Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008734.1 Hibiscus syriacus cultivar Beakdansim tig00111807_pilon, whole genome shotgun sequence
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: 415630
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 2 of 2
Found at i:276258 original size:23 final size:23
Alignment explanation
Indices: 276228--276276 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
276218 ATCTAGTACG
*
276228 TTATCATGAGCACATGTTTTGTC
1 TTATCATGAGCACATGTTTTATC
276251 TTATCATGAGCACATGTTTTATC
1 TTATCATGAGCACATGTTTTATC
276274 TTA
1 TTA
276277 CTTTTGTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.24, C:0.16, G:0.14, T:0.45
Consensus pattern (23 bp):
TTATCATGAGCACATGTTTTATC
Found at i:276441 original size:98 final size:98
Alignment explanation
Indices: 276262--276615 Score: 408
Period size: 99 Copynumber: 3.6 Consensus size: 98
276252 TATCATGAGC
* * * *
276262 ACATGTTTTATCTTACTTTTGTATAATATAAATGGTTTAATACTTATAACTTAAACAATTGACAT
1 ACATGTTTTATCTTACTTTTGCATAATATAAATAGTTTCATACTTATAACTTAAACGATTGACAT
* ** * * *
276327 AAAAAATGCGGTACCTACTATGTTACATGTGAA
66 AAAAAATACGCCACCTACTACGTTACACGAGAA
* * * *
276360 TA-ATATTTTGTCTTACTTTTGCATAATATAAATAGTTTCATACTTATAACTTAAACGGTTAACA
1 -ACATGTTTTATCTTACTTTTGCATAATATAAATAGTTTCATACTTATAACTTAAACGATTGACA
*
276424 TAAAAAATACGCCACCTACTACGTTTTCACGAGAA
65 TAAAAAATACGCCACCTACTACG-TTACACGAGAA
* * * *
276459 ACATGTTTTGTCTTACTTTTGCATAATATAAATAGTTTTATACTTATAACTCAAATGATTGACAT
1 ACATGTTTTATCTTACTTTTGCATAATATAAATAGTTTCATACTTATAACTTAAACGATTGACAT
* * *
276524 AAAAAA-ATGTCCTACCTACTACATTATTACGAGAA
66 AAAAAATACG-CC-ACCTACTACGTTA-CACGAGAA
* * *
276559 ATATGTTTTATCTTACTTTTGCATCATATAAA-CGATTTCATACTTATAACTTAAACG
1 ACATGTTTTATCTTACTTTTGCATAATATAAATAG-TTTCATACTTATAACTTAAACG
276616 GTTGTCATTT
Statistics
Matches: 217, Mismatches: 32, Indels: 11
0.83 0.12 0.04
Matches are distributed among these distances:
98 76 0.35
99 77 0.35
100 64 0.29
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (98 bp):
ACATGTTTTATCTTACTTTTGCATAATATAAATAGTTTCATACTTATAACTTAAACGATTGACAT
AAAAAATACGCCACCTACTACGTTACACGAGAA
Found at i:276494 original size:99 final size:99
Alignment explanation
Indices: 276262--276615 Score: 412
Period size: 98 Copynumber: 3.6 Consensus size: 99
276252 TATCATGAGC
* * * *
276262 ACATGTTTTATCTTACTTTTGTATAATATAAATGGTTTAATACTTATAACTTAAACAATTGACAT
1 ACATGTTTTATCTTACTTTTGCATAATATAAATAGTTTCATACTTATAACTTAAACGATTGACAT
* ** * * * *
276327 AAAAAATGCGGTACCTACTATG-TTACATGTGAA
66 AAAAAATACGCCACCTACTACGTTTTCACGAGAA
* * * *
276360 TA-ATATTTTGTCTTACTTTTGCATAATATAAATAGTTTCATACTTATAACTTAAACGGTTAACA
1 -ACATGTTTTATCTTACTTTTGCATAATATAAATAGTTTCATACTTATAACTTAAACGATTGACA
276424 TAAAAAATACGCCACCTACTACGTTTTCACGAGAA
65 TAAAAAATACGCCACCTACTACGTTTTCACGAGAA
* * * *
276459 ACATGTTTTGTCTTACTTTTGCATAATATAAATAGTTTTATACTTATAACTCAAATGATTGACAT
1 ACATGTTTTATCTTACTTTTGCATAATATAAATAGTTTCATACTTATAACTTAAACGATTGACAT
* *
276524 AAAAAA-ATGTCCTACCTACTACATTATT-ACGAGAA
66 AAAAAATACG-CC-ACCTACTACGTT-TTCACGAGAA
* * *
276559 ATATGTTTTATCTTACTTTTGCATCATATAAA-CGATTTCATACTTATAACTTAAACG
1 ACATGTTTTATCTTACTTTTGCATAATATAAATAG-TTTCATACTTATAACTTAAACG
276616 GTTGTCATTT
Statistics
Matches: 219, Mismatches: 30, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
98 76 0.35
99 75 0.34
100 66 0.30
101 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (99 bp):
ACATGTTTTATCTTACTTTTGCATAATATAAATAGTTTCATACTTATAACTTAAACGATTGACAT
AAAAAATACGCCACCTACTACGTTTTCACGAGAA
Found at i:276602 original size:100 final size:99
Alignment explanation
Indices: 276264--276652 Score: 398
Period size: 100 Copynumber: 3.9 Consensus size: 99
276254 TCATGAGCAC
* * *
276264 ATGTTTTATCTTACTTTTGTATAATATAAATG-GTTTAATACTTATAACTTAAACAATTGACAT-
1 ATGTTTTATCTTACTTTTGCATAATATAAA-GAGTTTCATACTTATAACTTAAACGATTGACATA
* * * * *
276327 AAAAAATGCGGTACCTACTATGTTA-CATGTG-AAT
65 AAAAAATGC-CTACCTACTACGTTATTACGAGAAAT
* * * * *
276361 AATATTTTGTCTTACTTTTGCATAATATAAATAGTTTCATACTTATAACTTAAACGGTTAACATA
1 -ATGTTTTATCTTACTTTTGCATAATATAAAGAGTTTCATACTTATAACTTAAACGATTGACATA
* *
276426 AAAAATACGCC-ACCTACTACGTT-TTCACGAGAAAC
65 AAAAA-ATGCCTACCTACTACGTTATT-ACGAGAAAT
* * * * *
276461 ATGTTTTGTCTTACTTTTGCATAATATAAATAGTTTTATACTTATAACTCAAATGATTGACATAA
1 ATGTTTTATCTTACTTTTGCATAATATAAAGAGTTTCATACTTATAACTTAAACGATTGACATAA
*
276526 AAAAATGTCCTACCTACTACATTATTACGAGAAAT
66 AAAAATG-CCTACCTACTACGTTATTACGAGAAAT
* * *
276561 ATGTTTTATCTTACTTTTGCATCATATAAACGA-TTTCATACTTATAACTTAAACGGTTGTCATT
1 ATGTTTTATCTTACTTTTGCATAATATAAA-GAGTTTCATACTTATAACTTAAACGATTGACA--
*
276625 TAAAAAAACATG-TTACCTACTACGTTAT
63 T-AAAAAA-ATGCCTACCTACTACGTTAT
276653 CAAACATAAC
Statistics
Matches: 243, Mismatches: 34, Indels: 24
0.81 0.11 0.08
Matches are distributed among these distances:
98 67 0.28
99 73 0.30
100 76 0.31
101 3 0.01
102 15 0.06
103 6 0.02
104 3 0.01
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.39
Consensus pattern (99 bp):
ATGTTTTATCTTACTTTTGCATAATATAAAGAGTTTCATACTTATAACTTAAACGATTGACATAA
AAAAATGCCTACCTACTACGTTATTACGAGAAAT
Found at i:276878 original size:132 final size:135
Alignment explanation
Indices: 276732--277014 Score: 346
Period size: 132 Copynumber: 2.1 Consensus size: 135
276722 ATATTTGTGG
* * * *
276732 AAAAGTATTGATACTCTGCAGCCTGCTCATTTTTCATGTTTTTTCTTTAAATTCGAAAGTATC-A
1 AAAAGTATCGATACTCTGCAGCCTGCTCATTTTCCATG-TTTTACTTTAAATTCGAAAATATCGA
** *
276796 CTA-C-TTTGAAAAAATATCCGTACTTTCGAA-TT-AAAAAACAT-AGAAATGGTATTTTAACTT
65 -TACCTTTTG-AAAAATATCAATACTTTCGAATTTAAAAAAACATGAGAAATGATATTTTAACTT
276856 T-AGAATTT
128 TCA-AATTT
* * ** *
276864 AAAAGTATCGATACTTTTCAGCCTTTTCATTTTCCATGTTTTACTTTAAATTTGAAAATATCGAT
1 AAAAGTATCGATACTCTGCAGCCTGCTCATTTTCCATGTTTTACTTTAAATTCGAAAATATCGAT
*
276929 ACCTTTTGAAAAATATCAATACTTTTGAATTTAAAAAAAACATGAGAAATGATATTTTAACTTTC
66 ACCTTTTGAAAAATATCAATACTTTCGAATTT-AAAAAAACATGAGAAATGATATTTTAACTTTC
276994 AAATTT
130 AAATTT
*
277000 AAAAGTAACGATACT
1 AAAAGTATCGATACT
277015 TTGGAAAAGT
Statistics
Matches: 129, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
131 23 0.18
132 52 0.40
133 6 0.05
135 9 0.07
136 38 0.29
137 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.39
Consensus pattern (135 bp):
AAAAGTATCGATACTCTGCAGCCTGCTCATTTTCCATGTTTTACTTTAAATTCGAAAATATCGAT
ACCTTTTGAAAAATATCAATACTTTCGAATTTAAAAAAACATGAGAAATGATATTTTAACTTTCA
AATTT
Found at i:276938 original size:19 final size:18
Alignment explanation
Indices: 276914--276957 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
276904 TTACTTTAAA
*
276914 TTTGAAAATATCGATACCT
1 TTTGAAAATATCAATA-CT
276933 TTTGAAAAATATCAATACT
1 TTTG-AAAATATCAATACT
276952 TTTGAA
1 TTTGAA
276958 TTTAAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 2 0.09
19 10 0.43
20 11 0.48
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (18 bp):
TTTGAAAATATCAATACT
Found at i:276943 original size:20 final size:19
Alignment explanation
Indices: 276914--276957 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
276904 TTACTTTAAA
*
276914 TTTG-AAAATATCGATACCT
1 TTTGAAAAATATCAATA-CT
276933 TTTGAAAAATATCAATACT
1 TTTGAAAAATATCAATACT
276952 TTTGAA
1 TTTGAA
276958 TTTAAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (19 bp):
TTTGAAAAATATCAATACT
Found at i:277022 original size:19 final size:19
Alignment explanation
Indices: 277000--277036 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
276990 TTTCAAATTT
277000 AAAAGTAACGATACTTTGG
1 AAAAGTAACGATACTTTGG
* *
277019 AAAAGTATCGATAGTTTG
1 AAAAGTAACGATACTTTG
277037 CAGCCTTCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.30
Consensus pattern (19 bp):
AAAAGTAACGATACTTTGG
Found at i:277244 original size:77 final size:76
Alignment explanation
Indices: 277115--277446 Score: 382
Period size: 77 Copynumber: 4.3 Consensus size: 76
277105 TTTTCCAATT
* ** * *
277115 TTTTA-TAATAGAAAA-ATTAACATTCCAGATTACAATTTACTTTCTTATTGAACCATAATATTC
1 TTTTATTAATA-AAAATATTAACATTCCAGATCACAACATA-TTTCTTAGTGAACCATAACATTC
277178 TTGTGCGAAACCTA
64 TTGTGCGAAACC-A
* *
277192 TTTTATTAATAAAAATATTAACATTCTAGATCACAACATATTTCTTAGTGAACCATGAA-ATTAT
1 TTTTATTAATAAAAATATTAACATTCCAGATCACAACATATTTCTTAGTGAACCAT-AACATTCT
* *
277256 TGGGGGAAACCCA
65 TGTGCGAAA-CCA
* * * * *
277269 TTTTATTAATAAAAATATTAGCATTCCATATCACAACCTATTTCTTAGTGAACCGTGACATTCTT
1 TTTTATTAATAAAAATATTAACATTCCAGATCACAACATATTTCTTAGTGAACCATAACATTCTT
** *
277334 ACGCGCAATCCA
66 GTGCG-AAACCA
* * *
277346 TTTTATTAATAAAAATATTAACATTCCAGATCGCAACATATTTCTTAGTGAACCATGACATTTTT
1 TTTTATTAATAAAAATATTAACATTCCAGATCACAACATATTTCTTAGTGAACCATAACATTCTT
* * *
