Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003198.1 Hibiscus syriacus cultivar Beakdansim tig00006731_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: 627338
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:299133 original size:15 final size:15
Alignment explanation
Indices: 299107--299145 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
299097 ATTGTAGATG
299107 AAAATGCAAAAAGGCA
1 AAAATGC-AAAAGGCA
*
299123 AAAATGCAAAATGCA
1 AAAATGCAAAAGGCA
*
299138 AGAATGCA
1 AAAATGCA
299146 TGAAATGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (15 bp):
AAAATGCAAAAGGCA
Found at i:302071 original size:18 final size:18
Alignment explanation
Indices: 302045--302079 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
302035 ATAAAAATAA
302045 TTAAGAATATATATATAT
1 TTAAGAATATATATATAT
* *
302063 TTAATAATATGTATATA
1 TTAAGAATATATATATA
302080 AAAAACTATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (18 bp):
TTAAGAATATATATATAT
Found at i:302186 original size:28 final size:28
Alignment explanation
Indices: 302174--302313 Score: 79
Period size: 30 Copynumber: 4.6 Consensus size: 28
302164 AATATTAAAG
302174 AAATATATATATAATAATAATAATAATA
1 AAATATATATATAATAATAATAATAATA
* *
302202 AAATATAGTAAAAAATCAAATGAA-AATAATTTA
1 AAATATA-TATATAAT--AAT-AATAATAA--TA
302235 ATATATATATATATACAT-ATAATAATAATA
1 A-A-ATATATATATA-ATAATAATAATAATA
* *
302265 ATAATA-ACATGAATAATAAAAATAAATGAATA
1 A-AATATATAT--ATAATAATAAT-AAT-AATA
**
302297 AAATATCCATATAATAA
1 AAATATATATATAATAA
302314 ATAAAGGGAC
Statistics
Matches: 89, Mismatches: 7, Indels: 30
0.71 0.06 0.24
Matches are distributed among these distances:
28 10 0.11
29 11 0.12
30 19 0.21
31 17 0.19
32 17 0.19
33 3 0.03
34 5 0.06
35 7 0.08
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.31
Consensus pattern (28 bp):
AAATATATATATAATAATAATAATAATA
Found at i:302192 original size:3 final size:3
Alignment explanation
Indices: 302184--302289 Score: 50
Period size: 3 Copynumber: 36.3 Consensus size: 3
302174 AAATATATAT
* *
302184 ATA ATA ATA ATA ATA ATA A-A AT- ATA GTA A-A A-A ATC A-A ATGA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
*
302225 A-A ATA AT- TTA ATA TATA TATA TATA CAT- ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA -ATA -ATA -ATA -ATA ATA ATA ATA ATA ATA ATA
* *
302271 A-C ATGA ATA ATA AAA ATA A
1 ATA AT-A ATA ATA ATA ATA A
302290 ATGAATAAAA
Statistics
Matches: 81, Mismatches: 11, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
2 15 0.19
3 49 0.60
4 17 0.21
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:302281 original size:18 final size:17
Alignment explanation
Indices: 302258--302301 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 17
302248 TACATATAAT
302258 AATAATAATAATAACATG
1 AATAATAATAATAA-ATG
*
302276 AATAATAAAAATAAATG
1 AATAATAATAATAAATG
302293 AATAA-AATA
1 AATAATAATA
302302 TCCATATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 8 0.33
18 13 0.54
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.25
Consensus pattern (17 bp):
AATAATAATAATAAATG
Found at i:309673 original size:28 final size:28
Alignment explanation
Indices: 309632--309699 Score: 102
Period size: 28 Copynumber: 2.5 Consensus size: 28
309622 GGAATGATTG
* *
309632 AAATA-CCCTGGATCTGTAAAATAACCA
1 AAATACCCCTAGATCTATAAAATAACCA
*
309659 AAATACCCCTAGATCTATAAAATTACCA
1 AAATACCCCTAGATCTATAAAATAACCA
309687 AAATACCCCTAGA
1 AAATACCCCTAGA
309700 GTGTAAATGA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
27 5 0.14
28 32 0.86
ACGTcount: A:0.46, C:0.25, G:0.07, T:0.22
Consensus pattern (28 bp):
AAATACCCCTAGATCTATAAAATAACCA
Found at i:315934 original size:45 final size:46
Alignment explanation
Indices: 315885--315975 Score: 130
Period size: 45 Copynumber: 2.0 Consensus size: 46
315875 GAATATCGAA
* * *
315885 TGCATTTTATGCATCGATGCA-TATACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
**
315930 TGCATTTGATGCATCGATGCACAAGATTATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
315976 GCTTTTTCAA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
45 20 0.50
46 20 0.50
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
Found at i:324564 original size:64 final size:63
Alignment explanation
Indices: 324469--324611 Score: 166
Period size: 64 Copynumber: 2.2 Consensus size: 63
324459 TTTCAAGGGC
* * **
324469 ATGCACCGATGCACCAATCCATGCATTGATGCA-TCA-ATTAATTTCTTGAACATCGAATGCATT
1 ATGCATCGATGCA-CAATCCATGCATCGATGCACTCAGATT--TTTC-AAAACATCGAATGCATT
324532 TT
62 TT
*
324534 ATGCATCGATGCAC-ATACCATGCATCGATGCACTCAGGCTTTTTCAAAACATCGAATGCATTTT
1 ATGCATCGATGCACAAT-CCATGCATCGATGCACTCA-GATTTTTCAAAACATCGAATGCATTTT
