Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008480.1 Hibiscus syriacus cultivar Beakdansim tig00111311_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: 2515485
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 13
Found at i:193116 original size:165 final size:165
Alignment explanation
Indices: 192931--193373 Score: 564
Period size: 165 Copynumber: 2.7 Consensus size: 165
192921 GTCTTTTGTT
* * * *
192931 GGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATAATATGCCTTGGAGCTGAGGGTAGTCG
1 GGCAAATAGCCCTTCTCGACTTAAGTTATGCTACAAATGATATGCCTTGGAGCTGAGCGTAGTCG
* * * * * *
192996 AACTCGAAGGTCTTTTGGTGACAAATAACCCTTCTAGCCTTGAGTTATGTTGTAACTGATGTGCC
66 AACTCGAAGGTCTTTTGGTGACAAATAACCCTTCTAGACTTAAGTTATGATGCAAATGATATGCC
*
193061 CTCGAAGCCGAGTGTAATCGAACTCGAGGGTCTTT
131 CTCGAAGCCGAGTGTAATCGAACTCGAGGGTCTTC
* * **
193096 GGCAAATAGCTCTTCTCGACTTAAGTTATACTGTAAATGATATGCCTTGGAGCTGAGCGTAGTCG
1 GGCAAATAGCCCTTCTCGACTTAAGTTATGCTACAAATGATATGCCTTGGAGCTGAGCGTAGTCG
* * * * * **
193161 AACTCGAAGATCTTGTGTTGGCATATAACCCTTCTCTACTTAAGTTATGATGCAAATGATATGCC
66 AACTCGAAGGTCTTTTGGTGACAAATAACCCTTCTAGACTTAAGTTATGATGCAAATGATATGCC
* * *
193226 CTTGAAGCTGATTGTAATCGAACTCGAGGGTCTTC
131 CTCGAAGCCGAGTGTAATCGAACTCGAGGGTCTTC
* * * *
193261 GGCATATAGCCCTTTTCGACTTAAGCTATGCTACAAATGATACGCCTTGGAGCTGAGCGTAGTCG
1 GGCAAATAGCCCTTCTCGACTTAAGTTATGCTACAAATGATATGCCTTGGAGCTGAGCGTAGTCG
* * * * *
193326 AACTCGAAGGTCTTTT-GTTAGCAGATAATCATTCTCGACTTAAGTTAT
66 AACTCGAAGGTCTTTTGGTGA-CAAATAACCCTTCTAGACTTAAGTTAT
193374 ACAACAAAAG
Statistics
Matches: 235, Mismatches: 42, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
164 1 0.00
165 234 1.00
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (165 bp):
GGCAAATAGCCCTTCTCGACTTAAGTTATGCTACAAATGATATGCCTTGGAGCTGAGCGTAGTCG
AACTCGAAGGTCTTTTGGTGACAAATAACCCTTCTAGACTTAAGTTATGATGCAAATGATATGCC
CTCGAAGCCGAGTGTAATCGAACTCGAGGGTCTTC
Found at i:193363 original size:249 final size:248
Alignment explanation
Indices: 192661--193375 Score: 717
Period size: 249 Copynumber: 2.9 Consensus size: 248
192651 CTGAATGTAA
* * * *
192661 TCGAACTCGGAGGTCTTCG-GTTGGCAGATAACCCTTCTCGACTTAAGCTAT-ACTACAAATGAT
1 TCGAACTCGAAGATCTT-GTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGA-TACAAATAAT
* * * * * * * * *
192724 GTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTCTGGTGACAGATAACCCTTCTAGCCTTG
64 ATGCCTTGAAGCTGAGGGTAATCGAACTCGAAGGTCTTTCGTGACAAATAACCCTTCTAGACTTA
* * ** ** * * * * *
192789 AGTTATGTTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTCGGCAGAT
129 AGCTATGCTACAAATGATACGCCCTCGAAGCCGAGCGTAATCGAACTCGAAGGTCTTTGGCAAAT
* * * *
192854 AGCA-CTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGTTGTGCGTAG
194 AG-ATCTTCTCGACTTAAGTTATACTGCAAATGATATGCCTTGGAGCTGAGCGTAG
* * *
192909 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATAATAT
1 TCGAACTCGAAGATCTTGTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGATACAAATAATAT
* * * * *
192974 GCCTTGGAGCTGAGGGTAGTCGAACTCGAAGGTCTTTTGGTGACAAATAACCCTTCTAGCCTTGA
66 GCCTTGAAGCTGAGGGTAATCGAACTCGAAGGTC-TTTCGTGACAAATAACCCTTCTAGACTTAA
* * ** * ** * *
193039 GTTATGTTGTAACTGATGTGCCCTCGAAGCCGAGTGTAATCGAACTCGAGGGTCTTTGGCAAATA
130 GCTATGCTACAAATGATACGCCCTCGAAGCCGAGCGTAATCGAACTCGAAGGTCTTTGGCAAATA
* *
193104 GCTCTTCTCGACTTAAGTTATACTGTAAATGATATGCCTTGGAGCTGAGCGTAG
195 GATCTTCTCGACTTAAGTTATACTGCAAATGATATGCCTTGGAGCTGAGCGTAG
* * * *
193158 TCGAACTCGAAGATCTTGTGTTGGCATATAACCCTTCTCTACTTAAGTTATGATGCAAATGATAT
1 TCGAACTCGAAGATCTTGTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGATACAAATAATAT
** * * * * *
193223 GCCCTTGAAGCTGATTGTAATCGAACTCGAGGGTC-TTCG-G-CATATAGCCCTTTTCGACTTAA
66 G-CCTTGAAGCTGAGGGTAATCGAACTCGAAGGTCTTTCGTGACAAATAACCCTTCTAGACTTAA
* * * *
193285 GCTATGCTACAAATGATACG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTAGCA
130 GCTATGCTACAAATGATACGCCCTCGAAGCCGAGCGTAATCGAACTCGAAGGTC-TTTG---GCA
*
193349 GATA-ATCATTCTCGACTTAAGTTATAC
191 AATAGATC-TTCTCGACTTAAGTTATAC
193376 AACAAAAGTT
Statistics
Matches: 404, Mismatches: 53, Indels: 19
0.85 0.11 0.04
Matches are distributed among these distances:
245 27 0.07
246 33 0.08
247 1 0.00
248 95 0.24
249 220 0.54
250 28 0.07
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (248 bp):
TCGAACTCGAAGATCTTGTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGATACAAATAATAT
GCCTTGAAGCTGAGGGTAATCGAACTCGAAGGTCTTTCGTGACAAATAACCCTTCTAGACTTAAG
CTATGCTACAAATGATACGCCCTCGAAGCCGAGCGTAATCGAACTCGAAGGTCTTTGGCAAATAG
ATCTTCTCGACTTAAGTTATACTGCAAATGATATGCCTTGGAGCTGAGCGTAG
Found at i:199014 original size:12 final size:12
Alignment explanation
Indices: 198997--199026 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
198987 CTGTTCGTGC
198997 AAGAGTTAAAGG
1 AAGAGTTAAAGG
199009 AAGAGTTAAAGG
1 AAGAGTTAAAGG
199021 AAGAGT
1 AAGAGT
199027 GAGATCGGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.33, T:0.17
Consensus pattern (12 bp):
AAGAGTTAAAGG
Found at i:202030 original size:17 final size:18
Alignment explanation
Indices: 202008--202041 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
201998 AAATATCCAT
202008 TAAATTT-TGGATTATTA
1 TAAATTTATGGATTATTA
*
202025 TAAATTTATGTATTATT
1 TAAATTTATGGATTATT
202042 TTAGGGTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (18 bp):
TAAATTTATGGATTATTA
Found at i:203368 original size:25 final size:25
Alignment explanation
Indices: 203331--203395 Score: 78
Period size: 24 Copynumber: 2.6 Consensus size: 25
203321 TATATTTTTG
*
203331 TACAACACTTTTAAAAATTCGTTTC
1 TACAATACTTTTAAAAATTCGTTTC
* * *
203356 TATAATACTTTT-AAAATTTGTTTT
1 TACAATACTTTTAAAAATTCGTTTC
*
203380 TACAATAATTTTAAAA
1 TACAATACTTTTAAAA
203396 CTCACTTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
24 20 0.61
25 13 0.39
ACGTcount: A:0.40, C:0.11, G:0.03, T:0.46
Consensus pattern (25 bp):
TACAATACTTTTAAAAATTCGTTTC
Found at i:206528 original size:16 final size:13
Alignment explanation
Indices: 206498--206522 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
206488 TATTTAAATA
206498 AAGAAAAAAACAT
1 AAGAAAAAAACAT
206511 AAGAAAAAAACA
1 AAGAAAAAAACA
206523 AGATAAACAA
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:0.80, C:0.08, G:0.08, T:0.04
Consensus pattern (13 bp):
AAGAAAAAAACAT
Found at i:206673 original size:19 final size:19
Alignment explanation
Indices: 206638--206697 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
206628 ATGTCAAAGT
206638 AAAAATAGAAATAGAAAGGA
1 AAAAATA-AAATAGAAAGGA
*
206658 AAAAATAAAA-AGGAAATGA
1 AAAAATAAAATA-GAAAGGA
*
206677 AAAGAT-AAATCA-AAAGGA
1 AAAAATAAAAT-AGAAAGGA
206695 AAA
1 AAA
206698 CAAATGCAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
18 12 0.35
19 14 0.41
20 8 0.24
ACGTcount: A:0.72, C:0.02, G:0.17, T:0.10
Consensus pattern (19 bp):
AAAAATAAAATAGAAAGGA
Found at i:206729 original size:17 final size:17
Alignment explanation
Indices: 206707--206742 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
206697 ACAAATGCAG
206707 AATAAATAAAAACGAAA
1 AATAAATAAAAACGAAA
206724 AATAAATAAAAACGAAA
1 AATAAATAAAAACGAAA
206741 AA
1 AA
206743 ACGAAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.78, C:0.06, G:0.06, T:0.11
Consensus pattern (17 bp):
AATAAATAAAAACGAAA
Found at i:206754 original size:18 final size:18
Alignment explanation
Indices: 206710--206753 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 18
206700 AATGCAGAAT
*
206710 AAATAAAAACG-AAAAAT
1 AAATAAAAACGAAAAAAG
206727 AAATAAAAACGAAAAAACG
1 AAATAAAAACGAAAAAA-G
206746 AAATAAAA
1 AAATAAAA
206754 CAAAAATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 11 0.46
18 5 0.21
19 8 0.33
ACGTcount: A:0.77, C:0.07, G:0.07, T:0.09
Consensus pattern (18 bp):
AAATAAAAACGAAAAAAG
Found at i:207980 original size:10 final size:10
Alignment explanation
Indices: 207962--208036 Score: 84
Period size: 10 Copynumber: 7.5 Consensus size: 10
207952 AAATAAATGG
*
207962 ATAAGAAATA
1 ATAATAAATA
207972 ATAATAAATA
1 ATAATAAATA
207982 ATAATAAATA
1 ATAATAAATA
*
207992 ACAAT-AAT-
1 ATAATAAATA
208000 A-AATAAATAA
1 ATAATAAAT-A
208010 ATATATAAATA
1 ATA-ATAAATA
208021 ATAATAAATAA
1 ATAATAAAT-A
208032 ATAAT
1 ATAAT
208037 TATATTAAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
7 3 0.05
8 4 0.07
9 3 0.05
10 30 0.53
11 11 0.19
12 6 0.11
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.28
Consensus pattern (10 bp):
ATAATAAATA
Found at i:207991 original size:4 final size:4
Alignment explanation
Indices: 207974--208035 Score: 62
Period size: 4 Copynumber: 16.2 Consensus size: 4
207964 AAGAAATAAT
*
207974 AATA AAT- AAT- AATA AATA ACA-A TAATA AATA AATA AATA TATA AAT-
1 AATA AATA AATA AATA AATA A-ATA -AATA AATA AATA AATA AATA AATA
208020 AAT- AATA AATA AATA A
1 AATA AATA AATA AATA A
208036 TTATATTAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
3 12 0.24
4 36 0.71
5 3 0.06
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (4 bp):
AATA
Found at i:208023 original size:26 final size:26
Alignment explanation
Indices: 207967--208041 Score: 102
Period size: 26 Copynumber: 3.0 Consensus size: 26
207957 AATGGATAAG
*
207967 AAATAATAATAAAT-AAT-AATAAAT
1 AAATAATAATAAATAAATAAATATAT
*
207991 -AACAATAATAAATAAATAAATATAT
1 AAATAATAATAAATAAATAAATATAT
*
208016 AAATAATAATAAATAAATAATTATAT
1 AAATAATAATAAATAAATAAATATAT
208042 TAAAAAAACT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
23 12 0.27
24 3 0.07
25 6 0.14
26 23 0.52
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (26 bp):
AAATAATAATAAATAAATAAATATAT
Found at i:208150 original size:18 final size:17
Alignment explanation
Indices: 208124--208186 Score: 60
Period size: 19 Copynumber: 3.6 Consensus size: 17
208114 CAAAAATGTT
208124 TTTTAAAAAACTATATAA
1 TTTTAAAAAACTATAT-A
208142 TTTTCAAAAAA-TACT-T-
1 TTTT-AAAAAACTA-TATA
208158 TTTTAAAAAACTATATGA
1 TTTTAAAAAACTATAT-A
208176 TTTTCAAAAAA
1 TTTT-AAAAAA
208187 TGTTTTCAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
15 7 0.18
16 7 0.18
18 11 0.29
19 13 0.34
ACGTcount: A:0.51, C:0.08, G:0.02, T:0.40
Consensus pattern (17 bp):
TTTTAAAAAACTATATA
Found at i:208260 original size:15 final size:15
Alignment explanation
Indices: 208242--208270 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
208232 AAAAACTTAA
208242 TTTTTTTTAAAAACG
1 TTTTTTTTAAAAACG
208257 TTTTTTTTAAAAAC
1 TTTTTTTTAAAAAC
208271 TACATATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.07, G:0.03, T:0.55
Consensus pattern (15 bp):
TTTTTTTTAAAAACG
Found at i:208317 original size:178 final size:180
Alignment explanation
