Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008355.1 Hibiscus syriacus cultivar Beakdansim tig00111092_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: 983659
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:890819 original size:2 final size:2
Alignment explanation
Indices: 890812--890839 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
890802 ACCTAGTGTA
890812 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
890840 TCAAATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:891276 original size:19 final size:20
Alignment explanation
Indices: 891249--891286 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
891239 AACTCCTAAA
* *
891249 TCCTTAATCTTTAA-CCTAT
1 TCCTAAATCCTTAATCCTAT
891268 TCCTAAATCCTTAATCCTA
1 TCCTAAATCCTTAATCCTA
891287 ACTTTGATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.42
Consensus pattern (20 bp):
TCCTAAATCCTTAATCCTAT
Found at i:892051 original size:20 final size:19
Alignment explanation
Indices: 892006--892064 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 19
891996 GTTTCACTCC
892006 CTTTATGGTATTTTTTTTAT
1 CTTT-TGGTATTTTTTTTAT
892026 GCTTTTGGTATGTTTTTTTGAT
1 -CTTTTGGTAT-TTTTTTT-AT
* *
892048 TTTTTGGCTCTTTTTTT
1 CTTTTGG-TATTTTTTT
892065 ATTTTTATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 6 0.18
21 23 0.70
22 4 0.12
ACGTcount: A:0.08, C:0.07, G:0.15, T:0.69
Consensus pattern (19 bp):
CTTTTGGTATTTTTTTTAT
Found at i:892052 original size:21 final size:19
Alignment explanation
Indices: 892011--892070 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 19
892001 ACTCCCTTTA
*
892011 TGGTATTTTTTTTATGCTTT
1 TGGTATTTTTTTTAT-TTTT
892031 TGGTATGTTTTTTTGATTTTT
1 TGGTAT-TTTTTTT-ATTTTT
*
892052 TGGCT-CTTTTTTTATTTTT
1 TGG-TATTTTTTTTATTTTT
892071 ATTTTAAGGG
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
19 6 0.17
20 13 0.37
21 13 0.37
22 3 0.09
ACGTcount: A:0.08, C:0.05, G:0.15, T:0.72
Consensus pattern (19 bp):
TGGTATTTTTTTTATTTTT
Found at i:893247 original size:3 final size:3
Alignment explanation
Indices: 893239--893266 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
893229 TCTAAGGTTC
893239 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
893267 AACAAGCTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:894268 original size:58 final size:58
Alignment explanation
Indices: 894198--894360 Score: 308
Period size: 58 Copynumber: 2.8 Consensus size: 58
894188 AATCTCGCGT
894198 TGATTCTAACTTTGTAAGGAAAATAGATTGTTGAATTTATTTTCTTGAGAATCTTTAA
1 TGATTCTAACTTTGTAAGGAAAATAGATTGTTGAATTTATTTTCTTGAGAATCTTTAA
894256 TGATTCTAACTTTGTAAGGAAAATAGATTGTTGAATTTATTTTCTTGAGAATCTTTAA
1 TGATTCTAACTTTGTAAGGAAAATAGATTGTTGAATTTATTTTCTTGAGAATCTTTAA
* *
894314 TGATTCTAACTTTGTAAGAAAAATAGATTATTGAATTTATTTTCTTG
1 TGATTCTAACTTTGTAAGGAAAATAGATTGTTGAATTTATTTTCTTG
894361 TGTTGAAAAC
Statistics
Matches: 103, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 103 1.00
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (58 bp):
TGATTCTAACTTTGTAAGGAAAATAGATTGTTGAATTTATTTTCTTGAGAATCTTTAA
Found at i:904076 original size:58 final size:58
Alignment explanation
Indices: 903966--904079 Score: 151
Period size: 58 Copynumber: 2.0 Consensus size: 58
903956 TAAAAAATTC
* **
903966 TAACTTTGTAAGGAAAATAAATTGTTGAATTTATTTCCTTGGAAATCTTGAATGATTT
1 TAACTTTGTAAGGAAAATAAATTGTCGAATTTATTTCCTTGGAAATAATGAATGATTT
* *
904024 TAACTTTGT-AGGAAAAATAAATTGTCGAATTTATTT-TTTTGAGAATAATGAATGAT
1 TAACTTTGTAAGG-AAAATAAATTGTCGAATTTATTTCCTTGGA-AATAATGAATGAT
904080 AATATCCTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
57 7 0.14
58 42 0.86
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.42
Consensus pattern (58 bp):
TAACTTTGTAAGGAAAATAAATTGTCGAATTTATTTCCTTGGAAATAATGAATGATTT
Found at i:904136 original size:58 final size:58
Alignment explanation
Indices: 903984--904188 Score: 155
Period size: 58 Copynumber: 3.5 Consensus size: 58
903974 TAAGGAAAAT
* * * ** * ** *
