consensus size: 5
18067878 CTCTTGCCTC
*
18067888 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
*
18067935 TCTTT T-TTT TGTTT TCT
1 TCTTT TCTTT TCTTT TCT
18067952 CTTTACAAGA
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
4 8 0.16
5 30 0.61
6 6 0.12
7 5 0.10
ACGTcount: A:0.02, C:0.16, G:0.05, T:0.78
Consensus pattern (5 bp):
TCTTT
Found at i:18067954 original size:21 final size:21
Alignment explanation
Indices: 18067886--18067955 Score: 83
Period size: 20 Copynumber: 3.3 Consensus size: 21
18067876 GCCTCTTGCC
18067886 TCTCTTTTCTTTTTATTTCGTTT
1 TCTCTTTTCTTTTT-TTT-GTTT
*
18067909 TCT-TTTTC-TTCTTTTGCTTT
1 TCTCTTTTCTTTTTTTTG-TTT
18067929 T-TCTTTTCTTTTTTTTGTTT
1 TCTCTTTTCTTTTTTTTGTTT
18067949 TCTCTTT
1 TCTCTTT
18067956 ACAAGAATGT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
19 2 0.05
20 16 0.39
21 15 0.37
22 5 0.12
23 3 0.07
ACGTcount: A:0.01, C:0.17, G:0.04, T:0.77
Consensus pattern (21 bp):
TCTCTTTTCTTTTTTTTGTTT
Found at i:18070588 original size:30 final size:30
Alignment explanation
Indices: 18070554--18070650 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
18070544 TAAACTAAAA
*
18070554 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
* * * * * * *
18070584 TGAGCTGAGATTAAACTCCTAAGCTGAAGC
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
*
18070614 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
18070643 ATGAGCTA
1 -TGAGCTA
18070651 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTAAAGT
Found at i:18078520 original size:15 final size:15
Alignment explanation
Indices: 18078502--18078535 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
18078492 GAAAGTTGTA
18078502 AAAAATAA-AAAAGAG
1 AAAAATAAGAAAA-AG
18078517 AAAAATAAGAAAAAG
1 AAAAATAAGAAAAAG
18078532 AAAA
1 AAAA
18078536 CAAAAGAGAG
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:0.82, C:0.00, G:0.12, T:0.06
Consensus pattern (15 bp):
AAAAATAAGAAAAAG
Found at i:18081562 original size:10 final size:10
Alignment explanation
Indices: 18081547--18081573 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
18081537 TACTCCTTCA
18081547 AGCTCAAATC
1 AGCTCAAATC
18081557 AGCTCAAATC
1 AGCTCAAATC
18081567 AGCTCAA
1 AGCTCAA
18081574 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:18082858 original size:30 final size:30
Alignment explanation
Indices: 18082773--18082869 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
18082763 TAAACTAAAA
* *
18082773 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
* * * * * *
18082803 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
18082833 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAGT
18082862 ATGAGCTA
1 -TGAGCTA
18082870 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:18086982 original size:27 final size:27
Alignment explanation
Indices: 18086952--18087004 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
18086942 CCCAAATTGA
18086952 TAAAATGACTGTTATGCCCCTATGAGG
1 TAAAATGACTGTTATGCCCCTATGAGG
*
18086979 TAAAATGACTGTTATGCCCTTATGAG
1 TAAAATGACTGTTATGCCCCTATGAG
18087005 ATGTATGACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (27 bp):
TAAAATGACTGTTATGCCCCTATGAGG
Found at i:18095286 original size:13 final size:14
Alignment explanation
Indices: 18095268--18095304 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
18095258 ATAAATCACT
18095268 TTTTTTTTTC-GAA
1 TTTTTTTTTCGGAA
18095281 TTTTTTTTTCGGAA
1 TTTTTTTTTCGGAA
18095295 TTTTTTTTTC
1 TTTTTTTTTC
18095305 AAACTTGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.11, C:0.08, G:0.08, T:0.73
Consensus pattern (14 bp):
TTTTTTTTTCGGAA
Found at i:18095286 original size:14 final size:15
Alignment explanation
Indices: 18095267--18095303 Score: 60
Period size: 13 Copynumber: 2.6 Consensus size: 15
18095257 CATAAATCAC
18095267 TTTTTTTTTTC-GAA
1 TTTTTTTTTTCGGAA
18095281 -TTTTTTTTTCGGAA
1 TTTTTTTTTTCGGAA
18095295 TTTTTTTTT
1 TTTTTTTTT
18095304 CAAACTTGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 10 0.48
14 3 0.14
15 8 0.38
ACGTcount: A:0.11, C:0.05, G:0.08, T:0.76
Consensus pattern (15 bp):
TTTTTTTTTTCGGAA
Found at i:18101338 original size:48 final size:48
Alignment explanation
Indices: 18101258--18101387 Score: 165
Period size: 48 Copynumber: 2.8 Consensus size: 48
18101248 GGAATGAAAA
**
18101258 AACGTGGTGCTAAGTGGATATACCACAATTACACATATTAATACATGT
1 AACGTGGTGCTAAGTGGATATACCACGGTTACACATATTAATACATGT
* * * *
18101306 AACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCAT-T
1 AACGTGGTGCTAAGTGGATATACCACGGTTACACATATTAATACATGT
* * *
18101353 AATGTAGTGCTAAG-GGATATACCACGGTTAAACAT
1 AACGTGGTGCTAAGTGGATATACCACGGTTACACAT
18101388 GTAACGTGGT
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
46 18 0.25
47 13 0.18
48 40 0.56
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (48 bp):
AACGTGGTGCTAAGTGGATATACCACGGTTACACATATTAATACATGT
Found at i:18103348 original size:19 final size:19
Alignment explanation
Indices: 18103303--18103348 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
18103293 ATTAACACAC
*
18103303 AATTAATTAAAATATAACT
1 AATTAATAAAAATATAACT
*
18103322 -ATTCATAAAAATCATAA-T
1 AATTAATAAAAAT-ATAACT
18103340 AATTAATAA
1 AATTAATAA
18103349 TTAAACAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.35
Consensus pattern (19 bp):
AATTAATAAAAATATAACT
Found at i:18105216 original size:18 final size:19
Alignment explanation
Indices: 18105193--18105231 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
18105183 TTTATCTTAA
*
18105193 TTTCTTTTTC-CACTCTTT
1 TTTCTTGTTCACACTCTTT
*
18105211 TTTCTTGTTCACATTCTTT
1 TTTCTTGTTCACACTCTTT
18105230 TT
1 TT
18105232 CTCTCTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.08, C:0.23, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTCTTGTTCACACTCTTT
Found at i:18105294 original size:18 final size:18
Alignment explanation
Indices: 18105253--18105298 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
18105243 TCTTTTTCAT
* *
18105253 TCTCTTTTTCAATCTTAT
1 TCTCTTTTTCAATCTCAA
* *
18105271 TTTCTTTTTCACTCTCAA
1 TCTCTTTTTCAATCTCAA
18105289 TCTCTTTTTC
1 TCTCTTTTTC
18105299 TTTTTCTTTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.13, C:0.26, G:0.00, T:0.61
Consensus pattern (18 bp):
TCTCTTTTTCAATCTCAA
Found at i:18111417 original size:30 final size:31
Alignment explanation
Indices: 18111383--18111480 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
18111373 AGCTCACTCC
*
18111383 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
18111413 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * *
18111443 CAGCTCAACTTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
18111474 TAGCTCA
1 TAGCTCA
18111481 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
30 29 0.57
31 22 0.43
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.29
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:18111984 original size:13 final size:13
Alignment explanation
Indices: 18111966--18111990 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18111956 GTATTGATCA
18111966 TGTGTTCACACCT
1 TGTGTTCACACCT
18111979 TGTGTTCACACC
1 TGTGTTCACACC
18111991 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:18116324 original size:20 final size:21
Alignment explanation
