Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1834
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: 246159
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
File 2 of 2
Found at i:180656 original size:20 final size:20
Alignment explanation
Indices: 180599--180670 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
180589 TTTTACAATC
* *
180599 TGTATCGATACATCAAGTTAG
1 TGTATCGATACAT-AAGTCAA
* *
180620 TGTATCAATACACAAGTCAA
1 TGTATCGATACATAAGTCAA
* *
180640 TGTATCGATATATAAGTGAA
1 TGTATCGATACATAAGTCAA
*
180660 TATATCGATAC
1 TGTATCGATAC
180671 TGGACCTTAT
Statistics
Matches: 41, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
20 30 0.73
21 11 0.27
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (20 bp):
TGTATCGATACATAAGTCAA
Found at i:184487 original size:15 final size:15
Alignment explanation
Indices: 184433--184497 Score: 51
Period size: 15 Copynumber: 4.4 Consensus size: 15
184423 TTGAAGTATC
184433 TATGCCGAAGGTAC-
1 TATGCCGAAGGTACT
* ** *
184447 CATGTTGAAGGTAGT
1 TATGCCGAAGGTACT
* *
184462 TGTGCCAAAGGTACT
1 TATGCCGAAGGTACT
* *
184477 TATGTCGAAGGTACC
1 TATGCCGAAGGTACT
184492 TATGCC
1 TATGCC
184498 AAAGATAATT
Statistics
Matches: 35, Mismatches: 15, Indels: 1
0.69 0.29 0.02
Matches are distributed among these distances:
14 10 0.29
15 25 0.71
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (15 bp):
TATGCCGAAGGTACT
Found at i:184498 original size:30 final size:29
Alignment explanation
Indices: 184432--184501 Score: 77
Period size: 30 Copynumber: 2.4 Consensus size: 29
184422 TTTGAAGTAT
* * *
184432 CTATGCCGAAGGTACCATGTTGAAGGTAG
1 CTATGCCAAAGGTACCATGTCGAAGGTAC
* * *
184461 TTGTGCCAAAGGTACTTATGTCGAAGGTAC
1 CTATGCCAAAGGTAC-CATGTCGAAGGTAC
184491 CTATGCCAAAG
1 CTATGCCAAAG
184502 ATAATTGTGC
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
29 12 0.38
30 20 0.62
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.26
Consensus pattern (29 bp):
CTATGCCAAAGGTACCATGTCGAAGGTAC
Found at i:185102 original size:17 final size:17
Alignment explanation
Indices: 185080--185112 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
185070 AGGCATTATC
185080 CGCAAGGTATTATTTGA
1 CGCAAGGTATTATTTGA
185097 CGCAAGGTATTATTTG
1 CGCAAGGTATTATTTG
185113 CGAGGTAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.36
Consensus pattern (17 bp):
CGCAAGGTATTATTTGA
Found at i:185522 original size:18 final size:15
Alignment explanation
Indices: 185499--185537 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
185489 TTTTCAATAG
185499 ATAAAAGATAAGATAAAA
1 ATAAAAGA-AA-AT-AAA
185517 ATAAAAGAAAATAAA
1 ATAAAAGAAAATAAA
185532 ATAAAA
1 ATAAAA
185538 TTTTAGAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 2 0.10
17 2 0.10
18 8 0.38
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (15 bp):
ATAAAAGAAAATAAA
Found at i:186069 original size:106 final size:101
Alignment explanation
Indices: 185898--186084 Score: 250
Period size: 106 Copynumber: 1.8 Consensus size: 101
185888 AGCATTTTTT
* * * * *
185898 AAAAAATAAATAAATAAGATATGTATGATCGTGATTTTTTTGTAACAGTATAATTTTATAAAAAA
1 AAAAAATAAATAAATAAAATATGCATGATCATGATTTTTTTGTAACAATAAAATTTTATAAAAAA
185963 TTTTTAATGATTTTTTATATTTTTGATTTTTGAAAG
66 TTTTTAATGATTTTTTATATTTTTGATTTTTGAAAG
*
185999 AAAAAATAAATAAATAAAATATGCATGATCATGACTCTTTTTTTTTAAAACAATAAAATTTT-TA
1 AAAAAATAAATAAATAAAATATGCATGATCATGA---TTTTTTTGT--AACAATAAAATTTTATA
*
186063 TGAAAATTTTTAATGATTTTTT
61 -AAAAATTTTTAATGATTTTTT
186085 TGAAAAAAAT
Statistics
Matches: 73, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
101 31 0.42
104 8 0.11
105 2 0.03
106 32 0.44
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.45
Consensus pattern (101 bp):
AAAAAATAAATAAATAAAATATGCATGATCATGATTTTTTTGTAACAATAAAATTTTATAAAAAA
TTTTTAATGATTTTTTATATTTTTGATTTTTGAAAG
Found at i:187053 original size:13 final size:13
Alignment explanation
Indices: 187035--187060 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
187025 TACAGCAAGT
187035 ATGTATCGATACA
1 ATGTATCGATACA
187048 ATGTATCGATACA
1 ATGTATCGATACA
187061 CAAAAATTTG
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:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:189310 original size:21 final size:21
Alignment explanation
Indices: 189277--189321 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
189267 TTGCAAGTTG
*
189277 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
189299 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
189319 AAA
1 AAA
189322 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:191214 original size:15 final size:15
Alignment explanation
Indices: 191160--191224 Score: 51
Period size: 15 Copynumber: 4.4 Consensus size: 15
191150 TTGAAGTATC
191160 TATGCCGAAGGTAC-
1 TATGCCGAAGGTACT
* ** *
191174 CATGTTGAAGGTAGT
1 TATGCCGAAGGTACT
* *
191189 TGTGCCAAAGGTACT
1 TATGCCGAAGGTACT
* *
191204 TATGTCGAAGGTACC
1 TATGCCGAAGGTACT
191219 TATGCC
1 TATGCC
191225 AAAGATAATT
Statistics
Matches: 35, Mismatches: 15, Indels: 1
0.69 0.29 0.02
Matches are distributed among these distances:
14 10 0.29
15 25 0.71
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (15 bp):
TATGCCGAAGGTACT
Found at i:191225 original size:30 final size:29
Alignment explanation
Indices: 191159--191228 Score: 77
Period size: 30 Copynumber: 2.4 Consensus size: 29
191149 TTTGAAGTAT
* * *
191159 CTATGCCGAAGGTACCATGTTGAAGGTAG
1 CTATGCCAAAGGTACCATGTCGAAGGTAC
* * *
191188 TTGTGCCAAAGGTACTTATGTCGAAGGTAC
1 CTATGCCAAAGGTAC-CATGTCGAAGGTAC
191218 CTATGCCAAAG
1 CTATGCCAAAG
191229 ATAATTGTGC
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
29 12 0.38
30 20 0.62
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.26
Consensus pattern (29 bp):
CTATGCCAAAGGTACCATGTCGAAGGTAC
Found at i:191829 original size:17 final size:17
Alignment explanation
Indices: 191807--191839 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
191797 AGGCATTATC
191807 CGCAAGGTATTATTTGA
1 CGCAAGGTATTATTTGA
191824 CGCAAGGTATTATTTG
1 CGCAAGGTATTATTTG
191840 CGAGGTAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.36
Consensus pattern (17 bp):
CGCAAGGTATTATTTGA
Found at i:192251 original size:18 final size:15
Alignment explanation
Indices: 192228--192266 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
192218 TTTTCAATAG
192228 ATAAAAGATAAGATAAAA
1 ATAAAAGA-AA-AT-AAA
192246 ATAAAAGAAAATAAA
1 ATAAAAGAAAATAAA
192261 ATAAAA
1 ATAAAA
192267 TTTTAGAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 2 0.10
17 2 0.10
18 8 0.38
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (15 bp):
ATAAAAGAAAATAAA
Found at i:192797 original size:106 final size:101
Alignment explanation
Indices: 192626--192812 Score: 250
Period size: 106 Copynumber: 1.8 Consensus size: 101
192616 AGCATTTTTT
* * * * *
192626 AAAAAATAAATAAATAAGATATGTATGATCGTGATTTTTTTGTAACAGTATAATTTTATAAAAAA
1 AAAAAATAAATAAATAAAATATGCATGATCATGATTTTTTTGTAACAATAAAATTTTATAAAAAA
192691 TTTTTAATGATTTTTTATATTTTTGATTTTTGAAAG
66 TTTTTAATGATTTTTTATATTTTTGATTTTTGAAAG
*
192727 AAAAAATAAATAAATAAAATATGCATGATCATGACTCTTTTTTTTTAAAACAATAAAATTTT-TA
1 AAAAAATAAATAAATAAAATATGCATGATCATGA---TTTTTTTGT--AACAATAAAATTTTATA
*
192791 TGAAAATTTTTAATGATTTTTT