903984 AAATTGTTGAATTTATTTCCTTG-GAAATCTTGAATGATTTTAACTTTGTAGGAA-AAAT
1 AAATTGTTAAATTTATTTTCTTGAG-AATCTTAAATGATAATATC-TTGTAAAAAGAAAC
** * ** *
904042 AAATTGTCGAATTTATTTTTTTGAGAATAATGAATGATAATATCCTT-TAAAAAGAAAC
1 AAATTGTTAAATTTATTTTCTTGAGAATCTTAAATGATAATAT-CTTGTAAAAAGAAAC
* ** * * * *
904100 AAATTGTTAAATTTATTTTCTTAAGAATCTTAAATGATTCTATTTTGTTAAAGGAAAT
1 AAATTGTTAAATTTATTTTCTTGAGAATCTTAAATGATAATATCTTGTAAAAAGAAAC
*
904158 AAATTGTTAAATTTATTTTCTTGGGAATCTT
1 AAATTGTTAAATTTATTTTCTTGAGAATCTT
904189 GAATAAAGAA
Statistics
Matches: 117, Mismatches: 26, Indels: 8
0.77 0.17 0.05
Matches are distributed among these distances:
57 6 0.05
58 109 0.93
59 2 0.02
ACGTcount: A:0.37, C:0.06, G:0.13, T:0.44
Consensus pattern (58 bp):
AAATTGTTAAATTTATTTTCTTGAGAATCTTAAATGATAATATCTTGTAAAAAGAAAC
Found at i:904302 original size:39 final size:39
Alignment explanation
Indices: 904259--904349 Score: 155
Period size: 39 Copynumber: 2.3 Consensus size: 39
904249 AAATCTTGGG
*
904259 ATTTATTTTCCTGTTTTGTAAAAGGAAATAAATTATTGA
1 ATTTATTTTCCTGTTTTGTAAAAGAAAATAAATTATTGA
* *
904298 ATTTATTTTCCTATTTTGTAAAAGAAAATAAATTGTTGA
1 ATTTATTTTCCTGTTTTGTAAAAGAAAATAAATTATTGA
904337 ATTTATTTTCCTG
1 ATTTATTTTCCTG
904350 AGAATCTCAC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 48 1.00
ACGTcount: A:0.34, C:0.07, G:0.11, T:0.48
Consensus pattern (39 bp):
ATTTATTTTCCTGTTTTGTAAAAGAAAATAAATTATTGA
Found at i:904537 original size:78 final size:79
Alignment explanation
Indices: 904419--904572 Score: 258
Period size: 78 Copynumber: 2.0 Consensus size: 79
904409 ATTTTCCTAT
* *
904419 TTTGTAAAAGGAAATAAATCGTTGGATTTATTTTCTTA-TTTTGTAAAAGGAAATAAATCATTTA
1 TTTGTAAAAGGAAATAAATCGTTGGATTTATTGTCCTATTTTTGTAAAAGGAAATAAATCA-TTA
904483 -ATTTATTTTTTTGG
65 GATTTATTTTTTTGG
*
904497 TTTGTAAAAGGAAATAAATCGTTGGATTTATTGTCCTATTTTTTTAAAAGGAAATAAATCATTAG
1 TTTGTAAAAGGAAATAAATCGTTGGATTTATTGTCCTATTTTTGTAAAAGGAAATAAATCATTAG
904562 ATTTATTTTTT
66 ATTTATTTTTT
904573 GGGAATCTTG
Statistics
Matches: 71, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
78 39 0.55
79 32 0.45
ACGTcount: A:0.35, C:0.05, G:0.14, T:0.47
Consensus pattern (79 bp):
TTTGTAAAAGGAAATAAATCGTTGGATTTATTGTCCTATTTTTGTAAAAGGAAATAAATCATTAG
ATTTATTTTTTTGG
Found at i:904555 original size:40 final size:39
Alignment explanation
Indices: 904390--904570 Score: 218
Period size: 39 Copynumber: 4.6 Consensus size: 39
904380 GAAATAAATC
* * *
904390 GAAAGAAATTGTTTGATTTATTTTCCTATTTTGTAAAAG
1 GAAATAAATCGTTGGATTTATTTTCCTATTTTGTAAAAG
*
904429 GAAATAAATCGTTGGATTTATTTTCTTATTTTGTAAAAG
1 GAAATAAATCGTTGGATTTATTTTCCTATTTTGTAAAAG
* ** ** **
904468 GAAATAAATCATTTAATTTATTTTTTTGGTTTGTAAAAG
1 GAAATAAATCGTTGGATTTATTTTCCTATTTTGTAAAAG
* *
904507 GAAATAAATCGTTGGATTTATTGTCCTATTTTTTTAAAAG
1 GAAATAAATCGTTGGATTTATTTTCCTA-TTTTGTAAAAG
* *
904547 GAAATAAATCATTAGATTTATTTT
1 GAAATAAATCGTTGGATTTATTTT
904571 TTGGGAATCT
Statistics
Matches: 119, Mismatches: 22, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
39 89 0.75
40 30 0.25
ACGTcount: A:0.35, C:0.05, G:0.14, T:0.46
Consensus pattern (39 bp):
GAAATAAATCGTTGGATTTATTTTCCTATTTTGTAAAAG
Found at i:907890 original size:2 final size:2
Alignment explanation
Indices: 907883--907909 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
907873 AAATGGTACC
907883 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
907910 GAATGATGAA
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:910428 original size:21 final size:20
Alignment explanation
Indices: 910397--910440 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
910387 ACCAAAAATA
*
910397 TTAAAAAAAATATTAATATT
1 TTAAAAAAAATAATAATATT
910417 TTAAATAAAAATAATAATATT
1 TTAAA-AAAAATAATAATATT
910438 TTA
1 TTA
910441 CGTAATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TTAAAAAAAATAATAATATT
Found at i:912181 original size:21 final size:21
Alignment explanation
Indices: 912155--912200 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
912145 AAAGGGATTG
