Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009635.1 Hibiscus syriacus cultivar Beakdansim tig00117038_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: 1009897
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:809573 original size:90 final size:90
Alignment explanation
Indices: 809452--809627 Score: 300
Period size: 90 Copynumber: 2.0 Consensus size: 90
809442 TAATTCTGAA
* *
809452 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATA-AAATCCCTAATATGA
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAGAAA-CCCTAATATGA
809516 TTAGGGTAACTTGGATATAAAAGGAT
65 TTAGGGTAACTTGGATATAAAAGGAT
*
809542 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAGAAACCGTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAGAAACCCTAATATGAT
*
809607 TAGGGTAACTTGGCTATAAAA
66 TAGGGTAACTTGGATATAAAA
809628 TGGTGTGTTA
Statistics
Matches: 81, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
90 78 0.96
91 3 0.04
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.38
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAGAAACCCTAATATGAT
TAGGGTAACTTGGATATAAAAGGAT
Found at i:816296 original size:89 final size:90
Alignment explanation
Indices: 816133--816309 Score: 286
Period size: 89 Copynumber: 2.0 Consensus size: 90
816123 TAATCCCGAA
* *
816133 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
1 TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAATCCCTAATATGAT
816198 TAGGGTAACTTGGATATAAAAGGAT
66 TAGGGTAACTTGGATATAAAAGGAT
*
816223 TATTAAATTTTAATTAATTAAATATAGATTTAATT-ATTTAAAATAATATAAA-CCCTAATATGA
1 TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTAAAATAATA-AAATCCCTAATATGA
* *
816286 TTAGGGTAACTTGGCTGTAAAAGG
65 TTAGGGTAACTTGGATATAAAAGG
816310 GTGTGTTAGG
Statistics
Matches: 81, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
89 45 0.56
90 36 0.44
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (90 bp):
TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAATCCCTAATATGAT
TAGGGTAACTTGGATATAAAAGGAT
Found at i:818308 original size:79 final size:79
Alignment explanation
Indices: 818177--818338 Score: 324
Period size: 79 Copynumber: 2.1 Consensus size: 79
818167 TCCCTTTTAC
818177 CTTTCTACTTTTCTTTGTTTTATAGTTAACCTTTAAGATTTTGTTTATACTTTATTCTTATTCTC
1 CTTTCTACTTTTCTTTGTTTTATAGTTAACCTTTAAGATTTTGTTTATACTTTATTCTTATTCTC
818242 AATTTTGTTGTTAA
66 AATTTTGTTGTTAA
818256 CTTTCTACTTTTCTTTGTTTTATAGTTAACCTTTAAGATTTTGTTTATACTTTATTCTTATTCTC
1 CTTTCTACTTTTCTTTGTTTTATAGTTAACCTTTAAGATTTTGTTTATACTTTATTCTTATTCTC
818321 AATTTTGTTGTTAA
66 AATTTTGTTGTTAA
818335 CTTT
1 CTTT
818339 GTTTGACTTT
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 83 1.00
ACGTcount: A:0.20, C:0.13, G:0.07, T:0.60
Consensus pattern (79 bp):
CTTTCTACTTTTCTTTGTTTTATAGTTAACCTTTAAGATTTTGTTTATACTTTATTCTTATTCTC
AATTTTGTTGTTAA
Found at i:821591 original size:2 final size:2
Alignment explanation
Indices: 821576--821617 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
821566 ATGGATTGCT
*
821576 TA TA TA -A TA GA TA TA TA TA TA TA -A 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 TA
821616 TA
1 TA
821618 GAGAGAGAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (2 bp):
TA
Found at i:821598 original size:17 final size:17
Alignment explanation
Indices: 821576--821619 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
821566 ATGGATTGCT
821576 TATATAATAGATATATA
1 TATATAATAGATATATA
*
821593 TATATAATATATATATA
1 TATATAATAGATATATA
821610 TATAT-ATAGA
1 TATATAATAGA
821620 GAGAGAGAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 4 0.16
17 21 0.84
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (17 bp):
TATATAATAGATATATA
Found at i:821696 original size:2 final size:2
Alignment explanation
Indices: 821689--821715 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
821679 GTCAATCTAC
821689 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
821716 ATTTACGACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:827730 original size:18 final size:19
Alignment explanation
Indices: 827707--827744 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
827697 GCTTATTTTT
827707 GTTTTCAAAATCAAA-ATA
1 GTTTTCAAAATCAAAGATA
*
827725 GTTTTCGAAATCAAAGATA
1 GTTTTCAAAATCAAAGATA
827744 G
1 G
827745 ACTTTGGTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.32
Consensus pattern (19 bp):
GTTTTCAAAATCAAAGATA
Found at i:829825 original size:6 final size:6
Alignment explanation
Indices: 829806--829877 Score: 60
Period size: 6 Copynumber: 12.2 Consensus size: 6
829796 GAGAAAAGAC
* * *
829806 AGAAAA AGAGAA AGAAAA AGAAAA TGAAAGA AAAAAA AG-AAA A-AAAA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAA-A AGAAAA AGAAAA AGAAAA
* *
829853 A-AAAA GGAAAT AGAGAAA AGAAAA A
1 AGAAAA AGAAAA AGA-AAA AGAAAA A
829878 CGAGAAAAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 8
0.74 0.14 0.11
Matches are distributed among these distances:
5 12 0.23
6 31 0.60
7 9 0.17
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (6 bp):
AGAAAA
Found at i:829851 original size:28 final size:28
Alignment explanation
Indices: 829808--829877 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 28
829798 GAAAAGACAG
* * *
829808 AAAAAGAGAAAGAAAAAGAAAATGAAAGA
1 AAAAAAAGAAA-AAAAAAAAAAGGAAAGA
*
829837 AAAAAAAGAAAAAAAAAAAAAGGAAATA
1 AAAAAAAGAAAAAAAAAAAAAGGAAAGA
* *
829865 GAGAAAAGAAAAA
1 AAAAAAAGAAAAA
829878 CGAGAAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
28 25 0.71
29 10 0.29
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (28 bp):
AAAAAAAGAAAAAAAAAAAAAGGAAAGA
Found at i:829853 original size:14 final size:14
Alignment explanation
Indices: 829808--829892 Score: 55
Period size: 14 Copynumber: 5.8 Consensus size: 14
829798 GAAAAGACAG
*
829808 AAAAAGAGAAAGAAA
1 AAAAAAAGAAA-AAA
* *
829823 AAGAAAATG-AAAGA
1 AA-AAAAAGAAAAAA
829837 AAAAAAAGAAAAAA
1 AAAAAAAGAAAAAA
* *
829851 AAAAAAAGGAAATA
1 AAAAAAAGAAAAAA
* *
829865 GAGAAAAGAAAAACGA
1 AAAAAAAGAAAAA--A
829881 GAAAAAAAGAAA
1 -AAAAAAAGAAA
829893 TGAAAACATA
Statistics
Matches: 52, Mismatches: 13, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
13 5 0.10
14 29 0.56
15 4 0.08
16 5 0.10
17 9 0.17
ACGTcount: A:0.79, C:0.01, G:0.18, T:0.02
Consensus pattern (14 bp):