Indices: 208065--208416 Score: 681
Period size: 178 Copynumber: 2.0 Consensus size: 180
208055 TAATATAATA
208065 TTTTTAAAAACGTTTCTTTTTTAAAAACTACATATTATATATAAATTTTCAAAAATGTTTTTTAA
1 TTTTTAAAAACGTTTCTTTTTTAAAAACTACATATTATATATAAATTTTCAAAAATGTTTTTTAA
208130 AAAACTATATAATTTTCAAAAAATACTTTTTTAAAAAACTATATGATTTTCAAAAAATGTTTTCA
66 AAAACTATATAATTTTCAAAAAATACTTTTTTAAAAAACTATATGATTTTCAAAAAATGTTTTCA
208195 AAAATAATATTTTATATAAGTTTTCAAAAATGTTTTTAAAAACTTAATTT
131 AAAATAATATTTTATATAAGTTTTCAAAAATGTTTTTAAAAACTTAATTT
208245 TTTTTAAAAACG-TT-TTTTTTAAAAACTACATATTATATATAAATTTTCAAAAATGTTTTTTAA
1 TTTTTAAAAACGTTTCTTTTTTAAAAACTACATATTATATATAAATTTTCAAAAATGTTTTTTAA
*
208308 AAAACTATATAATTTTCAAAAAATACTTTTTTTAAAAACTATATGATTTTCAAAAAATGTTTTCA
66 AAAACTATATAATTTTCAAAAAATACTTTTTTAAAAAACTATATGATTTTCAAAAAATGTTTTCA
208373 AAAATAATATTTTATATAAGTTTTCAAAAATGTTTTTAAAAACT
131 AAAATAATATTTTATATAAGTTTTCAAAAATGTTTTTAAAAACT
208417 ATATATTATA
Statistics
Matches: 171, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
178 157 0.92
179 2 0.01
180 12 0.07
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (180 bp):
TTTTTAAAAACGTTTCTTTTTTAAAAACTACATATTATATATAAATTTTCAAAAATGTTTTTTAA
AAAACTATATAATTTTCAAAAAATACTTTTTTAAAAAACTATATGATTTTCAAAAAATGTTTTCA
AAAATAATATTTTATATAAGTTTTCAAAAATGTTTTTAAAAACTTAATTT
Found at i:208325 original size:105 final size:103
Alignment explanation
Indices: 208207--208536 Score: 246
Period size: 114 Copynumber: 3.1 Consensus size: 103
208197 AATAATATTT
** * * * *
208207 TATATAAGTTTTC-AAAA-A-TGTTTTTAAAAACT-TAATTTTTTTTAAAAACGTTTTTTTTAAA
1 TATATAAGTTTTCAAAAATACTGTTTTTAAAAACTAT-ATGATTTTCAAAAA--ATGTTTTCAAA
208268 AACTACATATTATATATAAATTTTCAAAAATGTTTTTTAAAAAAC
63 AA-TA-ATATTATATATAAATTTTCAAAAATG-TTTTT-AAAAAC
*
208313 TATATAA-TTTTCAAAAAATACTTTTTTTAAAAACTATATGATTTTCAAAAAATGTTTTCAAAAA
1 TATATAAGTTTTC-AAAAATACTGTTTTTAAAAACTATATGATTTTCAAAAAATGTTTTCAAAAA
* *
208377 TAATATTTTATATAAGTTTTCAAAAATGTTTTTAAAAAC
65 TAATATTATATATAAATTTTCAAAAATGTTTTTAAAAAC
* *
208416 TATATATTATATAAATTTCAAAAA-A-TGTTTTTAAAAACTATATATTATATAAATTTCAAAAAA
1 TATATA--A-GT---TTTCAAAAATACTGTTTTTAAAAAC--TATA-T-GAT---TTTCAAAAAA
* * * *
208479 TATTTTTAAAAACT-ATA-TATTATATAAGTTTTCCAAAAATGATTTTAAAAAC
53 TGTTTTCAAAAA-TAATATTA-TATATAAATTTT-CAAAAATGTTTTTAAAAAC
208531 TATATA
1 TATATA
208537 TTATATATTT
Statistics
Matches: 187, Mismatches: 15, Indels: 35
0.79 0.06 0.15
Matches are distributed among these distances:
103 12 0.06
104 5 0.03
105 30 0.16
106 9 0.05
107 27 0.14
108 2 0.01
109 33 0.18
110 6 0.03
111 2 0.01
113 1 0.01
114 35 0.19
115 25 0.13
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.44
Consensus pattern (103 bp):
TATATAAGTTTTCAAAAATACTGTTTTTAAAAACTATATGATTTTCAAAAAATGTTTTCAAAAAT
AATATTATATATAAATTTTCAAAAATGTTTTTAAAAAC
Found at i:208328 original size:18 final size:17
Alignment explanation
Indices: 208282--208363 Score: 57
Period size: 18 Copynumber: 4.9 Consensus size: 17
208272 ACATATTATA
*
208282 TATAAATTTTCAAAAA-
1 TATATATTTTCAAAAAC
* *
208298 TGT-T-TTTTAAAAAAC
1 TATATATTTTCAAAAAC
208313 TATATAATTTTCAAAAA-
1 TATAT-ATTTTCAAAAAC
* *
208330 -ATACTTTTTTTAAAAAC
1 TATA-TATTTTCAAAAAC
208347 TATATGATTTTCAAAAA
1 TATAT-ATTTTCAAAAA
208364 ATGTTTTCAA
Statistics
Matches: 49, Mismatches: 9, Indels: 14
0.68 0.12 0.19
Matches are distributed among these distances:
14 9 0.18
15 2 0.04
16 15 0.31
17 2 0.04
18 21 0.43
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (17 bp):
TATATATTTTCAAAAAC
Found at i:208397 original size:39 final size:38
Alignment explanation
Indices: 208347--208650 Score: 349
Period size: 38 Copynumber: 8.2 Consensus size: 38
208337 TTTTAAAAAC
* * *
208347 TATATGATTTTCAAAAAATGTTTTCAAAAA-TAATATTT
1 TATATAATTTTCAAAAAATGTTTTTAAAAACT-ATATAT
208385 TATATAAGTTTTC-AAAAATGTTTTTAAAAACTATATAT
1 TATATAA-TTTTCAAAAAATGTTTTTAAAAACTATATAT
*
208423 TATATAAATTTCAAAAAATGTTTTTAAAAACTATATAT
1 TATATAATTTTCAAAAAATGTTTTTAAAAACTATATAT
* *
208461 TATATAAATTTCAAAAAATATTTTTAAAAACTATATAT
1 TATATAATTTTCAAAAAATGTTTTTAAAAACTATATAT
* *
208499 TATATAAGTTTTCCAAAAATGATTTTAAAAACTATATAT
1 TATATAA-TTTTCAAAAAATGTTTTTAAAAACTATATAT
** *
208538 TATAT-ATTTTCCTAAAAT-ATTTTAAAAACTATATAT
1 TATATAATTTTCAAAAAATGTTTTTAAAAACTATATAT
* * * *
208574 TATACAGTTTTC---AAGTG-TTTTAAAAACCATATAT
1 TATATAATTTTCAAAAAATGTTTTTAAAAACTATATAT
* *
208608 TATATACATTTT--TAAAATGTTTTTAGAAACTATATAT
1 TATATA-ATTTTCAAAAAATGTTTTTAAAAACTATATAT
208645 TATATA
1 TATATA
208651 CGTATTTTCA
Statistics
Matches: 237, Mismatches: 19, Indels: 21
0.86 0.07 0.08
Matches are distributed among these distances:
34 24 0.10
35 4 0.02
36 26 0.11
37 41 0.17
38 104 0.44
39 38 0.16
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (38 bp):
TATATAATTTTCAAAAAATGTTTTTAAAAACTATATAT
Found at i:208438 original size:76 final size:74
Alignment explanation
Indices: 208083--208650 Score: 369
Period size: 76 Copynumber: 7.8 Consensus size: 74
208073 AACGTTTCTT
* * *
208083 TTTTAAAAACTACATATTATATATAAATTTTCAAAAATGTTTTT-TAAA--A-A-ACTATATAAT
1 TTTTAAAAACTATATA-T-TATAT-AATTTTCAAAAATGTTTTTAAAAACTATATATTATATAAT
*
208143 TTTCAAAAAATAC
63 TTTCAAAAAAT-G
** * * * *
208156 TTTTTTAAA--A-A-ACTATATGATTTTCAAAAAATGTTTTCAAAAA-TAATATTTTATATAAGT
1 TTTTAAAAACTATATATTATATAATTTTC-AAAAATGTTTTTAAAAACT-ATATATTATATAA-T
208216 TTTC-AAAAATG
63 TTTCAAAAAATG
* *
208227 TTTTTAAAAACT-TA-ATT-T-T--TTTT-AAAAACGTTTTTTTTAAAAACTACATATTATATAT
1 -TTTTAAAAACTATATATTATATAATTTTCAAAAA---TGTTTTTAAAAACTATATA-T-TATAT
208285 AAATTTTC-AAAAATG
60 -AATTTTCAAAAAATG
** * * ** * *
208300 TTTTTTAAA--A-A-ACTATATAATTTTCAAAAAATACTTTTT-TTAA--A-A-ACTATATGATT
1 TTTTAAAAACTATATATTATATAATTTTC-AAAAAT-GTTTTTAAAAACTATATATTATATAATT
208356 TTCAAAAAATG
64 TTCAAAAAATG
* *
208367 TTTTCAAAAA-TAATATTTTATATAAGTTTTCAAAAATGTTTTTAAAAACTATATATTATATAAA
1 TTTT-AAAAACT-ATATATTATATAA-TTTTCAAAAATGTTTTTAAAAACTATATATTATATAAT
208431 TTTCAAAAAATG
63 TTTCAAAAAATG
* *
208443 TTTTTAAAAACTATATATTATATAAATTTCAAAAAATATTTTTAAAAACTATATATTATATAAGT
1 -TTTTAAAAACTATATATTATATAATTTTC-AAAAATGTTTTTAAAAACTATATATTATATAA-T
*
208508 TTTCCAAAAATG
63 TTTCAAAAAATG
* * * *
208520 ATTTTAAAAACTATATATTATAT-ATTTTCCTAAAAT-ATTTTAAAAACTATATATTATACAGTT
1 -TTTTAAAAACTATATATTATATAATTTT-CAAAAATGTTTTTAAAAACTATATATTATATAATT
*
208583 TTC---AAGTG
64 TTCAAAAAATG
* * *
208591 TTTTAAAAACCATATATTATATACATTTT-TAAAATGTTTTTAGAAACTATATATTATATA
1 TTTTAAAAACTATATATTATATA-ATTTTCAAAAATGTTTTTAAAAACTATATATTATATA
208651 CGTATTTTCA
Statistics
Matches: 399, Mismatches: 50, Indels: 94
0.73 0.09 0.17
Matches are distributed among these distances:
66 12 0.03
67 32 0.08
68 11 0.03
69 2 0.01
70 38 0.10
71 48 0.12
72 51 0.13
73 38 0.10
74 20 0.05
75 27 0.07
76 81 0.20
77 39 0.10
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (74 bp):
TTTTAAAAACTATATATTATATAATTTTCAAAAATGTTTTTAAAAACTATATATTATATAATTTT
CAAAAAATG
Found at i:208686 original size:2 final size:2
Alignment explanation
Indices: 208675--208703 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
208665 GTTTGCAAAC
208675 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
208704 CAATAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:209511 original size:84 final size:83
Alignment explanation
Indices: 209231--210104 Score: 846
Period size: 84 Copynumber: 10.5 Consensus size: 83
209221 GACAATTTAT
* * * * * * *
209231 TGACAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGTTGAGCGTAGTC
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTC
* ** * *
209296 AAACTTAAATGTATTTGG
66 GAACTCGAAGGTCTTTGG
* * * * * * **
209314 TGGCAGATAACCCTTTTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAAA
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG-CCTTGAAGCTGAGCGTAGT
209379 CGAACTCGAAGGTCTTTGG
65 CGAACTCGAAGGTCTTTGG
* * * * * *
209398 TTGGCAGATAGCCCTTCTCGACTTAAGTTATACTGCAAATGATGTGCCTTGGAGCTGAACGTAGT
1 -TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAGT
209463 CGAACTCGAAGGTCTTTTGG
65 CGAACTCGAAGGTC-TTTGG
* * * * ** * *
209483 TGACAGATAACCATTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCAAAGCTGAGTGTAAT
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG-CCTTGAAGCTGAGCGTAGT
**
209548 CGAACTCGGGGGTCTTT-G
65 CGAACTCGAAGGTCTTTGG
* * * * * *
209566 -GA-AGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCAGAACGTAGTC
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTC
209629 GAACTCGAAGGTCTTTTGG
66 GAACTCGAAGGTC-TTTGG
* * * * *
209648 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCTTGGAGCTGAGCGTAGTC
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTC
* *
209713 AAACTCGAAAGTCTTTGG
66 GAACTCGAAGGTCTTTGG
* * * * *
209731 TTGGA-AGATAACCCTTCTCGACTTAAGTTTTGCTGCAAATGACGTGCCATCGAAGCTGAGTGTA
1 -T-GACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCC-TTGAAGCTGAGCGTA
* **
209795 ATCGAACTCGGGGGTCTTT-G
63 GTCGAACTCGAAGGTCTTTGG
* * * *
209815 -G-CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTT-AAGATGAGCGTAGT
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCC-TTGAAGCTGAGCGTAGT
* * *
209877 CGAACTCAAAGGTCGTGTGT
65 CGAACTCGAAGGTC-TTTGG
* * * * *
209897 TGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTC
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTC
209962 GAACTCGAAGGTCTTTGG
66 GAACTCGAAGGTCTTTGG
* * * * * * * *
209980 TGACAGATAACCCTTATAGCCTTGAGTTATGCTGTAAATGATATGCCTTCGAAGTTGAGTGTAAT
1 TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTT-GAAGCTGAGCGTAGT
*
210045 CGAACTCGAAGGTCTTTTG
65 CGAACTCGAAGGTCTTTGG
* * * *
210064 TTAGCAGATAACCCTTCTCGACTTAAGTTATACTGTAAATG
1 TGA-CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATG
210105 TTGTCTTAAA
Statistics
Matches: 643, Mismatches: 129, Indels: 36
0.80 0.16 0.04
Matches are distributed among these distances:
80 46 0.07
81 80 0.12
82 3 0.00
83 96 0.15
84 289 0.45
85 129 0.20
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (83 bp):
TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTC
GAACTCGAAGGTCTTTGG
Found at i:209664 original size:249 final size:247
Alignment explanation
Indices: 209314--210104 Score: 1003
Period size: 249 Copynumber: 3.2 Consensus size: 247
209304 ATGTATTTGG
* * * * * * * * * **
209314 TGGCAGATAACCCTTTTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAAA
1 TGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGAAGCAGAGCGTAGT
* * * *
209379 CGAACTCGAAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGTTATACTGCAAATGATGTG
65 CGAACTCGAAGGTCTTTGG-TGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATG
* *
209444 CCTTGGAGCTGAACGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCATTCTAGCCTTGAG
129 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGACAGATAACCCTTCTAGCCTTGAG
* *
209509 TTATGCTGTAAATGATGTGCCCTCAAAGCTGAGTGTAATCGAACTCGGGGGTCTT
193 TTATGCTGTAAATGATGTGCCATCGAAGCTGAGTGTAATCGAACTCGGGGGTCTT
* * *
209564 TGGAAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCAGAACGTAGTC
1 TGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGAAGCAGAGCGTAGTC
* * * *
209629 GAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGC
66 GAACTCGAAGGTC-TTTGGTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGC
* * * * *
209694 CTTGGAGCTGAGCGTAGTCAAACTCGAAAGTCTTTGGTTGGA-AGATAACCCTTCTCGACTTAAG
130 CTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-T-GACAGATAACCCTTCTAGCCTTGAG
* * *
209758 TTTTGCTGCAAATGACGTGCCATCGAAGCTGAGTGTAATCGAACTCGGGGGTCTT
193 TTATGCTGTAAATGATGTGCCATCGAAGCTGAGTGTAATCGAACTCGGGGGTCTT
209813 TGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTT-AAG-ATGAGCGTAG
1 TGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC-TTGAAGCA-GAGCGTAG
* * * * *
209876 TCGAACTCAAAGGTCGTGTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATAT
64 TCGAACTCGAAGGTC-TTTGGTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATAT
*
209941 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTATAGCCTTGAG
128 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAG
* * * **
210006 TTATGCTGTAAATGATATGCCTTCGAAGTTGAGTGTAATCGAACTCGAAGGTCTTT
193 TTATGCTGTAAATGATGTGCCATCGAAGCTGAGTGTAATCGAACTCGGGGGTC-TT
* * * *
210062 TGTTAGCAGATAACCCTTCTCGACTTAAGTTATACTGTAAATG
1 TG---GCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATG
210105 TTGTCTTAAA
Statistics
Matches: 466, Mismatches: 65, Indels: 18
0.85 0.12 0.03
Matches are distributed among these distances:
247 2 0.00
248 70 0.15
249 313 0.67
250 47 0.10
252 34 0.07
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.30
Consensus pattern (247 bp):
TGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGAAGCAGAGCGTAGTC
GAACTCGAAGGTCTTTGGTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCC
TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTA
TGCTGTAAATGATGTGCCATCGAAGCTGAGTGTAATCGAACTCGGGGGTCTT
Found at i:209705 original size:333 final size:330
Alignment explanation
Indices: 209235--210104 Score: 1080
Period size: 333 Copynumber: 2.6 Consensus size: 330
209225 ATTTATTGAC
* * * * *
209235 AGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGTTGAGCGTAGTCAAAC
1 AGATAGCCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
** * * * * * * *
209300 TTAAATGTATTTGGTGGCAGATAACCCTTTTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCG
66 TCGAAGGTCTTTGGTGACAGATAACCCTTATAGCCTTGAGTTATGCTGTAAATGATATG-CCTTG
* *
209365 AAGCTGAGTGTAAACGAACTCGAAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGTTATA
130 AAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATA
* * * *
209430 CTGCAAATGATGTGCC-TTGGAGCTGAACGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAAC
195 CTGCAAATGACGTGCCATCGAAGCTGAACGTAATCGAACTCGAAGGTC-TTT-G-G-CAGATAAC
* * * * * *
209494 CATTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCAAAGCTGAGTGTAATCGAACTC-GGG
256 CATTCTAGACTTAAGCTATGCTGCAAATGATGTGCCCT-AAAGATGAGCGTAATCGAACTCAGGG
*
209558 GGTCT-TTGGA
320 CGTCTGTTGGA
* * *
209568 AGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCAGAACGTAGTCGAAC
1 AGATAGCCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
*
209633 TCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCTTG
66 TCGAAGGTC-TTTGGTGACAGATAACCCTTATAGCCTTGAGTTATGCTGTAAATGATATGCCTTG
* * * * * * * *
209698 GAGCTGAGCGTAGTCAAACTCGAAAGTCTTTGGTTGGAAGATAACCCTTCTCGACTTAAGTTTTG
130 AAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATA
** ** * *
209763 CTGCAAATGACGTGCCATCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTT
195 CTGCAAATGACGTGCCATCGAAGCTGAACGTAATCGAACTCGAAGGTCTTTGGCAGATAACCATT
* * * * *
209828 CTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTAAGATGAGCGTAGTCGAACTCAAAGGTCGT
260 CTAGACTTAAGCTATGCTGCAAATGATGTGCCCTAAAGATGAGCGTAATCGAACTC--AGGGCGT
* *
209893 GTGTTGGC
323 CTGTTGGA
* * * * *
209901 AGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAAC
1 AGATAGCCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
209966 TCGAAGGTCTTTGGTGACAGATAACCCTTATAGCCTTGAGTTATGCTGTAAATGATATGCCTTCG
66 TCGAAGGTCTTTGGTGACAGATAACCCTTATAGCCTTGAGTTATGCTGTAAATGATATGCCTT-G
* * *
210031 AAGTTGAGTGTAATCGAACTCGAAGGTCTTTTGTTAGCAGATAACCCTTCTCGACTTAAGTTATA
130 AAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATA
*
210096 CTGTAAATG
195 CTGCAAATG
210105 TTGTCTTAAA
Statistics
Matches: 459, Mismatches: 71, Indels: 14
0.84 0.13 0.03
Matches are distributed among these distances:
329 18 0.04
330 38 0.08
331 1 0.00
332 59 0.13
333 273 0.59
334 70 0.15
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (330 bp):
AGATAGCCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
TCGAAGGTCTTTGGTGACAGATAACCCTTATAGCCTTGAGTTATGCTGTAAATGATATGCCTTGA
AGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATAC
TGCAAATGACGTGCCATCGAAGCTGAACGTAATCGAACTCGAAGGTCTTTGGCAGATAACCATTC
TAGACTTAAGCTATGCTGCAAATGATGTGCCCTAAAGATGAGCGTAATCGAACTCAGGGCGTCTG
TTGGA
Found at i:215358 original size:24 final size:25
Alignment explanation
Indices: 215331--215390 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 25
215321 AAAAATATTT
* *
215331 AAATAAAGA-AAAAACATAAGAACA
1 AAATAAAGATAAAAACAAAAGAAAA
215355 AAAT-AAGATAAAAACAAAAGAAAA
1 AAATAAAGATAAAAACAAAAGAAAA
*
215379 AAATAATGATAA
1 AAATAAAGATAA
215391 TTAAATAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 4 0.13
24 21 0.68
25 6 0.19
ACGTcount: A:0.75, C:0.05, G:0.08, T:0.12
Consensus pattern (25 bp):
AAATAAAGATAAAAACAAAAGAAAA
Found at i:215362 original size:11 final size:11
Alignment explanation
Indices: 215331--215384 Score: 54
Period size: 12 Copynumber: 4.5 Consensus size: 11
215321 AAAAATATTT
215331 AAATAAAGAAAA
1 AAAT-AAGAAAA
*
215343 AACATAAGAACA
1 AA-ATAAGAAAA
215355 AAATAAGATAAA
1 AAATAAGA-AAA
*
215367 AACAAAAGAAAA
1 AA-ATAAGAAAA
215379 AAATAA
1 AAATAA
215385 TGATAATTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
11 9 0.26
12 19 0.54
13 7 0.20
ACGTcount: A:0.78, C:0.06, G:0.07, T:0.09
Consensus pattern (11 bp):
AAATAAGAAAA
Found at i:215510 original size:19 final size:19
Alignment explanation
Indices: 215475--215534 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
215465 ATGTAAAAGT
215475 AAAAATAGAAATAGAAAGGA
1 AAAAATA-AAATAGAAAGGA
*
215495 AAAAATAAAA-AGGAAATGA
1 AAAAATAAAATA-GAAAGGA
*
215514 AAAGAT-AAATCA-AAAGGA
1 AAAAATAAAAT-AGAAAGGA
215532 AAA
1 AAA
215535 CAAATGCAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
18 12 0.35
19 14 0.41
20 8 0.24
ACGTcount: A:0.72, C:0.02, G:0.17, T:0.10
Consensus pattern (19 bp):
AAAAATAAAATAGAAAGGA
Found at i:215565 original size:16 final size:16
Alignment explanation
Indices: 215544--215577 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
215534 ACAAATGCAG
*
215544 AATAAATAAAAAGGAA
1 AATAAATAAAAAAGAA
215560 AATAAATAAAAAAGAA
1 AATAAATAAAAAAGAA
215576 AA
1 AA
215578 AACGAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (16 bp):
AATAAATAAAAAAGAA
Found at i:216802 original size:7 final size:7
Alignment explanation
Indices: 216787--216848 Score: 65
Period size: 7 Copynumber: 8.7 Consensus size: 7
216777 AAATAAATGG
*
216787 ATAAGAA
1 ATAATAA
216794 ATAATAA
1 ATAATAA
216801 ATAAT-A
1 ATAATAA
216807 ATAAT-A
1 ATAATAA
216813 ATAATAA
1 ATAATAA
*
216820 ATAACAATA
1 ATAA-TA-A
216829 ATAAATAA
1 AT-AATAA
216837 ATAATAA
1 ATAATAA
216844 ATAAT
1 ATAAT
216849 TATATTAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
6 12 0.25
7 26 0.54
8 4 0.08
9 4 0.08
10 2 0.04
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (7 bp):
ATAATAA
Found at i:216806 original size:3 final size:3
Alignment explanation
Indices: 216793--216848 Score: 58
Period size: 3 Copynumber: 17.0 Consensus size: 3
216783 ATGGATAAGA
*
216793 AAT AAT AAAT AAT AAT AAT AAT AAT AAAT AAC AAT AAT AAAT AAAT AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT -AAT -AAT AAT
216842 AAAT AAT
1 -AAT AAT
216849 TATATTAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
3 31 0.66
4 16 0.34
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:216961 original size:33 final size:32
Alignment explanation
Indices: 216912--217003 Score: 96
Period size: 35 Copynumber: 2.8 Consensus size: 32
216902 CTTCATATTA
216912 TATATAAATTTT-AAAAAATGTTTTTTAAAAAAC
1 TATAT-AATTTTCAAAAAATGTTTTTT-AAAAAC
*
216945 TATATAATTTTCAAAAAAAATACTTTTTTAAAAAC
1 TATATAATTTTC--AAAAAAT-GTTTTTTAAAAAC
* **
216980 TATATGATTTTCTTAAAATGTTTT
1 TATATAATTTTCAAAAAATGTTTT
217004 CAAAAATTAT
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
32 10 0.20
33 10 0.20
35 24 0.48
36 6 0.12
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (32 bp):
TATATAATTTTCAAAAAATGTTTTTTAAAAAC
Found at i:216963 original size:35 final size:35
Alignment explanation
Indices: 216924--216991 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 35
216914 TATAAATTTT
*
216924 AAAAAAT-GTTTTTTAAAAAACTATATAATTTTCAA
1 AAAAAATACTTTTTT-AAAAACTATATAATTTTCAA
*
216959 AAAAAATACTTTTTTAAAAACTATATGATTTTC
1 AAAAAATACTTTTTTAAAAACTATATAATTTTC
216992 TTAAAATGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 24 0.80
36 6 0.20
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.41
Consensus pattern (35 bp):
AAAAAATACTTTTTTAAAAACTATATAATTTTCAA
Found at i:217036 original size:38 final size:36
Alignment explanation
Indices: 216980--217245 Score: 279
Period size: 38 Copynumber: 7.2 Consensus size: 36
216970 TTTTAAAAAC
* * * *
216980 TATATGATTTTCTTAAAATGTTTTCAAAAATTATATTT
1 TATATAATTTTC-AAAAATGTTTT-AAAAACTATATAT
217018 TATATAAGTTTTCAAAAATGTTTTTAAAAACTATATAT
1 TATATAA-TTTTCAAAAATG-TTTTAAAAACTATATAT
* *
217056 TATATAAATTTCAAAAAATATTTTTAAAAACTATATAT
1 TATATAATTTTC-AAAAAT-GTTTTAAAAACTATATAT
217094 TATATAAGTTTTCCAAAAATGATTTTAAAAACTATATAT
1 TATATAA-TTTT-CAAAAATG-TTTTAAAAACTATATAT
* *
217133 TATAT-ATTTTCCTAAAATATTTTAAAAACTATATAT
1 TATATAATTTT-CAAAAATGTTTTAAAAACTATATAT
* * *
217169 TATATAGTTTTC--AAGTGTTTTAAAAACCATATAT
1 TATATAATTTTCAAAAATGTTTTAAAAACTATATAT
* *
217203 TATATACATTTT-TAAAATGTTTTTAGAAACTATATAT
1 TATATA-ATTTTCAAAAATG-TTTTAAAAACTATATAT
217240 TATATA
1 TATATA
217246 CGTATTTTCA
Statistics
Matches: 198, Mismatches: 18, Indels: 25
0.82 0.07 0.10
Matches are distributed among these distances:
34 25 0.13
35 4 0.02
36 27 0.14
37 40 0.20
38 61 0.31
39 40 0.20
40 1 0.01