61 -AAAAATTTTTAATGATTTTTT
192813 TGAAAAAAAT
Statistics
Matches: 73, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
101 31 0.42
104 8 0.11
105 2 0.03
106 32 0.44
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.45
Consensus pattern (101 bp):
AAAAAATAAATAAATAAAATATGCATGATCATGATTTTTTTGTAACAATAAAATTTTATAAAAAA
TTTTTAATGATTTTTTATATTTTTGATTTTTGAAAG
Found at i:193781 original size:13 final size:13
Alignment explanation
Indices: 193763--193788 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
193753 TACAGCAAGT
193763 ATGTATCGATACA
1 ATGTATCGATACA
193776 ATGTATCGATACA
1 ATGTATCGATACA
193789 CAAAAATTTG
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:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:196038 original size:21 final size:21
Alignment explanation
Indices: 196005--196049 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
195995 TTGCAAGTTG
*
196005 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
196027 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
196047 AAA
1 AAA
196050 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:197873 original size:15 final size:15
Alignment explanation
Indices: 197853--197883 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
197843 TAAAAATGTC
*
197853 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
197868 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
197883 C
1 C
197884 CAAACGAAAT
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:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:199956 original size:13 final size:13
Alignment explanation
Indices: 199938--199976 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
199928 ACATTTTTCT
199938 TTGTATCGATACA
1 TTGTATCGATACA
199951 TTGTATCGATACA
1 TTGTATCGATACA
199964 TTGTATCGATACA
1 TTGTATCGATACA
199977 GGGTGATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:202150 original size:20 final size:19
Alignment explanation
Indices: 202127--202198 Score: 65
Period size: 20 Copynumber: 3.7 Consensus size: 19
202117 CAACTAGATG
* *
202127 TATCGATACATTATGCTTTA
1 TATCGATACATGAT-CATTA
*
202147 TATCGATACATGCTCATTA
1 TATCGATACATGATCATTA
* *
202166 TATCGATACAT-ACACAATTG
1 TATCGATACATGA-TC-ATTA
202186 TATCGATACATGA
1 TATCGATACATGA
202199 AACTGGCAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
19 16 0.37
20 26 0.60
21 1 0.02
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (19 bp):
TATCGATACATGATCATTA
Found at i:202168 original size:19 final size:20
Alignment explanation
Indices: 202144--202197 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
202134 ACATTATGCT
*
202144 TTATATCGATACATGCTC-A
1 TTATATCGATACATGCACAA
*
202163 TTATATCGATACATACACAA
1 TTATATCGATACATGCACAA
*
202183 TTGTATCGATACATG
1 TTATATCGATACATG
202198 AAACTGGCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (20 bp):
TTATATCGATACATGCACAA
Found at i:202264 original size:13 final size:13
Alignment explanation
Indices: 202246--202272 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
202236 CATGGGACAA
202246 TGTATCGATACAT
1 TGTATCGATACAT
202259 TGTATCGATACAT
1 TGTATCGATACAT
202272 T
1 T
202273 AAGAATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:202376 original size:125 final size:125
Alignment explanation
Indices: 202221--202488 Score: 482
Period size: 125 Copynumber: 2.1 Consensus size: 125
202211 CTACCCTAAG
* * *
202221 TGAAATGTATCGATACATGGGACAATGTATCGATACATTGTATCGATACATTAAGAATTGTATTG
1 TGAATTGTATCGATACATGGGACAATGTATCGATACATTGTATCGATACATGAAGAATTGTATCG
* * *
202286 ATATATTATGCCCAATAGCTATAAATGACTTTAATTTTAAATGTATGTATCGATACATTA
66 ATATATTATGCCCAACAGCTATAAACGACTTTAATTTTAAATGCATGTATCGATACATTA
202346 TGAATTGTATCGATACATGGGACAATGTATCGATACATTGTATCGATACATGAAGAATTGTATCG
1 TGAATTGTATCGATACATGGGACAATGTATCGATACATTGTATCGATACATGAAGAATTGTATCG
202411 ATATATTATGCCCAACAGCTATAAACGACTTTAATTTTAAATGCATGTATCGATACATTA
66 ATATATTATGCCCAACAGCTATAAACGACTTTAATTTTAAATGCATGTATCGATACATTA
202471 TGAATTGTATCGATACAT
1 TGAATTGTATCGATACAT
202489 AGTAACGAGA
Statistics
Matches: 137, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
125 137 1.00
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (125 bp):
TGAATTGTATCGATACATGGGACAATGTATCGATACATTGTATCGATACATGAAGAATTGTATCG
ATATATTATGCCCAACAGCTATAAACGACTTTAATTTTAAATGCATGTATCGATACATTA
Found at i:202389 original size:13 final size:13
Alignment explanation
Indices: 202371--202396 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
202361 CATGGGACAA
202371 TGTATCGATACAT
1 TGTATCGATACAT
202384 TGTATCGATACAT
1 TGTATCGATACAT
202397 GAAGAATTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:202408 original size:33 final size:33
Alignment explanation
Indices: 202349--202413 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
202339 TACATTATGA
*
202349 ATTGTATCGATACATGGGACAATGTATCGATAC
1 ATTGTATCGATACATGAGACAATGTATCGATAC
*
202382 ATTGTATCGATACATGAAGA-ATTGTATCGATA
1 ATTGTATCGATACATG-AGACAATGTATCGATA
202414 TATTATGCCC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 27 0.93
34 2 0.07
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.32
Consensus pattern (33 bp):
ATTGTATCGATACATGAGACAATGTATCGATAC
Found at i:204202 original size:14 final size:14
Alignment explanation
Indices: 204153--204202 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
204143 TACATTATGT
* *
204153 AAAATTATACTATA
1 AAAATTAAATTATA
204167 AAAATT-AATTA-A
1 AAAATTAAATTATA
*
204179 AAAGACTAAATTATA
1 AAA-ATTAAATTATA
204194 AAAATTAAA
1 AAAATTAAA
204203 AATTATTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
12 4 0.14
13 5 0.17
14 16 0.55
15 4 0.14
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (14 bp):
AAAATTAAATTATA
Found at i:204815 original size:153 final size:151
Alignment explanation
Indices: 204354--204808 Score: 524
Period size: 153 Copynumber: 3.0 Consensus size: 151
204344 AAAAAGATAC
* * * * * *
204354 AAAACTTATAAAATAAATTGAATCTTTAAAAAATGATTTAATATTAATTTAATAA-AATATTT-A
1 AAAACTCATAAAATAAATTAAATATTTCAAAAATGATTTAATA-TAAATTAAAAATAATATTTGA
* * * *
204417 ATGAATTTTGAAAATTATAAACTTAGAAAAATCCCACTAAAAAA-ATA-ATGGAGTAAAAAACTT
65 A-GAATTTTGAAAATTATAAACTTAAAAAAATCCTACCAAAAAATTTACA-GG-GTAAAAAACTT
*
204480 CGTATTTTGAAAACAAAAAAAATTTT
127 CGTATTTTG-AAACAAAAAAAATTCT
* *
204506 AAAACTCATAAAATAAATTGAAA-ATTTCAAAACTAATTTAATATAAATTAAACAATAATATTTG
1 AAAACTCATAAAATAAATT-AAATATTTCAAAAATGATTTAATATAAATTAAA-AATAATATTTG
* * * * *
204570 AAGAATTTTGAAAATTATAAAATCAATAAAATCCTACCAAAAAATTTACAGAGTAAAAAACTTTG
64 AAGAATTTTGAAAATTATAAACTTAAAAAAATCCTACCAAAAAATTTACAGGGTAAAAAACTTCG
* *
204635 TATCTTAGTAACAAAAAAAATTCT
129 TAT-TTTGAAACAAAAAAAATTCT
* * * * *
204659 AAAATTCATAAAATAAAGTAAATTTTTCAAAAATGATTTAATATGAACTAAGAAATAATATTTGA
1 AAAACTCATAAAATAAATTAAATATTTCAAAAATGATTTAATATAAATTAA-AAATAATATTTGA
* *
204724 AGAATTTTAAAAATTATAAACTTAAAAAAATCCTACCAAAGAAATTTACAGGGTAGAAAACTTCG
65 AGAATTTTGAAAATTATAAACTTAAAAAAATCCTACCAAA-AAATTTACAGGGTAAAAAACTTCG
204789 TATTTTGAAAGTCAAAAAAA
129 TATTTTGAAA--CAAAAAAA
204809 CCTAAAAGAA
Statistics
Matches: 255, Mismatches: 36, Indels: 21
0.82 0.12 0.07
Matches are distributed among these distances:
151 7 0.03
152 39 0.15
153 167 0.65
154 33 0.13
155 9 0.04
ACGTcount: A:0.53, C:0.08, G:0.07, T:0.31