AAAAAAAGAAAAAA
Found at i:831342 original size:45 final size:45
Alignment explanation
Indices: 831293--831619 Score: 224
Period size: 45 Copynumber: 7.3 Consensus size: 45
831283 GTCGTCATTA
* * *
831293 TTGACTTTCTCGTGAAGAGAGGTCGGTCTTTTAATAATGTTATTT
1 TTGACTTTCTCGTGAAGAGAGGTCGATCTTTTAGTAATGTTATTC
* **
831338 TTGACTTTCTCGTGAAGAGAAGTCGATCTTTTAGTGTTGTCT-TTC
1 TTGACTTTCTCGTGAAGAGAGGTCGATCTTTTAGTAATGT-TATTC
* ** **
831383 TTGACTTTCTCGCGAAGAG-GAGTCGATCTTTTAGTGTTGTCCTTC
1 TTGACTTTCTCGTGAAGAGAG-GTCGATCTTTTAGTAATGTTATTC
* *
831428 TTGACTTTTTCGTGAAGA-AGGGTCAATCTTTTAGTGAA-GTTATTC
1 TTGACTTTCTCGTGAAGAGA-GGTCGATCTTTTAGT-AATGTTATTC
* * ** *
831473 TTGACTTTCTCGTGAAGTG-GAGTCAATCTTTTAGTGTTGTCT-TTT
1 TTGACTTTCTCGTGAAGAGAG-GTCGATCTTTTAGTAATGT-TATTC
* * ** * *
831518 TTTACTTTCTCATGAAGA-AGAGTTAACCTTTTAGTGAT-TTCATTC
1 TTGACTTTCTCGTGAAGAGAG-GTCGATCTTTTAGTAATGTT-ATTC
* * * ** *
831563 TTAACTTTCTCGCGAAGAG-GAGTCAATCTTTTAGTGTTATCT-TTC
1 TTGACTTTCTCGTGAAGAGAG-GTCGATCTTTTAGTAATGT-TATTC
831608 TTGACTTTCTCG
1 TTGACTTTCTCG
831620 GGAGAGGAGT
Statistics
Matches: 231, Mismatches: 35, Indels: 32
0.78 0.12 0.11
Matches are distributed among these distances:
43 1 0.00
44 2 0.01
45 223 0.97
46 4 0.02
47 1 0.00
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.44
Consensus pattern (45 bp):
TTGACTTTCTCGTGAAGAGAGGTCGATCTTTTAGTAATGTTATTC
Found at i:831432 original size:90 final size:90
Alignment explanation
Indices: 831275--831652 Score: 388
Period size: 90 Copynumber: 4.2 Consensus size: 90
831265 TAAAAAATCA
* * * ** * ** *
831275 CTTTTAGTGTCGTCATTATTGACTTTCTCGTGAAGA-GAGGTCGGTCTTTTAATAATGT-TATTT
1 CTTTTAGTGTTGTCATTCTTGACTTTCTCGCGAAGAGGA-GTCAATCTTTTAGTGTTGTCT-TTC
*
831338 TTGACTTTCTCGTGAAG-AGAAGTCGAT
64 TTGACTTTCTCGTGAAGAAG-AGTCAAT
* * *
831365 CTTTTAGTGTTGTCTTTCTTGACTTTCTCGCGAAGAGGAGTCGATCTTTTAGTGTTGTCCTTCTT
1 CTTTTAGTGTTGTCATTCTTGACTTTCTCGCGAAGAGGAGTCAATCTTTTAGTGTTGTCTTTCTT
* *
831430 GACTTTTTCGTGAAGAAGGGTCAAT
66 GACTTTCTCGTGAAGAAGAGTCAAT
** * * * *
831455 CTTTTAGTGAAGTTATTCTTGACTTTCTCGTGAAGTGGAGTCAATCTTTTAGTGTTGTCTTTTTT
1 CTTTTAGTGTTGTCATTCTTGACTTTCTCGCGAAGAGGAGTCAATCTTTTAGTGTTGTCTTTCTT
* * * *
831520 TACTTTCTCATGAAGAAGAGTTAAC
66 GACTTTCTCGTGAAGAAGAGTCAAT
* *
831545 CTTTTAGTGATT-TCATTCTTAACTTTCTCGCGAAGAGGAGTCAATCTTTTAGTGTTATCTTTCT
1 CTTTTAGTG-TTGTCATTCTTGACTTTCTCGCGAAGAGGAGTCAATCTTTTAGTGTTGTCTTTCT
* * * *
831609 TGACTTTCTCG-GGAGAGGAGTTAAC
65 TGACTTTCTCGTGAAGAAGAGTCAAT
* *
831634 CTTTTAGCGATGTCATTCT
1 CTTTTAGTGTTGTCATTCT
831653 CAACTTGATT
Statistics
Matches: 241, Mismatches: 42, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
88 1 0.00
89 27 0.11
90 209 0.87
91 4 0.02
ACGTcount: A:0.20, C:0.15, G:0.21, T:0.43
Consensus pattern (90 bp):
CTTTTAGTGTTGTCATTCTTGACTTTCTCGCGAAGAGGAGTCAATCTTTTAGTGTTGTCTTTCTT
GACTTTCTCGTGAAGAAGAGTCAAT
Found at i:831525 original size:135 final size:134
Alignment explanation
Indices: 831275--831619 Score: 401
Period size: 135 Copynumber: 2.6 Consensus size: 134
831265 TAAAAAATCA
* * ** * *
831275 CTTTTAGTGTCGTCATTATTGACTTTCTCGTGAAGAGAGGTCGGTCTTTTAAT-AATGTTATTTT
1 CTTTTAGTGTTGTCATTCTTGACTTTCTCGTGAAGAG-GGTCAATCTTTTAGTGAA-GTTATTCT
* * *
831339 TGACTTTCTCGTGAAGAGAAGTCGATCTTTTAGTGTTGTCTTTCTTGACTTTCTCGCGAAGAGGA
64 TGACTTTCTCGTGAAGAGAAGTCAATCTTTTAGTGTTGTCTTTCTTGACTTTCTCACGAAGAAGA
* *
831404 GTCGAT
129 GTCAAC
* *
831410 CTTTTAGTGTTGTCCTTCTTGACTTTTTCGTGAAGAAGGGTCAATCTTTTAGTGAAGTTATTCTT
1 CTTTTAGTGTTGTCATTCTTGACTTTCTCGTGAAG-AGGGTCAATCTTTTAGTGAAGTTATTCTT
* * * * *
831475 GACTTTCTCGTGAAGTGGAGTCAATCTTTTAGTGTTGTCTTTTTTTACTTTCTCATGAAGAAGAG
65 GACTTTCTCGTGAAGAGAAGTCAATCTTTTAGTGTTGTCTTTCTTGACTTTCTCACGAAGAAGAG
*
831540 TTAAC
130 TCAAC
* * *
831545 CTTTTAGTGATT-TCATTCTTAACTTTCTCGCGAAGAGGAGTCAATCTTTTAGTGTTA-TCT-TT
1 CTTTTAGTG-TTGTCATTCTTGACTTTCTCGTGAAGAGG-GTCAATCTTTTAGTG-AAGT-TATT
831607 CTTGACTTTCTCG
62 CTTGACTTTCTCG
831620 GGAGAGGAGT
Statistics
Matches: 180, Mismatches: 24, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
134 3 0.02
135 169 0.94
136 8 0.04
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.44
Consensus pattern (134 bp):
CTTTTAGTGTTGTCATTCTTGACTTTCTCGTGAAGAGGGTCAATCTTTTAGTGAAGTTATTCTTG
ACTTTCTCGTGAAGAGAAGTCAATCTTTTAGTGTTGTCTTTCTTGACTTTCTCACGAAGAAGAGT
CAAC
Found at i:832663 original size:131 final size:130
Alignment explanation
Indices: 832355--833219 Score: 497
Period size: 131 Copynumber: 6.6 Consensus size: 130
832345 CTTGAAGGGA
* * * * * *
832355 AGTGAAGAAAAACTACCCCGATTCAATATTCTCTAAAGAGCAATGAAGTGAATC-AACATTTCTA
1 AGTGAA-AAAATCTACCTCGATTAAATCTTCTCTAAAGAGTAGTGAAGTGAATCAAAC-TTTCTA
* * * * * ** * * *
832419 GATCTGATCTACCCTGAAGAGAAGCAAAGCATATCGCTTTTTTTTAGATTTGATCTTC-CATTAG
64 GATATGATCTACCCTTAAGAGAAACAGAGCATATC-CCTTTTTCCAGATTTGATATTCTC-TAAA
832483 GAGC
127 GAGC
* * * * ** * *
832487 AGTGGAACAAATCTGCCTCGATTCAATCTTC-CATGAAGAACAGTGATGTGAATCAAACTTTCAA
1 AGT-GAAAAAATCTACCTCGATTAAATCTTCTC-TAAAGAGTAGTGAAGTGAATCAAACTTTCTA
832551 GATATGATCTACCCTTAAGA-ACAACAGAGCATATCCCTTTTTCCAGATTTGATATTCTCTAAAG
64 GATATGATCTACCCTTAAGAGA-AACAGAGCATATCCCTTTTTCCAGATTTGATATTCTCTAAAG
**
832615 AAT
128 AGC
**
832618 AGTGAAGAAAATAC-ACCTCGATTAAATCTTCTCTAAAGAGTAGTGAAGTGAATCAATGTTTCTA
1 AGTGAA-AAAAT-CTACCTCGATTAAATCTTCTCTAAAGAGTAGTGAAGTGAATCAAACTTTCTA
* ** * *** * * * *
832682 GATTTGATCTA-ATTTGAAGAGTAGTGGAGCAGATCCC-TTTT-CAGATTTGATCTTCCCTAAGG
64 GATATGATCTACCCTT-AAGAGAAACAGAGCATATCCCTTTTTCCAGATTTGATATTCTCTAAAG
832744 AGC
128 AGC
* * * * * * * *
832747 AGTGGAACAAATCTGCATTGATTAAATTTTCCCTGAAGAGTAGTGAAGTGAATCAAACTTTCAAG
1 AGT-GAAAAAATCTACCTCGATTAAATCTTCTCTAAAGAGTAGTGAAGTGAATCAAACTTTCTAG
* ** * * *
832812 ATCTGATCTA-CCTTGAAGAGAAACAGAGCATATCTTTTTTTCCAGATTTGTTATTCTATGAAGA
65 ATATGATCTACCCTT-AAGAGAAACAGAGCATATCCCTTTTTCCAGATTTGATATTCTCTAAAGA
832876 GC
129 GC
* * * * *
832878 AGTGACATAAATCCACCTCGTTTTAATCTTCTCTAAAGAGTAGTGAAGCGAATC-AACATTTCTA
1 AGTGA-AAAAATCTACCTCGATTAAATCTTCTCTAAAGAGTAGTGAAGTGAATCAAAC-TTTCTA
* * *** * * * * * * *
832942 G-TATGATCTACCCTGAAGAGCAGTGGAACAAAT-CCTTTTT-CAAATTTGATCTTCCCTGAGGA
64 GATATGATCTACCCTTAAGAGAAACAGAGCATATCCCTTTTTCCAGATTTGATATTCTCTAAAGA
833004 GC
129 GC
* ** * * * ** *
833006 AGTGGAACAAATCTGTCTCGATTAAATATTCACTGAAGAGTAGTCCAGTGAATC-AA-TTTCAAG
