Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003694.1 Hibiscus syriacus cultivar Beakdansim tig00007895_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: 787758
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:604863 original size:23 final size:23
Alignment explanation
Indices: 604819--604863 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
604809 TGAAAACGAT
* * *
604819 AAAATTCAAATAATTGTCTATAA
1 AAAAATCAAATAATTATATATAA
604842 AAAAATCAAATAATTATATATA
1 AAAAATCAAATAATTATATATA
604864 TGGCATAATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (23 bp):
AAAAATCAAATAATTATATATAA
Found at i:609290 original size:27 final size:27
Alignment explanation
Indices: 609259--609312 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
609249 CGGAAGTTGG
*
609259 TCTTTTAAAGCTCGGATGCTTTTATTT
1 TCTTTTAAAGCTCAGATGCTTTTATTT
609286 TCTTTTAAAGCTCAGATGCTTTTATTT
1 TCTTTTAAAGCTCAGATGCTTTTATTT
609313 GCACTACGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.20, C:0.15, G:0.13, T:0.52
Consensus pattern (27 bp):
TCTTTTAAAGCTCAGATGCTTTTATTT
Found at i:612322 original size:23 final size:21
Alignment explanation
Indices: 612283--612335 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
612273 CATAATTATT
612283 TAAAAAATTAAATAAAAATAC
1 TAAAAAATTAAATAAAAATAC
*
612304 TAAAAATATTTAATAAAAA-ATC
1 TAAAAA-ATTAAATAAAAATA-C
*
612326 AAAAAAATTA
1 TAAAAAATTA
612336 GGTTGAACTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (21 bp):
TAAAAAATTAAATAAAAATAC
Found at i:615199 original size:31 final size:31
Alignment explanation
Indices: 615127--615213 Score: 81
Period size: 31 Copynumber: 2.8 Consensus size: 31
615117 GCCCTATTTC
*
615127 AAAGTAATGATGTGATACATATTACTTGTCT
1 AAAGTAATGATGTGATACATATCACTTGTCT
* * *
615158 AAAATGATGATGTGATATATATCA-TGTGTTCT
1 AAAGTAATGATGTGATACATATCACT-TG-TCT
*
615190 -AAGTAATGATAG-GACACATATCAC
1 AAAGTAATGAT-GTGATACATATCAC
615214 ATGTTGTATC
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
30 1 0.02
31 39 0.89
32 4 0.09
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.34
Consensus pattern (31 bp):
AAAGTAATGATGTGATACATATCACTTGTCT
Found at i:615613 original size:20 final size:21
Alignment explanation
Indices: 615575--615614 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
615565 ATATTCAAAA
*
615575 AAAATATATATAGGCCAAACT
1 AAAATATATATAGACCAAACT
*
615596 AAAA-ATATATAGATCAAAC
1 AAAATATATATAGACCAAAC
615615 CAATTATTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.57, C:0.12, G:0.07, T:0.23
Consensus pattern (21 bp):
AAAATATATATAGACCAAACT
Found at i:617930 original size:16 final size:17
Alignment explanation
Indices: 617909--617943 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
617899 TTACTATTCA
617909 CGTGAATAGTG-AATTT
1 CGTGAATAGTGAAATTT
617925 CGTGAATAGTGAAATTT
1 CGTGAATAGTGAAATTT
617942 CG
1 CG
617944 GTCGGCGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.34
Consensus pattern (17 bp):
CGTGAATAGTGAAATTT
Found at i:618711 original size:15 final size:16
Alignment explanation
Indices: 618693--618725 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
618683 GTGGCAGATC
618693 AAAATCCAG-ACGGGA
1 AAAATCCAGAACGGGA
*
618708 AAAATCTAGAACGGGA
1 AAAATCCAGAACGGGA
618724 AA
1 AA
618726 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.52, C:0.15, G:0.24, T:0.09
Consensus pattern (16 bp):
AAAATCCAGAACGGGA
Found at i:623688 original size:23 final size:22
Alignment explanation
Indices: 623650--623692 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
623640 TTAATGAGCA
623650 TAAATATATTTGTTTAGTATTCG
1 TAAATATATTTGTTTA-TATTCG
623673 TAAATATATTCT-TTTATATT
1 TAAATATATT-TGTTTATATT
623693 TACTAACGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 4 0.21
23 14 0.74
24 1 0.05
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.56
Consensus pattern (22 bp):
TAAATATATTTGTTTATATTCG
Found at i:624294 original size:5 final size:5
Alignment explanation
Indices: 624284--624310 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
624274 GTTTCTGTCT
624284 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
624311 AATTAATTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:627410 original size:19 final size:20
Alignment explanation
Indices: 627386--627425 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
627376 AAATTGTTTT
*
627386 TATGAATAGTA-CTATACTG
1 TATGAATAGTATCGATACTG
627405 TATGAATAGTATCGATACTG
1 TATGAATAGTATCGATACTG
627425 T
1 T
627426 GCAAATAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (20 bp):
TATGAATAGTATCGATACTG
Found at i:628148 original size:31 final size:31
Alignment explanation
Indices: 628110--628230 Score: 149
Period size: 31 Copynumber: 4.0 Consensus size: 31
628100 CCCGAAAGAC
*
628110 CAGTCCATAGGTCTCGAAGAACCTAGGTAAA
1 CAGTCCATAGGTCTCGAAGAACATAGGTAAA
**
628141 CAGTCCATATAT-TCCGAAGAACATAGGTAAA
1 CAGTCCATAGGTCT-CGAAGAACATAGGTAAA
* * *
628172 CAGTCCATATGTCCCGAAGAACATAGGTAAT
1 CAGTCCATAGGTCTCGAAGAACATAGGTAAA
*
628203 CAGTCCAT-GTTCT-GAAGAACATAGGTAA
1 CAGTCCATAGGTCTCGAAGAACATAGGTAA
628231 CCCTCGACTC
Statistics
Matches: 79, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
29 15 0.19
30 3 0.04
31 61 0.77
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.22
Consensus pattern (31 bp):
CAGTCCATAGGTCTCGAAGAACATAGGTAAA
Found at i:628207 original size:62 final size:60
Alignment explanation
Indices: 628110--628230 Score: 170
Period size: 62 Copynumber: 2.0 Consensus size: 60
628100 CCCGAAAGAC
* *
628110 CAGTCCATAGGTCTCGAAGAACCTAGGTAAACAGTCCATATATTCCGAAGAACATAGGTAAA
1 CAGTCCATAGGTCCCGAAGAACATAGGTAAACAGTCC--ATATTCCGAAGAACATAGGTAAA
* * * *
628172 CAGTCCATATGTCCCGAAGAACATAGGTAATCAGTCCATGTTCTGAAGAACATAGGTAA
1 CAGTCCATAGGTCCCGAAGAACATAGGTAAACAGTCCATATTCCGAAGAACATAGGTAA
628231 CCCTCGACTC
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
60 20 0.38
62 33 0.62
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.22
Consensus pattern (60 bp):
CAGTCCATAGGTCCCGAAGAACATAGGTAAACAGTCCATATTCCGAAGAACATAGGTAAA
Found at i:637013 original size:43 final size:43
Alignment explanation
Indices: 636967--637123 Score: 219
Period size: 43 Copynumber: 3.7 Consensus size: 43
636957 AAAAAGTCGT
* * *
636967 TATCTATAGCAGCGTTTTTGGA-ACAAATGCCGCAAAAGGTCA
1 TATCTATAGCGGCGTTTTTTGATACAAACGCCGCAAAAGGTCA
*
637009 TTATCTATAGCGGCATTTTTTGATACAAACGCCGCAAAAGGTCA
1 -TATCTATAGCGGCGTTTTTTGATACAAACGCCGCAAAAGGTCA
* *
637053 GATCTATAGCGGCG-TTTTTGATATAAACGCCGCAAAAGGTCA
1 TATCTATAGCGGCGTTTTTTGATACAAACGCCGCAAAAGGTCA
* *
637095 AATCTATAACGGCGTTTTTTGATACAAAC
1 TATCTATAGCGGCGTTTTTTGATACAAAC
637124 TATGTATTTA
Statistics