Indices: 18116301--18116347 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
18116291 TCAGCTCCCA
*
18116301 TCAGCTTACTTGAGCTCG-AT
1 TCAGCTTACTTGAGCTAGAAT
**
18116321 TCAGCTTGTTTGAGCTAGAAT
1 TCAGCTTACTTGAGCTAGAAT
18116342 TCAGCT
1 TCAGCT
18116348 CAATCTAGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (21 bp):
TCAGCTTACTTGAGCTAGAAT
Found at i:18120424 original size:47 final size:49
Alignment explanation
Indices: 18120257--18120433 Score: 173
Period size: 50 Copynumber: 3.6 Consensus size: 49
18120247 CATGTGAGCT
* * * * * **
18120257 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACGGAAAGAGGAGAACC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGCCTC-GATATAAGAGAGTC
*
18120307 AGTGTAAGACCATGTCTGGGATATGGCATCGGCCTCGATATAAGAGAGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATC-GCCTCGATATAAGAGAGTC
* * * *
18120357 AGTGTAAGACCATGTTTGGGACATGGCATC-CACTC-A-ATATGTGATTAC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGC-CTCGATATAAGAGAGT-C
18120405 A-TGTAAGACCATGTCTGGGACATTGGCAT
1 AGTGTAAGACCATGTCTGGGACA-TGGCAT
18120434 TGTATTGTGA
Statistics
Matches: 109, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
47 27 0.25
48 10 0.09
49 3 0.03
50 66 0.61
51 3 0.03
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (49 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGCCTCGATATAAGAGAGTC
Found at i:18120457 original size:43 final size:42
Alignment explanation
Indices: 18120396--18120522 Score: 148
Period size: 43 Copynumber: 3.0 Consensus size: 42
18120386 CCACTCAATA
*
18120396 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
1 TGTGATTACATGTAAGACCATGTCTGGGATA-TGGCATTGTAT
* * * *
18120439 TGTGATTTCGTGTAAGACCATGTGTGGGATAGTGGCATCGATAT
1 TGTGATTACATGTAAGACCATGTCTGGGATA-TGGCATTG-TAT
* * *
18120483 T-TGATAACATGTAAGACCATATCTAGGATATGGCATTGTA
1 TGTGATTACATGTAAGACCATGTCTGGGATATGGCATTGTA
18120523 CGAGCTATAT
Statistics
Matches: 70, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
41 2 0.03
42 7 0.10
43 57 0.81
44 4 0.06
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.34
Consensus pattern (42 bp):
TGTGATTACATGTAAGACCATGTCTGGGATATGGCATTGTAT
Found at i:18125730 original size:29 final size:29
Alignment explanation
Indices: 18125687--18125795 Score: 125
Period size: 29 Copynumber: 3.9 Consensus size: 29
18125677 CATGATTATG
*
18125687 AATGTGA--TGGGCCTAACGGGCCATATA
1 AATGTGATTTGGGCCTAATGGGCCATATA
18125714 AATGTGATTTGGGCCTAATGGGCCATATA
1 AATGTGATTTGGGCCTAATGGGCCATATA
* * * *
18125743 CAGGTGGTTTGGGCCTAATGGGCCATATG
1 AATGTGATTTGGGCCTAATGGGCCATATA
* * *
18125772 AATATGA-TTCGGCTTAATGGGCCA
1 AATGTGATTTGGGCCTAATGGGCCA
18125796 GATACAGGTA
Statistics
Matches: 69, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
27 7 0.10
28 15 0.22
29 47 0.68
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.28
Consensus pattern (29 bp):
AATGTGATTTGGGCCTAATGGGCCATATA
Found at i:18125766 original size:58 final size:57
Alignment explanation
Indices: 18125694--18125804 Score: 159
Period size: 58 Copynumber: 1.9 Consensus size: 57
18125684 ATGAATGTGA
* * *
18125694 TGGGCCTAACGGGCCATATAAATGTGATTTGGGCCTAATGGGCCATATACAGGTGGTT
1 TGGGCCTAACGGGCCATATAAATATGA-TTCGGCCTAATGGGCCAGATACAGGTGGTT
* * *
18125752 TGGGCCTAATGGGCCATATGAATATGATTCGGCTTAATGGGCCAGATACAGGT
1 TGGGCCTAACGGGCCATATAAATATGATTCGGCCTAATGGGCCAGATACAGGT
18125805 ATGTATAATT
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
57 23 0.49
58 24 0.51
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (57 bp):
TGGGCCTAACGGGCCATATAAATATGATTCGGCCTAATGGGCCAGATACAGGTGGTT
Found at i:18128125 original size:13 final size:12
Alignment explanation
Indices: 18128107--18128140 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
18128097 ATACAAGTTT
18128107 GAAAAAAAAATCC
1 GAAAAAAAAAT-C
18128120 GAAAAAAAAATC
1 GAAAAAAAAATC
18128132 -AAAAAAAAA
1 GAAAAAAAAA
18128141 AGTTATTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.43
12 1 0.05
13 11 0.52
ACGTcount: A:0.79, C:0.09, G:0.06, T:0.06
Consensus pattern (12 bp):
GAAAAAAAAATC
Found at i:18128136 original size:12 final size:13
Alignment explanation
Indices: 18128108--18128141 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
18128098 TACAAGTTTG
*
18128108 AAAAAAAAATCCG
1 AAAAAAAAATCCA
18128121 AAAAAAAAAT-CA
1 AAAAAAAAATCCA
18128133 AAAAAAAAA
1 AAAAAAAAA
18128142 GTTATTTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.82, C:0.09, G:0.03, T:0.06
Consensus pattern (13 bp):
AAAAAAAAATCCA
Found at i:18133325 original size:21 final size:21
Alignment explanation
Indices: 18133291--18133339 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
18133281 TACTCCTTCA
18133291 AGCTCAA-ATCAACTCAAATC
1 AGCTCAACATCAACTCAAATC
* * *
18133311 AGCTCAACTTCAACTCAACTT
1 AGCTCAACATCAACTCAAATC
18133332 AGCTCAAC
1 AGCTCAAC
18133340 GAGCTCGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.39, C:0.33, G:0.06, T:0.22
Consensus pattern (21 bp):
AGCTCAACATCAACTCAAATC
Found at i:18135680 original size:28 final size:28
Alignment explanation
Indices: 18135628--18135682 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
18135618 ATTTATATAA
* *
18135628 ATGGAACTTAGTTTGCAAAGTATCTAGG
1 ATGGAACTTAGTGTGCAAAGCATCTAGG
18135656 ATGGAACTTAGTGTGCGAAA-CATCTAG
1 ATGGAACTTAGTGTGC-AAAGCATCTAG
18135683 AATAGCACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 21 0.88
29 3 0.12
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (28 bp):
ATGGAACTTAGTGTGCAAAGCATCTAGG
Found at i:18139142 original size:10 final size:10
Alignment explanation
Indices: 18139127--18139153 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
18139117 TTCGTAAGTA
18139127 AAAAAAATTC
1 AAAAAAATTC
18139137 AAAAAAATTC
1 AAAAAAATTC
18139147 AAAAAAA
1 AAAAAAA
18139154 AAGTGTGCTA
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:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (10 bp):
AAAAAAATTC
Found at i:18141691 original size:30 final size:30
Alignment explanation
Indices: 18141657--18141753 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
18141647 TAAACTAAAA
18141657 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
18141687 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
18141717 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
18141747 TGAGCTA
1 TGAGCTA
18141754 GGACTGAGCT
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:18142991 original size:30 final size:30
Alignment explanation
Indices: 18142957--18143057 Score: 87
Period size: 30 Copynumber: 3.4 Consensus size: 30
18142947 AGCTCACTCC
*
18142957 TAGCTCATTTTCAACTCACGAGCTAAACCT
1 TAGCTCATTTTCAGCTCACGAGCTAAACCT
** * * * * *
18142987 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCATTTTCAGCTCACGAGCTAAACCT
* * *
18143017 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTC-ATTTTCAGCTCACGAGCTAAACCT
18143047 TAGCTCATTTT
1 TAGCTCATTTT
18143058 AGTTTAAACT
Statistics
Matches: 51, Mismatches: 19, Indels: 3
0.70 0.26 0.04
Matches are distributed among these distances:
29 4 0.08
30 44 0.86
31 3 0.06
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.32
Consensus pattern (30 bp):
TAGCTCATTTTCAGCTCACGAGCTAAACCT
Found at i:18144198 original size:14 final size:14
Alignment explanation