1 AGT-GAAAAAATCTACCTCGATTAAATCTTCTCTAAAGAGTAGTGAAGTGAATCAAACTTTCTAG
* * * *** ** * * * *
833069 ATATGATCTA-TCTTGAAAAGTAGTGGAGCATATCTTTTTTTTCAGATTTGATCTTCCCTGAAGA
65 ATATGATCTACCCTT-AAGAGAAACAGAGCATATCCCTTTTTCCAGATTTGATATTCTCTAAAGA
*
833133 GA
129 GC
** * * * * * * **
833135 AGTGAAGCGAATCAACC-CTAATTCAGTCTTC-CTTAAATAGCAGTGAAGTGAATCAAAGGTTCT
1 AGTGAA-AAAATCTACCTC-GATTAAATCTTCTC-TAAAGAGTAGTGAAGTGAATCAAACTTTCT
* *
833198 AGATATGATTTACCCTGAAGAG
63 AGATATGATCTACCCTTAAGAG
833220 TAGCGGAGTA
Statistics
Matches: 563, Mismatches: 142, Indels: 57
0.74 0.19 0.07
Matches are distributed among these distances:
126 8 0.01
127 23 0.04
128 70 0.12
129 155 0.28
130 43 0.08
131 180 0.32
132 78 0.14
133 6 0.01
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Consensus pattern (130 bp):
AGTGAAAAAATCTACCTCGATTAAATCTTCTCTAAAGAGTAGTGAAGTGAATCAAACTTTCTAGA
TATGATCTACCCTTAAGAGAAACAGAGCATATCCCTTTTTCCAGATTTGATATTCTCTAAAGAGC
Found at i:832821 original size:260 final size:259
Alignment explanation
Indices: 832355--833085 Score: 864
Period size: 260 Copynumber: 2.8 Consensus size: 259
832345 CTTGAAGGGA
* * * * *
832355 AGTGAAGAAAA-ACTACCCCGATTCAATATTCTCTAAAGAGCAATGAAGTGAATCAACATTTCTA
1 AGTGAAGAAAATAC-ACCTCGATTAAATCTTCTCTAAAGAGTAGTGAAGTGAATCAACATTTCTA
* *** * * * *
832419 GATCTGATCTACCCTGAAGAGAAGCAAAGCATATCGCTTTTTTTTAGATTTGATCTTCCATTAGG
65 GATATGATCTACCCTGAAGAGAAGTGGAGCAAATC-C--TTTTTCAGATTTGATCTTCCCTAAGG
* * * ** *
832484 AGCAGTGGAACAAATCTGCCTCGATTCAATCTTCCATGAAGAACAGTGATGTGAATCAAACTTTC
127 AGCAGTGGAACAAATCTG-CTCGATTAAATATTCCCTGAAGAGTAGTGAAGTGAATCAAACTTTC
*
832549 AAGATATGATCTACCCTT-AAGA-ACAACAGAGCATATCCCTTTTTCCAGATTTGATATTCTCTA
191 AAGATATGATCTA-CCTTGAAGAGA-AACAGAGCATATCCCTTTTTCCAGATTTGATATTCTATA
*
832612 AAGAAT
254 AAGAAC
**
832618 AGTGAAGAAAATACACCTCGATTAAATCTTCTCTAAAGAGTAGTGAAGTGAATCAATGTTTCTAG
1 AGTGAAGAAAATACACCTCGATTAAATCTTCTCTAAAGAGTAGTGAAGTGAATCAACATTTCTAG
* *** * * *
832683 ATTTGATCTAATTTGAAGAGTAGTGGAGCAGATCCCTTTTCAGATTTGATCTTCCCTAAGGAGCA
66 ATATGATCTACCCTGAAGAGAAGTGGAGCAAATCCTTTTTCAGATTTGATCTTCCCTAAGGAGCA
* *
832748 GTGGAACAAATCTGCATTGATTAAATTTTCCCTGAAGAGTAGTGAAGTGAATCAAACTTTCAAGA
131 GTGGAACAAATCTGC-TCGATTAAATATTCCCTGAAGAGTAGTGAAGTGAATCAAACTTTCAAGA
* ** * * *
832813 TCTGATCTACCTTGAAGAGAAACAGAGCATATCTTTTTTTCCAGATTTGTTATTCTATGAAGAGC
195 TATGATCTACCTTGAAGAGAAACAGAGCATATCCCTTTTTCCAGATTTGATATTCTATAAAGAAC
* * * * *
832878 AGTGACA-TAAATCCACCTCGTTTTAATCTTCTCTAAAGAGTAGTGAAGCGAATCAACATTTCTA
1 AGTGA-AGAAAATACACCTCGATTAAATCTTCTCTAAAGAGTAGTGAAGTGAATCAACATTTCTA
* * * *
832942 G-TATGATCTACCCTGAAGAGCAGTGGAACAAATCCTTTTTCAAATTTGATCTTCCCTGAGGAGC
65 GATATGATCTACCCTGAAGAGAAGTGGAGCAAATCCTTTTTCAGATTTGATCTTCCCTAAGGAGC
* **
833006 AGTGGAACAAATCTGTCTCGATTAAATATTCACTGAAGAGTAGTCCAGTGAATC-AA-TTTCAAG
130 AGTGGAACAAATCTG-CTCGATTAAATATTCCCTGAAGAGTAGTGAAGTGAATCAAACTTTCAAG
*
833069 ATATGATCTATCTTGAA
194 ATATGATCTACCTTGAA
833086 AAGTAGTGGA
Statistics
Matches: 403, Mismatches: 59, Indels: 18
0.84 0.12 0.04
Matches are distributed among these distances:
257 22 0.05
258 2 0.00
259 105 0.26
260 189 0.47
261 2 0.00
262 1 0.00
263 80 0.20
264 2 0.00
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (259 bp):
AGTGAAGAAAATACACCTCGATTAAATCTTCTCTAAAGAGTAGTGAAGTGAATCAACATTTCTAG
ATATGATCTACCCTGAAGAGAAGTGGAGCAAATCCTTTTTCAGATTTGATCTTCCCTAAGGAGCA
GTGGAACAAATCTGCTCGATTAAATATTCCCTGAAGAGTAGTGAAGTGAATCAAACTTTCAAGAT
ATGATCTACCTTGAAGAGAAACAGAGCATATCCCTTTTTCCAGATTTGATATTCTATAAAGAAC
Found at i:833430 original size:3 final size:3
Alignment explanation
Indices: 833422--833471 Score: 68
Period size: 3 Copynumber: 16.7 Consensus size: 3
833412 TAACTGTTTT
833422 TTA TTA TTA TTA TTA TTA TT- TATA TTA TTA -TA TTA TTA TTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA -TTA
833467 TTA TT
1 TTA TT
833472 TTTCAGGTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
2 3 0.07
3 36 0.84
4 4 0.09
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:833459 original size:23 final size:24
Alignment explanation
Indices: 833422--833467 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 24
833412 TAACTGTTTT
833422 TTATTATTATTATTATTATTTATA
1 TTATTATTATTATTATTATTTATA
833446 TTATTA-TATTATTATTATTTAT
1 TTATTATTATTATTATTATTTAT
833468 TATTTTTCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (24 bp):
TTATTATTATTATTATTATTTATA
Found at i:834267 original size:19 final size:19
Alignment explanation
Indices: 834243--834280 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
834233 AAGTGAGAAA
*
834243 AATATGTTTTATGGAAAAC
1 AATATGTTTTATGAAAAAC
834262 AATATGTTTTATGAAAAAC
1 AATATGTTTTATGAAAAAC
834281 TGTAATACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.05, G:0.13, T:0.37
Consensus pattern (19 bp):
AATATGTTTTATGAAAAAC
Found at i:834943 original size:111 final size:110
Alignment explanation
Indices: 834747--835044 Score: 365
Period size: 111 Copynumber: 2.7 Consensus size: 110
834737 TTATGTGTAC
*
834747 TATCGACACTAAATGTGCAACCCACGTAATTCAT--T-ATATATTTATGAACGACCGTATCGACA
1 TATCGACACTAAATGTGCAACCAACG-AATTCATCATAATATATTTATGAACGACCGTATCGACA
* * * *
834809 CTAAGTGTGCAACCCACATAATTCATAATATATTTTTGAACGACCG
65 CTAAGTGTGCAACCCACAAAATTCATAATATATTTATAAACAACCG
* * * * *
834855 TATCAACACTAATTGTGCAACCTACAGAATTCATCATAATATGTTTATAAACGACCGTATCGACA
1 TATCGACACTAAATGTGCAACCAAC-GAATTCATCATAATATATTTATGAACGACCGTATCGACA
* *
834920 CTAAGCGTGCAACCCACAAAATTCATACTATATTTATAAACAACCG
65 CTAAGTGTGCAACCCACAAAATTCATAATATATTTATAAACAACCG
* * * *
834966 TATCGGCAGTAAGTGTGCAACCAACGAAAT--TCATAATATATTTATGAACGACCGTAT-GAACA
1 TATCGACACTAAATGTGCAACCAACGAATTCATCATAATATATTTATGAACGACCGTATCG-ACA
* *
835028 TTAAGTGTGCACCCCAC
65 CTAAGTGTGCAACCCAC
835045 GTAACTTATA
Statistics
Matches: 163, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
107 1 0.01
108 71 0.44
109 1 0.01
110 5 0.03
111 85 0.52
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (110 bp):
TATCGACACTAAATGTGCAACCAACGAATTCATCATAATATATTTATGAACGACCGTATCGACAC
TAAGTGTGCAACCCACAAAATTCATAATATATTTATAAACAACCG
Found at i:835056 original size:54 final size:54
Alignment explanation
Indices: 834747--835056 Score: 356
Period size: 54 Copynumber: 5.7 Consensus size: 54
834737 TTATGTGTAC
* *
834747 TATCGACACTAAATGTGCAACCCACGTAATTCATTATATATTTATGAACGACCG