324598 ATGCATCGATGCAC
1 ATGCATCGATGCAC
324612 TCTTAGTGCA
Statistics
Matches: 69, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
63 2 0.03
64 46 0.67
65 19 0.28
67 2 0.03
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.30
Consensus pattern (63 bp):
ATGCATCGATGCACAATCCATGCATCGATGCACTCAGATTTTTCAAAACATCGAATGCATTTT
Found at i:333376 original size:20 final size:21
Alignment explanation
Indices: 333330--333390 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
333320 TTCCCCTGTG
333330 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
333353 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
333373 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
333391 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:340854 original size:31 final size:31
Alignment explanation
Indices: 340819--340880 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
340809 ACCTCTGTAC
* *
340819 AGATCATAAAGGGATAAATTGAATTTTATCA
1 AGATCATAAAGGGAAAAATTGAATTTCATCA
*
340850 AGATCATAAAGGTAAAAATTGAATTTCATCA
1 AGATCATAAAGGGAAAAATTGAATTTCATCA
340881 TGCATGAACG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.47, C:0.08, G:0.15, T:0.31
Consensus pattern (31 bp):
AGATCATAAAGGGAAAAATTGAATTTCATCA
Found at i:343580 original size:20 final size:21
Alignment explanation
Indices: 343555--343594 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
343545 CAATTAAAAT
343555 ATAGCAGCGA-TCTTAAAACA
1 ATAGCAGCGACTCTTAAAACA
* *
343575 ATAGCATCGACTTTTAAAAC
1 ATAGCAGCGACTCTTAAAAC
343595 TCTAGATGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.25
Consensus pattern (21 bp):
ATAGCAGCGACTCTTAAAACA
Found at i:347697 original size:22 final size:21
Alignment explanation
Indices: 347672--347716 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
347662 TATGATTAAT
*
347672 TTTAATTTAAAATATTATCATA
1 TTTAATTTAAAAAATTAT-ATA
347694 TTTAATTTAAAAAATTATATA
1 TTTAATTTAAAAAATTATATA
347715 TT
1 TT
347717 GATAATAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTAATTTAAAAAATTATATA
Found at i:349245 original size:60 final size:60
Alignment explanation
Indices: 349073--349247 Score: 187
Period size: 60 Copynumber: 2.9 Consensus size: 60
349063 AGTATGACTC
* * * * * * *
349073 TCATTTTAAATTAGTCCCTAAA-TTTTTAAATATTTTAATTTTATCCCTAAACTATGATTA
1 TCATTCTAAATTAGTCCCCAAACTTTTTGAACATTTCAATTTCAT-CCTAAATTATGATTA
** *
349133 TCATTCTAAATTAGTCATCAGAC-TTTTGAACATTTCAATTTCATCCTCAAATTATGACCTT-
1 TCATTCTAAATTAGTCCCCAAACTTTTTGAACATTTCAATTTCATCCT-AAATTATGA--TTA
*
349194 T-ATTCTAAATTGGTCCCCAAACTTTTTGAACATTTCAATTTCATCCTAAATTAT
1 TCATTCTAAATTAGTCCCCAAACTTTTTGAACATTTCAATTTCATCCTAAATTAT
349248 ATGTACATAC
Statistics
Matches: 96, Mismatches: 14, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
59 3 0.03
60 66 0.69
61 25 0.26
62 2 0.02
ACGTcount: A:0.33, C:0.18, G:0.05, T:0.44
Consensus pattern (60 bp):
TCATTCTAAATTAGTCCCCAAACTTTTTGAACATTTCAATTTCATCCTAAATTATGATTA
Found at i:352169 original size:29 final size:29
Alignment explanation
Indices: 352105--352169 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 29
352095 TGTTATTTAT
*
352105 TTCTAACTACTAACTTTTATTTTACTTCA
1 TTCTAACTAATAACTTTTATTTTACTTCA
* *
352134 TAT-TAACTAATGATTTTTATTTTA-TTACA
1 T-TCTAACTAATAACTTTTATTTTACTT-CA
352163 TTCTAAC
1 TTCTAAC
352170 CATTGTTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
28 3 0.10
29 26 0.87
30 1 0.03
ACGTcount: A:0.31, C:0.15, G:0.02, T:0.52
Consensus pattern (29 bp):
TTCTAACTAATAACTTTTATTTTACTTCA
Found at i:352184 original size:4 final size:4
Alignment explanation
Indices: 352175--352200 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
352165 CTAACCATTG
352175 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
352201 GTTTATATTA
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:352376 original size:130 final size:127
Alignment explanation
Indices: 352183--352535 Score: 424
Period size: 130 Copynumber: 2.8 Consensus size: 127
352173 TGTTTATTTA
* * * * * *
352183 TTTATTTATTTATTTATTGTTTATATTATTCGATTCGGACTTTTGGTGACCTGATCCGGGGTATG
1 TTTATTTATTTATTTATTGTTTCTAATATTCGATTCGGCCTTGTGGTGACCAGATCTGGGGTATG
* *
352248 ATCCACATTATTATAGTTCGGACTCTGCTAACTACTAACTTTTATTTTATTACACTT-TAATC-A
66 ATCCGCATTATTATGGTTCGGACTCTGCTAACTACTAAC--TT-TTTT-TTACA-TTCTAA-CAA
352311 TTG
125 TTG
* * * * *
352314 -TTATTTATTTATTTATTGTTTCTAATATTCGATTTGGCCTTGTGGTAACCCGATATGTGGTATG
1 TTTATTTATTTATTTATTGTTTCTAATATTCGATTCGGCCTTGTGGTGACCAGATCTGGGGTATG
* * * *
352378 ATACGCATTATTATGGTTCAGACTCTGCTAACTACTGACTTTTTTTTGCATTCTAACAATTG
66 ATCCGCATTATTATGGTTCGGACTCTGCTAACTACTAACTTTTTTTTACATTCTAACAATTG
