Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 90 of 172
Found at i:30150713 original size:51 final size:47
Alignment explanation
Indices: 30150637--30150779 Score: 146
Period size: 51 Copynumber: 2.9 Consensus size: 47
30150627 TATGTGATAA
* *
30150637 AAAT-ATAATATAATAAATAATAAGTAATGATATATGTTAAAATATATATT
1 AAATAATAATATAA-AAAT-ATAAGTAAT-ATATATATTAAAATATA-AGT
* * *
30150687 AATATGATAATAGAAAAATATGAAGTAATATAATATAATAAAATATAAGT
1 AA-ATAATAATATAAAAATAT-AAGTAATAT-ATATATTAAAATATAAGT
30150737 AAATAATAATATAAAATATATAA-TACATATATATATTAAAATA
1 AAATAATAATATAAAA-ATATAAGTA-ATATATATATTAAAATA
30150780 AAATAATACA
Statistics
Matches: 80, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
48 14 0.17
49 18 0.22
50 14 0.17
51 26 0.32
52 8 0.10
ACGTcount: A:0.59, C:0.01, G:0.06, T:0.34
Consensus pattern (47 bp):
AAATAATAATATAAAAATATAAGTAATATATATATTAAAATATAAGT
Found at i:30150722 original size:5 final size:5
Alignment explanation
Indices: 30150712--30150761 Score: 50
Period size: 5 Copynumber: 10.0 Consensus size: 5
30150702 AAATATGAAG
* *
30150712 TAATA TAATA TAATA AAATA TAAGTA -AATAA TAATA TAAAA T-ATA TAATA
1 TAATA TAATA TAATA TAATA TAA-TA TAAT-A TAATA TAATA TAATA TAATA
30150762 CATATATATA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
4 4 0.11
5 28 0.76
6 5 0.14
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (5 bp):
TAATA
Found at i:30150745 original size:89 final size:89
Alignment explanation
Indices: 30150548--30150747 Score: 210
Period size: 89 Copynumber: 2.2 Consensus size: 89
30150538 CTGAAAATAT
* * *
30150548 ATATAATAGATAATAATAATATGAAATAATATATTGTTAAAATGTAAAATAATATAATAATATAA
1 ATATAAT--ATAATAATAATAAGAAATAATATATTGTTAAAATATAAAATAATATAATAATAGAA
* * *
30150613 AAATATATAAATATTATGTGATAAAA
64 AAATATATAAATATAATATAATAAAA
* * * * *
30150639 ATATAATATAATAAATAATAAGTAATGATATA-TGTTAAAATATATATTAATATGATAATAGAAA
1 ATATAATATAAT-AATAATAAGAAATAATATATTGTTAAAATATAAAATAATATAATAATAGAAA
30150703 AATATGA-AGTAATATAATATAAT-AAA
65 AATAT-ATA--AATATAATATAATAAAA
30150729 ATATAAGTA-AATAATAATA
1 ATATAA-TATAATAATAATA
30150748 TAAAATATAT
Statistics
Matches: 93, Mismatches: 11, Indels: 12
0.80 0.09 0.10
Matches are distributed among these distances:
89 45 0.48
90 29 0.31
91 19 0.20
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.34
Consensus pattern (89 bp):
ATATAATATAATAATAATAAGAAATAATATATTGTTAAAATATAAAATAATATAATAATAGAAAA
ATATATAAATATAATATAATAAAA
Found at i:30150772 original size:17 final size:17
Alignment explanation
Indices: 30150688--30150767 Score: 60
Period size: 18 Copynumber: 4.8 Consensus size: 17
30150678 ATATATATTA
* *
30150688 ATATGATAATAGAAAA-
1 ATATAATAATATAAAAT
*
30150704 ATATGAAGTAATATAATAT
1 ATAT-AA-TAATATAAAAT
*
30150723 A-ATAA-AATAT-AAGT
1 ATATAATAATATAAAAT
*
30150737 AAATAATAATATAAAAT
1 ATATAATAATATAAAAT
30150754 ATATAATACATATA
1 ATATAATA-ATATA
30150768 TATATTAAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
14 3 0.06
15 9 0.18
16 9 0.18
17 13 0.26
18 15 0.30
19 1 0.02
ACGTcount: A:0.61, C:0.01, G:0.06, T:0.31
Consensus pattern (17 bp):
ATATAATAATATAAAAT
Found at i:30150788 original size:26 final size:26
Alignment explanation
Indices: 30150748--30150807 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
30150738 AATAATAATA
* *
30150748 TAAAAT-ATATAATACATATA-TATAT
1 TAAAATAAAATAATACATATACAAT-T
30150773 TAAAATAAAATAATACATATACAATT
1 TAAAATAAAATAATACATATACAATT
30150799 TAAAATAAA
1 TAAAATAAA
30150808 TAAGTTATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
25 6 0.19
26 23 0.74
27 2 0.06
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (26 bp):
TAAAATAAAATAATACATATACAATT
Found at i:30152438 original size:44 final size:43
Alignment explanation
Indices: 30152388--30152470 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 43
30152378 CATGTTGATA
*
30152388 TCTTCGATCTGCTCTCCGCCGAACACAGAGACGCCAAATCTGCT
1 TCTTCGATCTGCTCTCCGAC-AACACAGAGACGCCAAATCTGCT
* * * * *
30152432 TCTTCGATTTGTTCTCTGACAATACAGAGAGGCCAAATC
1 TCTTCGATCTGCTCTCCGACAACACAGAGACGCCAAATC
30152471 ATCTTAGATT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
43 17 0.52
44 16 0.48
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (43 bp):
TCTTCGATCTGCTCTCCGACAACACAGAGACGCCAAATCTGCT
Found at i:30152943 original size:206 final size:206
Alignment explanation
Indices: 30152433--30152989 Score: 839
Period size: 207 Copynumber: 2.7 Consensus size: 206
30152423 AAATCTGCTT
* * *
30152433 CTTCGATTTGTTCTCTGACAATACAGAGAGGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCAT
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCAC
* * * * *
30152498 GCGAAAACCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAGCACCAGGATACCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
* * ** * *
30152563 GGATCTGCTTCAGTCTAATCATCTGAAGGTTAGATCTGCTATGTGTCTGCCCTTCGTCGAATATG
131 GGATCTGCTTCAGTATAAACATCTGAAGGCCAAATCTGCTATGTATCTGCCCTTCGTCGAATATG
*
30152628 GAGACGTCAAA
196 GAGACGCCAAA
* * *
30152639 CTTCGATTTTCTTCTCTGACAATACAGAGATGCAAAATCATCTTAGACTTGCTTCAGT-GTAAGC
1 CTTCGA-TTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCA-TCGTAAGC
* * *
30152703 ACGTGAAAGCTAAATCAGCTATGAT-TTCGATTTGTTCCTTGTAAACACAAGGATGCCAAATCAT
64 ACGTGAAAGCCAAATCAGCTATG-TCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCAT
*
30152767 CTTGGATCTGCTTCAGTATAAACATCTGAAGGCCAAATCTGCTATGTATCTGCTCTTCGTCGAAT
128 CTTGGATCTGCTTCAGTATAAACATCTGAAGGCCAAATCTGCTATGTATCTGCCCTTCGTCGAAT
30152832 ATGGAGACGCCAAA
193 ATGGAGACGCCAAA
* *
30152846 CTTTGATTTGTTCTCTGACAATATAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCAC
*
30152911 ATGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
30152976 GGATCTTGCTTCAG
131 GGATC-TGCTTCAG
30152990 CCAGATCTGC
Statistics
Matches: 314, Mismatches: 31, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
205 2 0.01
206 123 0.39
207 188 0.60
208 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.31
Consensus pattern (206 bp):
CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCAC
GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
GGATCTGCTTCAGTATAAACATCTGAAGGCCAAATCTGCTATGTATCTGCCCTTCGTCGAATATG
GAGACGCCAAA
Found at i:30166882 original size:25 final size:25
Alignment explanation
Indices: 30166830--30166894 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
30166820 TCCTGTACAT
*
30166830 GTATGCTCATATGAGCTATGATTCG
1 GTATGCTCATATGAGCTATAATTCG
30166855 GTATGCTC-TCATGAGCTATAAATT-G
1 GTATGCTCAT-ATGAGCTAT-AATTCG
* *
30166880 GTAAGCTTATATGAG
1 GTATGCTCATATGAG
30166895 TTGAGAATTG
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
24 1 0.03
25 29 0.85
26 4 0.12
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (25 bp):
GTATGCTCATATGAGCTATAATTCG
Found at i:30168961 original size:18 final size:18
Alignment explanation
Indices: 30168938--30168972 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
30168928 TTCGACTGCA
30168938 CCATGCGGAAATATGTGG
1 CCATGCGGAAATATGTGG
30168956 CCATGCGGAAATATGTG
1 CCATGCGGAAATATGTG
30168973 AGTGATAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.23
Consensus pattern (18 bp):
CCATGCGGAAATATGTGG
Found at i:30171032 original size:199 final size:199
Alignment explanation
Indices: 30170692--30171297 Score: 1185
Period size: 199 Copynumber: 3.0 Consensus size: 199
30170682 CTACTACTGG
*
30170692 AATTTTGTGCATACAAGTCAAGAGACTCAAACCCTTAATGTCGGTAATCGTCCATCCGATCACCC
1 AATTTTGGGCATACAAGTCAAGAGACTCAAACCCTTAATGTCGGTAATCGTCCATCCGATCACCC
30170757 CTTTATAATCTCTAAGAACTTGTACCAAATTTTCTTCTTACAACTTCAAGAGTTTACTTGAGATT
66 CTTTATAATCTCTAAGAACTTGTACCAAATTTTCTTCTTACAACTTCAAGAGTTTACTTGAGATT
30170822 ATTACTGGCAAGGTATTTCCTTCGCCCAGGAAGGCGTGCTTCAAATGGTTCGGTAGTGGTTTGAG
131 ATTACTGGCAAGGTATTTCCTTCGCCCAGGAAGGCGTGCTTCAAATGGTTCGGTAGTGGTTTGAG
30170887 TTCC
196 TTCC
30170891 AATTTTGGGCATACAAGTCAAGAGACTCAAACCCTTAATGTCGGTAATCGTCCATCCGATCACCC
1 AATTTTGGGCATACAAGTCAAGAGACTCAAACCCTTAATGTCGGTAATCGTCCATCCGATCACCC
30170956 CTTTATAATCTCTAAGAACTTGTACCAAATTTTCTTCTTACAACTTCAAGAGTTTACTTGAGATT
66 CTTTATAATCTCTAAGAACTTGTACCAAATTTTCTTCTTACAACTTCAAGAGTTTACTTGAGATT
30171021 ATTACTGGCAAGGTATTTCCTTCGCCCAGGAAGGCGTGCTTCAAATGGTTCGGTAGTGGTTTGAG
131 ATTACTGGCAAGGTATTTCCTTCGCCCAGGAAGGCGTGCTTCAAATGGTTCGGTAGTGGTTTGAG
30171086 TTCC
196 TTCC
30171090 AATTTTGGGCATACAAGTCAAGAGACTCAAACCCTTAATGTCGGTAATCGTCCATCCGATCACCC
1 AATTTTGGGCATACAAGTCAAGAGACTCAAACCCTTAATGTCGGTAATCGTCCATCCGATCACCC
30171155 CTTTATAATCTCTAAGAACTTGTACCAAATTTTCTTCTTACAACTTCAAGAGTTTACTTGAGATT
66 CTTTATAATCTCTAAGAACTTGTACCAAATTTTCTTCTTACAACTTCAAGAGTTTACTTGAGATT
* *
30171220 ATTACTGGCAAGGTATTTCCTTCGCCCAGGAAGGCGTGCTTCAGATGGTTCGATAGTGGTTTGAG
131 ATTACTGGCAAGGTATTTCCTTCGCCCAGGAAGGCGTGCTTCAAATGGTTCGGTAGTGGTTTGAG
30171285 TTCC
196 TTCC
30171289 AATTTTGGG
1 AATTTTGGG
30171298 GCCTACAAAA
Statistics
Matches: 404, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
199 404 1.00
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.33
Consensus pattern (199 bp):
AATTTTGGGCATACAAGTCAAGAGACTCAAACCCTTAATGTCGGTAATCGTCCATCCGATCACCC
CTTTATAATCTCTAAGAACTTGTACCAAATTTTCTTCTTACAACTTCAAGAGTTTACTTGAGATT
ATTACTGGCAAGGTATTTCCTTCGCCCAGGAAGGCGTGCTTCAAATGGTTCGGTAGTGGTTTGAG
TTCC
Found at i:30173127 original size:43 final size:42
Alignment explanation
Indices: 30173044--30173203 Score: 137
Period size: 43 Copynumber: 3.7 Consensus size: 42
30173034 AGGATTTCCG
* * *
30173044 ATATGTG-TTCTCGTGTAAGACCACGTATGGGACGTTGGCATCA
1 ATATGTGATT-TCGTGTAAGACCATGTCTGGGAC-ATGGCATCA
* *
30173087 ATATGTGATTTCGAGTAAGACCATGTCTAGGACATCGGCATCGTA
1 ATATGTGATTTCGTGTAAGACCATGTCTGGGACAT-GGCATC--A
* *
30173132 AT-TGTGATTT-GTGTAAGACCTTGTCTGGGACAGTGGCATCG
1 ATATGTGATTTCGTGTAAGACCATGTCTGGGACA-TGGCATCA
* * * * *
30173173 ACATGTGATTACATGTAAGCCCACGTCTGGG
1 ATATGTGATTTCGTGTAAGACCATGTCTGGG
30173204 TTGTTGGCAC
Statistics
Matches: 95, Mismatches: 15, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
41 1 0.01
42 8 0.08
43 72 0.76
44 11 0.12
45 3 0.03
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (42 bp):
ATATGTGATTTCGTGTAAGACCATGTCTGGGACATGGCATCA
Found at i:30183047 original size:16 final size:16
Alignment explanation
Indices: 30183026--30183076 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
30183016 TTAAAACTTG
30183026 AAATAATCTAAATTCA
1 AAATAATCTAAATTCA
* *
30183042 AAATAATTTAAA-TCC
1 AAATAATCTAAATTCA
* * *
30183057 TAATAAACTTAATTCA
1 AAATAATCTAAATTCA
30183073 AAAT
1 AAAT
30183077 TATCAATTTA
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
15 10 0.38
16 16 0.62
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (16 bp):
AAATAATCTAAATTCA
Found at i:30184353 original size:18 final size:19
Alignment explanation
Indices: 30184319--30184354 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
30184309 AGAGAAGAAG
*
30184319 AAAATGAAAACAAATAAAT
1 AAAAAGAAAACAAATAAAT
30184338 AAAAAGAAAA-AAATAAA
1 AAAAAGAAAACAAATAAA
30184355 AGTATAGGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.81, C:0.03, G:0.06, T:0.11
Consensus pattern (19 bp):
AAAAAGAAAACAAATAAAT
Found at i:30194634 original size:26 final size:26
Alignment explanation
Indices: 30194584--30194634 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
30194574 CCAACAAAGT
* *
30194584 TTTGATGATTTTACCCCTAATAAAAA
1 TTTGACGATTTTACCCCTAACAAAAA
* *
30194610 TTTGACGATTTTATCCCTGACAAAA
1 TTTGACGATTTTACCCCTAACAAAA
30194635 TTTCGAGAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (26 bp):
TTTGACGATTTTACCCCTAACAAAAA
Found at i:30197969 original size:27 final size:27
Alignment explanation
Indices: 30197939--30198115 Score: 169
Period size: 27 Copynumber: 6.5 Consensus size: 27
30197929 ATATTGAGCC
* *
30197939 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * *
30197966 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