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (36 bp):
TATATAATTTTCAAAAATGTTTTAAAAACTATATAT
Found at i:217270 original size:37 final size:37
Alignment explanation
Indices: 216980--217284 Score: 238
Period size: 38 Copynumber: 8.1 Consensus size: 37
216970 TTTTAAAAAC
* * *
216980 TATATGATTTTCTTAAAATGTTTTCAAAAATTATATTTTA
1 TATACGATTTTC--AAAATGTTTT-AAAAACTATATATTA
*
217020 TATAAG-TTTTCAAAAATGTTTTTAAAAACTATATATTA
1 TATACGATTTTC-AAAATG-TTTTAAAAACTATATATTA
* *
217058 TATA--AATTTCAAAAAATATTTTTAAAAACTATATATTA
1 TATACGATTTTC--AAAAT-GTTTTAAAAACTATATATTA
*
217096 TATAAG-TTTTCCAAAAATGATTTTAAAAACTATATATTA
1 TATACGATTTT-C-AAAATG-TTTTAAAAACTATATATTA
*
217135 TAT---ATTTTCCTAAAATATTTTAAAAACTATATATTA
1 TATACGATTTT-C-AAAATGTTTTAAAAACTATATATTA
* *
217171 TATA-G-TTTTC-AAGTGTTTTAAAAACCATATATTA
1 TATACGATTTTCAAAATGTTTTAAAAACTATATATTA
* *
217205 TATAC-ATTTTTAAAATGTTTTTAGAAACTATATATTA
1 TATACGATTTTCAAAATG-TTTTAAAAACTATATATTA
** *
217242 TATACGTATTTTCAAACCG-TTTACAAACTATAATATATA
1 TATACG-ATTTTCAAAATGTTTTAAAAACTAT-ATAT-TA
217281 TATA
1 TATA
217285 TATATATATA
Statistics
Matches: 225, Mismatches: 21, Indels: 39
0.79 0.07 0.14
Matches are distributed among these distances:
34 25 0.11
35 4 0.02
36 27 0.12
37 52 0.23
38 56 0.25
39 55 0.24
40 6 0.03
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (37 bp):
TATACGATTTTCAAAATGTTTTAAAAACTATATATTA
Found at i:217281 original size:2 final size:2
Alignment explanation
Indices: 217270--217308 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
217260 GTTTACAAAC
217270 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
217309 CAATAATAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:222167 original size:22 final size:22
Alignment explanation
Indices: 222140--222214 Score: 150
Period size: 22 Copynumber: 3.4 Consensus size: 22
222130 AATATCAAAT
222140 AATATATTTATAAAAATATTAA
1 AATATATTTATAAAAATATTAA
222162 AATATATTTATAAAAATATTAA
1 AATATATTTATAAAAATATTAA
222184 AATATATTTATAAAAATATTAA
1 AATATATTTATAAAAATATTAA
222206 AATATATTT
1 AATATATTT
222215 TTGATGGAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AATATATTTATAAAAATATTAA
Found at i:222177 original size:14 final size:13
Alignment explanation
Indices: 222140--222214 Score: 66
Period size: 9 Copynumber: 6.7 Consensus size: 13
222130 AATATCAAAT
222140 AATATATTTATAA
1 AATATATTTATAA
222153 AA-ATA--T-TAA
1 AATATATTTATAA
222162 AATATATTTATAA
1 AATATATTTATAA
222175 AA-ATA--T-TAA
1 AATATATTTATAA
222184 AATATATTTATAA
1 AATATATTTATAA
222197 AA-ATA--T-TAA
1 AATATATTTATAA
222206 AATATATTT
1 AATATATTT
222215 TTGATGGAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 23
0.69 0.00 0.31
Matches are distributed among these distances:
9 15 0.29
10 12 0.24
12 12 0.24
13 12 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
AATATATTTATAA
Found at i:224766 original size:3 final size:3
Alignment explanation
Indices: 224758--224790 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
224748 AGAAATAGTA
224758 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
224791 TTCACCCTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:225163 original size:2 final size:2
Alignment explanation
Indices: 225156--225185 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
225146 GGAAAACACA
225156 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
225186 TGAAGGGTCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:228708 original size:60 final size:61
Alignment explanation
Indices: 228582--228722 Score: 146
Period size: 60 Copynumber: 2.3 Consensus size: 61
228572 ATGACTTTCA
* * * **
228582 TTTAAATTA-TTCTTTAACTTTTAAACATTTCAATTTCATCGTCAAAAATATGGCTCTCAT
1 TTTAAATTAGTCCTTAAACTTCTAAACATTTCAATTTCATCGTCAAAAATATGAATCTCAT
* * * *
228642 TATAAATTAGTCCTTAAACTTCTGAACA-TTCGAATTTCATC-TCCAAACTATGAATCTCAT
1 TTTAAATTAGTCCTTAAACTTCTAAACATTTC-AATTTCATCGTCAAAAATATGAATCTCAT
*
228702 TTTAAATT-GATCCCTAAACTT
1 TTTAAATTAG-TCCTTAAACTT
228723 TAGATCTTCT
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
59 1 0.01
60 43 0.64
61 23 0.34
ACGTcount: A:0.34, C:0.19, G:0.06, T:0.41
Consensus pattern (61 bp):
TTTAAATTAGTCCTTAAACTTCTAAACATTTCAATTTCATCGTCAAAAATATGAATCTCAT
Found at i:230896 original size:60 final size:60
Alignment explanation
Indices: 230831--230974 Score: 137
Period size: 60 Copynumber: 2.4 Consensus size: 60
230821 CATACCCAAT
* * *
230831 CTATGACCCTCATT-TCAAATTAGTACCTAAATTTTTAAATATTTCAATTTCATCCTTAAA
1 CTATGACCATCATTCT-AAATTAGTACCTAAACTTTTAAACATTTCAATTTCATCCTTAAA
* * * * * * ** *
230891 CTATGACTATCATTCTAAATTAGTTCTTAAACTTTTGAACATTTCATTTTCGTCCTCGAG
1 CTATGACCATCATTCTAAATTAGTACCTAAACTTTTAAACATTTCAATTTCATCCTTAAA
* * *
230951 CTGTGATCTTCATTCTAAATTAGT
1 CTATGACCATCATTCTAAATTAGT
230975 CCCATGCTTT
Statistics
Matches: 67, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
60 66 0.99
61 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.08, T:0.43
Consensus pattern (60 bp):
CTATGACCATCATTCTAAATTAGTACCTAAACTTTTAAACATTTCAATTTCATCCTTAAA
Found at i:231207 original size:60 final size:59
Alignment explanation
Indices: 231140--231299 Score: 178
Period size: 60 Copynumber: 2.7 Consensus size: 59
231130 GATGAATTTA
* *
231140 GGGATAAAATAGAAATATCTAAAAGTTTAGGGACTAATTTACAATGAGATTCATAGTTTG
1 GGGATAAAATAGAAATGT-TAAAAGTTTAAGGACTAATTTACAATGAGATTCATAGTTTG
* * * * *
231200 GGGATAAAATTGAAATGTTCAAAAGTTTAAAGACTAATTTAGAATGTGATTCATATTTTG
1 GGGATAAAATAGAAATGTT-AAAAGTTTAAGGACTAATTTACAATGAGATTCATAGTTTG
* ** *
231260 AGGATGAAGTTA-AAACGTTTAAAAGTTTAAGGACTAATTT
1 GGGAT-AAAATAGAAATG-TTAAAAGTTTAAGGACTAATTT
231300 GACATAAGAG
Statistics
Matches: 84, Mismatches: 13, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
59 1 0.01
60 78 0.93
61 5 0.06
ACGTcount: A:0.41, C:0.06, G:0.19, T:0.34
Consensus pattern (59 bp):
GGGATAAAATAGAAATGTTAAAAGTTTAAGGACTAATTTACAATGAGATTCATAGTTTG
Found at i:236024 original size:40 final size:40
Alignment explanation
Indices: 235969--236051 Score: 166
Period size: 40 Copynumber: 2.1 Consensus size: 40
235959 TTTGACGTCA
235969 GATGAATGGAGAGGAACGTCAATCTGATGACAAAGTATGG
1 GATGAATGGAGAGGAACGTCAATCTGATGACAAAGTATGG
236009 GATGAATGGAGAGGAACGTCAATCTGATGACAAAGTATGG
1 GATGAATGGAGAGGAACGTCAATCTGATGACAAAGTATGG
236049 GAT
1 GAT
236052 TCGATTTTGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.37, C:0.10, G:0.33, T:0.20
Consensus pattern (40 bp):
GATGAATGGAGAGGAACGTCAATCTGATGACAAAGTATGG
Found at i:239296 original size:73 final size:73
Alignment explanation
Indices: 239186--239328 Score: 277
Period size: 73 Copynumber: 2.0 Consensus size: 73
239176 TATGATGGTA
239186 ACCTTGGAGGTATCCAATCCCATAATCATAGCCTCTAGTGAAACCATGCATGTTGCCTCTTGGAA
1 ACCTTGGAGGTATCCAATCCCATAATCATAGCCTCTAGTGAAACCATGCATGTTGCCTCTTGGAA
239251 TGATTGGG
66 TGATTGGG
*
239259 ACCTTGGAGGTATCCAATCCCATAATCATAGCCTCTAGTGAAAGCATGCATGTTGCCTCTTGGAA
1 ACCTTGGAGGTATCCAATCCCATAATCATAGCCTCTAGTGAAACCATGCATGTTGCCTCTTGGAA
239324 TGATT
66 TGATT
239329 TCCCAATCAC
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 69 1.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (73 bp):
ACCTTGGAGGTATCCAATCCCATAATCATAGCCTCTAGTGAAACCATGCATGTTGCCTCTTGGAA
TGATTGGG
Found at i:239752 original size:16 final size:16
Alignment explanation
Indices: 239731--239761 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
239721 GCTGCCTAAT
239731 AGCCGCCCATGTTGCC
1 AGCCGCCCATGTTGCC
239747 AGCCGCCCATGTTGC
1 AGCCGCCCATGTTGC
239762 TCAAAATCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.13, C:0.42, G:0.26, T:0.19
Consensus pattern (16 bp):
AGCCGCCCATGTTGCC
Found at i:245279 original size:21 final size:21
Alignment explanation
Indices: 245235--245293 Score: 79
Period size: 18 Copynumber: 3.0 Consensus size: 21
245225 GTGCCTGCTA
*
245235 CTGCTGCTACGACGACTGTGG
1 CTGCTGCTACGACTACTGTGG
245256 CTGCT-C--CGACTACTGTGG
1 CTGCTGCTACGACTACTGTGG
*
245274 CTGCTGCTACTACTACTGTG
1 CTGCTGCTACGACTACTGTG
245294 AGTGTTCCTG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 16 0.48
19 1 0.03
20 1 0.03
21 15 0.45
ACGTcount: A:0.14, C:0.31, G:0.27, T:0.29
Consensus pattern (21 bp):
CTGCTGCTACGACTACTGTGG
Found at i:247867 original size:16 final size:16
Alignment explanation
Indices: 247846--247926 Score: 144
Period size: 16 Copynumber: 5.1 Consensus size: 16
247836 CGTTTATTTA
*
247846 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
247862 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
247878 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
247894 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
247910 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
247926 A
1 A
247927 TAAACGTTGG
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 62 1.00
ACGTcount: A:0.57, C:0.22, G:0.12, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:247875 original size:10 final size:10
Alignment explanation
Indices: 247862--247932 Score: 53
Period size: 10 Copynumber: 7.3 Consensus size: 10
247852 ATAAATGAAC
247862 ACGAACATAA
1 ACGAACATAA
247872 ACGAAC----
1 ACGAACATAA
247878 ACGAACATAA
1 ACGAACATAA
**
247888 ACGAACACGA
1 ACGAACATAA
*
247898 AC-ATAAATGAA
1 ACGA-ACAT-AA
247909 CACGAACATAA
1 -ACGAACATAA
247920 ACGAACATAA
1 ACGAACATAA
247930 ACG
1 ACG
247933 TTGGAGACCC
Statistics
Matches: 47, Mismatches: 6, Indels: 16
0.68 0.09 0.23
Matches are distributed among these distances:
6 6 0.13
9 1 0.02
10 31 0.66
11 3 0.06
12 5 0.11
13 1 0.02
ACGTcount: A:0.56, C:0.23, G:0.13, T:0.08
Consensus pattern (10 bp):
ACGAACATAA
Found at i:248682 original size:10 final size:10
Alignment explanation
Indices: 248667--248714 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
248657 ATAAATGAAT
248667 GAACATAAAC
1 GAACATAAAC
248677 GAACATAATCGAAC
1 GAACAT-A---AAC
248691 GAACATAAAC
1 GAACATAAAC
*
248701 GAACATAACC
1 GAACATAAAC
248711 GAAC
1 GAAC
248715 GTTCACGAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 22 0.67
11 1 0.03
13 1 0.03
14 9 0.27
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.10
Consensus pattern (10 bp):
GAACATAAAC
Found at i:248691 original size:14 final size:14
Alignment explanation
Indices: 248674--248704 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
248664 AATGAACATA
*
248674 AACGAACATAATCG
1 AACGAACATAAACG
248688 AACGAACATAAACG
1 AACGAACATAAACG
248702 AAC
1 AAC
248705 ATAACCGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.23, G:0.13, T:0.10
Consensus pattern (14 bp):
AACGAACATAAACG
Found at i:248694 original size:24 final size:24
Alignment explanation