* * * * *
352440 TTTATTTATTTATTTATTATTTCTAATATTTGATTCGACCTTGTAGTGATCAGATCTGGGGTATG
1 TTTATTTATTTATTTATTGTTTCTAATATTCGATTCGGCCTTGTGGTGACCAGATCTGGGGTATG
*
352505 ATCTGCATTATTATGGTTCGGACTCTGCTAA
66 ATCCGCATTATTATGGTTCGGACTCTGCTAA
352536 TCGCTAATTA
Statistics
Matches: 190, Mismatches: 29, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
125 3 0.02
126 11 0.06
127 86 0.45
128 2 0.01
130 88 0.46
ACGTcount: A:0.23, C:0.14, G:0.16, T:0.47
Consensus pattern (127 bp):
TTTATTTATTTATTTATTGTTTCTAATATTCGATTCGGCCTTGTGGTGACCAGATCTGGGGTATG
ATCCGCATTATTATGGTTCGGACTCTGCTAACTACTAACTTTTTTTTACATTCTAACAATTG
Found at i:352503 original size:127 final size:129
Alignment explanation
Indices: 352183--352535 Score: 414
Period size: 127 Copynumber: 2.7 Consensus size: 129
352173 TGTTTATTTA
* * * * *
352183 TTTATTTATTTATTTATTGTTTATATTATTCGATTCGGA-CTTTTGGTGACCTGATCCGGGGTAT
1 TTTATTTATTTATTTATTGTTTCTAATATTCGATTC-GACCTTGTGGTGACCAGATCTGGGGTAT
* *
352247 GATCCACATTATTATAGTTCGGACTCTGCTAACTACTAACTTTTATTTTATTACACTTTAATCAT
65 GAT-CGCATTATTATGGTTCGGACTCTGCTAACTACTAAC-TTTATTTTATTACACTTTAATCAT
352312 TG
128 TG
* * * * * *
352314 -TTATTTATTTATTTATTGTTTCTAATATTCGATTTGGCCTTGTGGTAACCCGATATGTGGTATG
1 TTTATTTATTTATTTATTGTTTCTAATATTCGATTCGACCTTGTGGTGACCAGATCTGGGGTATG
* * *
352378 ATACGCATTATTATGGTTCAGACTCTGCTAACTACTGAC-TT-TTTT-TTGCA-TTCTAA-CAAT
66 AT-CGCATTATTATGGTTCGGACTCTGCTAACTACTAACTTTATTTTATTACACTT-TAATC-AT
352438 TG
128 TG
* * * *
352440 TTTATTTATTTATTTATTATTTCTAATATTTGATTCGACCTTGTAGTGATCAGATCTGGGGTATG
1 TTTATTTATTTATTTATTGTTTCTAATATTCGATTCGACCTTGTGGTGACCAGATCTGGGGTATG
352505 ATCTGCATTATTATGGTTCGGACTCTGCTAA
66 ATC-GCATTATTATGGTTCGGACTCTGCTAA
352536 TCGCTAATTA
Statistics
Matches: 190, Mismatches: 27, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
125 3 0.02
126 12 0.06
127 86 0.45
128 2 0.01
129 1 0.01
130 86 0.45
ACGTcount: A:0.23, C:0.14, G:0.16, T:0.47
Consensus pattern (129 bp):
TTTATTTATTTATTTATTGTTTCTAATATTCGATTCGACCTTGTGGTGACCAGATCTGGGGTATG
ATCGCATTATTATGGTTCGGACTCTGCTAACTACTAACTTTATTTTATTACACTTTAATCATTG
Found at i:352770 original size:24 final size:24
Alignment explanation
Indices: 352732--352797 Score: 66
Period size: 24 Copynumber: 2.7 Consensus size: 24
352722 TTCACCTTTA
352732 ATTTA-TGTTTATTTTA-AGTTTTTT
1 ATTTATTGTTT-TTTTACA-TTTTTT
352756 ATTTATTGTTTTTTTACTATTTTTT
1 ATTTATTGTTTTTTTAC-ATTTTTT
352781 A-TTATTGTACTTTTTTA
1 ATTTATTGT--TTTTTTA
352798 TTTTATTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
24 17 0.46
25 12 0.32
26 8 0.22
ACGTcount: A:0.20, C:0.03, G:0.06, T:0.71
Consensus pattern (24 bp):
ATTTATTGTTTTTTTACATTTTTT
Found at i:355129 original size:149 final size:149
Alignment explanation
Indices: 354866--355154 Score: 364
Period size: 149 Copynumber: 1.9 Consensus size: 149
354856 GCGTCAAGAG
* *
354866 GGAGTCTACATACTAAGGATACGAGCCAGACATCTGCCTACTAAGGTAACAAGTTCGACTCGAGA
1 GGAGTCTACATACCAAGGAGACGAGCCAGACATCTGCCTACTAAGGTAACAAGTTCGACTCGAGA
* * * * * ** ** * *
354931 CGATTCGAAGTTGAAGCCAATAGTTAAAGATCACGAATTAGCTTGAAAGATTTCTGGAAGTAGAA
66 CGATTCGAAGCTAAAGACAACAGTTAAAGATCACAAACCAGCTCAAAAGACTTCTGAAAGTAGAA
354996 GATGAAGTAGGAGCTAGAT
131 GATGAAGTAGGAGCTAGAT
* * * * * *
355015 GGAGTCTATC-TACCAAGGAGACGATCTAGACATTTGCCTGCTGAGGTAACAAGTTGGACTCGAG
1 GGAGTCTA-CATACCAAGGAGACGAGCCAGACATCTGCCTACTAAGGTAACAAGTTCGACTCGAG
* * *
355079 ACGATTCGACGCTAAAGACAACAGTTGAAGATCACAAACCAGCTCAAAAGACTTCTGAAAGTAGG
65 ACGATTCGAAGCTAAAGACAACAGTTAAAGATCACAAACCAGCTCAAAAGACTTCTGAAAGTAGA
355144 AGATGAAGTAG
130 AGATGAAGTAG
355155 AAGTTTTGAA
Statistics
Matches: 117, Mismatches: 22, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
149 116 0.99
150 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (149 bp):
GGAGTCTACATACCAAGGAGACGAGCCAGACATCTGCCTACTAAGGTAACAAGTTCGACTCGAGA
CGATTCGAAGCTAAAGACAACAGTTAAAGATCACAAACCAGCTCAAAAGACTTCTGAAAGTAGAA
GATGAAGTAGGAGCTAGAT
Found at i:356630 original size:15 final size:15
Alignment explanation
Indices: 356605--356680 Score: 61
Period size: 14 Copynumber: 5.2 Consensus size: 15
356595 AAGAGGAAAG
356605 AAAAACAAAGACAAA
1 AAAAACAAAGACAAA
* *
356620 AGAAGCAAAGA-AAA
1 AAAAACAAAGACAAA
356634 AAAAACAAAGAGCAAA
1 AAAAACAAAGA-CAAA
** *
356650 GAAAAGGAAA-A-AGA
1 -AAAAACAAAGACAAA
356664 AAAAACAAAGA-AAA
1 AAAAACAAAGACAAA
356678 AAA
1 AAA
356681 GTAAAAGAAA
Statistics
Matches: 47, Mismatches: 10, Indels: 9
0.71 0.15 0.14
Matches are distributed among these distances:
13 7 0.15
14 20 0.43
15 9 0.19
16 4 0.09
17 7 0.15
ACGTcount: A:0.78, C:0.08, G:0.14, T:0.00
Consensus pattern (15 bp):
AAAAACAAAGACAAA
Found at i:356632 original size:29 final size:28