30197993 CGCACACTTAGTGCTACATAGTCAGACT
1 CGCACACTTAGTGCTACATAATCA-ACT
** ** *
30198021 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
30198048 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
30198075 CGCACACTTAGTGCAACATAGTCGAA-T
1 CGCACACTTAGTGCTACATAATC-AACT
30198102 CGCACACTTAGTGC
1 CGCACACTTAGTGC
30198116 CGCACAATTT
Statistics
Matches: 127, Mismatches: 19, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
27 102 0.80
28 25 0.20
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:30198078 original size:82 final size:81
Alignment explanation
Indices: 30197960--30198119 Score: 232
Period size: 82 Copynumber: 2.0 Consensus size: 81
30197950 TGCTATATAA
* * *
30197960 TCAACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTCAGACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTC-GAATCGCA
30198025 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
30198042 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTTAGTGCAACATAGTCGAATCGCA
30198106 CACTTAGTGCCGCA
65 CACTTAGTGCCGCA
30198120 CAATTTAATC
Statistics
Matches: 70, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
81 23 0.33
82 47 0.67
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTCGAATCGCAC
ACTTAGTGCCGCATGG
Found at i:30199067 original size:18 final size:15
Alignment explanation
Indices: 30199027--30199056 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
30199017 GATCGGTAAC
30199027 TCTTTTGTTTTCATA
1 TCTTTTGTTTTCATA
30199042 TCTTTTGTTTTCATA
1 TCTTTTGTTTTCATA
30199057 ATTTCTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.13, G:0.07, T:0.67
Consensus pattern (15 bp):
TCTTTTGTTTTCATA
Found at i:30203437 original size:50 final size:50
Alignment explanation
Indices: 30203362--30203463 Score: 195
Period size: 50 Copynumber: 2.0 Consensus size: 50
30203352 TGACGTCGGG
30203362 GGAGGATGCCTCCTCTCGTGCGCGAATGGCATAGGCTCTAGCAGGAGTAC
1 GGAGGATGCCTCCTCTCGTGCGCGAATGGCATAGGCTCTAGCAGGAGTAC
*
30203412 GGAGGATGCCTCCTCTCGTGCGCGAATGGCATATGCTCTAGCAGGAGTAC
1 GGAGGATGCCTCCTCTCGTGCGCGAATGGCATAGGCTCTAGCAGGAGTAC
30203462 GG
1 GG
30203464 TTCTCGGCGC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.20, C:0.25, G:0.34, T:0.21
Consensus pattern (50 bp):
GGAGGATGCCTCCTCTCGTGCGCGAATGGCATAGGCTCTAGCAGGAGTAC
Found at i:30206209 original size:27 final size:27
Alignment explanation
Indices: 30206179--30206356 Score: 180
Period size: 27 Copynumber: 6.6 Consensus size: 27
30206169 ATATCGAGTC
* *
30206179 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
30206206 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
30206233 CGCACACTTAGTGCCACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
30206261 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
30206288 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
30206315 CGCACACTTAGTGCAACATAGTCGAA-T
1 CGCACACTTAGTGCTACATAATC-AACT
30206342 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
30206357 GTACAATTTA
Statistics
Matches: 131, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
27 105 0.80
28 26 0.20
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:30206318 original size:82 final size:81
Alignment explanation
Indices: 30206200--30206355 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
30206190 TGCTATATAA
*
30206200 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCCACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
30206265 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * ** *
30206282 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
30206346 CACTTAGTGC
65 CACTTAGTGC
30206356 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:30211053 original size:40 final size:39
Alignment explanation
Indices: 30210965--30211059 Score: 102
Period size: 40 Copynumber: 2.4 Consensus size: 39
30210955 TAAATCAGTA
*
30210965 TCGCACACTTAGTGCCTTCTATAGCCGAAGCTATTCCAAC
1 TCGCACACTTAGTG-CTTCTATAGCCGAAGCTATTCAAAC
* * * * *
30211005 TCGTACACTTAGTGCTATTTATAGCTGATGCTATATTAAAC
1 TCGCACACTTAGTGCT-TCTATAGCCGAAGCTAT-TCAAAC
30211046 -CGCACACTTAGTGC
1 TCGCACACTTAGTGC
30211060 CAATCATAGT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
39 2 0.04
40 40 0.87
41 4 0.09
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (39 bp):
TCGCACACTTAGTGCTTCTATAGCCGAAGCTATTCAAAC
Found at i:30215151 original size:26 final size:26
Alignment explanation
Indices: 30215122--30215182 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
30215112 ATTTACTAAA
* *
30215122 ATACCCCTAAGTATAAAATTACCATT
1 ATACCCCTAAGTACAAAATGACCATT
* * *
30215148 ATACCCCTAGGTGCAAAGTGACCATT
1 ATACCCCTAAGTACAAAATGACCATT
30215174 ATACCCCTA
1 ATACCCCTA
30215183 GGGTTAATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.36, C:0.28, G:0.10, T:0.26
Consensus pattern (26 bp):
ATACCCCTAAGTACAAAATGACCATT
Found at i:30215332 original size:28 final size:28
Alignment explanation
Indices: 30215287--30215376 Score: 105
Period size: 28 Copynumber: 3.3 Consensus size: 28
30215277 GGAAGAAGCG
**
30215287 TTCTGGTGGCTATGCCACAAATATCTGT
1 TTCTGGTGGCTACACCACAAATATCTGT
*
30215315 TTCTGGAGGCTACACCACAAATATCTG-
1 TTCTGGTGGCTACACCACAAATATCTGT
*
30215342 TTCTGGTGGCT-CTACCA-TAATATCTGT
1 TTCTGGTGGCTAC-ACCACAAATATCTGT
*
30215369 GTCTGGTG
1 TTCTGGTG
30215377 ACTCTGTCAC
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
26 9 0.17
27 21 0.39
28 24 0.44
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.34
Consensus pattern (28 bp):
TTCTGGTGGCTACACCACAAATATCTGT
Found at i:30215358 original size:27 final size:27
Alignment explanation
Indices: 30215286--30215401 Score: 121
Period size: 27 Copynumber: 4.3 Consensus size: 27
30215276 TGGAAGAAGC
* *
30215286 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTCTACCACAAATATCT
*
30215313 GTTTCTGGAGGCTAC-ACCACAAATATCT
1 G-TTCTGGTGGCT-CTACCACAAATATCT
*
30215341 GTTCTGGTGGCTCTACCA-TAATATCT
1 GTTCTGGTGGCTCTACCACAAATATCT
* **
30215367 GTGTCTGGTGACTCTGTCAC-AATATCT
1 GT-TCTGGTGGCTCTACCACAAATATCT
30215394 GTTCTGGT
1 GTTCTGGT
30215402 AGCCATGCTA
Statistics
Matches: 76, Mismatches: 8, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
26 16 0.21
27 37 0.49
28 23 0.30
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.35
Consensus pattern (27 bp):
GTTCTGGTGGCTCTACCACAAATATCT
Found at i:30221637 original size:40 final size:39
Alignment explanation
Indices: 30221548--30221643 Score: 120
Period size: 40 Copynumber: 2.4 Consensus size: 39
30221538 ATAAATCGGT
30221548 ATCGCACACTTAGTGCCTTCTATAGCCGAAGCTATACCAA
1 ATCGCACACTTAGTG-CTTCTATAGCCGAAGCTATACCAA
* * * ***
30221588 CTCGTACACTTAGTGCTATTTATAGCCGAAGCTATTTTAA
1 ATCGCACACTTAGTGCT-TCTATAGCCGAAGCTATACCAA
30221628 ATCGCACACTTAGTGC
1 ATCGCACACTTAGTGC
30221644 CAGTCATAGT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
39 2 0.04
40 45 0.96
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (39 bp):
ATCGCACACTTAGTGCTTCTATAGCCGAAGCTATACCAA
Found at i:30224398 original size:20 final size:20
Alignment explanation
Indices: 30224375--30224609 Score: 115
Period size: 20 Copynumber: 11.8 Consensus size: 20
30224365 TACTTCAGTA
30224375 CCCCTGATTGCACTTACATG
1 CCCCTGATTGCACTTACATG
* * * *
30224395 CCCCTGTTTGTA-TTTCAGTA
1 CCCCTGATTGCACTTACA-TG
* *
30224415 CCCCTAATTACACTTACATG
1 CCCCTGATTGCACTTACATG
* * *
30224435 CCCCTGTTTGTACTTTA-ATA
1 CCCCTGATTGCAC-TTACATG
* *
30224455 CCCCAGATTGCACTTACGTG
1 CCCCTGATTGCACTTACATG
* * * *
30224475 CCCCAG-TTGGTACTT-CGGTA
1 CCCCTGATT-GCACTTAC-ATG
* *
30224495 CTCCTGATTGCACTTACGTG
1 CCCCTGATTGCACTTACATG
* * *
30224515 CCCCTGTTTGTACTTA-AGTA
1 CCCCTGATTGCACTTACA-TG
**
30224535 CCTTTGATTGCACTTACATG
1 CCCCTGATTGCACTTACATG
* * *
30224555 CCCCTGTTTGTACTT-CAGTA
1 CCCCTGATTGCACTTACA-TG
*
30224575 CCCCTGATTGCACAT-CGATG
1 CCCCTGATTGCACTTAC-ATG
*
30224595 CCCCTGTTTGCACTT
1 CCCCTGATTGCACTT
30224610 TGGTGCCCCT
Statistics
Matches: 156, Mismatches: 47, Indels: 24
0.69 0.21 0.11
Matches are distributed among these distances:
19 12 0.08
20 132 0.85
21 12 0.08
ACGTcount: A:0.18, C:0.31, G:0.16, T:0.35
Consensus pattern (20 bp):
CCCCTGATTGCACTTACATG
Found at i:30224415 original size:40 final size:40
Alignment explanation
Indices: 30224361--30224609 Score: 329
Period size: 40 Copynumber: 6.2 Consensus size: 40
30224351 ATGTTCCCCA
30224361 TTTGTACTTCAGTACCCCTGATTGCACTTACATGCCCCTG
1 TTTGTACTTCAGTACCCCTGATTGCACTTACATGCCCCTG
* * *
30224401 TTTGTATTTCAGTACCCCTAATTACACTTACATGCCCCTG
1 TTTGTACTTCAGTACCCCTGATTGCACTTACATGCCCCTG
* * * * *
30224441 TTTGTACTTTAATACCCCAGATTGCACTTACGTGCCCCAG
1 TTTGTACTTCAGTACCCCTGATTGCACTTACATGCCCCTG
* * * *
30224481 TTGGTACTTCGGTACTCCTGATTGCACTTACGTGCCCCTG
1 TTTGTACTTCAGTACCCCTGATTGCACTTACATGCCCCTG
* **
30224521 TTTGTACTTAAGTACCTTTGATTGCACTTACATGCCCCTG
1 TTTGTACTTCAGTACCCCTGATTGCACTTACATGCCCCTG
*
30224561 TTTGTACTTCAGTACCCCTGATTGCACAT-CGATGCCCCTG
1 TTTGTACTTCAGTACCCCTGATTGCACTTAC-ATGCCCCTG
*
30224601 TTTGCACTT
1 TTTGTACTT
30224610 TGGTGCCCCT
Statistics
Matches: 178, Mismatches: 30, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
39 1 0.01
40 177 0.99
ACGTcount: A:0.18, C:0.30, G:0.16, T:0.36
Consensus pattern (40 bp):
TTTGTACTTCAGTACCCCTGATTGCACTTACATGCCCCTG
Found at i:30224616 original size:20 final size:20
Alignment explanation
Indices: 30224462--30224627 Score: 86
Period size: 20 Copynumber: 8.2 Consensus size: 20
30224452 ATACCCCAGA
*
30224462 TTGCACTTAC-GTGCCCCAGT
1 TTGCACTT-CGGTGCCCCTGT
* * * * *
30224482 TGGTACTTCGGTACTCCTGA
1 TTGCACTTCGGTGCCCCTGT
30224502 TTGCACTTAC-GTGCCCCTGT
1 TTGCACTT-CGGTGCCCCTGT
* ** * ** *
30224522 TTGTACTTAAGTACCTTTGA
1 TTGCACTTCGGTGCCCCTGT
*
30224542 TTGCACTTAC-ATGCCCCTGT
1 TTGCACTT-CGGTGCCCCTGT
* * * *
30224562 TTGTACTTCAGTACCCCTGA
1 TTGCACTTCGGTGCCCCTGT
* *
30224582 TTGCACATCGATGCCCCTGT
1 TTGCACTTCGGTGCCCCTGT
*
30224602 TTGCACTTTGGTGCCCCTGT
1 TTGCACTTCGGTGCCCCTGT
30224622 TGTGCA
1 T-TGCA
30224628 TCTATGATGC
Statistics
Matches: 103, Mismatches: 37, Indels: 11
0.68 0.25 0.07
Matches are distributed among these distances:
19 2 0.02
20 96 0.93
21 5 0.05
ACGTcount: A:0.15, C:0.30, G:0.20, T:0.36
Consensus pattern (20 bp):
TTGCACTTCGGTGCCCCTGT
Found at i:30229660 original size:21 final size:20
Alignment explanation
Indices: 30229636--30229674 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
30229626 GAGTACTTCG
30229636 ATGTTTAATGATAGATTATGA
1 ATGTTTAATGATAG-TTATGA
*
30229657 ATGTTTGATGATAGTTAT
1 ATGTTTAATGATAGTTAT
30229675 ACAAGTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (20 bp):
ATGTTTAATGATAGTTATGA
Found at i:30236984 original size:93 final size:93
Alignment explanation
Indices: 30236871--30237042 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
30236861 CGCCCATAAG
* * *
30236871 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCAGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCAGACTCAACTCA
30236936 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
* *
30236964 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCAGACTCAACTCA
30237029 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
30237043 TCAATCATCC
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCAGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:30237039 original size:46 final size:46
Alignment explanation
Indices: 30236864--30237039 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
30236854 TGTAACCCGC
* * * *
30236864 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCACAT
* *
30236910 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCACAT
*
30236960 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCACAT
*
30237003 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
30237040 TGCTCAATCA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
