Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006493.1 Hibiscus syriacus cultivar Beakdansim tig00015791_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: 75088
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:14195 original size:60 final size:59
Alignment explanation
Indices: 14052--14195 Score: 146
Period size: 60 Copynumber: 2.4 Consensus size: 59
14042 TTAGAGTAAA
* *
14052 TTACACAAATGGTCCCTCGACTATAGGGTACTACTTTGTTGAGTCCTCTAACTATTAAAAG
1 TTACA-AAATGGTCCCT-GACTATAGGATACTACTTTATTGAGTCCTCTAACTATTAAAAG
* ** ** * *
14113 TTACAAAATGATCTCCCAACTATAGGATGTTACTTTATTGAGTCC-CTCGACTATTAGAAG
1 TTACAAAATGGTC-CCTGACTATAGGATACTACTTTATTGAGTCCTCT-AACTATTAAAAG
*
14173 TTATAAAATGGTCACCTGACTAT
1 TTACAAAATGGTC-CCTGACTAT
14196 TCATATGTTC
Statistics
Matches: 67, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
59 2 0.03
60 58 0.87
61 7 0.10
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.33
Consensus pattern (59 bp):
TTACAAAATGGTCCCTGACTATAGGATACTACTTTATTGAGTCCTCTAACTATTAAAAG
Found at i:16135 original size:44 final size:44
Alignment explanation
Indices: 16072--16156 Score: 136
Period size: 44 Copynumber: 1.9 Consensus size: 44
16062 CGGTATAATT
*
16072 CGTCTAAATCAAAAGAGATAAACAATCAACAATCATTAATTTTC
1 CGTCTAAATCAAAAGAGATAAACAATCAACAATCATCAATTTTC
*
16116 CGTCTAAATCATAAA-AGATAAACCATCAACAATCATCAATT
1 CGTCTAAATCA-AAAGAGATAAACAATCAACAATCATCAATT
16157 CTCAATCGTC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
44 35 0.92
45 3 0.08
ACGTcount: A:0.48, C:0.20, G:0.06, T:0.26
Consensus pattern (44 bp):
CGTCTAAATCAAAAGAGATAAACAATCAACAATCATCAATTTTC
Found at i:16250 original size:44 final size:44
Alignment explanation
Indices: 16183--16277 Score: 145
Period size: 44 Copynumber: 2.2 Consensus size: 44
16173 TCACGATTAT
* * *
16183 AATTCTTCGTCTAAATTAGAAGAGATAAACAATCAACAATCATC
1 AATTCTCCGTCTAAATCAGAAGAGATAAACAACCAACAATCATC
* *
16227 AATTCTCCGTCTAAATCATAAGAGATAAACCACCAACAATCATC
1 AATTCTCCGTCTAAATCAGAAGAGATAAACAACCAACAATCATC
16271 AATTCTC
1 AATTCTC
16278 AATCGTCGTC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.43, C:0.23, G:0.07, T:0.26
Consensus pattern (44 bp):
AATTCTCCGTCTAAATCAGAAGAGATAAACAACCAACAATCATC
Found at i:16278 original size:118 final size:118
Alignment explanation
Indices: 16070--16516 Score: 752
Period size: 118 Copynumber: 3.8 Consensus size: 118
16060 ATCGGTATAA
* * * *
16070 TTCGTCTAAATCAAAAGAGATAAACAATCAACAATCATTAATTTTCCGTCTAAATCATAAAAGAT
1 TTCGTCTAAATCATAAGAGATAAACAATCAACAATCATCAATTCTCCGTCTAAATCATAAGAGAT
*
16135 AAACCATCAACAATCATCAATTCTCAATCGTCGTCTTATCACGATTATAATTC
66 AAACCACCAACAATCATCAATTCTCAATCGTCGTCTTATCACGATTATAATTC
* *
16188 TTCGTCTAAATTAGAAGAGATAAACAATCAACAATCATCAATTCTCCGTCTAAATCATAAGAGAT
1 TTCGTCTAAATCATAAGAGATAAACAATCAACAATCATCAATTCTCCGTCTAAATCATAAGAGAT
16253 AAACCACCAACAATCATCAATTCTCAATCGTCGTCTTATCACGATTATAATTC
66 AAACCACCAACAATCATCAATTCTCAATCGTCGTCTTATCACGATTATAATTC
* * * *
16306 TTCGTCTAAATCATAAGAGATAAACCATTAACAATCATCAATTCTCCATCTAAATCATAAGTGAT
1 TTCGTCTAAATCATAAGAGATAAACAATCAACAATCATCAATTCTCCGTCTAAATCATAAGAGAT
16371 AAACCACCAACAATCATCAATTCTCAATCGTCGTCTTATCACGATTATACA-TC
66 AAACCACCAACAATCATCAATTCTCAATCGTCGTCTTATCACGATTATA-ATTC
*
16424 TTCGTCTAAATCATAAGAGATAAACCATCAACAATCATCAATTCTCCGTCTAAATCATAAGAGAT
1 TTCGTCTAAATCATAAGAGATAAACAATCAACAATCATCAATTCTCCGTCTAAATCATAAGAGAT
**
16489 AAACCGTCAACAATCATCAATTCTCAAT
66 AAACCACCAACAATCATCAATTCTCAAT
16517 TGAATCTGGT
Statistics
Matches: 311, Mismatches: 17, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
118 310 1.00
119 1 0.00
ACGTcount: A:0.40, C:0.23, G:0.07, T:0.29
Consensus pattern (118 bp):
TTCGTCTAAATCATAAGAGATAAACAATCAACAATCATCAATTCTCCGTCTAAATCATAAGAGAT
AAACCACCAACAATCATCAATTCTCAATCGTCGTCTTATCACGATTATAATTC
Found at i:16364 original size:44 final size:44
Alignment explanation
Indices: 16301--16395 Score: 145
Period size: 44 Copynumber: 2.2 Consensus size: 44
16291 TCACGATTAT
* * **
16301 AATTCTTCGTCTAAATCATAAGAGATAAACCATTAACAATCATC
1 AATTCTCCATCTAAATCATAAGAGATAAACCACCAACAATCATC
*
16345 AATTCTCCATCTAAATCATAAGTGATAAACCACCAACAATCATC
1 AATTCTCCATCTAAATCATAAGAGATAAACCACCAACAATCATC
16389 AATTCTC
1 AATTCTC
16396 AATCGTCGTC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.42, C:0.24, G:0.05, T:0.28
Consensus pattern (44 bp):
AATTCTCCATCTAAATCATAAGAGATAAACCACCAACAATCATC
Found at i:16489 original size:44 final size:44
Alignment explanation
Indices: 16426--16513 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
16416 TATACATCTT
16426 CGTCTAAATCATAAGAGATAAACCATCAACAATCATCAATTCTC
1 CGTCTAAATCATAAGAGATAAACCATCAACAATCATCAATTCTC
*
16470 CGTCTAAATCATAAGAGATAAACCGTCAACAATCATCAATTCTC