Matches: 102, Mismatches: 10, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
42 39 0.38
43 44 0.43
44 19 0.19
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (43 bp):
TATCTATAGCGGCGTTTTTTGATACAAACGCCGCAAAAGGTCA
Found at i:637084 original size:42 final size:42
Alignment explanation
Indices: 636968--637123 Score: 206
Period size: 42 Copynumber: 3.6 Consensus size: 42
636958 AAAAGTCGTT
* * *
636968 ATCTATAGCAGCGTTTTTGGA-ACAAATGCCGCAAAAGGTCATT
1 ATCTATAGCGGCGTTTTT-GATACAAACGCCGCAAAAGGTCA-A
* *
637011 ATCTATAGCGGCATTTTTTGATACAAACGCCGCAAAAGGTCAG
1 ATCTATAGCGGC-GTTTTTGATACAAACGCCGCAAAAGGTCAA
*
637054 ATCTATAGCGGCGTTTTTGATATAAACGCCGCAAAAGGTCAA
1 ATCTATAGCGGCGTTTTTGATACAAACGCCGCAAAAGGTCAA
*
637096 ATCTATAACGGCGTTTTTTGATACAAAC
1 ATCTATAGCGGCG-TTTTTGATACAAAC
637124 TATGTATTTA
Statistics
Matches: 101, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
42 39 0.39
43 38 0.38
44 24 0.24
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (42 bp):
ATCTATAGCGGCGTTTTTGATACAAACGCCGCAAAAGGTCAA
Found at i:637271 original size:21 final size:21
Alignment explanation
Indices: 637245--637291 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
637235 AACTTAACAT
637245 CATAACAACAAACTTGAAATC
1 CATAACAACAAACTTGAAATC
*
637266 CATAACAAGAAACTTGAAATC
1 CATAACAACAAACTTGAAATC
637287 CATAA
1 CATAA
637292 TAATAAATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.53, C:0.21, G:0.06, T:0.19
Consensus pattern (21 bp):
CATAACAACAAACTTGAAATC
Found at i:640306 original size:41 final size:40
Alignment explanation
Indices: 640218--640689 Score: 398
Period size: 41 Copynumber: 11.5 Consensus size: 40
640208 ATTGCAGCAC
* * *
640218 GAGTCTATAGCGGCGTTTGTAAACACAAACACCACTAAAGTAT
1 GAGTCTTTAGCGGCGTTTGTATA-A-AAACGCCACTAAA-TAT
640261 GAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAGTAT
1 GAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAA-TAT
* *
640302 GAGTCTATAACGGCGTTTGTATAAAAACGCCACTAAATCAT
1 GAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAT-AT
* * * * *
640343 GATTCTTTAGCGGCGTTTGTAAAAAAAAGGCCACTAAACCAC
1 GAGTCTTTAGCGGCGTTTGT-ATAAAAACGCCACTAAA-TAT
* *
640385 GAGTCTTTAACGACGTTTGTATAAAAACGCCACTAAATCAT
1 GAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAT-AT
* * ** *
640426 GAGTCTATAGCAGCGTTTGTATAAAAATTCCACTAAATCAC
1 GAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAT-AT
* * * *
640467 GAGTCTATAGC-GTGTTTGTATAAAAAAGCCACTAAATCAC
1 GAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAT-AT
* * * * * *
640507 GAGTCTATAGCAGCATTTTTGA-AACAAACGCCGCTAAAGACT
1 GAGTCTTTAGCGGCGTTTGT-ATAA-AAACGCCACTAAATA-T
* * *
640549 -CGTACTATT-GCGGCATTTGTATAAAAATGCCACTAAAT-T
1 GAGT-CT-TTAGCGGCGTTTGTATAAAAACGCCACTAAATAT
* * * *
640588 ACAATCTTTAGCGGCGTTTTTATACAAACGCCACTAAAGTA-
1 -GAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAA-TAT
* * * *
640629 CATTCTTTAGCGGCGTTTTTATACAAACGCCACTATAATAT
1 GAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTA-AATAT
640670 GAGTCTTTAGCGGCGTTTGT
1 GAGTCTTTAGCGGCGTTTGT
640690 TCTAAAAATG
Statistics
Matches: 358, Mismatches: 53, Indels: 38
0.80 0.12 0.08
Matches are distributed among these distances:
39 3 0.01
40 100 0.28
41 174 0.49
42 59 0.16
43 22 0.06
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.29
Consensus pattern (40 bp):
GAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAATAT
Found at i:640478 original size:124 final size:123
Alignment explanation
Indices: 640215--640701 Score: 477
Period size: 124 Copynumber: 3.9 Consensus size: 123
640205 GCAATTGCAG
* * * * *
640215 CACGAGTCTATAGCGGCGTTTGTAAACACAAACACCACTAAAGTATGAGTCTTTAGCGGCGTTTG
1 CACGAGTCTATAGCGGCGTTTGTAAA-AAAAACGCCACTAAAGCACGAGTCTTTAGCGACGTTTG
* *
640280 TATAAAAACGCCACTAAAGTATGAGTCTATAACGGCGTTTGTATAAAAACGCCACTAAAT
65 TATAAAAACGCCACTAAA-TATGAGTCTATAGCGGCGTTTGTATAAAAATGCCACTAAAT
* * * * * *
640340 CATGATTCTTTAGCGGCGTTTGTAAAAAAAAGGCCACTAAACCACGAGTCTTTAACGACGTTTGT
1 CACGAGTCTATAGCGGCGTTTGTAAAAAAAACGCCACTAAAGCACGAGTCTTTAGCGACGTTTGT
* *
640405 ATAAAAACGCCACTAAATCATGAGTCTATAGCAGCGTTTGTATAAAAATTCCACTAAAT
66 ATAAAAACGCCACTAAAT-ATGAGTCTATAGCGGCGTTTGTATAAAAATGCCACTAAAT
* * * * * *
640464 CACGAGTCTATAGC-GTGTTTGTATAAAAAA-GCCACTAAATCACGAGTCTATAGC-AGCATTTT
1 CACGAGTCTATAGCGGCGTTTGTAAAAAAAACGCCACTAAAGCACGAGTCTTTAGCGA-CGTTTG
* * * * *
640526 TGA-AACAAACGCCGCTAAAGACT-CGTACTATTGCGGCATTTGTATAAAAATGCCACTAAAT
65 T-ATAA-AAACGCCACTAAATA-TGAGT-CTATAGCGGCGTTTGTATAAAAATGCCACTAAAT
* * * * * * * * * *
640587 TAC-AATCTTTAGCGGCGTTT-TTATACAAACGCCACTAAAGTAC-ATTCTTTAGCGGCGTTTTT
1 CACGAGTCTATAGCGGCGTTTGTAAAAAAAACGCCACTAAAGCACGAGTCTTTAGCGACGTTTGT
* * *
640649 ATACAAACGCCACTATAATATGAGTCTTTAGCGGCGTTTGTTCTAAAAATGCC
66 ATAAAAACGCCACTA-AATATGAGTCTATAGCGGCGTTTG-TATAAAAATGCC
640702 GCTATTAACC
Statistics
Matches: 295, Mismatches: 54, Indels: 29
0.78 0.14 0.08
Matches are distributed among these distances:
121 25 0.08
122 75 0.25
123 77 0.26
124 95 0.32
125 23 0.08
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (123 bp):
CACGAGTCTATAGCGGCGTTTGTAAAAAAAACGCCACTAAAGCACGAGTCTTTAGCGACGTTTGT
ATAAAAACGCCACTAAATATGAGTCTATAGCGGCGTTTGTATAAAAATGCCACTAAAT
Found at i:641256 original size:18 final size:18
Alignment explanation
Indices: 641233--641269 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
641223 TATTCCTTTA
*
641233 ATCAAACACGGTTATCTT
1 ATCAAACACGATTATCTT
641251 ATCAAACACGATTATCTT
1 ATCAAACACGATTATCTT
641269 A
1 A
641270 CATTCCTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.38, C:0.22, G:0.08, T:0.32
Consensus pattern (18 bp):
ATCAAACACGATTATCTT
Found at i:642204 original size:4 final size:4
Alignment explanation
Indices: 642195--642243 Score: 53
Period size: 4 Copynumber: 12.2 Consensus size: 4
642185 CACACTGAAA
* * * * *
642195 CTCT CTCT CTCT CTCT CTCT CCCT CTCT CCCT CTCC CTCC CTCC CTCT
1 CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT CTCT
642243 C
1 C
642244 AAAAGTTCAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (4 bp):
CTCT
Found at i:642214 original size:14 final size:14
Alignment explanation
Indices: 642197--642243 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 14
642187 CACTGAAACT
* *
642197 CTCTCTCTCTCTCT
1 CTCTCCCTCTCTCC
642211 CTCTCCCTCTCTCC
1 CTCTCCCTCTCTCC
*
642225 CTCTCCCTCCCTCC
1 CTCTCCCTCTCTCC
642239 CTCTC
1 CTCTC
642244 AAAAGTTCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (14 bp):
CTCTCCCTCTCTCC
Found at i:642911 original size:28 final size:28
Alignment explanation
Indices: 642871--642926 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
642861 TATGTAACTT
642871 TAATTCCTATTTTTAAAATAAAAATGTA
1 TAATTCCTATTTTTAAAATAAAAATGTA
642899 TAATTCCTATTTTTAAAATAAAAATGTA