277411 TTGCGTAAGCA
66 GTGCGAAACCA
277422 TTTTATTAATAAAAATATTAACATT
1 TTTTATTAATAAAAATATTAACATT
277447 TCATATATAA
Statistics
Matches: 219, Mismatches: 30, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
76 29 0.13
77 159 0.73
78 31 0.14
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.37
Consensus pattern (76 bp):
TTTTATTAATAAAAATATTAACATTCCAGATCACAACATATTTCTTAGTGAACCATAACATTCTT
GTGCGAAACCA
Found at i:277395 original size:154 final size:153
Alignment explanation
Indices: 277115--277483 Score: 424
Period size: 154 Copynumber: 2.4 Consensus size: 153
277105 TTTTCCAATT
* ** * * *
277115 TTTTA-TAATAGAAAA-ATTAACATTCCAGAT-TACAATTTACTTTCTTATTGAACCATAATATT
1 TTTTATTAATA-AAAATATTAACATTCCATATATA-AACCTA-TTTCTTAGTGAACCATGACATT
** * *
277177 CTTGTGCG-AAACCTATTTTATTAATAAAAATATTAACATTCTAGATCACAACATATTTCTTAGT
63 CTTACGCGCAATCC-ATTTTATTAATAAAAATATTAACATTCCAGATCACAACATATTTCTTAGT
*
277241 GAACCATGAAATTATTGGGGGAAACCCA
127 GAACCATGAAATTATTGGGCGAAA-CCA
* * *
277269 TTTTATTAATAAAAATATTAGCATTCCATATCA-CAACCTATTTCTTAGTGAACCGTGACATTCT
1 TTTTATTAATAAAAATATTAACATTCCATAT-ATAAACCTATTTCTTAGTGAACCATGACATTCT
*
277333 TACGCGCAATCCATTTTATTAATAAAAATATTAACATTCCAGATCGCAACATATTTCTTAGTGAA
65 TACGCGCAATCCATTTTATTAATAAAAATATTAACATTCCAGATCACAACATATTTCTTAGTGAA
* * ** * *
277398 CCATGACATTTTTTTGCGTAAGCA
130 CCATGAAATTATTGGGCGAAACCA
* * * *
277422 TTTTATTAATAAAAATATTAACATTTCATATATAAACTTGTTTCTTAGTTAACCATGACATT
1 TTTTATTAATAAAAATATTAACATTCCATATATAAACCTATTTCTTAGTGAACCATGACATT
277484 TTTAGGCCCA
Statistics
Matches: 181, Mismatches: 28, Indels: 13
0.82 0.13 0.06
Matches are distributed among these distances:
152 1 0.01
153 55 0.30
154 99 0.55
155 26 0.14
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.38
Consensus pattern (153 bp):
TTTTATTAATAAAAATATTAACATTCCATATATAAACCTATTTCTTAGTGAACCATGACATTCTT
ACGCGCAATCCATTTTATTAATAAAAATATTAACATTCCAGATCACAACATATTTCTTAGTGAAC
CATGAAATTATTGGGCGAAACCA
Found at i:277466 original size:76 final size:77
Alignment explanation
Indices: 277115--277483 Score: 347
Period size: 77 Copynumber: 4.8 Consensus size: 77
277105 TTTTCCAATT
* ** * * *
277115 TTTTA-TAATAGAAAA-ATTAACATTCCAGAT-TACAATTTACTTTCTTATTGAACCATAATATT
1 TTTTATTAATA-AAAATATTAACATTCCATATATA-AACATA-TTTCTTAGTGAACCATGACATT
*
277177 CTTGTGCGAAACCTA
63 CTTGTGCGAAACCCA
* * *
277192 TTTTATTAATAAAAATATTAACATT-C-TAGATCACAACATATTTCTTAGTGAACCATGAAATTA
1 TTTTATTAATAAAAATATTAACATTCCATATAT-A-AACATATTTCTTAGTGAACCATGACATTC
* *
277255 TTGGGGGAAACCCA
64 TTGTGCGAAACCCA
* * * *
277269 TTTTATTAATAAAAATATTAGCATTCCATATCA-CAACCTATTTCTTAGTGAACCGTGACATTCT
1 TTTTATTAATAAAAATATTAACATTCCATAT-ATAAACATATTTCTTAGTGAACCATGACATTCT
** * *
277333 TACGCGCAATCCA
65 TGTGCGAAACCCA
* *** *
277346 TTTTATTAATAAAAATATTAACATTCCAGATCGCAACATATTTCTTAGTGAACCATGACATTTTT
1 TTTTATTAATAAAAATATTAACATTCCATATATAAACATATTTCTTAGTGAACCATGACATTCTT
* * *
277411 TTGCGTAA-GCA
66 GTGCGAAACCCA
* * * *
277422 TTTTATTAATAAAAATATTAACATTTCATATATAAACTTGTTTCTTAGTTAACCATGACATT
1 TTTTATTAATAAAAATATTAACATTCCATATATAAACATATTTCTTAGTGAACCATGACATT
277484 TTTAGGCCCA
Statistics
Matches: 243, Mismatches: 41, Indels: 17
0.81 0.14 0.06
Matches are distributed among these distances:
76 57 0.23
77 162 0.67
78 21 0.09
79 2 0.01
80 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.38
Consensus pattern (77 bp):
TTTTATTAATAAAAATATTAACATTCCATATATAAACATATTTCTTAGTGAACCATGACATTCTT
GTGCGAAACCCA
Found at i:281553 original size:22 final size:21
Alignment explanation
Indices: 281494--281560 Score: 57
Period size: 22 Copynumber: 3.2 Consensus size: 21
281484 GATTCGTAAC
*
281494 GCGATTCT-GACTATCGCATT
1 GCGATTTTCGACTATCGCATT
* * *
281514 GCGATTTTCTA-AATTCGCGTT
1 GCGATTTTCGACTA-TCGCATT
*
281535 GCGATTTTTCGACTATCGCAAT
1 GCGA-TTTTCGACTATCGCATT
281557 GCGA
1 GCGA
281561 ATATGTAAAT
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
20 8 0.23
21 11 0.31
22 15 0.43
23 1 0.03
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (21 bp):
GCGATTTTCGACTATCGCATT
Found at i:281574 original size:20 final size:20
Alignment explanation
Indices: 281549--281660 Score: 145
Period size: 20 Copynumber: 5.6 Consensus size: 20
281539 TTTTTCGACT
281549 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
* ***
281569 ATCGCAATGCGAGTATGGCT
1 ATCGCAATGCGAATATGTAA
*
281589 ATCGCAACGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
281609 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
* *
281629 ATCGCAATGCGATTAT-TACT
1 ATCGCAATGCGAATATGTA-A
281649 ATCGCAATGCGA
1 ATCGCAATGCGA
281661 TTCTGACTAT
Statistics
Matches: 79, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
19 2 0.03
20 77 0.97
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:281661 original size:20 final size:21
Alignment explanation
Indices: 281546--281680 Score: 138
Period size: 20 Copynumber: 6.7 Consensus size: 21
281536 CGATTTTTCG
281546 ACTATCGCAATGCGAATATGT
1 ACTATCGCAATGCGAATATGT
* *
281567 A-AATCGCAATGCGAGTATG-
1 ACTATCGCAATGCGAATATGT
* *
281586 GCTATCGCAACGCGAATATGT
1 ACTATCGCAATGCGAATATGT
*
281607 A-AATCGCAATGCGAATATGT
1 ACTATCGCAATGCGAATATGT
* *
281627 A-AATCGCAATGCGATTAT-T
1 ACTATCGCAATGCGAATATGT
* *
281646 ACTATCGCAATGCGATTCTG-
1 ACTATCGCAATGCGAATATGT
*
281666 ACTATCGCAACGCGA
1 ACTATCGCAATGCGA
281681 TTTTCAAAGC
Statistics
Matches: 97, Mismatches: 13, Indels: 9
0.82 0.11 0.08
Matches are distributed among these distances:
19 2 0.02
20 94 0.97
21 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (21 bp):
ACTATCGCAATGCGAATATGT
Found at i:281673 original size:60 final size:60
Alignment explanation
Indices: 281545--281680 Score: 184
Period size: 60 Copynumber: 2.3 Consensus size: 60
281535 GCGATTTTTC
*
281545 GACTATCGCAATGCGAATATGTAAATCGCAATGCGAGTATGGCTATCGCAACGCGAATAT
1 GACTATCGCAATGCGAATATGTAAATCGCAATGCGAGTATGACTATCGCAACGCGAATAT
* * * * * *
281605 GTA-AATCGCAATGCGAATATGTAAATCGCAATGCGATTATTACTATCGCAATGCGATTCT
1 G-ACTATCGCAATGCGAATATGTAAATCGCAATGCGAGTATGACTATCGCAACGCGAATAT
*
281665 GACTATCGCAACGCGA
1 GACTATCGCAATGCGA
281681 TTTTCAAAGC
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
59 1 0.02
60 63 0.97
61 1 0.02
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (60 bp):
GACTATCGCAATGCGAATATGTAAATCGCAATGCGAGTATGACTATCGCAACGCGAATAT
Found at i:281682 original size:40 final size:40
Alignment explanation
Indices: 281545--281680 Score: 159
Period size: 40 Copynumber: 3.4 Consensus size: 40
281535 GCGATTTTTC
* *
281545 GACTATCGCAATGCGAATATGTAAATCGCAATGCGAGTAT
1 GACTATCGCAACGCGAATATGTAAATCGCAATGCGAATAT
*
281585 GGCTATCGCAACGCGAATATGTAAATCGCAATGCGAATAT
1 GACTATCGCAACGCGAATATGTAAATCGCAATGCGAATAT
* * * * * *
281625 GTA-AATCGCAATGCGATTAT-TACTATCGCAATGCGATTCT
1 G-ACTATCGCAACGCGAATATGTA-AATCGCAATGCGAATAT
281665 GACTATCGCAACGCGA
1 GACTATCGCAACGCGA
281681 TTTTCAAAGC
Statistics
Matches: 81, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
39 3 0.04
40 78 0.96
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (40 bp):
GACTATCGCAACGCGAATATGTAAATCGCAATGCGAATAT
Found at i:282512 original size:24 final size:24
Alignment explanation
Indices: 282478--282531 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
282468 GTATTCGAAA
*
282478 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
282502 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
282526 TTTGAT
1 TTTGAT
282532 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:282750 original size:14 final size:14
Alignment explanation
Indices: 282721--282757 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
282711 AGAAAAAAAA
282721 GAAGAAGAAATCCCC
1 GAAGAA-AAATCCCC
*
282736 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
282750 GAAGAAAA
1 GAAGAAAA
282758 TGCCACGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.51, C:0.22, G:0.22, T:0.05
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:284818 original size:18 final size:18
Alignment explanation
Indices: 284795--284829 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
284785 AGCAAAAGGC
*
284795 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
284813 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
284830 CAACCGTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:285032 original size:20 final size:20
Alignment explanation
Indices: 285007--285355 Score: 185
Period size: 20 Copynumber: 18.6 Consensus size: 20
284997 CATATTCATT
285007 TGACTATCGCAACGCGAATA
1 TGACTATCGCAACGCGAATA
285027 TGACTATCGCAACGCGAATA
1 TGACTATCGCAACGCGAATA
* *
285047 TGACTATCGCAACGTGAATT
1 TGACTATCGCAACGCGAATA
* *
