Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008747.1 Hibiscus syriacus cultivar Beakdansim tig00111837_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: 12616935
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 51 of 51
Found at i:12551349 original size:46 final size:46
Alignment explanation
Indices: 12551281--12551389 Score: 116
Period size: 46 Copynumber: 2.3 Consensus size: 46
12551271 TAGAAAAAAG
12551281 AAGAAAA-AAGAAAAAATGAGAAAAAATAAAAGAAAGA-GAAAAGGAA
1 AAGAAAAGAAGAAAAAA-GAGAAAAAATAAAA-AAAGAGGAAAAGGAA
** * *
12551327 AAGAAAAGAAGAAAGAAA-AGAAAAAATTGAAAATGAGGAAAATGAA
1 AAGAAAAGAAGAAA-AAAGAGAAAAAATAAAAAAAGAGGAAAAGGAA
12551373 AAGAAAATGAAAGAAAA
1 AAGAAAA-G-AAGAAAA
12551390 TCGATCAAAC
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
45 4 0.07
46 33 0.61
47 8 0.15
48 9 0.17
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.06
Consensus pattern (46 bp):
AAGAAAAGAAGAAAAAAGAGAAAAAATAAAAAAAGAGGAAAAGGAA
Found at i:12551351 original size:18 final size:18
Alignment explanation
Indices: 12551272--12551351 Score: 69
Period size: 17 Copynumber: 4.7 Consensus size: 18
12551262 AAAAAAAGAT
*
12551272 AGAAAA-AAGAAGAAAAA
1 AGAAAAGAAAAAGAAAAA
**
12551289 AGAAAA-AATGAGAAAAA
1 AGAAAAGAAAAAGAAAAA
* *
12551306 ATAAAAGAAAGAG-AAAA
1 AGAAAAGAAAAAGAAAAA
* *
12551323 GGAAAAG-AAAAGAAGAA
1 AGAAAAGAAAAAGAAAAA
12551340 AGAAAAGAAAAA
1 AGAAAAGAAAAA
12551352 ATTGAAAATG
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
16 4 0.08
17 38 0.75
18 9 0.18
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.03
Consensus pattern (18 bp):
AGAAAAGAAAAAGAAAAA
Found at i:12553810 original size:55 final size:55
Alignment explanation
Indices: 12553725--12554580 Score: 1140
Period size: 55 Copynumber: 15.8 Consensus size: 55
12553715 TGAAGCAAAA
* * * * *
12553725 GAAGATTGTTCGAGTCTTATACTCTTTGAAGGAAT-GGGGAGAAGACGCGATTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGG-GCAGACGCGATCGTT
* * * * *
12553780 GAAGATTGTCCGAGTCTCATACTCTCTGAAGAAATA-GGGGCTGACGCGATTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* * ** * * *
12553834 GAAGATTGTTCGAGTCTCATACTCTCTGAAGGAAT-GAGTAGAAGACGCGATTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAG-GGGGCAGACGCGATCGTT
* * * *
12553889 GAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGGAAGACGTGATTGATT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGG-GGCAGACGCGATCG-TT
*
12553946 -AAGATT-AT-G-GTTCTTATACTCTCTGAAGAAATA-GGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAG-TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* *
12553997 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
*
12554052 GAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* *
12554105 GAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* *
12554158 GAAGATTGTTTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* * *
12554213 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
*
12554268 GAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* * *
12554321 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGAAGCGATTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
*
12554376 GAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
*
12554429 GAAGATTG-T-GGGTCTTATACTCTCTGAA-AAATAGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* * *
12554481 GAAGATTGTTTGGGTTTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* *
12554536 GAAGATTGTTCGAGTATTATACTCTCTGAAG-AATAGGGAGCAGAC
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGAC
12554581 ATGTTATCCG
Statistics
Matches: 730, Mismatches: 52, Indels: 39
0.89 0.06 0.05
Matches are distributed among these distances:
51 2 0.00
52 49 0.07
53 223 0.31
54 127 0.17
55 309 0.42
56 19 0.03
57 1 0.00
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.28
Consensus pattern (55 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
Found at i:12554002 original size:163 final size:163
Alignment explanation
Indices: 12553725--12554580 Score: 1223
Period size: 163 Copynumber: 5.3 Consensus size: 163
12553715 TGAAGCAAAA
* * * *
12553725 GAAGATTGTTCGAGTCTTATACTCTTTGAAGGAAT-GGGGAGAAGACGCGATTGATGAAGATTGT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGG-GCAGACGCGATTGATTAAGATTGT
* * * * * *
12553789 CCGAGTCTCATACTCTCTGAAGAAATA-GGGGCTGACGCGATTGATGAAGATTGTTCGAGTCTCA
65 --GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTGTTCGAGTCTTA
* ** *
12553853 TACTCTCTGAAGGAAT-GAGTAGAAGACGCGATTGAT
128 TACTCTCTGAAGAAATAG-GGGGCAGACGCGATTGAT
* * * *
12553889 GAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGGAAGACGTGATTGATTAAGATTAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGG-GGCAGACGCGATTGATTAAGATTGT
*
12553954 GGTTCTTATACTCTCTGAAGAAATA-GGGGCAGACGCGATCGTTGAAGATTGTTCGAGTCTTATA
65 GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTGTTCGAGTCTTATA
12554018 CTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
130 CTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
* *
12554052 GAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCG-TTGAAGATTGT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATT-AAGATTGT
* * *
12554114 GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATCGTTGAAGATTGTTTGGGTCTTATA
65 GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTGTTCGAGTCTTATA
* *
12554179 CTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
130 CTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
* *
12554213 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTG
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATTAAGATTGTG
12554278 GGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTGTTCGAGTCTTATAC
66 GGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTGTTCGAGTCTTATAC
*
12554343 TCTCTGAAGAAATAGGGGGCAGAAGCGATTGAT