Indices: 18144181--18144225 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
18144171 TAAGCCTCTT
*
18144181 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
18144195 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
18144208 AATTTAATTTAATG
1 AGTTTAATTTAATG
18144222 AGTT
1 AGTT
18144226 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:18145233 original size:29 final size:29
Alignment explanation
Indices: 18145200--18145259 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
18145190 ATAACCAAAC
*
18145200 CTACAAAAACTTTATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
* *
18145229 CTACATAAACTTCATATCCATAAATCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
18145258 CT
1 CT
18145260 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:18145252 original size:15 final size:15
Alignment explanation
Indices: 18145206--18145252 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
18145196 AAACCTACAA
*
18145206 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
18145221 AAAC-CCATCTACAT
1 AAACTTCATATCCAT
18145235 AAACTTCATATCCAT
1 AAACTTCATATCCAT
18145250 AAA
1 AAA
18145253 TCCATCTTTG
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.30
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:18145771 original size:14 final size:14
Alignment explanation
Indices: 18145752--18145791 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
18145742 CGAATGGAAT
18145752 GGTAGGAACAAAAG
1 GGTAGGAACAAAAG
18145766 GGTAGGAACAAAAG
1 GGTAGGAACAAAAG
* *
18145780 GATATGAACAAA
1 GGTAGGAACAAA
18145792 TTGGTCGGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.53, C:0.07, G:0.30, T:0.10
Consensus pattern (14 bp):
GGTAGGAACAAAAG
Found at i:18148105 original size:20 final size:20
Alignment explanation
Indices: 18148082--18148127 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
18148072 TAAGCTCGGT
18148082 TGAGCTCAAACGAGCTGAAA
1 TGAGCTCAAACGAGCTGAAA
* *
18148102 TGAGCTCAAATGAGCTGAAT
1 TGAGCTCAAACGAGCTGAAA
18148122 TGAGCT
1 TGAGCT
18148128 GGACGGAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.22
Consensus pattern (20 bp):
TGAGCTCAAACGAGCTGAAA
Found at i:18148128 original size:10 final size:10
Alignment explanation
Indices: 18148082--18148128 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
18148072 TAAGCTCGGT
*
18148082 TGAGCTCAAA
1 TGAGCTGAAA
*
18148092 CGAGCTGAAA
1 TGAGCTGAAA
*
18148102 TGAGCTCAAA
1 TGAGCTGAAA
*
18148112 TGAGCTGAAT
1 TGAGCTGAAA
18148122 TGAGCTG
1 TGAGCTG
18148129 GACGGAGCTC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.34, C:0.17, G:0.28, T:0.21
Consensus pattern (10 bp):
TGAGCTGAAA
Found at i:18148887 original size:30 final size:30
Alignment explanation
Indices: 18148792--18148888 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
18148782 AGCTCACTCC
* * *
18148792 TAGCTC-ACTTTCAACTCACAAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAAGCT
* * * **
18148822 TAGCTCAACTTCAGCTTAGGAG-TTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAG-CT
*
18148852 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAGCT
18148882 TAGCTCA
1 TAGCTCA
18148889 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:18150556 original size:12 final size:12
Alignment explanation
Indices: 18150539--18150581 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
18150529 AATATAGTAC
18150539 AAAAAAATTCAA
1 AAAAAAATTCAA
18150551 AAAAAAATTCAA
1 AAAAAAATTCAA
* *
18150563 AAAAAATTTGAA
1 AAAAAAATTCAA
18150575 AAAAAAA
1 AAAAAAA
18150582 GTGTTTAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.16
Consensus pattern (12 bp):
AAAAAAATTCAA
Found at i:18151022 original size:11 final size:11
Alignment explanation
Indices: 18151006--18151046 Score: 66
Period size: 11 Copynumber: 3.7 Consensus size: 11
18150996 ATACAAGTTA
18151006 AAAAAAAATTC
1 AAAAAAAATTC
18151017 AAAAAAAATTC
1 AAAAAAAATTC
18151028 GAAAAAAAA-TC
1 -AAAAAAAATTC
18151039 AAAAAAAA
1 AAAAAAAA
18151047 AGAAAAAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
10 8 0.28
11 13 0.45
12 8 0.28
ACGTcount: A:0.78, C:0.07, G:0.02, T:0.12
Consensus pattern (11 bp):
AAAAAAAATTC
Found at i:18159224 original size:30 final size:30
Alignment explanation
Indices: 18159190--18159286 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
18159180 TAAACTAAAA
18159190 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
18159220 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
18159250 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
18159280 TGAGCTA
1 TGAGCTA
18159287 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:18160567 original size:30 final size:30
Alignment explanation
Indices: 18160496--18160578 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
18160486 CTTTTGTTTC
* *
18160496 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
18160527 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
18160556 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
18160579 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:18160578 original size:18 final size:18
Alignment explanation
Indices: 18160529--18160584 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
18160519 CACTCTCAAA
* *
18160529 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
18160546 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
18160564 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
18160583 TT
1 TT
18160585 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:18160585 original size:12 final size:12
Alignment explanation
Indices: 18160554--18160578 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18160544 TTTTTCAATC
18160554 TCATTTTCTTTT
1 TCATTTTCTTTT
18160566 TCATTTTCTTTT
1 TCATTTTCTTTT
18160578 T
1 T
18160579 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:18160657 original size:5 final size:5
Alignment explanation
Indices: 18160647--18160703 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
18160637 CTCTTGCCTC
*
18160647 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
18160694 TCTTT TCTTT
1 TCTTT TCTTT
18160704 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:18160687 original size:15 final size:14
Alignment explanation
Indices: 18160647--18160703 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
18160637 CTCTTGCCTC
*
18160647 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
18160662 TCATTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
18160677 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
18160694 TCTTTTCTTT
1 TCTTTTCTTT
18160704 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:18160704 original size:21 final size:21
Alignment explanation
Indices: 18160647--18160714 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
18160637 CTCTTGCCTC
* *
18160647 TCTTTTCTTTT-TATTTCATTT
1 TCTTTTCTTTTCT-TTGCTTTT
*
18160668 TCTTTT-TCTTCTTTTGCTTTT
1 TCTTTTCTTTTC-TTTGCTTTT
18160689 TCTTTTCTTTTCTTTG-TTTT
1 TCTTTTCTTTTCTTTGCTTTT
18160709 CTCTTT
1 -TCTTT
18160715 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:18163113 original size:5 final size:5
Alignment explanation
Indices: 18163103--18163159 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
18163093 CTCTTGCCTC
*