1 TAATTCCTATTTTTAAAATAAAAATGTA
642927 CTCTTTCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (28 bp):
TAATTCCTATTTTTAAAATAAAAATGTA
Found at i:647952 original size:2 final size:2
Alignment explanation
Indices: 647945--647976 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
647935 AATTTTCAAG
647945 TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
647977 TTGAATAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:648735 original size:66 final size:66
Alignment explanation
Indices: 648629--648761 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
648619 GGATGTTCTC
* * * *
648629 AAGTCTACAAGATTGTGTTTCTTCTATTAGTTTTTTATTAGAAGATCATATAAAAAAAGACACCT
1 AAGTCTACAAGATTGTATTTATTCTATTAATTTTTAATTAGAAGATCATATAAAAAAAGACACCT
648694 A
66 A
648695 AAGTCTACAAGATTGTATTTATTCTATTAATTTTTAATTAGAAGATCATATAAAAAAAGACACCT
1 AAGTCTACAAGATTGTATTTATTCTATTAATTTTTAATTAGAAGATCATATAAAAAAAGACACCT
648760 A
66 A
648761 A
1 A
648762 TACTAGATTT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.37
Consensus pattern (66 bp):
AAGTCTACAAGATTGTATTTATTCTATTAATTTTTAATTAGAAGATCATATAAAAAAAGACACCT
A
Found at i:656678 original size:157 final size:154
Alignment explanation
Indices: 656395--656705 Score: 595
Period size: 157 Copynumber: 2.0 Consensus size: 154
656385 AGATCGAACT
656395 TCCTAACTGATAGAATCGGTCAAATACTTGATTAGCGATAATGTACGAATTGAACGAGTTAAAAT
1 TCCTAACTGATAGAATCGGTCAAATACTTGATTAGCGATAATGTACGAATTGAACGAGTTAAAAT
656460 GTGTCAAAATCCAACTGCCGGTTTGATCCTAGAGGAGAGAAGCCCTTTACCCTCTCGCTTATTAG
66 GTGTCAAAATCCAACTGCCGGTTTGATCCTAGAGGAGAGAAGCCCTTTACCCTCTCGCTTATTAG
656525 TTGAAACATATATTAGCAATTTTA
131 TTGAAACATATATTAGCAATTTTA
656549 TCCTAACTGATAGAATCGGTCAAAATACTTGATTAGTCGATAATGTACGAATTGAACGAGTTAAA
1 TCCTAACTGATAGAATCGGTC-AAATACTTGATTAG-CGATAATGTACGAATTGAACGAGTTAAA
656614 ATGTGTCTAAAATCCAACTGCCGGTTTGATCCTAGAGGAGAGAAGCCCTTTACCCTCTCGCTTAT
64 ATGTGTC-AAAATCCAACTGCCGGTTTGATCCTAGAGGAGAGAAGCCCTTTACCCTCTCGCTTAT
656679 TAGTTGAAACATATATTAGCAATTTTA
128 TAGTTGAAACATATATTAGCAATTTTA
656706 AACTATCAAA
Statistics
Matches: 154, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
154 21 0.14
155 14 0.09
156 35 0.23
157 84 0.55
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (154 bp):
TCCTAACTGATAGAATCGGTCAAATACTTGATTAGCGATAATGTACGAATTGAACGAGTTAAAAT
GTGTCAAAATCCAACTGCCGGTTTGATCCTAGAGGAGAGAAGCCCTTTACCCTCTCGCTTATTAG
TTGAAACATATATTAGCAATTTTA
Found at i:659292 original size:29 final size:28
Alignment explanation
Indices: 659260--659318 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 28
659250 AATTTAAGGC
*
659260 AAAATGGTTTTTGGACTTGAATTGAATTTAA
1 AAAAT-GTTTTTGGACGT-AATTGAATTT-A
659291 AAAATGTTTTTGGACGTAATTGAATTTA
1 AAAATGTTTTTGGACGTAATTGAATTTA
659319 TTCAAAGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 1 0.04
29 10 0.37
30 11 0.41
31 5 0.19
ACGTcount: A:0.36, C:0.03, G:0.19, T:0.42
Consensus pattern (28 bp):
AAAATGTTTTTGGACGTAATTGAATTTA
Found at i:659330 original size:29 final size:30
Alignment explanation
Indices: 659260--659318 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
659250 AATTTAAGGC
*
659260 AAAATGGTTTTTGGACTTGAATTGAATTTAA
1 AAAAT-GTTTTTGGACGTGAATTGAATTTAA
659291 AAAATGTTTTTGGACGT-AATTGAATTTA
1 AAAATGTTTTTGGACGTGAATTGAATTTA
659319 TTCAAAGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 11 0.41
30 11 0.41
31 5 0.19
ACGTcount: A:0.36, C:0.03, G:0.19, T:0.42
Consensus pattern (30 bp):
AAAATGTTTTTGGACGTGAATTGAATTTAA
Found at i:659433 original size:21 final size:21
Alignment explanation
Indices: 659408--659508 Score: 124
Period size: 21 Copynumber: 5.1 Consensus size: 21
659398 TTCAAGATTG
* * *
659408 CCCAGGGGGTATAGATTCCCC
1 CCCAGAGGGTACAGATACCCC
*
659429 CCCAGGGGGTACAGATA---C
1 CCCAGAGGGTACAGATACCCC
659447 CCC--A-GGTACAGATACCCC
1 CCCAGAGGGTACAGATACCCC
659465 CCCAGAGGGTACAGATACCCC
1 CCCAGAGGGTACAGATACCCC
659486 CCCAGAGGGTACAGATACCCC
1 CCCAGAGGGTACAGATACCCC
659507 CC
1 CC
659509 TGCAGGTTTT
Statistics
Matches: 71, Mismatches: 3, Indels: 12
0.83 0.03 0.14
Matches are distributed among these distances:
15 10 0.14
18 8 0.11
20 1 0.01
21 52 0.73
ACGTcount: A:0.26, C:0.38, G:0.25, T:0.12
Consensus pattern (21 bp):
CCCAGAGGGTACAGATACCCC
Found at i:659456 original size:15 final size:15
Alignment explanation
Indices: 659436--659464 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
659426 CCCCCCAGGG
659436 GGTACAGATACCCCA
1 GGTACAGATACCCCA
659451 GGTACAGATACCCC
1 GGTACAGATACCCC
659465 CCCAGAGGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.34, G:0.21, T:0.14
Consensus pattern (15 bp):
GGTACAGATACCCCA
Found at i:659466 original size:36 final size:36
Alignment explanation
Indices: 659415--659485 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
659405 TTGCCCAGGG
* * *
659415 GGTATAGATTCCCCCCCAGGGGGTACAGATACCCCA
1 GGTACAGATACCCCCCCAGAGGGTACAGATACCCCA
659451 GGTACAGATACCCCCCCAGAGGGTACAGATACCCC
1 GGTACAGATACCCCCCCAGAGGGTACAGATACCCC
659486 CCCAGAGGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.27, C:0.35, G:0.24, T:0.14
Consensus pattern (36 bp):
GGTACAGATACCCCCCCAGAGGGTACAGATACCCCA
Found at i:659582 original size:20 final size:21
Alignment explanation
Indices: 659542--659584 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
659532 AACAGAATGT
659542 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
659563 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
659584 C
1 C
659585 TGTTCAACAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.44, G:0.28, T:0.14
Consensus pattern (21 bp):
CCAGGGGGTACCGATTCCCCC
Found at i:659645 original size:20 final size:21
Alignment explanation
Indices: 659620--659661 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
659610 ATTTGAATAT
*
659620 TATGAA-GGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
659640 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
659661 T
1 T
659662 CTTCTGGGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:659725 original size:20 final size:22
Alignment explanation
Indices: 659687--659726 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
659677 TTTGAGTATA
659687 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
659709 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
659727 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:659981 original size:34 final size:32
Alignment explanation
Indices: 659942--660011 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
659932 TTTTGTAAAG
*
659942 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
659976 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
660008 GGGA
1 GGGA