Indices: 248654--248715 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
248644 GATTGTGTTA
*
248654 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
248678 AACATAATCGAACGAACATAAACG
1 AACATAATCGAACGAACATAAACG
*
248702 AACATAACCGAACG
1 AACATAATCGAACG
248716 TTCACGAACG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 3 0.09
24 32 0.91
ACGTcount: A:0.55, C:0.19, G:0.13, T:0.13
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:251821 original size:17 final size:16
Alignment explanation
Indices: 251799--251832 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
251789 AAAACCGATC
*
251799 AAAAAAACTGAAAACCG
1 AAAAAAACCG-AAACCG
251816 AAAAAAACCGAAACCG
1 AAAAAAACCGAAACCG
251832 A
1 A
251833 TTTAGTGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.65, C:0.21, G:0.12, T:0.03
Consensus pattern (16 bp):
AAAAAAACCGAAACCG
Found at i:251829 original size:16 final size:17
Alignment explanation
Indices: 251784--251832 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 17
251774 CCAAAAAATT
251784 AACCGAAAACCGATCAAAAA
1 AACCGAAAACCG---AAAAA
*
251804 AACTGAAAACCGAAAAA
1 AACCGAAAACCGAAAAA
251821 AACCG-AAACCGA
1 AACCGAAAACCGA
251833 TTTAGTGTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 7 0.26
17 9 0.33
20 11 0.41
ACGTcount: A:0.59, C:0.24, G:0.12, T:0.04
Consensus pattern (17 bp):
AACCGAAAACCGAAAAA
Found at i:254664 original size:21 final size:21
Alignment explanation
Indices: 254638--254678 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
254628 CCGCGTAGAA
* *
254638 ATGTCCTGATGGACCACATAG
1 ATGTCCCGAAGGACCACATAG
254659 ATGTCCCGAAGGACCACATA
1 ATGTCCCGAAGGACCACATA
254679 TAACTCATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.27, G:0.22, T:0.20
Consensus pattern (21 bp):
ATGTCCCGAAGGACCACATAG
Found at i:254735 original size:21 final size:21
Alignment explanation
Indices: 254709--254788 Score: 63
Period size: 21 Copynumber: 3.8 Consensus size: 21
254699 ACCACTCCTT
254709 AAGGACTACATATATATTCTA
1 AAGGACTACATATATATTCTA
* * * * *
254730 AAGGACAAAATATGTGTT-TCG
1 AAGGACTACATATATATTCT-A
* * *
254751 AAGAACTACATATATGTTCCA
1 AAGGACTACATATATATTCTA
*
254772 AAGGATTACATATATAT
1 AAGGACTACATATATAT
254789 CCCGAAGGAC
Statistics
Matches: 43, Mismatches: 14, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
20 1 0.02
21 42 0.98
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.31
Consensus pattern (21 bp):
AAGGACTACATATATATTCTA
Found at i:254796 original size:21 final size:21
Alignment explanation
Indices: 254757--254797 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
254747 TTCGAAGAAC
* *
254757 TACATATATGTTCCAAAGGAT
1 TACATATATATCCCAAAGGAT
*
254778 TACATATATATCCCGAAGGA
1 TACATATATATCCCAAAGGA
254798 CCAAGTAGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (21 bp):
TACATATATATCCCAAAGGAT
Found at i:255964 original size:23 final size:23
Alignment explanation
Indices: 255930--255994 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
255920 CACCACAACT
* *
255930 CGTATAAATGCACTGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
255953 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
255976 CGTAGAAATGCACCGAAGT
1 CGTAGAAATGCACCGAAGT
255995 ACCATATAAG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.31, C:0.23, G:0.26, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:256691 original size:35 final size:35
Alignment explanation
Indices: 256645--256714 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
256635 CTGCCATACT
256645 CATAAACATATGTCACTTCTATTATTTCATTTATA
1 CATAAACATATGTCACTTCTATTATTTCATTTATA
256680 CATAAACATATGTCACTTCTATTATTTCATTTATA
1 CATAAACATATGTCACTTCTATTATTTCATTTATA
256715 TACTAATTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.34, C:0.17, G:0.03, T:0.46
Consensus pattern (35 bp):
CATAAACATATGTCACTTCTATTATTTCATTTATA
Found at i:257266 original size:20 final size:20
Alignment explanation
Indices: 257238--257276 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
257228 AACCATGAAA
*
257238 TACATATACAATAACATATC
1 TACACATACAATAACATATC
*
257258 TACACATACCATAACATAT
1 TACACATACAATAACATAT
257277 AACTAGACAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.28
Consensus pattern (20 bp):
TACACATACAATAACATATC
Found at i:258824 original size:20 final size:20
Alignment explanation
Indices: 258799--258875 Score: 109
Period size: 20 Copynumber: 3.8 Consensus size: 20
258789 TTTTAGCTTA
258799 ATAGTATCGATACTCTTACT
1 ATAGTATCGATACTCTTACT
258819 ATAGTATCGATACTCTTACT
1 ATAGTATCGATACTCTTACT
**
258839 ATAGTATCGATACTACCCACCT
1 ATAGTATCGATACT-CTTA-CT
*
258861 ATGGTATCGATACTC
1 ATAGTATCGATACTC
258876 CCCTAGGTAC
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
20 34 0.65
21 3 0.06
22 15 0.29
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (20 bp):
ATAGTATCGATACTCTTACT
Found at i:260342 original size:23 final size:23
Alignment explanation
Indices: 260298--260343 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
260288 TGTAAAGTAT
260298 TATTTATATATTTGAAAAAAAAA
1 TATTTATATATTTGAAAAAAAAA
* *
260321 TATTTGTA-ATTTGAAAACAAAA
1 TATTTATATATTTGAAAAAAAAA
260343 T
1 T
260344 CGACAACAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39
Consensus pattern (23 bp):
TATTTATATATTTGAAAAAAAAA
Found at i:267032 original size:16 final size:17
Alignment explanation
Indices: 267013--267045 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
267003 ATAAAATTTG
*
267013 AATATATAAAA-ATTAA
1 AATAAATAAAATATTAA
267029 AATAAATAAAATATTAA
1 AATAAATAAAATATTAA
267046 TATTTTAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AATAAATAAAATATTAA
Found at i:276154 original size:3 final size:3
Alignment explanation
Indices: 276148--276214 Score: 70
Period size: 3 Copynumber: 23.7 Consensus size: 3
276138 AATAATATAG
* * *
276148 TAT TAT T-T TAT TA- TAT TAA TAT TAT TAT TAT TA- TAT TAC AAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
276193 TAT TAT CA- TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
276215 CCAATATTAC
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
2 7 0.13
3 45 0.87
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:276180 original size:20 final size:20
Alignment explanation
Indices: 276148--276214 Score: 93
Period size: 20 Copynumber: 3.4 Consensus size: 20
276138 AATAATATAG
276148 TATTATT-TTATTATATTAA
1 TATTATTATTATTATATTAA
276167 TATTATTATTATTATATTACA
1 TATTATTATTATTATATTA-A
* *
276188 -ATTATTATTATCATATTAT
1 TATTATTATTATTATATTAA
276207 TATTATTA
1 TATTATTA
276215 CCAATATTAC
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
19 7 0.16
20 35 0.81
21 1 0.02
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (20 bp):
TATTATTATTATTATATTAA
Found at i:277901 original size:9 final size:9
Alignment explanation
Indices: 277887--277919 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
277877 TATCTTATAC
277887 TAATTAATT
1 TAATTAATT
277896 TAATTAATT
1 TAATTAATT
*
277905 TTA-TAATT
1 TAATTAATT
277913 TAATTAA
1 TAATTAA
277920 AGAATAACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
TAATTAATT
Found at i:284162 original size:1 final size:1
Alignment explanation
Indices: 284156--284237 Score: 119
Period size: 1 Copynumber: 82.0 Consensus size: 1
284146 ACATCAGAGG
* * * *
284156 AAAAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAGAAAAAAAAAAAAAAGA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
284221 AAAAAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAA
284238 GAAATTGAAT
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 71 1.00
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (1 bp):
A
Found at i:284188 original size:24 final size:24
Alignment explanation
Indices: 284156--284237 Score: 137
Period size: 24 Copynumber: 3.4 Consensus size: 24
284146 ACATCAGAGG
284156 AAAAAAAAAAAAAAGAAAAAAAAAA
1 AAAAAAAAAAAAAAG-AAAAAAAAA
*
284181 AAAAAAAAAAAAAAGAAAAAAAAG
1 AAAAAAAAAAAAAAGAAAAAAAAA
284205 AAAAAAAAAAAAAAGAAAAAAAAA
1 AAAAAAAAAAAAAAGAAAAAAAAA
*
284229 AAGAAAAAA
1 AAAAAAAAA
284238 GAAATTGAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
24 39 0.72
25 15 0.28
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (24 bp):
AAAAAAAAAAAAAAGAAAAAAAAA
Found at i:284190 original size:25 final size:25
Alignment explanation
Indices: 284156--284237 Score: 139
Period size: 25 Copynumber: 3.3 Consensus size: 25
284146 ACATCAGAGG
284156 AAAAAAAAAAAAAAGAAAAAAAAAA
1 AAAAAAAAAAAAAAGAAAAAAAAAA
*
284181 AAAAAAAAAAAAAAG-AAAAAAAAG
1 AAAAAAAAAAAAAAGAAAAAAAAAA
284205 AAAAAAAAAAAAAAGAAAAAAAAAA
1 AAAAAAAAAAAAAAGAAAAAAAAAA
*
284230 AGAAAAAA
1 AAAAAAAA
284238 GAAATTGAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
24 23 0.43
25 30 0.57
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (25 bp):
AAAAAAAAAAAAAAGAAAAAAAAAA
Found at i:284200 original size:34 final size:34
Alignment explanation
Indices: 284157--284241 Score: 145
Period size: 34 Copynumber: 2.5 Consensus size: 34
284147 CATCAGAGGA
284157 AAAAAAAAAAAAAGAAAAAAAAAAAAAA-AAAAA
1 AAAAAAAAAAAAAGAAAAAAAAAAAAAAGAAAAA
284190 AAAAAGAAAAAAAAGAAAAAAAAAAAAAAGAAAAA
1 AAAAA-AAAAAAAAGAAAAAAAAAAAAAAGAAAAA
*
284225 AAAAAAGAAAAAAGAAA
1 AAAAAAAAAAAAAGAAA
284242 TTGAATCAAG
Statistics
Matches: 49, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
33 5 0.10
34 34 0.69
35 10 0.20
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (34 bp):
AAAAAAAAAAAAAGAAAAAAAAAAAAAAGAAAAA
Found at i:287354 original size:3 final size:3
Alignment explanation
Indices: 287348--287428 Score: 121
Period size: 3 Copynumber: 27.7 Consensus size: 3
287338 TCCAATAATA
*
287348 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
287395 AAT TAT TAT TAT CA- TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
287429 CAAATATTAC
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
2 3 0.04
3 68 0.96
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:287865 original size:18 final size:18
Alignment explanation
Indices: 287842--287876 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
287832 ATTTCCCTAA
287842 AAAAAGGA-ACACAACGGG
1 AAAAAGGAGA-ACAACGGG
287860 AAAAAGGAGAACAACGG
1 AAAAAGGAGAACAACGG
287877 CAAGAACGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.94
19 1 0.06
ACGTcount: A:0.57, C:0.14, G:0.29, T:0.00
Consensus pattern (18 bp):
AAAAAGGAGAACAACGGG
Found at i:289179 original size:9 final size:9
Alignment explanation
Indices: 289165--289197 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
289155 TATCTTATAC
289165 TAATTAATT
1 TAATTAATT
289174 TAATTAATT
1 TAATTAATT
*