18163103 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
18163150 TCTTT TCTTT
1 TCTTT TCTTT
18163160 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:18163143 original size:15 final size:14
Alignment explanation
Indices: 18163103--18163159 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
18163093 CTCTTGCCTC
*
18163103 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
18163118 TCGTTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
18163133 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
18163150 TCTTTTCTTT
1 TCTTTTCTTT
18163160 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:18163160 original size:21 final size:21
Alignment explanation
Indices: 18163103--18163170 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
18163093 CTCTTGCCTC
* *
18163103 TCTTTTCTTTT-TATTTCGTTT
1 TCTTTTCTTTTCT-TTGCTTTT
*
18163124 TCTTTT-TCTTCTTTTGCTTTT
1 TCTTTTCTTTTC-TTTGCTTTT
18163145 TCTTTTCTTTTCTTTG-TTTT
1 TCTTTTCTTTTCTTTGCTTTT
18163165 CTCTTT
1 -TCTTT
18163171 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:18164092 original size:12 final size:12
Alignment explanation
Indices: 18164075--18164131 Score: 73
Period size: 13 Copynumber: 4.7 Consensus size: 12
18164065 CATAAATCAC
18164075 TTTTTTTTC-AA
1 TTTTTTTTCGAA
18164086 TTTTTTTT-GAA
1 TTTTTTTTCGAA
18164097 TTTTATTTTTCGAA
1 -TTT-TTTTTCGAA
18164111 TTTTTTTTCGAAA
1 TTTTTTTTCG-AA
18164124 TTTTTTTT
1 TTTTTTTT
18164132 TGGTTTTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
11 10 0.24
12 10 0.24
13 18 0.44
14 3 0.07
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.72
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:18164100 original size:10 final size:11
Alignment explanation
Indices: 18164075--18164145 Score: 61
Period size: 11 Copynumber: 6.0 Consensus size: 11
18164065 CATAAATCAC
18164075 TTTTTTTTCAA
1 TTTTTTTTCAA
*
18164086 TTTTTTTTGAA
1 TTTTTTTTCAA
18164097 TTTTATTTTTCGAA
1 -TTT-TTTTTC-AA
18164111 TTTTTTTTCGAAA
1 TTTTTTTTC--AA
***
18164124 TTTTTTTTTGG
1 TTTTTTTTCAA
18164135 TTTTTTTTCAA
1 TTTTTTTTCAA
18164146 ACTTGTATAA
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
11 18 0.38
12 9 0.19
13 18 0.38
14 2 0.04
ACGTcount: A:0.17, C:0.06, G:0.07, T:0.70
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:18164105 original size:14 final size:13
Alignment explanation
Indices: 18164075--18164132 Score: 70
Period size: 14 Copynumber: 4.6 Consensus size: 13
18164065 CATAAATCAC
18164075 TTTTTTTTC-AA-
1 TTTTTTTTCGAAT
18164086 TTTTTTTT-GAAT
1 TTTTTTTTCGAAT
18164098 TTTATTTTTCGAA-
1 TTT-TTTTTCGAAT
18164111 TTTTTTTTCGAAAT
1 TTTTTTTTCG-AAT
18164125 TTTTTTTT
1 TTTTTTTT
18164133 GGTTTTTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
11 10 0.24
12 10 0.24
13 10 0.24
14 11 0.27
ACGTcount: A:0.17, C:0.05, G:0.05, T:0.72
Consensus pattern (13 bp):
TTTTTTTTCGAAT
Found at i:18166638 original size:19 final size:20
Alignment explanation
Indices: 18166606--18166646 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
18166596 GAATGAAATC
18166606 GAGAGAAGAAACAAAGAAAA
1 GAGAGAAGAAACAAAGAAAA
18166626 GAGAGAA-AAACAAAGAAAA
1 GAGAGAAGAAACAAAGAAAA
18166645 GA
1 GA
18166647 AAATGAAAAA
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:0.71, C:0.05, G:0.24, T:0.00
Consensus pattern (20 bp):
GAGAGAAGAAACAAAGAAAA
Found at i:18166658 original size:12 final size:12
Alignment explanation
Indices: 18166641--18166666 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
18166631 AAAAACAAAG
18166641 AAAAGAAAATGA
1 AAAAGAAAATGA
18166653 AAAAGAAAATGA
1 AAAAGAAAATGA
18166665 AA
1 AA
18166667 TTGAGATTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (12 bp):
AAAAGAAAATGA
Found at i:18166679 original size:30 final size:30
Alignment explanation
Indices: 18166645--18166713 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
18166635 ACAAAGAAAA
*
18166645 GAAAATGAAAAAGAAAATGAAA-TTGAGATT
1 GAAAAAGAAAAAGAAAA-GAAATTTGAGATT
* * **
18166675 GAAAAAGAGAACGAAAAGAAATTTGAGAGA
1 GAAAAAGAAAAAGAAAAGAAATTTGAGATT
18166705 GAAAAAGAA
1 GAAAAAGAA
18166714 TGTGAACAAG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 4 0.12
30 28 0.88
ACGTcount: A:0.62, C:0.01, G:0.23, T:0.13
Consensus pattern (30 bp):
GAAAAAGAAAAAGAAAAGAAATTTGAGATT
Found at i:18166742 original size:18 final size:19
Alignment explanation
Indices: 18166706--18166744 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
18166696 TTTGAGAGAG
*
18166706 AAAAAGAATGTGAACAAGA
1 AAAAAGAATGTGAAAAAGA
*
18166725 AAAAAGAGTG-GAAAAAGA
1 AAAAAGAATGTGAAAAAGA
18166743 AA
1 AA
18166745 TTGAGATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.67, C:0.03, G:0.23, T:0.08
Consensus pattern (19 bp):
AAAAAGAATGTGAAAAAGA
Found at i:18168383 original size:29 final size:29
Alignment explanation
Indices: 18168350--18168409 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
18168340 AAGGATTCAA
18168350 AGATGGGTTTATGGATATGA-AGTTTATGT
1 AGATGGGTTTATGGATAT-ACAGTTTATGT
*
18168379 AGATGGGTTTATGGATATACAGTTTTTGT
1 AGATGGGTTTATGGATATACAGTTTATGT
18168408 AG
1 AG
18168410 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 1 0.03
29 28 0.97
ACGTcount: A:0.27, C:0.02, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATACAGTTTATGT
Found at i:18168390 original size:14 final size:14
Alignment explanation
Indices: 18168350--18168393 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
18168340 AAGGATTCAA
18168350 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
18168364 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
18168379 AGATGGGTTTATGG
1 AGATGGGTTTATGG
18168393 A
1 A
18168394 TATACAGTTT
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:18169437 original size:14 final size:14
Alignment explanation
Indices: 18169420--18169453 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
18169410 GTACGAATGG
18169420 AATGGTAGGAACAA
1 AATGGTAGGAACAA
*
18169434 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
18169448 ATTGGT
1 AATGGT
18169454 CGGTTTAGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.06, G:0.26, T:0.24
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:18171142 original size:14 final size:14
Alignment explanation
Indices: 18171100--18171144 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
18171090 TTAAAGAAGC
18171100 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
18171114 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
18171127 AACTCATTTAATTA
1 AACTCATTAAATTA
18171141 AACT
1 AACT
18171145 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:18171646 original size:20 final size:21
Alignment explanation
Indices: 18171623--18171669 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
18171613 TCAGCTCCCA
*
18171623 TCAGCTCACTTGAGCTCG-AT
1 TCAGCTCACTTGAGCTAGAAT
**
18171643 TCAGCTCGTTTGAGCTAGAAT
1 TCAGCTCACTTGAGCTAGAAT
18171664 TCAGCT
1 TCAGCT
18171670 TGATCTAGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (21 bp):
TCAGCTCACTTGAGCTAGAAT
Found at i:18174946 original size:26 final size:26
Alignment explanation
Indices: 18174909--18174981 Score: 128
Period size: 26 Copynumber: 2.8 Consensus size: 26
18174899 TGATACAAAT
*
18174909 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