131 TCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
* *
12554376 GAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCG-TTGAAGATTGT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATT-AAGATTGT
* * *
12554438 GGGTCTTATACTCTCTGAA-AAATAGGGGGCAGACGCGATCGTTGAAGATTGTTTGGGTTTTATA
65 GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTGTTCGAGTCTTATA
* *
12554502 CTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
130 CTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
* *
12554536 GAAGATTGTTCGAGTATTATACTCTCTGAAG-AATAGGGAGCAGAC
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGAC
12554581 ATGTTATCCG
Statistics
Matches: 629, Mismatches: 52, Indels: 25
0.89 0.07 0.04
Matches are distributed among these distances:
159 2 0.00
160 124 0.20
161 182 0.29
162 21 0.03
163 241 0.38
164 34 0.05
165 24 0.04
166 1 0.00
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.28
Consensus pattern (163 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATTAAGATTGTG
GGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTGTTCGAGTCTTATAC
TCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
Found at i:12554029 original size:108 final size:108
Alignment explanation
Indices: 12553738--12554580 Score: 1229
Period size: 108 Copynumber: 7.8 Consensus size: 108
12553728 GATTGTTCGA
* * * * * * *
12553738 GTCTTATACTCTTTGAAGGAAT-GGGGAGAAGACGCGATTGATGAAGATTGTCCGAGTCTCATAC
1 GTCTTATACTCTCTGAAGAAATAGGGG-GCAGACGCGATCGTTGAAGATTGTTCGAGTCTTATAC
* *
12553802 TCTCTGAAGAAATA-GGGGCTGACGCGATTGATGAAGATTGTTCGA
65 TCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTG-T-GG
* * ** * * * *
12553847 GTCTCATACTCTCTGAAGGAAT-GAGTAGAAGACGCGATTGATGAAGATTGTTCGAGTCTCATAC
1 GTCTTATACTCTCTGAAGAAATAG-GGGGCAGACGCGATCGTTGAAGATTGTTCGAGTCTTATAC
* * * *
12553911 TCTCTGAAGAAATAGGGAGGAAGACGTGATTGATTAAGATTATGG
65 TCTCTGAAGAAATAGGG-GGCAGACGCGATTGATGAAGATTGTGG
*
12553956 TTCTTATACTCTCTGAAGAAATA-GGGGCAGACGCGATCGTTGAAGATTGTTCGAGTCTTATACT
1 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTGTTCGAGTCTTATACT
12554020 CTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGG
66 CTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGG
*
12554063 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTG-T-GGGTCTTATACT
1 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTGTTCGAGTCTTATACT
* * *
12554126 CTCTGAAGAAATAGGGGGCAGACACGATCGTTGAAGATTGTTTGG
66 CTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTG--TGG
*
12554171 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATTCGAGTCTTATACT
1 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTGTTCGAGTCTTATACT
12554236 CTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGG
66 CTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGG
12554279 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTGTTCGAGTCTTATACT
1 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTGTTCGAGTCTTATACT
*
12554344 CTCTGAAGAAATAGGGGGCAGAAGCGATTGATGAAGATTGTGG
66 CTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGG
*
12554387 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTG-T-GGGTCTTATACT
1 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTGTTCGAGTCTTATACT
* *
12554450 CTCTGAA-AAATAGGGGGCAGACGCGATCGTTGAAGATTGTTTGG
66 CTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTG--TGG
* *
12554494 GTTTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTGTTCGAGTATTATACT
1 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTGTTCGAGTCTTATACT
*
12554559 CTCTGAAG-AATAGGGAGCAGAC
66 CTCTGAAGAAATAGGGGGCAGAC
12554581 ATGTTATCCG
Statistics
Matches: 676, Mismatches: 44, Indels: 28
0.90 0.06 0.04
Matches are distributed among these distances:
105 29 0.04
106 66 0.10
107 99 0.15
108 289 0.43
109 122 0.18
110 52 0.08
111 19 0.03
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.28
Consensus pattern (108 bp):
GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTGTTCGAGTCTTATACT
CTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGG
Found at i:12558224 original size:17 final size:17
Alignment explanation
Indices: 12558202--12558234 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
12558192 ATTCTTCTAG
12558202 ATGTTAGGGAATATTCA
1 ATGTTAGGGAATATTCA
12558219 ATGTTAGGGAATATTC
1 ATGTTAGGGAATATTC
12558235 GAAATCACCC
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:0.33, C:0.06, G:0.24, T:0.36
Consensus pattern (17 bp):
ATGTTAGGGAATATTCA
Found at i:12558971 original size:64 final size:64
Alignment explanation
Indices: 12558892--12559016 Score: 232
Period size: 64 Copynumber: 2.0 Consensus size: 64
12558882 TTGTAAACCA
12558892 CCTTAATTAACTATGTTTTCTGTTGACCGTCAACATTTTCATGCATTAAAACGTGAAACATCTG
1 CCTTAATTAACTATGTTTTCTGTTGACCGTCAACATTTTCATGCATTAAAACGTGAAACATCTG
* *
12558956 CCTTAATTAATTATGTTTTCTGTTGACTGTCAACATTTTCATGCATTAAAACGTGAAACAT
1 CCTTAATTAACTATGTTTTCTGTTGACCGTCAACATTTTCATGCATTAAAACGTGAAACAT
12559017 TTCTGACCAA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 59 1.00
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (64 bp):
CCTTAATTAACTATGTTTTCTGTTGACCGTCAACATTTTCATGCATTAAAACGTGAAACATCTG
Found at i:12559600 original size:50 final size:51
Alignment explanation
Indices: 12559453--12559600 Score: 122
Period size: 50 Copynumber: 2.9 Consensus size: 51
12559443 GAGTTCGTCT
* * * * * *
12559453 AAATA-ATATTTTTTATTTAAATTCGTCACCTCGAGGTGATGATTTTTAATA
1 AAATATATATTTTTTATTAAAATTCATCACATCGAAGTGAAGA-GTTTAATA
* ** * * * *
12559504 AAAAATATATTTTTTATTAATTTTTATCACAACGAAGAT-AAAAGTTTGA-A
1 AAATATATATTTTTTATTAAAATTCATCACATCGAAG-TGAAGAGTTTAATA
* *
12559554 AAATATATATTTTTTATTAAAACTCATCACATCGAAGTGACGAGTTT
1 AAATATATATTTTTTATTAAAATTCATCACATCGAAGTGAAGAGTTT
12559601 CATGTACTGT
Statistics
Matches: 73, Mismatches: 21, Indels: 7