1 TATCGACACTAAGTGTGCAACCCACGTAATTCATAATATATTTATGAACGACCG
* *
834801 TATCGACACTAAGTGTGCAACCCACATAATTCATAATATATTTTTGAACGACCG
1 TATCGACACTAAGTGTGCAACCCACGTAATTCATAATATATTTATGAACGACCG
* * * * *
834855 TATCAACACTAATTGTGCAACCTACAG-AATTCATCATAATATGTTTATAAACGACCG
1 TATCGACACTAAGTGTGCAACCCAC-GTAA-T--TCATAATATATTTATGAACGACCG
* ** * * *
834912 TATCGACACTAAGCGTGCAACCCACAAAATTCATACTATATTTATAAACAACCG
1 TATCGACACTAAGTGTGCAACCCACGTAATTCATAATATATTTATGAACGACCG
* * * *
834966 TATCGGCAGTAAGTGTGCAACCAACGAAATTCATAATATATTTATGAACGACCG
1 TATCGACACTAAGTGTGCAACCCACGTAATTCATAATATATTTATGAACGACCG
* *
835020 TAT-GAACATTAAGTGTGCACCCCACGTAACTT-ATAAT
1 TATCG-ACACTAAGTGTGCAACCCACGTAA-TTCATAAT
835057 GATTTGAAAC
Statistics
Matches: 217, Mismatches: 32, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
53 1 0.00
54 168 0.77
55 3 0.01
56 1 0.00
57 44 0.20
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (54 bp):
TATCGACACTAAGTGTGCAACCCACGTAATTCATAATATATTTATGAACGACCG
Found at i:840643 original size:53 final size:54
Alignment explanation
Indices: 840387--840725 Score: 391
Period size: 54 Copynumber: 6.3 Consensus size: 54
840377 TACTATTGGT
* * *
840387 ACTAAGTGTGCATCCCACGA-AATTCATAATATATTTATGAACGACCGTACCGAC
1 ACTAAGTGTGCAACCCAC-ATAATTCATAATATGTTTATGAACGACCGTATCGAC
*
840441 ACTAAGTGTGCAACCCATATAATTCATAATATGTTTATGAACGACCGTATCAGGA-
1 ACTAAGTGTGCAACCCACATAATTCATAATATGTTTATGAACGACCGTATC--GAC
** *** * *
840496 A-TAAGTGCACAACCCATGGAATTCATAATATGTTTATGAAGGACCGTATCGAA
1 ACTAAGTGTGCAACCCACATAATTCATAATATGTTTATGAACGACCGTATCGAC
* * * * *
840549 AATAAGTGTGCAACCCATAGAATTCATAAAATGTTTATGAACGACCATATCGAC
1 ACTAAGTGTGCAACCCACATAATTCATAATATGTTTATGAACGACCGTATCGAC
** * *
840603 ACTAAGTGTTTAACCCACA-AATTCATAACATGTTTATGAACGACCTTATCGAC
1 ACTAAGTGTGCAACCCACATAATTCATAATATGTTTATGAACGACCGTATCGAC
** *
840656 ACTAAGTGTGCAACCCA-ATAATTCATAATATGTTTATGAATAACTGTATCGAC
1 ACTAAGTGTGCAACCCACATAATTCATAATATGTTTATGAACGACCGTATCGAC
* *
840709 ATTAAGTGTGCACCCCA
1 ACTAAGTGTGCAACCCA
840726 TAGAACTTAT
Statistics
Matches: 248, Mismatches: 31, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
52 3 0.01
53 93 0.38
54 149 0.60
55 1 0.00
56 2 0.01
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (54 bp):
ACTAAGTGTGCAACCCACATAATTCATAATATGTTTATGAACGACCGTATCGAC
Found at i:841474 original size:78 final size:76
Alignment explanation
Indices: 841335--841591 Score: 268
Period size: 78 Copynumber: 3.3 Consensus size: 76
841325 ATCATAGTTT
* * * *
841335 TTATGTGATGGAATCGAGCA-AAAT-AATTA-TATTTTAAAGGAAACAATCTCTAGTGATATAAT
1 TTATGTGAT-GAATCGAG-AGAAATGAAATATTATTTCAAGGGAAACAATCTC-AGTGAGATAAT
*
841397 GCTGATCCAACTCC
63 GTTGATCCAACTCC
*
841411 TTATGTGATAGAATCTAGAGAAATGAAATATTATTTCAAGGGAAACAATCTTCAGTGAGATAATG
1 TTATGTGAT-GAATCGAGAGAAATGAAATATTATTTCAAGGGAAACAATC-TCAGTGAGATAATG
841476 TTGATCCAACTCC
64 TTGATCCAACTCC
* * * * ** *
841489 ATATGCGATGCAATCGAGTGAAATGAAATCTTGGTTCGAGGGAAACAATCATCAGTGAGATAATG
1 TTATGTGATG-AATCGAGAGAAATGAAATATTATTTCAAGGGAAACAATC-TCAGTGAGATAATG
841554 TTGATCCAACTCC
64 TTGATCCAACTCC
* * * *
841567 CTATGTAATGGAACCGAGCGAAATG
1 TTATGTGAT-GAATCGAGAGAAATG
841592 TTGATGATGA
Statistics
Matches: 154, Mismatches: 21, Indels: 10
0.83 0.11 0.05
Matches are distributed among these distances:
75 1 0.01
76 20 0.13
77 5 0.03
78 125 0.81
79 3 0.02
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (76 bp):
TTATGTGATGAATCGAGAGAAATGAAATATTATTTCAAGGGAAACAATCTCAGTGAGATAATGTT
GATCCAACTCC
Found at i:859745 original size:21 final size:21
Alignment explanation
Indices: 859719--859764 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
859709 TGTGTAAGTC
*
859719 TCCTAGACTTACCTCTTGGGA
1 TCCTAGACCTACCTCTTGGGA
*
859740 TCCTAGACCTACCTCTTGGGC
1 TCCTAGACCTACCTCTTGGGA
859761 TCCT
1 TCCT
859765 CCATGAACTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.15, C:0.35, G:0.17, T:0.33
Consensus pattern (21 bp):
TCCTAGACCTACCTCTTGGGA
Found at i:860248 original size:21 final size:21
Alignment explanation
Indices: 860219--860264 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
860209 CCTAGTTGAT
*
860219 GGTGTCACCCATCAGCAAGGA
1 GGTGACACCCATCAGCAAGGA
*
860240 GGTGACACCCTTCAGCAAGGA
1 GGTGACACCCATCAGCAAGGA
860261 GGTG
1 GGTG
860265 GCACACTCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.26, C:0.26, G:0.33, T:0.15
Consensus pattern (21 bp):
GGTGACACCCATCAGCAAGGA
Found at i:863078 original size:19 final size:19
Alignment explanation
Indices: 863050--863095 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
863040 AAAAATATGA
* *
863050 ATTAACTTATTTTTATTTT
1 ATTAATTTATTTTAATTTT
863069 ATTAATTTATTTTAATTTT
1 ATTAATTTATTTTAATTTT
*
863088 TTTAATTT
1 ATTAATTT
863096 TAATTTAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (19 bp):
ATTAATTTATTTTAATTTT
Found at i:863090 original size:9 final size:9
Alignment explanation
Indices: 863059--863096 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
863049 AATTAACTTA
863059 TTTTT-ATT
1 TTTTTAATT
*
863067 TTATTAATT
1 TTTTTAATT
863076 TATTTTAATT
1 T-TTTTAATT
863086 TTTTTAATT
1 TTTTTAATT
863095 TT
1 TT
863097 AATTTAGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
8 4 0.15
9 14 0.54
10 8 0.31
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTTTAATT
Found at i:864512 original size:20 final size:20
Alignment explanation
Indices: 864467--864504 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
864457 ATTAGTTGTC
864467 AAGTATCGATACCCAAGGTG
1 AAGTATCGATACCCAAGGTG
*
864487 AAGTATCGATACTCAAGG
1 AAGTATCGATACCCAAGG
864505 GCTAGTATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.18, G:0.24, T:0.21
Consensus pattern (20 bp):
AAGTATCGATACCCAAGGTG
Found at i:868380 original size:32 final size:33
Alignment explanation
Indices: 868331--868415 Score: 92
Period size: 32 Copynumber: 2.8 Consensus size: 33
868321 GTACTTAAAG
* *
868331 TATTTTTTTGATCAAAATATGTATCTAAAGTTA
1 TATTTTTTTGATCAAAATAGGTACCTAAAGTTA
*
868364 TATTTTTTTG-TTAAAATAGGTACCTAAAG---
1 TATTTTTTTGATCAAAATAGGTACCTAAAGTTA
*
868393 TA--TTATTGATCAAAATAGGTACC
1 TATTTTTTTGATCAAAATAGGTACC
868416 AAAAATATTA
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
27 5 0.11
28 13 0.28
29 2 0.04
32 16 0.35
33 10 0.22
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.44
Consensus pattern (33 bp):