1 CGTCTAAATCATAAGAGATAAACCATCAACAATCATCAATTCTC
16514 AATTGAATCT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.42, C:0.25, G:0.08, T:0.25
Consensus pattern (44 bp):
CGTCTAAATCATAAGAGATAAACCATCAACAATCATCAATTCTC
Found at i:20540 original size:2 final size:2
Alignment explanation
Indices: 20533--20557 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20523 AGTTCAATAA
20533 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
20558 TTAAACCCCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:21932 original size:15 final size:15
Alignment explanation
Indices: 21912--21941 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
21902 TCTTTTATTA
21912 TTATTATTATATTTT
1 TTATTATTATATTTT
21927 TTATTATTATATTTT
1 TTATTATTATATTTT
21942 CTTTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TTATTATTATATTTT
Found at i:23806 original size:19 final size:19
Alignment explanation
Indices: 23772--23816 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
23762 ATTTAGACAT
23772 TTTGCA-TTTCTTATTTTC
1 TTTGCATTTTCTTATTTTC
*
23790 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTCTTATTTTC
23809 TTTGCATT
1 TTTGCATT
23817 CACATTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.11, C:0.13, G:0.09, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTCTTATTTTC
Found at i:27366 original size:165 final size:165
Alignment explanation
Indices: 27001--27578 Score: 630
Period size: 165 Copynumber: 3.5 Consensus size: 165
26991 AAAGACCTTT
* * * * * * * *
27001 GAGTTTGACTACGATCAGC-TCAACGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTA
1 GAGTTCGACTACGCTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTA
*** * * * *
27065 TCTG-C--C-AAAGACCCCCGAGTTCGACTACGCTCAGCTTCGAGGGCACATCATTTACAGCATA
66 TCTGCCAACAAAAGACCTTTGAGTTCGACTACGATCAGC-TCCAAGGCACATCATTTGCAGCATA
* * * * * * **
27126 ACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGATCTTC
130 GCTTAAGTCGAGAAGGGCTATC--TG-CC-AAAGACCCCC
* * * * * * * *
27166 GAGTTAGACTACGCTCGGC-TCCAAGGCATATCATTTGCAGCACAACTTAAGTCTACAAGGGTTG
1 GAGTTCGACTACGCTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTA
* *
27230 TCTGCCAACAAAAGACCTTTGAGTTTGACTACGATCAGCT-CAACGGCACATCATTTGCAGTATA
66 TCTGCCAACAAAAGACCTTTGAGTTCGACTACGATCAGCTCCAA-GGCACATCATTTGCAGCATA
27294 GCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCC
130 GCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCC
* * *
27330 GAGTTCGACTACGCTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTA
1 GAGTTCGACTACGCTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTA
** * *
27395 TCTGTGACCAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAG
66 TCTGCCAACAAAAGACCTTTGAGTTCGACTACGATCAGCTCCAAGGCACATCATTTGCAGCATAG
**
27460 CTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTC
131 CTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCC
* * * *
27495 GAGTTCGATTACACTCAGCTCCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTA
1 GAGTTCGACTACGCTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTA
*
27560 TCTGCCAACCAAAGACCTT
66 TCTGCCAACAAAAGACCTT
27579 AAGGCACATC
Statistics
Matches: 346, Mismatches: 60, Indels: 14
0.82 0.14 0.03
Matches are distributed among these distances:
164 24 0.07
165 254 0.73
166 6 0.02
167 1 0.00
168 37 0.11
169 24 0.07
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (165 bp):
GAGTTCGACTACGCTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTA
TCTGCCAACAAAAGACCTTTGAGTTCGACTACGATCAGCTCCAAGGCACATCATTTGCAGCATAG
CTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCC
Found at i:27387 original size:249 final size:249
Alignment explanation
Indices: 26949--27567 Score: 1014
Period size: 249 Copynumber: 2.5 Consensus size: 249
26939 AAAACAAACT
26949 ATTTGCAGCACAACTTAAGTCTACAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTTGACTACG
1 ATTTGCAGCACAACTTAAGTCTACAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTTGACTACG
27014 ATCAGCTCAACGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCC
66 ATCAGCTCAACGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCC
27079 CCGAGTTCGACTACGCTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGT
131 CCGAGTTCGACTACGCTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGT
* * *
27144 TATCTGTGACCAAAAGATCTTCGAGTTAGACTACGCTCGGCTCCAAGGCATATC
196 TATCTGTGACCAAAAGACCTTCGAGTTAGACTACGCTCAGCTCCAAGGCACATC
27198 ATTTGCAGCACAACTTAAGTCTACAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTTGACTACG
1 ATTTGCAGCACAACTTAAGTCTACAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTTGACTACG
27263 ATCAGCTCAACGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCC
66 ATCAGCTCAACGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCC
27328 CCGAGTTCGACTACGCTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGT
131 CCGAGTTCGACTACGCTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGT
* *
27393 TATCTGTGACCAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATC
196 TATCTGTGACCAAAAGACCTTCGAGTTAGACTACGCTCAGCTCCAAGGCACATC
* * * * * * * * *
27447 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-C--C-AAAGACCTTCGAGTTCGATTAC-
1 ATTTGCAGCACAACTTAAGTCTACAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTTGACTACG
* * * * *
27507 ACTCAGCTCCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAA
66 A-TCAGCT-CAACGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAA
27568 CCAAAGACCT
Statistics
Matches: 349, Mismatches: 19, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
244 1 0.00
245 25 0.07
246 48 0.14
248 1 0.00
249 274 0.79
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (249 bp):
ATTTGCAGCACAACTTAAGTCTACAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTTGACTACG
ATCAGCTCAACGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCC
CCGAGTTCGACTACGCTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGT
TATCTGTGACCAAAAGACCTTCGAGTTAGACTACGCTCAGCTCCAAGGCACATC
Found at i:27696 original size:142 final size:142
Alignment explanation
Indices: 27437--27705 Score: 484
Period size: 142 Copynumber: 1.9 Consensus size: 142
27427 GCTCAGCTCC
*
27437 AAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCG
1 AAGGCACATCATTTGCAGCATAGCTTAAGTCGAAAAGGGCTATCTGCCAAAGACCTTCGAGTTCG
* * *
27502 ATTACACTCAGCTCCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCA
66 ATTACACTCAGCTCCGAGGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGCCA
27567 ACCAAAGACCTT
131 ACCAAAGACCTT
27579 AAGGCACATCATTTGCAGCATAGCTTAAGTCGAAAAGGGCTATCTGCCAAAGACCTTCGAGTTCG
1 AAGGCACATCATTTGCAGCATAGCTTAAGTCGAAAAGGGCTATCTGCCAAAGACCTTCGAGTTCG
* *
27644 ATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG
66 ATTACACTCAGCTCCGAGGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTG
27706 TGACTAAAAG
Statistics
Matches: 121, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
142 121 1.00
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (142 bp):
AAGGCACATCATTTGCAGCATAGCTTAAGTCGAAAAGGGCTATCTGCCAAAGACCTTCGAGTTCG
ATTACACTCAGCTCCGAGGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGCCA
ACCAAAGACCTT
Found at i:27830 original size:307 final size:306
Alignment explanation
Indices: 27274--27884 Score: 997
Period size: 307 Copynumber: 2.0 Consensus size: 306
27264 TCAGCTCAAC
* *
27274 GGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGAC
1 GGCACATCATTTGCAGCATAGCTTAAGTCGAAAAGGGCTATCTGCCAAAGACCCCCGAGTTCGAC
*
27339 TACGCTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACC
66 TACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACC
* *
27404 AAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCG
131 AAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAGCTTAAGTCG
* * **
27469 AGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGATTACACTCAGCTCCGAGGGCACATCATTTGC
196 AGAAGGGCTATCTGCCAAAGACCCTCGAGTTCAATTACACTCAGCTCCGAGGGCACATCATTCAC
* * *
27534 AGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTAA
261 AACATAACTCAAGGCGAGAAGGGTTATCTGCC-ACCAAAGACCTTAA
** *
27581 GGCACATCATTTGCAGCATAGCTTAAGTCGAAAAGGGCTATCTGCCAAAGACCTTCGAGTTCGAT
1 GGCACATCATTTGCAGCATAGCTTAAGTCGAAAAGGGCTATCTGCCAAAGACCCCCGAGTTCGAC
*
27646 TACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACT
66 TACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACC
* *
27711 AAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTACAGTATAGCTTAAGTCG
131 AAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAGCTTAAGTCG
* **
27776 AGAAGGGCTATCTGCCAAAGACCCTCGAGTTCAATTACTCTCAGCTTGGAGGGCACATCATTCAC
196 AGAAGGGCTATCTGCCAAAGACCCTCGAGTTCAATTACACTCAGCTCCGAGGGCACATCATTCAC
* * *
27841 AATATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTT
261 AACATAACTCAAGGCGAGAAGGGTTATCTGCCACCAAAGACCTT
27885 TGAGTTCGAC
Statistics
Matches: 280, Mismatches: 24, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
306 12 0.04
307 268 0.96
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (306 bp):
GGCACATCATTTGCAGCATAGCTTAAGTCGAAAAGGGCTATCTGCCAAAGACCCCCGAGTTCGAC
TACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACC
AAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAGCTTAAGTCG
AGAAGGGCTATCTGCCAAAGACCCTCGAGTTCAATTACACTCAGCTCCGAGGGCACATCATTCAC
AACATAACTCAAGGCGAGAAGGGTTATCTGCCACCAAAGACCTTAA
Found at i:27962 original size:164 final size:165
Alignment explanation
Indices: 27578--28043 Score: 682
Period size: 164 Copynumber: 2.8 Consensus size: 165