18174935 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
18174961 TGATAATGGGTTAGGTAAATG
1 TGATAATGGGTTAGGTAAATG
18174982 GGTTTTAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 45 1.00
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:18175661 original size:11 final size:11
Alignment explanation
Indices: 18175632--18175666 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
18175622 TATAAGACAA
18175632 ACATATTAAAC
1 ACATATTAAAC
18175643 ACAT-TTAAAC
1 ACATATTAAAC
*
18175653 ACTTATTAAAC
1 ACATATTAAAC
18175664 ACA
1 ACA
18175667 AAACACATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.51, C:0.20, G:0.00, T:0.29
Consensus pattern (11 bp):
ACATATTAAAC
Found at i:18175681 original size:9 final size:9
Alignment explanation
Indices: 18175630--18175685 Score: 55
Period size: 9 Copynumber: 6.2 Consensus size: 9
18175620 GCTATAAGAC
*
18175630 AAACATATT
1 AAACACATT
18175639 AAACACATTT
1 AAACACA-TT
18175649 AAACACTTATT
1 AAACAC--ATT
18175660 AAACACA--
1 AAACACATT
18175667 AAACACATT
1 AAACACATT
18175676 AAACAC-TT
1 AAACACATT
18175684 AA
1 AA
18175686 CTTAAATAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
7 7 0.17
8 4 0.10
9 13 0.32
10 8 0.20
11 8 0.20
12 1 0.02
ACGTcount: A:0.55, C:0.20, G:0.00, T:0.25
Consensus pattern (9 bp):
AAACACATT
Found at i:18176013 original size:15 final size:16
Alignment explanation
Indices: 18175993--18176026 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
18175983 TAAAATATGC
*
18175993 AAACTTATTTAAA-TA
1 AAACTTAATTAAATTA
18176008 AAACTTAATTAAATTA
1 AAACTTAATTAAATTA
18176024 AAA
1 AAA
18176027 ATCCTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (16 bp):
AAACTTAATTAAATTA
Found at i:18180762 original size:26 final size:26
Alignment explanation
Indices: 18180726--18180809 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
18180716 CATGAAATTC
18180726 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
18180752 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
18180778 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
18180804 TTATCA
1 TTATCA
18180810 ATTTGTATCA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:18185672 original size:20 final size:21
Alignment explanation
Indices: 18185629--18185675 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
18185619 AGCTAGATCA
*
18185629 AGCTGAATTCTAGCTCAAACG
1 AGCTGAATTCGAGCTCAAACG
**
18185650 AGCTGAA-TCGAGCTCAAGTG
1 AGCTGAATTCGAGCTCAAACG
18185670 AGCTGA
1 AGCTGA
18185676 TGGGAGCTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.21
Consensus pattern (21 bp):
AGCTGAATTCGAGCTCAAACG
Found at i:18186174 original size:14 final size:14
Alignment explanation
Indices: 18186155--18186199 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
18186145 AACTCATCTT
*
18186155 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
18186169 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
18186182 AATTTAATTTAATG
1 AGTTTAATTTAATG
18186196 AGTT
1 AGTT
18186200 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:18187868 original size:14 final size:14
Alignment explanation
Indices: 18187846--18187893 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
18187836 ACCTAAACCG
* *
18187846 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
18187860 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
18187874 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
18187888 ACCATT
1 ACCATT
18187894 CCATTCGTAC
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:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:18188938 original size:29 final size:29
Alignment explanation
Indices: 18188905--18188964 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
18188895 ATAACCAAAC
18188905 CTACAAAAACTGT-ATATCCATAAACCCAT
1 CTACAAAAACT-TCATATCCATAAACCCAT
*
18188934 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
18188963 CT
1 CT
18188965 TTGAATCCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 1 0.03
29 28 0.97
ACGTcount: A:0.42, C:0.30, G:0.02, T:0.27
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:18188957 original size:15 final size:14
Alignment explanation
Indices: 18188918--18188962 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
18188908 CAAAAACTGT
18188918 ATATCCATAAACCC
1 ATATCCATAAACCC
* * *
18188932 ATCTACATAAACTTC
1 ATATCCATAAAC-CC
18188947 ATATCCATAAACCC
1 ATATCCATAAACCC
18188961 AT
1 AT
18188963 CTTTGAATCC
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.42, C:0.31, G:0.00, T:0.27
Consensus pattern (14 bp):
ATATCCATAAACCC
Found at i:18190593 original size:18 final size:19
Alignment explanation
Indices: 18190570--18190608 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
18190560 TTTATCTCAA
*
18190570 TTTCTTTTTC-CACTCTTT
1 TTTCTTGTTCACACTCTTT
*
18190588 TTTCTTGTTCACATTCTTT
1 TTTCTTGTTCACACTCTTT
18190607 TT
1 TT
18190609 CTCTCTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.08, C:0.23, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTCTTGTTCACACTCTTT
Found at i:18190665 original size:12 final size:12
Alignment explanation
Indices: 18190648--18190673 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
18190638 TCAATCTCAA
18190648 TTTCATTTTCTT
1 TTTCATTTTCTT
18190660 TTTCATTTTCTT
1 TTTCATTTTCTT
18190672 TT
1 TT
18190674 CTTTGTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTCATTTTCTT
Found at i:18190669 original size:30 final size:30
Alignment explanation
Indices: 18190612--18190669 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
18190602 TCTTTTTCTC
*
18190612 TCTCAAATTTCTTTTCGTTCTCTTTTTCAA
1 TCTCAAATTTCTTTTCGTTCTCATTTTCAA
* *
18190642 TCTC-AATTTCATTTTCTTTTTCATTTTC
1 TCTCAAATTTC-TTTTCGTTCTCATTTTC
18190670 TTTTCTTTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 6 0.25
30 18 0.75
ACGTcount: A:0.16, C:0.22, G:0.02, T:0.60
Consensus pattern (30 bp):
TCTCAAATTTCTTTTCGTTCTCATTTTCAA
Found at i:18190692 original size:19 final size:20
Alignment explanation
Indices: 18190668--18190708 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
18190658 TTTTTCATTT
18190668 TCTTTTCTTTGTTT-TTCTC
1 TCTTTTCTTTGTTTCTTCTC
18190687 TCTTTTCTTTGTTTCTTCTC
1 TCTTTTCTTTGTTTCTTCTC
18190707 TC
1 TC
18190709 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:18193156 original size:14 final size:13
Alignment explanation
Indices: 18193131--18193199 Score: 78
Period size: 12 Copynumber: 5.6 Consensus size: 13
18193121 TACAAGTTTG
18193131 AAAAAAAA--CGA
1 AAAAAAAATTCGA
18193142 AAAAAAAATTTCG-
1 AAAAAAAA-TTCGA
18193155 AAAAAAAATTCGA
1 AAAAAAAATTCGA
18193168 AAAATAAAATTC--
1 AAAA-AAAATTCGA
18193180 AAAAAAAATT-GA
1 AAAAAAAATTCGA
18193192 AAAAAAAA
1 AAAAAAAA
18193200 GTGATTTATG
Statistics
Matches: 51, Mismatches: 0, Indels: 13
0.80 0.00 0.20
Matches are distributed among these distances:
11 14 0.27
12 16 0.31
13 12 0.24
14 9 0.18
ACGTcount: A:0.74, C:0.06, G:0.06, T:0.14
Consensus pattern (13 bp):
AAAAAAAATTCGA
Found at i:18193158 original size:13 final size:12
Alignment explanation
Indices: 18193130--18193198 Score: 74
Period size: 11 Copynumber: 5.8 Consensus size: 12
18193120 ATACAAGTTT
18193130 GAAAAAAAA--C
1 GAAAAAAAATTC
18193140 GAAAAAAAAATTTC
1 G-AAAAAAAA-TTC
18193154 GAAAAAAAATTC
1 GAAAAAAAATTC