285067 TGAATATCGCAA--CG-AGA
1 TGACTATCGCAACGCGAATA
** *
285084 T-A--ATCGCAATACGAAAA
1 TGACTATCGCAACGCGAATA
*
285101 TGACTATCGCAACG-G--GA
1 TGACTATCGCAACGCGAATA
* *
285118 T-A--ATCGCAATGCGAAAA
1 TGACTATCGCAACGCGAATA
* *
285135 TGACTATCGCAATG-GGATA
1 TGACTATCGCAACGCGAATA
* *
285154 --A-T-T-GCAATGCGAAAA
1 TGACTATCGCAACGCGAATA
* * *
285169 TGACTATTGCAATGCGAAAA
1 TGACTATCGCAACGCGAATA
*
285189 TGACTATCGCAACGCGAAAA
1 TGACTATCGCAACGCGAATA
* *
285209 TGACTATCGTAACACGAATA
1 TGACTATCGCAACGCGAATA
* * *
285229 TGACAATAGCAACGCGAATT
1 TGACTATCGCAACGCGAATA
* * * *
285249 TAAC-CT-GCAAAATCACGAATT
1 TGACTATCGC--AA-CGCGAATA
*
285270 TGACTATCGCAA--CG-AGA
1 TGACTATCGCAACGCGAATA
*
285287 T-A--ATCGCAATGCGAA-A
1 TGACTATCGCAACGCGAATA
*
285303 TGACTATCGCAACGCGAATT
1 TGACTATCGCAACGCGAATA
* * *
285323 TGATTATCGCAACGGGAATT
1 TGACTATCGCAACGCGAATA
285343 TGACTATCGCAAC
1 TGACTATCGCAAC
285356 AAGAAAATCG
Statistics
Matches: 261, Mismatches: 38, Indels: 60
0.73 0.11 0.17
Matches are distributed among these distances:
14 28 0.11
15 5 0.02
16 10 0.04
17 15 0.06
18 8 0.03
19 18 0.07
20 162 0.62
21 12 0.05
22 1 0.00
23 2 0.01
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.22
Consensus pattern (20 bp):
TGACTATCGCAACGCGAATA
Found at i:285109 original size:34 final size:34
Alignment explanation
Indices: 285071--285180 Score: 175
Period size: 34 Copynumber: 3.2 Consensus size: 34
285061 TGAATTTGAA
* *
285071 TATCGCAACGAGATAATCGCAATACGAAAATGAC
1 TATCGCAACGGGATAATCGCAATGCGAAAATGAC
285105 TATCGCAACGGGATAATCGCAATGCGAAAATGAC
1 TATCGCAACGGGATAATCGCAATGCGAAAATGAC
* *
285139 TATCGCAATGGGATAATTGCAATGCGAAAATGAC
1 TATCGCAACGGGATAATCGCAATGCGAAAATGAC
*
285173 TATTGCAA
1 TATCGCAA
285181 TGCGAAAATG
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 71 1.00
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.21
Consensus pattern (34 bp):
TATCGCAACGGGATAATCGCAATGCGAAAATGAC
Found at i:285144 original size:54 final size:55
Alignment explanation
Indices: 285086--285217 Score: 137
Period size: 54 Copynumber: 2.4 Consensus size: 55
285076 CAACGAGATA
* **
285086 ATCGCAATACGAAAATGACTATCGC-AACGGGA-TAATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACTATCGCGAAAAGGACT-ATCGCAATGCGAAAATGACT
* * * * *
285140 ATCGCAATGGGATAATTG-CAAT-GCGAAAATGACTATTGCAATGCGAAAATGACT
1 ATCGCAATGCGA-AAATGACTATCGCGAAAAGGACTATCGCAATGCGAAAATGACT
*
285194 ATCGCAACGCGAAAATGACTATCG
1 ATCGCAATGCGAAAATGACTATCG
285218 TAACACGAAT
Statistics
Matches: 61, Mismatches: 12, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
53 6 0.10
54 49 0.80
55 6 0.10
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.20
Consensus pattern (55 bp):
ATCGCAATGCGAAAATGACTATCGCGAAAAGGACTATCGCAATGCGAAAATGACT
Found at i:285531 original size:36 final size:34
Alignment explanation
Indices: 285490--285569 Score: 114
Period size: 30 Copynumber: 2.4 Consensus size: 34
285480 TCAACTTTTA
285490 ATCAATTAAACAAGCACAAATAAGAATTATTTACAC
1 ATCAATTAAACAA--ACAAATAAGAATTATTTACAC
285526 ATCAATT----AAACAAATAAGAATTATTTACAC
1 ATCAATTAAACAAACAAATAAGAATTATTTACAC
285556 ATCAATTAAACAAA
1 ATCAATTAAACAAA
285570 TCAACTCTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
30 28 0.70
32 2 0.05
34 3 0.08
36 7 0.17
ACGTcount: A:0.55, C:0.15, G:0.04, T:0.26
Consensus pattern (34 bp):
ATCAATTAAACAAACAAATAAGAATTATTTACAC
Found at i:285540 original size:30 final size:30
Alignment explanation
Indices: 285505--285570 Score: 132
Period size: 30 Copynumber: 2.2 Consensus size: 30
285495 TTAAACAAGC
285505 ACAAATAAGAATTATTTACACATCAATTAA
1 ACAAATAAGAATTATTTACACATCAATTAA
285535 ACAAATAAGAATTATTTACACATCAATTAA
1 ACAAATAAGAATTATTTACACATCAATTAA
285565 ACAAAT
1 ACAAAT
285571 CAACTCTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.55, C:0.14, G:0.03, T:0.29
Consensus pattern (30 bp):
ACAAATAAGAATTATTTACACATCAATTAA
Found at i:286985 original size:21 final size:21
Alignment explanation
Indices: 286956--287036 Score: 74
Period size: 21 Copynumber: 3.9 Consensus size: 21
286946 GAATGTTGGG
* *
286956 AGGGACCTCTTCAACGATGAT
1 AGGGGCCTCTTGAACGATGAT
* * **
286977 AGTGGCCTCTTGAACGGTGGG
1 AGGGGCCTCTTGAACGATGAT
* *
286998 AGGGGACTCTT-AAGAGATGAT
1 AGGGGCCTCTTGAA-CGATGAT
287019 AGGGGCCTCTTGAACGAT
1 AGGGGCCTCTTGAACGAT
287037 AGGGGAGGCC
Statistics
Matches: 44, Mismatches: 14, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
20 2 0.05
21 40 0.91
22 2 0.05
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.23
Consensus pattern (21 bp):
AGGGGCCTCTTGAACGATGAT
Found at i:287050 original size:42 final size:42
Alignment explanation
Indices: 286971--287051 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
286961 CCTCTTCAAC
* * *
286971 GATGATAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTAAGA
1 GATGATAGGGGCCTCTTGAACGATGGGAGAGGACTCTTAAGA
*
287013 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTA
1 GATGATAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTA
287052 CGGATTCTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 31 0.91
43 3 0.09
ACGTcount: A:0.23, C:0.16, G:0.37, T:0.23
Consensus pattern (42 bp):
GATGATAGGGGCCTCTTGAACGATGGGAGAGGACTCTTAAGA
Found at i:287541 original size:18 final size:18
Alignment explanation
Indices: 287518--287563 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
287508 GAAACTTAAA
**
287518 ATCGCAACACGAATGACT
1 ATCGCAACAAAAATGACT
287536 ATCGCAACGCAAAAATGACT
1 ATCGCAA--CAAAAATGACT
287556 ATCGCAAC
1 ATCGCAAC
287564 GAGAGAATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 8 0.33
20 16 0.67
ACGTcount: A:0.41, C:0.28, G:0.15, T:0.15
Consensus pattern (18 bp):
ATCGCAACAAAAATGACT
Found at i:287661 original size:20 final size:20
Alignment explanation
Indices: 287608--287674 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
287598 CGATTCTTTT
**
287608 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCATTTTCGC
287628 GTTGCGATAGTCATTTTCGC
1 GTTGCGATAGTCATTTTCGC
*
287648 GTTGCGATAGTCATTTCCGC
1 GTTGCGATAGTCATTTTCGC
*
287668 TTTGCGA
1 GTTGCGA
287675 AAGTAAACTA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.18, C:0.21, G:0.25, T:0.36
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGC
Found at i:287845 original size:18 final size:18
Alignment explanation
Indices: 287822--287871 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
287812 TTTACTAAGC
287822 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
287840 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
287858 AATCTAAGTGAAAT
1 AATCTAAGTGAAAT
287872 TACGAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (18 bp):
AATCTAAGTGAAATGGTT
Found at i:289675 original size:20 final size:20
Alignment explanation
Indices: 289587--289713 Score: 124
Period size: 20 Copynumber: 6.7 Consensus size: 20
289577 GAAACTTAAA
*
289587 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
289607 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
** *
289627 ATCGCAACGCGAATTTGATT
1 ATCGCAACGCGAAAATGACT
**
289647 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
289667 ATCGCAACGCG---A-GA--
1 ATCGCAACGCGAAAATGACT
* *
289681 ATCGCAACGTG-AAATGACA
1 ATCGCAACGCGAAAATGACT
289700 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
289714 CTAAAATCGC
Statistics
Matches: 93, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
14 10 0.11
16 3 0.03
17 2 0.02
19 10 0.11
20 68 0.73
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:289708 original size:33 final size:34
Alignment explanation
Indices: 289647--289711 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
289637 GAATTTGATT
* *
289647 ATCGCAACGCGAATTTGACTATCGCAACGCGAGA
1 ATCGCAACGCGAATATGACAATCGCAACGCGAGA
*
289681 ATCGCAACGTGAA-ATGACAATCGCAACGCGA
1 ATCGCAACGCGAATATGACAATCGCAACGCGA
289712 AACTAAAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 16 0.57
34 12 0.43
ACGTcount: A:0.35, C:0.26, G:0.23, T:0.15
Consensus pattern (34 bp):
ATCGCAACGCGAATATGACAATCGCAACGCGAGA
Found at i:290137 original size:22 final size:22
Alignment explanation
Indices: 290109--290162 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
290099 GGAGATAGAT
290109 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCGCCGGAGATGGGGAC
* *
290131 TGATTTCGTCGGAGATGGGGAC
1 GGATTTCGCCGGAGATGGGGAC
*
290153 GGATGTCGCC
1 GGATTTCGCC
290163 TTAGAGAGTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.17, C:0.19, G:0.43, T:0.22
Consensus pattern (22 bp):
GGATTTCGCCGGAGATGGGGAC
Found at i:290380 original size:20 final size:20
Alignment explanation
Indices: 290326--290520 Score: 72