Alignment explanation
Indices: 356600--356706 Score: 89
Period size: 29 Copynumber: 3.8 Consensus size: 28
356590 AAGCTAAGAG
*
356600 GAAAGAAAAACAAAGACAAAAGAAGCAAA
1 GAAAGAAAAACAAAGACAAAAAAAG-AAA
* *
356629 GAAAAAAAAACAAAGAGCAAAGAAAAGGAA
1 GAAAGAAAAACAAAGA-CAAA-AAAAGAAA
*
356659 -AAAGAAAAAACAAAG--AAAAAAAG-TA
1 GAAAG-AAAAACAAAGACAAAAAAAGAAA
*
356684 -AAAGAAAAAGCAAAGAGAAAAAA
1 GAAAGAAAAA-CAAAGACAAAAAA
356707 GAATATAAGA
Statistics
Matches: 67, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
24 5 0.07
25 10 0.15
26 5 0.07
27 9 0.13
29 18 0.27
30 16 0.24
31 4 0.06
ACGTcount: A:0.76, C:0.07, G:0.17, T:0.01
Consensus pattern (28 bp):
GAAAGAAAAACAAAGACAAAAAAAGAAA
Found at i:356645 original size:46 final size:44
Alignment explanation
Indices: 356595--356680 Score: 109
Period size: 46 Copynumber: 1.9 Consensus size: 44
356585 AATCAAAGCT
* *
356595 AAGAGGAAAGAAAAACAAAGACAAAAGAAGCAAAGAAAAAAAAACA
1 AAGAGCAAAGAAAAACAAAAACAAAA-AA-CAAAGAAAAAAAAACA
** *
356641 AAGAGCAAAGAAAAGGAAAAAGAAAAAACAAAGAAAAAAA
1 AAGAGCAAAGAAAAACAAAAACAAAAAACAAAGAAAAAAA
356681 GTAAAAGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 12 0.34
45 2 0.06
46 21 0.60
ACGTcount: A:0.76, C:0.07, G:0.17, T:0.00
Consensus pattern (44 bp):
AAGAGCAAAGAAAAACAAAAACAAAAAACAAAGAAAAAAAAACA
Found at i:356660 original size:23 final size:23
Alignment explanation
Indices: 356634--356677 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
356624 GCAAAGAAAA
* *
356634 AAAAACAAAGAGCAAAGAAAAGG
1 AAAAACAAAAAACAAAGAAAAGG
*
356657 AAAAAGAAAAAACAAAGAAAA
1 AAAAACAAAAAACAAAGAAAA
356678 AAAGTAAAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.77, C:0.07, G:0.16, T:0.00
Consensus pattern (23 bp):
AAAAACAAAAAACAAAGAAAAGG
Found at i:356669 original size:30 final size:28
Alignment explanation
Indices: 356601--356706 Score: 103
Period size: 30 Copynumber: 3.8 Consensus size: 28
356591 AGCTAAGAGG
*
356601 AAAG-AAAAACAAAGACAAAAGAAGCAA
1 AAAGAAAAAACAAAGACAAAAAAAGCAA
* *
356628 AGAAAAAAAAACAAAGAGCAAAGAAAAGGAA
1 A-AAGAAAAAACAAAGA-CAAA-AAAAGCAA
*
356659 AAAGAAAAAACAAAG--AAAAAAAG-TA
1 AAAGAAAAAACAAAGACAAAAAAAGCAA
* *
356684 AAAGAAAAAGCAAAGAGAAAAAA
1 AAAGAAAAAACAAAGACAAAAAA
356707 GAATATAAGA
Statistics
Matches: 67, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
25 15 0.22
26 5 0.07
27 10 0.15
28 2 0.03
29 11 0.16
30 17 0.25
31 7 0.10
ACGTcount: A:0.76, C:0.07, G:0.16, T:0.01
Consensus pattern (28 bp):
AAAGAAAAAACAAAGACAAAAAAAGCAA
Found at i:356679 original size:25 final size:26
Alignment explanation
Indices: 356601--356709 Score: 105
Period size: 25 Copynumber: 4.0 Consensus size: 26
356591 AGCTAAGAGG
*
356601 AAAG-AAAAACAAAGACAAAAGAAGCAA
1 AAAGAAAAAACAAAGAGAAAA-AAG-AA
*
356628 AGAAAAAAAAACAAAGAGCAAAGAAAAGGAA
1 A-AAGAAAAAACAAAGAG--AA-AAAA-GAA
*
356659 AAAGAAAAAACAAAGA-AAAAAAGTA
1 AAAGAAAAAACAAAGAGAAAAAAGAA
*
356684 AAAGAAAAAGCAAAGAGAAAAAAGAA
1 AAAGAAAAAACAAAGAGAAAAAAGAA
356710 TATAAGAAGA
Statistics
Matches: 69, Mismatches: 6, Indels: 15
0.77 0.07 0.17
Matches are distributed among these distances:
25 17 0.25
26 12 0.17
27 3 0.04
28 2 0.03
29 11 0.16
30 14 0.20
31 7 0.10
32 3 0.04
ACGTcount: A:0.76, C:0.06, G:0.17, T:0.01
Consensus pattern (26 bp):
AAAGAAAAAACAAAGAGAAAAAAGAA
Found at i:356691 original size:12 final size:12
Alignment explanation
Indices: 356622--356705 Score: 59
Period size: 12 Copynumber: 7.2 Consensus size: 12
356612 AAGACAAAAG
356622 AAGC-AAAGAAA
1 AAGCAAAAGAAA
*
356633 AA--AAAACAAA
1 AAGCAAAAGAAA
*
356643 GAGC-AAAGAAA
1 AAGCAAAAGAAA
* *
356654 AGGAAAAAGAAA
1 AAGCAAAAGAAA
* *
356666 AAACAAAGAAAAA
1 AAGCAAA-AGAAA
*
356679 AAGTAAAAGAAA
1 AAGCAAAAGAAA
356691 AAGCAAAGAGAAA
1 AAGCAAA-AGAAA
356704 AA
1 AA
356706 AGAATATAAG
Statistics
Matches: 53, Mismatches: 14, Indels: 10
0.69 0.18 0.13
Matches are distributed among these distances:
10 7 0.13
11 9 0.17
12 21 0.40
13 16 0.30
ACGTcount: A:0.76, C:0.06, G:0.17, T:0.01
Consensus pattern (12 bp):
AAGCAAAAGAAA
Found at i:358294 original size:75 final size:75
Alignment explanation
Indices: 358166--358407 Score: 308
Period size: 75 Copynumber: 3.2 Consensus size: 75
358156 ATAAAAAAAA
* * * * *
358166 TTTATCTCACTTGAGATTGTTTTTCTCAAAA-CAAGTTTTGTCTCAC-TGTAGACAGTTTCCCTT
1 TTTATCTCACTTGAGATGGTTTTTCTTAAAACCAA-TTTCGTCTCACTTG-AGACAATTTCCATT
358229 GAAACAAGAAAT
64 GAAACAAGAAAT
* * **
358241 TTTATCTTACTTGTGATGGTTTTTCTTAAAACCAATTTCGTCTCACTTGAGACAATTTCTGTTGA
1 TTTATCTCACTTGAGATGGTTTTTCTTAAAACCAATTTCGTCTCACTTGAGACAATTTCCATTGA
358306 AACAAGAAAT
66 AACAAGAAAT
* * * * *
358316 TTTATCGCACTCGAGATGGTTTTTCTTAAAACCAACTTCGTCTCGCTTGAGACAATTTTCGATTG