18193166 GAAAAATAAAATTC
1 G-AAAA-AAAATTC
18193180 -AAAAAAAATT-
1 GAAAAAAAATTC
18193190 GAAAAAAAA
1 GAAAAAAAA
18193199 AGTGATTTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 13
0.80 0.00 0.20
Matches are distributed among these distances:
10 1 0.02
11 22 0.42
12 8 0.15
13 12 0.23
14 9 0.17
ACGTcount: A:0.72, C:0.06, G:0.07, T:0.14
Consensus pattern (12 bp):
GAAAAAAAATTC
Found at i:18193160 original size:26 final size:25
Alignment explanation
Indices: 18193131--18193187 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 25
18193121 TACAAGTTTG
18193131 AAAAAAAACGAAAAA-AAAATTTCGAA
1 AAAAAAAACGAAAAATAAAA-TTC-AA
**
18193157 AAAAAATTCGAAAAATAAAATTCAA
1 AAAAAAAACGAAAAATAAAATTCAA
18193182 AAAAAA
1 AAAAAA
18193188 TTGAAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 8 0.29
26 16 0.57
27 4 0.14
ACGTcount: A:0.74, C:0.07, G:0.05, T:0.14
Consensus pattern (25 bp):
AAAAAAAACGAAAAATAAAATTCAA
Found at i:18193199 original size:13 final size:13
Alignment explanation
Indices: 18193141--18193199 Score: 50
Period size: 13 Copynumber: 4.6 Consensus size: 13
18193131 AAAAAAAACG
**
18193141 AAAAAAAAATTTC
1 AAAAAAAAATTGA
*
18193154 GAAAAAAAATTCGA
1 AAAAAAAAATT-GA
*
18193168 AAAATAAAATT--
1 AAAAAAAAATTGA
*
18193179 CAAAAAAAATTGA
1 AAAAAAAAATTGA
18193192 AAAAAAAA
1 AAAAAAAA
18193200 GTGATTTATG
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
11 9 0.26
13 17 0.49
14 9 0.26
ACGTcount: A:0.73, C:0.05, G:0.05, T:0.17
Consensus pattern (13 bp):
AAAAAAAAATTGA
Found at i:18194140 original size:21 final size:20
Alignment explanation
Indices: 18194106--18194173 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
18194096 ACATTCTTGT
18194106 AAAGAGAAAA-CAAAGAAAAGA
1 AAAGA-AAAAGCAAA-AAAAGA
*
18194127 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAGCAAAAAAAG-A
* *
18194148 AAAGAAAACGAAATAAAAAGA
1 AAAGAAAAAGCAA-AAAAAGA
18194169 AAAGA
1 AAAGA
18194174 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:0.04, G:0.18, T:0.01
Consensus pattern (20 bp):
AAAGAAAAAGCAAAAAAAGA
Found at i:18194141 original size:6 final size:5
Alignment explanation
Indices: 18194117--18194173 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
18194107 AAGAGAAAAC
*
18194117 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAACGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
18194164 AAAGA AAAGA
1 AAAGA AAAGA
18194174 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:0.04, G:0.18, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:18194148 original size:15 final size:14
Alignment explanation
Indices: 18194117--18194173 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
18194107 AAGAGAAAAC
18194117 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
18194133 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
18194148 AAAGAAAACGAAATAA
1 AAAGAAAA-G-AAGAA
18194164 AAAGAAAAGA
1 AAAGAAAAGA
18194174 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:0.04, G:0.18, T:0.02
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:18201825 original size:26 final size:26
Alignment explanation
Indices: 18201789--18201872 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
18201779 CATGAAATTC
18201789 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
18201815 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
18201841 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
18201867 TTATCA
1 TTATCA
18201873 ATTTGTATCA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:18203709 original size:14 final size:14
Alignment explanation
Indices: 18203690--18203720 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
18203680 TTAATCGGGA
18203690 ATGCAAATCACTAC
1 ATGCAAATCACTAC
18203704 ATGCAAATCACTAC
1 ATGCAAATCACTAC
18203718 ATG
1 ATG
18203721 AAGAACACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.42, C:0.26, G:0.10, T:0.23
Consensus pattern (14 bp):
ATGCAAATCACTAC
Found at i:18204418 original size:30 final size:30
Alignment explanation
Indices: 18204348--18204429 Score: 87
Period size: 30 Copynumber: 2.7 Consensus size: 30
18204338 TTTTGTTTCA
* *
18204348 ATTTCTTTTTCATCTTCTTTTTCACTCTCAG
1 ATTTCTTTTTCTTC-TCTTTTTCAATCTCAG
18204379 ATTTC-TTTTCGTTCTCTTTTTCAATCTCA-
1 ATTTCTTTTTC-TTCTCTTTTTCAATCTCAG
* *
18204408 TTTTCTTTTTCATTTTCTTTTT
1 ATTTCTTTTTC-TTCTCTTTTT
18204430 GCTTTTCAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
29 4 0.09
30 33 0.75
31 7 0.16
ACGTcount: A:0.11, C:0.22, G:0.02, T:0.65
Consensus pattern (30 bp):
ATTTCTTTTTCTTCTCTTTTTCAATCTCAG
Found at i:18204429 original size:18 final size:18
Alignment explanation
Indices: 18204380--18204435 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
18204370 CACTCTCAGA
* *
18204380 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
18204397 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
18204415 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
18204434 TT
1 TT
18204436 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:18204436 original size:12 final size:12
Alignment explanation
Indices: 18204405--18204429 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18204395 TTTTTCAATC
18204405 TCATTTTCTTTT
1 TCATTTTCTTTT
18204417 TCATTTTCTTTT
1 TCATTTTCTTTT
18204429 T
1 T
18204430 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:18204447 original size:12 final size:12
Alignment explanation
Indices: 18204432--18204462 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
18204422 TTCTTTTTGC
18204432 TTTTCAAAGGCT
1 TTTTCAAAGGCT
18204444 TTTTCAAAGGCT
1 TTTTCAAAGGCT
18204456 TTTTCAA
1 TTTTCAA
18204463 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:18204520 original size:5 final size:5
Alignment explanation
Indices: 18204510--18204566 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
18204500 CTCTTGCCTC
*
18204510 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
18204557 TCTTT TCTTT
1 TCTTT TCTTT
18204567 ATTTTCTCTT
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:18204550 original size:15 final size:14
Alignment explanation
Indices: 18204510--18204566 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
18204500 CTCTTGCCTC
*
18204510 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
18204525 TCATTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
18204540 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
18204557 TCTTTTCTTT
1 TCTTTTCTTT
18204567 ATTTTCTCTT
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:18204576 original size:21 final size:20
Alignment explanation
Indices: 18204508--18204577 Score: 63
Period size: 20 Copynumber: 3.4 Consensus size: 20
18204498 GCCTCTTGCC
18204508 TCTCTTTTCTTTTTATTTCATTT
1 TCTCTTTTC-TTTT-TTT-ATTT
**
18204531 TCT-TTTTCTTCTTTTGCTTT
1 TCTCTTTTCTT-TTTTTATTT
18204551 T-TCTTTTCTTTTCTTTATTT
1 TCTCTTTTCTTTT-TTTATTT
18204571 TCTCTTT
1 TCTCTTT
18204578 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:0.04, C:0.19, G:0.01, T:0.76
Consensus pattern (20 bp):
TCTCTTTTCTTTTTTTATTT
Found at i:18205499 original size:11 final size:11
Alignment explanation
Indices: 18205483--18205540 Score: 52
Period size: 11 Copynumber: 5.6 Consensus size: 11
18205473 ATTAAACACT
18205483 TTTTTTTCAAA
1 TTTTTTTCAAA