289183 TTA-TAATT
1 TAATTAATT
289191 TAATTAA
1 TAATTAA
289198 AGAATAACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
TAATTAATT
Found at i:293103 original size:31 final size:31
Alignment explanation
Indices: 293041--293104 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
293031 GGAAGATTGT
**
293041 TGAAAATCAAAGGTTGGCACTGAATGCTGCA
1 TGAAAATCAAAGGTTGGCACCAAATGCTGCA
* *
293072 TGAAAATCAAAGTTTGGCACCAAATGGTGCA
1 TGAAAATCAAAGGTTGGCACCAAATGCTGCA
293103 TG
1 TG
293105 GTCAAAAGCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (31 bp):
TGAAAATCAAAGGTTGGCACCAAATGCTGCA
Found at i:297335 original size:36 final size:36
Alignment explanation
Indices: 297288--297360 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
297278 GTTGACATGA
* * *
297288 ACTATGCTAAATTCTAAGTTTAGTGTGTATATTTAT
1 ACTATGCTAAATTCGAAGTTTAGTGTGCATATATAT
*
297324 ACTATGCTAAATTCGAAGTTTATTGTGCATATATAT
1 ACTATGCTAAATTCGAAGTTTAGTGTGCATATATAT
297360 A
1 A
297361 TATATAGACA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.44
Consensus pattern (36 bp):
ACTATGCTAAATTCGAAGTTTAGTGTGCATATATAT
Found at i:298526 original size:21 final size:21
Alignment explanation
Indices: 298479--298527 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
298469 TGCAGAGGAA
298479 GAAGAAGAAATAATGGATGAAG
1 GAAGAAGAAATAA-GGATGAAG
*
298501 G-AGAAGAAATGA-GATGAGAG
1 GAAGAAGAAATAAGGATGA-AG
298521 GAAGAAG
1 GAAGAAG
298528 TGCACAGCCC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 5 0.21
20 3 0.12
21 15 0.62
22 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.37, T:0.10
Consensus pattern (21 bp):
GAAGAAGAAATAAGGATGAAG
Found at i:300073 original size:46 final size:46
Alignment explanation
Indices: 300006--300099 Score: 179
Period size: 46 Copynumber: 2.0 Consensus size: 46
299996 CTGAGACCCG
300006 ACCCGACCAAAACAAGTTTTCACCCGACCCGATATATAACTTAAAA
1 ACCCGACCAAAACAAGTTTTCACCCGACCCGATATATAACTTAAAA
*
300052 ACCCGACCAAAATAAGTTTTCACCCGACCCGATATATAACTTAAAA
1 ACCCGACCAAAACAAGTTTTCACCCGACCCGATATATAACTTAAAA
300098 AC
1 AC
300100 TCGGCCGACT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.41, C:0.30, G:0.09, T:0.20
Consensus pattern (46 bp):
ACCCGACCAAAACAAGTTTTCACCCGACCCGATATATAACTTAAAA
Found at i:300077 original size:21 final size:21
Alignment explanation
Indices: 300006--300080 Score: 60
Period size: 21 Copynumber: 3.4 Consensus size: 21
299996 CTGAGACCCG
*
300006 ACCCGACCAAAACAAGTTTTC
1 ACCCGACCAAAATAAGTTTTC
* * ***
300027 ACCCGACCCGATATATAACTTAAAA
1 ACCCGA-CC-A-AAATAAGTT-TTC
300052 ACCCGACCAAAATAAGTTTTC
1 ACCCGACCAAAATAAGTTTTC
300073 ACCCGACC
1 ACCCGACC
300081 CGATATATAA
Statistics
Matches: 39, Mismatches: 11, Indels: 8
0.67 0.19 0.14
Matches are distributed among these distances:
21 14 0.36
22 9 0.23
23 2 0.05
24 8 0.21
25 6 0.15
ACGTcount: A:0.39, C:0.33, G:0.09, T:0.19
Consensus pattern (21 bp):
ACCCGACCAAAATAAGTTTTC
Found at i:301988 original size:2 final size:2
Alignment explanation
Indices: 301981--302065 Score: 156
Period size: 2 Copynumber: 43.5 Consensus size: 2
301971 TATAACATCA
301981 AT AT AT AT AT AT AT AT AT AT -T 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
302022 AT AT AT AT A- 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
302063 AT A
1 AT A
302066 ACATAAAATT
Statistics
Matches: 81, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 2 0.02
2 79 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:315606 original size:35 final size:35
Alignment explanation
Indices: 315560--315626 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
315550 AGTCGATTAA
**
315560 TTATTATCTTTGCAATGGAACTTATGGATTCAGAC
1 TTATTATCTTTGCAATCAAACTTATGGATTCAGAC
315595 TTATTATCTTTGCAATCAAACTTATGGATTCA
1 TTATTATCTTTGCAATCAAACTTATGGATTCA
315627 TGCTTAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (35 bp):
TTATTATCTTTGCAATCAAACTTATGGATTCAGAC
Found at i:318575 original size:5 final size:5
Alignment explanation
Indices: 318565--318589 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
318555 CGAGGTAATT
318565 TCCCC TCCCC TCCCC TCCCC TCCCC
1 TCCCC TCCCC TCCCC TCCCC TCCCC
318590 CTTGTTGCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.80, G:0.00, T:0.20
Consensus pattern (5 bp):
TCCCC
Found at i:320685 original size:23 final size:24
Alignment explanation
Indices: 320650--320710 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
320640 TGAATAAGAA
320650 TCTCTG-TCATTGTGACACAT-TTT
1 TCTCTGCTC-TTGTGACACATGTTT
*
320673 TTTCTGCTCTTGTGACACATGTTT
1 TCTCTGCTCTTGTGACACATGTTT
320697 TCTCTGCTCTTGTG
1 TCTCTGCTCTTGTG
320711 GCACGATCCA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
23 16 0.47
24 18 0.53
ACGTcount: A:0.11, C:0.23, G:0.16, T:0.49
Consensus pattern (24 bp):
TCTCTGCTCTTGTGACACATGTTT
Found at i:322220 original size:17 final size:18
Alignment explanation
Indices: 322198--322231 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
322188 TTGATTTTTT
322198 TTTCAAAATTTG-GTTTA
1 TTTCAAAATTTGTGTTTA
322215 TTTCAAAATTTGTGTTT
1 TTTCAAAATTTGTGTTT
322232 TCTTTATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.26, C:0.06, G:0.12, T:0.56
Consensus pattern (18 bp):
TTTCAAAATTTGTGTTTA
Found at i:327891 original size:54 final size:54
Alignment explanation
Indices: 327669--327903 Score: 238
Period size: 54 Copynumber: 4.3 Consensus size: 54
327659 CTGAATCCAT
* * * *
327669 AGCACCTCTTTTCTTCAATCGAGAACTGACACCTCTGTGTAGCCAAAAGTGATTG
1 AGCACCTCTGTGCTTCAATCGAGAACTGACACCTCTGTGCAGCCAAAA-TGACTG
* **
327724 AGCACCTGTGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAATGACTG
1 AGCACCTCTGTGCTTCAATCGAGAACTGACACCTCTGTGCAG---CCAAAATGACTG
** * * * * * * *
327781 AGCACCTCTGTGCTTCAGCCGAGAGCTGACACCTCTGTGTATCTAAGACGATTG
1 AGCACCTCTGTGCTTCAATCGAGAACTGACACCTCTGTGCAGCCAAAATGACTG
* * *
327835 AGCACCTCTGTGCTTCAAACGATG-ACTGAAATCTCTGTGCAGCCAAAATGACTG
1 AGCACCTCTGTGCTTCAATCGA-GAACTGACACCTCTGTGCAGCCAAAATGACTG
*
327889 AGCACCTCTATGCTT
1 AGCACCTCTGTGCTT
327904 TTACAAATGA
Statistics
Matches: 146, Mismatches: 30, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
54 62 0.42
55 39 0.27
57 41 0.28
58 4 0.03
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.26
Consensus pattern (54 bp):
AGCACCTCTGTGCTTCAATCGAGAACTGACACCTCTGTGCAGCCAAAATGACTG
Found at i:327897 original size:27 final size:27
Alignment explanation
Indices: 327771--327897 Score: 66
Period size: 27 Copynumber: 4.7 Consensus size: 27
327761 TGCAGTTAAA
327771 AAAATGACTGAGCACCTCTGTGCTTCAGCC
1 AAAATGACTGAGCACCTCTGTG---CAGCC
* * * * *
327801 GAGA-G-CTGA-CACCTCTGTGTATCT
1 AAAATGACTGAGCACCTCTGTGCAGCC
* * * **
327825 AAGACGATTGAGCACCTCTGTGC-TTC
1 AAAATGACTGAGCACCTCTGTGCAGCC
* *
327851 AAACGATGACTGA-AATCTCTGTGCAGCC
1 AAA--ATGACTGAGCACCTCTGTGCAGCC
327879 AAAATGACTGAGCACCTCT
1 AAAATGACTGAGCACCTCT
327898 ATGCTTTTAC
Statistics
Matches: 71, Mismatches: 19, Indels: 17
0.66 0.18 0.16
Matches are distributed among these distances:
24 5 0.07
25 1 0.01
26 14 0.20
27 34 0.48
28 14 0.20
29 1 0.01
30 2 0.03
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (27 bp):
AAAATGACTGAGCACCTCTGTGCAGCC
Found at i:328686 original size:29 final size:31
Alignment explanation
Indices: 328629--328697 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 31
328619 GATGGTCACG
*
328629 ACAC-CTAAATGAGTAACGAAATGAAACATT
1 ACACACTAAATGAGTAACAAAATGAAACATT
** *
328659 AGGCACTAAATTAG-AACAAAAT-AAACATT
1 ACACACTAAATGAGTAACAAAATGAAACATT
328688 ACACACTAAA
1 ACACACTAAA
328698 CTGGAAAAAG
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
29 15 0.47
30 9 0.28
31 8 0.25
ACGTcount: A:0.54, C:0.17, G:0.10, T:0.19
Consensus pattern (31 bp):
ACACACTAAATGAGTAACAAAATGAAACATT
Found at i:329060 original size:24 final size:24
Alignment explanation
Indices: 329026--329074 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
329016 AATCATAAGG
*
329026 AACGTGTCACAAGAGCAGAGAAAA
1 AACGTGCCACAAGAGCAGAGAAAA
329050 AACGTGCCACAAGAGCAGAGAAAA
1 AACGTGCCACAAGAGCAGAGAAAA
329074 A
1 A
329075 TGTGTCACAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.51, C:0.18, G:0.24, T:0.06
Consensus pattern (24 bp):
AACGTGCCACAAGAGCAGAGAAAA
Found at i:331494 original size:29 final size:30
Alignment explanation
Indices: 331444--331503 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
331434 ACCTTAATGA
331444 GTAACGAAATTAAACATTAGACACTAAACT
1 GTAACGAAATTAAACATTAGACACTAAACT
**
331474 GTAACGAAA-TAAATGTTAGACACTAAACT
1 GTAACGAAATTAAACATTAGACACTAAACT
331503 G
1 G
331504 AAAAAAGGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
29 19 0.68
30 9 0.32
ACGTcount: A:0.48, C:0.15, G:0.13, T:0.23
Consensus pattern (30 bp):
GTAACGAAATTAAACATTAGACACTAAACT
Found at i:333978 original size:18 final size:18
Alignment explanation
Indices: 333955--333995 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
333945 TAAATGCTGC
333955 TTATAAATGATCTTCCAA
1 TTATAAATGATCTTCCAA
333973 TTATAAATGATCTTCCAA
1 TTATAAATGATCTTCCAA
333991 TTATA
1 TTATA
333996 GGGTATTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.39, C:0.15, G:0.05, T:0.41
Consensus pattern (18 bp):
TTATAAATGATCTTCCAA
Found at i:335707 original size:3 final size:3
Alignment explanation
Indices: 335699--335783 Score: 89
Period size: 3 Copynumber: 27.7 Consensus size: 3
335689 ACGTTATTTA
* * * * *
335699 TAT TAT TAT TAT TAT TAT AAT AAT TAT TAT TAT TAT AAT AAT AAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
335747 TAT TAT TAT TAT TAA TAT ATAT TATT TAT TAA TAT TA
1 TAT TAT TAT TAT TAT TAT -TAT TA-T TAT TAT TAT TA
335784 CAAAACCCAA
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
3 66 0.92
4 6 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:335724 original size:21 final size:21
Alignment explanation
Indices: 335700--335777 Score: 113
Period size: 21 Copynumber: 3.6 Consensus size: 21
335690 CGTTATTTAT
335700 ATTATTATTATTATTATAATA
1 ATTATTATTATTATTATAATA
*
335721 ATTATTATTATTATAATAATA
1 ATTATTATTATTATTATAATA
335742 ATTATTATTATTATTATTAAT-
1 ATTATTATTATTATTA-TAATA
335763 ATATATTATTTATTA
1 AT-TATTA-TTATTA
335778 ATATTACAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
21 37 0.71
22 9 0.17
23 6 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
ATTATTATTATTATTATAATA
Found at i:337898 original size:24 final size:24
Alignment explanation
Indices: 337857--337907 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
337847 TTAATTTATA
*
337857 ATTTTTTTAATATATATACATATT
1 ATTTTTATAATATATATACATATT
* * *
337881 ATTTTTATAGTATTTATATATATT
1 ATTTTTATAATATATATACATATT