0.72 0.21 0.07
Matches are distributed among these distances:
49 1 0.01
50 38 0.52
51 8 0.11
52 25 0.34
53 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.41
Consensus pattern (51 bp):
AAATATATATTTTTTATTAAAATTCATCACATCGAAGTGAAGAGTTTAATA
Found at i:12560196 original size:31 final size:31
Alignment explanation
Indices: 12560121--12560198 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
12560111 ATAACGATGG
*
12560121 AGTGATCATTTTGTTATAAATCGAAAATGTT
1 AGTGATCAATTTGTTATAAATCGAAAATGTT
* * *
12560152 AGT-AACAATTTTGTTATAGATCGATAATGTT
1 AGTGATCAA-TTTGTTATAAATCGAAAATGTT
*
12560183 CGTGATCAATTTGTTA
1 AGTGATCAATTTGTTA
12560199 CTTTTGAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
30 3 0.08
31 32 0.82
32 4 0.10
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.42
Consensus pattern (31 bp):
AGTGATCAATTTGTTATAAATCGAAAATGTT
Found at i:12563612 original size:23 final size:25
Alignment explanation
Indices: 12563561--12563613 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
12563551 TGCTTTCTCT
*
12563561 TTGATTCTCTCTTGATTCTTGATTC
1 TTGATTCTCTCTTGATTCTTGATTA
* *
12563586 TTGATTCTC-GTTGTTTCTTG-TTA
1 TTGATTCTCTCTTGATTCTTGATTA
12563609 TTGAT
1 TTGAT
12563614 CAATGACTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 7 0.28
24 9 0.36
25 9 0.36
ACGTcount: A:0.11, C:0.15, G:0.15, T:0.58
Consensus pattern (25 bp):
TTGATTCTCTCTTGATTCTTGATTA
Found at i:12563895 original size:45 final size:45
Alignment explanation
Indices: 12563826--12563931 Score: 135
Period size: 45 Copynumber: 2.4 Consensus size: 45
12563816 GGTGCACTAA
* *
12563826 GAGTGCATCGATGCATGAAGTGCATTCGATG-TTTCA-AAATAGCCT
1 GAGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAA-A-CCT
*
12563871 GAGTGCATCGATGCATAAAATGCATTTGATGTTTTCATAAAACCT
1 GAGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACCT
* *
12563916 GAATGCATCGACGCAT
1 GAGTGCATCGATGCAT
12563932 GGTATGTGCA
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
45 45 0.83
46 6 0.11
47 3 0.06
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (45 bp):
GAGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACCT
Found at i:12565445 original size:5 final size:5
Alignment explanation
Indices: 12565435--12565460 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
12565425 TTTTATCTCC
12565435 TGTTT TGTTT TGTTT TGTTT TGTTT T
1 TGTTT TGTTT TGTTT TGTTT TGTTT T
12565461 TCTCACTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (5 bp):
TGTTT
Found at i:12566477 original size:134 final size:134
Alignment explanation
Indices: 12566254--12566614 Score: 467
Period size: 134 Copynumber: 2.7 Consensus size: 134
12566244 GTTCTGGTCG
* * * * **
12566254 TCTAAGGGTGACACGGCTCCTACGTGATGAGAAAATTTGGTCGACGGATGACACT-GTTCCTACG
1 TCTAAGGGTGACGCGGCTCCTACGTGATGAGGAGATATGGTCGGTGGATGACA-TGGTTCCTACG
* * *
12566318 TGATGAGGACGTCTTGGCCAT-TTTAGGGATGATGATAACACAGTTCCTACGCGATGAGGATGAC
65 TGATGAGGACGAC-TGGCCATCTTTAGGGATGATGATAACACAGTTCCTACGCGACGAGGACGAC
*
12566382 TGATTA
129 TGATAA
*
12566388 TCTAAGGTTGACGCGGCTCCTACGTGATGAGGAGATATGGTCGGTGGATGACATGGTTCCTACGT
1 TCTAAGGGTGACGCGGCTCCTACGTGATGAGGAGATATGGTCGGTGGATGACATGGTTCCTACGT
* ** * *
12566453 GATGATGATAACTGACCATCTTTAGGGATGATGATAACACAGTTCCTACGTGACGAGGACGACTG
66 GATGAGGACGACTGGCCATCTTTAGGGATGATGATAACACAGTTCCTACGCGACGAGGACGACTG
*
12566518 GTAA
131 ATAA
* * * * * *
12566522 TCTAAGGGTGATGCGACTTCTACGTGATGAGGAGATCT-GTCAGTGGATGACACGGTTCCTACGT
1 TCTAAGGGTGACGCGGCTCCTACGTGATGAGGAGATATGGTCGGTGGATGACATGGTTCCTACGT
*
12566586 GATGAGGACGGCTGGCCATCTTTAGGGAT
66 GATGAGGACGACTGGCCATCTTTAGGGAT
12566615 AATATTTCAA
Statistics
Matches: 196, Mismatches: 29, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
133 55 0.28
134 141 0.72
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (134 bp):
TCTAAGGGTGACGCGGCTCCTACGTGATGAGGAGATATGGTCGGTGGATGACATGGTTCCTACGT
GATGAGGACGACTGGCCATCTTTAGGGATGATGATAACACAGTTCCTACGCGACGAGGACGACTG
ATAA
Found at i:12566783 original size:65 final size:66
Alignment explanation
Indices: 12566651--12566793 Score: 234
Period size: 65 Copynumber: 2.2 Consensus size: 66
12566641 GATTTTTTTT
* * * *
12566651 TGTTTTAAGAAAAACTGTCTCAAGAGTGACAAAACTTTGTTTCAAGGGAAACGATATCAAAGTTG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACGATATCAAAGATG
12566716 A
66 A
*
12566717 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACGATCTCAAAGATG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACGATATCAAAGATG
12566781 A
66 A
12566782 TGTTTCAAGAGA
1 TGTTTCAAGAGA
12566794 GACAAAATTC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
65 41 0.57
66 31 0.43
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.27
Consensus pattern (66 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACGATATCAAAGATG
A
Found at i:12566811 original size:50 final size:50
Alignment explanation
Indices: 12566736--12566843 Score: 207
Period size: 50 Copynumber: 2.2 Consensus size: 50
12566726 AGAAACTGTC
*
12566736 TCAAGAGAGACAAAATTTGTTTCAAGGGAAACGATCTCAAAGATGATGTT
1 TCAAGAGAGACAAAATTCGTTTCAAGGGAAACGATCTCAAAGATGATGTT
12566786 TCAAGAGAGACAAAATTCGTTTCAAGGGAAACGATCTCAAAGATGATGTT
1 TCAAGAGAGACAAAATTCGTTTCAAGGGAAACGATCTCAAAGATGATGTT
12566836 TCAAGAGA
1 TCAAGAGA
12566844 AACTATCTCA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 57 1.00
ACGTcount: A:0.41, C:0.13, G:0.22, T:0.24
Consensus pattern (50 bp):
TCAAGAGAGACAAAATTCGTTTCAAGGGAAACGATCTCAAAGATGATGTT
Found at i:12566826 original size:115 final size:116
Alignment explanation
Indices: 12566670--12566908 Score: 374
Period size: 115 Copynumber: 2.1 Consensus size: 116
12566660 AAAAACTGTC
* * * *
12566670 TCAAGAGTGACAAAACTTTGTTTCAAGGGAAACGATATCAAAGTTGATGTTTCAAGAGAAACTGT
1 TCAAGAGAGACAAAACTTCGTTTCAAGGGAAACGATATCAAAGATGATGTTTCAAGAGAAACTAT
*