Consensus pattern (151 bp):
AAAACTCATAAAATAAATTAAATATTTCAAAAATGATTTAATATAAATTAAAAATAATATTTGAA
GAATTTTGAAAATTATAAACTTAAAAAAATCCTACCAAAAAATTTACAGGGTAAAAAACTTCGTA
TTTTGAAACAAAAAAAATTCT
Found at i:205009 original size:14 final size:14
Alignment explanation
Indices: 204990--205031 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
204980 AATTCATCAA
204990 GAATTATATAAAAT
1 GAATTATATAAAAT
*
205004 GAATTAAATAAAAT
1 GAATTATATAAAAT
*
205018 -ATATTATCTAAAAT
1 GA-ATTATATAAAAT
205032 ATTTTCTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 1 0.04
14 23 0.96
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (14 bp):
GAATTATATAAAAT
Found at i:206036 original size:43 final size:43
Alignment explanation
Indices: 205958--206138 Score: 170
Period size: 43 Copynumber: 4.2 Consensus size: 43
205948 GACAATATGA
* * * **
205958 ACCAACAAGTTAGAAATGTGTTGGC-CATGATGAAACCATATGT
1 ACCAACAAGTTAGAAGTGTGTTGGCTGA-GACGAAACCATACAT
* * * *
206001 ACCAACGAGTT-GGAGTGGTGTTGGTTGGGACGAAACCATACAT
1 ACCAACAAGTTAGAAGT-GTGTTGGCTGAGACGAAACCATACAT
*
206044 ACCAACAAGTTAGAAGTGTGTTGGCTGAGACGAAACCATGCAT
1 ACCAACAAGTTAGAAGTGTGTTGGCTGAGACGAAACCATACAT
** * * *
206087 ACCAACAAGTTAGAAAG-GCATTGGCCGAGAGGAAACCATACAC
1 ACCAACAAGTTAG-AAGTGTGTTGGCTGAGACGAAACCATACAT
*
206130 ACTAACAAG
1 ACCAACAAG
206139 GAAAAGTTGA
Statistics
Matches: 113, Mismatches: 21, Indels: 8
0.80 0.15 0.06
Matches are distributed among these distances:
42 3 0.03
43 103 0.91
44 7 0.06
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.20
Consensus pattern (43 bp):
ACCAACAAGTTAGAAGTGTGTTGGCTGAGACGAAACCATACAT
Found at i:206498 original size:21 final size:22
Alignment explanation
Indices: 206456--206500 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
206446 TTAGAAAATG
206456 TTGAAAGAATCTTCTCTTTTTT
1 TTGAAAGAATCTTCTCTTTTTT
* *
206478 TTGAAGGAATC-TCTTTTTTTT
1 TTGAAAGAATCTTCTCTTTTTT
206499 TT
1 TT
206501 TTTAATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.20, C:0.11, G:0.11, T:0.58
Consensus pattern (22 bp):
TTGAAAGAATCTTCTCTTTTTT
Found at i:209784 original size:13 final size:13
Alignment explanation
Indices: 209766--209790 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
209756 AGATTGCACA
209766 GTATCGATACATT
1 GTATCGATACATT
209779 GTATCGATACAT
1 GTATCGATACAT
209791 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:209803 original size:20 final size:21
Alignment explanation
Indices: 209778--209830 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
209768 ATCGATACAT
**
209778 TGTATCGATACATGACCA-AA
1 TGTATCGATACATGAAAAGAA
*
209798 TGTATCAATACATGAAAAGAA
1 TGTATCGATACATGAAAAGAA
209819 TGTATCGATACA
1 TGTATCGATACA
209831 GGTCATTGCA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.26
Consensus pattern (21 bp):
TGTATCGATACATGAAAAGAA
Found at i:209927 original size:33 final size:32
Alignment explanation
Indices: 209862--209929 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 32
209852 GTAGCCAAAT
* *
209862 TTGTATCGATCCACACAATATGGATCGATACA
1 TTGTATCGATACACACAAAATGGATCGATACA
* *
209894 TTGTATCGATACATCCCAAAATGTATCGATACA
1 TTGTATCGATACA-CACAAAATGGATCGATACA
209927 TTG
1 TTG
209930 GCTTGTAACG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 12 0.39
33 19 0.61
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.31
Consensus pattern (32 bp):
TTGTATCGATACACACAAAATGGATCGATACA
Found at i:215188 original size:8 final size:8
Alignment explanation
Indices: 215177--215202 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
215167 ATTTGATTAT
215177 ATTTTGTG
1 ATTTTGTG
215185 ATTTTGTG
1 ATTTTGTG
215193 ATTTTGTG
1 ATTTTGTG
215201 AT
1 AT
215203 GAAATGATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.23, T:0.62
Consensus pattern (8 bp):
ATTTTGTG
Found at i:215876 original size:20 final size:21
Alignment explanation
Indices: 215846--215893 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 21
215836 CCTAGGCAAT
215846 ACCCACTAGGTCACAACC-GGC
1 ACCC-CTAGGTCACAACCAGGC
*
215867 ACCCCTAGGTCGCAACCAGGC
1 ACCCCTAGGTCACAACCAGGC
215888 AGCCCC
1 A-CCCC
215894 CACACTAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 12 0.50
21 8 0.33
22 4 0.17
ACGTcount: A:0.25, C:0.46, G:0.21, T:0.08
Consensus pattern (21 bp):
ACCCCTAGGTCACAACCAGGC
Found at i:217879 original size:13 final size:13
Alignment explanation
Indices: 217861--217885 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
217851 AGATTGCACA
217861 GTATCGATACATT
1 GTATCGATACATT
217874 GTATCGATACAT
1 GTATCGATACAT
217886 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:217898 original size:20 final size:21
Alignment explanation
Indices: 217873--217925 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
217863 ATCGATACAT
**
217873 TGTATCGATACATGACCA-AA
1 TGTATCGATACATGAAAAGAA
*
217893 TGTATCGATACTTGAAAAGAA
1 TGTATCGATACATGAAAAGAA
217914 TGTATCGATACA
1 TGTATCGATACA
217926 GGTCATTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGAAAAGAA
Found at i:221725 original size:19 final size:18
Alignment explanation
Indices: 221701--221764 Score: 66
Period size: 19 Copynumber: 3.7 Consensus size: 18
221691 AGCGATACAT
221701 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
*
221720 TGTATCGGTAC--A--T-
1 TGTATCGATACAAACTTA
221733 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
221752 TGTATCGATACAA
1 TGTATCGATACAA
221765 TTATTGTTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
13 10 0.27
14 1 0.03
16 2 0.05
18 1 0.03
19 23 0.62
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:221737 original size:32 final size:32
Alignment explanation
Indices: 221693--221763 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
221683 AGCTTCGTAG
221693 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
* *
221725 CGGTACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
221757 CGATACA
1 CGATACA
221764 ATTATTGTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.32
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:221791 original size:19 final size:20
Alignment explanation
Indices: 221732--221791 Score: 70
Period size: 19 Copynumber: 3.0 Consensus size: 20
221722 TATCGGTACA
* *
221732 TTGTATCGATACAACACT-T
1 TTGTATCGATACAATATTGT
*
221751 ATGTATCGATACAATTATTGT
1 TTGTATCGATACAA-TATTGT
221772 TTGTATCGATACAA-ATTGT
1 TTGTATCGATACAATATTGT
221791 T
1 T
221792 GAAATTCAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
19 19 0.54
20 2 0.06
21 14 0.40
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (20 bp):
TTGTATCGATACAATATTGT
Found at i:222652 original size:52 final size:49
Alignment explanation
Indices: 222535--224212 Score: 510
Period size: 48 Copynumber: 36.7 Consensus size: 49
222525 CGAGGAATGA
* * * *
222535 CAATGTGCTGATTCATGGCCAGCGACATTTAGACTT--GAA-GAAAAATGC
1 CAATATGCTGATTCAAGGCCAGCGACA-TTGGACTTAGGAATG-AAAGTGC
* * ** *
222583 CAATGTGTTGAGGCAAGGCCAGCGACATTGGGCTTAGGAATGTTAAAGATGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGGAATG--AAAG-TGC
* * * *
222635 CAATACGCTGATTCAAGGCCAACGATATTGGACTTAAGG-ATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTT-AGGAATGAAAGTGC
* * * * *
222684 TAATGTGCTGATTCAAGGCCAGCGACATTGG-TTTGAAAGATGACGAAAGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTT--AGGA--ATGAAAGTGC