660012 GTTGTAAGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:663034 original size:24 final size:25
Alignment explanation
Indices: 662988--663034 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
662978 TAGTGTTTAT
* **
662988 TTTAAGGGAAGAAGAGGCGGGGGGA
1 TTTAAGGGAAGAAGAAGAAGGGGGA
663013 TTTAA-GGAAGAAGAAGAAGGGG
1 TTTAAGGGAAGAAGAAGAAGGGG
663035 CAGATGAGCG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 14 0.74
25 5 0.26
ACGTcount: A:0.38, C:0.02, G:0.47, T:0.13
Consensus pattern (25 bp):
TTTAAGGGAAGAAGAAGAAGGGGGA
Found at i:663598 original size:2 final size:2
Alignment explanation
Indices: 663593--663633 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
663583 TTTTACTTAA
663593 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT A
663634 GAGAGAGAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:663638 original size:2 final size:2
Alignment explanation
Indices: 663633--663666 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
663623 ATATATATAT
663633 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
663667 TATTAAATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:669751 original size:27 final size:27
Alignment explanation
Indices: 669720--669782 Score: 126
Period size: 27 Copynumber: 2.3 Consensus size: 27
669710 TTTTCTTCTT
669720 TAAAATTTTATAAATTCTCTCATAGCA
1 TAAAATTTTATAAATTCTCTCATAGCA
669747 TAAAATTTTATAAATTCTCTCATAGCA
1 TAAAATTTTATAAATTCTCTCATAGCA
669774 TAAAATTTT
1 TAAAATTTT
669783 GTGTTCCATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.41, C:0.13, G:0.03, T:0.43
Consensus pattern (27 bp):
TAAAATTTTATAAATTCTCTCATAGCA
Found at i:671909 original size:194 final size:190
Alignment explanation
Indices: 671560--671943 Score: 732
Period size: 194 Copynumber: 2.0 Consensus size: 190
671550 AAATATTAGT
671560 TTTATATATGTTATTTTCTTTAATTTTTTAACATTATTTGATGACCTCAAAGACTTCATAATGTT
1 TTTATATATGTTATTTTCTTTAATTTTTTAACATTATTTGATGACCTCAAAGACTTCATAATGTT
671625 CCGGAGGATACTCACATGAAAGTGGACATAAAAAAGAGAATGATTCCGTACAATGGCATACTTGG
66 CCGGAGGATACTCACATGAAAGTGGACATAAAAAAGAGAATGATTCCGTACAATGGCATACTTGG
671690 GACGAAGGTTCACGAGCAAGTTTACCAGAAGTCCGTCCCACAGGACACCGAAGAAATTGG
131 GACGAAGGTTCACGAGCAAGTTTACCAGAAGTCCGTCCCACAGGACACCGAAGAAATTGG
671750 TTTATATATGTTATTTTCTTTAATTTTTTAACATTAGTTTGATGACCTCAAAGACTTCATAATGT
1 TTTATATATGTTATTTTCTTTAATTTTTTAACATTA-TTTGATGACCTCAAAGACTTCATAATGT
671815 TCCGGAGGATACTCCACATGAAAGTGGACATAAAAAAGAGAATGATTCCGTTAACAATGGCATAC
65 TCCGGAGGATACT-CACATGAAAGTGGACATAAAAAAGAGAATGATTCCG-T-ACAATGGCATAC
671880 TTGGGACGAAGGTTCACGAGCAAGTTTACCAGAAGTCCGTCCCACAGGACACCGAAGAAATTGG
127 TTGGGACGAAGGTTCACGAGCAAGTTTACCAGAAGTCCGTCCCACAGGACACCGAAGAAATTGG
671944 GACCAGAAGC
Statistics
Matches: 190, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
190 36 0.19
191 41 0.22
192 36 0.19
193 1 0.01
194 76 0.40
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (190 bp):
TTTATATATGTTATTTTCTTTAATTTTTTAACATTATTTGATGACCTCAAAGACTTCATAATGTT
CCGGAGGATACTCACATGAAAGTGGACATAAAAAAGAGAATGATTCCGTACAATGGCATACTTGG
GACGAAGGTTCACGAGCAAGTTTACCAGAAGTCCGTCCCACAGGACACCGAAGAAATTGG
Found at i:680300 original size:102 final size:100
Alignment explanation
Indices: 680124--680327 Score: 381
Period size: 102 Copynumber: 2.0 Consensus size: 100
680114 TGAAAGTTTT
*
680124 TTGTACAAATATTATTTTATATTCACTCAAAACTCAAAAGATAACTTCTAATTTGTCTAATATTT
1 TTGTACAAATATTATCTTATATTCACTCAAAACTCAAAAGATAACTTCTAATTTGTCTAATATTT
680189 AAACTTACAATGACTTATATTATAATTAGACTAAAAA
66 AAACTTACAATGACTTATA-T-TAATTAGACTAAAAA
680226 TTGTACAAATATTATCTTATATTCACTCAAAACTCAAAAGATAACTTCTAATTTGTCTAATATTT
1 TTGTACAAATATTATCTTATATTCACTCAAAACTCAAAAGATAACTTCTAATTTGTCTAATATTT
680291 AAACTTACAATGACTTATATTAATTAGACTAAAAA
66 AAACTTACAATGACTTATATTAATTAGACTAAAAA
680326 TT
1 TT
680328 TGAGAACACT
Statistics
Matches: 101, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
100 17 0.17
101 1 0.01
102 83 0.82
ACGTcount: A:0.43, C:0.13, G:0.05, T:0.39
Consensus pattern (100 bp):
TTGTACAAATATTATCTTATATTCACTCAAAACTCAAAAGATAACTTCTAATTTGTCTAATATTT
AAACTTACAATGACTTATATTAATTAGACTAAAAA
Found at i:680412 original size:17 final size:17
Alignment explanation
Indices: 680386--680423 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
680376 TTTTAAATTT
*
680386 AAATATTTATATGAACTA
1 AAATATTTAT-TAAACTA
680404 AAATA-TTATTAAACTA
1 AAATATTTATTAAACTA
680420 AAAT
1 AAAT
680424 TATATCAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 10 0.53
17 4 0.21
18 5 0.26
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (17 bp):
AAATATTTATTAAACTA
Found at i:691058 original size:19 final size:20
Alignment explanation
Indices: 691034--691086 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 20
691024 TTTAATCTAC
*
691034 TTTAATATATTATAT-TATG
1 TTTAATATATTATATATATA
* *
691053 TTTAAT-TTTTATTTATATA
1 TTTAATATATTATATATATA
691072 TTTAATTATATTATA
1 TTTAA-TATATTATA
691087 ATAAAGCGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
18 6 0.23
19 14 0.54
20 1 0.04
21 5 0.19
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
TTTAATATATTATATATATA
Found at i:696973 original size:2 final size:2
Alignment explanation
Indices: 696966--697019 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
696956 GATTTTCCTA
696966 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
697008 AT AT AT AT AT AT
1 AT AT AT AT AT AT
697020 TTCTGCTGTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:701236 original size:38 final size:36
Alignment explanation
Indices: 701160--701236 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 36
701150 TTTTTATATT
*
701160 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
701196 TTTAATTTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAA-TTTTGTAAA-AAAATTATATAAATATTAT-CAA
701234 TTT
1 TTT
701237 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 5 0.14
37 21 0.60
38 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:701499 original size:5 final size:6
Alignment explanation
Indices: 701469--701502 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
701459 CACATATTAT
701469 CACGAC CACGAC CACGAC CACGAC C-CGAC C-CGAC
1 CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC
701503 ACGGACGGCG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 9 0.32
6 19 0.68
ACGTcount: A:0.29, C:0.53, G:0.18, T:0.00
Consensus pattern (6 bp):
CACGAC
Found at i:701996 original size:6 final size:6
Alignment explanation
Indices: 701985--702018 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
701975 GTCGTTCGTC
*
701985 TCGTGG TCGTGG TCGTGG TCGTGG TTGTGG TCGT
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGT
702019 AGTAATACGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.15, G:0.47, T:0.38
Consensus pattern (6 bp):
TCGTGG
Found at i:702203 original size:21 final size:21
Alignment explanation
Indices: 702178--702250 Score: 119
Period size: 21 Copynumber: 3.5 Consensus size: 21
702168 GATTTACATA
702178 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
702199 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
702220 TTCGCAATGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
702241 TTCGCGTTGC
1 TTCGCATTGC
702251 AAATCTGGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.22, C:0.23, G:0.26, T:0.29
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:702406 original size:2 final size:2
Alignment explanation
Indices: 702399--702433 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
702389 TTATTTTCTC
702399 AT AT AT AT 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 AT AT AT AT A
702434 ACATGTAATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:704314 original size:13 final size:13
Alignment explanation
Indices: 704298--704334 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
704288 TATTTGCTTA
704298 TATTATTTATTAT
1 TATTATTTATTAT
704311 TATTATGTTA-TAT
1 TATTAT-TTATTAT
704324 TATTA-TTATTA
1 TATTATTTATTA
704335 AATAATACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 3 0.14
12 2 0.09
13 14 0.64
14 3 0.14
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (13 bp):
TATTATTTATTAT
Found at i:705963 original size:13 final size:14
Alignment explanation
Indices: 705934--705964 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
705924 AAAAATCCTA
705934 TTTATAAATTTAAT
1 TTTATAAATTTAAT
705948 TTTATAAA-TTAAT
1 TTTATAAATTTAAT
705961 TTTA
1 TTTA
705965 AGAAAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTTATAAATTTAAT
Found at i:708704 original size:3 final size:3
Alignment explanation
Indices: 708696--708740 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
708686 TTACCATTCT
708696 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
708741 ATCTGATATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:712414 original size:139 final size:142
Alignment explanation
Indices: 712158--712441 Score: 520
Period size: 139 Copynumber: 2.0 Consensus size: 142
712148 ATAGTGGGAA
712158 AATTAACTTGTTTACATAAGGTGTTGGAGAATTTCCCCCCCCCCCCACCCGAATAGAGTGTATGC
1 AATTAACTTGTTTACATAAGGTGTTGGAGAATTT---CCCCCCCCCACCCGAATAGAGTGTATGC
712223 TAAAATACTAATAGAAAATTACATGAATCACTTAACGTTTTTGGGAAGATACACGAAAGACACAT
63 TAAAATACTAATAGAAAATTACATGAATCACTTAACGTTTTTGGGAAGATACACGAAAGACACAT
712288 TGTCTTCTCTTATTT
128 TGTCTTCTCTTATTT
712303 AATTAACTTGTTTACATAAGGTGTTGGAGAA-TT-CCCCCCCC-CCCGAATAGAGTGTATGCTAA
1 AATTAACTTGTTTACATAAGGTGTTGGAGAATTTCCCCCCCCCACCCGAATAGAGTGTATGCTAA
712365 AATACTAATAGAAAATTACATGAATCACTTAACGTTTTTGGGAAGATACACGAAAGACACATTGT
66 AATACTAATAGAAAATTACATGAATCACTTAACGTTTTTGGGAAGATACACGAAAGACACATTGT
712430 CTTCTCTTATTT
131 CTTCTCTTATTT
712442 GCTCTCGTGC
Statistics
Matches: 139, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
139 98 0.71
140 8 0.06
144 2 0.01
145 31 0.22
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.31
Consensus pattern (142 bp):
AATTAACTTGTTTACATAAGGTGTTGGAGAATTTCCCCCCCCCACCCGAATAGAGTGTATGCTAA
AATACTAATAGAAAATTACATGAATCACTTAACGTTTTTGGGAAGATACACGAAAGACACATTGT
CTTCTCTTATTT
Found at i:714203 original size:6 final size:6
Alignment explanation
Indices: 714140--714201 Score: 106
Period size: 6 Copynumber: 10.3 Consensus size: 6
714130 TAGATTCATG
714140 TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA
1 TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA
* *
714188 TTAATA TATATA TA
1 TAAATA TAAATA TA
714202 TAAAGCGTGT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (6 bp):
TAAATA
Found at i:714510 original size:2 final size:2
Alignment explanation
Indices: 714503--714535 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
714493 AATGAATCAT
714503 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
714536 CTAAAAATCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:719142 original size:22 final size:22
Alignment explanation
Indices: 719110--719161 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
719100 CAGATTCAAT
*
719110 CCGGAGCGTCATATTAGGGTCA
1 CCGGAGCGTCACATTAGGGTCA
*
719132 CCGGAGTGTCACATTAGGGTCA
1 CCGGAGCGTCACATTAGGGTCA
719154 CCGGAGCG
1 CCGGAGCG
719162 ACCCACCGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.21, C:0.25, G:0.35, T:0.19
Consensus pattern (22 bp):
CCGGAGCGTCACATTAGGGTCA
Found at i:719249 original size:20 final size:21
Alignment explanation
Indices: 719224--719266 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
719214 GTATAAAATC
*
719224 ATTTATGAGTA-CAAAATAAA
1 ATTTATCAGTATCAAAATAAA
719244 ATTTATCAGTATTCAAAATAAA
1 ATTTATCAGTA-TCAAAATAAA
719266 A
1 A
719267 CAGATTTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
22 10 0.50
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (21 bp):
ATTTATCAGTATCAAAATAAA
Found at i:726121 original size:43 final size:42
Alignment explanation
Indices: 726076--726511 Score: 579
Period size: 43 Copynumber: 10.2 Consensus size: 42
726066 CTATAGTTCA
726076 AGATCTATAGCGGCGTTTTTGGAACAAACGTCGCAAAAGGTC
1 AGATCTATAGCGGCGTTTTTGGAACAAACGTCGCAAAAGGTC
* * *
726118 AAGATCTCTAGCGGCGTTTATGGAACAAATGTCGCAAAAGGTC
1 -AGATCTATAGCGGCGTTTTTGGAACAAACGTCGCAAAAGGTC
*
726161 GAGATCTATAGCGGCGTTTTTGTAACAAACGTCGCAAAAGGTC
1 -AGATCTATAGCGGCGTTTTTGGAACAAACGTCGCAAAAGGTC
*
726204 GAGATCTATAGCGGCGTTTTTGTAACAAACGTCGCAAAAGGTC
1 -AGATCTATAGCGGCGTTTTTGGAACAAACGTCGCAAAAGGTC
* *
726247 GAGATCTATAGCGGCGTTTTTGTAACAAACGTCGCAAAAGGTT
1 -AGATCTATAGCGGCGTTTTTGGAACAAACGTCGCAAAAGGTC
* * * *
726290 AGATATTTAGCGGCGTTTTTGGAAACAAACGCCGCAAAAGGTT
1 AGATCTATAGCGGCGTTTTTGG-AACAAACGTCGCAAAAGGTC
* * *
726333 AGATATTTAGCGGCGTTTTTGGATACAAACG-CTACAAAA-GTAC
1 AGATCTATAGCGGCGTTTTTGGA-ACAAACGTC-GCAAAAGGT-C
*
726376 AGATCTATAGCGGCGTTTTTGGACACAAACGCCGCAAAAGGTC
1 AGATCTATAGCGGCGTTTTTGGA-ACAAACGTCGCAAAAGGTC
* *
726419 AGATCTATAGCGGTGTTTTTGGACACAAACGCCGCAAAAGGTC
1 AGATCTATAGCGGCGTTTTTGGA-ACAAACGTCGCAAAAGGTC
* * *
726462 AGATCTATAGCGACGTTTTTGGACACAAACGCCGCAAAAAGTC
1 AGATCTATAGCGGCGTTTTTGGA-ACAAACGTCGCAAAAGGTC
726505 AGATCTA
1 AGATCTA
726512 AATTACCATT
Statistics
Matches: 364, Mismatches: 23, Indels: 12
0.91 0.06 0.03
Matches are distributed among these distances:
42 23 0.06
43 338 0.93
44 3 0.01
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.25
Consensus pattern (42 bp):
AGATCTATAGCGGCGTTTTTGGAACAAACGTCGCAAAAGGTC
Found at i:727375 original size:26 final size:26
Alignment explanation
Indices: 727346--727399 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