12566735 CTCAAGAGAGACAAAATTTGTTTCAAGGGAAACGATCTCAAAGATGA-TGTT
66 CTCAAGAAAGACAAAATTTGTTTCAAGGGAAACGATCTCAAAGAT-ATTGTT
*
12566786 TCAAGAGAGACAAAA-TTCGTTTCAAGGGAAACGATCTCAAAGATGATGTTTCAAGAGAAACTAT
1 TCAAGAGAGACAAAACTTCGTTTCAAGGGAAACGATATCAAAGATGATGTTTCAAGAGAAACTAT
* * *
12566850 CTCAAGAAATATAAAATTTGTTTCAAGGGAAACGATCTCTAAGATATTGTT
66 CTCAAGAAAGACAAAATTTGTTTCAAGGGAAACGATCTCAAAGATATTGTT
12566901 TCAAGAGA
1 TCAAGAGA
12566909 AACTGTCTCA
Statistics
Matches: 113, Mismatches: 9, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
114 1 0.01
115 98 0.87
116 14 0.12
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (116 bp):
TCAAGAGAGACAAAACTTCGTTTCAAGGGAAACGATATCAAAGATGATGTTTCAAGAGAAACTAT
CTCAAGAAAGACAAAATTTGTTTCAAGGGAAACGATCTCAAAGATATTGTT
Found at i:12566837 original size:29 final size:30
Alignment explanation
Indices: 12566799--12566970 Score: 127
Period size: 29 Copynumber: 5.4 Consensus size: 30
12566789 AGAGAGACAA
12566799 AATTCGTTTCAAGGGAAACGATCTCAAAGAT
1 AATT-GTTTCAAGGGAAACGATCTCAAAGAT
* * * *
12566830 GA-TGTTTCAAGAGAAACTATCTCAAGAAATAT
1 AATTGTTTCAAGGGAAACGATCTC---AAAGAT
*
12566862 AAAATTTGTTTCAAGGGAAACGATCTCTAAGAT
1 --AA-TTGTTTCAAGGGAAACGATCTCAAAGAT
*
12566895 -ATTGTTTCAAGAGAAACTG-TCTCAAGAGAGAT
1 AATTGTTTCAAGGGAAAC-GATCTC-A-A-AGAT
12566927 AAAATTTGTTTCAAGGGAAACGATCTCAAAGAT
1 --AA-TTGTTTCAAGGGAAACGATCTCAAAGAT
*
12566960 GA-TGTTTCAAG
1 AATTGTTTCAAG
12566971 AGAGACACAA
Statistics
Matches: 112, Mismatches: 13, Indels: 34
0.70 0.08 0.21
Matches are distributed among these distances:
29 46 0.41
30 3 0.03
31 3 0.03
32 9 0.08
33 8 0.07
34 2 0.02
35 3 0.03
36 38 0.34
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (30 bp):
AATTGTTTCAAGGGAAACGATCTCAAAGAT
Found at i:12566855 original size:65 final size:65
Alignment explanation
Indices: 12566786--12566973 Score: 306
Period size: 65 Copynumber: 2.9 Consensus size: 65
12566776 AGATGATGTT
* *
12566786 TCAAGAGAGACAAAATTCGTTTCAAGGGAAACGATCTCAAAGATGATGTTTCAAGAGAAACTATC
1 TCAAGAGAGATAAAATTTGTTTCAAGGGAAACGATCTCAAAGATGATGTTTCAAGAGAAACTATC
* * * *
12566851 TCAAGAAATATAAAATTTGTTTCAAGGGAAACGATCTCTAAGAT-ATTGTTTCAAGAGAAACTGT
1 TCAAGAGAGATAAAATTTGTTTCAAGGGAAACGATCTCAAAGATGA-TGTTTCAAGAGAAACTAT
12566915 C
65 C
12566916 TCAAGAGAGATAAAATTTGTTTCAAGGGAAACGATCTCAAAGATGATGTTTCAAGAGA
1 TCAAGAGAGATAAAATTTGTTTCAAGGGAAACGATCTCAAAGATGATGTTTCAAGAGA
12566974 GACACAACTT
Statistics
Matches: 112, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
64 1 0.01
65 110 0.98
66 1 0.01
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.27
Consensus pattern (65 bp):
TCAAGAGAGATAAAATTTGTTTCAAGGGAAACGATCTCAAAGATGATGTTTCAAGAGAAACTATC
Found at i:12566882 original size:36 final size:34
Alignment explanation
Indices: 12566832--12566955 Score: 118
Period size: 36 Copynumber: 3.7 Consensus size: 34
12566822 TCAAAGATGA
*
12566832 TGTTTCAAGAGAAACTATCTCAAGAAATATAAAATT
1 TGTTTCAAGAGAAACGATCTCAAG-AA-ATAAAATT
*
12566868 TGTTTCAAGGGAAACGATCTCTAAG--AT---A-T
1 TGTTTCAAGAGAAACGATCTC-AAGAAATAAAATT
12566897 TGTTTCAAGAGAAACTG-TCTCAAGAGAGATAAAATT
1 TGTTTCAAGAGAAAC-GATCTCAAGA-A-ATAAAATT
*
12566933 TGTTTCAAGGGAAACGATCTCAA
1 TGTTTCAAGAGAAACGATCTCAA
12566956 AGATGATGTT
Statistics
Matches: 73, Mismatches: 4, Indels: 22
0.74 0.04 0.22
Matches are distributed among these distances:
28 3 0.04
29 19 0.26
30 2 0.03
32 2 0.03
33 2 0.03
35 2 0.03
36 40 0.55
37 3 0.04
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (34 bp):
TGTTTCAAGAGAAACGATCTCAAGAAATAAAATT
Found at i:12566933 original size:180 final size:181
Alignment explanation
Indices: 12566681--12567005 Score: 539
Period size: 180 Copynumber: 1.8 Consensus size: 181
12566671 CAAGAGTGAC
*
12566681 AAAACTTTGTTTCAAGGGAAACGATATCAAAGTTGATGTTTCAAGAGAAACTGTCTCAAGAGAGA
1 AAAACTTTGTTTCAAGGGAAACGATATCAAAGATGATGTTTCAAGAGAAACTGTCTCAAGAGAGA
12566746 CAAAATTTGTTTCAAGGGAAACGATCTCAAAGATGATGTTTCAAGAGAGACA-AAATTCGTTTCA
66 CAAAATTTGTTTCAAGGGAAACGATCTCAAAGATGATGTTTCAAGAGAGACACAAATT-GTTTCA
* *
12566810 AGGGAAACGATCTCAAAGATGATGTTTCAAGAGAAACTATCTCAAGAAATAT
130 AGAGAAACAATCTCAAAGATGATGTTTCAAGAGAAACTATCTCAAGAAATAT
* *
12566862 AAAA-TTTGTTTCAAGGGAAACGATCTCTAAGAT-ATTGTTTCAAGAGAAACTGTCTCAAGAGAG
1 AAAACTTTGTTTCAAGGGAAACGATATCAAAGATGA-TGTTTCAAGAGAAACTGTCTCAAGAGAG
* *
12566925 ATAAAATTTGTTTCAAGGGAAACGATCTCAAAGATGATGTTTCAAGAGAGACACAACTTGTTTCA
65 ACAAAATTTGTTTCAAGGGAAACGATCTCAAAGATGATGTTTCAAGAGAGACACAAATTGTTTCA
*
12566990 AGATAAACAATCTCAA
130 AGAGAAACAATCTCAA
12567006 GGTTTAAGTT
Statistics
Matches: 134, Mismatches: 8, Indels: 5
0.91 0.05 0.03
Matches are distributed among these distances:
179 1 0.01
180 125 0.93
181 8 0.06
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.27
Consensus pattern (181 bp):
AAAACTTTGTTTCAAGGGAAACGATATCAAAGATGATGTTTCAAGAGAAACTGTCTCAAGAGAGA
CAAAATTTGTTTCAAGGGAAACGATCTCAAAGATGATGTTTCAAGAGAGACACAAATTGTTTCAA
GAGAAACAATCTCAAAGATGATGTTTCAAGAGAAACTATCTCAAGAAATAT
Found at i:12567307 original size:36 final size:38
Alignment explanation
Indices: 12567260--12567344 Score: 122
Period size: 38 Copynumber: 2.3 Consensus size: 38
12567250 GGAAAACTAC
* *
12567260 CTCAAG-GAGAC-AAATTTTTTTTTGAG-AAAAATTGT
1 CTCAAGCGAGACAAAATTTGTTTTTAAGAAAAAATTGT
12567295 CTCAAGCGAGACAAAATTTGTTTTTAAGAAAAAATTGT
1 CTCAAGCGAGACAAAATTTGTTTTTAAGAAAAAATTGT
*
12567333 CTCTAGCGAGAC
1 CTCAAGCGAGAC
12567345 GACACTTTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
35 6 0.14
36 5 0.11
37 13 0.30
38 20 0.45
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.32
Consensus pattern (38 bp):
CTCAAGCGAGACAAAATTTGTTTTTAAGAAAAAATTGT
Found at i:12569864 original size:15 final size:15
Alignment explanation
Indices: 12569846--12569901 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
12569836 CCTTTTTTAT
12569846 TTTTTTCTTTGCTTC