44 2 0.02
45 2 0.02
46 62 0.56
47 28 0.25
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCACAT
Found at i:30239352 original size:27 final size:26
Alignment explanation
Indices: 30239322--30239454 Score: 115
Period size: 27 Copynumber: 4.9 Consensus size: 26
30239312 TACCCCTGGG
*
30239322 TTGTAAAGTTATCGAAATACCCTTGAT
1 TTGTAAA-TTACCGAAATACCCTTGAT
* **
30239349 TTGTGAAATTACCCAAATACCCTCAAT
1 TTGT-AAATTACCGAAATACCCTTGAT
* ** *
30239376 TTTTGAAATTACCGAAATACCCCAGAC
1 TTGT-AAATTACCGAAATACCCTTGAT
* *
30239403 TTGTAAAATTACTGAAATACCCCT-AGT
1 TTGT-AAATTACCGAAATACCCTTGA-T
30239430 TTGTATAATTACCGAAATACCCTTG
1 TTGTA-AATTACCGAAATACCCTTG
30239455 TAGTGTAAAA
Statistics
Matches: 85, Mismatches: 17, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 80 0.94
28 3 0.04
ACGTcount: A:0.35, C:0.21, G:0.11, T:0.32
Consensus pattern (26 bp):
TTGTAAATTACCGAAATACCCTTGAT
Found at i:30239474 original size:27 final size:26
Alignment explanation
Indices: 30239404--30239492 Score: 79
Period size: 27 Copynumber: 3.3 Consensus size: 26
30239394 ACCCCAGACT
* * *
30239404 TGTAAAATTACTGAAATACCCCTAGTT
1 TGTAAAATTACAGAAATA-CCCTTGTA
* *
30239431 TGTATAATTACCGAAATACCCTTGTA
1 TGTAAAATTACAGAAATACCCTTGTA
* **
30239457 GTGTAAAATTACAAAAATATTCTTGTA
1 -TGTAAAATTACAGAAATACCCTTGTA
30239484 TGGTAAAAT
1 T-GTAAAAT
30239493 GACTATTTTA
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
26 7 0.14
27 44 0.86
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.35
Consensus pattern (26 bp):
TGTAAAATTACAGAAATACCCTTGTA
Found at i:30239475 original size:54 final size:53
Alignment explanation
Indices: 30239292--30239475 Score: 156
Period size: 54 Copynumber: 3.4 Consensus size: 53
30239282 TAGGACCCCC
* * * * * *
30239292 GACTTGTAAAGTTCCTAAAATACCCCTGGGTTGTAAAGTTATCGAAATACCCTT
1 GACTTGTAAAATTACAAAAATACCCCTAGTTTGTAAA-TTACCGAAATACCCTT
* * ** * * **
30239346 GATTTGTGAAATTACCCAAATA-CCCTCAATTTTTGAAATTACCGAAATACCCCA
1 GACTTGTAAAATTACAAAAATACCCCT-AGTTTGT-AAATTACCGAAATACCCTT
**
30239400 GACTTGTAAAATTACTGAAATACCCCTAGTTTGTATAATTACCGAAATACCCTT
1 GACTTGTAAAATTACAAAAATACCCCTAGTTTGTA-AATTACCGAAATACCCTT
*
30239454 GTA-GTGTAAAATTACAAAAATA
1 G-ACTTGTAAAATTACAAAAATA
30239476 TTCTTGTATG
Statistics
Matches: 101, Mismatches: 24, Indels: 10
0.75 0.18 0.07
Matches are distributed among these distances:
53 5 0.05
54 88 0.87
55 8 0.08
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.31
Consensus pattern (53 bp):
GACTTGTAAAATTACAAAAATACCCCTAGTTTGTAAATTACCGAAATACCCTT
Found at i:30240988 original size:50 final size:50
Alignment explanation
Indices: 30240930--30241029 Score: 191
Period size: 50 Copynumber: 2.0 Consensus size: 50
30240920 GTTTTCGAAA
*
30240930 AACACTTCAATGTGACATGTCAGATCGGGTTTGGGGTGTTACAAACTAAC
1 AACACTTCAATGTGACATGTCAGATCAGGTTTGGGGTGTTACAAACTAAC
30240980 AACACTTCAATGTGACATGTCAGATCAGGTTTGGGGTGTTACAAACTAAC
1 AACACTTCAATGTGACATGTCAGATCAGGTTTGGGGTGTTACAAACTAAC
30241030 TAATGCTCCT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (50 bp):
AACACTTCAATGTGACATGTCAGATCAGGTTTGGGGTGTTACAAACTAAC
Found at i:30243671 original size:25 final size:25
Alignment explanation
Indices: 30243643--30243690 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
30243633 TTATATTATG
* * *
30243643 AAAATGACTGTTTTGCCCCTAGGTA
1 AAAATGACCGTTATACCCCTAGGTA
30243668 AAAATGACCGTTATACCCCTAGG
1 AAAATGACCGTTATACCCCTAGG
30243691 GTTTACTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (25 bp):
AAAATGACCGTTATACCCCTAGGTA
Found at i:30243832 original size:27 final size:26
Alignment explanation
Indices: 30243802--30243923 Score: 185
Period size: 26 Copynumber: 4.7 Consensus size: 26
30243792 GAGGAAGTGC
30243802 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
30243828 AAAAAGGGGTTATGCCCCAGTTTATTG
1 -AAAAGGGCTTATGCCCCAGTTTATTG
*
30243855 AAAAGGGCTGATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
**
30243881 AAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
30243906 AAAAGGGCTT-TGCCCCAG
1 AAAAGGGCTTATGCCCCAG
30243924 GTATTAAAGA
Statistics
Matches: 89, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
25 31 0.35
26 33 0.37
27 25 0.28
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.26
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:30245009 original size:17 final size:17
Alignment explanation
Indices: 30244987--30245019 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
30244977 AGTGAAAACG
30244987 AGTAAAACA-ACATAATC
1 AGTAAAA-ATACATAATC
30245004 AGTAAAAATACATAAT
1 AGTAAAAATACATAAT
30245020 GTTCATAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.07
17 14 0.93
ACGTcount: A:0.61, C:0.12, G:0.06, T:0.21
Consensus pattern (17 bp):
AGTAAAAATACATAATC
Found at i:30245964 original size:47 final size:47
Alignment explanation
Indices: 30245895--30246060 Score: 271
Period size: 47 Copynumber: 3.5 Consensus size: 47
30245885 AGACACATAG
30245895 GACAAGGATACCATGTAAGACCATGTTTGGAACATGGAATTTGGTAA
1 GACAAGGATACCATGTAAGACCATGTTTGGAACATGGAATTTGGTAA
* *
30245942 GACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGCAA
1 GACAAGGATACCATGTAAGACCATGTTTGGAACATGGAATTTGGTAA
*
30245989 GACAAGGATACCATGTAAGACCATGTTTGGAACA-CGACATTTGGTAA
1 GACAAGGATACCATGTAAGACCATGTTTGGAACATGGA-ATTTGGTAA
* *
30246036 GATAAGGATATCATGTAAGACCATG
1 GACAAGGATACCATGTAAGACCATG
30246061 CCAAGGCATG
Statistics
Matches: 111, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
46 1 0.01
47 110 0.99
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.24
Consensus pattern (47 bp):
GACAAGGATACCATGTAAGACCATGTTTGGAACATGGAATTTGGTAA
Found at i:30271087 original size:46 final size:46
Alignment explanation
Indices: 30271037--30271212 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
30271027 TGGTTGAGCA
30271037 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
30271083 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* **
30271128 CATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACA
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
30271176 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
30271213 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 62 0.57
47 28 0.26
48 2 0.02
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:30271193 original size:93 final size:93
Alignment explanation
Indices: 30271034--30271205 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
30271024 GGATGGTTGA
***
30271034 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAGT
30271099 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
30271127 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACACCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAGT
30271192 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
30271206 CTTATGGGCG
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:30279550 original size:11 final size:11
Alignment explanation
Indices: 30279496--30279553 Score: 52
Period size: 11 Copynumber: 5.6 Consensus size: 11
30279486 CATGGTATGT
30279496 ATGATATGCAC
1 ATGATATGCAC
* *
30279507 ATGACATG--T
1 ATGATATGCAC
30279516 ATGATATGCAC
1 ATGATATGCAC
* *
30279527 ATAATATG--T
1 ATGATATGCAC
30279536 ATGATATGCAC
1 ATGATATGCAC
30279547 ATGATAT
1 ATGATAT
30279554 ATTCATAAAT
Statistics
Matches: 35, Mismatches: 8, Indels: 8
0.69 0.16 0.16
Matches are distributed among these distances:
9 14 0.40
11 21 0.60
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:30279553 original size:20 final size:20
Alignment explanation
Indices: 30279485--30279553 Score: 111
Period size: 20 Copynumber: 3.5 Consensus size: 20
30279475 ATTTTGATAA
*
30279485 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
30279505 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
*
30279525 ACATAATATGTATGATATGC
1 ACATGATATGTATGATATGC
30279545 ACATGATAT
1 ACATGATAT
30279554 ATTCATAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:30279663 original size:24 final size:23
Alignment explanation
Indices: 30279601--30279747 Score: 143
Period size: 24 Copynumber: 6.2 Consensus size: 23
30279591 GAGGAAGTGA
*
30279601 AAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTACGCCCCAGTTAT
* *
30279624 TAAAGGGCTT-CTGCCCTAGTTAT
1 AAAAGGGCTTAC-GCCCCAGTTAT
* *
30279647 CAAAAGGACTTACGCCCTAGTTAT
1 -AAAAGGGCTTACGCCCCAGTTAT
*
30279671 CAAAAGGGCTTACGGCCCAGTTAT
1 -AAAAGGGCTTACGCCCCAGTTAT
* *
30279695 TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTACGCCCCAGTTAT
** *
30279718 AAAAAGGGCTTTTGCCCCATTTATT
1 -AAAAGGGCTTACGCCCCAGTTA-T
30279743 AAAAG
1 AAAAG
30279748 AGGTAAGGCC
Statistics
Matches: 105, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
23 39 0.37
24 64 0.61
25 2 0.02
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (23 bp):
AAAAGGGCTTACGCCCCAGTTAT
Found at i:30279742 original size:47 final size:46
Alignment explanation
Indices: 30279602--30279745 Score: 162
Period size: 47 Copynumber: 3.1 Consensus size: 46
30279592 AGGAAGTGAA
* * * *
30279602 AAAGGGCTTATGCCCCAGTTATTAAAGGGCTTCTGCCCTAGTTATCA
1 AAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTAT-T
* * * * *
30279649 AAAGGACTTACGCCCTAGTTATCAAAAGGGCTTACGGCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATT
* *
30279696 AAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTTTGCCCCATTTATT
1 AAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATT
30279743 AAA
1 AAA
30279746 AGAGGTAAGG
Statistics
Matches: 79, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
47 61 0.77
48 18 0.23
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.28
Consensus pattern (46 bp):
AAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
Found at i:30279747 original size:71 final size:71
Alignment explanation
Indices: 30279601--30279747 Score: 195
Period size: 71 Copynumber: 2.1 Consensus size: 71
30279591 GAGGAAGTGA
* * * * *
30279601 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTCTGCCCTAGTTATCAAAAGGACTTACGCCCTA
1 AAAAGGGCTTACGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATAAAAAGGACTTACGCCCCA
30279666 GTTATC
66 GTTATC
* * **
30279672 AAAAGGGCTTACGGCCCAGTTATTAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTTTGCCCCA
1 AAAAGGGCTTACGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATAAAAAGGACTTACGCCCCA
* *
30279737 TTTATT
66 GTTATC
30279743 AAAAG
1 AAAAG
30279748 AGGTAAGGCC
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
71 65 1.00
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (71 bp):
AAAAGGGCTTACGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATAAAAAGGACTTACGCCCCA
GTTATC
Found at i:30279995 original size:31 final size:31
Alignment explanation
Indices: 30279960--30280023 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
30279950 CGTTTACAGT
* *
30279960 AAAGGCTTCGGCCCAGTAATATGAAATTTGA
1 AAAGGCTTCGGCCCAATAATATGAAATATGA
**
30279991 AAAGGCTTCGGCCCAATGTTATGAAATATGA
1 AAAGGCTTCGGCCCAATAATATGAAATATGA
30280022 AA
1 AA
30280024 TATGAAAAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAATAATATGAAATATGA
Found at i:30282441 original size:29 final size:29
Alignment explanation
Indices: 30282390--30282455 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
30282380 TGTATAACTG
* *
30282390 AGTGTGCGAGCTTGAAATGCATGGCGCTA
1 AGTGTGCGAGCTTGAAATACATGGCACTA
*
30282419 AGTGTGCGAG-TTTAAAGTACATGGCACTA
1 AGTGTGCGAGCTTGAAA-TACATGGCACTA
30282448 AGTGTGCG
1 AGTGTGCG
30282456 CGGTTGATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 5 0.15
29 28 0.85
ACGTcount: A:0.26, C:0.15, G:0.33, T:0.26
Consensus pattern (29 bp):
AGTGTGCGAGCTTGAAATACATGGCACTA
Found at i:30290124 original size:27 final size:28
Alignment explanation
Indices: 30290040--30290137 Score: 126
Period size: 27 Copynumber: 3.5 Consensus size: 28