27568 CCAAAGACCT
* * *
27578 TAAGGCACATCATTTGCAGCATAGCTTAAGTCGAAAAGGGCTATCTGCCAAAGACCTTCGAGTTC
1 TAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTC
* *
27643 GATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTG
66 GATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTC
27708 ACTAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
131 ACTAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
*
27743 TAAGGCACATCATTTACAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTC
1 TAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTC
* * * * *
27808 AATTACTCTCAGCTTGGAGGGCACATCATTCACAATATAACTCAAGGCTAGAAGGGTTATCTGTC
66 GATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTC
* *
27873 AC-CAAAGACCTTTGAGTTCGACTACGCTCAGCTC
131 ACTAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
* * * * * *
27907 TCAGGCACATCATTGGCAGTATAACTTAAGTCGAGAAGAGTTATCTGCCAAAGACCCTCGAGTTT
1 TAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTC
* * * * * * *
27972 GATTACACTCAACTTCGAGGTCATATCGTTTACAACATAGCTCAAGGCAAGAAGGGTTATTTGTC
66 GATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTC
*
28037 AATAAAA
131 ACTAAAA
28044 TTGTCGAGTT
Statistics
Matches: 266, Mismatches: 34, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
164 142 0.53
165 124 0.47
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (165 bp):
TAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTC
GATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTC
ACTAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
Found at i:29723 original size:22 final size:22
Alignment explanation
Indices: 29696--29737 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
29686 CTGACCCTTA
*
29696 TTTTATTATTATTT-TTTTTACT
1 TTTTATT-TCATTTCTTTTTACT
29718 TTTTATTTCATTTCTTTTTA
1 TTTTATTTCATTTCTTTTTA
29738 TCAGTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTTATTTCATTTCTTTTTACT
Found at i:29856 original size:15 final size:15
Alignment explanation
Indices: 29836--29865 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
29826 TCTTTTATTA
29836 TTATTATTATATTTT
1 TTATTATTATATTTT
29851 TTATTATTATATTTT
1 TTATTATTATATTTT
29866 CTTTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TTATTATTATATTTT
Found at i:37592 original size:2 final size:2
Alignment explanation
Indices: 37585--37622 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
37575 AATTCTACTT
37585 TA TA 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
37623 AAGGCTTATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39453 original size:26 final size:27
Alignment explanation
Indices: 39424--39474 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
39414 TTTATATATA
39424 TATATATA-AAACTTAATTTATTTTTC
1 TATATATACAAACTTAATTTATTTTTC
* * *
39450 TATATTTACAAATTTTATTTATTTT
1 TATATATACAAACTTAATTTATTTT
39475 ATATTTTGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 7 0.33
27 14 0.67
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (27 bp):
TATATATACAAACTTAATTTATTTTTC
Found at i:42635 original size:31 final size:31
Alignment explanation
Indices: 42599--42658 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
42589 AACTTAAAAG
* *
42599 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
42630 AGTTTTACAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
42659 CATACAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:43157 original size:16 final size:17
Alignment explanation
Indices: 43136--43179 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
43126 AATTAAAATA
43136 AATATAAAATTTTA-AT
1 AATATAAAATTTTATAT
*
43152 AATATAAAAATTTATAT
1 AATATAAAATTTTATAT
*
43169 GATATAAAATT
1 AATATAAAATT
43180 AAATATCTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 13 0.54
17 11 0.46
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (17 bp):
AATATAAAATTTTATAT
Found at i:43182 original size:23 final size:21
Alignment explanation
Indices: 43156--43208 Score: 52
Period size: 23 Copynumber: 2.4 Consensus size: 21
43146 TTTAATAATA
43156 TAAAAATTTATATGATATAAAAT
1 TAAAAATTTATA--ATATAAAAT
* * *
43179 TAAATATCTATAATATAATAT
1 TAAAAATTTATAATATAAAAT
43200 TGAAAAATT
1 T-AAAAATT
43209 ATTATTTAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
21 9 0.38
22 5 0.21
23 10 0.42
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.40
Consensus pattern (21 bp):
TAAAAATTTATAATATAAAAT
Found at i:43229 original size:24 final size:24
Alignment explanation
Indices: 43202--43247 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
43192 TATAATATTG
* * *
43202 AAAAATTATTATTTAATTTATTTA
1 AAAAATTAATATTAAAATTATTTA
43226 AAAAATTAATATTAAAATTATT
1 AAAAATTAATATTAAAATTATT