1 TTTTTTCTTTGCTTC
*
12569861 TTTTCTCTTTGCTTC
1 TTTTTTCTTTGCTTC
* * * *
12569876 ATTTATCTTTGTTTT
1 TTTTTTCTTTGCTTC
12569891 TTTCTTTCTTT
1 TTT-TTTCTTT
12569902 TCTTTTCCTC
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
15 27 0.82
16 6 0.18
ACGTcount: A:0.04, C:0.18, G:0.05, T:0.73
Consensus pattern (15 bp):
TTTTTTCTTTGCTTC
Found at i:12569884 original size:22 final size:20
Alignment explanation
Indices: 12569858--12569918 Score: 52
Period size: 22 Copynumber: 2.9 Consensus size: 20
12569848 TTTTCTTTGC
12569858 TTCTTTTCTCTTTGCTTCATT
1 TTCTTTTCTCTTTGCTTC-TT
* *
12569879 TATCTTTGT-TTTTTTCTTTCTT
1 T-TCTTT-TCTCTTTGC-TTCTT
12569901 TTCTTTTCCTCTTTGCTT
1 TTCTTTT-CTCTTTGCTT
12569919 TGATTTGATC
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
20 1 0.03
21 8 0.26
22 18 0.58
23 4 0.13
ACGTcount: A:0.03, C:0.21, G:0.05, T:0.70
Consensus pattern (20 bp):
TTCTTTTCTCTTTGCTTCTT
Found at i:12571269 original size:21 final size:20
Alignment explanation
Indices: 12571239--12571278 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
12571229 AAAAAATGAA
*
12571239 ATACAGATGCAAAATGCAAAT
1 ATACAAATGC-AAATGCAAAT
*
12571260 ATACAAATGCAGATGCAAA
1 ATACAAATGCAAATGCAAA
12571279 AAGATTGATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.53, C:0.15, G:0.15, T:0.17
Consensus pattern (20 bp):
ATACAAATGCAAATGCAAAT
Found at i:12574786 original size:6 final size:6
Alignment explanation
Indices: 12574770--12574828 Score: 61
Period size: 6 Copynumber: 9.8 Consensus size: 6
12574760 CTCATCATTT
*
12574770 TTTTCTC TTTTTC -TTTTC -TTTTC TTTTTTC TATTTT- TTCTTC TTTTTC
1 TTTT-TC TTTTTC TTTTTC TTTTTC -TTTTTC T-TTTTC TTTTTC TTTTTC
12574818 TTTTTC TTTTT
1 TTTTTC TTTTT
12574829 ATTATATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
5 13 0.28
6 20 0.43
7 13 0.28
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTTC
Found at i:12574786 original size:16 final size:16
Alignment explanation
Indices: 12574767--12574822 Score: 69
Period size: 17 Copynumber: 3.3 Consensus size: 16
12574757 TCTCTCATCA
12574767 TTTTTTTCTCTTTTTC
1 TTTTTTTCTCTTTTTC
12574783 TTTTCTTT-TCTTTTTTC
1 TTTT-TTTCTC-TTTTTC
12574800 TATTTTTTCTTCTTTTTC
1 T-TTTTTTC-TCTTTTTC
12574818 TTTTT
1 TTTTT
12574823 CTTTTTATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
16 6 0.17
17 17 0.49
18 10 0.29
19 2 0.06
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTTTTCTCTTTTTC
Found at i:12574796 original size:24 final size:25
Alignment explanation
Indices: 12574769--12574828 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 25
12574759 TCTCATCATT
12574769 TTTTTCTCTTTTTCTT-TTC-TTTTC
1 TTTTTCTCTTTTT-TTCTTCTTTTTC
12574793 TTTTT-TCTATTTTTTCTTCTTTTTC
1 TTTTTCTCT-TTTTTTCTTCTTTTTC
12574818 TTTTTCT-TTTT
1 TTTTTCTCTTTT
12574829 ATTATATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
23 5 0.16
24 15 0.47
25 11 0.34
26 1 0.03
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.82
Consensus pattern (25 bp):
TTTTTCTCTTTTTTTCTTCTTTTTC
Found at i:12574805 original size:25 final size:25
Alignment explanation
Indices: 12574768--12574822 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
12574758 CTCTCATCAT
* *
12574768 TTTTTTCT-CTTTTTCTTTTCTTTTC
1 TTTTTTCTATTTTTTCTTCT-TTTTC
12574793 TTTTTTCTATTTTTTCTTCTTTTTC
1 TTTTTTCTATTTTTTCTTCTTTTTC
12574818 TTTTT
1 TTTTT
12574823 CTTTTTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 18 0.67
26 9 0.33
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (25 bp):
TTTTTTCTATTTTTTCTTCTTTTTC
Found at i:12574807 original size:9 final size:8
Alignment explanation
Indices: 12574767--12574822 Score: 60
Period size: 9 Copynumber: 6.6 Consensus size: 8
12574757 TCTCTCATCA
12574767 TTTTTTTC
1 TTTTTTTC
*
12574775 TCTTTTTC
1 TTTTTTTC
12574783 TTTTCTTT-
1 TTTT-TTTC
12574791 TCTTTTTTC
1 T-TTTTTTC
12574800 TATTTTTTC
1 T-TTTTTTC
12574809 TTCTTTTTC
1 TT-TTTTTC
12574818 TTTTT
1 TTTTT
12574823 CTTTTTATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
8 18 0.44
9 23 0.56
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTTTC
Found at i:12577788 original size:45 final size:45
Alignment explanation
Indices: 12577685--12577957 Score: 361
Period size: 45 Copynumber: 6.0 Consensus size: 45
12577675 ATAACATTTC
* * * *
12577685 TTACCAATATACTAACCATTTAATCCCATAAGCTCGTAAGCTTTTT
1 TTACCAATAAACTTACCATTT-ATTCCATAAGCTCGTAAGCTTATT
*
12577731 TTACAAAT-AACTTACCATTTATTCCATAAGCTCGTAAGCTTATT
1 TTACCAATAAACTTACCATTTATTCCATAAGCTCGTAAGCTTATT
12577775 TTACCAATAAACTTACCATTTATTCCATAAGCTCGTAAGCTTATT
1 TTACCAATAAACTTACCATTTATTCCATAAGCTCGTAAGCTTATT
* *
12577820 TTACCAATATACCATAAACCATTTATTCCATAAGCTCGTAAGCTTATT
1 TTACCAATA-AAC-T-TACCATTTATTCCATAAGCTCGTAAGCTTATT
* * *
12577868 TTACTAATATACTTACCATTTATTACATAAGCTCGTAAGCTTATT
1 TTACCAATAAACTTACCATTTATTCCATAAGCTCGTAAGCTTATT
* * * * *
12577913 TTATCAATATATTTGCCA-TTATTCCATAAGCTTGTAAGCTTATT
1 TTACCAATAAACTTACCATTTATTCCATAAGCTCGTAAGCTTATT
12577957 T
1 T
12577958 CATACTTACC
Statistics
Matches: 204, Mismatches: 19, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
44 54 0.26
45 99 0.49
46 10 0.05
47 2 0.01
48 39 0.19
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.40
Consensus pattern (45 bp):
TTACCAATAAACTTACCATTTATTCCATAAGCTCGTAAGCTTATT
Found at i:12577860 original size:93 final size:90
Alignment explanation
Indices: 12577685--12577957 Score: 374
Period size: 93 Copynumber: 3.0 Consensus size: 90
12577675 ATAACATTTC
* * *
12577685 TTACCAATATACTAACCATTTAATCCCATAAGCTCGTAAGCTTTTTTTACAA-ATA-ACTTACCA
1 TTACCAATATACTTACCATTT-ATTCCATAAGCTCGTAAGCTTATTTTACAATATACA-TTACCA
12577748 TTTATTCCATAAGCTCGTAAGCTTATT
64 TTTATTCCATAAGCTCGTAAGCTTATT
* *
12577775 TTACCAATAAACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACCATAAACC
1 TTACCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTA-CAATATA-CAT-TACC
12577840 ATTTATTCCATAAGCTCGTAAGCTTATT
63 ATTTATTCCATAAGCTCGTAAGCTTATT
* * * *
12577868 TTACTAATATACTTACCATTTATTACATAAGCTCGTAAGCTTATTTTATCAATATA-TTTGCCA-
1 TTACCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTA-CAATATACATTACCAT
*
12577931 TTATTCCATAAGCTTGTAAGCTTATT
65 TTATTCCATAAGCTCGTAAGCTTATT
12577957 T
1 T
12577958 CATACTTACC
Statistics
Matches: 165, Mismatches: 13, Indels: 11
0.87 0.07 0.06
Matches are distributed among these distances:
89 51 0.31
90 25 0.15
91 4 0.02
92 1 0.01
93 84 0.51
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.40
Consensus pattern (90 bp):
TTACCAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACAATATACATTACCATT
TATTCCATAAGCTCGTAAGCTTATT
Found at i:12577897 original size:138 final size:134
Alignment explanation
Indices: 12577685--12577957 Score: 413
Period size: 137 Copynumber: 2.0 Consensus size: 134
12577675 ATAACATTTC
*
12577685 TTACCAATATACTAACCATTTAATCCCATAAGCTCGTAAGCTTTTTTTACAAATAACTTACCATT
1 TTACCAATATACTAACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACAAATAACTTACCATT
*
12577750 TATTCCATAAGCTCGTAAGCTTATTTTACCAATAAACTTACCATTTATTCCATAAGCTCGTAAGC
66 TATTACATAAGCTCGTAAGCTTATTTTACCAATAAACTTACCA-TTATTCCATAAGCTCGTAAGC
12577815 TTATT
130 TTATT
* *
12577820 TTACCAATATACCATAAACCATTT-ATTCCATAAGCTCGTAAGCTTATTTTACTAATATACTTAC
1 TTACCAATATA-C-T-AACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACAAATA-ACTTAC
* * * * *
12577884 CATTTATTACATAAGCTCGTAAGCTTATTTTATCAATATATTTGCCATTATTCCATAAGCTTGTA
62 CATTTATTACATAAGCTCGTAAGCTTATTTTACCAATAAACTTACCATTATTCCATAAGCTCGTA
12577949 AGCTTATT
127 AGCTTATT
12577957 T
1 T
12577958 CATACTTACC
Statistics
Matches: 125, Mismatches: 9, Indels: 6
0.89 0.06 0.04
Matches are distributed among these distances:
135 11 0.09
136 1 0.01
137 57 0.46
138 56 0.45
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.40
Consensus pattern (134 bp):
TTACCAATATACTAACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACAAATAACTTACCATT
TATTACATAAGCTCGTAAGCTTATTTTACCAATAAACTTACCATTATTCCATAAGCTCGTAAGCT
TATT
Found at i:12580277 original size:22 final size:23
Alignment explanation
Indices: 12580226--12580285 Score: 56
Period size: 22 Copynumber: 2.7 Consensus size: 23
12580216 CTTTTTATTA
* *
12580226 TTCTTTTTTATCTC-ATGTTTGT
1 TTCTTTTTTCTCTCTATATTTGT
12580248 TT-TGTTTTTCTCTCTATATTT-T
1 TTCT-TTTTTCTCTCTATATTTGT
*
12580270 TTC-TTTTTCTTTCTAT
1 TTCTTTTTTCTCTCTAT
12580286 TCAACCTCTC
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
21 13 0.41
22 14 0.44
23 5 0.16
ACGTcount: A:0.08, C:0.15, G:0.05, T:0.72
Consensus pattern (23 bp):
TTCTTTTTTCTCTCTATATTTGT
Found at i:12588629 original size:23 final size:23
Alignment explanation
Indices: 12588603--12588661 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
12588593 AGATCCTCAT
*
12588603 GGTTATTCACACGGGTATGGTTC
1 GGTTATTCACACGGGTACGGTTC
*
12588626 GGTTATTCACACGGGTACGGTTT
1 GGTTATTCACACGGGTACGGTTC
*
12588649 GGTTATTCTCACG
1 GGTTATTCACACG
12588662 ATTCGGCTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.17, C:0.19, G:0.29, T:0.36
Consensus pattern (23 bp):
GGTTATTCACACGGGTACGGTTC
Found at i:12594623 original size:20 final size:20
Alignment explanation
Indices: 12594584--12594638 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 20
12594574 GAGAAAAGAG
*
12594584 CAAAGAAAAAAAAGCAAAAATA
1 CAAAGAAAGAAAAG-AAAAA-A
12594606 CAAA-AAAGCAAAAGAAAAAA
1 CAAAGAAAG-AAAAGAAAAAA
12594626 CAAAGAAAGAAAA
1 CAAAGAAAGAAAA
12594639 AAAGACAAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
20 9 0.30
21 12 0.40
22 9 0.30
ACGTcount: A:0.78, C:0.09, G:0.11, T:0.02
Consensus pattern (20 bp):
CAAAGAAAGAAAAGAAAAAA
Found at i:12595823 original size:36 final size:37
Alignment explanation
Indices: 12595774--12595897 Score: 180
Period size: 36 Copynumber: 3.4 Consensus size: 37
12595764 GACTATCGAC
**
12595774 CTTGAGATTATTTTCT-TAAAAACAAATTTTGTCTCG
1 CTTGAGACAATTTTCTCTAAAAACAAATTTTGTCTCG
*
12595810 CTTGAGACAATTTTATCTAAAAACAAATTTTGTCTCG
1 CTTGAGACAATTTTCTCTAAAAACAAATTTTGTCTCG
* *
12595847 CTTGAGACAA-TTTCTCTCAAAACAAATTTTGTCTAG
1 CTTGAGACAATTTTCTCTAAAAACAAATTTTGTCTCG
*
12595883 CTTGAGACATTTTTC
1 CTTGAGACAATTTTC
12595898 CTTTGAGGTA
Statistics
Matches: 79, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
36 45 0.57
37 34 0.43
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.40
Consensus pattern (37 bp):
CTTGAGACAATTTTCTCTAAAAACAAATTTTGTCTCG
Found at i:12595838 original size:37 final size:37
Alignment explanation
Indices: 12595790--12595896 Score: 171
Period size: 37 Copynumber: 2.9 Consensus size: 37
12595780 ATTATTTTCT
12595790 TAAAAACAAATTTTGTCTCGCTTGAGACAATTTTATC
1 TAAAAACAAATTTTGTCTCGCTTGAGACAATTTTATC
*
12595827 TAAAAACAAATTTTGTCTCGCTTGAGACAA-TTTCTC
1 TAAAAACAAATTTTGTCTCGCTTGAGACAATTTTATC
* * *
12595863 TCAAAACAAATTTTGTCTAGCTTGAGACATTTTT
1 TAAAAACAAATTTTGTCTCGCTTGAGACAATTTT
12595897 CCTTTGAGGT
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
36 32 0.49
37 33 0.51
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (37 bp):
TAAAAACAAATTTTGTCTCGCTTGAGACAATTTTATC
Found at i:12596155 original size:29 final size:29
Alignment explanation
Indices: 12596123--12596232 Score: 87
Period size: 29 Copynumber: 3.6 Consensus size: 29
12596113 TCTTGAGACA
12596123 GTTTCTCTTGAAACAAGATCTTTGAGATT
1 GTTTCTCTTGAAACAAGATCTTTGAGATT
* * **
12596152 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCTCTTGAAAC-AA----G-ATCT-TTGAGATT
**
12596188 GTTTCTCTTGAAACATCATCTTTGAG-TAT
1 GTTTCTCTTGAAACAAGATCTTTGAGAT-T
12596217 GTTTCTCTTGAAACAA
1 GTTTCTCTTGAAACAA
12596233 ATCCCTAAAG
Statistics
Matches: 62, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