1 TTTATCTCACTTGAGATGGTTTTTCTTAAAACCAATTTCGTCTCACTTGAGACAA-TTTCCATTG
358381 AAACAAGAAAT
65 AAACAAGAAAT
*
358392 TTTATCTCACTCGAGA
1 TTTATCTCACTTGAGA
358408 GAACTTCTCT
Statistics
Matches: 147, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
75 109 0.74
76 38 0.26
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (75 bp):
TTTATCTCACTTGAGATGGTTTTTCTTAAAACCAATTTCGTCTCACTTGAGACAATTTCCATTGA
AACAAGAAAT
Found at i:358887 original size:117 final size:117
Alignment explanation
Indices: 358681--359037 Score: 588
Period size: 117 Copynumber: 3.1 Consensus size: 117
358671 AAGATAAACC
* * * ** *
358681 GATCAATATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCAACGAATGAGAAGAAATTCA
1 GATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCA
358746 TAATGAGAAGAACTTGTTCAACCTTGGTTCGATTCCATCACAGAATGAGGTG
66 TAATGAGAAGAACTTGTTCAACCTTGGTTCGATTCCATCACAGAATGAGGTG
*
358798 GATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAGAAGTTCA
1 GATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCA
358863 TAATGAGAAGAACTTGTTCAACCTTGGTTCGATTCCATCACAGAATGAGGTG
66 TAATGAGAAGAACTTGTTCAACCTTGGTTCGATTCCATCACAGAATGAGGTG
* * *
358915 GATAAACATTTACAGTGGAGAGTTCATAATGAGAAGAACTCATTCAACGAGGGAGAAGAAGTTCA
1 GATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCA
* * * *
358980 TAATGAGAAGAATTTGTTCAACCTTGGTTCGATTCTATCACAGAAGGAGGTA
66 TAATGAGAAGAACTTGTTCAACCTTGGTTCGATTCCATCACAGAATGAGGTG
359032 GATCAA
1 GATCAA
359038 ACATCAACAT
Statistics
Matches: 224, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
117 224 1.00
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (117 bp):
GATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCA
TAATGAGAAGAACTTGTTCAACCTTGGTTCGATTCCATCACAGAATGAGGTG
Found at i:359886 original size:17 final size:17
Alignment explanation
Indices: 359864--359896 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
359854 ACAAGGAAGG
359864 TGGCCACCATCTTTCGA
1 TGGCCACCATCTTTCGA
359881 TGGCCACCATCTTTCG
1 TGGCCACCATCTTTCG
359897 GTGGTCGTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.15, C:0.36, G:0.18, T:0.30
Consensus pattern (17 bp):
TGGCCACCATCTTTCGA
Found at i:360199 original size:29 final size:29
Alignment explanation
Indices: 360135--360199 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
360125 TGTTATTTAT
*
360135 TTCTAACTACTAACTTTTATTTTATTGCA
1 TTCTAACTACTAACTTTTATTTTATTACA
* *
360164 TAT-TAACTACTGATTTTTATTTTATTACA
1 T-TCTAACTACTAACTTTTATTTTATTACA
360193 TTCTAAC
1 TTCTAAC
360200 CATTGTTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
28 1 0.03
29 29 0.94
30 1 0.03
ACGTcount: A:0.29, C:0.15, G:0.03, T:0.52
Consensus pattern (29 bp):
TTCTAACTACTAACTTTTATTTTATTACA
Found at i:360324 original size:135 final size:132
Alignment explanation
Indices: 360167--360552 Score: 409
Period size: 132 Copynumber: 3.0 Consensus size: 132
360157 TATTGCATAT
* *
360167 TAACTACTGATTTTTATTTTATTACATTCTAACCATTGTTTATTTATTTATTTATTTATTGTTTC
1 TAACTACTGA-TTTTATTTTATTGCATTCTAATCATTGTTTATTTATTTATTTA-TTA---TTTC
* * * * * * * **
360232 TATTATTCGATT-TG-GTCTTGTGGTGACCCGATCTGGGGTATGATTTGCATTATTATGGTTCGA
61 GAATATTCGATTCGGAGCCTTATGGTAACCCGATCCGGGGTATGATCCGCATTATTATGGTTCGA
360295 ACTCTGC
126 ACTCTGC
*
360302 TAACTACTAACTTTTATTTTATTGCACTT-TAATCATT-TTTATTTATTTATTTATTATTTCGAA
1 TAACTACTGA-TTTTATTTTATTGCA-TTCTAATCATTGTTTATTTATTTATTTATTATTTCGAA
* * *
360365 TATTCGATTCGGAGCCTTATGGTAATCTGATCCGGGGTATGATCCGTATTATTATGGTTCGAACT
64 TATTCGATTCGGAGCCTTATGGTAACCCGATCCGGGGTATGATCCGCATTATTATGGTTCGAACT
360430 CTGC
129 CTGC
* * *
360434 TAACTTCTGA-TTT-TTTTATTTGCATTCTAATGATTGTTTATTTATTTA--T-TT-TTTCTAAT
1 TAACTACTGATTTTATTTTA-TTGCATTCTAATCATTGTTTATTTATTTATTTATTATTTCGAAT
* * ** *
360493 ATTTGATTC-GA-CCTTATGGTGACCATATCCGGGATATGATCCGCATTATTATGGTTCGAA
65 ATTCGATTCGGAGCCTTATGGTAACCCGATCCGGGGTATGATCCGCATTATTATGGTTCGAA
360553 TTACTAATTG
Statistics
Matches: 218, Mismatches: 27, Indels: 22
0.82 0.10 0.08
Matches are distributed among these distances:
125 43 0.20
126 2 0.01
127 15 0.07
128 2 0.01
129 8 0.04
130 29 0.13
131 13 0.06
132 55 0.25
133 3 0.01
134 16 0.07
135 30 0.14
136 2 0.01
ACGTcount: A:0.23, C:0.14, G:0.15, T:0.48
Consensus pattern (132 bp):
TAACTACTGATTTTATTTTATTGCATTCTAATCATTGTTTATTTATTTATTTATTATTTCGAATA
TTCGATTCGGAGCCTTATGGTAACCCGATCCGGGGTATGATCCGCATTATTATGGTTCGAACTCT
GC
Found at i:360783 original size:22 final size:22
Alignment explanation
Indices: 360750--360793 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
360740 TTTATGTTTA
360750 TTTTATG-TTTTTTATTTATTGT
1 TTTTATGTTTTTTTA-TTATTGT
360772 TTTTACTG-TTTTTTATTATTGT
1 TTTTA-TGTTTTTTTATTATTGT