43248 ATCTATAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAAATTAATATTAAAATTATTTA
Found at i:43242 original size:12 final size:12
Alignment explanation
Indices: 43227--43333 Score: 60
Period size: 12 Copynumber: 8.7 Consensus size: 12
43217 ATTTATTTAA
43227 AAAATTAATATT
1 AAAATTAATATT
*
43239 AAAATTATTATCT
1 AAAATTAATAT-T
*
43252 ATAATATAATATT
1 AAAAT-TAATATT
*
43265 AAAAATTTATTATT
1 -AAAA-TTAATATT
* *
43279 -TAATTTAT-TT
1 AAAATTAATATT
43289 AAAAAATTAATATT
1 --AAAATTAATATT
*
43303 AAAATTAA-AAT
1 AAAATTAATATT
*
43314 CAAATATAATA-T
1 AAAAT-TAATATT
43326 AAAATTAA
1 AAAATTAA
43334 ATATAAAACC
Statistics
Matches: 72, Mismatches: 13, Indels: 21
0.68 0.12 0.20
Matches are distributed among these distances:
10 2 0.03
11 12 0.17
12 28 0.39
13 13 0.18
14 16 0.22
15 1 0.01
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (12 bp):
AAAATTAATATT
Found at i:43253 original size:64 final size:64
Alignment explanation
Indices: 43173--43329 Score: 250
Period size: 64 Copynumber: 2.5 Consensus size: 64
43163 TTATATGATA
43173 TAAAATTAAATATCTATAATATAATATTGAAAAA-TTATTATTTAATTTATTTAAAAAATTAATA
1 TAAAATT-AATATCTATAATATAATATT-AAAAATTTATTATTTAATTTATTTAAAAAATTAATA
43237 T
64 T
*
43238 TAAAATTATTATCTATAATATAATATTAAAAATTTATTATTTAATTTATTTAAAAAATTAATAT
1 TAAAATTAATATCTATAATATAATATTAAAAATTTATTATTTAATTTATTTAAAAAATTAATAT
*
43302 TAAAATTAAAATC-A-AATATAATA-TAAAA
1 TAAAATTAATATCTATAATATAATATTAAAA
43330 TTAAATATAA
Statistics
Matches: 88, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
61 5 0.06
62 9 0.10
63 6 0.07
64 61 0.69
65 7 0.08
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (64 bp):
TAAAATTAATATCTATAATATAATATTAAAAATTTATTATTTAATTTATTTAAAAAATTAATAT
Found at i:43282 original size:21 final size:24
Alignment explanation
Indices: 43230--43282 Score: 58
Period size: 26 Copynumber: 2.2 Consensus size: 24
43220 TATTTAAAAA
*
43230 ATTAATATTAAAATTATTATCTAT
1 ATTAATATTAAAAATATTATCTAT
43254 AATATAATATTAAAAAT-TTAT-TAT
1 -AT-TAATATTAAAAATATTATCTAT
43278 -TTAAT
1 ATTAAT
43283 TTATTTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 4 0.15
22 1 0.04
24 3 0.12
25 6 0.23
26 12 0.46
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (24 bp):
ATTAATATTAAAAATATTATCTAT
Found at i:43336 original size:12 final size:12
Alignment explanation
Indices: 43291--43341 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
43281 ATTTATTTAA
43291 AAAATT-AATATT
1 AAAATTAAATA-T
43303 AAAATTAAA-AT
1 AAAATTAAATAT
*
43314 CAAA-TATAATAT
1 AAAATTA-AATAT
43326 AAAATTAAATAT
1 AAAATTAAATAT
43338 AAAA
1 AAAA
43342 CCTCTTTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
10 2 0.06
11 6 0.18
12 21 0.64
13 4 0.12
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (12 bp):
AAAATTAAATAT
Found at i:45143 original size:30 final size:30
Alignment explanation
Indices: 45072--45131 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
45062 ACAATTTAAG
45072 GCAAAATGTTTTTGGACTGGAATTGAATTT
1 GCAAAATGTTTTTGGACTGGAATTGAATTT
* *
45102 GCAAAATGTTTTTGGATTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTGGAATTGAATTT
45132 ATTCAAAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.30, C:0.05, G:0.22, T:0.43
Consensus pattern (30 bp):
GCAAAATGTTTTTGGACTGGAATTGAATTT
Found at i:45237 original size:21 final size:21
Alignment explanation
Indices: 45211--45268 Score: 116
Period size: 21 Copynumber: 2.8 Consensus size: 21
45201 AGGGTGTCAA
45211 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
45232 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
45253 AGTGCATCCATGCATC
1 AGTGCATCCATGCATC
45269 TGCACTAATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (21 bp):
AGTGCATCCATGCATCCCTGC
Found at i:45357 original size:21 final size:21
Alignment explanation
Indices: 45331--45406 Score: 127
Period size: 21 Copynumber: 3.7 Consensus size: 21
45321 ATGCAATTAG
45331 TGCATCGATGCATCCTTGCCA
1 TGCATCGATGCATCCTTGCCA
45352 TGCATCGATGCATCCTTGCCA
1 TGCATCGATGCATCCTTGCCA
*
45373 TGCATCGATGCATCC-TGTCA
1 TGCATCGATGCATCCTTGCCA
*
45393 TGCATCCATGCATC
1 TGCATCGATGCATC
45407 AAGGCTGCAA
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
20 17 0.32
21 36 0.68
ACGTcount: A:0.20, C:0.33, G:0.18, T:0.29
Consensus pattern (21 bp):
TGCATCGATGCATCCTTGCCA
Found at i:45838 original size:32 final size:33
Alignment explanation
Indices: 45771--45840 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 33
45761 TTTTGTAAAG
* *
45771 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-GTAAAAACTA
*
45805 GGGAAAGGTTCTAGTTTAGCCC-GTAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGTAAAAACTA
45837 GGGA
1 GGGA
45841 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 13 0.39