Period size: 20 Copynumber: 9.7 Consensus size: 20
290316 GTGCTTTGAA
* *
290326 AATCGTATTGCGACAGTCAG
1 AATCGCATTGCGATAGTCAG
* *
290346 AATTGCGTTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
* * *
290366 AATCGCATTGAGATAGTAAT
1 AATCGCATTGCGATAGTCAG
** * *
290386 AATCATATTGCGAT-TTACAT
1 AATCGCATTGCGATAGT-CAG
* * ** *
290406 ATTCGCGTTGCGATAACCAT
1 AATCGCATTGCGATAGTCAG
* * *
290426 ACTCGCATTGCGAT-TTACAT
1 AATCGCATTGCGATAGT-CAG
* *
290446 ATTCGCATTGCGATAGTCGGAA
1 AATCGCATTGCGATAGTC--AG
** * **
290468 AATCGCAACGCGA-ATTTGG
1 AATCGCATTGCGATAGTCAG
*
290487 AAATCGCAATGCGATAGTCAG
1 -AATCGCATTGCGATAGTCAG
*
290508 AATCGCGTTGCGA
1 AATCGCATTGCGA
290521 ATCTGAAAAC
Statistics
Matches: 127, Mismatches: 40, Indels: 16
0.69 0.22 0.09
Matches are distributed among these distances:
19 1 0.01
20 109 0.86
21 6 0.05
22 11 0.09
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (20 bp):
AATCGCATTGCGATAGTCAG
Found at i:291743 original size:29 final size:29
Alignment explanation
Indices: 291710--291769 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
291700 GTTTAAATCT
291710 TACATTTTTTAATTGAATAAACT-TGATTG
1 TACATTTTTTAATTGAATAAACTGT-ATTG
291739 TACATTTTTTAATTGAATAAACTGTATTG
1 TACATTTTTTAATTGAATAAACTGTATTG
291768 TA
1 TA
291770 AAAGTTATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 29 0.97
30 1 0.03
ACGTcount: A:0.35, C:0.07, G:0.10, T:0.48
Consensus pattern (29 bp):
TACATTTTTTAATTGAATAAACTGTATTG
Found at i:294116 original size:35 final size:35
Alignment explanation
Indices: 294070--294141 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
294060 TTTGAACTAG
294070 GTTCATATATGATAACATCATTCATATGAGCCTGT
1 GTTCATATATGATAACATCATTCATATGAGCCTGT
294105 GTTCATATATGATAACATCATTCATATGAGCCTGT
1 GTTCATATATGATAACATCATTCATATGAGCCTGT
294140 GT
1 GT
294142 AAGCATGTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.38
Consensus pattern (35 bp):
GTTCATATATGATAACATCATTCATATGAGCCTGT
Found at i:299041 original size:6 final size:6
Alignment explanation
Indices: 299030--299133 Score: 120
Period size: 6 Copynumber: 17.2 Consensus size: 6
299020 ATAGGTACTG
*
299030 AAATTC AAATTC AAATTC AAATTC AAATTC AAATTC AAATTC AAATCC
1 AAATTC AAATTC AAATTC AAATTC AAATTC AAATTC AAATTC AAATTC
* * * * * *
299078 AAATCC AAATCC AAA-TC CAATTCC AAATCC AAATCC AAATCC AAATTTC
1 AAATTC AAATTC AAATTC AAATT-C AAATTC AAATTC AAATTC AAA-TTC
299127 AAATTC A
1 AAATTC A
299134 TGTTTCTAAG
Statistics
Matches: 89, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
5 3 0.03
6 77 0.87
7 9 0.10
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (6 bp):
AAATTC
Found at i:303100 original size:21 final size:22
Alignment explanation
Indices: 303059--303101 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
303049 CATTATTTTA
* *
303059 TTGTTGTATGTTGATGACATGC
1 TTGTTGTAGGTTCATGACATGC
303081 TTGTTGTAGGTTCA-GACATGC
1 TTGTTGTAGGTTCATGACATGC
303102 AAGAGATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.19, C:0.12, G:0.28, T:0.42
Consensus pattern (22 bp):
TTGTTGTAGGTTCATGACATGC
Found at i:306949 original size:25 final size:26
Alignment explanation
Indices: 306890--306949 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
306880 TTTTATAAAC
* *
306890 TTATTTCTTTTCTTTTCTTTTCAAGTT
1 TTATTT-TTTTATTTTATTTTCAAGTT
306917 TT-TCTTTTTTATTTTATTTT-AAGTT
1 TTAT-TTTTTTATTTTATTTTCAAGTT
306942 TTATTTTT
1 TTATTTTT
306950 CAACATGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
25 11 0.38
26 14 0.48
27 4 0.14
ACGTcount: A:0.13, C:0.08, G:0.03, T:0.75
Consensus pattern (26 bp):
TTATTTTTTTATTTTATTTTCAAGTT
Found at i:313679 original size:30 final size:30
Alignment explanation
Indices: 313627--313689 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
313617 ATAAATAACA
* *
313627 TGAAAGAAGCTATATGTCTATATGTATATG
1 TGAAAGAAGCTATATGTCTATATGAACATG
313657 TGAAAGAAGCTATGA-G-CTTATATGAACATG
1 TGAAAGAAGCTAT-ATGTC-TATATGAACATG
313687 TGA
1 TGA
313690 TATGAAAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 1 0.03
30 27 0.93
31 1 0.03
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.32
Consensus pattern (30 bp):
TGAAAGAAGCTATATGTCTATATGAACATG
Found at i:313814 original size:18 final size:18
Alignment explanation
Indices: 313791--313860 Score: 122
Period size: 18 Copynumber: 3.9 Consensus size: 18
313781 GGGTCTACGC
313791 GGTCCTTCGGGACATAGT
1 GGTCCTTCGGGACATAGT
313809 GGTCCTTCGGGACATAGT
1 GGTCCTTCGGGACATAGT
*
313827 GGTCCTTCAGGACATAGT
1 GGTCCTTCGGGACATAGT
*
313845 GGTCTTTCGGGACATA
1 GGTCCTTCGGGACATA
313861 TGTGTTATAT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 49 1.00
ACGTcount: A:0.19, C:0.21, G:0.31, T:0.29
Consensus pattern (18 bp):
GGTCCTTCGGGACATAGT
Found at i:316712 original size:15 final size:15
Alignment explanation
Indices: 316692--316721 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
316682 CAAAACAAAG
316692 GTTAGTTTCTGGTTA
1 GTTAGTTTCTGGTTA
*
316707 GTTAGTTTCTTGTTA
1 GTTAGTTTCTGGTTA
316722 AATTTAAGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.07, G:0.23, T:0.57
Consensus pattern (15 bp):
GTTAGTTTCTGGTTA
Found at i:318110 original size:18 final size:18
Alignment explanation
Indices: 318074--318124 Score: 95
Period size: 18 Copynumber: 2.9 Consensus size: 18
318064 GGGTCTATGC
318074 GGTCCTTCGGGAC-TAGT
1 GGTCCTTCGGGACATAGT
318091 GGTCCTTCGGGACATAGT
1 GGTCCTTCGGGACATAGT
318109 GGTCCTTCGGGACATA
1 GGTCCTTCGGGACATA
318125 TGTGTTATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 13 0.39
18 20 0.61
ACGTcount: A:0.16, C:0.24, G:0.33, T:0.27
Consensus pattern (18 bp):
GGTCCTTCGGGACATAGT
Found at i:319591 original size:80 final size:78
Alignment explanation
Indices: 319483--319639 Score: 296
Period size: 80 Copynumber: 2.0 Consensus size: 78
319473 AACACACAAC
319483 TCAGAATTTACTATCTCTTATTTCTAGTTTTATAAACTTATTTCTTTTCTTTTCTTTTCTTTTCA
1 TCAGAATTTACTATCTCTTATTTCTAGTTTTATAAACTTATTTCTTTTCTTTTCTTTTCTTTTCA
319548 TGTTTTCATTTTA
66 TGTTTTCATTTTA
319561 TCAGAATTTACTATTCTTCTTATTTCTAGTTTTATAAACTTATTTCTTTTCTTTTCTTTTCTTTT
1 TCAGAATTTACTA-TC-TCTTATTTCTAGTTTTATAAACTTATTTCTTTTCTTTTCTTTTCTTTT
319626 CATGTTTTCATTTT
64 CATGTTTTCATTTT
319640 TATTTTATTT
Statistics
Matches: 77, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
78 13 0.17
79 2 0.03
80 62 0.81
ACGTcount: A:0.18, C:0.15, G:0.04, T:0.62
Consensus pattern (78 bp):
TCAGAATTTACTATCTCTTATTTCTAGTTTTATAAACTTATTTCTTTTCTTTTCTTTTCTTTTCA
TGTTTTCATTTTA
Found at i:322155 original size:21 final size:22
Alignment explanation
Indices: 322131--322205 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 22
322121 GAATAGCAAC
322131 CCTC-TTTTCTAGAACAACATA
1 CCTCATTTTCTAGAACAACATA
*
322152 CCTCATTTTTTCTAGAACAATA-A
1 CCTCA--TTTTCTAGAACAACATA
* * *
322175 TCTTC-TTTTCCAGAACAACATC
1 -CCTCATTTTCTAGAACAACATA
322197 CCTCATTTT
1 CCTCATTTT
322206 TTCCAGAACA
Statistics
Matches: 42, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
21 20 0.48
22 4 0.10
23 1 0.02
24 17 0.40
ACGTcount: A:0.29, C:0.28, G:0.04, T:0.39
Consensus pattern (22 bp):
CCTCATTTTCTAGAACAACATA
Found at i:322165 original size:24 final size:24
Alignment explanation
Indices: 322135--322216 Score: 91
Period size: 24 Copynumber: 3.5 Consensus size: 24
322125 AGCAACCCTC
*
322135 TTTTCTAGAACAACATACCTCATT
1 TTTTCCAGAACAACATACCTCATT
* *
322159 TTTTCTAGAAC-A-ATA-ATC-TT
1 TTTTCCAGAACAACATACCTCATT
*
322179 CTTTTCCAGAACAACATCCCTCATT
1 -TTTTCCAGAACAACATACCTCATT
322204 TTTTCCAGAACAA
1 TTTTCCAGAACAA
322217 TAGCCCACTT
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 2 0.04
21 12 0.24
22 4 0.08
23 3 0.06
24 26 0.53
25 2 0.04
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.37
Consensus pattern (24 bp):
TTTTCCAGAACAACATACCTCATT
Found at i:322182 original size:45 final size:45
Alignment explanation
Indices: 322133--322218 Score: 145
Period size: 45 Copynumber: 1.9 Consensus size: 45
322123 ATAGCAACCC
* *
322133 TCTTTTCTAGAACAACATACCTCATTTTTTCTAGAACAATAATCT
1 TCTTTTCCAGAACAACATACCTCATTTTTTCCAGAACAATAATCT
*
322178 TCTTTTCCAGAACAACATCCCTCATTTTTTCCAGAACAATA
1 TCTTTTCCAGAACAACATACCTCATTTTTTCCAGAACAATA
322219 GCCCACTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.37
Consensus pattern (45 bp):
TCTTTTCCAGAACAACATACCTCATTTTTTCCAGAACAATAATCT
Found at i:322228 original size:45 final size:45
Alignment explanation
Indices: 322128--322229 Score: 132
Period size: 45 Copynumber: 2.3 Consensus size: 45
322118 ATAGAATAGC
* * *
322128 AACCCTCTTTTCTAGAACAACATACCTCATTTTTTCTAGAACAAT
1 AACCCACTTTTCCAGAACAACATACCTCATTTTTTCCAGAACAAT