912155 ATCCTTTAAGGGAAATGATCA
1 ATCCTTTAAGGGAAATGATCA
912176 ATCCTTTAAGGGAAATGATCA
1 ATCCTTTAAGGGAAATGATCA
912197 ATCC
1 ATCC
912201 ATTTTCAAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.28
Consensus pattern (21 bp):
ATCCTTTAAGGGAAATGATCA
Found at i:912252 original size:22 final size:21
Alignment explanation
Indices: 912212--912252 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
912202 TTTTCAAGGG
* *
912212 GATCGATCTTTTGGTCAAAGT
1 GATCGATCCTTTGGCCAAAGT
912233 GATCGATCCTTTGAGCCAAA
1 GATCGATCCTTTG-GCCAAA
912253 AATCCTTGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.32
Consensus pattern (21 bp):
GATCGATCCTTTGGCCAAAGT
Found at i:913399 original size:24 final size:24
Alignment explanation
Indices: 913354--913401 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
913344 TGTTCGGTTC
* *
913354 GTTTAACATTCGCGAACGTGTTTT
1 GTTTAACATTCGCAAACATGTTTT
* *
913378 GTTTAACGTTGGCAAACATGTTTT
1 GTTTAACATTCGCAAACATGTTTT
913402 CCGTTAAGAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.23, C:0.15, G:0.21, T:0.42
Consensus pattern (24 bp):
GTTTAACATTCGCAAACATGTTTT
Found at i:920743 original size:19 final size:20
Alignment explanation
Indices: 920719--920761 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
920709 AAAACCAGAA
*
920719 CCCTA-GGGGGTATCAATTC
1 CCCTAGGGGGGAATCAATTC
*
920738 CCCTAGGGGGGAATCGATTC
1 CCCTAGGGGGGAATCAATTC
920758 CCCT
1 CCCT
920762 TAAAAGGGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.19, C:0.30, G:0.28, T:0.23
Consensus pattern (20 bp):
CCCTAGGGGGGAATCAATTC
Found at i:920803 original size:22 final size:21
Alignment explanation
Indices: 920723--920804 Score: 60
Period size: 23 Copynumber: 3.8 Consensus size: 21
920713 CCAGAACCCT
* *
920723 AGGGGGTATCAATTCCCC-TA
1 AGGGGGAATCGATTCCCCTTA
*
920743 GGGGGGAATCGATTCCCCTTAAA
1 AGGGGGAATCGATTCCCCTT--A
*
920766 AGGGGGAAT-TAGTTCCCCTTCA
1 AGGGGGAATCGA-TTCCCCTT-A
* *
920788 AGGGGGTATTGATTCCC
1 AGGGGGAATCGATTCCC
920805 TCTGCCCTAT
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
20 15 0.31
21 1 0.02
22 15 0.31
23 18 0.37
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (21 bp):
AGGGGGAATCGATTCCCCTTA
Found at i:928673 original size:23 final size:23
Alignment explanation
Indices: 928640--928696 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
928630 AATCGACAAG
*
928640 CGGAACAGTTTGCAAAGAGGAGT
1 CGGAACGGTTTGCAAAGAGGAGT
*
928663 CGGAATGGTTTGCAAAGAGGAGT
1 CGGAACGGTTTGCAAAGAGGAGT
928686 CGGAACGGTTT
1 CGGAACGGTTT
928697 TGTGTTTAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.30, C:0.12, G:0.37, T:0.21
Consensus pattern (23 bp):
CGGAACGGTTTGCAAAGAGGAGT
Found at i:929183 original size:21 final size:21
Alignment explanation
Indices: 929152--929207 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
929142 AGTCGTATAT
929152 AGCCG-TTGGGGATGTTTTGA
1 AGCCGTTTGGGGATGTTTTGA
* *
929172 AGCTGTTTGGGGATGTTTTGG
1 AGCCGTTTGGGGATGTTTTGA
*
929193 AGCCGTTTAGGGATG
1 AGCCGTTTGGGGATG
929208 AGAATCAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 4 0.13
21 27 0.87
ACGTcount: A:0.14, C:0.09, G:0.41, T:0.36
Consensus pattern (21 bp):
AGCCGTTTGGGGATGTTTTGA
Found at i:929267 original size:21 final size:21
Alignment explanation
Indices: 929241--929292 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
929231 GGAGCGTGGG
929241 GGGAATCGGTACCCCCTCATA
1 GGGAATCGGTACCCCCTCATA
929262 GGGAATCGGTACCCCCTCATA
1 GGGAATCGGTACCCCCTCATA
929283 GGGAATCGGT
1 GGGAATCGGT
929293 TCCCTAAGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.23, C:0.29, G:0.29, T:0.19
Consensus pattern (21 bp):
GGGAATCGGTACCCCCTCATA
Found at i:930856 original size:20 final size:20
Alignment explanation
Indices: 930831--930880 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
930821 TCTAAATTAT
930831 TTTTCAAAATTTCATTTTGA
1 TTTTCAAAATTTCATTTTGA
930851 TTTTCAAAATTTCATTTTGA
1 TTTTCAAAATTTCATTTTGA
930871 TTTTCAAAAT
1 TTTTCAAAAT