* * *
222736 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTA-AAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGGA-ATGAAAGTGC
* ** * * *
222785 CAATGTATTGACTCAAGGCCAGCGACATTAGACTTA-AAGATGACGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGGA-ATGA--AA-GTGC
* * ** *
222837 CAATATGCTAATTCAAGGCCAGCGATACCGGACTTA--AA-GACGAAGATAC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGGAATGA--AAG-TGC
* * * * **
222886 CAATGTGCTAATTCAAGGCCAGTGACATTGGACTTAAAGATAACAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTT-AGGA-ATGAAA-GTGC
* *
222938 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A-G--AGTGG
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGGAATGAAAGTGC
* *
222980 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTA--AA-GACAAAG-GC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGGAATG--AAAGTGC
* *
223027 ATCAATATGCCGATTCAAGGCCAGCGATATTGGACTTA--AA-G---GTGC
1 --CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGGAATGAAAGTGC
* * * *
223072 GAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTA--AA-GACACGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGGAATGA-A-AGTGC
* * * * *
223120 CAATATGCTAATTCAAAGCCAACGATATTGGGC-T-----T---A-TGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGGAATGAAAGTGC
* * *
223159 CAATGTGCTGATTCAAGGCCAACGAC-TTGGTCTTA--AA-GACAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGGAATGA-AA-GTGC
* *
223206 CAATATGCTGATTCAAGGCCAGCGATATTGGGC-T-----T---A-TGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGGAATGAAAGTGC
* *
223245 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTA--AA-GACAAAG-GCAC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGGAATG--AAAGTG--C
** * *
223294 CAATATGCTGATTCAAGGCCAATGATATTGGACTTA--AA-G---TTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGGAATGAAAGTGC
* * * *
223337 CAATGTGTTGATTCAAGGCCAGCAACATTGGTCTTA--AA-GACAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGGAATGA-AA-GTGC
* *
223385 CAATATGCTGATTCAAGGCCAGCGATATTGGGC-T-----T---A-TGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGGAATGAAAGTGC
* *
223424 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTA--AA-GACAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGGAATGA-AA-GTGC
** *
223472 CAATATGCTGATTCAAGGCCAGC-A-A-T--A-TT-GGGCT--TA-TGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGGAATGAAAGTGC
* *
223511 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTA--AA-GACAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGGAATGA-AA-GTGC
* *
223559 CAATATGCTGATTCAAGGCCAGCGATATTGGGC-T-----T---A-TGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGGAATGAAAGTGC
* *
223598 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTA--AA-GACAAAG-GCAC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGGAATG--AAAGTG--C
** * *
223647 CAATATGCTGATTCAAGGCCAATGATATTGGACTTA--AA-G---TTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGGAATGAAAGTGC
* * * *
223690 CAATGTGTTGATTCAAGGCCAGCAACATTGGTCTTA--AA-GACAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGGAATGA-AA-GTGC
* *
223738 CAATATGCTGATTCAAGGCCAGCGATATTGGGC-T-----T---A-TGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGGAATGAAAGTGC
* *
223777 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTA--AA-GACAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGGAATGA-AA-GTGC
* **
223825 CAATATGCTGATTCAAGGCC-GC-A-A-T--A-TT-GG--GGTTA-TGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGGAATGAAAGTGC
* *
223863 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTA--AA-GACAAAG-GCAC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGGAATG--AAAGTG--C
* * *
223912 CAATATGCTGATTCAAAGCCAGTGATATTGGACTTA--AA-G---GTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGGAATGAAAGTGC
* * *
223955 CAATGTGCTGATTCAAGGCTAGCGACATTGGCCTTA--AA-GATAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGGAATGA-AA-GTGC
* * *
224003 CAATATGCTAATTCAAGGCCAGCGATATTGGGC-T-----T---A-TGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGGAATGAAAGTGC
* *
224042 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTA--AA-GACAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGGAATGA-AA-GTGC
* ** *
224090 CAATATGCTGATTCAAGGCTAGC-A-A-T--A-TT-GGGCT--TA-TGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGGAATGAAAGTGC
* * * *
224129 CAATGTGCTGATTCAAGGCCAGCAACATTGGTCTTA--AA-GACAAGGTCC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGGAATGA-AA-GTGC
* **
224177 CAATATGCTGGTTCAAGGCCAGCGATTTTGGACTTA
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTA
224213 AAAGAAGATG
Statistics
Matches: 1255, Mismatches: 203, Indels: 344
0.70 0.11 0.19
Matches are distributed among these distances:
38 27 0.02
39 241 0.19
40 9 0.01
41 13 0.01
42 42 0.03
43 135 0.11
44 5 0.00
45 16 0.01
46 9 0.01
47 49 0.04
48 293 0.23
49 259 0.21
50 7 0.01
51 6 0.00
52 136 0.11
53 7 0.01
54 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (49 bp):
CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGGAATGAAAGTGC
Found at i:223173 original size:39 final size:40
Alignment explanation
Indices: 223117--224165 Score: 563
Period size: 39 Copynumber: 24.0 Consensus size: 40
223107 AAAGACACGG
* * * *
223117 TGCCAATATGCTAATTCAAAGCCAACGATATTGGGCTT-A
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAA
* * *
223156 TGCCAATGTGCTGATTCAAGGCCAACGA-CTTGGTCTTAAAGACAA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTT------AA
*
223201 GGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT-A
1 --TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAA
* *
223242 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTT-------AA
* ** *
223289 GGCACCAATATGCTGATTCAAGGCCAATGATATTGGACTTAAA
1 TG--CCAATATGCTGATTCAAGGCCAGCGATATTGGTCTT-AA
* * * *
223332 GTTGCCAATGTGTTGATTCAAGGCCAGCAACATTGGTCTTAAAGACAA
1 --TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTT------AA
*
223380 GGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT-A
1 --TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAA
* *
223421 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTT------AA
* *
223467 GGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGGCTT-A
1 --TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAA
* *
223508 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTT------AA
*
223554 GGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT-A
1 --TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAA
* *
223595 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTT-------AA
* ** *
223642 GGCACCAATATGCTGATTCAAGGCCAATGATATTGGACTTAAA
1 TG--CCAATATGCTGATTCAAGGCCAGCGATATTGGTCTT-AA
* * * *
223685 GTTGCCAATGTGTTGATTCAAGGCCAGCAACATTGGTCTTAAAGACAA
1 --TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTT------AA
*
223733 GGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT-A
1 --TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAA
* *
223774 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTT------AA
* **
223820 GGTGCCAATATGCTGATTCAAGGCC-GCAATATTGGGGTT-A
1 --TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAA
* *