360794 ACTTTATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.14, C:0.02, G:0.09, T:0.75
Consensus pattern (22 bp):
TTTTATGTTTTTTTATTATTGT
Found at i:360799 original size:23 final size:22
Alignment explanation
Indices: 360751--360809 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
360741 TTATGTTTAT
*
360751 TTTATGTTTTTTATTTATTGTT
1 TTTATGTTTTTTATTTATTGTC
360773 TTTACTGTTTTTTA-TTATTGTAC
1 TTTA-TGTTTTTTATTTATTGT-C
*
360796 TTTATTTTGTTTTA
1 TTTATGTT-TTTTA
360810 ATTAAGTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 14 0.44
23 18 0.56
ACGTcount: A:0.15, C:0.03, G:0.08, T:0.73
Consensus pattern (22 bp):
TTTATGTTTTTTATTTATTGTC
Found at i:374105 original size:19 final size:19
Alignment explanation
Indices: 374081--374129 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
374071 ATATATGTTC
374081 TGATCTCTGATTTGAGTTA
1 TGATCTCTGATTTGAGTTA
374100 TGATCTCTGATTTGAGTTA
1 TGATCTCTGATTTGAGTTA
*
374119 TGATATCTGAT
1 TGATCTCTGAT
374130 CTTTGCTCTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.22, C:0.10, G:0.20, T:0.47
Consensus pattern (19 bp):
TGATCTCTGATTTGAGTTA
Found at i:380544 original size:6 final size:6
Alignment explanation
Indices: 380512--380559 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
380502 GATTATAATC
* * * * *
380512 ATATAT GTATAC ATACAT ATACAT ATATGT ATATAT ATATAT ATATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
380560 GTGTGTGTGT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (6 bp):
ATATAT
Found at i:380548 original size:4 final size:4
Alignment explanation
Indices: 380512--380559 Score: 51
Period size: 4 Copynumber: 12.0 Consensus size: 4
380502 GATTATAATC
* * * * *
380512 ATAT ATGT ATAC ATAC ATAT ACAT ATAT GTAT ATAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
380560 GTGTGTGTGT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (4 bp):
ATAT
Found at i:380564 original size:2 final size:2
Alignment explanation
Indices: 380559--380606 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
380549 TATATATATA
*
380559 TG TG TG TG TG TG TG TG TG TG TG TG T- TG TG TG TG TG TT TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
380600 TG TG TG T
1 TG TG TG T
380607 ATATTAGTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.00, C:0.00, G:0.46, T:0.54
Consensus pattern (2 bp):
TG
Found at i:383159 original size:31 final size:31
Alignment explanation
Indices: 383119--383207 Score: 103
Period size: 31 Copynumber: 2.9 Consensus size: 31
383109 CTAAGGGAGC
383119 ATCTTGGGGCCTGAGAGCCTACCCAAGAAAG
1 ATCTTGGGGCCTGAGAGCCTACCCAAGAAAG
*
383150 -T-TTCCGGGGCCTCG-GGGCCTACCCAAGAAAG
1 ATCTT--GGGGCCT-GAGAGCCTACCCAAGAAAG
* *
383181 ATCTTGGAGCCTTAGAGCCTACCCAAG
1 ATCTTGGGGCCTGAGAGCCTACCCAAG
383208 GGTCGCCTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
29 2 0.04
30 1 0.02
31 41 0.85
32 2 0.04
33 2 0.04
ACGTcount: A:0.25, C:0.29, G:0.28, T:0.18
Consensus pattern (31 bp):
ATCTTGGGGCCTGAGAGCCTACCCAAGAAAG
Found at i:384003 original size:20 final size:20
Alignment explanation
Indices: 383963--384003 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
383953 CAAAGTCAAT
* **
383963 GGGTCGGGTCAAGTCGGTTC
1 GGGTCGGGTCAACTCAATTC
383983 GGGTCGGGTCAACTCAATTC
1 GGGTCGGGTCAACTCAATTC
384003 G
1 G
384004 AGTTCGATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.22, G:0.39, T:0.24
Consensus pattern (20 bp):
GGGTCGGGTCAACTCAATTC
Found at i:391190 original size:20 final size:20
Alignment explanation
Indices: 391153--391195 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
391143 AAAGTCAACA
* *
391153 GGTCAGGTCAAGTCGGTTTG
1 GGTCAGGTCAACTCGGTTCG
* *
391173 GGTCGGGTCAACTTGGTTCG
1 GGTCAGGTCAACTCGGTTCG
391193 GGT
1 GGT
391196 TCGGTCTATC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.12, C:0.16, G:0.42, T:0.30
Consensus pattern (20 bp):
GGTCAGGTCAACTCGGTTCG
Found at i:399975 original size:17 final size:17
Alignment explanation
Indices: 399948--400006 Score: 75
Period size: 17 Copynumber: 3.5 Consensus size: 17
399938 GTGTTTGTTG
* * *
399948 CTCGAACGAGAGTTTTT
1 CTCGAAAGAGAATTTCT
*
399965 CTCGATAGAGAATTTCT
1 CTCGAAAGAGAATTTCT
399982 CTCGAAAGAGAATTTCT
1 CTCGAAAGAGAATTTCT
399999 CTC-AAAGA
1 CTCGAAAGA
400007 AAATGAAGGG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
16 5 0.14
17 32 0.86
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Consensus pattern (17 bp):
CTCGAAAGAGAATTTCT
Found at i:408602 original size:20 final size:20
Alignment explanation
Indices: 408577--408623 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
408567 ATAGTTATAG
*
408577 GGGTATCGATACCTTAAGAA