TATTTTTTTGATCAAAATAGGTACCTAAAGTTA
Found at i:868552 original size:28 final size:28
Alignment explanation
Indices: 868506--868603 Score: 79
Period size: 28 Copynumber: 3.4 Consensus size: 28
868496 AAAAAGTTTG
* *
868506 AATAATTTAGGTACCTATTTTAACATAA
1 AATAATTTAGGTAACTATTTTAACAAAA
* * *
868534 AATATTTTAGGTAATTATTTTGACAAAAA
1 AATAATTTAGGTAACTATTTTAAC-AAAA
** *
868563 AGATAACTTTAGGTATTTATTTTGACCAAAA
1 A-ATAA-TTTAGGTAACTATTTT-AACAAAA
*
868594 AATAGTTTAG
1 AATAATTTAG
868604 TTACTTAAAT
Statistics
Matches: 56, Mismatches: 10, Indels: 7
0.77 0.14 0.10
Matches are distributed among these distances:
28 20 0.36
29 9 0.16
30 6 0.11
31 20 0.36
32 1 0.02
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.40
Consensus pattern (28 bp):
AATAATTTAGGTAACTATTTTAACAAAA
Found at i:888864 original size:28 final size:27
Alignment explanation
Indices: 888799--888865 Score: 64
Period size: 27 Copynumber: 2.4 Consensus size: 27
888789 TTTGTTTTCA
* * *
888799 TTTTCCTTGTCTTTAACCTTTTCTTTAC
1 TTTTCCTT-TCTTGAAACATTTCTTTAC
*
888827 -TTTCATTTTCTTGAAACATTTCTTCTAC
1 TTTTC-CTTTCTTGAAACATTTCTT-TAC
888855 TTTTCCTTTCT
1 TTTTCCTTTCT
888866 ACCCTAACCT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
27 17 0.55
28 10 0.32
29 4 0.13
ACGTcount: A:0.13, C:0.24, G:0.03, T:0.60
Consensus pattern (27 bp):
TTTTCCTTTCTTGAAACATTTCTTTAC
Found at i:899357 original size:30 final size:30
Alignment explanation
Indices: 899321--899377 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
899311 GTTTTTAACT
* *
899321 ATAAAATATTAC-ACAATTATTTTAAAAATC
1 ATAAAATAATACAAC-ATTATTCTAAAAATC
899351 ATAAAATAATACAACATTATTCTAAAA
1 ATAAAATAATACAACATTATTCTAAAA
899378 TATTAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 22 0.92
31 2 0.08
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (30 bp):
ATAAAATAATACAACATTATTCTAAAAATC
Found at i:899435 original size:17 final size:17
Alignment explanation
Indices: 899415--899449 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
899405 AAAACAATAT
899415 AAAATATAAAATGTTAA
1 AAAATATAAAATGTTAA
* *
899432 AAAATATTAAATTTTAA
1 AAAATATAAAATGTTAA
899449 A
1 A
899450 GATTTGTTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (17 bp):
AAAATATAAAATGTTAA
Found at i:905885 original size:40 final size:40
Alignment explanation
Indices: 905830--905911 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
905820 TGCAGGTTTA
905830 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
905870 TAATACACTTCGGTGTATCTGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
905910 TA
1 TA
905912 GCACTACGGT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:906110 original size:47 final size:44
Alignment explanation
Indices: 906016--906127 Score: 125
Period size: 47 Copynumber: 2.5 Consensus size: 44
906006 GTAACCATGC
* * *
906016 AAATAAGCTTATGAGCTTACGGAATAATGGCAAGTATATAGGAA
1 AAATAAGCTTACGAGCTTATGAAATAATGGCAAGTATATAGGAA
* * * *
906060 AAATAAGCTTACGAGCTTATGAAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGAAA--T-AATGGCAAGTATATAGGAA
*
906107 AAATAAGCTTTCGAGCTTATG
1 AAATAAGCTTACGAGCTTATG
906128 GGATAAATGG
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
44 21 0.37
46 1 0.02
47 35 0.61
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.31
Consensus pattern (44 bp):
AAATAAGCTTACGAGCTTATGAAATAATGGCAAGTATATAGGAA
Found at i:913051 original size:40 final size:40
Alignment explanation
Indices: 912996--913077 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
912986 TGCAGGTTTA
912996 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
913036 TAATACACTTCGGTGTATCTGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
913076 TA
1 TA
913078 GCACTACGGT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:931547 original size:45 final size:44
Alignment explanation
Indices: 931478--931616 Score: 170
Period size: 45 Copynumber: 3.1 Consensus size: 44
931468 ATAAAACACA
* * *
931478 AAACTTACCCAATAATGGCATAAGAAATTTGTTCATTAATGTCAT
1 AAACTTACCCAAGAATGGCCTAAGAAA-TTGTTCATTAACGTCAT
* * **
931523 AAACTTAGCCAAGAATGACCTAAGAACAAGGTTCATTAACGTCAT
1 AAACTTACCCAAGAATGGCCTAAGAA-ATTGTTCATTAACGTCAT
* *
931568 AAACTTACCCAAGAATGGCCTAAGAACTTGCTTCATTAACATCAT
1 AAACTTACCCAAGAATGGCCTAAGAAATTG-TTCATTAACGTCAT
931613 AAAC
1 AAAC
931617 GTACACAAAA
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
44 1 0.01
45 77 0.97
46 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.27
Consensus pattern (44 bp):
AAACTTACCCAAGAATGGCCTAAGAAATTGTTCATTAACGTCAT
Found at i:939522 original size:30 final size:30
Alignment explanation
Indices: 939486--939582 Score: 90
Period size: 29 Copynumber: 3.3 Consensus size: 30
939476 CATTTTATAG
* *
939486 AAATAGCACCCCTTTTTGAATTAATTACCA
1 AAATAGCACCACATTTTGAATTAATTACCA
*
939516 AAATAGCA-CACATTTTGAATTAATTTCCA
1 AAATAGCACCACATTTTGAATTAATTACCA
* * ** * * *
939545 TAATAACACCA-AAATCGAATAAATTCCCA
1 AAATAGCACCACATTTTGAATTAATTACCA
939574 AAATAGCAC
1 AAATAGCAC
939583 TGGTCAACGG
Statistics
Matches: 54, Mismatches: 12, Indels: 3
0.78 0.17 0.04
Matches are distributed among these distances:
29 44 0.81
30 10 0.19
ACGTcount: A:0.44, C:0.22, G:0.06, T:0.28
Consensus pattern (30 bp):
AAATAGCACCACATTTTGAATTAATTACCA
Found at i:939614 original size:18 final size:17
Alignment explanation
Indices: 939584--939618 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
939574 AAATAGCACT
939584 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
939601 GGTCAACGGGTCGGGTCG
1 GGTCAAC-GGTCGGGTCG
939619 TGACCGGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.11, C:0.23, G:0.49, T:0.17
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:944402 original size:40 final size:40
Alignment explanation
Indices: 944342--944456 Score: 162
Period size: 40 Copynumber: 2.9 Consensus size: 40
944332 ATTGTAGTTC
944342 TTACACATAAGGT-GTGCCCACCATATGCACCGAA-ATGCA
1 TTACACATAAGGTCGTGCCCACCATATGCACCGAAGA-GCA
* *
944381 TTGCACATAAGCTCGTGCCCACCATATGCACCGAAGAGCA
1 TTACACATAAGGTCGTGCCCACCATATGCACCGAAGAGCA
* * *
944421 TTACATATACGGTCGTTCCCACCATATGCACCGAAG
1 TTACACATAAGGTCGTGCCCACCATATGCACCGAAG
944457 TGCTTAATCG
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
39 11 0.16
40 55 0.82
41 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.21