930881 CAACTTTTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.32, C:0.10, G:0.04, T:0.54
Consensus pattern (20 bp):
TTTTCAAAATTTCATTTTGA
Found at i:930888 original size:20 final size:19
Alignment explanation
Indices: 930831--930902 Score: 69
Period size: 20 Copynumber: 3.7 Consensus size: 19
930821 TCTAAATTAT
930831 TTTTCAAAATTTC-ATTTTGA
1 TTTTCAAAA--TCAATTTTGA
930851 TTTTCAAAATTTC-ATTTTGA
1 TTTTCAAAA--TCAATTTTGA
930871 TTTTCAAAATCAACTTTTG-
1 TTTTCAAAATCAA-TTTTGA
*
930890 CTTTCAAAATCAA
1 TTTTCAAAATCAA
930903 ATTATCTTTA
Statistics
Matches: 49, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
18 2 0.04
19 13 0.27
20 34 0.69
ACGTcount: A:0.33, C:0.14, G:0.04, T:0.49
Consensus pattern (19 bp):
TTTTCAAAATCAATTTTGA
Found at i:931379 original size:12 final size:12
Alignment explanation
Indices: 931362--931405 Score: 79
Period size: 12 Copynumber: 3.7 Consensus size: 12
931352 TGCCTACCTC
*
931362 TTTCTTCTTCTT
1 TTTCTTCTTGTT
931374 TTTCTTCTTGTT
1 TTTCTTCTTGTT
931386 TTTCTTCTTGTT
1 TTTCTTCTTGTT
931398 TTTCTTCT
1 TTTCTTCT
931406 CTTCTCTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.00, C:0.20, G:0.05, T:0.75
Consensus pattern (12 bp):
TTTCTTCTTGTT
Found at i:942872 original size:21 final size:23
Alignment explanation
Indices: 942816--942885 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 23
942806 ATATTTACAA
942816 AAATTATTAAAAAGTTATAATATATT
1 AAATT-TTAAAAA--TATAATATATT
**
942842 AAATAATAAAAATAT-ATAT-TT
1 AAATTTTAAAAATATAATATATT
*
942863 AAATTTTAAATA-ATAAT-TATT
1 AAATTTTAAAAATATAATATATT
942884 AA
1 AA
942886 CTCAAAAACT
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
20 3 0.08
21 17 0.46
22 4 0.11
23 3 0.08
25 6 0.16
26 4 0.11
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (23 bp):
AAATTTTAAAAATATAATATATT
Found at i:943434 original size:18 final size:17
Alignment explanation
Indices: 943411--943451 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
943401 TTATTTTTTC
*
943411 AAAAATAAAATTTTATTT
1 AAAAAT-AAATATTATTT
*
943429 AAAAATATATATTATTT
1 AAAAATAAATATTATTT
943446 AAAAAT
1 AAAAAT
943452 TGAACATGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAAAATAAATATTATTT
Found at i:964141 original size:3 final size:3
Alignment explanation
Indices: 964133--964235 Score: 172
Period size: 3 Copynumber: 34.7 Consensus size: 3
964123 TTTTTATCCA
* *
964133 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAA TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
964181 TAT TAT TAT TAT TAT TAT TAT TAT TTT TAT TAT TAT TAT TAT TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
964228 TAT TAT TA
1 TAT TAT TA
964236 AATATATTAA
Statistics
Matches: 93, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
2 2 0.02
3 91 0.98
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:965674 original size:24 final size:22
Alignment explanation
Indices: 965626--965674 Score: 53
Period size: 24 Copynumber: 2.1 Consensus size: 22
965616 GTTTTAATAG
* *
965626 TATTTTTATTTTTATGAATAAA
1 TATTTTTATTTTCATAAATAAA
*
965648 TATTTTTATATATTCATAAATATA
1 TATTTTTAT-T-TTCATAAATAAA
965672 TAT
1 TAT
965675 ATAATGGTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 9 0.41
23 1 0.05
24 12 0.55
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (22 bp):
TATTTTTATTTTCATAAATAAA
Found at i:976933 original size:5 final size:5
Alignment explanation
Indices: 976923--977004 Score: 62
Period size: 5 Copynumber: 15.6 Consensus size: 5
976913 TGCTTGAAGA
*
976923 AAAAG AAAAG AAAAAG AAAAG -AAAG AAAAG AAAAAAG AAAAG AAAAAA
1 AAAAG AAAAG -AAAAG AAAAG AAAAG AAAAG --AAAAG AAAAG -AAAAG
*
976971 AAATAG AAAATG -AAA- AAAAG AGAAG AAAAAG AAA
1 AAA-AG AAAA-G AAAAG AAAAG AAAAG -AAAAG AAA
977005 GGGGGTCAAG
Statistics
Matches: 63, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
4 7 0.11
5 33 0.52
6 18 0.29
7 5 0.08
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (5 bp):
AAAAG
Found at i:976942 original size:16 final size:16
Alignment explanation