30290030 TGAGAGATTG
* * **
30290040 GCACTAAGTGTGCGGGTTTAAATTGCATA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
*
30290069 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
30290097 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
30290124 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
30290138 GACTTAATAT
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
27 24 0.39
28 21 0.34
29 17 0.27
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:30290148 original size:27 final size:27
Alignment explanation
Indices: 30290066--30290150 Score: 91
Period size: 27 Copynumber: 3.1 Consensus size: 27
30290056 TTTAAATTGC
* * *
30290066 ATAGCACTAAGTGTGCAAGTTTGATTAT
1 ATAGCACTAAGTGTGCGA-CTTGAATAT
* *
30290094 ATAGCACTAAGTGTGCGAGTTGATTAT
1 ATAGCACTAAGTGTGCGACTTGAATAT
*
30290121 ATAGCACTGAGTGTGCGGACTT-AATAT
1 ATAGCACTAAGTGTGC-GACTTGAATAT
30290148 ATA
1 ATA
30290151 CTTTTGAATC
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
27 30 0.59
28 21 0.41
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.33
Consensus pattern (27 bp):
ATAGCACTAAGTGTGCGACTTGAATAT
Found at i:30299629 original size:20 final size:20
Alignment explanation
Indices: 30299600--30299646 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
30299590 ATTTTGATAA
*
30299600 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
30299620 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
30299640 ACATGAT
1 ACATGAT
30299647 GTATTCATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:30299758 original size:24 final size:23
Alignment explanation
Indices: 30299696--30299841 Score: 202
Period size: 24 Copynumber: 6.2 Consensus size: 23
30299686 GAGGAAGTGA
30299696 AAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
* *
30299719 TAACGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
*
30299742 CAAAAGGACTTATGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
*
30299766 CAAAAGGGCTTACGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
*
30299790 TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
*
30299813 AAAAAGGGCTTTTGCCCCAGTTATT
1 -AAAAGGGCTTATGCCCCAGTTA-T
30299838 AAAA
1 AAAA
30299842 TAGGTAAGGC
Statistics
Matches: 109, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
23 42 0.39
24 66 0.61
25 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (23 bp):
AAAAGGGCTTATGCCCCAGTTAT
Found at i:30299765 original size:47 final size:47
Alignment explanation
Indices: 30299696--30299841 Score: 204
Period size: 47 Copynumber: 3.1 Consensus size: 47
30299686 GAGGAAGTGA
* *
30299696 AAAAGGGCTTATGCCCCAGTTAT-TAACGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCAGTTAT
* * *
30299742 CAAAAGGACTTATGCCCCAGTTATCAAAAGGGCTTACGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCAGTTAT
* *
30299790 TAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCAGTTA-T
30299838 AAAA
1 AAAA
30299842 TAGGTAAGGC
Statistics
Matches: 87, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
47 63 0.72
48 24 0.28
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCAGTTAT
Found at i:30299812 original size:71 final size:71
Alignment explanation
Indices: 30299696--30299841 Score: 238
Period size: 71 Copynumber: 2.1 Consensus size: 71
30299686 GAGGAAGTGA
* * *
30299696 AAAAGGGCTTATGCCCCAGTTATTAACGGGCTTATGCCCCAGTTATCAAAAGGACTTATGCCCCA
1 AAAAGGGCTTACGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATAAAAAGGACTTATGCCCCA
30299761 GTTATC
66 GTTATC
* *
30299767 AAAAGGGCTTACGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTTTGCCCCA
1 AAAAGGGCTTACGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATAAAAAGGACTTATGCCCCA
*
30299832 GTTATT
66 GTTATC
30299838 AAAA
1 AAAA
30299842 TAGGTAAGGC
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (71 bp):
AAAAGGGCTTACGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATAAAAAGGACTTATGCCCCA
GTTATC
Found at i:30300093 original size:31 final size:31
Alignment explanation
Indices: 30300055--30300118 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
30300045 CGTTTACAGT
*
30300055 AAAGGCTTCAGCCCAGTAATATGAAATTTGA
1 AAAGGCTTCAGCCCAGTAATATGAAATATGA
* **
30300086 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCAGCCCAGTAATATGAAATATGA
30300117 AA
1 AA
30300119 TATGAAAAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCAGCCCAGTAATATGAAATATGA
Found at i:30304784 original size:21 final size:21
Alignment explanation
Indices: 30304732--30304777 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
30304722 TAAGGACAAG
*
30304732 AATAAAATAA-AAATGAAATA
1 AATAAAATAATTAATGAAATA
30304752 AATAAAATAATTAATGAAAT-
1 AATAAAATAATTAATGAAATA
30304772 AATAAA
1 AATAAA
30304778 GGAAATTCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (21 bp):
AATAAAATAATTAATGAAATA
Found at i:30304872 original size:3 final size:3
Alignment explanation
Indices: 30304864--30305043 Score: 134
Period size: 3 Copynumber: 60.3 Consensus size: 3
30304854 TGGTTTTAAA
* * * *
30304864 AAT AAT AAT AAT AAA AAT AAT AGT AAT AAT AAT ACT AAT AAT ACT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * * **
30304911 AAT AAT AAT GAC AGT AGT GAT AA- AAT AAT AAT AAT AGT GGT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * *
30304958 AAT AAT AAT AAT AAT AAC AAT AAT AAT AGT AAC AGT AAT AAC AAA AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
30305006 AAT AAC AGA- AAT AAT AAT AA- ATAT AAT AAT AAT GAAT A
1 AAT AAT A-AT AAT AAT AAT AAT A-AT AAT AAT AAT -AAT A
30305044 TAAAACTCAA
Statistics
Matches: 138, Mismatches: 32, Indels: 14
0.75 0.17 0.08
Matches are distributed among these distances:
2 5 0.04
3 128 0.93
4 5 0.04
ACGTcount: A:0.61, C:0.04, G:0.07, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:30306121 original size:46 final size:46
Alignment explanation
Indices: 30306016--30306121 Score: 106
Period size: 46 Copynumber: 2.3 Consensus size: 46
30306006 AAAGTTCAAG
* *
30306016 GAGATAAGAATTG-GTAATTTCAACCTGCTCCACTGCAACTTCAGG
1 GAGATAAGAATTGTGTAATTTCAACCTGCTCCACTACAACTTCAGA
* ** * * ** * *
30306061 GAAATAAGGTTTGTGTATTTTTATTCTTCTCTACTACAACTTCAGA
1 GAGATAAGAATTGTGTAATTTCAACCTGCTCCACTACAACTTCAGA
30306107 GAGATAAGAATTGTG
1 GAGATAAGAATTGTG
30306122 GCTTCGATCT
Statistics
Matches: 46, Mismatches: 14, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
45 10 0.22
46 36 0.78
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (46 bp):
GAGATAAGAATTGTGTAATTTCAACCTGCTCCACTACAACTTCAGA
Found at i:30306221 original size:179 final size:179
Alignment explanation
Indices: 30305921--30306254 Score: 483
Period size: 179 Copynumber: 1.9 Consensus size: 179
30305911 TCCATTGTAT
*
30305921 CTTCAGAGGTATAGGAATTGGTGCTTCGATCCGCTCCAATGTAACTTCAGGGAAAAAAGATTTGT
1 CTTCAGAGGTATAAGAATTGGTGCTTCGATCCGCTCCAATGTAACTTCAGGGAAAAAAGATTTGT
* ** * *
30305986 AGCTTCGATCTACTCTGCTGAAAGTTCAAGGAGATAAGAATTGGTAATTTCAACCTGCTCCACTG
66 AGCTTCAATCTACTCCACTGAAACTTCAAGGAGATAAGAATTGGTAATTTCAACCTGCTCCACCG
30306051 CAACTTCAGGGAAATAAGGTTTGTGTATTTTTATTCTTCTCTACTACAA
131 CAACTTCAGGGAAATAAGGTTTGTGTATTTTTATTCTTCTCTACTACAA
* * * *
30306100 CTTCAGAGAG-ATAAGAATT-GTGGCTTCGATCTGCTCCAATGTAATTTCAGGGAGAAGAGATTT
1 CTTCAGAG-GTATAAGAATTGGT-GCTTCGATCCGCTCCAATGTAACTTCAGGGAAAAAAGATTT
* * * * * *
30306163 GTAGCTTCAATCTACTCCACTGGAACTTCAAGTAGGTAAGAGTTGGTACTTTCAACCTGCTTCAC
64 GTAGCTTCAATCTACTCCACTGAAACTTCAAGGAGATAAGAATTGGTAATTTCAACCTGCTCCAC
*
30306228 CGCAACTTCAGGGAGATAAGGTTTGTG
129 CGCAACTTCAGGGAAATAAGGTTTGTG
30306255 GTCTTCAGTC
Statistics
Matches: 136, Mismatches: 17, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
178 2 0.01
179 133 0.98
180 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (179 bp):
CTTCAGAGGTATAAGAATTGGTGCTTCGATCCGCTCCAATGTAACTTCAGGGAAAAAAGATTTGT
AGCTTCAATCTACTCCACTGAAACTTCAAGGAGATAAGAATTGGTAATTTCAACCTGCTCCACCG
CAACTTCAGGGAAATAAGGTTTGTGTATTTTTATTCTTCTCTACTACAA
Found at i:30306253 original size:89 final size:88
Alignment explanation
Indices: 30305963--30306519 Score: 325
Period size: 89 Copynumber: 6.2 Consensus size: 88
30305953 GCTCCAATGT
* * * * ** *
30305963 AACTTCAGGGAAAAAAGATTTGTAGCTTCGATCTACTCTGCTGA-AAGTTCAAGGAGATAAGAAT
1 AACTTCAGGGAGATAAGGTTTGTAGCTTCAATCTACTCCACT-ACAACTTCAAGGAGATAAGAAT
* *
30306027 TGGTAATTTCAACCTGCTCCACTGC
65 TGGT-ACTTCAACCTGCTCCACCGC
* ** * * * *
30306052 AACTTCAGGGAAATAAGGTTTGTGTATTTTTATTCTTCTCTACTACAACTTC-AGAGAGATAAGA
1 AACTTCAGGGAGATAAGG-TT-TGTAGCTTCAATCTACTCCACTACAACTTCAAG-GAGATAAGA
* * * ** *
30306116 ATT-GTGGCTTCGATCTGCTCCAATGT
63 ATTGGT-ACTTCAACCTGCTCCACCGC
* * ** * * *
30306142 AATTTCAGGGAGA-AGAGATTTGTAGCTTCAATCTACTCCACTGGAACTTCAAGTAGGTAAGAGT
1 AACTTCAGGGAGATA-AGGTTTGTAGCTTCAATCTACTCCACTACAACTTCAAGGAGATAAGAAT
*
30306206 TGGTACTTTCAACCTGCTTCACCGC
65 TGGTAC-TTCAACCTGCTCCACCGC
* * * * * * *
30306231 AACTTCAGGGAGATAAGGTTTGTGGTCTTCAGTCTGCTCCACTACAACTTGAGGGAGATAATACT
1 AACTTCAGGGAGATAAGGTTTGTAG-CTTCAATCTACTCCACTACAACTTCAAGGAGATAAGAAT
* *
30306296 TGCTACTTCAACCTGCTCTACCGC
65 TGGTACTTCAACCTGCTCCACCGC
* * * * * * * *
30306320 AATTTCAGAGAGATAAGGTTTGCTATCTTCGATCTATTTCACAATAACTTC-AGGAAGATAAG-A
1 AACTTCAGGGAGATAAGGTTTG-TAGCTTCAATCTACTCCACTACAACTTCAAGG-AGATAAGAA
* ** * **
30306383 TCTGCTATCTTCAGTCTACTCCACTAC
64 T-TGGTA-CTTCAACCTGCTCCACCGC
* *** * * * * * *
30306410 AACTTCTGGGAGATAATACTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACT
1 AACTTCAGGGAGATAAGGTTTG-TAGCTTCAATCTACTCCACTACAACTTCAAGGAGATAAGAAT
* * * *
30306475 TGCTACTTCAACCTACTCTACTGC
65 TGGTACTTCAACCTGCTCCACCGC
* *
30306499 AACTTTAGAGAGATAAGGTTT
1 AACTTCAGGGAGATAAGGTTT
30306520 TTCATTTTCG
Statistics
Matches: 351, Mismatches: 101, Indels: 32
0.73 0.21 0.07
Matches are distributed among these distances:
88 35 0.10
89 149 0.42
90 132 0.38
91 35 0.10
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (88 bp):
AACTTCAGGGAGATAAGGTTTGTAGCTTCAATCTACTCCACTACAACTTCAAGGAGATAAGAATT
GGTACTTCAACCTGCTCCACCGC
Found at i:30306305 original size:134 final size:134
Alignment explanation
Indices: 30306167--30306519 Score: 349
Period size: 134 Copynumber: 2.6 Consensus size: 134
30306157 AGATTTGTAG
* * * * * *
30306167 CTTCAATCTACTCCACTGGAACTTCAAGTAGGTAAGAGTTGGTACTTTCAACCTGCTTCACCGCA
1 CTTCAATCTGCTCCACTGCAACTTCAAG-AGATAAGAGTTGCTACTTTCAACCTACTTCACAGCA
* * *
30306232 ACTTCAGGGAGATAAGGTTTG-TGGTCTTCAGTCTGCTCCACTACAACTTGAGGGAGATAATACT
65 ACTTCAGGGAGATAAGGTTTGCT-ATCTTCAGTCTACTCCACTACAACTTCAGGGAGATAATACT
30306296 TGCTA-
129 TGCTAT
* * * * * * * *
30306301 CTTCAACCTGCTCTACCGCAATTTCAGAGAGATAAG-GTTTGCTA-TCTTCGATCTATTTCACAA
1 CTTCAATCTGCTCCACTGCAACTTCA-AGAGATAAGAG-TTGCTACT-TTCAACCTACTTCACAG
* * * * *
30306364 TAACTTCAGGAAGATAAGATCTGCTATCTTCAGTCTACTCCACTACAACTTCTGGGAGATAATAC
63 CAACTTCAGGGAGATAAGGTTTGCTATCTTCAGTCTACTCCACTACAACTTCAGGGAGATAATAC
30306429 TTGCTAT
128 TTGCTAT
* * * *
30306436 CTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTAC-TTCAACCTAC-TCTACTGC
1 CTTCAATCTGCTCCACTGCAACTTCA-AGAGATAAGAGTTGCTACTTTCAACCTACTTC-ACAGC
* *
30306499 AACTTTAGAGAGATAAGGTTT
64 AACTTCAGGGAGATAAGGTTT
30306520 TTCATTTTCG
Statistics
Matches: 171, Mismatches: 40, Indels: 16
0.75 0.18 0.07
Matches are distributed among these distances:
133 4 0.02
134 128 0.75
135 39 0.23
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (134 bp):
CTTCAATCTGCTCCACTGCAACTTCAAGAGATAAGAGTTGCTACTTTCAACCTACTTCACAGCAA
CTTCAGGGAGATAAGGTTTGCTATCTTCAGTCTACTCCACTACAACTTCAGGGAGATAATACTTG
CTAT
Found at i:30306371 original size:179 final size:176
Alignment explanation
Indices: 30306010--30306519 Score: 488
Period size: 179 Copynumber: 2.9 Consensus size: 176
30306000 CTGCTGAAAG
* *
30306010 TTCAAGGAGATAAGAATTGGTAATTTCAACCTGCTCCACTGCAACTTCAGGGAAATAAGGTTTGT
1 TTCAAGAAGATAAG-ATTGGT-ATTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGT
* * * * * * * * * * * *
30306075 GTATTTTTATTCTTCTCTACTACAACTTCAGAGAGATAAGAATTG-TGGCTTCGATCTGCTCCAA
64 G-ATCTTCAGTCTGCTCCACTACAACTTCAGGGAGATAAGACTTGCT-ACTTCAACCTGCTCTAC
* * * **
30306139 TGTAATTTCAGGGAGA-AGAGATTTGTAGCTTCAATCTACTCCACTGGAAC
127 TGCAATTTCAGAGAGATA-AGGTTTGTAGCTTCAATCTACTCCACAAGAAC
* * * *
30306189 TTCAAGTAGGTAAGAGTTGGTACTTTCAACCTGCTTCACCGCAACTTCAGGGAGATAAGGTTTGT
1 TTCAAGAAGATAAGA-TTGGTA-TTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGT
* * * *
30306254 GGTCTTCAGTCTGCTCCACTACAACTTGAGGGAGATAATACTTGCTACTTCAACCTGCTCTACCG
64 GATCTTCAGTCTGCTCCACTACAACTTCAGGGAGATAAGACTTGCTACTTCAACCTGCTCTACTG
* * * * *
30306319 CAATTTCAGAGAGATAAGGTTTGCTATCTTCGATCTATTTCACAATAAC
129 CAATTTCAGAGAGATAAGGTTTG-TAGCTTCAATCTACTCCACAAGAAC
* * ** * * * ***
30306368 TTCAGGAAGATAAGATCTGCTATCTTCAGTCTACTCCACTACAACTTCTGGGAGATAATACTTGC
1 TTCAAGAAGATAAGAT-TGGTAT-TTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTG-
* *
30306433 T-ATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTACTTCAACCTACTCTACT
63 TGATCTTCAGTCTGCTCCACTACAACTTCAGGGAGATAAGACTTGCTACTTCAACCTGCTCTACT
30306497 GCAACTTT-AGAGAGATAAGGTTT
128 GCAA-TTTCAGAGAGATAAGGTTT
30306520 TTCATTTTCG
Statistics
Matches: 271, Mismatches: 51, Indels: 18
0.80 0.15 0.05
Matches are distributed among these distances:
178 68 0.25
179 199 0.73
180 4 0.01
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (176 bp):
TTCAAGAAGATAAGATTGGTATTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTGA
TCTTCAGTCTGCTCCACTACAACTTCAGGGAGATAAGACTTGCTACTTCAACCTGCTCTACTGCA
ATTTCAGAGAGATAAGGTTTGTAGCTTCAATCTACTCCACAAGAAC
Found at i:30306414 original size:45 final size:45
Alignment explanation
Indices: 30306230--30306515 Score: 231
Period size: 45 Copynumber: 6.4 Consensus size: 45
30306220 TGCTTCACCG
** * *
30306230 CAACTTCAGGGAGATAAGGTTTG-TGGTCTTCAGTCTGCTCCACTA
1 CAACTTCAGGGAGATAAGACTTGCT-ATCTTCAGTCTACTCCACTA
* * ** * * **
30306275 CAACTTGAGGGAGATAATACTTGCTA-CTTCAACCTGCTCTACCG
1 CAACTTCAGGGAGATAAGACTTGCTATCTTCAGTCTACTCCACTA
* * ** * * *
30306319 CAATTTCAGAGAGATAAGGTTTGCTATCTTC-GATCTATTTCACAA
1 CAACTTCAGGGAGATAAGACTTGCTATCTTCAG-TCTACTCCACTA
* *
30306364 TAACTTCAGGAAGATAAGA-TCTGCTATCTTCAGTCTACTCCACTA
1 CAACTTCAGGGAGATAAGACT-TGCTATCTTCAGTCTACTCCACTA
* * * *
30306409 CAACTTCTGGGAGATAATACTTGCTATCTTCAGTCTGCTCCACTG
1 CAACTTCAGGGAGATAAGACTTGCTATCTTCAGTCTACTCCACTA
** * *
30306454 CAACTTCAGGGAGATAAGACTTGCTA-CTTCAACCTACTCTACTG
1 CAACTTCAGGGAGATAAGACTTGCTATCTTCAGTCTACTCCACTA
* *
30306498 CAACTTTAGAGAGATAAG
1 CAACTTCAGGGAGATAAG
30306516 GTTTTTCATT
Statistics
Matches: 189, Mismatches: 46, Indels: 13
0.76 0.19 0.05
Matches are distributed among these distances:
44 64 0.34
45 122 0.65
46 3 0.02
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.30
Consensus pattern (45 bp):
CAACTTCAGGGAGATAAGACTTGCTATCTTCAGTCTACTCCACTA
Found at i:30310148 original size:66 final size:68
Alignment explanation
Indices: 30310019--30310148 Score: 158
Period size: 66 Copynumber: 1.9 Consensus size: 68
30310009 GGGATGTATC
* * *
30310019 CCATGTAGACAAGAGAGCTACGTGCGAGATAAATGTAGCTAGGTTGCATGAGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGC-AC-TACGAGATAAATG-AGCTAGGTCGCATGAGTGATACCAAGTGA
30310084 AGGACA
63 AGGACA
* *
30310090 CCATGTAGACAAGAGAG-A-TACGAGATAAATCG-GCTAGGTCGCATGAGTGGTACTAAGTG
1 CCATGTAGACAAGAGAGCACTACGAGATAAAT-GAGCTAGGTCGCATGAGTGATACCAAGTG
30310149 TTCACCATGT
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
66 23 0.43
67 11 0.21
68 1 0.02
69 1 0.02
71 17 0.32
ACGTcount: A:0.34, C:0.15, G:0.30, T:0.21
Consensus pattern (68 bp):
CCATGTAGACAAGAGAGCACTACGAGATAAATGAGCTAGGTCGCATGAGTGATACCAAGTGAAGG
ACA
Found at i:30317648 original size:66 final size:67
Alignment explanation
Indices: 30317519--30317648 Score: 174
Period size: 66 Copynumber: 1.9 Consensus size: 67
30317509 GGGATGTATC
*
30317519 CCATGTAGACAAGAGAGCTACGTGAGAGATAAATGTAGCTAGGTCGCATGAGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTAC--G-GAGATAAATG-AGCTAGGTCGCATGAGTGATACCAAGTGA
30317584 AGGATA
62 AGGATA
* *
30317590 CCATGTAGACAAGAGAGCTAC-GAGATAAATCG-GCTAGGTCGCATGAGTGGTACTAAGTG
1 CCATGTAGACAAGAGAGCTACGGAGATAAAT-GAGCTAGGTCGCATGAGTGATACCAAGTG
30317649 TTCACCATGT
Statistics
Matches: 55, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
66 24 0.44
67 9 0.16
68 1 0.02
71 21 0.38
ACGTcount: A:0.34, C:0.15, G:0.30, T:0.21
Consensus pattern (67 bp):
CCATGTAGACAAGAGAGCTACGGAGATAAATGAGCTAGGTCGCATGAGTGATACCAAGTGAAGGA
TA
Found at i:30325093 original size:15 final size:15
Alignment explanation
Indices: 30325070--30325113 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
30325060 GAAGCCCAGA
30325070 ATAAGGAAATCCAAG
1 ATAAGGAAATCCAAG
* *
30325085 ATAAAGAAATCCATG
1 ATAAGGAAATCCAAG
30325100 ATAAGGAAATCCAA
1 ATAAGGAAATCCAA
30325114 TTTACAGCAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.55, C:0.14, G:0.16, T:0.16
Consensus pattern (15 bp):
ATAAGGAAATCCAAG
Found at i:30332205 original size:10 final size:10
Alignment explanation
Indices: 30332192--30332236 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
30332182 AGCTCACTTG
30332192 AGCTCGTTTT
1 AGCTCGTTTT
*
30332202 AGCTCGTTTG
1 AGCTCGTTTT
*
30332212 AGCTTGATTTT
1 AGCTCG-TTTT
*
30332223 AGCTCGTTTC
1 AGCTCGTTTT
30332233 AGCT
1 AGCT
30332237 TATTTCTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
10 21 0.72
11 8 0.28
ACGTcount: A:0.13, C:0.20, G:0.22, T:0.44
Consensus pattern (10 bp):
AGCTCGTTTT
Found at i:30332205 original size:20 final size:21
Alignment explanation
Indices: 30332182--30332227 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
30332172 AGCTCCAACC
30332182 AGCTCACTTGAGCTCG-TTTT
1 AGCTCACTTGAGCTCGATTTT
** *
30332202 AGCTCGTTTGAGCTTGATTTT
1 AGCTCACTTGAGCTCGATTTT
30332223 AGCTC
1 AGCTC
30332228 GTTTCAGCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.41
Consensus pattern (21 bp):
AGCTCACTTGAGCTCGATTTT
Found at i:30332224 original size:21 final size:21
Alignment explanation
Indices: 30332189--30332241 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
30332179 ACCAGCTCAC
*
30332189 TTGAGCTCG-TTTTAGCTCGT
1 TTGAGCTTGATTTTAGCTCGT
30332209 TTGAGCTTGATTTTAGCTCGT
1 TTGAGCTTGATTTTAGCTCGT
*
30332230 TTCAGCTT-ATTT
1 TTGAGCTTGATTT
30332242 CTTTTTCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 12 0.40
21 18 0.60
ACGTcount: A:0.13, C:0.17, G:0.21, T:0.49
Consensus pattern (21 bp):
TTGAGCTTGATTTTAGCTCGT
Found at i:30332477 original size:15 final size:15
Alignment explanation
Indices: 30332457--30332487 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
30332447 ATTATATGAA
30332457 TAATTATATTTTATT
1 TAATTATATTTTATT
*
30332472 TAATTATTTTTTATT
1 TAATTATATTTTATT
30332487 T
1 T
30332488 CTTTGTAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TAATTATATTTTATT
Found at i:30332634 original size:21 final size:23
Alignment explanation
Indices: 30332588--30332635 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 23
30332578 GTTCAATGCT
*
30332588 TGGAGGAATTATATTTATGTACA
1 TGGAGGAATTATATTTATGCACA
30332611 TGGAGG-ATTA-ATTTCATGCA-A
1 TGGAGGAATTATATTT-ATGCACA
30332632 TGGA
1 TGGA
30332636 TATGAAGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 9 0.39
22 8 0.35
23 6 0.26
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.35
Consensus pattern (23 bp):
TGGAGGAATTATATTTATGCACA
Found at i:30335787 original size:21 final size:22
Alignment explanation
Indices: 30335751--30335807 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 22
30335741 TGAGAGTGGA
*
30335751 AAAAGAAAGTGAAAATGAAAAAG
1 AAAAGAAA-AGAAAATGAAAAAG
*
30335774 -AAAGAAAAGAAAATGAAAGAG
1 AAAAGAAAAGAAAATGAAAAAG
30335795 AAAAGAACAAGAA
1 AAAAGAA-AAGAA
30335808 TTGTGATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 12 0.40
22 13 0.43
23 5 0.17
ACGTcount: A:0.72, C:0.02, G:0.21, T:0.05
Consensus pattern (22 bp):
AAAAGAAAAGAAAATGAAAAAG
Found at i:30335791 original size:15 final size:16
Alignment explanation
Indices: 30335749--30335807 Score: 57
Period size: 15 Copynumber: 3.6 Consensus size: 16
30335739 TATGAGAGTG
30335749 GAAAAAGAAAGTGAAAAT
1 GAAAAAGAAA--GAAAAT
30335767 GAAAAAGAAAGAAAA-
1 GAAAAAGAAAGAAAAT
* *
30335782 GAAAATGAAAGAGAAAA
1 GAAAAAGAAAGA-AAAT
*
30335799 GAACAAGAA
1 GAAAAAGAA
30335808 TTGTGATAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
15 11 0.31
16 8 0.22
17 7 0.19
18 10 0.28
ACGTcount: A:0.71, C:0.02, G:0.22, T:0.05
Consensus pattern (16 bp):
GAAAAAGAAAGAAAAT
Found at i:30338374 original size:27 final size:26
Alignment explanation
Indices: 30338336--30338422 Score: 111
Period size: 27 Copynumber: 3.3 Consensus size: 26
30338326 TGGAGGAAGC
*
30338336 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTCTGCCAC-AATATCT
*
30338363 GTTCTGGTGGCTCTGCCACAATATTT
1 GTTCTGGTGGCTCTGCCACAATATCT
* * *
30338389 GTATCCGGTGACTCTGTCACAATATCT
1 GT-TCTGGTGGCTCTGCCACAATATCT
30338416 GTTCTGG
1 GTTCTGG
30338423 CAGCCATGCT
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
26 12 0.23
27 40 0.77
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (26 bp):
GTTCTGGTGGCTCTGCCACAATATCT
Found at i:30341051 original size:100 final size:101
Alignment explanation
Indices: 30340857--30341038 Score: 294
Period size: 100 Copynumber: 1.8 Consensus size: 101
30340847 TGAATACAAC
* *
30340857 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCATACTGTTAAGTCGCATGTGTAGTACTAAGT
1 TGTGTAGTACTAAGTACAGGCTACTACGTGTACCAGACTGTTAAGTCGCATGTGTAGTACTAAGT
30340922 GCAGGCTACTATGCGTACTCAATGACTTCGATCACG
66 GCAGGCTACTATGCGTACTCAATGACTTCGATCACG
* * * *
30340958 TGTGTAGTACTAAGTACAGGCTACTACGTGTATCGGATTGTT-GGTCGCATGTGTAGTACTAAGT
1 TGTGTAGTACTAAGTACAGGCTACTACGTGTACCAGACTGTTAAGTCGCATGTGTAGTACTAAGT
*
30341022 GTAGGCTACTATGCGTA
66 GCAGGCTACTATGCGTA
30341039 TCAGATAGCT
Statistics
Matches: 74, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
100 37 0.50
101 37 0.50
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (101 bp):
TGTGTAGTACTAAGTACAGGCTACTACGTGTACCAGACTGTTAAGTCGCATGTGTAGTACTAAGT
GCAGGCTACTATGCGTACTCAATGACTTCGATCACG
Found at i:30345160 original size:34 final size:33
Alignment explanation
Indices: 30345116--30345184 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 33
30345106 AGACTGAATA
30345116 GTGTCAACAAAGTTTTGAGAA-CTTGAAAGAGCG
1 GTGTCAACAAAGTTTTGAGAAGC-TGAAAGAGCG
30345149 GNTGTCAACAAAGTTTTGAGAAGCTGAAAGAGCG
1 G-TGTCAACAAAGTTTTGAGAAGCTGAAAGAGCG
30345183 GT
1 GT
30345185 TGACCAAAGC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 2 0.06
34 31 0.91
35 1 0.03
ACGTcount: A:0.35, C:0.12, G:0.29, T:0.23
Consensus pattern (33 bp):
GTGTCAACAAAGTTTTGAGAAGCTGAAAGAGCG
Found at i:30348246 original size:50 final size:49
Alignment explanation
Indices: 30348056--30348245 Score: 168
Period size: 50 Copynumber: 3.8 Consensus size: 49
30348046 ATTGTGAATA
* * *
30348056 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCATACT-GTTAAGT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGCGTATCAT--TGGTTAGGT
* * * * * * *
30348106 CGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACTCAATGACTTCGAT
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGCGTA-TCATTG-GTTAGGT
* * ** *
30348157 CACGTCTGTAGTAC-AACATGCAGGCTACTACATGTATCAGTTGGTGAGGT
1 CACGTGTGTAGTACTAA-GTGCAGGCTACTACGCGTATCA-TTGGTTAGGT
*
30348207 CACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTATCA
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACGCGTATCA
30348246 GATAGCTTCG
Statistics
Matches: 107, Mismatches: 27, Indels: 12
0.73 0.18 0.08
Matches are distributed among these distances:
49 1 0.01
50 71 0.66
51 35 0.33
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.29
Consensus pattern (49 bp):
CACGTGTGTAGTACTAAGTGCAGGCTACTACGCGTATCATTGGTTAGGT