Consensus pattern (40 bp):
TTACACATAAGGTCGTGCCCACCATATGCACCGAAGAGCA
Found at i:944644 original size:22 final size:24
Alignment explanation
Indices: 944619--944671 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 24
944609 TCATTCACGG
* *
944619 TAAATAT-A-ATATATGTTCATGA
1 TAAATATCATATATACGATCATGA
* *
944641 TAAACATCATATGTACGATCATGA
1 TAAATATCATATATACGATCATGA
944665 TAAATAT
1 TAAATAT
944672 TTTATATTCA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
22 6 0.25
23 1 0.04
24 17 0.71
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (24 bp):
TAAATATCATATATACGATCATGA
Found at i:946455 original size:377 final size:378
Alignment explanation
Indices: 945807--946535 Score: 1337
Period size: 377 Copynumber: 1.9 Consensus size: 378
945797 CTCAAACATT
945807 AATTTACAACATAGTACATCAAATTAAACAATTACAAAAAAATCCATAACTTTTTCAAAAATTAT
1 AATTTACAACATAGTACATCAAATTAAACAATTACAAAAAAATCCATAACTTTTTCAAAAATTAT
945872 CATTTTGGTCCCCAACTATTAAAAAATTACATAATGTTCCCCAAATTTTTCCAAGTCTCTTAGAA
66 CATTTTGGTCCCCAACTATTAAAAAATTACATAATGTTCCCCAAATTTTTCCAAGTCTCTTAGAA
945937 TACTTCCTACATCATTTCCAGTCCTTACAATTTTTTCTAAAATTTTTGTCATCCATTTAAGCCAA
131 TACTTCCTACATCATTTCCAGTCCTTACAATTTTTTCTAAAATTTTTGTCATCCATTTAAGCCAA
*
946002 GGCTGAACACATCAAGGTTCCAAGACTATGGTTTTCATGATTTTGCTCGTTTTGATTCGATTCAA
196 GGCTGAACACATCAAGGTTCCAAGACTATGGTTTTCATGATCTTGCTCGTTTTGATTCGATTCAA
946067 GCATGAATCAACTTCGATTCAACC-T-TACAATTTCTAAAATCAAAACCCTAACTTAATTTCATC
261 GCATGAATCAACTTCGATTCAACCTTATACAATTTCTAAAATCAAAACCCTAACTTAATTTCATC
946130 -AAACACATATTTATATCCTAAGATTATGCTCAATAATATCAAAATTCTTCATCA
326 AAAACACATA-TT-TATCCTAAGATTATGCTCAATAATATCAAAATTCTTCATCA
946184 AATTTACAACATAGTACATCAAATATTAAACAATTACAAAAAAATCCATAAC-TTTTCAAAAATT
1 AATTTACAACATAGTACATC-AA-ATTAAACAATTACAAAAAAATCCATAACTTTTTCAAAAATT
*
946248 ATCATTTTGGT-CCCAACTATTAAAAAATTACATAATGTTCCCCAAATTTTTCCAAGTCTCTTAT
64 ATCATTTTGGTCCCCAACTATTAAAAAATTACATAATGTTCCCCAAATTTTTCCAAGTCTCTTAG
946312 AATACTTCCTACATCATTTCCAGTCCTTACAA-TTTTTCT-AAATTTTTGTCATCCATTTAAGCC
129 AATACTTCCTACATCATTTCCAGTCCTTACAATTTTTTCTAAAATTTTTGTCATCCATTTAAGCC
946375 AAGGCTGAACACATCAAGGTTCCAAGACTATGGTTTTCATGATCTTGCTCTGTTTTGATTCGATT
194 AAGGCTGAACACATCAAGGTTCCAAGACTATGGTTTTCATGATCTTGCTC-GTTTTGATTCGATT
946440 CAAGCATGAAATCAACTTCGATTCAACCTTATACAATTTCTAAAATCAAAACCCTAACTTAATTT
258 CAAGCATG-AATCAACTTCGATTCAACCTTATACAATTTCTAAAATCAAAACCCTAACTTAATTT
946505 CATCAAAACACATATTTATCCTAAGATTATG
322 CATCAAAACACATATTTATCCTAAGATTATG
946536 GTTAGGTCAA
Statistics
Matches: 343, Mismatches: 2, Indels: 13
0.96 0.01 0.04
Matches are distributed among these distances:
375 73 0.21
376 29 0.08
377 123 0.36
378 41 0.12
379 68 0.20
380 9 0.03
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (378 bp):
AATTTACAACATAGTACATCAAATTAAACAATTACAAAAAAATCCATAACTTTTTCAAAAATTAT
CATTTTGGTCCCCAACTATTAAAAAATTACATAATGTTCCCCAAATTTTTCCAAGTCTCTTAGAA
TACTTCCTACATCATTTCCAGTCCTTACAATTTTTTCTAAAATTTTTGTCATCCATTTAAGCCAA
GGCTGAACACATCAAGGTTCCAAGACTATGGTTTTCATGATCTTGCTCGTTTTGATTCGATTCAA
GCATGAATCAACTTCGATTCAACCTTATACAATTTCTAAAATCAAAACCCTAACTTAATTTCATC
AAAACACATATTTATCCTAAGATTATGCTCAATAATATCAAAATTCTTCATCA
Found at i:949275 original size:15 final size:16
Alignment explanation
Indices: 949255--949297 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
949245 AGTTATCATC
949255 ATAATAACTATAGAT-
1 ATAATAACTATAGATG
949270 ATAATATA-TATAGATG
1 ATAATA-ACTATAGATG
*
949286 AAAATAACTATA
1 ATAATAACTATA
949298 TTAAAACTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.33
Consensus pattern (16 bp):
ATAATAACTATAGATG
Found at i:952219 original size:14 final size:13
Alignment explanation
Indices: 952192--952263 Score: 62
Period size: 13 Copynumber: 5.5 Consensus size: 13
952182 TTGGCTTGCA
*
952192 TTCTTTTTTACTT
1 TTCTTTTTTTCTT
952205 TTCTTCTTTTTCTT
1 TTCTT-TTTTTCTT
952219 TTCTTTTTTT-TT
1 TTCTTTTTTTCTT
952231 TT-TTGAATTTTTC--
1 TTCTT---TTTTTCTT
*
952244 TTCTTTTTGTCTT
1 TTCTTTTTTTCTT
952257 TTCTTTT
1 TTCTTTT
952264 CTTTTAGTAC
Statistics
Matches: 49, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
11 7 0.14
12 4 0.08
13 19 0.39
14 19 0.39
ACGTcount: A:0.04, C:0.14, G:0.03, T:0.79
Consensus pattern (13 bp):
TTCTTTTTTTCTT
Found at i:959666 original size:22 final size:22
Alignment explanation
Indices: 959641--959686 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
959631 TGAATACTCA
959641 TCTAAATGCACTTGAATAAACT
1 TCTAAATGCACTTGAATAAACT
*
959663 TCTAAATGCACTTGAATACACT
1 TCTAAATGCACTTGAATAAACT
959685 TC
1 TC
959687 AATGACTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.37, C:0.22, G:0.09, T:0.33
Consensus pattern (22 bp):
TCTAAATGCACTTGAATAAACT
Found at i:961607 original size:15 final size:17
Alignment explanation
Indices: 961587--961625 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
961577 ACATAAGTAG
961587 TAATTTTA-TCAA-AAA
1 TAATTTTATTCAATAAA
961602 TAATTTTATTCAATAAA
1 TAATTTTATTCAATAAA
961619 TAGATTT
1 TA-ATTT
961626 ATTGAGTGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.38
16 4 0.19
17 5 0.24
18 4 0.19
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (17 bp):
TAATTTTATTCAATAAA
Found at i:962634 original size:12 final size:12
Alignment explanation
Indices: 962617--962648 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
962607 TTTTGATGAC
962617 AGTTGATTAGGG
1 AGTTGATTAGGG
962629 AGTTGATTAGGG
1 AGTTGATTAGGG
*
962641 ATTTGATT
1 AGTTGATT
962649 GTATAGATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.25, C:0.00, G:0.34, T:0.41
Consensus pattern (12 bp):
AGTTGATTAGGG
Found at i:962877 original size:29 final size:30
Alignment explanation
Indices: 962836--962902 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
962826 ATGCCTTAGA
* *
962836 AAAATTTAGGGACC-ATTAT-ATAATTTTTG
1 AAAAGTTAGGGACCAATT-TGATAATTTTGG
*
962865 AAAAGTTAGGGACCAATTTGGTAATTTTGG
1 AAAAGTTAGGGACCAATTTGATAATTTTGG
962895 AAAAGTTA
1 AAAAGTTA
962903 TGAATGATTG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 14 0.42
30 19 0.58
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.36
Consensus pattern (30 bp):
AAAAGTTAGGGACCAATTTGATAATTTTGG
Found at i:963739 original size:40 final size:40
Alignment explanation
Indices: 963684--963921 Score: 397
Period size: 40 Copynumber: 6.0 Consensus size: 40