Indices: 976922--977004 Score: 96
Period size: 16 Copynumber: 4.9 Consensus size: 16
976912 ATGCTTGAAG
976922 AAAAAGAAAAGAAAAA
1 AAAAAGAAAAGAAAAA
*
976938 GAAAAG-AAAGAAAAGA
1 AAAAAGAAAAGAAAA-A
976954 AAAAAGAAAAGAAAAA
1 AAAAAGAAAAGAAAAA
976970 AAAATAGAAAATGAAAAA
1 AAAA-AGAAAA-GAAAAA
976988 AAGAGAAGAAAAAGAAA
1 AA-A-AAG-AAAAGAAA
977005 GGGGGTCAAG
Statistics
Matches: 58, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
15 8 0.14
16 16 0.28
17 14 0.24
18 8 0.14
19 7 0.12
20 5 0.09
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (16 bp):
AAAAAGAAAAGAAAAA
Found at i:976954 original size:31 final size:32
Alignment explanation
Indices: 976919--977004 Score: 106
Period size: 31 Copynumber: 2.7 Consensus size: 32
976909 ATTATGCTTG
976919 AAGAAAAAGAAAAGAAAAAGAAA-AGAAAGA-A
1 AAGAAAAAGAAAAGAAAAAGAAATAGAAA-ATA
* *
976950 AAGAAAAAAGAAAAGAAAAAAAAATAGAAAATG
1 AAG-AAAAAGAAAAGAAAAAGAAATAGAAAATA
*
976983 AA-AAAAAGAGAAGAAAAAGAAA
1 AAGAAAAAGAAAAGAAAAAGAAA
977005 GGGGGTCAAG
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
31 21 0.44
32 20 0.42
33 7 0.15
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (32 bp):
AAGAAAAAGAAAAGAAAAAGAAATAGAAAATA
Found at i:976966 original size:43 final size:42
Alignment explanation
Indices: 976919--977004 Score: 120
Period size: 43 Copynumber: 2.0 Consensus size: 42
976909 ATTATGCTTG
*
976919 AAGAAAAAGAAA-AGAAAAAGAAAAGAAAGAAAAGAAAAAAGAA
1 AAGAAAAAAAAATAGAAAAAGAAAA-AAAGAAAAG-AAAAAGAA
* *
976962 AAGAAAAAAAAATAGAAAATGAAAAAAAGAGAAGAAAAAGAA
1 AAGAAAAAAAAATAGAAAAAGAAAAAAAGAAAAGAAAAAGAA
977004 A
1 A
977005 GGGGGTCAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
42 9 0.23
43 19 0.49
44 11 0.28
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (42 bp):
AAGAAAAAAAAATAGAAAAAGAAAAAAAGAAAAGAAAAAGAA
Found at i:976988 original size:17 final size:15
Alignment explanation
Indices: 976922--976994 Score: 76
Period size: 17 Copynumber: 4.5 Consensus size: 15
976912 ATGCTTGAAG
976922 AAAAAGAAAAGAAAA
1 AAAAAGAAAAGAAAA
976937 AGAAAAG-AAAGAAAAGA
1 A-AAAAGAAAAG-AAA-A
976954 AAAAAGAAAAGAAAAA
1 AAAAAGAAAAG-AAAA
976970 AAAATAGAAAATGAAAA
1 AAAA-AGAAAA-GAAAA
*
976987 AAAGAGAA
1 AAAAAGAA
976995 GAAAAAGAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 11
0.81 0.02 0.17
Matches are distributed among these distances:
15 5 0.10
16 22 0.43
17 23 0.45
18 1 0.02
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (15 bp):
AAAAAGAAAAGAAAA
Found at i:977811 original size:52 final size:52
Alignment explanation
Indices: 977733--978284 Score: 1018
Period size: 52 Copynumber: 10.6 Consensus size: 52
977723 ATGCCAATAG
*
977733 CATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAA
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAA
977785 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAA
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAA
*
977837 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAA
977889 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAA
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAA
977941 CATCTTCTGGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAA
1 CATCTTCT-GGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAA
977994 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAA
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAA
978046 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAA
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAA
* *
978098 CATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGACAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAA
*
978150 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAA
* *
978202 CATCTTCTGGAAGTGTTCTTTGAGTTA--TGATCTGGTTAGACAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAA
978252 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
978285 TGGACAGAAT
Statistics
Matches: 490, Mismatches: 7, Indels: 6
0.97 0.01 0.01
Matches are distributed among these distances:
50 49 0.10
52 389 0.79
53 52 0.11
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.37
Consensus pattern (52 bp):
CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAA
Found at i:978197 original size:261 final size:258
Alignment explanation
Indices: 977733--978284 Score: 1032
Period size: 261 Copynumber: 2.1 Consensus size: 258
977723 ATGCCAATAG
*
977733 CATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAACATCTTCTGGAAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAACATCTTCTGGAAG
977798 TGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAACATCTTCTGGAAGTGTTCTTTGAGTT
66 TGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAACATCTTCTGGAAGTGTTCTTTGAGTT
*
977863 ATCTGATCTGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
131 ATCTAATCTGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
*
977928 GGACAGAACATAACATCTTCTGGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATA
196 GGACAGAACATAACATCTTCT-GGAAGTGTTCTTTGAGTTA--TGATCTGGTTAGACAGAACATA
977993 A
258 A
977994 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAACATCTTCTGGAAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAACATCTTCTGGAAG
978059 TGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAACATCTTCTGGAAGTGTTCTTTGAGTT
66 TGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAACATCTTCTGGAAGTGTTCTTTGAGTT
978124 ATCTAATCTGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
131 ATCTAATCTGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
* *
978189 GGACAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATGATCTGGTTAGACAGAACATAG
196 GGACAGAACATAACATCTTCTGGAAGTGTTCTTTGAGTTATGATCTGGTTAGACAGAACATAA
978252 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
978285 TGGACAGAAT
Statistics
Matches: 286, Mismatches: 5, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
258 54 0.19
260 19 0.07
261 213 0.74
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.37
Consensus pattern (258 bp):
CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAACATCTTCTGGAAG
TGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAACATCTTCTGGAAGTGTTCTTTGAGTT
ATCTAATCTGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT
GGACAGAACATAACATCTTCTGGAAGTGTTCTTTGAGTTATGATCTGGTTAGACAGAACATAA
Found at i:979124 original size:118 final size:118
Alignment explanation
Indices: 978919--979554 Score: 963
Period size: 117 Copynumber: 5.5 Consensus size: 118
978909 GACTCAAATC
* * ** * *
978919 CATCATTTGATGGATCAGCTTTTCC--AGTTAGAGTTCATAATGAAAAGAACTCATCATCTGAAG
1 CATCACTTGATGGATCATCTTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAG
*
978982 AAGGAAGAAG-AGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATT
979034 CATCACTTGATGGATCATTCTTTTCCAGAGGAAGAGTTCATAATGAGAAG-ACTCGTCATCTGAA
1 CATCACTTGATGGATCA-TCTTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAA
979098 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG-ATT
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATT
* *
979151 CATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAA
1 CATC-ACTTGATGGATCATCTTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAA
*
979216 GAAGGAAGAAGAAG-TCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATT
979269 CATCACTTGATGGATCATTCTTTTCCAGAGGAAGAGTTCATAATGAGAAG-A-TCGTCATCTGAA
1 CATCACTTGATGGATCA-TCTTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAA
*
979332 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATT
* * *
979386 CATCACTTGATGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATATGAAG
1 CATCACTTGATGGATCATCTTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAG
*
979451 AAGG-A-AAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATT
* * * ** *
979502 CATCATTTGATGGAACATCATCCCCAGCA-GAA-AGTTCGTAATGAGAAGAACTC
1 CATCACTTGATGGATCATCTTTTCCAG-AGGAAGAGTTCATAATGAGAAGAACTC
979555 ATCTGGAGAA
Statistics
Matches: 486, Mismatches: 23, Indels: 24
0.91 0.04 0.05
Matches are distributed among these distances:
115 36 0.07
116 132 0.27
117 168 0.35
118 150 0.31
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.29
Consensus pattern (118 bp):
CATCACTTGATGGATCATCTTTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATT
Found at i:979389 original size:235 final size:234
Alignment explanation
Indices: 978948--979573 Score: 1000
Period size: 235 Copynumber: 2.7 Consensus size: 234
978938 TTTTCCAGTT
* *
978948 AGAGTTCATAATGAAAAGAACTCATCATCTGAAGAAGGAAGAAG-AGTTCATAATGAGAAGAACT
1 AGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
979012 TGTTCAATCTTTTGCTTGAATTCATCACTTGATGGATCATTCTTTTCCAGAGGAAGAGTTCATAA
66 TGTTCAATCTTTTGCTTGAATTCATCACTTGATGGATCATTCTTTTCCAGAGGAAGAGTTCATAA
979077 TGAGAAGACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
131 TGAGAAGA-TCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
*
979142 TGCTTGATTCATCAAATTGATGGATCATCATTTCCAGAGGA
195 TGCTTGATTCATC-AATTGATGGATCATCATTTCCAGAGAA
*
979183 AGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAG-TCATAATGAGAAGAATT
1 AGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
*
979247 TGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCATTCTTTTCCAGAGGAAGAGTTCATAA
66 TGTTCAATCTTTTGCTTGAATTCATCACTTGATGGATCATTCTTTTCCAGAGGAAGAGTTCATAA
*
979312 TGAGAAGATCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
131 TGAGAAGATCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT
*
979377 GCTTGAATTCATCACTTGATGGATCATCATTTCCAGAGAA
196 GCTTG-ATTCATCAATTGATGGATCATCATTTCCAGAGAA
*
979417 AGAGTTCATAATGAGAAGAACTCGTCATATGAAGAAGG-A-AAGAAGTTCATAATGAGAAGAACT
1 AGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
* * * ** *
979480 TGTTCAATCTTTTGCTTGAATTCATCATTTGATGGAACA-TCATCCCCAGCA-GAA-AGTTCGTA
66 TGTTCAATCTTTTGCTTGAATTCATCACTTGATGGATCATTCTTTTCCAG-AGGAAGAGTTCATA
* * *
979542 ATGAGAAGAAC-TCATCTGGAGAA-AAAGAAGAA
130 ATGAGAAGATCGTCATCTGAAGAAGGAAGAAGAA
979574 TTTATTCAAT
Statistics
Matches: 368, Mismatches: 19, Indels: 14
0.92 0.05 0.03
Matches are distributed among these distances:
229 8 0.02
230 11 0.03
231 17 0.05
232 16 0.04
233 54 0.15
234 123 0.33
235 137 0.37
236 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (234 bp):
AGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
TGTTCAATCTTTTGCTTGAATTCATCACTTGATGGATCATTCTTTTCCAGAGGAAGAGTTCATAA
TGAGAAGATCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT
GCTTGATTCATCAATTGATGGATCATCATTTCCAGAGAA
Found at i:979717 original size:3 final size:3
Alignment explanation
Indices: 979709--979802 Score: 129
Period size: 3 Copynumber: 31.7 Consensus size: 3
979699 TTTTTATCCA
* * *
979709 TAT TAT TAT TAT TAT TAT TAA TAT TAT TAT TAT CAT TAT TAA TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
979757 TAT TAT TAT TAT TAT T-T TTT TA- TAT TAT TAT TAT TATT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT
979801 TA
1 TA
979803 AATATATTAA
Statistics
Matches: 81, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
2 4 0.05
3 74 0.91
4 3 0.04
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:980161 original size:21 final size:21
Alignment explanation
Indices: 980136--980179 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
980126 GCCGTCCACG
*
980136 CCATGGCTACT-CGGTGAGTCA
1 CCATGG-TACTCCGGTGACTCA
*
980157 CCATGGTAGTCCGGTGACTCA
1 CCATGGTACTCCGGTGACTCA
980178 CC
1 CC
980180 GAAACTCACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.18, C:0.32, G:0.27, T:0.23
Consensus pattern (21 bp):
CCATGGTACTCCGGTGACTCA
Found at i:980275 original size:6 final size:6
Alignment explanation
Indices: 980266--980292 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
980256 AAAAAAAAAA
980266 AGAGAC AGAGAC AGAGAC AGAGAC AGA
1 AGAGAC AGAGAC AGAGAC AGAGAC AGA
980293 ACCGAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.15, G:0.33, T:0.00
Consensus pattern (6 bp):
AGAGAC
Found at i:981170 original size:13 final size:15
Alignment explanation
Indices: 981144--981175 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