29 33 0.53
30 5 0.08
34 1 0.02
35 4 0.06
36 19 0.31
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (29 bp):
GTTTCTCTTGAAACAAGATCTTTGAGATT
Found at i:12596171 original size:65 final size:64
Alignment explanation
Indices: 12595950--12596234 Score: 233
Period size: 65 Copynumber: 4.4 Consensus size: 64
12595940 TTGATCTCAC
** ** * * * *
12595950 TTGAGATTGTTTTTCTCAAAACAAACTTTGTCACGCTTGAGACAATCTTC-CTT-AAGACAAA-C
1 TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGT-TTCTCTTGAA-ACAAATC
12596012 T
64 T
* * ** * * * *
12596013 TTGAAATT-TTCCCCTTGAAACAAAGTGGTGTTTCCCTTGAGACGGTTT-TCCTTTAAACACAAA
1 TTGAGATTGTTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGACAGTTTCT-C-TTGAA-ACAAA
*
12596076 TAT
62 TCT
* * *
12596079 TT-ACGATCGTTTCCCTTTAAACGAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAGATC
1 TTGA-GATTGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAA-ATC
12596143 T
64 T
*
12596144 TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATCATCT
1 TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA-AATCT
*
12596209 TTGAG-TATGTTTCTCTTGAAACAAAT
1 TTGAGAT-TGTTTCCCTTGAAACAAAT
12596235 CCCTAAAGAT
Statistics
Matches: 176, Mismatches: 33, Indels: 24
0.76 0.14 0.10
Matches are distributed among these distances:
62 13 0.07
63 21 0.12
64 7 0.04
65 96 0.55
66 25 0.14
67 14 0.08
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.39
Consensus pattern (64 bp):
TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATCT
Found at i:12596317 original size:40 final size:37
Alignment explanation
Indices: 12596273--12596405 Score: 88
Period size: 40 Copynumber: 3.3 Consensus size: 37
12596263 CATAGGAACT
12596273 GTGTCATCCCCCCACCAAACCTCCTCATCACGTAGGAGTC
1 GTGTCA-CCCCCCA-CAAACCTCCTCATCACGTAGGAG-C
** *
12596313 GTGTCA-CCCTTAGATAACTAGTCGTCCTCATCACGTAGGAAGC
1 GTGTCACCCCCCACA-AAC----C-TCCTCATCACGTAGG-AGC
** *
12596356 GTGTCATCCACCGAACAAACCTTCTCATCACGTAGGAGCC
1 GTGTCA-CC-CCCCACAAACCTCCTCATCACGTAGGAG-C
12596396 GTGTCACCCC
1 GTGTCACCCC
12596406 TAGATAACCA
Statistics
Matches: 75, Mismatches: 7, Indels: 24
0.71 0.07 0.23
Matches are distributed among these distances:
37 1 0.01
38 9 0.12
39 4 0.05
40 27 0.36
41 1 0.01
42 1 0.01
43 22 0.29
44 2 0.03
45 4 0.05
46 4 0.05
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.22
Consensus pattern (37 bp):
GTGTCACCCCCCACAAACCTCCTCATCACGTAGGAGC
Found at i:12596391 original size:83 final size:82
Alignment explanation
Indices: 12596265--12596442 Score: 248
Period size: 83 Copynumber: 2.1 Consensus size: 82
12596255 CCTCATTGCA
* * * *
12596265 TAGGAACTGTGTCATCCCCCCACCAAACCTCCTCATCACGTAGGAGTCGTGTCACCCTTAGATAA
1 TAGGAAC-GTGTCATCCACCCAACAAACCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAA
* *
12596330 CTAGTCGTCCTCATCACG
65 CCAATCGTCCTCATCACG
* *
12596348 TAGGAAGCGTGTCATCCACCGAACAAACCTTCTCATCACGTAGGAGCCGTGTCACCCCTAGATAA
1 TAGGAA-CGTGTCATCCACCCAACAAACCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAA
*
12596413 CCAATCGTCCTCATCGCG
65 CCAATCGTCCTCATCACG
12596431 TAGGAACCGTGT
1 TAGGAA-CGTGT
12596443 TATCACTCTA
Statistics
Matches: 84, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
83 83 0.99
84 1 0.01
ACGTcount: A:0.25, C:0.33, G:0.19, T:0.22
Consensus pattern (82 bp):
TAGGAACGTGTCATCCACCCAACAAACCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAAC
CAATCGTCCTCATCACG
Found at i:12596441 original size:43 final size:43
Alignment explanation
Indices: 12596294--12596442 Score: 146
Period size: 43 Copynumber: 3.5 Consensus size: 43
12596284 CCACCAAACC
** * * *
12596294 TCCTCATCACGTAGGAGTCGTGTCACCCTTAGATAACTAGTCG
1 TCCTCATCACGTAGGAACCGTGTCACCCCTAGATAACCAATCG
* * *
12596337 TCCTCATCACGTAGGAAGCGTGTCATCCACC--G--AA-CAAACC
1 TCCTCATCACGTAGGAACCGTGTCA-CC-CCTAGATAACCAATCG
* *
12596377 TTCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAATCG
1 TCCTCATCACGTAGGAACCGTGTCACCCCTAGATAACCAATCG
*
12596420 TCCTCATCGCGTAGGAACCGTGT
1 TCCTCATCACGTAGGAACCGTGT
12596443 TATCACTCTA
Statistics
Matches: 84, Mismatches: 15, Indels: 14
0.74 0.13 0.12
Matches are distributed among these distances:
38 2 0.02
39 2 0.02
40 25 0.30
41 2 0.02
42 2 0.02
43 48 0.57
44 2 0.02
45 1 0.01
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.23
Consensus pattern (43 bp):
TCCTCATCACGTAGGAACCGTGTCACCCCTAGATAACCAATCG
Found at i:12596736 original size:3 final size:3
Alignment explanation
Indices: 12596728--12596779 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
12596718 GGTTTTTAAA
*
12596728 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ACT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
12596776 ATT A
1 ATT A
12596780 CATTTTTGCA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:12598008 original size:23 final size:23
Alignment explanation
Indices: 12597982--12598027 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
12597972 ATTTGTAAAT
* *
12597982 CATTTATTTTAGTCATTGTTTGG
1 CATTTAGTTTAATCATTGTTTGG
* *
12598005 CATTTGGTTTAATTATTGTTTGG
1 CATTTAGTTTAATCATTGTTTGG
12598028 TCCTTTATGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.17, C:0.07, G:0.20, T:0.57
Consensus pattern (23 bp):
CATTTAGTTTAATCATTGTTTGG
Found at i:12599516 original size:16 final size:17
Alignment explanation
Indices: 12599485--12599517 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
12599475 TATGTCCAAC
12599485 TTGAGAGCCATCCTTTG
1 TTGAGAGCCATCCTTTG
*
12599502 TTGAGA-CCATTCTTTG
1 TTGAGAGCCATCCTTTG
12599518 ACAGAGTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.39
Consensus pattern (17 bp):
TTGAGAGCCATCCTTTG
Found at i:12609136 original size:3 final size:3
Alignment explanation
Indices: 12609130--12609201 Score: 112
Period size: 3 Copynumber: 24.0 Consensus size: 3
12609120 TTTTTTATAT