963674 AAGGACAATT
* * *
963684 GGTGCATATGGTGGGCATGACCTTATGTATAATGCACTCA
1 GGTGCATATGGTGGGCACGACCTTATGTGTAATGCACTTA
963724 GGTGCATATGGTGGGCACGACCTTATGTGTAATGCACTTA
1 GGTGCATATGGTGGGCACGACCTTATGTGTAATGCACTTA
*
963764 GGTGCATATGGTGGGCATC-ACCTTATTTGTAATGCACTTA
1 GGTGCATATGGTGGGCA-CGACCTTATGTGTAATGCACTTA
*
963804 GGTGCATATGGTGGGCACGACCTTATATGTAATGCACTTA
1 GGTGCATATGGTGGGCACGACCTTATGTGTAATGCACTTA
*
963844 GGCGCATATGGTGGGCACGACCTTATGTGTAATGCACTTA
1 GGTGCATATGGTGGGCACGACCTTATGTGTAATGCACTTA
*
963884 GGTGCATATGGTGGGAACGACCTTATGTGTAATGCACT
1 GGTGCATATGGTGGGCACGACCTTATGTGTAATGCACT
963922 ACGATGTATA
Statistics
Matches: 187, Mismatches: 9, Indels: 4
0.94 0.05 0.02
Matches are distributed among these distances:
39 1 0.01
40 185 0.99
41 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.30
Consensus pattern (40 bp):
GGTGCATATGGTGGGCACGACCTTATGTGTAATGCACTTA
Found at i:967618 original size:23 final size:20
Alignment explanation
Indices: 967586--967637 Score: 59
Period size: 23 Copynumber: 2.4 Consensus size: 20
967576 CTTTTAAATC
*
967586 TTCTTCTTAATCTTCTTTCACTT
1 TTCTT-TTAATATTCTTT-A-TT
967609 TTCTCTTTAATATTCTTTATT
1 TTCT-TTTAATATTCTTTATT
967630 TTCTTTTA
1 TTCTTTTA
967638 CTTTTATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 4 0.15
21 6 0.22
22 1 0.04
23 15 0.56
24 1 0.04
ACGTcount: A:0.15, C:0.19, G:0.00, T:0.65
Consensus pattern (20 bp):
TTCTTTTAATATTCTTTATT
Found at i:967645 original size:16 final size:16
Alignment explanation
Indices: 967624--967655 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
967614 TTTAATATTC
*
967624 TTTATTTTCTTTTACT
1 TTTATTTTATTTTACT
967640 TTTATTTTATTTTACT
1 TTTATTTTATTTTACT
967656 CTGTTCATCT
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:0.16, C:0.09, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTATTTTATTTTACT
Found at i:978748 original size:45 final size:45
Alignment explanation
Indices: 978682--978820 Score: 210
Period size: 45 Copynumber: 3.1 Consensus size: 45
978672 ATAACACGCA
*
978682 AAACTTACCCAAGAATTGCCTAAGAACATTGTTTATTAACTAT-AT
1 AAACTTACCCAAGAATGGCCTAAGAACATTGTTTATTAAC-ATCAT
* * *
978727 AAACTTATCCAAGAATGGCCTAAGAACATGGTTAATTAACATCAT
1 AAACTTACCCAAGAATGGCCTAAGAACATTGTTTATTAACATCAT
978772 AAACTTACCCAAGAATGGCCTAAGAACA-TGTTTCATTAACATCAT
1 AAACTTACCCAAGAATGGCCTAAGAACATTGTTT-ATTAACATCAT
978817 AAAC
1 AAAC
978821 GTACACAAAA
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
44 5 0.06
45 80 0.94
ACGTcount: A:0.42, C:0.19, G:0.11, T:0.28
Consensus pattern (45 bp):
AAACTTACCCAAGAATGGCCTAAGAACATTGTTTATTAACATCAT
Found at i:988103 original size:45 final size:45
Alignment explanation
Indices: 988048--988207 Score: 216
Period size: 44 Copynumber: 3.6 Consensus size: 45
988038 TTTGTATCAA
* *
988048 TTATCCCATAAGCTTGTAAGCTTATTTTACCAAAATACTTACCAT
1 TTATCCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCAT
* * *
988093 TTAACCCATAAACTCGTAAGC-TATTTTAACAATATACTTACCAT
1 TTATCCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCAT
* * *
988137 TTGTTCCATAAGCTCGTGAGCTTATTTTACCAATATACTTACCA-
1 TTATCCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCAT
* *
988181 TTATTCCATAAGCTCGGAAGCTTATTT
1 TTATCCCATAAGCTCGTAAGCTTATTT
988208 GCATGCTTAC
Statistics
Matches: 100, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
44 61 0.61
45 39 0.39
ACGTcount: A:0.32, C:0.22, G:0.09, T:0.38
Consensus pattern (45 bp):
TTATCCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCAT
Found at i:988355 original size:40 final size:40
Alignment explanation
Indices: 988311--988472 Score: 261
Period size: 40 Copynumber: 4.0 Consensus size: 40
988301 ACCGTAGTGC
*
988311 TACACATAAGGTCATGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
988351 TACACATAAGGTTGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* *
988391 TACACATAAGGTCGTGCCCACTATATACGCCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* * *
988431 TACATATAAGGTCGTGCCCACCATATACACCAAACTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
988471 TA
1 TA
988473 TAAACCCGAA
Statistics
Matches: 112, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 112 1.00
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:992343 original size:6 final size:6
Alignment explanation
Indices: 992327--992451 Score: 78
Period size: 6 Copynumber: 19.8 Consensus size: 6
992317 TCTCTCATTG
* *
992327 TTTTCTC TTTTTC -TTTTC -TTATC TTTTTC TATATATAT- TTTTTC ATTTTC
1 TTTT-TC TTTTTC TTTTTC TTTTTC TTTTTC T-T-T-T-TC TTTTTC TTTTTC
* * * *
992377 ATTTTC TTTTTG TTCCTTGTC TTTTTT TCTTTTC TTTTTC TTTTTC TGTTT-
1 TTTTTC TTTTTC TT--TT-TC TTTTTC T-TTTTC TTTTTC TTTTTC TTTTTC
992428 TTTTTC TTTTTC TTCTTTC TTTTT
1 TTTTTC TTTTTC TT-TTTC TTTTT
992452 TTATAATATT
Statistics
Matches: 96, Mismatches: 10, Indels: 25
0.73 0.08 0.19
Matches are distributed among these distances:
5 14 0.15
6 53 0.55
7 19 0.20
8 4 0.04
9 5 0.05
10 1 0.01
ACGTcount: A:0.06, C:0.16, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTTTC
Found at i:992401 original size:15 final size:13
Alignment explanation
Indices: 992381--992453 Score: 57
Period size: 13 Copynumber: 5.7 Consensus size: 13
992371 ATTTTCATTT
992381 TCTTTTTGTTCCTTG
1 TCTTTTT-TT-CTTG
*
992396 TCTTTTTTTCTTT
1 TCTTTTTTTCTTG
992409 TCTTTTTCTT-TT-
1 TCTTTTT-TTCTTG
*
992421 TCTGTTTTT-TT-
1 TCTTTTTTTCTTG
992432 TCTTTTTCTTCTT-
1 TCTTTTT-TTCTTG
992445 TCTTTTTTT
1 TCTTTTTTT
992454 ATAATATTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
11 10 0.19
12 10 0.19
13 21 0.40
14 4 0.08
15 7 0.13
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.79
Consensus pattern (13 bp):
TCTTTTTTTCTTG
Found at i:992436 original size:23 final size:23
Alignment explanation
Indices: 992396--992453 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
992386 TTGTTCCTTG
*
992396 TCTTT-TTTTCTTTTCTTTTTCT
1 TCTTTCTTTTTTTTTCTTTTTCT
992418 T-TTTCTGTTTTTTTTCTTTTTCT
1 TCTTTCT-TTTTTTTTCTTTTTCT
992441 TCTTTCTTTTTTT
1 TCTTTCTTTTTTT
992454 ATAATATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
21 3 0.09
22 2 0.06
23 22 0.69
24 5 0.16
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.83
Consensus pattern (23 bp):
TCTTTCTTTTTTTTTCTTTTTCT
Found at i:992436 original size:36 final size:34