34 20 0.61
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (33 bp):
GGGAAAGGTTCTAGCTTAGCCCGGTAAAAACTA
Found at i:46726 original size:19 final size:20
Alignment explanation
Indices: 46702--46749 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
46692 AATGATTTTC
*
46702 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
46721 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
46741 TTTTGAAAA
1 TTTTGAAAA
46750 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:47967 original size:89 final size:88
Alignment explanation
Indices: 47866--48043 Score: 347
Period size: 89 Copynumber: 2.0 Consensus size: 88
47856 AAGGGGAGCT
47866 TAACATTTTCATATATTTTCCAACAATTGGTAACAATTGATATCTTTTTCATTAAACAATTTATT
1 TAACATTTTCATATATTTTCCAACAATTGGTAACAATTGATATCTTTTTCATTAAACAATTTATT
47931 AAGGGGGAGTTTTGCCAAAACCAA
66 AA-GGGGAGTTTTGCCAAAACCAA
47955 TAACATTTTCATATATTTTCCAACAATTGGTAACAATTGATATCTTTTTCATTAAACAATTTATT
1 TAACATTTTCATATATTTTCCAACAATTGGTAACAATTGATATCTTTTTCATTAAACAATTTATT
48020 AAGGGGAGTTTTGCCAAAACCAA
66 AAGGGGAGTTTTGCCAAAACCAA
48043 T
1 T
48044 TTTTCAAATG
Statistics
Matches: 89, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
88 22 0.25
89 67 0.75
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.39
Consensus pattern (88 bp):
TAACATTTTCATATATTTTCCAACAATTGGTAACAATTGATATCTTTTTCATTAAACAATTTATT
AAGGGGAGTTTTGCCAAAACCAA
Found at i:48148 original size:30 final size:30
Alignment explanation
Indices: 48112--48171 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
48102 ACAATTTAAG
*
48112 GCAAAATGTTTTTGGACTGGAATTGAATTT
1 GCAAAATATTTTTGGACTGGAATTGAATTT
* *
48142 GCAAAATATTTTTGGATTTGAATTGAATTT
1 GCAAAATATTTTTGGACTGGAATTGAATTT
48172 ATTCAAAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.43
Consensus pattern (30 bp):
GCAAAATATTTTTGGACTGGAATTGAATTT
Found at i:48376 original size:20 final size:20
Alignment explanation
Indices: 48351--48404 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
48341 ATGCAATTAG
*
48351 TGCATCGATGCATCTTGCCA
1 TGCATCGATGCATCCTGCCA
*
48371 TGCATCGATGCATCCTGTCA
1 TGCATCGATGCATCCTGCCA
*
48391 TGCATCCATGCATC
1 TGCATCGATGCATC
48405 AAGGCTGCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.20, C:0.31, G:0.19, T:0.30
Consensus pattern (20 bp):
TGCATCGATGCATCCTGCCA
Found at i:49088 original size:21 final size:21
Alignment explanation
Indices: 49064--49121 Score: 116
Period size: 21 Copynumber: 2.8 Consensus size: 21
49054 AAATCCCAAA
49064 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
49085 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
49106 AGTGCATCCATGCATC
1 AGTGCATCCATGCATC
49122 TGCACTAATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (21 bp):
AGTGCATCCATGCATCCCTGC
Found at i:49225 original size:20 final size:21
Alignment explanation
Indices: 49184--49238 Score: 94
Period size: 20 Copynumber: 2.7 Consensus size: 21
49174 ATGCAATTAG
49184 TGCATCGATGCATCCTTGCCA
1 TGCATCGATGCATCCTTGCCA
49205 TGCATCGATGCATCC-TGCCA
1 TGCATCGATGCATCCTTGCCA
*
49225 TGCATCCATGCATC
1 TGCATCGATGCATC
49239 AAGGCTGCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 18 0.55
21 15 0.45
ACGTcount: A:0.20, C:0.35, G:0.18, T:0.27
Consensus pattern (21 bp):
TGCATCGATGCATCCTTGCCA
Found at i:49642 original size:34 final size:32
Alignment explanation
Indices: 49603--49672 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
49593 TTTTGTAAAG
* *
49603 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
49637 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
49669 GGGA
1 GGGA
49673 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:49866 original size:844 final size:833
Alignment explanation
Indices: 48252--49906 Score: 3139
Period size: 844 Copynumber: 2.0 Consensus size: 833
48242 AGGGTGTCAA
*
48252 AGTGCATCCATGCATCCCTGTAGTGCATCCATGCATCTGCACTAATGCATCGATGCATCAGGCAA
1 AGTGCATCCATGCATCCCTGCAGTGCATCCATGCATCTGCACTAATGCATCGATGCATCAGGCAA
48317 TGCATCCATGCATCCAAACATCGAATGCAATTAGTGCATCGATGCATCTTGCCATGCATCGATGC
66 TGCATCCATGCATCCAAACATCGAATGCAATTAGTGCATCGATGCATCTTGCCATGCATCGATGC
*
48382 ATCCTGTCATGCATCCATGCATCAAGGCTGCAACGGCTAGTTTATTTGAATTTAATGAAGGGGTA
131 ATCCTGCCATGCATCCATGCATCAAGGCTGCAACGGCTAGTTTATTTGAATTTAATGAAGGGGTA
48447 TCGATGCACCTTGATCATGCATCGATGCATCATGTTATGGGCAGCCTTTTTGAGTAGAAAAATCA
196 TCGATGCACCTTGATCATGCATCGATGCATCATGTTATGGGCAGCCTTTTTGAGTAGAAAAATCA
48512 TCCCCAAACGACTCCAAAACATCCCCAACGGCTATATACAACATCAAACACATTCCAAGCTATAA
261 TCCCCAAACGACTCCAAAACATCCCCAACGGCTATATACAACATCAAACACATTCCAAGCTATAA
48577 ATACAAGCTGAGGACACTTGAAGAAGTAAGAGAACAACTATCCAAGCAATCAAACACAAGAGAAG
326 ATACAAGCTGAGGACACTTGAAGAAGTAAGAGAACAACTATCCAAGCAATCAAACACAAGAGAAG