18205494 TTTTTTT----
1 TTTTTTTCAAA
*
18205501 TTCTTTTCAAA
1 TTTTTTTCAAA
**
18205512 TTTTTTTTGAA
1 TTTTTTTCAAA
*
18205523 TTTTTTTCGAA
1 TTTTTTTCAAA
18205534 TTTTTTT
1 TTTTTTT
18205541 TCGATTTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
7 6 0.16
11 32 0.84
ACGTcount: A:0.17, C:0.07, G:0.03, T:0.72
Consensus pattern (11 bp):
TTTTTTTCAAA
Found at i:18205499 original size:12 final size:12
Alignment explanation
Indices: 18205499--18205552 Score: 69
Period size: 11 Copynumber: 4.7 Consensus size: 12
18205489 TCAAATTTTT
*
18205499 TTTTCTTTTCAAA
1 TTTT-TTTTCGAA
18205512 TTTTTTTT-GAA
1 TTTTTTTTCGAA
18205523 -TTTTTTTCGAA
1 TTTTTTTTCGAA
18205534 TTTTTTTTCG-A
1 TTTTTTTTCGAA
18205545 TTTTTTTT
1 TTTTTTTT
18205553 ACTTGTATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
10 7 0.18
11 14 0.37
12 13 0.34
13 4 0.11
ACGTcount: A:0.15, C:0.07, G:0.06, T:0.72
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:18205515 original size:17 final size:17
Alignment explanation
Indices: 18205482--18205519 Score: 67
Period size: 18 Copynumber: 2.2 Consensus size: 17
18205472 CATTAAACAC
18205482 TTTTTTTTCAAATTTTT
1 TTTTTTTTCAAATTTTT
18205499 TTTTCTTTTCAAATTTTT
1 TTTT-TTTTCAAATTTTT
18205517 TTT
1 TTT
18205520 GAATTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTTTTCAAATTTTT
Found at i:18205526 original size:19 final size:18
Alignment explanation
Indices: 18205486--18205526 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
18205476 AAACACTTTT
**
18205486 TTTTCAAATTTTTTTTTC
1 TTTTCAAATTTTTTTTAA
18205504 TTTTCAAATTTTTTTTGAA
1 TTTTCAAATTTTTTTT-AA
18205523 TTTT
1 TTTT
18205527 TTTCGAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.20, C:0.07, G:0.02, T:0.71
Consensus pattern (18 bp):
TTTTCAAATTTTTTTTAA
Found at i:18205547 original size:22 final size:22
Alignment explanation
Indices: 18205483--18205552 Score: 76
Period size: 22 Copynumber: 3.3 Consensus size: 22
18205473 ATTAAACACT
18205483 TTTTTTTCAAA-TTTTTTT---
1 TTTTTTTCAAATTTTTTTTGAA
*
18205501 TTCTTTTCAAATTTTTTTTGAA
1 TTTTTTTCAAATTTTTTTTGAA
* *
18205523 TTTTTTTCGAATTTTTTTTCGAT
1 TTTTTTTCAAATTTTTTTT-GAA
18205546 TTTTTTT
1 TTTTTTT
18205553 ACTTGTATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
18 10 0.23
19 7 0.16
22 17 0.40
23 9 0.21
ACGTcount: A:0.16, C:0.07, G:0.04, T:0.73
Consensus pattern (22 bp):
TTTTTTTCAAATTTTTTTTGAA
Found at i:18207820 original size:164 final size:164
Alignment explanation
Indices: 18207549--18207876 Score: 423
Period size: 164 Copynumber: 2.0 Consensus size: 164
18207539 GAGTTATTCT
* * * *
18207549 TAGCTCCTCCAACGTTATAGAGCTGGTTATCATCCCAAATGCGCATCACAAAGGCTGATATAGCA
1 TAGCTCCTCCAACGTCATAGACCTGGTTATCATCCCAAATACGCAACACAAAGGCTGATATAGCA
* * *
18207614 TCTTGAAGTTGCTTGGTTCGAGCTCGGGTCATGGGACCTTTTGGCAGCTC-AATAGATCCTTGGT
66 TCTTGAAGTTGCTTGGTTCGAGCTCGAGTCATGGGACCTTTTGGAAGCTCGAATAGAT-CTTGAT
* * **
18207678 GTGCATTCGAGGATGCCCCGGGTGTGCTCACATCA
130 GTGCATTCGAAGAAGCCCCGGGCATGCTCACATCA
* *
18207713 TAGCTCCTCCAACGTCATAGACCTTGTTGTCATCCCAAATACGCAACACCAAA-GCTGATA-AGG
1 TAGCTCCTCCAACGTCATAGACCTGGTTATCATCCCAAATACGCAACA-CAAAGGCTGATATA-G
* *
18207776 CGTCTTGAA-TTCGCTTGGTTCGAGCTCGAGTCATAGGG-CCTTTTGGAAGCTCGATTAGATCTT
64 CATCTTGAAGTT-GCTTGGTTCGAGCTCGAGTCAT-GGGACCTTTTGGAAGCTCGAATAGATCTT
* *
18207839 GATTTGCATTCGAAGAAGCCCCGTGCATGCTCACATCA
127 GATGTGCATTCGAAGAAGCCCCGGGCATGCTCACATCA
18207877 GTAGGCTTTC
Statistics
Matches: 142, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
163 3 0.02
164 126 0.89
165 13 0.09
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.28
Consensus pattern (164 bp):
TAGCTCCTCCAACGTCATAGACCTGGTTATCATCCCAAATACGCAACACAAAGGCTGATATAGCA
TCTTGAAGTTGCTTGGTTCGAGCTCGAGTCATGGGACCTTTTGGAAGCTCGAATAGATCTTGATG
TGCATTCGAAGAAGCCCCGGGCATGCTCACATCA
Found at i:18211929 original size:9 final size:10
Alignment explanation
Indices: 18211922--18211978 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
18211912 AAGAGAAAAC
18211922 AAAGAAAAGA
1 AAAGAAAAGA
18211932 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
18211944 AAAGAAGA-A
1 AAAGAAAAGA
18211953 AAAGAAAATGA
1 AAAGAAAA-GA
18211964 AATA-AAAAGA
1 AA-AGAAAAGA
18211974 AAAGA
1 AAAGA
18211979 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:18211945 original size:21 final size:20
Alignment explanation
Indices: 18211911--18211978 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
18211901 ACATTCTTGT
18211911 AAAGAGAAAA-CAAAGAAAAGA
1 AAAGA-AAAAGCAAA-AAAAGA
*
18211932 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAGCAAAAAAAG-A
* *
18211953 AAAGAAAATGAAATAAAAAGA
1 AAAGAAAAAGCAA-AAAAAGA
18211974 AAAGA
1 AAAGA
18211979 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:18211946 original size:6 final size:5
Alignment explanation
Indices: 18211922--18211978 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
18211912 AAGAGAAAAC
*
18211922 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
18211969 AAAGA AAAGA
1 AAAGA AAAGA
18211979 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:18211953 original size:15 final size:14
Alignment explanation
Indices: 18211922--18211978 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
18211912 AAGAGAAAAC
18211922 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
18211938 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
18211953 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
18211969 AAAGAAAAGA
1 AAAGAAAAGA
18211979 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:18216722 original size:29 final size:29
Alignment explanation
Indices: 18216689--18216748 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
18216679 ATAACCAAAC
* *
18216689 CTACAAAAACTTTATATCCATAAATCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
18216718 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
18216747 CT
1 CT
18216749 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:18216741 original size:15 final size:15
Alignment explanation
Indices: 18216695--18216742 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
18216685 AAACCTACAA
*
18216695 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
18216710 AAA-TCCATCTACAT
1 AAACTTCATATCCAT
18216724 AAACTTCATATCCAT
1 AAACTTCATATCCAT
18216739 AAAC
1 AAAC
18216743 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:18218774 original size:21 final size:22
Alignment explanation
Indices: 18218748--18218791 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
18218738 AAACGAGCTC
18218748 GTTGAGCTAAGTTGAG-TTGAA
1 GTTGAGCTAAGTTGAGCTTGAA
* *
18218769 GTTGAGCTGATTTGAGCTTGAA
1 GTTGAGCTAAGTTGAGCTTGAA
18218791 G
1 G
18218792 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:18223188 original size:19 final size:18
Alignment explanation
Indices: 18223146--18223189 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
18223136 AAAAGAAAAA
*
18223146 AGAAAAAGTGGAAAAGAG
1 AGAAAAAGTAGAAAAGAG
*
18223164 AGGAAAAAGTAAGAAAAGTG
1 A-GAAAAAGT-AGAAAAGAG
18223184 AGAAAA
1 AGAAAA
18223190 GTGATTCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 1 0.05
19 13 0.59
20 8 0.36
ACGTcount: A:0.64, C:0.00, G:0.30, T:0.07
Consensus pattern (18 bp):
AGAAAAAGTAGAAAAGAG
Found at i:18229941 original size:24 final size:23