Alignment explanation
Indices: 992364--992451 Score: 98
Period size: 29 Copynumber: 2.7 Consensus size: 34
992354 TCTATATATA
*
992364 TTTTTTCATTTTCATTTTCTTTTTGTTCCTTGTCT
1 TTTTTTC-TTTTCTTTTTCTTTTTGTTCCTTGTCT
992399 TTTTTTCTTTTCTTTTTC--TTT-TT-C-TGT-T
1 TTTTTTCTTTTCTTTTTCTTTTTGTTCCTTGTCT
992427 TTTTTTCTTTTTCTTCTTTCTTTTT
1 TTTTTTC-TTTTCTT-TTTCTTTTT
992452 TTATAATATT
Statistics
Matches: 48, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
28 8 0.17
29 10 0.21
30 5 0.10
31 2 0.04
32 6 0.12
34 10 0.21
35 7 0.15
ACGTcount: A:0.02, C:0.16, G:0.03, T:0.78
Consensus pattern (34 bp):
TTTTTTCTTTTCTTTTTCTTTTTGTTCCTTGTCT
Found at i:992438 original size:29 final size:29
Alignment explanation
Indices: 992372--992452 Score: 94
Period size: 28 Copynumber: 2.8 Consensus size: 29
992362 TATTTTTTCA
* * **
992372 TTTTCATTTTCTTTTTGTTCCTTGTCTTT
1 TTTTCTTTTTCTTTTTCTTTTTTGTCTTT
992401 TTTTC-TTTTCTTTTTCTTTTTCTGT-TTT
1 TTTTCTTTTTCTTTTTCTTTTT-TGTCTTT
992429 TTTTCTTTTTCTTCTTTCTTTTTT
1 TTTTCTTTTTCTT-TTTCTTTTTT
992453 TATAATATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
28 21 0.46
29 16 0.35
30 9 0.20
ACGTcount: A:0.01, C:0.16, G:0.04, T:0.79
Consensus pattern (29 bp):
TTTTCTTTTTCTTTTTCTTTTTTGTCTTT
Found at i:995319 original size:44 final size:45
Alignment explanation
Indices: 995250--995406 Score: 205
Period size: 44 Copynumber: 3.5 Consensus size: 45
995240 GTATCAATTA
* * *
995250 TCCCATAAGCTTGTAAACTTATTTTACCAAAATACTTACCATTTAG
1 TCCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTT-G
* *
995296 -CCCATAAACTCGTAAGC-TATTTTAACAATATACTTACCATTTG
1 TCCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTG
*
995339 TTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTAT-
1 TCCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATT-TG
*
995384 T-CCATAAGCTCATAAGCTTATTT
1 TCCCATAAGCTCGTAAGCTTATTT
995407 GCATGCTTAC
Statistics
Matches: 99, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
43 1 0.01
44 59 0.60
45 38 0.38
46 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.38
Consensus pattern (45 bp):
TCCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTG
Found at i:995568 original size:40 final size:40
Alignment explanation
Indices: 995511--995592 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
995501 ATCGTAGTGC
995511 TACACATAAGGTCGTGCCCACCATATACACTGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACTGAAGTGTAT
* *
995551 TACACATAAGGTTGTGCCCACCATATATACTGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACTGAAGTGTAT
995591 TA
1 TA
995593 TAAACCTGCA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACTGAAGTGTAT
Found at i:1001280 original size:29 final size:28
Alignment explanation
Indices: 1001210--1001282 Score: 85
Period size: 29 Copynumber: 2.6 Consensus size: 28
1001200 TTTTGTGCTC
* * *
1001210 TATATATA-AAACTATTTTATATGTGTA
1 TATATATATAAATTATTTTATATATATA
*
1001237 TATATATTTAAATTATTTTAATATATATA
1 TATATATATAAATTATTTT-ATATATATA
*
1001266 TATATATATATATTATT
1 TATATATATAAATTATT
1001283 CAAAAACTCC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 7 0.18
28 9 0.24
29 22 0.58
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.53
Consensus pattern (28 bp):
TATATATATAAATTATTTTATATATATA
Found at i:1001445 original size:28 final size:27
Alignment explanation
Indices: 1001408--1001490 Score: 85
Period size: 30 Copynumber: 2.9 Consensus size: 27
1001398 AATTATAAAA
* * *
1001408 AAATTGTTTTTAAATATAAAATATTAC
1 AAATTATTTTAAAATATAAAATAATAC
1001435 ACAATTATTTTAAAAATCATAAAATAATAC
1 A-AATTATTTT-AAAAT-ATAAAATAATAC
* *
1001465 AACATTATTCTAAAATATTAAATAAT
1 AA-ATTATTTTAAAATATAAAATAAT
1001491 TATTTAAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
27 1 0.02
28 17 0.36
29 10 0.21
30 19 0.40
ACGTcount: A:0.53, C:0.07, G:0.01, T:0.39
Consensus pattern (27 bp):
AAATTATTTTAAAATATAAAATAATAC
Found at i:1001537 original size:17 final size:17
Alignment explanation
Indices: 1001517--1001551 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1001507 AAAACAATAT
1001517 AAAATATAAAATGTTAA
1 AAAATATAAAATGTTAA
* *
1001534 AAAATATTAAATTTTAA
1 AAAATATAAAATGTTAA
1001551 A
1 A
1001552 GATTCGTTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (17 bp):
AAAATATAAAATGTTAA
Found at i:1002318 original size:3 final size:3
Alignment explanation
Indices: 1002310--1002341 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
1002300 GAGGTAAAGA
1002310 ATT ATT ATT ATT A-T ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1002342 TATGAAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1002329 original size:14 final size:14
Alignment explanation
Indices: 1002310--1002337 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1002300 GAGGTAAAGA
1002310 ATTATTATTATTAT
1 ATTATTATTATTAT
1002324 ATTATTATTATTAT
1 ATTATTATTATTAT
1002338 TATTTATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
ATTATTATTATTAT
Found at i:1002332 original size:17 final size:16
Alignment explanation
Indices: 1002310--1002344 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
1002300 GAGGTAAAGA
1002310 ATTATTATTATTATATT
1 ATTATTATTATTAT-TT
1002327 ATTATTATTATTATTT
1 ATTATTATTATTATTT
1002343 AT
1 AT
1002345 GAAAAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
ATTATTATTATTATTT
Found at i:1004088 original size:14 final size:14
Alignment explanation
Indices: 1004069--1004096 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1004059 ATAAATGTGA
1004069 AACATATGTTGAGG
1 AACATATGTTGAGG
1004083 AACATATGTTGAGG
1 AACATATGTTGAGG
1004097 CAAAATTAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.29, T:0.29
Consensus pattern (14 bp):
AACATATGTTGAGG
Found at i:1006381 original size:37 final size:37
Alignment explanation
Indices: 1006308--1006382 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 37
1006298 GTTGGAAAAT
*
1006308 ATTTATATATTTTCTTTAAAAAATGTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATGTAAAATCATAAA
* *
1006345 ATTTATATAATTTTTTTTACAAAAT-TGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATGT-AAAATCATAAA
1006382 A
1 A
1006383 ATGTTCAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 15 0.45
38 18 0.55
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATGTAAAATCATAAA
Done.