223860 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTT-------AA
* * * *
223907 GGCACCAATATGCTGATTCAAAGCCAGTGATATTGGACTTAAA
1 TG--CCAATATGCTGATTCAAGGCCAGCGATATTGGTCTT-AA
* * * *
223950 GGTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGCCTTAAAGATAA
1 --TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTC-T-----TAA
* *
223998 GGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGGCTT-A
1 --TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAA
* *
224039 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTT------AA
* * *
224085 GGTGCCAATATGCTGATTCAAGGCTAGCAATATTGGGCTT-A
1 --TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAA
* * *
224126 TGCCAATGTGCTGATTCAAGGCCAGCAACATTGGTCTTAA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAA
224166 AGACAAGGTC
Statistics
Matches: 795, Mismatches: 115, Indels: 199
0.72 0.10 0.18
Matches are distributed among these distances:
38 29 0.04
39 277 0.35
40 2 0.00
41 7 0.01
42 1 0.00
43 95 0.12
44 1 0.00
45 4 0.01
46 4 0.01
47 43 0.05
48 238 0.30
49 94 0.12
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.26
Consensus pattern (40 bp):
TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAA
Found at i:223452 original size:87 final size:87
Alignment explanation
Indices: 222885--224212 Score: 1960
Period size: 87 Copynumber: 15.0 Consensus size: 87
222875 GACGAAGATA
* * *
222885 CCAATGTGCTAATTCAAGGCCAGTGACATTGGACTTAAAGATAACAAAGGTGCCAATATGCTGAT
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAG---AC-AAGGTGCCAATATGCTGAT
*
222950 TCAAGGCCAGCGATATTGGACTTAGAGTG
62 TCAAGGCCAGCGATATTGGGCTT--A-TG
* * *
222979 GCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAG-GCATCAATATGCCGATTC
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGC--CAATATGCTGATTC
*
223043 AAGGCCAGCGATATTGGACTTAAAGGTG
64 AAGGCCAGCGATATTGGGCTT--A--TG
* * *
223071 CGAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACACGGTGCCAATATGCTAATTCAA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
* *
223136 AGCCAACGATATTGGGCTTATG
66 GGCCAGCGATATTGGGCTTATG
*
223158 CCAATGTGCTGATTCAAGGCCAACGAC-TTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
223222 GGCCAGCGATATTGGGCTTATG
66 GGCCAGCGATATTGGGCTTATG
**
223244 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGCACCAATATGCTGATTCA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAC-AAGGTGCCAATATGCTGATTCA
** *
223309 AGGCCAATGATATTGGACTTAAAGTTG
65 AGGCCAGCGATATTGGGCTT--A--TG
* *
223336 CCAATGTGTTGATTCAAGGCCAGCAACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
223401 GGCCAGCGATATTGGGCTTATG
66 GGCCAGCGATATTGGGCTTATG
223423 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
*
223488 GGCCAGCAATATTGGGCTTATG
66 GGCCAGCGATATTGGGCTTATG
223510 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
223575 GGCCAGCGATATTGGGCTTATG
66 GGCCAGCGATATTGGGCTTATG
**
223597 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGCACCAATATGCTGATTCA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAC-AAGGTGCCAATATGCTGATTCA
** *
223662 AGGCCAATGATATTGGACTTAAAGTTG
65 AGGCCAGCGATATTGGGCTT--A--TG
* *
223689 CCAATGTGTTGATTCAAGGCCAGCAACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
223754 GGCCAGCGATATTGGGCTTATG
66 GGCCAGCGATATTGGGCTTATG
223776 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
* *
223841 GGCC-GCAATATTGGGGTTATG
66 GGCCAGCGATATTGGGCTTATG
**
223862 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGCACCAATATGCTGATTCA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAC-AAGGTGCCAATATGCTGATTCA
* * *
223927 AAGCCAGTGATATTGGACTTAAAGGTG
65 AGGCCAGCGATATTGGGCTT--A--TG
* * * *
223954 CCAATGTGCTGATTCAAGGCTAGCGACATTGGCCTTAAAGATAAGGTGCCAATATGCTAATTCAA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
224019 GGCCAGCGATATTGGGCTTATG
66 GGCCAGCGATATTGGGCTTATG
224041 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
* *
224106 GGCTAGCAATATTGGGCTTATG
66 GGCCAGCGATATTGGGCTTATG
* * *
224128 CCAATGTGCTGATTCAAGGCCAGCAACATTGGTCTTAAAGACAAGGTCCCAATATGCTGGTTCAA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
* *
224193 GGCCAGCGATTTTGGACTTA
66 GGCCAGCGATATTGGGCTTA
224213 AAAGAAGATG
Statistics
Matches: 1129, Mismatches: 84, Indels: 49
0.89 0.07 0.04
Matches are distributed among these distances:
86 138 0.12
87 509 0.45
88 84 0.07
89 6 0.01
90 6 0.01
91 178 0.16
92 170 0.15
93 2 0.00
94 36 0.03
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (87 bp):
CCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAA
GGCCAGCGATATTGGGCTTATG
Found at i:224159 original size:618 final size:619
Alignment explanation
Indices: 222579--224212 Score: 2275
Period size: 618 Copynumber: 2.6 Consensus size: 619
222569 TTGAAGAAAA
* ** * ** *** *
222579 ATGCCAATGTGTTGAGGCAAGGCCAGCGACATTGGGCTTAGGAATGTTAAAGATGCCAATACGCT
1 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTA--AA-GACAAAGGCACCAATATGCT
* * * *
222644 GATTCAAGGCCAACGATATTGGACTTAAGGATGAAGGTGCTAATGTGCTGATTCAAGGCCAGCGA
63 GATTCAAAGCCAATGATATTGGACTT----A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCAA
* * * *
222709 CATTGG-TTTGAAAGATGACGAAAGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAA
122 CATTGGCCTT--AA-A-GAC-AAGGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGGC-T--
** * * *
222773 AGATGAAGGTGCCAATGTATTGACTCAAGGCCAGCGACATTAGACTTAAAGATGACGAAGGTGCC
179 ---T--A--TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT-AA-A-GAC-AAGGTGCC
* * ** * * *
222838 AATATGCTAATTCAAGGCCAGCGATACCGGACTTAAAGACGAAGATACCAATGTGCTAATTCAAG
233 AATATGCTGATTCAAGGCCAGCAATATTGGGCTT----------ATGCCAATGTGCTGATTCAAG
* *
222903 GCCAGTGACATTGGACTTAAAGATAACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTG
288 GCCAGCGACATTGGTCTTAAAG---AC-AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTG
* *
222968 GACTTAGAGTGGCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGCATCAAT
349 GACTT--AGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGCACCAAT
* * *
223033 ATGCCGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCGAATGTGCTGATTCAAGGCCAGCGAC
412 ATGCCGATTCAAGGCCAACGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCAAC
*
223098 ATTGGTCTTAAAGACACGGTGCCAATATGCTAATTCAAAGCCAACGATATTGGGCTTATGCCAAT
477 ATTGGTCTTAAAGACAAGGTGCCAATATGCTAATTCAAAGCCAACGATATTGGGCTTATGCCAAT
223163 GTGCTGATTCAAGGCCAACGACTTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAG
542 GTGCTGATTCAAGGCCAACGACTTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAG
*
223228 CGATATTGGGCTT
607 CAATATTGGGCTT
223241 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGCACCAATATGCTGAT
1 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGCACCAATATGCTGAT
* * * *
223306 TCAAGGCCAATGATATTGGACTTAAAGTTGCCAATGTGTTGATTCAAGGCCAGCAACATTGGTCT
66 TCAAAGCCAATGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGCCT
*
223371 TAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTATGCCAATGTGCTGAT
131 TAAAGACAAGGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGGCTTATGCCAATGTGCTGAT
223436 TCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATT
196 TCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATT
223501 GGGCTTATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATG
261 GGGCTTATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATG
*
223566 CTGATTCAAGGCCAGCGATATTGGGCTTA-TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGT
326 CTGATTCAAGGCCAGCGATATTGGACTTAGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGT
* * *
223630 CTTAAAGACAAAGGCACCAATATGCTGATTCAAGGCCAATGATATTGGACTTAAAGTTGCCAATG
391 CTTAAAGACAAAGGCACCAATATGCCGATTCAAGGCCAACGATATTGGACTTAAAGGTGCCAATG
* * * *
223695 TGTTGATTCAAGGCCAGCAACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAG
456 TGCTGATTCAAGGCCAGCAACATTGGTCTTAAAGACAAGGTGCCAATATGCTAATTCAAAGCCAA
*
223760 CGATATTGGGCTTATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGC
521 CGATATTGGGCTTATGCCAATGTGCTGATTCAAGGCCAACGAC-TTGGTCTTAAAGACAAGGTGC
*
223825 CAATATGCTGATTCAAGGCC-GCAATATTGGGGTT
585 CAATATGCTGATTCAAGGCCAGCAATATTGGGCTT
223859 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGCACCAATATGCTGAT
1 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGCACCAATATGCTGAT
* * *
223924 TCAAAGCCAGTGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGCCT
66 TCAAAGCCAATGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGCCT
*
223989 TAAAGATAAGGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGGCTTATGCCAATGTGCTGAT
131 TAAAGACAAGGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGGCTTATGCCAATGTGCTGAT
*
224054 TCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGCTAGCAATATT
196 TCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATT
* *
224119 GGGCTTATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGTCTTAAAGACAAGGTCCCAATATG
261 GGGCTTATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATG
* *
224184 CTGGTTCAAGGCCAGCGATTTTGGACTTA
326 CTGATTCAAGGCCAGCGATATTGGACTTA
224213 AAAGAAGATG
Statistics
Matches: 906, Mismatches: 64, Indels: 48
0.89 0.06 0.05
Matches are distributed among these distances:
618 545 0.60
619 42 0.05
621 41 0.05
622 2 0.00
625 39 0.04
635 37 0.04
636 3 0.00
637 1 0.00
638 2 0.00
639 33 0.04
641 1 0.00
643 1 0.00
648 1 0.00
649 38 0.04
650 3 0.00
651 1 0.00
652 2 0.00
653 34 0.04
654 2 0.00
655 1 0.00
659 39 0.04
660 2 0.00
662 36 0.04
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (619 bp):
ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGCACCAATATGCTGAT
TCAAAGCCAATGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGCCT
TAAAGACAAGGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGGCTTATGCCAATGTGCTGAT
TCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATT
GGGCTTATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATG
CTGATTCAAGGCCAGCGATATTGGACTTAGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGT
CTTAAAGACAAAGGCACCAATATGCCGATTCAAGGCCAACGATATTGGACTTAAAGGTGCCAATG
TGCTGATTCAAGGCCAGCAACATTGGTCTTAAAGACAAGGTGCCAATATGCTAATTCAAAGCCAA
CGATATTGGGCTTATGCCAATGTGCTGATTCAAGGCCAACGACTTGGTCTTAAAGACAAGGTGCC
AATATGCTGATTCAAGGCCAGCAATATTGGGCTT
Found at i:224214 original size:265 final size:267
Alignment explanation
Indices: 222685--224214 Score: 2040
Period size: 265 Copynumber: 5.7 Consensus size: 267
222675 TGAAGGTGCT
*
222685 AATGTGCTGATTCAAGGCCAGCGACATTGGT-TTGAAAGATGACGAAAGTGCCAATATGCTGATT
1 AATGTGCTGATTCAAGGCCAGCGACATTGGTCTT--AA-A-GAC-AAGGTGCCAATATGCTGATT
** *
222749 CAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTATTGACTCAAGGCCAGCGACATT
61 CAAGGCCAGCGATATTGGAC-T-----T-AA-GTGCCAATGTGCTGATTCAAGGCCAGCGACATT
* * * * * **
222814 AGACTTAAAGATGACGAAGGTGCCAATATGCTAATTCAAGGCCAGCGATACCGGACTTAAAGACG
118 GGTCTT-AA-A-GACAAAGGTCCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--
* * * *
222879 AAGATACCAATGTGCTAATTCAAGGCCAGTGACATTGGACTTAAAGATAACAAAGGTGCCAATAT
174 AAG-TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAG---AC-AAGGTGCCAATAT
* *
222944 GCTGATTCAAGGCCAGCGATATTGGACTTAGAGTGGC
234 GCTGATTCAAGGCCAGCGATATTGGGCTT--A-TGCC
* *
222981 AATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAG-GCATCAATATGCCGATTCAA
1 AATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGC--CAATATGCTGATTCAA
*
223045 GGCCAGCGATATTGGACTTAAAGGTGCGAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAA
64 GGCCAGCGATATTGGACTT-AA-GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAA
* * * * * *
223110 GAC-ACGGTGCCAATATGCTAATTCAAAGCCAACGATATTGGGCTT--A-TGCCAATGTGCTGAT
127 GACAAAGGTCCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGTGCCAATGTGCTGAT
*
223171 TCAAGGCCAACGAC-TTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATT
192 TCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATT
223235 GGGCTTATGCC
257 GGGCTTATGCC
**
223246 AATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGCACCAATATGCTGATTCAAG
1 AATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAC-AAGGTGCCAATATGCTGATTCAAG
** * *
223311 GCCAATGATATTGGACTTAAAGTTGCCAATGTGTTGATTCAAGGCCAGCAACATTGGTCTTAAAG
65 GCCAGCGATATTGGACTT-AAG-TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAG
* *
223376 AC-AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT--A-TGCCAATGTGCTGATT
128 ACAAAGGTCCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGTGCCAATGTGCTGATT
*
223437 CAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTG
193 CAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTG
223502 GGCTTATGCC
258 GGCTTATGCC
223512 AATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGG
1 AATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGG
*
223577 CCAGCGATATTGGGCTT-A-TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACA
66 CCAGCGATATTGGACTTAAGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACA
** *
223640 AAGG-CACCAATATGCTGATTCAAGGCCAATGATATTGGACTTAAAGTTGCCAATGTGTTGATTC
131 AAGGTC-CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG-TGCCAATGTGCTGATTC
*
223704 AAGGCCAGCAACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGG
194 AAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGG
223769 GCTTATGCC
259 GCTTATGCC
223778 AATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGG
1 AATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGG
* **
223843 CC-GCAATATTGGGGTT-A-TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACA
66 CCAGCGATATTGGACTTAAGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACA
* *
223905 AAGG-CACCAATATGCTGATTCAAAGCCAGTGATATTGGACTTAAAGGTGCCAATGTGCTGATTC
131 AAGGTC-CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA-GTGCCAATGTGCTGATTC
* * * *
223969 AAGGCTAGCGACATTGGCCTTAAAGATAAGGTGCCAATATGCTAATTCAAGGCCAGCGATATTGG
194 AAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGG
224034 GCTTATGCC
259 GCTTATGCC
224043 AATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGG
1 AATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGG
* * * *
224108 CTAGCAATATTGGGCTT-A-TGCCAATGTGCTGATTCAAGGCCAGCAACATTGGTCTTAAAGAC-
66 CCAGCGATATTGGACTTAAGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACA
* *
224170 AAGGTCCCAATATGCTGGTTCAAGGCCAGCGATTTTGGACTTAAA
131 AAGGTCCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
224215 AGAAGATGCC
Statistics
Matches: 1152, Mismatches: 66, Indels: 63
0.90 0.05 0.05
Matches are distributed among these distances:
261 42 0.04
262 37 0.03
263 1 0.00
264 2 0.00
265 514 0.45
266 318 0.28
267 1 0.00
268 41 0.04
269 2 0.00
272 11 0.01
273 25 0.02
275 1 0.00