Found at i:30354467 original size:30 final size:30
Alignment explanation
Indices: 30354433--30354493 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
30354423 CCCCTAGTAC
30354433 AAACTTTGGCAAAATTAC-CATTTTGCCCCT
1 AAACTTTGGCAAAATTACAC-TTTTGCCCCT
* * *
30354463 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGCAAAATTACACTTTTGCCCCT
30354493 A
1 A
30354494 GGCTCGAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.28, C:0.26, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGCAAAATTACACTTTTGCCCCT
Found at i:30364103 original size:27 final size:26
Alignment explanation
Indices: 30364065--30364152 Score: 113
Period size: 27 Copynumber: 3.3 Consensus size: 26
30364055 TGGAGGAAGC
*
30364065 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTCTGCCAC-AATATCT
*
30364092 GTTCTGGTGGCTCTGCCACAATATTT
1 GTTCTGGTGGCTCTGCCACAATATCT
** *
30364118 GTATCTGGTGATTCTGTCACAATATCT
1 GT-TCTGGTGGCTCTGCCACAATATCT
30364145 GTTCTGGT
1 GTTCTGGT
30364153 AGCCATGCTG
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
26 14 0.26
27 40 0.74
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.39
Consensus pattern (26 bp):
GTTCTGGTGGCTCTGCCACAATATCT
Found at i:30365308 original size:21 final size:20
Alignment explanation
Indices: 30365273--30365321 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
30365263 ACCAGCTCAC
*
30365273 TTGAGCTCGTTTTAGCTTGT
1 TTGAGCTCGTTTTAGCTCGT
*
30365293 TTGAGCTTGATTTTAGCTCGT
1 TTGAGCTCG-TTTTAGCTCGT
*
30365314 TTCAGCTC
1 TTGAGCTC
30365322 ATTTGTTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.47
Consensus pattern (20 bp):
TTGAGCTCGTTTTAGCTCGT
Found at i:30367909 original size:134 final size:134
Alignment explanation
Indices: 30367708--30367953 Score: 368
Period size: 134 Copynumber: 1.8 Consensus size: 134
30367698 CTACTTCAGG
* * * * *
30367708 GAGATGAGGCTGGTGGCCTAAATCTGTTCCATTGCTACTTCAAGAAGATAAGATTTGTCGTCTTT
1 GAGATAAGACTGGTGGCCTAAATCTGTTCCATTGCTACCTCAAGAAGATAAGATTTGTCATCATT
* *
30367773 GATCTGCTCCACTTCTATCTCAAAGAGATAAGATCTACAATCTTCAGCCTACTCCTTTGCTACCT
66 GATCTACTCCACTGCTATCTCAAAGAGATAAGATCTACAATCTTCAGCCTACTCCTTTGCTACCT
30367838 CAAA
131 CAAA
* * *
30367842 GAGATAAGACTGGTGGCTTAAATCTGCTTCCCTT-CTGCCTCAAGAAGATAAGATTTGTCATCAT
1 GAGATAAGACTGGTGGCCTAAATCTG-TTCCATTGCTACCTCAAGAAGATAAGATTTGTCATCAT
* *
30367906 TGATCTATTCCACTGCTATCTCAAGGAGATAAGATCTACAATCTTCAG
65 TGATCTACTCCACTGCTATCTCAAAGAGATAAGATCTACAATCTTCAG
30367954 TCTGCTTCCT
Statistics
Matches: 99, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
134 93 0.94
135 6 0.06
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (134 bp):
GAGATAAGACTGGTGGCCTAAATCTGTTCCATTGCTACCTCAAGAAGATAAGATTTGTCATCATT
GATCTACTCCACTGCTATCTCAAAGAGATAAGATCTACAATCTTCAGCCTACTCCTTTGCTACCT
CAAA
Found at i:30368002 original size:134 final size:134
Alignment explanation
Indices: 30367747--30368004 Score: 322
Period size: 134 Copynumber: 1.9 Consensus size: 134
30367737 CATTGCTACT
* * * *
30367747 TCAAGAAGATAAGATTTGTCGTCTTTGATCTGCTCCACTTCTATCTCAAAGAGATAAGATCTACA
1 TCAAGAAGATAAGATTTGTCATCATTGATCTACTCCACTGCTATCTCAAAGAGATAAGATCTACA
* ****
30367812 ATCTTCAGCCTACTCCTTTGCTACCTCAAAGAGATAAGACTGGTGGCTTAAATCTGCTTCCCTTC
66 ATCTTCAGCCTACTCCTTTGATACCTCAAAGAGATAAGACTACAAGCTTAAATCTGCTTCCCTTC
30367877 TGCC
131 TGCC
* *
30367881 TCAAGAAGATAAGATTTGTCATCATTGATCTATTCCACTGCTATCTCAAGGAGATAAGATCTACA
1 TCAAGAAGATAAGATTTGTCATCATTGATCTACTCCACTGCTATCTCAAAGAGATAAGATCTACA
* * ** * * *
30367946 ATCTTCAGTCTGCTTCC-TTGATACCTC-GGGAAGATAAGACTACAATCTTCAGTCTGCTT
66 ATCTTCAGCCTAC-TCCTTTGATACCTCAAAG-AGATAAGACTACAAGCTTAAATCTGCTT
30368005 ATGTCAAATG
Statistics
Matches: 104, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
133 1 0.01
134 100 0.96
135 3 0.03
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (134 bp):
TCAAGAAGATAAGATTTGTCATCATTGATCTACTCCACTGCTATCTCAAAGAGATAAGATCTACA
ATCTTCAGCCTACTCCTTTGATACCTCAAAGAGATAAGACTACAAGCTTAAATCTGCTTCCCTTC
TGCC
Found at i:30374434 original size:46 final size:46
Alignment explanation
Indices: 30374384--30374556 Score: 208
Period size: 46 Copynumber: 3.7 Consensus size: 46
30374374 TGGTTGAGCA
*
30374384 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * * *
30374430 TCCGAACTCGTTGAGTTGAGTTCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
*
30374477 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCAAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
30374523 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
30374557 GGGGCGGGTT
Statistics
Matches: 106, Mismatches: 14, Indels: 14
0.79 0.10 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 60 0.57
47 28 0.26
48 3 0.03
50 6 0.06
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:30374540 original size:93 final size:93
Alignment explanation
Indices: 30374381--30374551 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
30374371 GGATGGTTGA
* *
30374381 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
*
30374446 TGAGTTCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
30374474 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCAAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
30374539 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
30374552 ACTTAGGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:30376522 original size:25 final size:25
Alignment explanation
Indices: 30376494--30376550 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
30376484 TTTGGCTTGA
**
30376494 CATTTACTAAGCAATATCGGATATT
1 CATTTACTAAGCAATATCAAATATT
* *
30376519 CATTTATTAGGCAATATCAAATATT
1 CATTTACTAAGCAATATCAAATATT
30376544 CAATTTA
1 C-ATTTA
30376551 TTCTTTAACA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
25 22 0.81
26 5 0.19
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.39
Consensus pattern (25 bp):
CATTTACTAAGCAATATCAAATATT
Found at i:30378726 original size:2 final size:2
Alignment explanation
Indices: 30378721--30378747 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
30378711 GGGGGGGGGA
30378721 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
30378748 TCATCCATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:30382766 original size:9 final size:9
Alignment explanation
Indices: 30382748--30382820 Score: 61
Period size: 9 Copynumber: 8.6 Consensus size: 9
30382738 TTTATTTAAG
30382748 TTAA-GTGT
1 TTAATGTGT
30382756 TTAATGTGT
1 TTAATGTGT
30382765 TT--TGTGT
1 TTAATGTGT
30382772 TTAATAAGTGT
1 TTAAT--GTGT
30382783 TTAAATGTGT
1 TT-AATGTGT
*
30382793 TTAATATG-
1 TTAATGTGT
30382801 TT--TGT-T
1 TTAATGTGT
30382807 TTAATGTGT
1 TTAATGTGT
30382816 TTAAT
1 TTAAT
30382821 TGTAGGTGTC
Statistics
Matches: 53, Mismatches: 2, Indels: 19
0.72 0.03 0.26
Matches are distributed among these distances:
6 4 0.08
7 7 0.13
8 9 0.17
9 18 0.34
10 6 0.11
11 6 0.11
12 3 0.06
ACGTcount: A:0.25, C:0.00, G:0.19, T:0.56
Consensus pattern (9 bp):
TTAATGTGT
Found at i:30382793 original size:21 final size:22
Alignment explanation
Indices: 30382767--30382820 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 22
30382757 TAATGTGTTT
30382767 TGTGTTTAATAAG-TGTTTAAA
1 TGTGTTTAATAAGTTGTTTAAA
* *
30382788 TGTGTTTAATATGTTTGTTTTAA
1 TGTGTTTAATAAG-TTGTTTAAA
30382811 TGTGTTTAAT
1 TGTGTTTAAT
30382821 TGTAGGTGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 12 0.41
23 17 0.59
ACGTcount: A:0.26, C:0.00, G:0.19, T:0.56
Consensus pattern (22 bp):
TGTGTTTAATAAGTTGTTTAAA
Found at i:30385656 original size:30 final size:30
Alignment explanation
Indices: 30385622--30385682 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
30385612 TCCTTAACTC
30385622 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
30385652 AAACTTTTGCACATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
30385682 A
1 A
30385683 GGATCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.25, G:0.08, T:0.36
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:30390100 original size:30 final size:30
Alignment explanation
Indices: 30390066--30390126 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
30390056 TCCTTAACTC
30390066 AAACTTTAGAAAAATTACAATTTTGCCCCT
1 AAACTTTAGAAAAATTACAATTTTGCCCCT
* * * * *
30390096 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTAGAAAAATTACAATTTTGCCCCT
30390126 A
1 A
30390127 GGCTGGGAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.38
Consensus pattern (30 bp):
AAACTTTAGAAAAATTACAATTTTGCCCCT
Found at i:30392000 original size:28 final size:29
Alignment explanation
Indices: 30391943--30392002 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
30391933 ATTTATTTAA
*
30391943 CAATTTAACCCCTCAATTTACACTTTTGT
1 CAATTTAACCCCTCAATTGACACTTTTGT
*
30391972 CAATTTAATCCCT-AATTGACA-TTGTTGT
1 CAATTTAACCCCTCAATTGACACTT-TTGT
30392000 CAA
1 CAA
30392003 AAATCACTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 2 0.07
28 14 0.50
29 12 0.43
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (29 bp):
CAATTTAACCCCTCAATTGACACTTTTGT
Found at i:30396034 original size:18 final size:18
Alignment explanation
Indices: 30396013--30396062 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
30396003 AAAAGAAAAA
30396013 GAGAAGGAAAAAGAGAT-C
1 GAGAAGGAAAAAGA-ATGC
*
30396031 GAG-AGTGAAAAAGAATGT
1 GAGAAG-GAAAAAGAATGC
30396049 GAGAA-GAAAAAGAA
1 GAGAAGGAAAAAGAA
30396063 AATTGAAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 13 0.46
18 14 0.50
19 1 0.04
ACGTcount: A:0.58, C:0.02, G:0.32, T:0.08
Consensus pattern (18 bp):
GAGAAGGAAAAAGAATGC
Found at i:30397384 original size:27 final size:27
Alignment explanation
Indices: 30397350--30397416 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 27
30397340 TGGATAAGTT
* *
30397350 GTAGAATTACTGAAATACCCCTGTAAG
1 GTAGAATTACCGAAATACCCCTATAAG
*
30397377 GTAGAATTACCGAAATACCCCTATAGG
1 GTAGAATTACCGAAATACCCCTATAAG
* *
30397404 GTAGGACTACCGA
1 GTAGAATTACCGA
30397417 TTTACCCTCA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (27 bp):
GTAGAATTACCGAAATACCCCTATAAG
Found at i:30398210 original size:27 final size:26
Alignment explanation
Indices: 30398158--30398217 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
30398148 ACATATATAT
*
30398158 ATATCTGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
30398184 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
30398211 ATATCTG
1 ATATCTG
30398218 GCAGCCTCGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:30404857 original size:27 final size:27
Alignment explanation
Indices: 30404821--30404878 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
30404811 TGGATAAGTT
30404821 GTAGAATTACCGAAATACCCCTGTAAG
1 GTAGAATTACCGAAATACCCCTGTAAG
* *
30404848 GTAGAGTTACCGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAAG
30404875 GTAG
1 GTAG
30404879 GACTACCAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.22
Consensus pattern (27 bp):
GTAGAATTACCGAAATACCCCTGTAAG
Found at i:30415687 original size:16 final size:16
Alignment explanation
Indices: 30415666--30415699 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
30415656 TTCCAAAGTT
30415666 AGAATAGAGGATTCCG
1 AGAATAGAGGATTCCG
30415682 AGAATAGAGGATTCCG
1 AGAATAGAGGATTCCG
30415698 AG
1 AG
30415700 CTCATTCTGA
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:0.38, C:0.12, G:0.32, T:0.18
Consensus pattern (16 bp):
AGAATAGAGGATTCCG
Found at i:30416391 original size:53 final size:54
Alignment explanation
Indices: 30416265--30416398 Score: 252
Period size: 54 Copynumber: 2.5 Consensus size: 54
30416255 CATCTTATGG
30416265 CGGGATTACCAGTCCAGGCTAAATCCCCCCAAATATAAACTCATAGACTGATGT
1 CGGGATTACCAGTCCAGGCTAAATCCCCCCAAATATAAACTCATAGACTGATGT
*
30416319 CGGGATTACCAGTCCAGGCTAAATCCCCCCAAATATAAACTCATAGAGTGATGT
1 CGGGATTACCAGTCCAGGCTAAATCCCCCCAAATATAAACTCATAGACTGATGT