727336 TAAAATAATT
727346 AATGATTAAAATCACAAAATGCAGGG
1 AATGATTAAAATCACAAAATGCAGGG
727372 AATGATTAAAATCACAAAATGCAGGG
1 AATGATTAAAATCACAAAATGCAGGG
727398 AA
1 AA
727400 ACAAGATACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.52, C:0.11, G:0.19, T:0.19
Consensus pattern (26 bp):
AATGATTAAAATCACAAAATGCAGGG
Found at i:730587 original size:41 final size:41
Alignment explanation
Indices: 730540--730849 Score: 196
Period size: 41 Copynumber: 7.6 Consensus size: 41
730530 ACTTTCGACA
* * *
730540 TTGTATATAAACACCACTAAAGTATAATTGTATAACGGCGT
1 TTGTATATAAACGCCACTAAAGTACAAGTGTATAACGGCGT
* * * * *
730581 TTGTATAAAAATGCCACGAAAGAACAAGTGTATAGCGGCGT
1 TTGTATATAAACGCCACTAAAGTACAAGTGTATAACGGCGT
* * * * * * *
730622 TTTTATATAAACGCCTCTAAAGTACGAGTCTTTAGCGGAGT
1 TTGTATATAAACGCCACTAAAGTACAAGTGTATAACGGCGT
* * * * *
730663 TTTTATAAAAACGCCACTAAAGTACAAGTCTATAGCGTCGT
1 TTGTATATAAACGCCACTAAAGTACAAGTGTATAACGGCGT
* * * * * * *
730704 TTATATAAAAACGCTACTAAAGTACGAGTCTATAGCGTCG-
1 TTGTATATAAACGCCACTAAAGTACAAGTGTATAACGGCGT
* * ** * *
730744 TT-TATAGAAACGCCACTAAAGTACGAGAATTTAGCGGCGT
1 TTGTATATAAACGCCACTAAAGTACAAGTGTATAACGGCGT
* * * * * *
730784 TTGTGCT-TAAAATGCCACTAAAGTA-TAGTATTTAGCGGCGT
1 TTGT-ATAT-AAACGCCACTAAAGTACAAGTGTATAACGGCGT
* * *
730825 TTATACAAAAACGCCACTAAAGTAC
1 TTGTATATAAACGCCACTAAAGTAC
730850 GAGCATTTAG
Statistics
Matches: 220, Mismatches: 43, Indels: 12
0.80 0.16 0.04
Matches are distributed among these distances:
39 31 0.14
40 19 0.09
41 154 0.70
42 16 0.07
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.28
Consensus pattern (41 bp):
TTGTATATAAACGCCACTAAAGTACAAGTGTATAACGGCGT
Found at i:730690 original size:82 final size:81
Alignment explanation
Indices: 730575--731049 Score: 447
Period size: 82 Copynumber: 5.8 Consensus size: 81
730565 AATTGTATAA
* * * * * * * *
730575 CGGCGTTTGTATAAAAATGCCACGAAAGAACAAGTGTATAGCGGCGTTT-T-TATATAAACGCCT
1 CGGCGTTTATATAAAAACGCCACTAAAGTACGAGTATTTAGCGGCGTTTGTCT-TA-AAACGCCA
*
730638 CTAAAGTACGAGTCTTTAG
64 CTAAAGTAC-AGTATTTAG
* * * * * * * * * *
730657 CGGAGTTTTTATAAAAACGCCACTAAAGTACAAGTCTATAGCGTCGTTTATATAAAAACGCTACT
1 CGGCGTTTATATAAAAACGCCACTAAAGTACGAGTATTTAGCGGCGTTTGTCTTAAAACGCCACT
* *
730722 AAAGTACGAGTCTATAG
66 AAAGTAC-AGTATTTAG
* * * *
730739 CGTCG-TT-TATAGAAACGCCACTAAAGTACGAGAATTTAGCGGCGTTTGTGCTTAAAATGCCAC
1 CGGCGTTTATATAAAAACGCCACTAAAGTACGAGTATTTAGCGGCGTTTGT-CTTAAAACGCCAC
*
730802 TAAAGTATAGTATTTAG
65 TAAAGTACAGTATTTAG
* * *
730819 CGGCGTTTATACAAAAACGCCACTAAAGTACGAGCATTTAGCGGCGTTTGTGCTTAAAACGTCAC
1 CGGCGTTTATATAAAAACGCCACTAAAGTACGAGTATTTAGCGGCGTTTGT-CTTAAAACGCCAC
* *
730884 TATAGTACATTATTTAG
65 TAAAGTACAGTATTTAG
* * * *
730901 CGGCGTCTATATAGAAATGCCACTAAAGTACGAGCATTTAGCGGCGTTTGTGCTTAAAACGCCAC
1 CGGCGTTTATATAAAAACGCCACTAAAGTACGAGTATTTAGCGGCGTTTGT-CTTAAAACGCCAC
** *
730966 TATTGTACATTATTTAG
65 TAAAGTACAGTATTTAG
** ** * * *
730983 CGGCGTTTATACGAAAACGCCACTAAAGTAC-AGTAGGTAGCGGCGTTTATATAAAAACGCCACT
1 CGGCGTTTATATAAAAACGCCACTAAAGTACGAGTATTTAGCGGCGTTTGTCTTAAAACGCCACT
731047 AAA
66 AAA
731050 CCACAAGTAT
Statistics
Matches: 333, Mismatches: 55, Indels: 12
0.83 0.14 0.03
Matches are distributed among these distances:
80 59 0.18
81 35 0.11
82 236 0.71
83 2 0.01
84 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.28
Consensus pattern (81 bp):
CGGCGTTTATATAAAAACGCCACTAAAGTACGAGTATTTAGCGGCGTTTGTCTTAAAACGCCACT
AAAGTACAGTATTTAG
Found at i:730858 original size:41 final size:41
Alignment explanation
Indices: 730613--731049 Score: 352
Period size: 41 Copynumber: 10.7 Consensus size: 41
730603 AACAAGTGTA
* * * *
730613 TAGCGGCGTTTTTATATAAACGCCTCTAAAGTACGAGTC-TT
1 TAGCGGCGTTTATACAAAAACGCCACTAAAGTACGAG-CATT
* * * * *
730654 TAGCGGAGTTTTTATAAAAACGCCACTAAAGTACAAGTC-TA
1 TAGCGGCGTTTATACAAAAACGCCACTAAAGTACGAG-CATT
* * * *
730695 TAGCGTCGTTTATATAAAAACGCTACTAAAGTACGAGTC-TA
1 TAGCGGCGTTTATACAAAAACGCCACTAAAGTACGAG-CATT
* * *
730736 TAGCGTCGTTTAT--AGAAACGCCACTAAAGTACGAGAATT
1 TAGCGGCGTTTATACAAAAACGCCACTAAAGTACGAGCATT
* * * * * *
730775 TAGCGGCGTTTGTGCTTAAAATGCCACTAAAGTA-TAGTATT
1 TAGCGGCGTTTATAC-AAAAACGCCACTAAAGTACGAGCATT
730816 TAGCGGCGTTTATACAAAAACGCCACTAAAGTACGAGCATT
1 TAGCGGCGTTTATACAAAAACGCCACTAAAGTACGAGCATT
* * * * * **
730857 TAGCGGCGTTTGTGCTTAAAACGTCACTATAGTAC-ATTATT
1 TAGCGGCGTTTATAC-AAAAACGCCACTAAAGTACGAGCATT
* * * *
730898 TAGCGGCGTCTATATAGAAATGCCACTAAAGTACGAGCATT
1 TAGCGGCGTTTATACAAAAACGCCACTAAAGTACGAGCATT
* * * ** **
730939 TAGCGGCGTTTGTGCTTAAAACGCCACTATTGTAC-ATTATT
1 TAGCGGCGTTTATAC-AAAAACGCCACTAAAGTACGAGCATT
* * **
730980 TAGCGGCGTTTATACGAAAACGCCACTAAAGTAC-AGTAGG
1 TAGCGGCGTTTATACAAAAACGCCACTAAAGTACGAGCATT
*
731020 TAGCGGCGTTTATATAAAAACGCCACTAAA
1 TAGCGGCGTTTATACAAAAACGCCACTAAA
731050 CCACAAGTAT
Statistics
Matches: 322, Mismatches: 66, Indels: 17
0.80 0.16 0.04
Matches are distributed among these distances:
39 32 0.10
40 77 0.24
41 168 0.52
42 45 0.14
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.29
Consensus pattern (41 bp):
TAGCGGCGTTTATACAAAAACGCCACTAAAGTACGAGCATT
Found at i:730947 original size:164 final size:161
Alignment explanation
Indices: 730630--731049 Score: 504
Period size: 164 Copynumber: 2.6 Consensus size: 161
730620 GTTTTTATAT
* * * * *
730630 AAACGCCTCTAAAGTACGAGTCTTTAGCGGAGTTTTTATAAAAACGCCACTAAAGTACAAGTC-T
1 AAACGCCACTAAAGTAC-AGTATTTAGCGGCGTTTATACAAAAACGCCACTAAAGTAC-AG-CAT
* * *
730694 ATAGCGTCGTTTATATAAAAACGCTACTAAAGTACGAGTCTATAGCGTCGTTTATAGAAACGCCA
63 ATAGCGGCGTTTATATAAAAACGCTACTAAAGTACGAGTATATAGCGGCGTTTATAGAAACGCCA
730759 CTAAAGTACGAGAATTTAGCGGCGTTTGTGCTTA
128 CTAAAGTACGAGAATTTAGCGGCGTTTGTGCTTA
* * *
730793 AAATGCCACTAAAGTATAGTATTTAGCGGCGTTTATACAAAAACGCCACTAAAGTACGAGCATTT
1 AAACGCCACTAAAGTACAGTATTTAGCGGCGTTTATACAAAAACGCCACTAAAGTAC-AGCATAT
* * * * * * *
730858 AGCGGCGTTTGTGCTTAAAACG-TCACTATAGTAC-ATTATTTAGCGGCGTCTATATAGAAATGC
65 AGCGGCGTTTAT-ATAAAAACGCT-ACTAAAGTACGAGTATATAGCGGCGT-T-TATAGAAACGC
*
730921 CACTAAAGTACGAGCATTTAGCGGCGTTTGTGCTTA
126 CACTAAAGTACGAGAATTTAGCGGCGTTTGTGCTTA
** * * * **
730957 AAACGCCACTATTGTACATTATTTAGCGGCGTTTATACGAAAACGCCACTAAAGTACAGTAGGTA
1 AAACGCCACTAAAGTACAGTATTTAGCGGCGTTTATACAAAAACGCCACTAAAGTACAGCATATA
*
731022 GCGGCGTTTATATAAAAACGCCACTAAA
66 GCGGCGTTTATATAAAAACGCTACTAAA
731050 CCACAAGTAT
Statistics
Matches: 217, Mismatches: 34, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
161 1 0.00
162 74 0.34
163 46 0.21
164 96 0.44
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.28
Consensus pattern (161 bp):
AAACGCCACTAAAGTACAGTATTTAGCGGCGTTTATACAAAAACGCCACTAAAGTACAGCATATA
GCGGCGTTTATATAAAAACGCTACTAAAGTACGAGTATATAGCGGCGTTTATAGAAACGCCACTA