283 36 0.03
284 3 0.00
285 1 0.00
286 2 0.00
287 37 0.03
291 2 0.00
292 5 0.00
293 35 0.03
294 1 0.00
295 2 0.00
296 31 0.03
297 2 0.00
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.25
Consensus pattern (267 bp):
AATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGG
CCAGCGATATTGGACTTAAGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACA
AAGGTCCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGTGCCAATGTGCTGATTCAA
GGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGC
TTATGCC
Found at i:224327 original size:33 final size:33
Alignment explanation
Indices: 224290--224610 Score: 235
Period size: 33 Copynumber: 10.4 Consensus size: 33
224280 TGCCACTTAC
*
224290 TTGTGGGCTTAAAAAGAGAAAGATGCCACGGAG
1 TTGTGGACTTAAAAAGAGAAAGATGCCACGGAG
*
224323 TTGTGGACTT-AAAAG-G---G-TGCCACGGAA
1 TTGTGGACTTAAAAAGAGAAAGATGCCACGGAG
* *
224350 TTGTGGACTTAAAAGGA-AAAGGTGCCACGGAG
1 TTGTGGACTTAAAAAGAGAAAGATGCCACGGAG
* *
224382 TTGTGGACTTAAAAGGA-AAAAAGTGCCACGGAG
1 TTGTGGACTTAAAAAGAGAAAGA-TGCCACGGAG
* * *
224415 TTGTGGACTTAAAAGGAAAAAGATGCCATGGAG
1 TTGTGGACTTAAAAAGAGAAAGATGCCACGGAG
* *
224448 TTGTGGACTTAAAAGGAAAAAGATGCCACGGA-
1 TTGTGGACTTAAAAAGAGAAAGATGCCACGGAG
* * * **
224480 TGTGTGCACTT-AAAAGGGACAAGGTGCCATAGAG
1 T-TGTGGACTTAAAAAGAGA-AAGATGCCACGGAG
*
224514 TTGTGGACTT--AAA-AG---GATGCCATGGAG
1 TTGTGGACTTAAAAAGAGAAAGATGCCACGGAG
* *
224541 TTGTGGGCTT-TAAA-AG--AG-TGCCACGGAG
1 TTGTGGACTTAAAAAGAGAAAGATGCCACGGAG
* * *
224569 TTGTGGGCTT-TAAA-AG--AG-TGCCACGGGG
1 TTGTGGACTTAAAAAGAGAAAGATGCCACGGAG
224597 TTGTGGACTTAAAA
1 TTGTGGACTTAAAA
224611 GGATGCCATG
Statistics
Matches: 249, Mismatches: 25, Indels: 32
0.81 0.08 0.10
Matches are distributed among these distances:
27 38 0.15
28 55 0.22
29 3 0.01
31 3 0.01
32 43 0.17
33 102 0.41
34 5 0.02
ACGTcount: A:0.33, C:0.12, G:0.32, T:0.22
Consensus pattern (33 bp):
TTGTGGACTTAAAAAGAGAAAGATGCCACGGAG
Found at i:224463 original size:66 final size:64
Alignment explanation
Indices: 224339--224530 Score: 278
Period size: 66 Copynumber: 2.9 Consensus size: 64
224329 ACTTAAAAGG
*
224339 GTGCCACGGAATTGTGGACTTAAAAGGAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAA
1 GTGCCACGG-ATTGTGGACTTAAAAGGAAAAGGTGCCATGGAGTTGTGGACTTAAAAGGAAAAAA
*
224404 GTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGATGCCATGGAGTTGTGGACTTAAAAGG-AAAA
1 GTGCCACGGA-TTGTGGACTTAAAAGG-AAAAGGTGCCATGGAGTTGTGGACTTAAAAGGAAAAA
224468 A
64 A
* * *
224469 GATGCCACGGATGTGTGCACTTAAAAGGGACAAGGTGCCATAGAGTTGTGGACTTAAAAGGA
1 G-TGCCACGGAT-TGTGGACTTAAAA-GGAAAAGGTGCCATGGAGTTGTGGACTTAAAAGGA
224531 TGCCATGGAG
Statistics
Matches: 115, Mismatches: 6, Indels: 10
0.88 0.05 0.08
Matches are distributed among these distances:
64 1 0.01
65 32 0.28
66 80 0.70
67 2 0.02
ACGTcount: A:0.36, C:0.12, G:0.31, T:0.20
Consensus pattern (64 bp):
GTGCCACGGATTGTGGACTTAAAAGGAAAAGGTGCCATGGAGTTGTGGACTTAAAAGGAAAAAA
Found at i:224493 original size:99 final size:93
Alignment explanation
Indices: 224308--224629 Score: 296
Period size: 99 Copynumber: 3.5 Consensus size: 93
224298 TTAAAAAGAG
*
224308 AAAGATGCCACGGAGTTGTGGACTTAAAAGG-GTGCCACGGAATTGTGGACTTAAAAGGAAAAGG
1 AAAG-TGCCACGGAGTTGTGGACTTAAAAGGAGTGCCACGGAATTGTGGACTTAAAAGGAAAAGA
*
224372 TGCCACGGAGTTGTGGACTTAAAAGGAAA
65 TGCCACGGAGTTGTGCACTTAAAAGGAAA
* *
224401 AAAGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGATGCCATGGAGTTGTGGACTTAAAAGGAA
1 AAAGTGCCACGGAGTTGTGGACTTAAAAGG----AG-TGCCACGGAATTGTGGACTTAAAAGG-A
* *
224466 AAAGATGCCACGGA-TGTGTGCACTTAAAAGGGAC
60 AAAGATGCCACGGAGT-TGTGCACTTAAAAGGAAA
* ** * * *
224500 AAGGTGCCATAGAGTTGTGGACTTAAAAGGA-TGCCATGGAGTTGTGGGCTTTAAAA-G---AG-
1 AAAGTGCCACGGAGTTGTGGACTTAAAAGGAGTGCCACGGAATTGTGGAC-TTAAAAGGAAAAGA
**
224559 TGCCACGGAGTTGTGGGCTTTAAAA-G---
65 TGCCACGGAGTTGTGCAC-TTAAAAGGAAA
* * *
224585 --AGTGCCACGGGGTTGTGGACTTAAAAGGA-TGCCATGGAGTTGTGG
1 AAAGTGCCACGGAGTTGTGGACTTAAAAGGAGTGCCACGGAATTGTGG
224630 GCTTTGGGAC
Statistics
Matches: 202, Mismatches: 16, Indels: 32
0.81 0.06 0.13
Matches are distributed among these distances:
83 41 0.20
88 15 0.07
89 9 0.04
92 26 0.13
93 22 0.11
94 6 0.03
95 1 0.00
97 1 0.00
98 25 0.12
99 56 0.28
ACGTcount: A:0.32, C:0.13, G:0.33, T:0.22
Consensus pattern (93 bp):
AAAGTGCCACGGAGTTGTGGACTTAAAAGGAGTGCCACGGAATTGTGGACTTAAAAGGAAAAGAT
GCCACGGAGTTGTGCACTTAAAAGGAAA
Found at i:224554 original size:28 final size:28
Alignment explanation
Indices: 224500--224634 Score: 163
Period size: 28 Copynumber: 4.9 Consensus size: 28
224490 TAAAAGGGAC
* *
224500 AAGG-TGCCATAGAGTTGTGGAC-TTAA
1 AAGGATGCCATGGAGTTGTGGGCTTTAA
224526 AAGGATGCCATGGAGTTGTGGGCTTTAA
1 AAGGATGCCATGGAGTTGTGGGCTTTAA
*
224554 AA-GAGTGCCACGGAGTTGTGGGCTTTAA
1 AAGGA-TGCCATGGAGTTGTGGGCTTTAA
* * *
224582 AA-GAGTGCCACGGGGTTGTGGAC-TTAA
1 AAGGA-TGCCATGGAGTTGTGGGCTTTAA
224609 AAGGATGCCATGGAGTTGTGGGCTTT
1 AAGGATGCCATGGAGTTGTGGGCTTT
224635 GGGACAAAAT
Statistics
Matches: 96, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
26 4 0.04
27 39 0.41
28 53 0.55
ACGTcount: A:0.25, C:0.13, G:0.36, T:0.27
Consensus pattern (28 bp):
AAGGATGCCATGGAGTTGTGGGCTTTAA
Found at i:224630 original size:55 final size:56
Alignment explanation
Indices: 224500--224634 Score: 163
Period size: 55 Copynumber: 2.5 Consensus size: 56
224490 TAAAAGGGAC
* * * *
224500 AAGG-TGCCATAGAGTTGTGGAC-TTAAAAGGATGCCATGGAGTTGTGGGCTTTAA
1 AAGGATGCCATGGAGTTGTGGGCTTTAAAAGGATGCCACGGAGTTGTGGACTTTAA
* *
224554 AA-GAGTGCCACGGAGTTGTGGGCTTTAAAA-GAGTGCCACGGGGTTGTGGAC-TTAA
1 AAGGA-TGCCATGGAGTTGTGGGCTTTAAAAGGA-TGCCACGGAGTTGTGGACTTTAA
224609 AAGGATGCCATGGAGTTGTGGGCTTT
1 AAGGATGCCATGGAGTTGTGGGCTTT
224635 GGGACAAAAT
Statistics
Matches: 69, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
53 1 0.01
54 2 0.03
55 43 0.62
56 23 0.33
ACGTcount: A:0.25, C:0.13, G:0.36, T:0.27
Consensus pattern (56 bp):
AAGGATGCCATGGAGTTGTGGGCTTTAAAAGGATGCCACGGAGTTGTGGACTTTAA
Found at i:224663 original size:30 final size:31
Alignment explanation
Indices: 224642--224701 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
224632 TTTGGGACAA
224642 AATGCCACTGAGTCGTAGGCTTTGAGAAGAG
1 AATGCCACTGAGTCGTAGGCTTTGAGAAGAG
* *
224673 ATTGCCACTGAGTCGT-GGACTTTAAGAAG
1 AATGCCACTGAGTCGTAGG-CTTTGAGAAG
224702 GTACTTGAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 2 0.08
31 24 0.92
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.25
Consensus pattern (31 bp):
AATGCCACTGAGTCGTAGGCTTTGAGAAGAG
Found at i:225997 original size:9 final size:8
Alignment explanation
Indices: 225982--226029 Score: 57
Period size: 8 Copynumber: 6.1 Consensus size: 8
225972 TTTGCACTTT
225982 TTTTTTTG
1 TTTTTTTG
225990 TGTTTTTTG
1 T-TTTTTTG
225999 ---TTTTG
1 TTTTTTTG
226004 TTTTTTTG
1 TTTTTTTG
226012 TTGTTTTTG
1 TT-TTTTTG
226021 TTTTTTTG
1 TTTTTTTG
226029 T
1 T
226030 GTTTGTACTT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
5 5 0.14
8 15 0.43
9 15 0.43
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (8 bp):
TTTTTTTG
Found at i:226007 original size:25 final size:25
Alignment explanation
Indices: 225979--226029 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
225969 GCCTTTGCAC
*
225979 TTTTTTTTTTGTGTTTT-TTGTTTTG
1 TTTTTTTGTTGT-TTTTGTTGTTTTG
*
226004 TTTTTTTGTTGTTTTTGTTTTTTTG