30416373 CGGGATTA-CAGTCCAGGCTAAATCCC
1 CGGGATTACCAGTCCAGGCTAAATCCC
30416399 TTGTGACAAC
Statistics
Matches: 79, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
53 18 0.23
54 61 0.77
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.22
Consensus pattern (54 bp):
CGGGATTACCAGTCCAGGCTAAATCCCCCCAAATATAAACTCATAGACTGATGT
Found at i:30419392 original size:15 final size:15
Alignment explanation
Indices: 30419374--30419417 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
30419364 GAAGCCCAGA
30419374 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
30419389 ATAAAGAAATTCATG
1 ATAAAGAAATCCAAG
*
30419404 ATAAGGAAATCCAA
1 ATAAAGAAATCCAA
30419418 TTTACAGCTC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.57, C:0.11, G:0.14, T:0.18
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:30423869 original size:40 final size:40
Alignment explanation
Indices: 30423839--30424291 Score: 451
Period size: 39 Copynumber: 11.5 Consensus size: 40
30423829 GCTACTCGTT
*
30423839 CAAATGCCTTCGGGACATAGCCCGATTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGATTATAGTAACTCGCA
*
30423879 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCC-GATTATAGTAACTCGCA
* *
30423919 CCAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCC-GATTATAGTAACTCGCA
* *
30423958 CCAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCC-GATTATAGTAACTCGCA
* *
30423997 CCAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCC-GATTATAGTAACTCGCA
* *
30424036 CCAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCC-GATTATAGTAACTCGCA
* *
30424075 CCAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCC-GATTATAGTAACTCGCA
* *
30424114 CCAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCC-GATTATAGTAACTCGCA
* *
30424153 CCAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCC-GATTATAGTAACTCGCA
* *
30424192 CCAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCC-GATTATAGTAACTCGCA
* * * * *
30424231 CCAATGCCTTC-GGATCTTAGTCCGGA-TATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAG-CCCGATTATAGTAAC-TCGCA
30424272 CAAA-GCCTTCGGGACTTAGC
1 CAAATGCCTTCGGGACTTAGC
30424292 ACGGACATCA
Statistics
Matches: 396, Mismatches: 10, Indels: 15
0.94 0.02 0.04
Matches are distributed among these distances:
38 2 0.01
39 309 0.78
40 69 0.17
41 16 0.04
ACGTcount: A:0.24, C:0.30, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGATTATAGTAACTCGCA
Found at i:30423953 original size:39 final size:39
Alignment explanation
Indices: 30423841--30424243 Score: 727
Period size: 39 Copynumber: 10.3 Consensus size: 39
30423831 TACTCGTTCA
* * *
30423841 AATGCCTTCGGGACATAGCCC-GATTATAGTAACTCGCACA
1 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACC
* *
30423881 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
1 AATGCCTTCGGG-CTTAGCCCGGAATTAGTAACTCGCACC
30423921 AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACC
1 AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACC
30423960 AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACC
1 AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACC
30423999 AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACC
1 AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACC
30424038 AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACC
1 AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACC
30424077 AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACC
1 AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACC
30424116 AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACC
1 AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACC
30424155 AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACC
1 AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACC
30424194 AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACC
1 AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACC
30424233 AATGCCTTCGG
1 AATGCCTTCGG
30424244 ATCTTAGTCC
Statistics
Matches: 357, Mismatches: 5, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
39 309 0.87
40 44 0.12
41 4 0.01
ACGTcount: A:0.24, C:0.30, G:0.23, T:0.23
Consensus pattern (39 bp):
AATGCCTTCGGGCTTAGCCCGGAATTAGTAACTCGCACC
Found at i:30425089 original size:64 final size:64
Alignment explanation
Indices: 30424304--30425069 Score: 1532
Period size: 64 Copynumber: 12.0 Consensus size: 64
30424294 GGACATCATT
30424304 CGAATAACCATGCACATTTAACAATAAATCATGACACATTCGTATTTCATTTTCATTAGCAAAA
1 CGAATAACCATGCACATTTAACAATAAATCATGACACATTCGTATTTCATTTTCATTAGCAAAA
30424368 CGAATAACCATGCACATTTAACAATAAATCATGACACATTCGTATTTCATTTTCATTAGCAAAA
1 CGAATAACCATGCACATTTAACAATAAATCATGACACATTCGTATTTCATTTTCATTAGCAAAA
30424432 CGAATAACCATGCACATTTAACAATAAATCATGACACATTCGTATTTCATTTTCATTAGCAAAA
1 CGAATAACCATGCACATTTAACAATAAATCATGACACATTCGTATTTCATTTTCATTAGCAAAA
30424496 CGAATAACCATGCACATTTAACAATAAATCATGACACATTCGTATTTCATTTTCATTAGCAAAA
1 CGAATAACCATGCACATTTAACAATAAATCATGACACATTCGTATTTCATTTTCATTAGCAAAA
30424560 CGAATAACCATGCACATTTAACAATAAATCATGACACATTCGTATTTCATTTTCATTAGCAAAA
1 CGAATAACCATGCACATTTAACAATAAATCATGACACATTCGTATTTCATTTTCATTAGCAAAA
30424624 CGAATAACCATGCACATTTAACAATAAATCATGACACATTCGTATTTCATTTTCATTAGCAAAA
1 CGAATAACCATGCACATTTAACAATAAATCATGACACATTCGTATTTCATTTTCATTAGCAAAA
30424688 CGAATAACCATGCACATTTAACAATAAATCATGACACATTCGTATTTCATTTTCATTAGCAAAA
1 CGAATAACCATGCACATTTAACAATAAATCATGACACATTCGTATTTCATTTTCATTAGCAAAA
30424752 CGAATAACCATGCACATTTAACAATAAATCATGACACATTCGTATTTCATTTTCATTAGCAAAA
1 CGAATAACCATGCACATTTAACAATAAATCATGACACATTCGTATTTCATTTTCATTAGCAAAA
30424816 CGAATAACCATGCACATTTAACAATAAATCATGACACATTCGTATTTCATTTTCATTAGCAAAA
1 CGAATAACCATGCACATTTAACAATAAATCATGACACATTCGTATTTCATTTTCATTAGCAAAA
30424880 CGAATAACCATGCACATTTAACAATAAATCATGACACATTCGTATTTCATTTTCATTAGCAAAA
1 CGAATAACCATGCACATTTAACAATAAATCATGACACATTCGTATTTCATTTTCATTAGCAAAA
30424944 CGAATAACCATGCACATTTAACAATAAATCATGACACATTCGTATTTCATTTTCATTAGCAAAA
1 CGAATAACCATGCACATTTAACAATAAATCATGACACATTCGTATTTCATTTTCATTAGCAAAA
30425008 CGAATAACCATGCACATTTAACAATAAATCATGACACATTCGTATTTCATTTTCATTAGCAA
1 CGAATAACCATGCACATTTAACAATAAATCATGACACATTCGTATTTCATTTTCATTAGCAA
30425070 NGGAGACAAT
Statistics
Matches: 702, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 702 1.00
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.31
Consensus pattern (64 bp):
CGAATAACCATGCACATTTAACAATAAATCATGACACATTCGTATTTCATTTTCATTAGCAAAA
Found at i:30429474 original size:30 final size:30
Alignment explanation
Indices: 30429440--30429496 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
30429430 CGTAGTTTTA
30429440 TTTATTGATGACATTTTGATTTACTCTGTG
1 TTTATTGATGACATTTTGATTTACTCTGTG
30429470 TTTATTGATGACATTTTGATTTACTCT
1 TTTATTGATGACATTTTGATTTACTCT
30429497 CATGATGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.21, C:0.11, G:0.14, T:0.54
Consensus pattern (30 bp):
TTTATTGATGACATTTTGATTTACTCTGTG
Found at i:30434899 original size:20 final size:20
Alignment explanation
Indices: 30434874--30434975 Score: 64
Period size: 20 Copynumber: 5.1 Consensus size: 20
30434864 GGAGTATAAA
30434874 CAGGGGCACGTATGTGCATT
1 CAGGGGCACGTATGTGCATT
* * *
30434894 CAGGGGTACCG-AAGTACAATT
1 CAGGGGCA-CGTATGTGC-ATT
* *
30434915 C-GGGGCATGTATATGCATT
1 CAGGGGCACGTATGTGCATT
* ** * * *
30434934 CAGGGGTACCAAAGTACACT
1 CAGGGGCACGTATGTGCATT
*
30434954 CAGGGGCACATATGTGCATT
1 CAGGGGCACGTATGTGCATT
30434974 CA
1 CA
30434976 AGGGTACCAA
Statistics
Matches: 56, Mismatches: 22, Indels: 8
0.65 0.26 0.09
Matches are distributed among these distances:
19 5 0.09
20 45 0.80
21 6 0.11
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (20 bp):
CAGGGGCACGTATGTGCATT
Found at i:30434932 original size:40 final size:40
Alignment explanation
Indices: 30434874--30435094 Score: 230
Period size: 40 Copynumber: 5.5 Consensus size: 40
30434864 GGAGTATAAA
30434874 CAGGGGCACGTATGTGCATTCAGGGGTACCGAAGTACAATT
1 CAGGGGCACGTATGTGCATTCAGGGGTACCGAAGTACAA-T
* * * *
30434915 C-GGGGCATGTATATGCATTCAGGGGTACCAAAGTACACT
1 CAGGGGCACGTATGTGCATTCAGGGGTACCGAAGTACAAT
* * * * *
30434954 CAGGGGCACATATGTGCATTCAAGGGTACCAAAGAACAAA
1 CAGGGGCACGTATGTGCATTCAGGGGTACCGAAGTACAAT
* * **
30434994 CAGGGGCACGAATGTGCATTCAAGGGTATTGAAGTACAAT
1 CAGGGGCACGTATGTGCATTCAGGGGTACCGAAGTACAAT
* * * *
30435034 CTGTGGCATGAATGTGCATTCAGGGGTACCGAAGTACAAAT
1 CAGGGGCACGTATGTGCATTCAGGGGTACCGAAGTAC-AAT
* **
30435075 C-GGGGTACAAATGTGCATTC
1 CAGGGGCACGTATGTGCATTC
30435095 TTCAATAATT
Statistics
Matches: 150, Mismatches: 28, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
39 2 0.01
40 143 0.95
41 5 0.03
ACGTcount: A:0.31, C:0.19, G:0.29, T:0.22
Consensus pattern (40 bp):
CAGGGGCACGTATGTGCATTCAGGGGTACCGAAGTACAAT
Found at i:30435089 original size:120 final size:120
Alignment explanation
Indices: 30434871--30435094 Score: 317
Period size: 120 Copynumber: 1.9 Consensus size: 120
30434861 ACTGGAGTAT
* * *
30434871 AAACAGGGGCACGTATGTGCATTCAGGGGTACCGAAGTACAATTCGGGGCATGTATATGCATTCA
1 AAACAGGGGCACGAATGTGCATTCAAGGGTACCGAAGTACAATTCGGGGCATGAATATGCATTCA
* *
30434936 GGGGTACCAAAGTACACTCAGGGGCACATATGTGCATTCAAGGGTACCAAAGAAC
66 GGGGTACCAAAGTACAATCAGGGGCACAAATGTGCATTCAAGGGTACCAAAGAAC
** * *
30434991 AAACAGGGGCACGAATGTGCATTCAAGGGTATTGAAGTACAA-TCTGTGGCATGAATGTGCATTC
1 AAACAGGGGCACGAATGTGCATTCAAGGGTACCGAAGTACAATTC-GGGGCATGAATATGCATTC
* *
30435055 AGGGGTACCGAAGTACAAATC-GGGGTACAAATGTGCATTC
65 AGGGGTACCAAAGTAC-AATCAGGGGCACAAATGTGCATTC
30435095 TTCAATAATT
Statistics
Matches: 91, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
119 2 0.02
120 86 0.95
121 3 0.03
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (120 bp):
AAACAGGGGCACGAATGTGCATTCAAGGGTACCGAAGTACAATTCGGGGCATGAATATGCATTCA
GGGGTACCAAAGTACAATCAGGGGCACAAATGTGCATTCAAGGGTACCAAAGAAC
Found at i:30436360 original size:21 final size:21
Alignment explanation
Indices: 30436334--30436376 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
30436324 TTTTGGGTTT
* *
30436334 AAGTCTCGAGACAAGTTGAAC
1 AAGTCTAGAGACAAGATGAAC
30436355 AAGTCTAGAGACAAGATGAAC
1 AAGTCTAGAGACAAGATGAAC
30436376 A
1 A
30436377 TTTTTAAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.16, G:0.23, T:0.16
Consensus pattern (21 bp):
AAGTCTAGAGACAAGATGAAC
Found at i:30437345 original size:21 final size:21
Alignment explanation
Indices: 30437321--30437363 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
30437311 AATAAAAAAT
*
30437321 TTAGAATTTTATTGTGATTAA
1 TTAGAATTTTATAGTGATTAA
* *
30437342 TTAGGATTTTATAGTTATTAA
1 TTAGAATTTTATAGTGATTAA
30437363 T
1 T
30437364 AATGTATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (21 bp):
TTAGAATTTTATAGTGATTAA
Found at i:30438343 original size:30 final size:29
Alignment explanation
Indices: 30438307--30438371 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
30438297 ATAATTTATG
* *
30438307 AAAATTGAATC-AAATCAAAATTTCATGTAT
1 AAAATTGAA-CAAAATC-AAAGTTCATATAT
*
30438337 AAAATTGCACAAAATCAAAGTTCATATAT
1 AAAATTGAACAAAATCAAAGTTCATATAT
30438366 AAAATT
1 AAAATT
30438372 ATATATTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 18 0.58
30 13 0.42
ACGTcount: A:0.52, C:0.11, G:0.06, T:0.31
Consensus pattern (29 bp):
AAAATTGAACAAAATCAAAGTTCATATAT
Found at i:30441745 original size:15 final size:15
Alignment explanation
Indices: 30441725--30441756 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
30441715 CCCTTCATTC
30441725 TTAACTCACTCACCA
1 TTAACTCACTCACCA
30441740 TTAACTCACTCACCA
1 TTAACTCACTCACCA
30441755 TT
1 TT
30441757 TCCCTTTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.38, G:0.00, T:0.31
Consensus pattern (15 bp):
TTAACTCACTCACCA
Found at i:30443112 original size:56 final size:56
Alignment explanation
Indices: 30443050--30443160 Score: 186
Period size: 56 Copynumber: 2.0 Consensus size: 56