* ** *
322173 AATCTTCTTTTCCAGAACAACATCCCTCATTTTTTCCAGAACAAT
1 AACCCACTTTTCCAGAACAACATACCTCATTTTTTCCAGAACAAT
*
322218 AGCCCACTTTTC
1 AACCCACTTTTC
322230 TATAATAGCA
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.30, C:0.29, G:0.05, T:0.35
Consensus pattern (45 bp):
AACCCACTTTTCCAGAACAACATACCTCATTTTTTCCAGAACAAT
Found at i:324415 original size:3 final size:3
Alignment explanation
Indices: 324407--324431 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
324397 TGGTTCAAAC
324407 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
324432 AACCCTATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:332416 original size:38 final size:37
Alignment explanation
Indices: 332334--332417 Score: 132
Period size: 38 Copynumber: 2.2 Consensus size: 37
332324 TGAATTAAAT
*
332334 TTTAGAAAAACAGGGATTCTAAACAAATTAAATATCA
1 TTTAGAAAAACAGGGATTCTAAACAAATTAAATAGCA
*
332371 TTATAGAAAAACAGGGATTCTAAACAAATTAAATCGCTA
1 TT-TAGAAAAACAGGGATTCTAAACAAATTAAATAGC-A
332410 TTTAGAAA
1 TTTAGAAA
332418 CATTATAATT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
37 2 0.05
38 38 0.88
39 3 0.07
ACGTcount: A:0.50, C:0.11, G:0.12, T:0.27
Consensus pattern (37 bp):
TTTAGAAAAACAGGGATTCTAAACAAATTAAATAGCA
Found at i:333429 original size:27 final size:26
Alignment explanation
Indices: 333350--333435 Score: 74
Period size: 27 Copynumber: 3.4 Consensus size: 26
333340 ATTTCTGATG
333350 TTTTGATTGAGTTGTATTCGGTGATTT
1 TTTTGATTGAGTTGTATTC-GTGATTT
* * * *
333377 TTTTTATTTTA-TT-T-TT-TTGA-TG
1 TTTTGA-TTGAGTTGTATTCGTGATTT
333399 TTTTGATTGAGTTGTATTCAGTGATTT
1 TTTTGATTGAGTTGTATTC-GTGATTT
333426 TTTTGATTGA
1 TTTTGATTGA
333436 ATGGTGGAGT
Statistics
Matches: 44, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
21 3 0.07
22 8 0.18
23 4 0.09
24 2 0.05
25 2 0.05
26 4 0.09
27 18 0.41
28 3 0.07
ACGTcount: A:0.16, C:0.02, G:0.20, T:0.62
Consensus pattern (26 bp):
TTTTGATTGAGTTGTATTCGTGATTT
Found at i:344089 original size:21 final size:21
Alignment explanation
Indices: 344047--344090 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
344037 ACTCCGGGAG
*
344047 CTAGTTCCTCACGAGCTGCTC
1 CTAGTTCCTCACGAGCTCCTC
* * *
344068 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCCTCACGAGCTCCTC
344089 CT
1 CT
344091 CCTCCTCCGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.39, G:0.16, T:0.36
Consensus pattern (21 bp):
CTAGTTCCTCACGAGCTCCTC
Found at i:345360 original size:64 final size:63
Alignment explanation
Indices: 345191--345370 Score: 193
Period size: 64 Copynumber: 2.8 Consensus size: 63
345181 GAATAAATTG
* * * * * * *
345191 AACATCAAATGCATTTCATGCATCGATGCACTCTCTGTGCATCGATGAACTTGGGTTTTATTAA
1 AACATCGAATGCATTTCATGCATCGATGCACACT-TGTGCACCGATGCACTAGGCTATTATTAA
** *
345255 AACATCGAATGCATTTCATGCATCGATGCACAAGC-AATGCACCGATGCACTCAGGCTATT-TTC
1 AACATCGAATGCATTTCATGCATCGATGCAC-A-CTTGTGCACCGATGCACT-AGGCTATTATTA
345318 A
63 A
* *
345319 AACATCGAATGCATTTTATGAATCGATGCACACTTGGTGCACCGATGCACTA
1 AACATCGAATGCATTTCATGCATCGATGCACACTT-GTGCACCGATGCACTA
345371 AGTGTTCCAA
Statistics
Matches: 97, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 88 0.91
65 5 0.05
66 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (63 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTTGTGCACCGATGCACTAGGCTATTATTAA
Found at i:346314 original size:11 final size:11
Alignment explanation
Indices: 346300--346359 Score: 66
Period size: 11 Copynumber: 5.4 Consensus size: 11
346290 TTACTTGCTG
*
346300 TTTATTTGTTG
1 TTTATTTGTTA
*
346311 TTTATTTGATA
1 TTTATTTGTTA
* *
346322 TTTTAGTTGATA
1 -TTTATTTGTTA
346334 TTTATTTGTTA
1 TTTATTTGTTA
*
346345 TTTATTTGCTA
1 TTTATTTGTTA
346356 TTTA
1 TTTA
346360 GTTGCTGTGA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
11 32 0.76
12 10 0.24
ACGTcount: A:0.20, C:0.02, G:0.12, T:0.67
Consensus pattern (11 bp):
TTTATTTGTTA
Found at i:346326 original size:23 final size:22
Alignment explanation
Indices: 346300--346359 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 22
346290 TTACTTGCTG
* *
346300 TTTATTTGTTGTTTATTTGATA
1 TTTATTTGATATTTATTTGATA
* *
346322 TTTTAGTTGATATTTATTTGTTA
1 -TTTATTTGATATTTATTTGATA
*
346345 TTTATTTGCTATTTA
1 TTTATTTGATATTTA
346360 GTTGCTGTGA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
22 13 0.42
23 18 0.58
ACGTcount: A:0.20, C:0.02, G:0.12, T:0.67
Consensus pattern (22 bp):
TTTATTTGATATTTATTTGATA
Found at i:346341 original size:34 final size:33
Alignment explanation
Indices: 346300--346363 Score: 101
Period size: 34 Copynumber: 1.9 Consensus size: 33
346290 TTACTTGCTG
*
346300 TTTATTTGTTGTTTATTTGATATTTTAGTTGATA
1 TTTATTTGTTATTTATTTGATA-TTTAGTTGATA
*
346334 TTTATTTGTTATTTATTTGCTATTTAGTTG
1 TTTATTTGTTATTTATTTGATATTTAGTTG
346364 CTGTGAATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 8 0.29
34 20 0.71
ACGTcount: A:0.19, C:0.02, G:0.14, T:0.66
Consensus pattern (33 bp):
TTTATTTGTTATTTATTTGATATTTAGTTGATA
Found at i:346364 original size:11 final size:11
Alignment explanation
Indices: 346323--346365 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
346313 TATTTGATAT
*
346323 TTTAGTTGATA
1 TTTAGTTGCTA
* *
346334 TTTATTTGTTA
1 TTTAGTTGCTA
*
346345 TTTATTTGCTA
1 TTTAGTTGCTA
346356 TTTAGTTGCT
1 TTTAGTTGCT
346366 GTGAATTCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.19, C:0.05, G:0.14, T:0.63
Consensus pattern (11 bp):
TTTAGTTGCTA
Found at i:346439 original size:11 final size:11
Alignment explanation
Indices: 346420--346451 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
346410 TAATTGCTAT
*
346420 TTTATTTGTTA
1 TTTAGTTGTTA
346431 TTTAGTTGTTA
1 TTTAGTTGTTA
346442 TTTAGTTGTT
1 TTTAGTTGTT
346452 GTGAATTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.69
Consensus pattern (11 bp):
TTTAGTTGTTA
Found at i:346537 original size:11 final size:11
Alignment explanation
Indices: 346500--346552 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
346490 TATTGGATGT
346500 TTTAGTTGTTA
1 TTTAGTTGTTA
* *
346511 TTTTAGTTGATG
1 -TTTAGTTGTTA
*
346523 TTTATTTGTTA
1 TTTAGTTGTTA
* *
346534 TTTATTTGCTA
1 TTTAGTTGTTA
346545 TTTAGTTG
1 TTTAGTTG
346553 CTGTGAATTT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
11 25 0.74
12 9 0.26
ACGTcount: A:0.17, C:0.02, G:0.17, T:0.64
Consensus pattern (11 bp):
TTTAGTTGTTA
Found at i:346609 original size:11 final size:11
Alignment explanation
Indices: 346597--346637 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
346587 TTATTGGATG
*
346597 TTTAGTTGCTG
1 TTTAGTTGCTA
* *
346608 TTTATTTGTTA
1 TTTAGTTGCTA
346619 TTTAGTTGCTA
1 TTTAGTTGCTA
346630 TTTAGTTG
1 TTTAGTTG
346638 TTGTGAATTC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.15, C:0.05, G:0.20, T:0.61
Consensus pattern (11 bp):
TTTAGTTGCTA
Found at i:346612 original size:85 final size:85
Alignment explanation
Indices: 346512--346786 Score: 352
Period size: 85 Copynumber: 3.1 Consensus size: 85
346502 TAGTTGTTAT
* * *
346512 TTTAGTTGATGTTTATTTGTTATTTATTTGCTATTTAGTTGCTGTGAATTTAATATTATTGGATA
1 TTTAGTTGCTGTTTATTTGTTATTTATTTGCTATTTAGTTGTTGTGAATTCAATATTATTGGATA
*
346577 TTATGTCTATTTATTGGATG
66 TTATGTCTGTTTATTGGATG
*
346597 TTTAGTTGCTGTTTATTTGTTATTTAGTTGCTATTTAGTTGTTGTGAATTCAATATTATTGGATA
1 TTTAGTTGCTGTTTATTTGTTATTTATTTGCTATTTAGTTGTTGTGAATTCAATATTATTGGATA
*
346662 TTATGTCTGTTTATTAGATGTTTAGTTATTAT
66 TTATGTCTGTTTA-T---TG----G--A-T-G
* * *
346694 TTTAGTTGCTATTTATTTGTTATTTATTTTCTATTTAGTTGTTGTGAATTCAATATTATTAGATA
1 TTTAGTTGCTGTTTATTTGTTATTTATTTGCTATTTAGTTGTTGTGAATTCAATATTATTGGATA
*
346759 TTATGTCTGTTTATTTGATG
66 TTATGTCTGTTTATTGGATG
346779 TTTAGTTG
1 TTTAGTTG
346787 TTATGTTAGA
Statistics
Matches: 166, Mismatches: 12, Indels: 24
0.82 0.06 0.12
Matches are distributed among these distances:
85 81 0.49
86 2 0.01
87 1 0.01
89 3 0.02
93 2 0.01
95 1 0.01
96 2 0.01
97 74 0.45
ACGTcount: A:0.22, C:0.04, G:0.17, T:0.57
Consensus pattern (85 bp):
TTTAGTTGCTGTTTATTTGTTATTTATTTGCTATTTAGTTGTTGTGAATTCAATATTATTGGATA
TTATGTCTGTTTATTGGATG
Found at i:346622 original size:22 final size:22
Alignment explanation
Indices: 346597--346639 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
346587 TTATTGGATG
* *
346597 TTTAGTTGCTGTTTATTTGTTA
1 TTTAGTTGCTATTTAGTTGTTA
346619 TTTAGTTGCTATTTAGTTGTT
1 TTTAGTTGCTATTTAGTTGTT
346640 GTGAATTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.14, C:0.05, G:0.19, T:0.63
Consensus pattern (22 bp):
TTTAGTTGCTATTTAGTTGTTA
Found at i:346698 original size:97 final size:97
Alignment explanation
Indices: 346597--346795 Score: 335
Period size: 97 Copynumber: 2.1 Consensus size: 97