337905 ATT
1 ATT
337908 AATATTTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (24 bp):
ATTTTTATAATATATATACATATT
Found at i:337901 original size:22 final size:21
Alignment explanation
Indices: 337850--337912 Score: 58
Period size: 22 Copynumber: 3.0 Consensus size: 21
337840 CATATATTTA
337850 ATTTATA-ATTTTTTTAATAT
1 ATTTATATATTTTTTTAATAT
* *
337870 ATATACATATTATTTTT-ATAGT
1 ATTTATATATT-TTTTTAATA-T
* *
337892 ATTTATATATATTATTAATAT
1 ATTTATATATTTTTTTAATAT
337913 TTCATTTTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
20 5 0.15
21 11 0.33
22 17 0.52
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
ATTTATATATTTTTTTAATAT
Found at i:341162 original size:15 final size:15
Alignment explanation
Indices: 341142--341173 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
341132 GATCAATACC
341142 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
341157 TTTTGCATACATTCA
1 TTTTGCATACATGCA
341172 TT
1 TT
341174 ATTCATTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:348514 original size:8 final size:8
Alignment explanation
Indices: 348503--348557 Score: 65
Period size: 8 Copynumber: 6.6 Consensus size: 8
348493 AGAGAAAAAG
348503 AAAAGAAA
1 AAAAGAAA
*
348511 AAAAGAGA
1 AAAAGAAA
348519 AAAAGAAA
1 AAAAGAAA
*
348527 AAAGGAAA
1 AAAAGAAA
*
348535 AAGAGAAAA
1 AAAAG-AAA
348544 AAGAAGAAA
1 AA-AAGAAA
348553 AAAAG
1 AAAAG
348558 GGGGGTCAAG
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
8 27 0.69
9 10 0.26
10 2 0.05
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (8 bp):
AAAAGAAA
Found at i:348517 original size:21 final size:21
Alignment explanation
Indices: 348492--348557 Score: 91
Period size: 21 Copynumber: 3.1 Consensus size: 21
348482 ATTATGCTTG
348492 AAGAGAAAAAGAAAAGAAAAA
1 AAGAGAAAAAGAAAAGAAAAA
348513 AAGAGAAAAAGAAAA-AAGGAAA
1 AAGAGAAAAAGAAAAGAA--AAA
*
348535 AAGAGAAAAA-AGAAGAAAAA
1 AAGAGAAAAAGAAAAGAAAAA
348555 AAG
1 AAG
348558 GGGGGTCAAG
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
20 8 0.20
21 18 0.44
22 15 0.37
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (21 bp):
AAGAGAAAAAGAAAAGAAAAA
Found at i:348521 original size:15 final size:15
Alignment explanation
Indices: 348497--348553 Score: 64
Period size: 16 Copynumber: 3.7 Consensus size: 15
348487 GCTTGAAGAG
348497 AAAA-AGAAAAGAAA
1 AAAAGAGAAAAGAAA
348511 AAAAGAGAAAAAGAAA
1 AAAAGAG-AAAAGAAA
*
348527 AAAGGA-AAAAGAGAA
1 AAAAGAGAAAAGA-AA
348542 AAAAGAAGAAAA
1 AAAAG-AGAAAA
348554 AAAGGGGGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
14 10 0.28
15 8 0.22
16 14 0.39
17 4 0.11
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAAGAGAAAAGAAA
Found at i:348524 original size:16 final size:16
Alignment explanation
Indices: 348503--348554 Score: 72
Period size: 16 Copynumber: 3.2 Consensus size: 16
348493 AGAGAAAAAG
348503 AAAAGAAAAAAAGAGA
1 AAAAGAAAAAAAGAGA
348519 AAAAG-AAAAAAG-GA
1 AAAAGAAAAAAAGAGA
348533 AAAAGAGAAAAAAGAAGA
1 AAAAGA-AAAAAAG-AGA
348551 AAAA
1 AAAA
348555 AAGGGGGGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
14 7 0.22
15 7 0.22
16 12 0.38
18 6 0.19
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAAAAGAGA
Found at i:349841 original size:83 final size:83
Alignment explanation
Indices: 349702--349921 Score: 386
Period size: 83 Copynumber: 2.7 Consensus size: 83
349692 GAACAAATGC
* *
349702 AATGTACTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
*
349767 TATTGAATTTGAAAGATG
66 CATTGAATTTGAAAGATG
* *
349785 AATGTGCTAATAGCATCTTCTGTAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
349850 CATTGAATTTGAAAGATG
66 CATTGAATTTGAAAGATG
*
349868 AATGTGCTCATAGCATCTTCTGGAAGTGCTCTTTGAGTTATCTGATCTGGTTTG
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
349922 ATATGAAACC
Statistics
Matches: 129, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 129 1.00
ACGTcount: A:0.26, C:0.13, G:0.22, T:0.39
Consensus pattern (83 bp):
AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
CATTGAATTTGAAAGATG
Found at i:351476 original size:338 final size:339
Alignment explanation
Indices: 350859--351496 Score: 1136
Period size: 338 Copynumber: 1.9 Consensus size: 339
350849 GCAAAGATTT
350859 AAATCCATCATTCAATGGATCAACAGTGCCAGTTCGAGTTCATAATGAGAAGAACTCATCCGAAG
1 AAATCCATCATTCAATGGATCAACAGTGCCAGTTCGAGTTCATAATGAGAAGAACTCATCCGAAG
*
350924 AAGGAAAAAGAAGTTCATAATGAGAAGAATTTGTTCAAACTTTTGCTAAAATCCATCACTTGATG
66 AAGGAAAAAGAAGTTCATAATGAGAAGAATTTGTTCAAACCTTTGCTAAAATCCATCACTTGATG
350989 GATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
131 GATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
351054 TAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCCAGTT
196 TAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCCAGTT
* *
351119 CGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
261 AGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
351184 TCAACCTTTTGCTC
326 TCAACCTTTTGCTC
* ** * *
351198 AAATCCATCACTT-GATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAA
1 AAATCCATCA-TTCAATGGATCAACAGTGCCAGTTCGAGTTCATAATGAGAAGAACTCATCCGAA
* *
351262 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC-AACCTTTGCTCAAATCCATCACTTGAT
65 GAAGGAAAAAGAAGTTCATAATGAGAAGAATTTGTTCAAACCTTTGCTAAAATCCATCACTTGAT
*
351326 GGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC
130 GGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTC
* *
351391 ATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATTAGCTTTTCCAGT
195 ATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCCAGT
351456 TAGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAA
260 TAGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAA
351497 CTTGTTCAAC
Statistics
Matches: 285, Mismatches: 13, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
338 191 0.67
339 92 0.32
340 2 0.01
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (339 bp):
AAATCCATCATTCAATGGATCAACAGTGCCAGTTCGAGTTCATAATGAGAAGAACTCATCCGAAG
AAGGAAAAAGAAGTTCATAATGAGAAGAATTTGTTCAAACCTTTGCTAAAATCCATCACTTGATG
GATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
TAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCCAGTT
AGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
TCAACCTTTTGCTC
Found at i:351504 original size:113 final size:113
Alignment explanation
Indices: 350859--351496 Score: 1136
Period size: 113 Copynumber: 5.7 Consensus size: 113
350849 GCAAAGATTT
* ** * *
350859 AAATCCATCA-TTCAATGGATCAACAGTGCCAGTTCGAGTTCATAATGAGAAGAACTCATCCGAA
1 AAATCCATCACTT-GATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAA
* * *
350923 GAAGGAAAAAGAAGTTCATAATGAGAAGAATTTGTTCAAACTTTTGCTA
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
350972 AAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
351037 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
351085 AAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
351150 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
351198 AAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
351263 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACC-TTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
*
351310 AAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
351375 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * *
351423 AAATCCATCACTTGATGGATTAGCTTTTCCAGTTAGAGTTCATAATAAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
351488 AAGGAAGAA
66 AAGGAAGAA
351497 CTTGTTCAAC
Statistics
Matches: 511, Mismatches: 12, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
112 111 0.22
113 398 0.78
114 2 0.00
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (113 bp):
AAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
Found at i:351542 original size:92 final size:93
Alignment explanation
Indices: 351398--351582 Score: 246
Period size: 92 Copynumber: 2.0 Consensus size: 93
351388 TTCATAATGA
* * * * * * ** *
351398 GAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATTAGCTTTTCCAGTTAGAGTT
1 GAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTTAATAGATCAACTTTTACAGAGAAAGTT
351463 CATAATAAGAAGAACTCATCTGAAGAAG
66 CATAATAAGAAGAACTCATCTGAAGAAG
** *
351491 GAAGAACTTGTTCAA-CTTTTGCTTGAATTCATCACTTAATAGATCAACTTTTACAGAGAAAGTT
1 GAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTTAATAGATCAACTTTTACAGAGAAAGTT
*
351555 CATAATGAGAAGAACTCATCTGAAGAAG
66 CATAATAAGAAGAACTCATCTGAAGAAG
351583 AGAAAGTTCA
Statistics
Matches: 79, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
92 65 0.82
93 14 0.18
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (93 bp):
GAAGAACTTGTTCAACCTTTTGCTCAAATCCATCACTTAATAGATCAACTTTTACAGAGAAAGTT
CATAATAAGAAGAACTCATCTGAAGAAG
Found at i:351859 original size:3 final size:3
Alignment explanation
Indices: 351851--351924 Score: 98
Period size: 3 Copynumber: 24.7 Consensus size: 3
351841 ACATTATTTA
*
351851 TAT TAT TAT TAT AAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
351898 TAT TA- TAT ATAT TATT TAT TAA TAT TA
1 TAT TAT TAT -TAT TA-T TAT TAT TAT TA
351925 CAAAACCCAA
Statistics
Matches: 63, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
2 4 0.06
3 53 0.84
4 6 0.10
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:358392 original size:14 final size:14
Alignment explanation
Indices: 358373--358457 Score: 67
Period size: 14 Copynumber: 6.5 Consensus size: 14
358363 AAATAAATTA
358373 AATATTAATTTTTT
1 AATATTAATTTTTT
* *
358387 AATATT-ATATTAT
1 AATATTAATTTTTT
358400 AGATATTAA--TTTT
1 A-ATATTAATTTTTT
*
358413 AATATTAAATTTTT
1 AATATTAATTTTTT
* *
358427 AA-A-TAA--ATTA
1 AATATTAATTTTTT
358437 AATATTAATTTTTT
1 AATATTAATTTTTT
358451 AATATTA
1 AATATTA
358458 TATTATAGAT
Statistics
Matches: 56, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
10 4 0.07
11 1 0.02
12 13 0.23
13 11 0.20
14 26 0.46
15 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (14 bp):
AATATTAATTTTTT
Found at i:358398 original size:26 final size:28
Alignment explanation
Indices: 358352--358423 Score: 86
Period size: 26 Copynumber: 2.8 Consensus size: 28
358342 ATTTTAATAT
358352 TATT-ATTTTTTAA-A-TAAATTA-A-A
1 TATTAATTTTTTAATATTAAATTATAGA
*
358375 TATTAATTTTTTAATATTATATTATAGA
1 TATTAATTTTTTAATATTAAATTATAGA
358403 TATTAA--TTTTAATATTAAATT
1 TATTAATTTTTTAATATTAAATT
358424 TTTAAATAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
23 4 0.10
24 9 0.21
25 1 0.02
26 20 0.48
27 1 0.02
28 7 0.17
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (28 bp):
TATTAATTTTTTAATATTAAATTATAGA
Found at i:358417 original size:40 final size:37
Alignment explanation