981134 TCTTTTATTT
981144 TATTGTTTTAAATA-
1 TATTGTTTTAAATAG
981158 TATTGTTTT-AATAG
1 TATTGTTTTAAATAG
981172 TATT
1 TATT
981176 TTTATTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.59
Consensus pattern (15 bp):
TATTGTTTTAAATAG
Found at i:982268 original size:2 final size:2
Alignment explanation
Indices: 982261--982285 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
982251 AACTCCCCCA
982261 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
982286 TTTGCAGGTT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:982921 original size:61 final size:58
Alignment explanation
Indices: 982800--983041 Score: 179
Period size: 59 Copynumber: 4.1 Consensus size: 58
982790 GTCTTTTTGT
* * * * *
982800 CTCAATTTTGACGATATTTAGCTTTATCTTATAGCTGAAACTGAGAATAC-GTA--TTTCA
1 CTCAA-TTTGACGCTATTTAGCTTAATCGTATAGCTG-AACTGAAAAT-CTATATTTTTCA
* * * *
982858 CTCCAATTTAACGCTTTTTAGCTTAATCGTTTAGATGAATCTGAAAATCTATATGTTTTCA
1 CT-CAATTTGACGCTATTTAGCTTAATCGTATAGCTGAA-CTGAAAATCTATAT-TTTTCA
* * * * *
982919 CTCAGTGTTGACGCTATTTAGCTCT-ATC-TAAAGCTGAACTGAGAATCTTTTTTTTTTTCA
1 CTCAAT-TTGACGCTATTTAGCT-TAATCGTATAGCTGAACTGAAAATC--TATATTTTTCA
* * * * *
982979 CTCTATTTGACGATCTTTAGCTTAATCGTGTAGCTGAAGCTGAAAATCTATGTTTTTCA
1 CTCAATTTGACGCTATTTAGCTTAATCGTATAGCTGAA-CTGAAAATCTATATTTTTCA
983038 CTCA
1 CTCA
983042 GTATGGACTC
Statistics
Matches: 143, Mismatches: 28, Indels: 25
0.73 0.14 0.13
Matches are distributed among these distances:
57 3 0.02
58 36 0.25
59 40 0.28
60 28 0.20
61 35 0.24
62 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.41
Consensus pattern (58 bp):
CTCAATTTGACGCTATTTAGCTTAATCGTATAGCTGAACTGAAAATCTATATTTTTCA
Found at i:982947 original size:119 final size:115
Alignment explanation
Indices: 982807--983043 Score: 269
Period size: 120 Copynumber: 2.0 Consensus size: 115
982797 TGTCTCAATT
* *
982807 TTGACGATATTTAGCTTTATCTTATAGCTGAAACTGAGAATAC-GTATTTCACTCCAATTTAACG
1 TTGACGATATTTAGCTCTATC-TAAAGCTG-AACTGAGAAT-CTGTATTTCACT-CAATTTAACG
* * * *
982871 CTTTTTAGCTTAATCGTTTAGATGAATCTGAAAATCTATATGTTTTCACTCAGTG
62 ATCTTTAGCTTAATCGTGTAGATGAAGCTGAAAATCTATAT-TTTTCACTCAGTG
* * * * *
982926 TTGACGCTATTTAGCTCTATCTAAAGCTGAACTGAGAATCTTTTTTTTTTTCACTCTATTTGACG
1 TTGACGATATTTAGCTCTATCTAAAGCTGAACTGAGAATC----TGTATTTCACTCAATTTAACG
* *
982991 ATCTTTAGCTTAATCGTGTAGCTGAAGCTGAAAATCTATGTTTTTCACTCAGT
62 ATCTTTAGCTTAATCGTGTAGATGAAGCTGAAAATCTATATTTTTCACTCAGT
983044 ATGGACTCTT
Statistics
Matches: 100, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
116 1 0.01
117 10 0.10
118 7 0.07
119 31 0.31
120 43 0.43
121 8 0.08
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (115 bp):
TTGACGATATTTAGCTCTATCTAAAGCTGAACTGAGAATCTGTATTTCACTCAATTTAACGATCT
TTAGCTTAATCGTGTAGATGAAGCTGAAAATCTATATTTTTCACTCAGTG
Found at i:983088 original size:120 final size:117
Alignment explanation
Indices: 982874--983120 Score: 252
Period size: 120 Copynumber: 2.1 Consensus size: 117
982864 TTTAACGCTT
* * * *
982874 TTTAGCTTAATCGTTTAGATGAATCTGAAAATCTATATGTTTTCACTCAGTGTTGACGCTATTTA
1 TTTAGCTTAATCGTGTAGATGAAGCTGAAAATCTATATGTTTTCACTCAGTATGGAC-CTATTTA
*
982939 GCTCTATCTAAAGCTGAACTGAGAATCTTTT-TTTTTTTCACTCTATTTGACGATC
65 GCTCTATCTAAA-CTGAACTGAGAATCTTTTATTTTTTT-ACTC-ATTTGACGATA
* * *
982994 TTTAGCTTAATCGTGTAGCTGAAGCTGAAAATCTATGT-TTTTCACTCAGTATGGA-CTCTTTAG
1 TTTAGCTTAATCGTGTAGATGAAGCTGAAAATCTATATGTTTTCACTCAGTATGGACCTATTTAG
* * * *
983057 CTCTATCATTTTAA-TGAAAACTGA-ATTTCTTTTAATTTTTTTACTCCTTTGACGCTA
66 CTCTATC---TAAACTG--AACTGAGA-ATCTTTT-ATTTTTTTACTCATTTGACGATA
983114 TTTAGCT
1 TTTAGCT
983121 CAATTTTCTG
Statistics
Matches: 107, Mismatches: 12, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
117 14 0.13
118 2 0.02
119 16 0.15
120 64 0.60
121 4 0.04
122 7 0.07
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.44
Consensus pattern (117 bp):
TTTAGCTTAATCGTGTAGATGAAGCTGAAAATCTATATGTTTTCACTCAGTATGGACCTATTTAG
CTCTATCTAAACTGAACTGAGAATCTTTTATTTTTTTACTCATTTGACGATA
Done.