346587 TTATTGGATG
* *
346597 TTTAGTTGCTGTTTATTTGTTATTTAGTTGCTATTTAGTTGTTGTGAATTCAATATTATTGGATA
1 TTTAGTTGCTATTTATTTGTTATTTAGTTGCTATTTAGTTGTTGTGAATTCAATATTATTAGATA
346662 TTATGTCTGTTTATTAGATGTTTAGTTATTAT
66 TTATGTCTGTTTATTAGATGTTTAGTTATTAT
* *
346694 TTTAGTTGCTATTTATTTGTTATTTATTTTCTATTTAGTTGTTGTGAATTCAATATTATTAGATA
1 TTTAGTTGCTATTTATTTGTTATTTAGTTGCTATTTAGTTGTTGTGAATTCAATATTATTAGATA
* *
346759 TTATGTCTGTTTATTTGATGTTTAGTTGTTAT
66 TTATGTCTGTTTATTAGATGTTTAGTTATTAT
*
346791 GTTAG
1 TTTAG
346796 AATTTACTTG
Statistics
Matches: 95, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
97 95 1.00
ACGTcount: A:0.22, C:0.04, G:0.17, T:0.58
Consensus pattern (97 bp):
TTTAGTTGCTATTTATTTGTTATTTAGTTGCTATTTAGTTGTTGTGAATTCAATATTATTAGATA
TTATGTCTGTTTATTAGATGTTTAGTTATTAT
Found at i:347809 original size:29 final size:28
Alignment explanation
Indices: 347769--347828 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
347759 AGCTTCAATA
* *
347769 TGTTGATGGATGTTAACTGCCATTTTTTG
1 TGTTGATAGATG-TAACTGCCATCTTTTG
* *
347798 TGTTGATAGATGTACCTGTCATCTTTTG
1 TGTTGATAGATGTAACTGCCATCTTTTG
347826 TGT
1 TGT
347829 CATTTTTTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 16 0.59
29 11 0.41
ACGTcount: A:0.17, C:0.12, G:0.23, T:0.48
Consensus pattern (28 bp):
TGTTGATAGATGTAACTGCCATCTTTTG
Found at i:348285 original size:35 final size:35
Alignment explanation
Indices: 348237--348332 Score: 156
Period size: 35 Copynumber: 2.7 Consensus size: 35
348227 AAGTATTTTA
* *
348237 GAATTTGGGGTTTAGAATGTAATTGAATTACTTTG
1 GAATTTGGTGTTTAGAATGAAATTGAATTACTTTG
*
348272 GAATTTGGTGTTTAAAATGAAATTGAATTACTTTG
1 GAATTTGGTGTTTAGAATGAAATTGAATTACTTTG
*
348307 GAATTTGGTGTTTAGAATAAAATTGA
1 GAATTTGGTGTTTAGAATGAAATTGA
348333 GGATTGTTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 56 1.00
ACGTcount: A:0.33, C:0.02, G:0.23, T:0.42
Consensus pattern (35 bp):
GAATTTGGTGTTTAGAATGAAATTGAATTACTTTG
Found at i:350880 original size:77 final size:78
Alignment explanation
Indices: 350741--350896 Score: 280
Period size: 77 Copynumber: 2.0 Consensus size: 78
350731 CTAGCCCTTC
350741 CTCATTCCAAGGAAGTTGAGTGAAGTTAGTGAGGTCGATGTTGAGTTCTGTTCCTGATACTGAAT
1 CTCATTCCAAGGAAGTTGAGTGAAGTTAGT-AGGTCGATGTTGAGTTCTGTTCCTGATACTGAAT
350806 CAGTGAG-TCAGTTG
65 -AGTGAGTTCAGTTG
350820 CTCATTCCAAGGAAGTTGAGTGAAGTTAGT-GGTCGATGTTGAGTTCTGTTCCTGATACTGAATA
1 CTCATTCCAAGGAAGTTGAGTGAAGTTAGTAGGTCGATGTTGAGTTCTGTTCCTGATACTGAATA
350884 GTGAGTTCAGTTG
66 GTGAGTTCAGTTG
350897 TGGATGAGGA
Statistics
Matches: 76, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
76 6 0.08
77 40 0.53
79 30 0.39
ACGTcount: A:0.24, C:0.13, G:0.29, T:0.34
Consensus pattern (78 bp):
CTCATTCCAAGGAAGTTGAGTGAAGTTAGTAGGTCGATGTTGAGTTCTGTTCCTGATACTGAATA
GTGAGTTCAGTTG
Found at i:355497 original size:30 final size:30
Alignment explanation
Indices: 355461--355522 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
355451 ATACAGAAGC
355461 ATAGAGTGACTTGGCATGAATTTGAGGCTG
1 ATAGAGTGACTTGGCATGAATTTGAGGCTG
355491 ATAGAGTGACTTGGCATGAATTTGAGGCTG
1 ATAGAGTGACTTGGCATGAATTTGAGGCTG
355521 AT
1 AT
355523 TTGTGTCATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.27, C:0.10, G:0.32, T:0.31
Consensus pattern (30 bp):
ATAGAGTGACTTGGCATGAATTTGAGGCTG
Found at i:361221 original size:36 final size:36
Alignment explanation
Indices: 361181--361249 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
361171 AACTAAAATG
*
361181 TAAGTCTATTCACAAAGTGACATAACTTATTATTAA
1 TAAGTCTATTCACAAAGTGACACAACTTATTATTAA
*
361217 TAAGTCTATTCACCAAGTGACACAACTTATTAT
1 TAAGTCTATTCACAAAGTGACACAACTTATTAT
361250 AAAGAGCATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (36 bp):
TAAGTCTATTCACAAAGTGACACAACTTATTATTAA
Found at i:362834 original size:26 final size:26
Alignment explanation
Indices: 362798--362862 Score: 121
Period size: 26 Copynumber: 2.5 Consensus size: 26
362788 AATCATGCGC
*
362798 CATTGGTTATTGTCTCATTGGCTTTG
1 CATTTGTTATTGTCTCATTGGCTTTG
362824 CATTTGTTATTGTCTCATTGGCTTTG
1 CATTTGTTATTGTCTCATTGGCTTTG
362850 CATTTGTTATTGT
1 CATTTGTTATTGT
362863 TGTAACGTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.12, C:0.14, G:0.20, T:0.54
Consensus pattern (26 bp):
CATTTGTTATTGTCTCATTGGCTTTG
Found at i:365192 original size:18 final size:18
Alignment explanation
Indices: 365147--365192 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 18
365137 ACCCCAATGA
*
365147 AGTAAAGAAAATAAAAAG
1 AGTAAAAAAAATAAAAAG
*
365165 AGATACAAAAAATAAAAAG
1 AG-TAAAAAAAATAAAAAG
365184 AGTAAAAAA
1 AGTAAAAAA
365193 TGAATAAGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.74, C:0.02, G:0.13, T:0.11
Consensus pattern (18 bp):
AGTAAAAAAAATAAAAAG
Found at i:365207 original size:9 final size:9
Alignment explanation
Indices: 365189--365372 Score: 66
Period size: 9 Copynumber: 19.9 Consensus size: 9
365179 AAAAGAGTAA
*
365189 AAAATGAAT
1 AAAATAAAT
*
365198 AAGATAAAT
1 AAAATAAAT
365207 AAAATAAAT
1 AAAATAAAT
365216 AAAATGAAAT
1 AAAAT-AAAT
365226 AATAATAATAT
1 AA-AATAA-AT
* *
365237 ATACA-CAAT
1 A-AAATAAAT
365246 -AAATAAAT
1 AAAATAAAT
*
365254 AAAAATTAGAAG
1 -AAAA-TA-AAT
365266 AAAATAAA-
1 AAAATAAAT
365274 AAAATAAAT
1 AAAATAAAT
*
365283 -ACATAAA-
1 AAAATAAAT
365290 ACAAAT--AT
1 A-AAATAAAT
*
365298 AAAGGAGAAA-
1 AAA--ATAAAT
365308 AAGAATAAGAT
1 AA-AATAA-AT
* *
365319 GAAGATAAAG
1 -AAAATAAAT
365329 AATAA-AAAT
1 AA-AATAAAT
365338 AAAAATAAA-
1 -AAAATAAAT
365347 AGAAATAAAT
1 A-AAATAAAT
365357 -AAATAAAT
1 AAAATAAAT
365365 AAAATAAA
1 AAAATAAA
365373 ATTAAAAATG
Statistics
Matches: 132, Mismatches: 16, Indels: 54
0.65 0.08 0.27
Matches are distributed among these distances:
7 5 0.04
8 27 0.20
9 52 0.39
10 24 0.18
11 19 0.14
12 5 0.04
ACGTcount: A:0.71, C:0.02, G:0.08, T:0.19
Consensus pattern (9 bp):
AAAATAAAT
Found at i:365225 original size:19 final size:19
Alignment explanation
Indices: 365142--365233 Score: 57
Period size: 19 Copynumber: 4.8 Consensus size: 19
365132 AAATAACCCC
*
365142 AATGAAGTAAAGA-AAATAA
1 AATGAAATAAA-ATAAATAA
* *
365161 AAAGAGATACAAA-AAATAA
1 AATGAAATA-AAATAAATAA
* *
365180 AAAGAGTAA-AAAATGAATAA
1 AATGA--AATAAAATAAATAA
*
365200 GAT-AAATAAAATAAATAA
1 AATGAAATAAAATAAATAA
365218 AATGAAATAATAATAA
1 AATGAAATAA-AATAA
365234 TATATACACA
Statistics
Matches: 57, Mismatches: 9, Indels: 13
0.72 0.11 0.16
Matches are distributed among these distances:
17 2 0.04
18 12 0.21
19 28 0.49
20 14 0.25
21 1 0.02
ACGTcount: A:0.71, C:0.01, G:0.11, T:0.17
Consensus pattern (19 bp):
AATGAAATAAAATAAATAA
Found at i:365233 original size:34 final size:32
Alignment explanation
Indices: 365188--365281 Score: 86
Period size: 34 Copynumber: 2.9 Consensus size: 32
365178 AAAAAGAGTA
365188 AAAAATGAATAAGATAAATAAAATAAATAAAAT
1 AAAAAT-AATAAGATAAATAAAATAAATAAAAT
* * * *
365221 GAAATAATAATAATATATACACAATAAAT-AAAT
1 -AAA-AATAATAAGATAAATAAAATAAATAAAAT
* *
365254 AAAAATTAGAAGA-AAATAAAA-AAATAAA
1 AAAAATAATAAGATAAATAAAATAAATAAA
365282 TACATAAAAC
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
29 4 0.08
30 7 0.15
31 7 0.15
32 3 0.06
33 4 0.08
34 20 0.42
35 3 0.06
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.21
Consensus pattern (32 bp):
AAAAATAATAAGATAAATAAAATAAATAAAAT
Found at i:365344 original size:12 final size:12
Alignment explanation
Indices: 365323--365381 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 12
365313 TAAGATGAAG
365323 ATAAAGAATAAAA
1 ATAAA-AATAAAA
365336 ATAAAAATAAAA
1 ATAAAAATAAAA
365348 GA-AATAAATAAATA
1 -ATAA-AAATAAA-A
365362 A-ATAAAATAAAA
1 ATA-AAAATAAAA
*
365374 TTAAAAAT
1 ATAAAAAT
365382 GTATAAAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
12 15 0.38
13 23 0.57
14 2 0.05
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.20
Consensus pattern (12 bp):
ATAAAAATAAAA
Found at i:365362 original size:17 final size:17
Alignment explanation
Indices: 365340--365372 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
365330 ATAAAAATAA
365340 AAATAAA-AGAAATAAAT
1 AAATAAATA-AAATAAAT
365357 AAATAAATAAAATAAA
1 AAATAAATAAAATAAA
365373 ATTAAAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 14 0.93
18 1 0.07
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (17 bp):
AAATAAATAAAATAAAT
Found at i:365511 original size:11 final size:11
Alignment explanation
Indices: 365495--365521 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
365485 ATAAAAAAAT
365495 TAAAATATATA
1 TAAAATATATA
365506 TAAAATATATA
1 TAAAATATATA
365517 TAAAA
1 TAAAA
365522 CAAAATAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