Alignment explanation
Indices: 18229908--18229968 Score: 86
Period size: 24 Copynumber: 2.6 Consensus size: 23
18229898 TGCTTAGACA
* *
18229908 GATTTTATGAGCTTCTGGTTGAC
1 GATTTAATGAGCTGCTGGTTGAC
18229931 TGATTTAATGAGCTGCTGGTTGAC
1 -GATTTAATGAGCTGCTGGTTGAC
18229955 GAATTTAATGAGCT
1 G-ATTTAATGAGCT
18229969 ATTGGTTTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
23 1 0.03
24 33 0.97
ACGTcount: A:0.23, C:0.11, G:0.26, T:0.39
Consensus pattern (23 bp):
GATTTAATGAGCTGCTGGTTGAC
Found at i:18229974 original size:24 final size:23
Alignment explanation
Indices: 18229908--18229975 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 23
18229898 TGCTTAGACA
*
18229908 GATTTTATGAGCTTCTGGTTGACT
1 GATTTAATGAGCTT-TGGTTGACT
*
18229932 GATTTAATGAGCTGCTGGTTGAC-
1 GATTTAATGAGCT-TTGGTTGACT
18229955 GAATTTAATGAGCTATTGGTT
1 G-ATTTAATGAGCT-TTGGTT
18229976 TCTTTTTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
23 1 0.03
24 37 0.97
ACGTcount: A:0.22, C:0.10, G:0.26, T:0.41
Consensus pattern (23 bp):
GATTTAATGAGCTTTGGTTGACT
Found at i:18235473 original size:71 final size:71
Alignment explanation
Indices: 18235389--18235552 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
18235379 CGATTTGTCT
18235389 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
18235454 CTTTCA
66 CTTTCA
18235460 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
18235525 CTTTCA
66 CTTTCA
18235531 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
18235553 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:18235590 original size:71 final size:70
Alignment explanation
Indices: 18235389--18235586 Score: 258
Period size: 71 Copynumber: 2.8 Consensus size: 70
18235379 CGATTTGTCT
* * * *
18235389 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
18235454 CTTTCA
65 CTTTCA
* * * *
18235460 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
18235525 CTTTCA
65 CTTTCA
* *
18235531 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
18235587 TACAGGGTGT
Statistics
Matches: 120, Mismatches: 6, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
68 22 0.18
69 1 0.01
70 1 0.01
71 96 0.80
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:18237495 original size:16 final size:16
Alignment explanation
Indices: 18237474--18237507 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
18237464 TCGACACTTA
18237474 CGACCATACAAGGCTT
1 CGACCATACAAGGCTT
18237490 CGACCATACAAGGCTT
1 CGACCATACAAGGCTT
18237506 CG
1 CG
18237508 TACGGTGCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.32, G:0.21, T:0.18
Consensus pattern (16 bp):
CGACCATACAAGGCTT
Found at i:18243067 original size:71 final size:71
Alignment explanation
Indices: 18242983--18243146 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
18242973 CGATTTGTCT
18242983 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
18243048 CTTTCA
66 CTTTCA
18243054 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
18243119 CTTTCA
66 CTTTCA
18243125 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
18243147 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:18243184 original size:71 final size:70
Alignment explanation
Indices: 18242983--18243180 Score: 258
Period size: 71 Copynumber: 2.8 Consensus size: 70
18242973 CGATTTGTCT
* * * *
18242983 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
18243048 CTTTCA
65 CTTTCA
* * * *
18243054 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
18243119 CTTTCA
65 CTTTCA
* *
18243125 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
18243181 TACAGGGTGT
Statistics
Matches: 120, Mismatches: 6, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
68 22 0.18
69 1 0.01
70 1 0.01
71 96 0.80
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:18246506 original size:17 final size:18
Alignment explanation
Indices: 18246464--18246512 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
18246454 AGTTGAAAAG
18246464 GAGCATGATTGTCATACTT
1 GAGCATGA-TGTCATACTT
*
18246483 G-GCCATGATG-CATTCTT
1 GAG-CATGATGTCATACTT
18246500 GAGCATGAT-TCAT
1 GAGCATGATGTCAT
18246513 GCTTCTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 16 0.62
18 4 0.15
19 6 0.23
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (18 bp):
GAGCATGATGTCATACTT
Found at i:18247401 original size:40 final size:40
Alignment explanation
Indices: 18247335--18247501 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
18247325 AAATTGAATG
* * *
18247335 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * **
18247374 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
18247414 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
18247454 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
18247494 ATATCCGG
1 ATATCCGG
18247502 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:18254507 original size:17 final size:18
Alignment explanation
Indices: 18254465--18254513 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
18254455 AGTTGAAAAG
18254465 GAGCATGATTGTCATACTT
1 GAGCATGA-TGTCATACTT
*
18254484 G-GCCATGATG-CATTCTT
1 GAG-CATGATGTCATACTT
18254501 GAGCATGAT-TCAT
1 GAGCATGATGTCAT
18254514 GCTTCTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 16 0.62
18 4 0.15
19 6 0.23
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (18 bp):
GAGCATGATGTCATACTT
Found at i:18255401 original size:40 final size:40
Alignment explanation
Indices: 18255335--18255501 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
18255325 AAATTGAATG
* * *
18255335 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * **
18255374 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
18255414 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
18255454 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
18255494 ATATCCGG
1 ATATCCGG
18255502 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:18260101 original size:55 final size:56
Alignment explanation
Indices: 18260036--18260150 Score: 137
Period size: 55 Copynumber: 2.1 Consensus size: 56
18260026 AGCATGGCTG
* * *
18260036 CCAGATACAGA-AAATGTGACAGAGTCACCAGATACAGATATTTTGTGGCAGT-GCCA
1 CCAGATACAGATAAACGTGACAGAGCCACCAGA-ACAGATAATTTGTGGCA-TAGCCA
* * *
18260092 CCAGA-ACAGATATACGTGGCAGGGCCACCAGAACAGATAATTTGTGGCATAGCCA
1 CCAGATACAGATAAACGTGACAGAGCCACCAGAACAGATAATTTGTGGCATAGCCA
18260147 CCAG
1 CCAG
18260151 GACACTTCCT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
54 1 0.02
55 29 0.57
56 21 0.41
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (56 bp):
CCAGATACAGATAAACGTGACAGAGCCACCAGAACAGATAATTTGTGGCATAGCCA
Found at i:18260147 original size:28 final size:27
Alignment explanation
Indices: 18260061--18260150 Score: 101
Period size: 27 Copynumber: 3.2 Consensus size: 27
18260051 GTGACAGAGT
*
18260061 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATAATTTGTGGCA-TGC
** *
18260090 CACCAGAACAGAT-ATACGTGGCAGGGC
1 CACCAGAACAGATAATTTGTGGCA-TGC
18260117 CACCAGAACAGATAATTTGTGGCATAGC
1 CACCAGAACAGATAATTTGTGGCAT-GC
18260145 CACCAG
1 CACCAG
18260151 GACACTTCCT
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
27 23 0.44
28 22 0.42
29 7 0.13
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.19
Consensus pattern (27 bp):
CACCAGAACAGATAATTTGTGGCATGC
Done.