1 GGGTATCGATAACTTAAGAA
*
408597 GGGTATCGATAACTTAGGAA
1 GGGTATCGATAACTTAAGAA
408617 GGGTATC
1 GGGTATC
408624 AATATTACAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.32, C:0.13, G:0.30, T:0.26
Consensus pattern (20 bp):
GGGTATCGATAACTTAAGAA
Found at i:412272 original size:21 final size:21
Alignment explanation
Indices: 412247--412287 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
412237 ATTTGGTGGA
412247 AAATGTAATAGGTTAAAAGTG
1 AAATGTAATAGGTTAAAAGTG
412268 AAATGTAATAGGTTAAAAGT
1 AAATGTAATAGGTTAAAAGT
412288 TAAACACAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.22, T:0.29
Consensus pattern (21 bp):
AAATGTAATAGGTTAAAAGTG
Found at i:412298 original size:21 final size:21
Alignment explanation
Indices: 412253--412298 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
412243 TGGAAAATGT
***
412253 AATAGGTTAAAAGTGAAATGT
1 AATAGGTTAAAAGTGAAACAC
*
412274 AATAGGTTAAAAGTTAAACAC
1 AATAGGTTAAAAGTGAAACAC
412295 AATA
1 AATA
412299 TATTATAATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.04, G:0.17, T:0.26
Consensus pattern (21 bp):
AATAGGTTAAAAGTGAAACAC
Found at i:412751 original size:77 final size:77
Alignment explanation
Indices: 412643--412911 Score: 271
Period size: 77 Copynumber: 3.5 Consensus size: 77
412633 AGTTCACTAG
* * * * * *
412643 GTTGTGATCT-AGAATGCTGAT-TTTTTCATTAATAAAATATGTTGCGCCCAATAATATCATGGT
1 GTTGTGATCTGA-AATGTTAATATTTTT-ATTAATAAAATATGTTGCACCAAAGAATGTCATGGT
412706 TCACTAAGAAATAA
64 TCACTAAGAAATAA
* * * *
412720 GTTGTGATCTGAAATGTTAATATTTTTATTAATAAAATAGGTTGTACCTAAGAATGTCATGGTTT
1 GTTGTGATCTGAAATGTTAATATTTTTATTAATAAAATATGTTGCACCAAAGAATGTCATGGTTC
412785 ACTAAGAAATAA
66 ACTAAGAAATAA
** * * * * *
412797 GTTACGAACTGGAATGTTAATATTTTTATTAATAAAATGA-ATTGCATCAAAGAATGT-ATGATT
1 GTTGTGATCTGAAATGTTAATATTTTTATTAATAAAAT-ATGTTGCACCAAAGAATGTCATGGTT
* * *
412860 CGCTAAGAGAGTAG
65 CACTAAGA-AATAA
*
412874 GTTGTGATCTGAAATATTAATA-TTTTATT-ATAAAATAT
1 GTTGTGATCTGAAATGTTAATATTTTTATTAATAAAATAT
412912 TCGAAAGTAA
Statistics
Matches: 160, Mismatches: 27, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
74 1 0.01
75 7 0.04
76 18 0.11
77 127 0.79
78 7 0.04
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.38
Consensus pattern (77 bp):
GTTGTGATCTGAAATGTTAATATTTTTATTAATAAAATATGTTGCACCAAAGAATGTCATGGTTC
ACTAAGAAATAA
Found at i:414509 original size:19 final size:18
Alignment explanation
Indices: 414485--414540 Score: 52
Period size: 19 Copynumber: 3.3 Consensus size: 18
414475 ATAATCCCTT
414485 CATAATCCTCTCAGCACTA
1 CATAATCCTCTCA-CACTA
414504 CATAA---T-T--CACTA
1 CATAATCCTCTCACACTA
414516 CATAATCCTCTCAACACTA
1 CATAATCCTCTC-ACACTA
414535 CATAAT
1 CATAAT
414541 TCATCTCCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 14
0.68 0.00 0.32
Matches are distributed among these distances:
12 10 0.33
15 2 0.07
16 2 0.07
19 16 0.53
ACGTcount: A:0.38, C:0.32, G:0.02, T:0.29
Consensus pattern (18 bp):
CATAATCCTCTCACACTA
Found at i:414521 original size:31 final size:31
Alignment explanation
Indices: 414485--414543 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
414475 ATAATCCCTT
*
414485 CATAATCCTCTCAGCACTACATAATTCACTA
1 CATAATCCTCTCAACACTACATAATTCACTA
414516 CATAATCCTCTCAACACTACATAATTCA
1 CATAATCCTCTCAACACTACATAATTCA
414544 TCTCCTTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.37, C:0.32, G:0.02, T:0.29
Consensus pattern (31 bp):
CATAATCCTCTCAACACTACATAATTCACTA
Found at i:419408 original size:32 final size:31
Alignment explanation
Indices: 419357--419417 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 31
419347 TTGGTCTGGG
**
419357 TCAATATCAGATCGGTTGATATTTAGATTTAA
1 TCAATATCAGATCAATTGAT-TTTAGATTTAA
*
419389 TCAATATCAGATCAATTGATTTTCGATTT
1 TCAATATCAGATCAATTGATTTTAGATTT
419418 GGGTCAACCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 8 0.31
32 18 0.69
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.43
Consensus pattern (31 bp):
TCAATATCAGATCAATTGATTTTAGATTTAA
Found at i:419615 original size:16 final size:16
Alignment explanation
Indices: 419596--419646 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
419586 TTCAGATTGC
419596 TTTCGATTCGGATTAA
1 TTTCGATTCGGATTAA
*
419612 TTTCAGATT-GGGTTAA
1 TTTC-GATTCGGATTAA
*
419628 ATTCGATTC-GAGTTAA
1 TTTCGATTCGGA-TTAA
419644 TTT
1 TTT
419647 TAGTTCGAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
15 5 0.18
16 19 0.68
17 4 0.14
ACGTcount: A:0.25, C:0.10, G:0.20, T:0.45
Consensus pattern (16 bp):
TTTCGATTCGGATTAA
Found at i:420582 original size:22 final size:23
Alignment explanation
Indices: 420529--420585 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