*
48642 AGTTTTTTATTCTTATTTCATCATTCTCTTGTAAATATTTTGTTCTTGTGAGCTCAATCTTGTAA
391 AGTTTTTCATTCTTATTTCATCATTCTCTTGTAAATATTTTGTTCTTGTGAGCTCAATCTTGTAA
*
48707 ACACCTACCTTAGAGAGGTTTTCTTGTTTACATCTTTTATCCTTTTGTAAAGGGGAAATGTTCTA
456 ACACCTACCTTAGAGAGGTTTTCTTGTTTACATCTTTTATCCTTTTGTAAAGGGGAAAGGTTCTA
48772 GCTTATCCCGTGTAAAAGCTAGGGAAAGGTTCTAGTTTAGCCCGAAAAAACTAGGGAGTTGTAAG
521 GCTTATCCCGTGTAAAAGCTAGGGAAAGGTTCTAGTTTAGCCCGAAAAAACTAGGGAGTTGTAAG
48837 GTTATATCTTTGTCCTCAAAAGAAAGAACAAATTAGTGAATTTGTTGGAAAATCCTTGGTGAGGA
586 GTTATATCTTTGTCCTCAAAAGAAAGAACAAATTAGTGAATTTGTTGGAAAATCCTTGGTGAGGA
48902 GCTAAGGTAGTGGATGTAGACTTTGATTGAGAAAGTCGAACCACTCTAAATCGCTGTGCAATTTT
651 GCTAAGGTAGTGGATGTAGACTTTGATTGAGAAAGTCGAACCACTCTAAATCGCTGTGCAATTTT
48967 CTATCTTTCAATCTCCTTACTCCCTAAACACAAAACCGTTCCGACCCCTCTTTGCAAACCTTTCC
716 CTATCTTTCAATCTCCTTACTCCCTAAACACAAAACCGTTCCGACCCCTCTTTGCAAACCTTTCC
49032 GGTTGTCTATTCGAGCGTCCGAAAATCCCAAAAGTGCATCCATGCATCCCTGC
781 GGTTGTCTATTCGAGCGTCCGAAAATCCCAAAAGTGCATCCATGCATCCCTGC
49085 AGTGCATCCATGCATCCCTGCAGTGCATCCATGCATCTGCACTAATGCATCGATGCATCAGGCAA
1 AGTGCATCCATGCATCCCTGCAGTGCATCCATGCATCTGCACTAATGCATCGATGCATCAGGCAA
49150 TGCATCCATGCATCCAAACATCGAATGCAATTAGTGCATCGATGCATCCTTGCCATGCATCGATG
66 TGCATCCATGCATCCAAACATCGAATGCAATTAGTGCATCGATGCAT-CTTGCCATGCATCGATG
49215 CATCCTGCCATGCATCCATGCATCAAGGCTGCAACGGCTAGTAACGACTAGTTTATTTGAATTTA
130 CATCCTGCCATGCATCCATGCATCAAGGCTGCAA---C--G----G-CTAGTTTATTTGAATTTA
49280 ATGAAGGGGTATCGATGCACCTTGATCATGCATCGATGCATCATGTTATGGGCAGCCTTTTTGAG
185 ATGAAGGGGTATCGATGCACCTTGATCATGCATCGATGCATCATGTTATGGGCAGCCTTTTTGAG
49345 TAGAAAAATCATCCCCAAACGACTCCAAAACATCCCCAACGGCTATATACAACATCAAACACATT
250 TAGAAAAATCATCCCCAAACGACTCCAAAACATCCCCAACGGCTATATACAACATCAAACACATT
49410 CCAAGCTATAAATACAAGCTGAGGACACTTGAAGAAGTAAGAGAACAACTATCCAAGCAATCAAA
315 CCAAGCTATAAATACAAGCTGAGGACACTTGAAGAAGTAAGAGAACAACTATCCAAGCAATCAAA
49475 CACAAGAGAAGAGTTTTTCATTCTTATTTCATCATTCTCTTGTAAATATTTTGTTCTTGTGAGCT
380 CACAAGAGAAGAGTTTTTCATTCTTATTTCATCATTCTCTTGTAAATATTTTGTTCTTGTGAGCT
49540 CAATCTTGTAAACACCTACCTTAGAGAGGTTTTCTTGTTTACATCTTTTATCCTTTTGTAAAGGG
445 CAATCTTGTAAACACCTACCTTAGAGAGGTTTTCTTGTTTACATCTTTTATCCTTTTGTAAAGGG
*
49605 GAAAGGTTCTAGCTTATCCCGTGTAAAAGCTAGGGAAAGGTTCTAGTTTAGCCCGGAAAAACTAG
510 GAAAGGTTCTAGCTTATCCCGTGTAAAAGCTAGGGAAAGGTTCTAGTTTAGCCCGAAAAAACTAG
*
49670 GGAGTTGTAAGGTTATCTCTTTGTCCTCAAAAGAAAGAACAAATTAGTGAATTTGTTGGAAAATC
575 GGAGTTGTAAGGTTATATCTTTGTCCTCAAAAGAAAGAACAAATTAGTGAATTTGTTGGAAAATC
* *
49735 CTTGGTGAGGAGCTAAGGTAGTGGATGTAGACTTTGGTTGAGAGAGTCGAACCACTCTAAATCGC
640 CTTGGTGAGGAGCTAAGGTAGTGGATGTAGACTTTGATTGAGAAAGTCGAACCACTCTAAATCGC
49800 TGTGCAATTTTCTATCTTTCAATCTCCTTACTCCCTAAACACAAAACCGTTCCGACCCCTCTTTG
705 TGTGCAATTTTCTATCTTTCAATCTCCTTACTCCCTAAACACAAAACCGTTCCGACCCCTCTTTG
49865 CAAACCTTTCCGGTTGTCTATTCGAGCGTCCGAAAATCCCAA
770 CAAACCTTTCCGGTTGTCTATTCGAGCGTCCGAAAATCCCAA
49907 CAGACTATAA
Statistics
Matches: 803, Mismatches: 8, Indels: 11
0.98 0.01 0.01
Matches are distributed among these distances:
833 111 0.14
834 50 0.06
837 1 0.00
839 1 0.00
843 1 0.00
844 639 0.80
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.29
Consensus pattern (833 bp):
AGTGCATCCATGCATCCCTGCAGTGCATCCATGCATCTGCACTAATGCATCGATGCATCAGGCAA
TGCATCCATGCATCCAAACATCGAATGCAATTAGTGCATCGATGCATCTTGCCATGCATCGATGC
ATCCTGCCATGCATCCATGCATCAAGGCTGCAACGGCTAGTTTATTTGAATTTAATGAAGGGGTA
TCGATGCACCTTGATCATGCATCGATGCATCATGTTATGGGCAGCCTTTTTGAGTAGAAAAATCA
TCCCCAAACGACTCCAAAACATCCCCAACGGCTATATACAACATCAAACACATTCCAAGCTATAA
ATACAAGCTGAGGACACTTGAAGAAGTAAGAGAACAACTATCCAAGCAATCAAACACAAGAGAAG
AGTTTTTCATTCTTATTTCATCATTCTCTTGTAAATATTTTGTTCTTGTGAGCTCAATCTTGTAA
ACACCTACCTTAGAGAGGTTTTCTTGTTTACATCTTTTATCCTTTTGTAAAGGGGAAAGGTTCTA
GCTTATCCCGTGTAAAAGCTAGGGAAAGGTTCTAGTTTAGCCCGAAAAAACTAGGGAGTTGTAAG
GTTATATCTTTGTCCTCAAAAGAAAGAACAAATTAGTGAATTTGTTGGAAAATCCTTGGTGAGGA
GCTAAGGTAGTGGATGTAGACTTTGATTGAGAAAGTCGAACCACTCTAAATCGCTGTGCAATTTT
CTATCTTTCAATCTCCTTACTCCCTAAACACAAAACCGTTCCGACCCCTCTTTGCAAACCTTTCC
GGTTGTCTATTCGAGCGTCCGAAAATCCCAAAAGTGCATCCATGCATCCCTGC
Found at i:51007 original size:3 final size:3
Alignment explanation
Indices: 50999--51048 Score: 55
Period size: 3 Copynumber: 16.0 Consensus size: 3
50989 AATCATTATT
* * *
50999 TAA TAA TAA TAAA TAAA TAA TGA TAA TAA TAA AAA TAA TAA TAA TGA
1 TAA TAA TAA T-AA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
51046 TAA
1 TAA
51049 AAAAAGGGAC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
3 33 0.82
4 7 0.17
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:51036 original size:18 final size:18
Alignment explanation
Indices: 50999--51051 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 18
50989 AATCATTATT