Indices: 358373--358457 Score: 100
Period size: 38 Copynumber: 2.2 Consensus size: 37
358363 AAATAAATTA
* *
358373 AATATTAATTTTTTAATATTATATTATAGATATTAA-TTTT
1 AATATTAAATTTTTAA-A-TAAATTA-A-ATATTAATTTTT
358413 AATATTAAATTTTTAAATAAATTAAATATTAATTTTTT
1 AATATTAAATTTTTAAATAAATTAAATATTAA-TTTTT
358451 AATATTA
1 AATATTA
358458 TATTATAGAT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
36 7 0.17
37 1 0.02
38 17 0.41
39 1 0.02
40 15 0.37
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (37 bp):
AATATTAAATTTTTAAATAAATTAAATATTAATTTTT
Found at i:358427 original size:64 final size:65
Alignment explanation
Indices: 358320--358478 Score: 254
Period size: 64 Copynumber: 2.5 Consensus size: 65
358310 TTATATTTAA
* *
358320 TTTT-ATATTATATT-T-GATTTTAATTTTAATATTATTATTTTTTAAATAAATTAAATATTAAT
1 TTTTAATATTATATTATAGATATTAATTTTAATATTA-TAATTTTTAAATAAATTAAATATTAAT
358382 T
65 T
358383 TTTTAATATTATATTATAGATATTAATTTTAATATTA-AATTTTTAAATAAATTAAATATTAATT
1 TTTTAATATTATATTATAGATATTAATTTTAATATTATAATTTTTAAATAAATTAAATATTAATT
358447 TTTTAATATTATATTATAGATATTTAATTTTA
1 TTTTAATATTATATTATAGATA-TTAATTTTA
358479 TATCATATAA
Statistics
Matches: 90, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
63 4 0.04
64 58 0.64
65 10 0.11
66 18 0.20
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (65 bp):
TTTTAATATTATATTATAGATATTAATTTTAATATTATAATTTTTAAATAAATTAAATATTAATT
Found at i:358515 original size:64 final size:62
Alignment explanation
Indices: 358318--358523 Score: 185
Period size: 64 Copynumber: 3.3 Consensus size: 62
358308 TTTTATATTT
* *
358318 AATTTT-ATATTATATT-T-GATTTTAATTTTAATATTATTATTTTTTAAATAAATTAAATATTA
1 AATTTTAATATTATATTATAGATATTAATTTTAATATTA--AATTTTT--ATAAATTAAATATTA
358380 A
62 A
**
358381 TTTTTTAATATTATATTATAGATATTAATTTTAATATTAAATTTTTAAATAAATTAAATATTAA
1 AATTTTAATATTATATTATAGATATTAATTTTAATATTAAATTTTT--ATAAATTAAATATTAA
** * *
358445 TTTTTTAATATTATATTATAGATATTTAATTTTATATCATATAAATTATTT-TATA-T-ATTATT
1 AATTTTAATATTATATTATAGATA-TTAATTTTA-AT-AT-TAAATT-TTTATAAATTAAATATT
358507 AA
61 AA
358509 AATTTT-ATATT-TATT
1 AATTTTAATATTATATT
358524 TTAATTATTT
Statistics
Matches: 127, Mismatches: 8, Indels: 17
0.84 0.05 0.11
Matches are distributed among these distances:
62 4 0.03
63 9 0.07
64 69 0.54
65 11 0.09
66 23 0.18
67 2 0.02
68 6 0.05
69 3 0.02
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (62 bp):
AATTTTAATATTATATTATAGATATTAATTTTAATATTAAATTTTTATAAATTAAATATTAA
Found at i:358546 original size:20 final size:20
Alignment explanation
Indices: 358488--358547 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
358478 ATATCATATA
358488 AATTATTTTATATATTA--TT
1 AATTATTTTATAT-TTAGTTT
* *
358507 AA-AATTTTATATTTATTTT
1 AATTATTTTATATTTAGTTT
358526 AATTATTTTA-ATTTAAGTTT
1 AATTATTTTATATTT-AGTTT
358546 AA
1 AA
358548 ATATAATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
17 3 0.09
18 9 0.26
19 10 0.29
20 12 0.35
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
AATTATTTTATATTTAGTTT
Found at i:359219 original size:22 final size:23
Alignment explanation
Indices: 359169--359220 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
359159 CTTCTTTTAT
* *
359169 TGCAGATGTGGTTCGCAGATGCA
1 TGCAAATGTAGTTCGCAGATGCA
* *
359192 TACAAATGTAGTTCGCA-ATGCC
1 TGCAAATGTAGTTCGCAGATGCA
359214 TGCAAAT
1 TGCAAAT
359221 ATGATCCAAG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 10 0.42
23 14 0.58
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (23 bp):
TGCAAATGTAGTTCGCAGATGCA
Found at i:362079 original size:19 final size:19
Alignment explanation
Indices: 362055--362095 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
362045 GGCATACCTT
362055 ATACCCAATTAGAATTTAC
1 ATACCCAATTAGAATTTAC
362074 ATACCCAATTAGAATTTAC
1 ATACCCAATTAGAATTTAC
362093 ATA
1 ATA
362096 GAACTTTACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.44, C:0.20, G:0.05, T:0.32
Consensus pattern (19 bp):
ATACCCAATTAGAATTTAC
Found at i:368317 original size:13 final size:13
Alignment explanation
Indices: 368301--368332 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
368291 GTTCATGCGC
368301 TCTGCTACGCCAT
1 TCTGCTACGCCAT
368314 TCTGCTACGCCAT
1 TCTGCTACGCCAT
368327 TCTGCT
1 TCTGCT
368333 GCGGTGTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.12, C:0.38, G:0.16, T:0.34
Consensus pattern (13 bp):
TCTGCTACGCCAT
Found at i:370149 original size:16 final size:16
Alignment explanation
Indices: 370125--370156 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
370115 TATCGCCGAC
*
370125 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
370141 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
370157 TGTGAATAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.25, G:0.06, T:0.34
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:375741 original size:18 final size:18
Alignment explanation
Indices: 375718--375764 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
375708 CCCCGAATTA
375718 GTTGGCTATGATGATAGG
1 GTTGGCTATGATGATAGG
375736 GTTGGCTATGATGATAGG
1 GTTGGCTATGATGATAGG
*
375754 GATGGCT-TGAT
1 GTTGGCTATGAT
375765 TTTGTTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 4 0.14
18 24 0.86
ACGTcount: A:0.21, C:0.06, G:0.38, T:0.34
Consensus pattern (18 bp):
GTTGGCTATGATGATAGG
Found at i:376232 original size:3 final size:3
Alignment explanation
Indices: 376212--376290 Score: 101
Period size: 3 Copynumber: 26.7 Consensus size: 3
376202 GGGATATAAA
* *
376212 TAT TA- TAT TAT GAT TAT TAT TA- TAT TA- TAT GAT TAT TAT TAT TATT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T
376258 TAT TAT TAT TAT TAT TAT TAT TAT TATT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TA
376291 CAACTATTTT
Statistics
Matches: 67, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
2 6 0.09
3 55 0.82
4 6 0.09
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:376239 original size:22 final size:22
Alignment explanation
Indices: 376211--376290 Score: 110
Period size: 22 Copynumber: 3.6 Consensus size: 22
376201 TGGGATATAA
*
376211 ATATTATATTATGATTATTATT
1 ATATTATATTATTATTATTATT
*
376233 ATATTATATGATTATTATTATT
1 ATATTATATTATTATTATTATT
376255 AT-TTATTATTATTATTATTATT
1 ATATTA-TATTATTATTATTATT
376277 ATTATTAT-TTATTA
1 A-TATTATATTATTA
376291 CAACTATTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
21 3 0.06
22 44 0.85
23 2 0.04
24 3 0.06
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (22 bp):
ATATTATATTATTATTATTATT
Found at i:376244 original size:19 final size:19
Alignment explanation
Indices: 376212--376290 Score: 99
Period size: 19 Copynumber: 4.1 Consensus size: 19
376202 GGGATATAAA
376212 TATTATATTATGATTATTAT
1 TATTAT-TTATGATTATTAT
376232 TA-TATTATATGATTATTAT
1 TATTATT-TATGATTATTAT
*
376251 TATTATTTATTATTATTAT
1 TATTATTTATGATTATTAT
*
376270 TATTA-TTATTATTATTTAT
1 TATTATTTATGATTA-TTAT
376289 TA
1 TA
376291 CAACTATTTT
Statistics
Matches: 55, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
18 10 0.18
19 39 0.71
20 6 0.11
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (19 bp):
TATTATTTATGATTATTAT
Found at i:376298 original size:28 final size:28
Alignment explanation
Indices: 376243--376298 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
376233 ATATTATATG
** *
376243 ATTATTATTATTATTTATTATTATTATT
1 ATTATTATTATTATTTATTACAACTATT
376271 ATTATTATTATTATTTATTACAACTATT
1 ATTATTATTATTATTTATTACAACTATT
376299 TTTAGGCCCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (28 bp):
ATTATTATTATTATTTATTACAACTATT
Found at i:376606 original size:20 final size:20
Alignment explanation
Indices: 376581--376622 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
376571 AGAGGCTTTC
376581 GGTGGAATGAAGGAAATAAA
1 GGTGGAATGAAGGAAATAAA
376601 GGTGGAATGAAGGAAATAAA
1 GGTGGAATGAAGGAAATAAA
376621 GG
1 GG
376623 GAGTACAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.48, C:0.00, G:0.38, T:0.14
Consensus pattern (20 bp):
GGTGGAATGAAGGAAATAAA
Found at i:382581 original size:102 final size:102
Alignment explanation
Indices: 382402--382607 Score: 304
Period size: 102 Copynumber: 2.0 Consensus size: 102
382392 ATGAATTCAA
* * * * *
382402 AAATGTTTTTAAAAGGAAACATTTGTATATATTAACAATATAAATTTTTTATAAGAATATACACA
1 AAATGTTTTTAAAAGAAAACATTCGTATATATTAACAATATAAAATTCTTATAAGAATAGACACA
382467 AATAAAACTTTAAGGAATCATAATTAATTACATATAT
66 AATAAAACTTTAAGGAATCATAATTAATTACATATAT
* * * * *
382504 AAATGTTTTTAAAAGAAAACATTCGTATATATTAACGATATAAAATTCTTATAAGAGTGGATATA
1 AAATGTTTTTAAAAGAAAACATTCGTATATATTAACAATATAAAATTCTTATAAGAATAGACACA
* *
382569 AATAAAATTTTAAGGAATCATAATTAATTACATGTAT
66 AATAAAACTTTAAGGAATCATAATTAATTACATATAT
382606 AA
1 AA
382608 TTACCCAATG
Statistics
Matches: 92, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
102 92 1.00
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.36
Consensus pattern (102 bp):
AAATGTTTTTAAAAGAAAACATTCGTATATATTAACAATATAAAATTCTTATAAGAATAGACACA
AATAAAACTTTAAGGAATCATAATTAATTACATATAT
Found at i:383212 original size:42 final size:43
Alignment explanation
Indices: 383128--383349 Score: 131
Period size: 43 Copynumber: 5.2 Consensus size: 43
383118 ATTTTATGAA
* * *
383128 ATTGTAAAAAATTAGAGGCCTTAATTATAAAGGTAAAAATTGAG
1 ATTG-AAAAAAATAAAGGCCTCAATTATAAAGGTAAAAATTGAG
* *
383172 ATTGAAAAAAATAAAGGCCTCAATTGTAAAGGT-ATAATTGAG
1 ATTGAAAAAAATAAAGGCCTCAATTATAAAGGTAAAAATTGAG
* *** ** * * *
383214 ATCGAAAATTCTTAGGGGCCTCAATTAGAAAGTTAGAAAGTT-AG
1 ATTGAAAA-AAATAAAGGCCTCAATTATAAAGGTA-AAAATTGAG
* * *
383258 ATT------AATTAAGGCCCTCAATTATAAAGTTAAAAAAAAGTGAG
1 ATTGAAAAAAATAAAGG-CCTCAATTATAAAGGT---AAAAATTGAG
** *
383299 ATT--AAAAAATATGGGCCTCAATTATAAAGGTAGAAATTGAG
1 ATTGAAAAAAATAAAGGCCTCAATTATAAAGGTAAAAATTGAG
383340 ATTGAAAAAA
1 ATTGAAAAAA
383350 TTTAAAGACC
Statistics
Matches: 133, Mismatches: 31, Indels: 29
0.69 0.16 0.15
Matches are distributed among these distances:
37 3 0.02
38 15 0.11
40 4 0.03
41 17 0.13
42 15 0.11
43 47 0.35
44 23 0.17
45 9 0.07
ACGTcount: A:0.47, C:0.08, G:0.18, T:0.27
Consensus pattern (43 bp):
ATTGAAAAAAATAAAGGCCTCAATTATAAAGGTAAAAATTGAG
Found at i:383595 original size:28 final size:28
Alignment explanation
Indices: 383564--383619 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
383554 AATTAAGGAT
* *
383564 TTAATTATAATGATAAAAAATAGGGGCC
1 TTAATTACAAGGATAAAAAATAGGGGCC
*
383592 TTAATTACAAGGATAAAAAATGGGGGCC
1 TTAATTACAAGGATAAAAAATAGGGGCC
383620 CTAAGCACTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.45, C:0.09, G:0.21, T:0.25
Consensus pattern (28 bp):
TTAATTACAAGGATAAAAAATAGGGGCC
Done.