1 TTTTTTTGTTGTTTTTGTTGTTTTG
226029 T
1 T
226030 GTTTGTACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (25 bp):
TTTTTTTGTTGTTTTTGTTGTTTTG
Found at i:226025 original size:23 final size:22
Alignment explanation
Indices: 225982--226024 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
225972 TTTGCACTTT
225982 TTTTTTTGTGTTTTTTGTTTTG
1 TTTTTTTGTGTTTTTTGTTTTG
226004 TTTTTTTGT-TGTTTTTGTTTT
1 TTTTTTTGTGT-TTTTTGTTTT
226025 TTTGTGTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (22 bp):
TTTTTTTGTGTTTTTTGTTTTG
Found at i:226029 original size:14 final size:14
Alignment explanation
Indices: 225979--226035 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
225969 GCCTTTGCAC
225979 TTTTT-TTTTTGTGT
1 TTTTTGTTTTTGT-T
*
225993 TTTTTGTTTTGTTTT
1 TTTTTGTTTT-TGTT
226008 TTTGTTGTTTTTGTT
1 TTT-TTGTTTTTGTT
*
226023 TTTTTGTGTTTGT
1 TTTTTGTTTTTGT
226036 ACTTTTAAGG
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
14 14 0.38
15 14 0.38
16 9 0.24
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (14 bp):
TTTTTGTTTTTGTT
Found at i:226041 original size:22 final size:20
Alignment explanation
Indices: 225982--226035 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
225972 TTTGCACTTT
225982 TTTTTTTGTGTTT-TTTGTT-
1 TTTTTTTGTGTTTGTTT-TTG
*
226001 TTGTTTTTTTG-TTGTTTTTG
1 TT-TTTTTGTGTTTGTTTTTG
226021 TTTTTTTGTGTTTGT
1 TTTTTTTGTGTTTGT
226036 ACTTTTAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (20 bp):
TTTTTTTGTGTTTGTTTTTG
Found at i:228848 original size:9 final size:9
Alignment explanation
Indices: 228809--228849 Score: 64
Period size: 9 Copynumber: 4.6 Consensus size: 9
228799 GAGGGTAAAG
228809 AATGATCAA
1 AATGATCAA
*
228818 AATCATCAA
1 AATGATCAA
*
228827 AATCATCAA
1 AATGATCAA
228836 AATGATCAA
1 AATGATCAA
228845 AATGA
1 AATGA
228850 CTGAAGGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.56, C:0.15, G:0.07, T:0.22
Consensus pattern (9 bp):
AATGATCAA
Found at i:229885 original size:19 final size:19
Alignment explanation
Indices: 229861--229974 Score: 117
Period size: 19 Copynumber: 6.6 Consensus size: 19
229851 AGCGATACAT
* *
229861 TGTATCGATACAAAACTAA
1 TGTATCGATACAACACTTA
229880 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
229893 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
229912 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
229931 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
*
229944 TGTGTCGATACAACACTTA
1 TGTATCGATACAACACTTA
229963 TGTATCGATACA
1 TGTATCGATACA
229975 GTTACTGTTT
Statistics
Matches: 79, Mismatches: 4, Indels: 24
0.74 0.04 0.22
Matches are distributed among these distances:
13 17 0.22
14 1 0.01
16 11 0.14
18 2 0.03
19 48 0.61
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.32
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:229894 original size:32 final size:32
Alignment explanation
Indices: 229853--229923 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
229843 AGCTTCGTAG
229853 CGATACATTGTATCGATACAAAACTAATGTAT
1 CGATACATTGTATCGATACAAAACTAATGTAT
* *
229885 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTAATGTAT
229917 CGATACA
1 CGATACA
229924 ACACTTATGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTAATGTAT
Found at i:229898 original size:13 final size:13
Alignment explanation
Indices: 229880--229904 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
229870 ACAAAACTAA
229880 TGTATCGATACAT
1 TGTATCGATACAT
229893 TGTATCGATACA
1 TGTATCGATACA
229905 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:229937 original size:51 final size:51
Alignment explanation
Indices: 229861--229974 Score: 201
Period size: 51 Copynumber: 2.2 Consensus size: 51
229851 AGCGATACAT
229861 TGTATCGATACAAAACTAATGTATCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACAAAACTAATGTATCGATACATTGTATCGATACAACACTTA
* * *
229912 TGTATCGATACAACACTTATGTATCGATACATTGTGTCGATACAACACTTA
1 TGTATCGATACAAAACTAATGTATCGATACATTGTATCGATACAACACTTA
229963 TGTATCGATACA
1 TGTATCGATACA
229975 GTTACTGTTT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.32
Consensus pattern (51 bp):
TGTATCGATACAAAACTAATGTATCGATACATTGTATCGATACAACACTTA
Found at i:236437 original size:13 final size:13
Alignment explanation
Indices: 236419--236444 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
236409 ACATTTGGTC
236419 ATGTATCGATACA
1 ATGTATCGATACA
236432 ATGTATCGATACA
1 ATGTATCGATACA
236445 TCTTGTATGT
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:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:236439 original size:33 final size:32
Alignment explanation
Indices: 236397--236464 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 32
236387 CGTTACAAGC
236397 CAATGTATCGATACAT-TTGGTCATGTATCGATA
1 CAATGTATCGATACATCTT-GT-ATGTATCGATA
236430 CAATGTATCGATACATCTTGTATGTATCGATA
1 CAATGTATCGATACATCTTGTATGTATCGATA
236462 CAA
1 CAA
236465 ACAGTTAAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
32 14 0.41
33 18 0.53
34 2 0.06
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATCTTGTATGTATCGATA
Found at i:237666 original size:20 final size:19
Alignment explanation
Indices: 237611--237666 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
237601 AAAACCCTTA
*
237611 AAAGTATCGATACATAATTC
1 AAAGTATCGATACAT-GTTC
237631 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACATGTT-C
*
237651 AATGTATCGATACATG
1 AAAGTATCGATACATG
237667 AAAAAGATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 2 0.06
20 31 0.94
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (19 bp):
AAAGTATCGATACATGTTC
Found at i:237760 original size:20 final size:20
Alignment explanation
Indices: 237717--237768 Score: 88
Period size: 19 Copynumber: 2.6 Consensus size: 20
237707 GTAGCCAAAC
*
237717 TTGTATCGATACACAAAATA
1 TTGTATCGATACACAAAAAA
237737 -TGTATCGATACACAAAAAA
1 TTGTATCGATACACAAAAAA
237756 TTGTATCGATACA
1 TTGTATCGATACA
237769 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.60
20 12 0.40
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:239989 original size:21 final size:21
Alignment explanation
Indices: 239956--240005 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
239946 TTGCAAGTTG
*
239956 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
239978 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
239999 AAATAAA
1 AAATAAA
240006 AATTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:241823 original size:15 final size:15
Alignment explanation
Indices: 241803--241833 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
241793 TAAAAATATC
*
241803 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
241818 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
241833 C
1 C
241834 CAAACGAAAT
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:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:243931 original size:13 final size:13
Alignment explanation
Indices: 243913--243950 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
243903 CATTTTTCTT
243913 TGTATCGATACAA
1 TGTATCGATACAA
*
243926 TGTATCGATACAC
1 TGTATCGATACAA
243939 TGTATCGATACA
1 TGTATCGATACA
243951 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Done.