AAGTACGAGAATTTAGCGGCGTTTGTGCTTA
Found at i:739550 original size:57 final size:57
Alignment explanation
Indices: 739489--739602 Score: 219
Period size: 57 Copynumber: 2.0 Consensus size: 57
739479 TAATGTCAAT
739489 TATATAATTATTATTTCTAAAATATTAAATCATTATTTTTAAAATATCAGTAGAGAA
1 TATATAATTATTATTTCTAAAATATTAAATCATTATTTTTAAAATATCAGTAGAGAA
*
739546 TATATAATTATTATTTTTAAAATATTAAATCATTATTTTTAAAATATCAGTAGAGAA
1 TATATAATTATTATTTCTAAAATATTAAATCATTATTTTTAAAATATCAGTAGAGAA
739603 GAGATGAATT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (57 bp):
TATATAATTATTATTTCTAAAATATTAAATCATTATTTTTAAAATATCAGTAGAGAA
Found at i:740589 original size:16 final size:16
Alignment explanation
Indices: 740565--740620 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
740555 AAATTATTCG
740565 AATTTAATTTAGTTAA
1 AATTTAATTTAGTTAA
* * *
740581 AATTCAA-TTATTTCGA
1 AATTTAATTTAGTT-AA
740597 AA-TTAATTTAGTTAA
1 AATTTAATTTAGTTAA
740612 AATTTAATT
1 AATTTAATT
740621 AATATTTAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
15 11 0.35
16 20 0.65
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (16 bp):
AATTTAATTTAGTTAA
Found at i:740603 original size:31 final size:30
Alignment explanation
Indices: 740556--740621 Score: 105
Period size: 31 Copynumber: 2.2 Consensus size: 30
740546 ACGGTTAATA
*
740556 AATTATTCGAATTTAATTTAGTTAAAATTC
1 AATTATTCGAAATTAATTTAGTTAAAATTC
*
740586 AATTATTTCGAAATTAATTTAGTTAAAATTT
1 AATTA-TTCGAAATTAATTTAGTTAAAATTC
740617 AATTA
1 AATTA
740622 ATATTTAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
30 5 0.15
31 28 0.85
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.47
Consensus pattern (30 bp):
AATTATTCGAAATTAATTTAGTTAAAATTC
Found at i:745086 original size:13 final size:14
Alignment explanation
Indices: 745068--745103 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
745058 GAAAATATTC
745068 TAAATTATAATA-A
1 TAAATTATAATACA
745081 TAAATTA-AATACA
1 TAAATTATAATACA
745094 T-AATTATAAT
1 TAAATTATAAT
745104 TTCTTATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (14 bp):
TAAATTATAATACA
Found at i:745551 original size:21 final size:20
Alignment explanation
Indices: 745524--745574 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
745514 TGTAAAATTA
* *
745524 AAAATAAATAAATATATAAT
1 AAAATAAATAAAAAGATAAT
745544 ACAAATAAATAAAAAGATAAT
1 A-AAATAAATAAAAAGATAAT
*
745565 AAAAAAAATA
1 AAAATAAATA
745575 TCAATAATCG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 9 0.33
21 18 0.67
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.22
Consensus pattern (20 bp):
AAAATAAATAAAAAGATAAT
Found at i:756271 original size:4 final size:4
Alignment explanation
Indices: 756264--756289 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
756254 TAAACCTCAG
756264 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
756290 ACCTCAGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:760304 original size:3 final size:3
Alignment explanation
Indices: 760296--760322 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
760286 ACTCAATTGA
760296 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
760323 ATAATAGGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:761129 original size:2 final size:2
Alignment explanation
Indices: 761122--761188 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
761112 GTTAACTTGG
761122 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
761164 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 A
761189 AATTCATCAA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:772611 original size:12 final size:12
Alignment explanation
Indices: 772596--772666 Score: 54
Period size: 12 Copynumber: 5.9 Consensus size: 12
772586 TGATACATTA
772596 TCTGAATTCTGT
1 TCTGAATTCTGT
* *
772608 TCTGATTTCTGA
1 TCTGAATTCTGT
* *
772620 TATGGATTCTGT
1 TCTGAATTCTGT
* *
772632 TATGATATT-TGA
1 TCTGA-ATTCTGT
772644 TCTGAATTCTGT
1 TCTGAATTCTGT
* *
772656 TTTGATTTCTG
1 TCTGAATTCTG
772667 ATATCTCCGT
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
11 3 0.07
12 39 0.87
13 3 0.07
ACGTcount: A:0.18, C:0.11, G:0.18, T:0.52
Consensus pattern (12 bp):
TCTGAATTCTGT
Found at i:772616 original size:48 final size:48
Alignment explanation
Indices: 772560--772670 Score: 127
Period size: 48 Copynumber: 2.3 Consensus size: 48
772550 AAATATTTTA
*
772560 TCTGATTTCCGACT-TGAATTATGTTCTGATACATT-ATCTGAATTCTGT
1 TCTGATTTCCGA-TATGAATTATGTTATGATA-ATTGATCTGAATTCTGT
* * * *
772608 TCTGATTTCTGATATGGATTCTGTTATGATATTTGATCTGAATTCTGT
1 TCTGATTTCCGATATGAATTATGTTATGATAATTGATCTGAATTCTGT
* *
772656 TTTGATTTCTGATAT
1 TCTGATTTCCGATAT
772671 CTCCGTTTAC
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
47 3 0.05
48 52 0.95
ACGTcount: A:0.22, C:0.13, G:0.16, T:0.50
Consensus pattern (48 bp):
TCTGATTTCCGATATGAATTATGTTATGATAATTGATCTGAATTCTGT
Found at i:772628 original size:24 final size:24
Alignment explanation
Indices: 772598--772670 Score: 94
Period size: 24 Copynumber: 3.0 Consensus size: 24
772588 ATACATTATC
*
772598 TGAATTCTGTTCTGATTTCTGATA
1 TGAATTCTGTTATGATTTCTGATA
* *
772622 TGGATTCTGTTATGATATT-TGATC
1 TGAATTCTGTTATGAT-TTCTGATA
*
772646 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTATGATTTCTGATA
772670 T
1 T
772671 CTCCGTTTAC
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
23 2 0.05
24 37 0.90
25 2 0.05
ACGTcount: A:0.21, C:0.10, G:0.18, T:0.52
Consensus pattern (24 bp):
TGAATTCTGTTATGATTTCTGATA
Found at i:773463 original size:20 final size:18
Alignment explanation
Indices: 773440--773481 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 18
773430 TTAATTTTAA
773440 AAATTATTATTAATAATGAT
1 AAATTATTATTAA-AAT-AT
773460 AAATTATTATTAAAATAT
1 AAATTATTATTAAAATAT
773478 AAAT
1 AAAT
773482 AATAAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 6 0.27
19 3 0.14
20 13 0.59
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
AAATTATTATTAAAATAT
Found at i:777904 original size:33 final size:30
Alignment explanation
Indices: 777858--777928 Score: 79
Period size: 33 Copynumber: 2.3 Consensus size: 30
777848 TATTTCTATA
* *
777858 AATATTTTTATTATAAATATTAAATGATATTAT
1 AATAATTTGATTATAAA-ATTAAAT-AT-TTAT
* *
777891 ATTAATTTGATTATAAAATTATATATTTAT
1 AATAATTTGATTATAAAATTAAATATTTAT
777921 AATAATTT
1 AATAATTT
777929 TTTAATTATG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
30 11 0.33
31 2 0.06
32 6 0.18
33 14 0.42
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (30 bp):
AATAATTTGATTATAAAATTAAATATTTAT
Found at i:782407 original size:21 final size:21
Alignment explanation
Indices: 782367--782421 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
782357 GATTCTTGAC