TAAAATATATA
Found at i:367754 original size:84 final size:84
Alignment explanation
Indices: 367464--368675 Score: 1424
Period size: 84 Copynumber: 14.4 Consensus size: 84
367454 TTTTATTGAG
* * * * * * * * * *
367464 AGATAACTCTTCTTGCCTTGAGCTATACTGTAAATTTGATTTGCCTCTGAGTTGAATGTAATCAA
1 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAA--TGATGTGCCTTTGAGCTGAGTGTAATCGA
* * * *
367529 AATTGAAGGTC-TTTGATGAC
64 ACTCGAAGGTCTTTTGTTGGC
* * ** * **
367549 AGATAACCCTTATCGCCTTGAGTTATGCTATAAAACTGATGTGCCTTTGAGTTGAGTGTAATTAA
1 AGATAACCCTTCTAGCCTTGAGTTATGCT-GCAAA-TGATGTGCCTTTGAGCTGAGTGTAATCGA
*
367614 ACTCGAAGGTC-TTGGTTGGC
64 ACTCGAAGGTCTTTTGTTGGC
* * * *
367634 AGATAACCCTTTTTGCCTTGAGTTATGCTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCAAAC
1 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAAC
*
367699 TCGAAGGCCTTTTGTTGGC
66 TCGAAGGTCTTTTGTTGGC
* ** * * * *
367718 AGATAGCCCTTCTTTCCTTGAGCTATGCTGCAAATGATGCGTCTTTGAGATGAGTGTAATCGAAC
1 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAAC
*
367783 TCGAAGGTCTTTTGTTAGC
66 TCGAAGGTCTTTTGTTGGC
* * *
367802 AGATAACCCTTATAGCCTTGAGTTATGCTGCAAATGAAGTGCCTTTGAGCTGAATGTAATCGAAC
1 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAAC
*
367867 TCGAATGTC-TTTGATTGGC
66 TCGAAGGTCTTTTG-TTGGC
* * * *
367886 AGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAAC
1 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAAC
*
367951 TCGAAGGTCTTTGGTTGGC
66 TCGAAGGTCTTTTGTTGGC
* * *
367970 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCATTTGAGCTGAATGTAATCAAAC
1 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAAC
* * *
368035 TTGAAGGTCTTTGGTTGGA
66 TCGAAGGTCTTTTGTTGGC
* * * *
368054 AGATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAAC
1 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAAC
*
368119 TCGAAGGTC-TTTGTTGAC
66 TCGAAGGTCTTTTGTTGGC
* * * * * * *
368137 AGATAACCTTTCTAGCCTTGAGTTATGATGTACATAATATGCCTTTGAGATGAGTGTAATCGAAC
1 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAAC
* * *
368202 TCAAAGGTCTCTTGCTGGC
66 TCGAAGGTCTTTTGTTGGC
* * * * * *
368221 AGATAACTCTTCTTGCCTTGAGCTATGCTGTAAATGATGCGCCTTTGAGCTGAGTGTAATTGAAC
1 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAAC
*
368286 TCGAAGGTCTTTTGTTGGT
66 TCGAAGGTCTTTTGTTGGC
* * * *
368305 AGATAACCCTTCTAGGCTTGAGTTATGCTGCAAATGATGTGCCTTTAAGCTGAGTGTAATTGAAA
1 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAAC
* * *
368370 TCAAAGGTATTTGGTTGGC
66 TCGAAGGTCTTTTGTTGGC
* * * * * * ** * *
368389 AGATAGCCCTTATCGACTTAAGCTATAATGTAAATGATGTGCCTTTGAGCTTAGTGTAATCGAAC
1 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAAC
*
368454 TCGAAGGTCTTTTGTTGGT
66 TCGAAGGTCTTTTGTTGGC
* *
368473 AGATAACCCTTCTAGCCTTGAGTTATGCTACAAATGATGTGCCTTTGAGTTGAGTGTAATCGAAC
1 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAAC
*
368538 TCGAAGGTCTTTGGTTGGC
66 TCGAAGGTCTTTTGTTGGC
* * * * * *
368557 AGATAACCCTTCTCGACTTAAGATATGTTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAAC
1 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAAC
*
368622 TCGAAGGTCTTTTGTTCGC
66 TCGAAGGTCTTTTGTTGGC
* * *
368641 AGATAACCCTTCTAGCCTCGAGTTATACTGTAAAT
1 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAAT
368676 AAAAAAAATC
Statistics
Matches: 955, Mismatches: 167, Indels: 11
0.84 0.15 0.01
Matches are distributed among these distances:
83 109 0.11
84 749 0.78
85 94 0.10
86 3 0.00
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.34
Consensus pattern (84 bp):
AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAAC
TCGAAGGTCTTTTGTTGGC
Found at i:368533 original size:503 final size:502
Alignment explanation
Indices: 367464--368677 Score: 1662
Period size: 503 Copynumber: 2.4 Consensus size: 502
367454 TTTTATTGAG
* * * * * * *
367464 AGATAACTCTTCTTGCCTTGAGCTATACTGTAAATTTGATTTGCCTCTGAGTTGAATGTAATCAA
1 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAA--TGATGTGCCTTTGAGTTGAATGTAATCAA
* * * * * * *
367529 AATTGAAGGTCTTT-GAT-GACAGATAACCCTTATCGCCTTGAGTTATGCTATAAAACTGATGTG
64 ACTTGAAGGTCTTTGGTTGGA-AGATAACCCTTCTCGACTTAAGATATGCT-GAAAA-TGATGTG
* ** * *
367592 CCTTTGAGTTGAGTGTAATTAAACTCGAAGGTCTTGGTTGGCAGATAACCCTTT-TTGCCTTGAG
126 CCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTT-GCAGATAA-CCTTTCTAGCCTTGAG
* * * * * * *
367656 TTATGCTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGCCTTTTGTTGGCAGA
189 TTATGATGTAAATAATATGCCTTTGAGATGAGTGTAATCAAACTCAAAGGCCTCTTGCTGGCAGA
* * *
367721 TAGCCCTTCTTTCCTTGAGCTATGCTGCAAATGATGCGTCTTTGAGATGAGTGTAATCGAACTCG
254 TAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGCGCCTTTGAGATGAGTGTAATCGAACTCG
*
367786 AAGGTCTTTTGTTAGCAGATAACCCTTATAGCCTTGAGTTATGCTGCAAATGAAGTGCCTTTGAG
319 AAGGTCTTTTGTTAGCAGATAACCCTTATAGCCTTGAGTTATGCTGCAAATGAAGTGCCTTTAAG
* * * * * **
367851 CTGAATGTAATCGAACTCGAATGTCTTTGATTGGCAGATAACCCTTCTCGACTTAAGCTATGCTG
384 CTGAATGTAATCGAAATCAAAGGTATTTGATTGGCAGATAACCCTTATCGACTTAAGCTATAATG
367916 CAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGC
449 CAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGC
* *
367970 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCATTTGAGCTGAATGTAATCAAAC
1 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGTTGAATGTAATCAAAC
* * *
368035 TTGAAGGTCTTTGGTTGGAAGATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTT
66 TTGAAGGTCTTTGGTTGGAAGATAACCCTTCTCGACTTAAGATATGCTGAAAATGATGTGCCTTT
368100 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCTTTCTAGCCTTGAGTTATGA
131 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTG-CAGATAACCTTTCTAGCCTTGAGTTATGA
* * * *
368165 TGTACATAATATGCCTTTGAGATGAGTGTAATCGAACTCAAAGGTCTCTTGCTGGCAGATAACTC
195 TGTAAATAATATGCCTTTGAGATGAGTGTAATCAAACTCAAAGGCCTCTTGCTGGCAGATAACCC
* * *
368230 TTCTTGCCTTGAGCTATGCTGTAAATGATGCGCCTTTGAGCTGAGTGTAATTGAACTCGAAGGTC
260 TTCTTGCCTTGAGCTATGCTGCAAATGATGCGCCTTTGAGATGAGTGTAATCGAACTCGAAGGTC
* * * * * *
368295 TTTTGTTGGTAGATAACCCTTCTAGGCTTGAGTTATGCTGCAAATGATGTGCCTTTAAGCTGAGT
325 TTTTGTTAGCAGATAACCCTTATAGCCTTGAGTTATGCTGCAAATGAAGTGCCTTTAAGCTGAAT
* * * *
368360 GTAATTGAAATCAAAGGTATTTGGTTGGCAGATAGCCCTTATCGACTTAAGCTATAATGTAAATG
390 GTAATCGAAATCAAAGGTATTTGATTGGCAGATAACCCTTATCGACTTAAGCTATAATGCAAATG
* * *
368425 ATGTGCCTTTGAGCTTAGTGTAATCGAACTCGAAGGTCTTTTGTTGGT
455 ATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGC
* * *
368473 AGATAACCCTTCTAGCCTTGAGTTATGCTACAAATGATGTGCCTTTGAGTTGAGTGTAATCGAAC
1 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGTTGAATGTAATCAAAC
* * * *
368538 TCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGATATGTTGTAAATGATGTGCCTTT
66 TTGAAGGTCTTTGGTTGGAAGATAACCCTTCTCGACTTAAGATATGCTGAAAATGATGTGCCTTT
* *
368603 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTCGCAGATAACCCTTCTAGCCTCGAGTTAT-
131 GAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTT-GCAGATAACCTTTCTAGCCTTGAGTTATG
368667 ACTGTAAATAA
194 A-TGTAAATAA
368678 AAAAAATCGC
Statistics
Matches: 626, Mismatches: 75, Indels: 16
0.87 0.10 0.02
Matches are distributed among these distances:
502 6 0.01
503 482 0.77
504 80 0.13
505 27 0.04
506 31 0.05
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (502 bp):
AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAGTTGAATGTAATCAAAC
TTGAAGGTCTTTGGTTGGAAGATAACCCTTCTCGACTTAAGATATGCTGAAAATGATGTGCCTTT
GAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGCAGATAACCTTTCTAGCCTTGAGTTATGAT
GTAAATAATATGCCTTTGAGATGAGTGTAATCAAACTCAAAGGCCTCTTGCTGGCAGATAACCCT
TCTTGCCTTGAGCTATGCTGCAAATGATGCGCCTTTGAGATGAGTGTAATCGAACTCGAAGGTCT
TTTGTTAGCAGATAACCCTTATAGCCTTGAGTTATGCTGCAAATGAAGTGCCTTTAAGCTGAATG
TAATCGAAATCAAAGGTATTTGATTGGCAGATAACCCTTATCGACTTAAGCTATAATGCAAATGA
TGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGC
Found at i:369924 original size:84 final size:86
Alignment explanation
Indices: 369825--370046 Score: 259
Period size: 95 Copynumber: 2.5 Consensus size: 86
369815 GGCTAGCTGG
** **
369825 ATCCATAAAATCGGGGTGTTTAACCAATTGCTCTAGAGGGACAGC-TTA-ATATTATAATCACCT
1 ATCCATAAAGCCGGGGCATTTAACCAATTGCTCTAGAGGGACAGCTTTATATATTATAATCACCT
*
369888 TTATCATGCTAGCTGAATATT
66 TTATCAGGCTAGCTGAATATT
*
369909 ATCCATAAAGCCGGGGCATTTAACCAATTGCTCTAGAGAGACAACTCAAGCTTTATTGTATATTA
1 ATCCATAAAGCCGGGGCATTTAACCAATTGCTCTAGAG-G--GA--C-AGCTTTA---TATATTA
* *
369974 TAATCTCCTTTATCAGGCTAGCTGAATCTT
57 TAATCACCTTTATCAGGCTAGCTGAATATT
* *
370004 ATCCATAAAGCCGAGGCATCTAACCAATTGCTCTAGAGGGACA
1 ATCCATAAAGCCGGGGCATTTAACCAATTGCTCTAGAGGGACA
370047 ACTCAAGCTT
Statistics
Matches: 116, Mismatches: 11, Indels: 17
0.81 0.08 0.12
Matches are distributed among these distances:
84 34 0.29
85 1 0.01
87 1 0.01
89 2 0.02
90 4 0.03
91 3 0.03
92 1 0.01
94 1 0.01
95 69 0.59
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (86 bp):
ATCCATAAAGCCGGGGCATTTAACCAATTGCTCTAGAGGGACAGCTTTATATATTATAATCACCT
TTATCAGGCTAGCTGAATATT
Found at i:370036 original size:95 final size:95
Alignment explanation
Indices: 369873--370073 Score: 339
Period size: 95 Copynumber: 2.1 Consensus size: 95
369863 GGACAGCTTA
* * *
369873 ATATTATAATCACCTTTATCATGCTAGCTGAATATTATCCATAAAGCCGGGGCATTTAACCAATT
1 ATATTATAATCACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGAGGCATCTAACCAATT
369938 GCTCTAGAGAGACAACTCAAGCTTTATTGT
66 GCTCTAGAGAGACAACTCAAGCTTTATTGT
* *
369968 ATATTATAATCTCCTTTATCAGGCTAGCTGAATCTTATCCATAAAGCCGAGGCATCTAACCAATT
1 ATATTATAATCACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGAGGCATCTAACCAATT
*
370033 GCTCTAGAGGGACAACTCAAGCTTTATTGT
66 GCTCTAGAGAGACAACTCAAGCTTTATTGT
370063 ATATATATAAT
1 ATAT-TATAAT
370074 TATAATTTGG
Statistics
Matches: 99, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
95 93 0.94
96 6 0.06
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (95 bp):
ATATTATAATCACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGAGGCATCTAACCAATT
GCTCTAGAGAGACAACTCAAGCTTTATTGT
Found at i:372792 original size:19 final size:19
Alignment explanation
Indices: 372745--372814 Score: 74
Period size: 18 Copynumber: 3.8 Consensus size: 19
372735 AAACCAATGA
372745 AGTAAAGAAAAT-AAAAAG
1 AGTAAAGAAAATAAAAAAG
372763 AG-ATAAGAAAATAAAAAAG
1 AGTA-AAGAAAATAAAAAAG
* * *
372782 AGTAAAAAAAATGAATAAG
1 AGTAAAGAAAATAAAAAAG
*
372801 A-TAAATAAAATAAA
1 AGTAAAGAAAATAAA
372815 TAAAATGAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
17 1 0.02
18 21 0.48
19 21 0.48
20 1 0.02
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.14
Consensus pattern (19 bp):
AGTAAAGAAAATAAAAAAG
Found at i:372807 original size:9 final size:9
Alignment explanation
Indices: 372707--372833 Score: 62
Period size: 9 Copynumber: 13.8 Consensus size: 9
372697 GGAAAGAATG
372707 AAAATAAAT
1 AAAATAAAT
* *
372716 AAAACAAAG
1 AAAATAAAT
* *
372725 AAAGTAAAA
1 AAAATAAAT
**
372734 AAAACCAAT
1 AAAATAAAT
* * *
372743 GAAGTAAAG
1 AAAATAAAT
372752 AAAATAAA-
1 AAAATAAAT
*
372760 AAGAGAT-AAG
1 AA-A-ATAAAT
372770 AAAATAAA-
1 AAAATAAAT
*
372778 AAAGAGTAAAA
1 AAA-A-TAAAT
*
372789 AAAATGAAT
1 AAAATAAAT
*
372798 AAGATAAAT
1 AAAATAAAT
372807 AAAATAAAT
1 AAAATAAAT
372816 AAAATGAAAT
1 AAAAT-AAAT
372826 AATAATAA
1 AA-AATAA
372834 TATATACACA
Statistics
Matches: 88, Mismatches: 21, Indels: 17
0.70 0.17 0.13
Matches are distributed among these distances:
8 7 0.08
9 58 0.66
10 17 0.19
11 6 0.07
ACGTcount: A:0.72, C:0.02, G:0.10, T:0.15
Consensus pattern (9 bp):
AAAATAAAT
Found at i:372926 original size:12 final size:12
Alignment explanation
Indices: 372905--372970 Score: 55
Period size: 12 Copynumber: 5.2 Consensus size: 12
372895 TAAGATGAAG
372905 ATAAAGAATAAAA
1 ATAAA-AATAAAA
372918 ATAAAAATAAAA
1 ATAAAAATAAAA
372930 GA-AAAAATAAATAA
1 -ATAAAAAT-AA-AA
372944 ATAAATAA-ATAAA
1 ATAAA-AATA-AAA
*
372957 ATAAAAGTAAAA
1 ATAAAAATAAAA
372969 AT
1 AT
372971 TTATAAAAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 15
0.74 0.02 0.25
Matches are distributed among these distances:
12 19 0.42
13 18 0.40
14 6 0.13
15 2 0.04
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (12 bp):
ATAAAAATAAAA
Found at i:373085 original size:11 final size:11
Alignment explanation
Indices: 373069--373094 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
373059 GAGTATAAGG
373069 ATAATAAATAA
1 ATAATAAATAA
373080 ATAATAAATAA
1 ATAATAAATAA
373091 ATAA
1 ATAA
373095 AATATATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
ATAATAAATAA
Found at i:373143 original size:25 final size:26
Alignment explanation
Indices: 373106--373154 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
373096 ATATATATAT
*
373106 ATATAACAAAATAAGTAATAAAACAA
1 ATATAACAAAATAAATAATAAAACAA
* *
373132 ATAT-ACATAATAAATATTAAAAC
1 ATATAACAAAATAAATAATAAAAC
373155 TACCCCCATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.65, C:0.08, G:0.02, T:0.24
Consensus pattern (26 bp):
ATATAACAAAATAAATAATAAAACAA
Found at i:373144 original size:18 final size:17
Alignment explanation
Indices: 373080--373145 Score: 55
Period size: 18 Copynumber: 3.6 Consensus size: 17
373070 TAATAAATAA
373080 ATAATAAATAAATA-AAAT
1 ATAAT-AATAAA-ACAAAT
*
373098 ATATATATATATAACAAA-
1 ATA-ATA-ATAAAACAAAT
373116 ATAAGTAATAAAACAAAT
1 ATAA-TAATAAAACAAAT
373134 ATACATAATAAA
1 ATA-ATAATAAA
373146 TATTAAAACT
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
17 10 0.25
18 20 0.50
19 10 0.25
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.27
Consensus pattern (17 bp):
ATAATAATAAAACAAAT
Found at i:373213 original size:2 final size:2
Alignment explanation
Indices: 373206--373284 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
373196 GACAAAACAA
373206 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
373248 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
373285 GGATTTAAAA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:374836 original size:90 final size:91
Alignment explanation
Indices: 374683--374868 Score: 356
Period size: 90 Copynumber: 2.1 Consensus size: 91
374673 TAAGATCAAG
374683 TTTTTCTGAAGAATTACTTGTTCTTGTGATTTCAGTATTCCTTTATATAAAAATTAATCATCTCA
1 TTTTTCTGAAGAATTACTTGTTCTTGTGATTTCAGTATTCCTTTATATAAAAATTAATCATCTCA
374748 AAT-GAGAGATAAACTCTAAATAAGT
66 AATGGAGAGATAAACTCTAAATAAGT
*
374773 TTTTTCTGAAGAATTACTTGTTCTTGTGATTTTAGTATTCCTTTATATAAAAATTAATCATCTCA
1 TTTTTCTGAAGAATTACTTGTTCTTGTGATTTCAGTATTCCTTTATATAAAAATTAATCATCTCA
374838 AATGGAGAGATAAACTCTAAATAAGT
66 AATGGAGAGATAAACTCTAAATAAGT
374864 TTTTT
1 TTTTT
374869 TCTTATTATG
Statistics
Matches: 94, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
90 67 0.71
91 27 0.29
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (91 bp):
TTTTTCTGAAGAATTACTTGTTCTTGTGATTTCAGTATTCCTTTATATAAAAATTAATCATCTCA
AATGGAGAGATAAACTCTAAATAAGT
Found at i:378585 original size:45 final size:47
Alignment explanation
Indices: 378520--378630 Score: 163
Period size: 45 Copynumber: 2.3 Consensus size: 47
378510 TATGACAACC
378520 GATATATCTGCAACAAGCATACTGTAAT-AAAAAAAA-CCAAAAGTT
1 GATATATCTGCAACAAGCATACTGTAATAAAAAAAAACCCAAAAGTT
* *
378565 GATATGTCTGCAACAGGCATACTGTAATGAAAAAAAAAACCCCAAAAGTT
1 GATATATCTGCAACAAGCATACTGTAAT--AAAAAAAAA-CCCAAAAGTT
378615 GATATATCTGCAACAA
1 GATATATCTGCAACAA
378631 AAAAGTTTCA
Statistics
Matches: 57, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
45 26 0.46
48 8 0.14
50 23 0.40
ACGTcount: A:0.48, C:0.17, G:0.14, T:0.22
Consensus pattern (47 bp):
GATATATCTGCAACAAGCATACTGTAATAAAAAAAAACCCAAAAGTT
Found at i:381669 original size:13 final size:13
Alignment explanation
Indices: 381651--381676 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
381641 CTTTAAACAC
381651 CTAAAGTTAATTT
1 CTAAAGTTAATTT
381664 CTAAAGTTAATTT
1 CTAAAGTTAATTT
381677 TATGTATTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (13 bp):
CTAAAGTTAATTT
Found at i:382072 original size:2 final size:2
Alignment explanation
Indices: 382054--382107 Score: 87
Period size: 2 Copynumber: 28.5 Consensus size: 2
382044 TCATAAAAAC
382054 AT AT A- AT AT -T A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
382093 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
382108 CCATGCAAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
1 3 0.06
2 46 0.94
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:387558 original size:28 final size:28
Alignment explanation
Indices: 387487--387542 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
387477 AAGGCTCCCA
* *
387487 AATTT-TATATTGATAATTGGGGTTTTT
1 AATTTCTATATTTATAATTAGGGTTTTT
387514 AATTTCTATATTTATAATTAGGGTTTTT
1 AATTTCTATATTTATAATTAGGGTTTTT
387542 A
1 A
387543 TTTTTTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 5 0.19
28 21 0.81
ACGTcount: A:0.29, C:0.02, G:0.14, T:0.55
Consensus pattern (28 bp):
AATTTCTATATTTATAATTAGGGTTTTT
Found at i:393158 original size:14 final size:15
Alignment explanation
Indices: 393125--393160 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
393115 CCAGTCACCA
*
393125 AGTCAACTCGGTCTG
1 AGTCAACTCGGTCCG
393140 AGTCAACTC-GTCCG
1 AGTCAACTCGGTCCG
393154 AGTCAAC
1 AGTCAAC
393161 CCGTTGACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 11 0.55
15 9 0.45
ACGTcount: A:0.25, C:0.31, G:0.22, T:0.22
Consensus pattern (15 bp):
AGTCAACTCGGTCCG
Done.