*
50999 TAATAATAATAA-ATAAA
1 TAATAATAATAATAAAAA
*
51016 TAATGATAATAATAAAAA
1 TAATAATAATAATAAAAA
*
51034 TAATAATAATGATAAAAA
1 TAATAATAATAATAAAAA
51052 AAGGGACAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 11 0.35
18 20 0.65
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (18 bp):
TAATAATAATAATAAAAA
Found at i:60150 original size:15 final size:16
Alignment explanation
Indices: 60125--60154 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
60115 GAAAAAGAAA
60125 TTCGTATAGATACCCC
1 TTCGTATAGATACCCC
60141 TTCG-ATAGATACCC
1 TTCGTATAGATACCC
60155 TTACCAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.27, C:0.30, G:0.13, T:0.30
Consensus pattern (16 bp):
TTCGTATAGATACCCC
Found at i:65670 original size:24 final size:24
Alignment explanation
Indices: 65638--65722 Score: 100
Period size: 24 Copynumber: 3.5 Consensus size: 24
65628 AAATATTTTA
65638 TCTGATTTCTGA-CTTGAATTCTGT
1 TCTGATTTCTGATC-TGAATTCTGT
*
65662 TCTGATTTCTGATCTGGATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
* * * *
65686 TATGATATATGTTCTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
*
65710 TTTGATTTCTGAT
1 TCTGATTTCTGAT
65723 ATCTCCGTTT
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
24 49 0.98
25 1 0.02
ACGTcount: A:0.18, C:0.13, G:0.18, T:0.52
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTCTGT
Found at i:65671 original size:12 final size:12
Alignment explanation
Indices: 65638--65720 Score: 62
Period size: 12 Copynumber: 6.9 Consensus size: 12
65628 AAATATTTTA
65638 TCTGATTTCTG-
1 TCTGATTTCTGT
* *
65649 ACTTGAATTCTGT
1 TC-TGATTTCTGT
*
65662 TCTGATTTCTGA
1 TCTGATTTCTGT
65674 TCTGGA-TTCTGT
1 TCT-GATTTCTGT
* * *
65686 TATGATATATGT
1 TCTGATTTCTGT
*
65698 TCTGAATTCTGT
1 TCTGATTTCTGT
*
65710 TTTGATTTCTG
1 TCTGATTTCTG
65721 ATATCTCCGT
Statistics
Matches: 53, Mismatches: 15, Indels: 7
0.71 0.20 0.09
Matches are distributed among these distances:
11 3 0.06
12 47 0.89
13 3 0.06
ACGTcount: A:0.17, C:0.13, G:0.18, T:0.52
Consensus pattern (12 bp):
TCTGATTTCTGT
Found at i:68520 original size:31 final size:30
Alignment explanation
Indices: 68482--68557 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 30
68472 AAAAATTGAA
* *
68482 AGTTTAGATACTAAAACGGGCAAGAAATGAT
1 AGTTTAGATACTAAAACGGACAA-AAATAAT
* *
68513 AGTTTAGATACTAAAACGGATAAAACTAAT
1 AGTTTAGATACTAAAACGGACAAAAATAAT
*
68543 AATTTAGATACTAAA
1 AGTTTAGATACTAAA
68558 TACGAATTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 19 0.47
31 21 0.52
ACGTcount: A:0.49, C:0.09, G:0.16, T:0.26
Consensus pattern (30 bp):
AGTTTAGATACTAAAACGGACAAAAATAAT
Found at i:68551 original size:30 final size:31
Alignment explanation
Indices: 68484--68557 Score: 96
Period size: 30 Copynumber: 2.4 Consensus size: 31
68474 AAATTGAAAG
* * *
68484 TTTAGATACTAAAACGGGCAAGAAATGATAG
1 TTTAGATACTAAAACGGACAAGAAATAATAA
* *
68515 TTTAGATACTAAAACGGATAA-AACTAATAA
1 TTTAGATACTAAAACGGACAAGAAATAATAA
68545 TTTAGATACTAAA
1 TTTAGATACTAAA
68558 TACGAATTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
30 19 0.50
31 19 0.50
ACGTcount: A:0.49, C:0.09, G:0.15, T:0.27
Consensus pattern (31 bp):
TTTAGATACTAAAACGGACAAGAAATAATAA
Found at i:68986 original size:26 final size:26
Alignment explanation
Indices: 68926--68995 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 26
68916 AAAGAAAACT
* *
68926 TATAGTTTTTTAAAAAATTATATGAA
1 TATAATTTTTTAAAAAATTAAATGAA
* *
68952 AACAATTTTTTAAAAAATTAAAATG-A
1 TATAATTTTTTAAAAAATT-AAATGAA
* *
68978 TATATTTTTTTGAAAAAT
1 TATAATTTTTTAAAAAAT
68996 CATTCTTCAA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
26 31 0.89
27 4 0.11
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.44
Consensus pattern (26 bp):
TATAATTTTTTAAAAAATTAAATGAA
Found at i:72506 original size:25 final size:25
Alignment explanation
Indices: 72451--72505 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
72441 TTCGTTAATA
*
72451 AAAAATAATGAATATGAACACCTTT
1 AAAAATAATGAATATGAACACATTT
*
72476 AAAAATAATTAA-ATGAACACGATATT
1 AAAAATAATGAATATGAACAC-AT-TT
72502 AAAA
1 AAAA
72506 TTTTAAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 8 0.31
25 12 0.46
26 6 0.23
ACGTcount: A:0.58, C:0.09, G:0.07, T:0.25
Consensus pattern (25 bp):
AAAAATAATGAATATGAACACATTT
Found at i:72997 original size:16 final size:16
Alignment explanation
Indices: 72976--73007 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
72966 ATCTACATTT
72976 TTTTTCAAAAAAAATA
1 TTTTTCAAAAAAAATA
*
72992 TTTTTCAAAATAAATA
1 TTTTTCAAAAAAAATA
73008 ACTTCTACTT
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:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (16 bp):
TTTTTCAAAAAAAATA
Done.