30443040 TTGTGAACTT
* * *
30443050 ATTAATTGTTGAGTGATTTTGAATATAGTTTATCCTATAATGAGTTAATTGACCAC
1 ATTAATTGTTAAGTGATTTTGAATACAATTTATCCTATAATGAGTTAATTGACCAC
*
30443106 ATTAATTGTTAAGTGATTTTGAATACAATTTATCTTATAATGAGTTAATTGACCA
1 ATTAATTGTTAAGTGATTTTGAATACAATTTATCCTATAATGAGTTAATTGACCA
30443161 TATCAAATAT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 51 1.00
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.43
Consensus pattern (56 bp):
ATTAATTGTTAAGTGATTTTGAATACAATTTATCCTATAATGAGTTAATTGACCAC
Found at i:30445520 original size:173 final size:175
Alignment explanation
Indices: 30445191--30445541 Score: 643
Period size: 173 Copynumber: 2.0 Consensus size: 175
30445181 TATATAAACA
*
30445191 TCAATGTGAAGGAAGATTCAAGAACTGTTTCATAGATGTGATGAGGATTTATTAATTATAATTGG
1 TCAATGTGAAGGAAGATTCAAGAACTGTTTCATAGATGTGATGAGGATTTAGTAATTATAATTGG
*
30445256 TTTAGCTGTTTTTCTTTAAAGATCATTCATTGGTCAGAGTTGAAATTTTTGGTGAAATTTTATGT
66 TTTAGCTGTTTTTCTTTAAAGATCATTCAGTGGTCAGAGTTGAAATTTTTGGTGAAATTTTATGT
*
30445321 TTAAGCACATTATTGAAGCATTGACCAGTTAGGTAATTTATTATT
131 TTAAGCACATTATTGAAGCATTGACCAATTAGGTAATTTATTATT
30445366 TCAATGTGAAGGAAGATTCAAGAACTGTTTCATAGATGTGATGAGGATTTAGTAATTATAATTGG
1 TCAATGTGAAGGAAGATTCAAGAACTGTTTCATAGATGTGATGAGGATTTAGTAATTATAATTGG
30445431 TTTAGCTG-TTTT-TTTAAAGATCATTCAGTGGTCAGAGTTGAAATTTTTGGTGAAATTTTATGT
66 TTTAGCTGTTTTTCTTTAAAGATCATTCAGTGGTCAGAGTTGAAATTTTTGGTGAAATTTTATGT
* *
30445494 TTAAGCACATTATTGAAGCATTGACCAATTATGTAATTTATTCTT
131 TTAAGCACATTATTGAAGCATTGACCAATTAGGTAATTTATTATT
30445539 TCA
1 TCA
30445542 CTTTGTTGAT
Statistics
Matches: 171, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
173 95 0.56
174 4 0.02
175 72 0.42
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.41
Consensus pattern (175 bp):
TCAATGTGAAGGAAGATTCAAGAACTGTTTCATAGATGTGATGAGGATTTAGTAATTATAATTGG
TTTAGCTGTTTTTCTTTAAAGATCATTCAGTGGTCAGAGTTGAAATTTTTGGTGAAATTTTATGT
TTAAGCACATTATTGAAGCATTGACCAATTAGGTAATTTATTATT
Found at i:30450025 original size:13 final size:13
Alignment explanation
Indices: 30450009--30450040 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
30449999 CTCGTAGGAT
30450009 GAGCTCGCAAGTC
1 GAGCTCGCAAGTC
30450022 GAGCTCGCAAGTC
1 GAGCTCGCAAGTC
*
30450035 AAGCTC
1 GAGCTC
30450041 ACTCTCTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.25, C:0.31, G:0.28, T:0.16
Consensus pattern (13 bp):
GAGCTCGCAAGTC
Found at i:30452492 original size:28 final size:28
Alignment explanation
Indices: 30452454--30453391 Score: 1563
Period size: 28 Copynumber: 33.5 Consensus size: 28
30452444 TAAATTGTAC
*
30452454 AGCACTAAGTGTGCGAGCTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
30452482 AGCACTAAGTGTGCGAATTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
30452510 AGCACTAGGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
30452538 AGCACTAAGTGTGCGAATTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
30452566 AGCACTAGGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
30452594 AGCACTAAGTGTGCGAATTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
30452622 AGCACTAGGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
30452650 AGCACTAAGTGTGCGAATTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
30452678 AGCACTAGGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
30452706 AGCACTAAGTGTGCGAATTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
30452734 AGCACTAGGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
30452762 AGCACTAAGTGTGCGAATTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
30452790 AGCACTAGGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
30452818 AGCACTAAGTGTGCGAATTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
30452846 AGCACTAGGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
30452874 AGCACTAAGTGTGCGAATTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
30452902 AGCACTAGGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
30452930 AGCACTAAGTGTGCGAATTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
30452958 AGCACTAGGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
30452986 AGCACTAAGTGTGCGAATTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
30453014 AGCACTAGGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
30453042 AGCACTAAGTGTGCGAATTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
30453070 AGCACTAGGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
30453098 AGCACTAAGTGTGCGAATTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
30453126 AGCACTAGGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
30453154 AGCACTAAGTGTGCGAATTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
30453182 AGCACTAGGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
30453210 AGCACTAAGTGTGCGAATTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
30453238 AGCACTAGGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
30453266 AGCACTAAGTGTGCGAATTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
30453294 AGCACTAGGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
30453322 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
30453350 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
30453377 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
30453392 GACTTAATAT
Statistics
Matches: 847, Mismatches: 63, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
27 24 0.03
28 823 0.97
ACGTcount: A:0.25, C:0.11, G:0.29, T:0.35
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATGT
Found at i:30452522 original size:56 final size:56
Alignment explanation
Indices: 30452454--30453391 Score: 1806
Period size: 56 Copynumber: 16.8 Consensus size: 56
30452444 TAAATTGTAC
* *
30452454 AGCACTAAGTGTGCGAGCTTGATTATGTAGCACTAAGTGTGCGAATTTGATTATGT
1 AGCACTAGGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAATTTGATTATGT
30452510 AGCACTAGGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAATTTGATTATGT
1 AGCACTAGGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAATTTGATTATGT
30452566 AGCACTAGGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAATTTGATTATGT
1 AGCACTAGGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAATTTGATTATGT
30452622 AGCACTAGGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAATTTGATTATGT
1 AGCACTAGGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAATTTGATTATGT
30452678 AGCACTAGGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAATTTGATTATGT
1 AGCACTAGGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAATTTGATTATGT
30452734 AGCACTAGGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAATTTGATTATGT
1 AGCACTAGGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAATTTGATTATGT
30452790 AGCACTAGGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAATTTGATTATGT
1 AGCACTAGGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAATTTGATTATGT
30452846 AGCACTAGGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAATTTGATTATGT
1 AGCACTAGGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAATTTGATTATGT
30452902 AGCACTAGGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAATTTGATTATGT
1 AGCACTAGGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAATTTGATTATGT
30452958 AGCACTAGGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAATTTGATTATGT
1 AGCACTAGGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAATTTGATTATGT
30453014 AGCACTAGGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAATTTGATTATGT
1 AGCACTAGGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAATTTGATTATGT
30453070 AGCACTAGGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAATTTGATTATGT
1 AGCACTAGGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAATTTGATTATGT
30453126 AGCACTAGGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAATTTGATTATGT
1 AGCACTAGGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAATTTGATTATGT
30453182 AGCACTAGGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAATTTGATTATGT
1 AGCACTAGGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAATTTGATTATGT
30453238 AGCACTAGGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAATTTGATTATGT
1 AGCACTAGGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAATTTGATTATGT
* *
30453294 AGCACTAGGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAGGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAATTTGATTATGT
* * *
30453350 AGCACTAAGTGTGCGAG-TTGATTATATAGCACTGAGTGTGCG
1 AGCACTAGGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCG
30453392 GACTTAATAT
Statistics
Matches: 875, Mismatches: 7, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
55 23 0.03
56 852 0.97
ACGTcount: A:0.25, C:0.11, G:0.29, T:0.35
Consensus pattern (56 bp):
AGCACTAGGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAATTTGATTATGT
Found at i:30458112 original size:43 final size:43
Alignment explanation
Indices: 30458028--30458138 Score: 134
Period size: 43 Copynumber: 2.6 Consensus size: 43
30458018 TAAGCTCATA
* * ** *
30458028 CAATGCCCCAGATATGGTCTTACATGTTATCATATATCGATGC
1 CAATGTCCCAGATATGGTCTTACACGAAATCATATAACGATGC
* *
30458071 CACTGTCCCAGATAGGGTCTTACACGAAATCA-ATTAACGATGC
1 CAATGTCCCAGATATGGTCTTACACGAAATCATA-TAACGATGC
*
30458114 CAATGTCCCAGACATGGTCTTACAC
1 CAATGTCCCAGATATGGTCTTACAC
30458139 ATAATCTCAA
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 1 0.02
43 56 0.98
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (43 bp):
CAATGTCCCAGATATGGTCTTACACGAAATCATATAACGATGC
Found at i:30458787 original size:21 final size:21
Alignment explanation
Indices: 30458763--30458802 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
30458753 TTCAATATCT
* *
30458763 ATCATCAAGCTTTCAAAATTC
1 ATCAACAAGCATTCAAAATTC
*
30458784 ATCAACAATCATTCAAAAT
1 ATCAACAAGCATTCAAAAT
30458803 ATCAAGCATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.23, G:0.03, T:0.30
Consensus pattern (21 bp):
ATCAACAAGCATTCAAAATTC
Found at i:30465774 original size:68 final size:67
Alignment explanation
Indices: 30465702--30465851 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
30465692 CATCATGTGT
* * * *
30465702 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
30465764 ATGTAG
62 ATGTAG
** * *
30465770 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
30465835 AG
66 AG
30465837 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
30465852 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:30465807 original size:64 final size:64
Alignment explanation
Indices: 30465726--30465909 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
30465716 AGACATTATG
* *
30465726 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
30465790 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
30465855 AA
63 AA
* * * *
30465857 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
30465910 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:30469242 original size:41 final size:41
Alignment explanation
Indices: 30469197--30469279 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
30469187 ATCATTCATG
30469197 TGACCATCGATTCTTAATGTTATTTAGACTCTAGAATTGAA
1 TGACCATCGATTCTTAATGTTATTTAGACTCTAGAATTGAA
*
30469238 TGACCATTGATTCTTAATGTTATTTAGACTCTAGAATTGAA
1 TGACCATCGATTCTTAATGTTATTTAGACTCTAGAATTGAA
30469279 T
1 T
30469280 TATTAGCCCT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.41
Consensus pattern (41 bp):
TGACCATCGATTCTTAATGTTATTTAGACTCTAGAATTGAA
Found at i:30470450 original size:5 final size:5
Alignment explanation
Indices: 30470434--30470465 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
30470424 TCCAAGTGCC
*
30470434 ATTTT ATCTT ATTTT ATTTT ATTTT ATTTT AT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT AT
30470466 CTTTTTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (5 bp):
ATTTT
Done.