12609130 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
12609176 TTA -TA TTA TTA TTA -TA TTA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA
12609202 CAGGCCCAAA
Statistics
Matches: 65, Mismatches: 0, Indels: 8
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.06
3 55 0.85
4 6 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:12611241 original size:26 final size:27
Alignment explanation
Indices: 12611189--12611246 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
12611179 TAATTCTTTC
*
12611189 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCAAAATATTTATATATAC-TATTA
* *
12611217 TTTTCATAATATTTATATGTA-TATTA
1 TTTTCAAAATATTTATATATACTATTA
12611243 TTTT
1 TTTT
12611247 ATTAATGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 9 0.33
28 18 0.67
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (27 bp):
TTTTCAAAATATTTATATATACTATTA
Found at i:12616596 original size:11 final size:11
Alignment explanation
Indices: 12616580--12616617 Score: 62
Period size: 10 Copynumber: 3.6 Consensus size: 11
12616570 CTCATCCAGC
12616580 AAAGAAAGAAA
1 AAAGAAAGAAA
12616591 AAAGAAA-AAA
1 AAAGAAAGAAA
12616601 AAA-AAAGAAA
1 AAAGAAAGAAA
12616611 AAAGAAA
1 AAAGAAA
12616618 AATGAGAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 3 0.12
10 12 0.48
11 10 0.40
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (11 bp):
AAAGAAAGAAA
Found at i:12616601 original size:8 final size:8
Alignment explanation
Indices: 12616580--12616696 Score: 57
Period size: 7 Copynumber: 14.2 Consensus size: 8
12616570 CTCATCCAGC
12616580 AAAGAAAGA
1 AAAGAAA-A
12616589 AAA-AAGAA
1 AAAGAA-AA
12616597 AAA-AAAA
1 AAAGAAAA
12616604 AAAG-AAA
1 AAAGAAAA
12616611 AAAG-AAA
1 AAAGAAAA
* *
12616618 AATG-AGA
1 AAAGAAAA
*
12616625 AATGAGAAA
1 AAAGA-AAA
*
12616634 AAAG-GAA
1 AAAGAAAA
*
12616641 AAAGGAAA
1 AAAGAAAA
12616649 AAAGAAAAA
1 AAAG-AAAA
12616658 AAATGAAAA
1 AAA-GAAAA
12616667 AAATGAGAAA
1 AAA-GA-AAA
12616677 AAAGGGAAAA
1 AAA--GAAAA
*
12616687 AAGGAAAA
1 AAAGAAAA
12616695 AA
1 AA
12616697 TTGAACCAAG
Statistics
Matches: 90, Mismatches: 9, Indels: 19
0.76 0.08 0.16
Matches are distributed among these distances:
7 30 0.33
8 21 0.23
9 25 0.28
10 12 0.13
11 2 0.02
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (8 bp):
AAAGAAAA
Found at i:12616602 original size:9 final size:9
Alignment explanation
Indices: 12616584--12616696 Score: 54
Period size: 9 Copynumber: 12.1 Consensus size: 9
12616574 TCCAGCAAAG
12616584 AAAGAAAAA
1 AAAGAAAAA
12616593 AGAA-AAAAA
1 A-AAGAAAAA
12616602 AAA-AAGAAA
1 AAAGAA-AAA
12616611 AAAGAAAAA
1 AAAGAAAAA
**
12616620 TGAGAAATGAGA
1 AAAGAAA--A-A
*
12616632 AAA-AAGGAA
1 AAAGAA-AAA
*
12616641 AAAG-GAAA
1 AAAGAAAAA
12616649 AAAGAAAAA
1 AAAGAAAAA
12616658 AAATGAAAAA
1 AAA-GAAAAA
*
12616668 AATGAGAAAA
1 AAAGA-AAAA
* *
12616678 AAGGGAAAA
1 AAAGAAAAA
*
12616687 AAGGAAAAA
1 AAAGAAAAA
12616696 A
1 A
12616697 TTGAACCAAG
Statistics
Matches: 81, Mismatches: 12, Indels: 22
0.70 0.10 0.19
Matches are distributed among these distances:
8 10 0.12
9 46 0.57
10 20 0.25
11 3 0.04
12 2 0.02
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.04
Consensus pattern (9 bp):
AAAGAAAAA
Found at i:12616643 original size:43 final size:40
Alignment explanation
Indices: 12616586--12616688 Score: 118
Period size: 43 Copynumber: 2.4 Consensus size: 40
12616576 CAGCAAAGAA
*
12616586 AGAAAAAAGAAAAAAAAAAAAGAAAAAAGAA-AAATGAGAAATG
1 AGAAAAAAGGAAAAAAAAAAAGAAAAAA-AAGAAA--A-AAATG
12616629 AGAAAAAAGGAAAAAGGAAAAAAGAAAAAAAATGAAAAAAATG
1 AGAAAAAAGGAAAAA--AAAAAAGAAAAAAAA-GAAAAAAATG
*
12616672 AGAAAAAAGGGAAAAAA
1 AGAAAAAAGGAAAAAAA
12616689 GGAAAAAATT
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
41 2 0.04
43 33 0.61
44 3 0.06
45 13 0.24
46 3 0.06
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (40 bp):
AGAAAAAAGGAAAAAAAAAAAGAAAAAAAAGAAAAAAATG
Found at i:12616667 original size:7 final size:7
Alignment explanation
Indices: 12616584--12616658 Score: 89
Period size: 7 Copynumber: 10.4 Consensus size: 7
12616574 TCCAGCAAAG
12616584 AAAGAAA
1 AAAGAAA
12616591 AAAGAAA
1 AAAGAAA
12616598 AAA-AAA
1 AAAGAAA
12616604 AAAGAAA
1 AAAGAAA
12616611 AAAGAAA
1 AAAGAAA
12616618 AATGAGAAA
1 AA--AGAAA
**
12616627 TGAGAAA
1 AAAGAAA
12616634 AAAGGAAA
1 AAA-GAAA
*
12616642 AAGGAAA
1 AAAGAAA
12616649 AAAGAAA
1 AAAGAAA
12616656 AAA
1 AAA
12616659 AATGAAAAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
6 6 0.10
7 41 0.71
8 6 0.10
9 5 0.09
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (7 bp):
AAAGAAA
Found at i:12616677 original size:17 final size:17
Alignment explanation
Indices: 12616615--12616677 Score: 51
Period size: 17 Copynumber: 3.8 Consensus size: 17
12616605 AAGAAAAAAG
12616615 AAAAATGAG-AAATGAGA
1 AAAAATGAGAAAATGA-A
* *
12616632 AAAAAGGA-AAAAGGAA
1 AAAAATGAGAAAATGAA
* *
12616648 AAAAGA-AAAAAAATGAA
1 AAAA-ATGAGAAAATGAA
12616665 AAAAATGAGAAAA
1 AAAAATGAGAAAA
12616678 AAGGGAAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
16 7 0.19
17 29 0.81
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06
Consensus pattern (17 bp):
AAAAATGAGAAAATGAA
Found at i:12616687 original size:10 final size:9
Alignment explanation
Indices: 12616631--12616696 Score: 66
Period size: 9 Copynumber: 7.6 Consensus size: 9
12616621 GAGAAATGAG
12616631 AAAAAAGG-
1 AAAAAAGGA
12616639 -AAAAAGG-
1 AAAAAAGGA
*
12616646 AAAAAAGAA
1 AAAAAAGGA
*
12616655 AAAAAATGA
1 AAAAAAGGA
*
12616664 AAAAAATGA
1 AAAAAAGGA
*
12616673 GAAAAAAGGG
1 -AAAAAAGGA
12616683 AAAAAAGGA
1 AAAAAAGGA
12616692 AAAAA
1 AAAAA
12616697 TTGAACCAAG
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
7 7 0.14
8 6 0.12
9 29 0.59
10 7 0.14
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (9 bp):
AAAAAAGGA
Done.