782367 AATCGCAATGCGATAGTACA-
1 AATCGCAATGCGATAGTACAG
* **
782387 AATTCGCATTGCGATTTTACAG
1 AA-TCGCAATGCGATAGTACAG
*
782409 AATCGCAACGCGA
1 AATCGCAATGCGA
782422 ATATGAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 2 0.07
21 24 0.86
22 2 0.07
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.24
Consensus pattern (21 bp):
AATCGCAATGCGATAGTACAG
Found at i:782523 original size:20 final size:20
Alignment explanation
Indices: 782409--782657 Score: 245
Period size: 20 Copynumber: 12.4 Consensus size: 20
782399 GATTTTACAG
* ** *
782409 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
782429 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
* *
782449 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
782469 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
782489 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
782509 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
782529 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
782549 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
782569 AATCGCAACG-ATAATCAGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
782589 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
782609 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
782629 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
782649 AATCACAAC
1 AATCGCAAC
782658 ACTGAAATTT
Statistics
Matches: 198, Mismatches: 25, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
19 2 0.01
20 194 0.98
21 2 0.01
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:783389 original size:24 final size:24
Alignment explanation
Indices: 783350--783396 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
783340 AAATTTGGTC
783350 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
783374 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
783397 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:785915 original size:33 final size:33
Alignment explanation
Indices: 785864--786081 Score: 136
Period size: 34 Copynumber: 6.2 Consensus size: 33
785854 CGGAAATTAC
* *
785864 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACAAGAAAATCGCAATGCGAAATGAA
* *
785897 AATCCCAACAAGAAAATCGCAATGCGGAACTGAA
1 AATCGCAACAAGAAAATCGCAATGC-GAAATGAA
* * * *
785931 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCAC
1 AATCGCAA--C--AA-GAAAATCGCAATGCGA-AATGAA
* *
785970 AATGCGGAA-ATGAAAATCGCAATGCGAAATGAA
1 AAT-CGCAACAAGAAAATCGCAATGCGAAATGAA
* * *
786003 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-C
1 AATCGCAA--C--AA-GAAAATCGCAATGCGA-AAT-GAA
* *
786042 AATGCGGAA-ATGAAAATCGCAATGCGAAATGAA
1 AAT-CGCAACAAGAAAATCGCAATGCGAAATGAA
786075 AATCGCA
1 AATCGCA
786082 TTGCGATTCT
Statistics
Matches: 140, Mismatches: 27, Indels: 37
0.69 0.13 0.18
Matches are distributed among these distances:
32 8 0.06
33 35 0.25
34 42 0.30
35 2 0.01
36 1 0.01
37 1 0.01
38 18 0.13
39 24 0.17
40 9 0.06
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (33 bp):
AATCGCAACAAGAAAATCGCAATGCGAAATGAA
Found at i:786005 original size:72 final size:72
Alignment explanation
Indices: 785908--786087 Score: 324
Period size: 72 Copynumber: 2.5 Consensus size: 72
785898 ATCCCAACAA
*
785908 GAAAATCGCAATGCGGAACTGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCACAAT
1 GAAAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCACAAT
785973 GCGGAAAT
65 GCGGAAAT
*
785981 GAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATG
1 GAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCACAATG
786046 CGGAAAT
66 CGGAAAT
*
786053 GAAAATCGCAATGCGAAATGAAAATCGCATTGCGA
1 GAAAATCGCAATGCGAAATGAAAATCGCAATGCGA
786088 TTCTCTCGTT
Statistics
Matches: 104, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
72 90 0.87
73 14 0.13
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.14
Consensus pattern (72 bp):
GAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCACAATG
CGGAAAT
Found at i:786064 original size:53 final size:53
Alignment explanation
Indices: 785864--786081 Score: 229
Period size: 53 Copynumber: 4.1 Consensus size: 53
785854 CGGAAATTAC
* *
785864 AATCGCAACGA-GAGAATCGCAATGCGAAATGAAAATCCCAA--C--AA-GAA
1 AATCGCAACGATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
* * * *
785911 AATCGCAATGCGGAACTGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCAC
1 AATCGCAA--C-G-A-TGAAAATCGCAATGCGAAATGAAAATCGCAATGCGA-AATGAA
*
785970 AATGCGGAA--ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AAT-CGCAACGATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
786022 AATCGCAACGA-GAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGATGAAAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
786075 AATCGCA
1 AATCGCA
786082 TTGCGATTCT
Statistics
Matches: 143, Mismatches: 12, Indels: 26
0.79 0.07 0.14
Matches are distributed among these distances:
47 8 0.06
49 1 0.01
50 1 0.01
51 5 0.03
52 20 0.14
53 97 0.68
54 1 0.01
58 2 0.01
59 4 0.03
60 4 0.03
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (53 bp):
AATCGCAACGATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:786121 original size:53 final size:52
Alignment explanation
Indices: 786058--786173 Score: 160
Period size: 53 Copynumber: 2.2 Consensus size: 52
786048 GAAATGAAAA
*
786058 TCGCAATGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
** ** **
786110 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
786163 TCGCATTGCGA
1 TCGCATTGCGA
786174 TTTTCATTTC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
52 11 0.20
53 45 0.80
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:786136 original size:19 final size:19
Alignment explanation
Indices: 786096--786183 Score: 123
Period size: 19 Copynumber: 4.8 Consensus size: 19
786086 GATTCTCTCG
786096 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
786116 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
786135 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
786149 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
786168 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
786184 AACATAATGC
Statistics
Matches: 61, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
14 6 0.10
16 7 0.11
17 7 0.11
19 26 0.43
20 15 0.25
ACGTcount: A:0.14, C:0.23, G:0.16, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:786293 original size:14 final size:14
Alignment explanation
Indices: 786274--786310 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
786264 CATCAATTAC
786274 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
786288 ACAAATCATCTTTT
1 ACAAATCAACTTTT
786302 ACAAATCAA
1 ACAAATCAA
786311 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Done.