420519 TTAGATAGTA
420529 TAATGATTAAAATATTTATATGATT
1 TAAT-ATTAAAATATTTATA-GATT
** *
420554 TTTTATTCAAATATTTATA-ATT
1 TAATATTAAAATATTTATAGATT
420576 TAATATTAAA
1 TAATATTAAA
420586 GTTTAGCACA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
22 10 0.38
24 14 0.54
25 2 0.08
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.51
Consensus pattern (23 bp):
TAATATTAAAATATTTATAGATT
Found at i:429055 original size:24 final size:24
Alignment explanation
Indices: 429028--429151 Score: 90
Period size: 24 Copynumber: 5.2 Consensus size: 24
429018 TATATCAAAA
429028 ATCAAAACATAAAT-CAGGTCAAGT
1 ATCAAAACA-AAATCCAGGTCAAGT
* *
429052 ATCATATCAAAATCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * * *
429076 ATCAGATCAGAATCCAAGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * * *
429100 ATCAGATCAGAATCCATGTC-AGAT
1 ATCAAAACAAAATCCAGGTCAAG-T
* * * *
429124 ATCAGATCAGAATCCATGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
429148 ATCA
1 ATCA
429152 GATCAGAATT
Statistics
Matches: 91, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
23 6 0.07
24 83 0.91
25 2 0.02
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.23
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGGTCAAGT
Found at i:429152 original size:24 final size:24
Alignment explanation
Indices: 429045--429160 Score: 180
Period size: 24 Copynumber: 4.8 Consensus size: 24
429035 CATAAATCAG
* * *
429045 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAT
*
429069 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
429093 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
429117 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
429141 GTCAAGTATCAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
429161 TCAAATCGAA
Statistics
Matches: 86, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
23 2 0.02
24 82 0.95
25 2 0.02
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:429176 original size:48 final size:48
Alignment explanation
Indices: 429045--429178 Score: 146
Period size: 48 Copynumber: 2.8 Consensus size: 48
429035 CATAAATCAG
* * ** *
429045 GTCAAGTATCATATCAAAATCCAGGTCA-AGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAAATCAGA-AATCAGATCAGAATCCAA
** * *
429093 GTCAAGTATCAGATCAGAATCCATGTCAGATATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAAATCAGAAATCAGATCAGAATCCAA
*
429141 GTCAAGTATCAGATCAGAATTCAAATC-GAAAATCAGAT
1 GTCAAGTATCAGATCAGAATCCAAATCAG-AAATCAGAT
429179 AAAATATTCA
Statistics
Matches: 76, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
47 1 0.01
48 74 0.97
49 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (48 bp):
GTCAAGTATCAGATCAGAATCCAAATCAGAAATCAGATCAGAATCCAA
Found at i:430320 original size:17 final size:18
Alignment explanation
Indices: 430287--430320 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
430277 TCCATTCTGT
*
430287 CTTATTATTTAATTCCAA
1 CTTATCATTTAATTCCAA
430305 CTTATCATTT-ATTCCA
1 CTTATCATTTAATTCCA
430321 GACCTTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (18 bp):
CTTATCATTTAATTCCAA
Found at i:431617 original size:18 final size:18
Alignment explanation
Indices: 431596--431632 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
431586 CACCGGTCAA
* *
431596 CGGGTCAACGGGTTGGGT
1 CGGGTAAACGGGTCGGGT
431614 CGGGTAAACGGGTCGGGT
1 CGGGTAAACGGGTCGGGT
431632 C
1 C
431633 AAGTTGGAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.19, G:0.49, T:0.19
Consensus pattern (18 bp):
CGGGTAAACGGGTCGGGT
Found at i:433655 original size:35 final size:35
Alignment explanation
Indices: 433601--433695 Score: 145
Period size: 35 Copynumber: 2.7 Consensus size: 35
433591 CAAGTCCAGT
* * *
433601 AGGCTCTGAGCACACAGCCGAGGAGCTGGTAAGTA
1 AGGCCCTGAGCACACAGCCGAGGAGCCGATAAGTA
*
433636 AGGCCCTGAGCACATAGCCGAGGAGCCGATAAGTA
1 AGGCCCTGAGCACACAGCCGAGGAGCCGATAAGTA
*
433671 AGGCCATGAGCACACAGCCGAGGAG
1 AGGCCCTGAGCACACAGCCGAGGAG
433696 TCTCCAAGTA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 54 1.00
ACGTcount: A:0.31, C:0.25, G:0.34, T:0.11
Consensus pattern (35 bp):
AGGCCCTGAGCACACAGCCGAGGAGCCGATAAGTA
Found at i:433793 original size:24 final size:24
Alignment explanation
Indices: 433766--433841 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
433756 TATATCAAAA
433766 ATCAAAACATAAAT-CAGGTCAAGT
1 ATCAAAACA-AAATCCAGGTCAAGT
* *
433790 ATCATATCAAAATCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * * * *
433814 GTCAGATCAGAATCCAAGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
433838 ATCA
1 ATCA
433842 GATCAGAATC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 4 0.09
24 40 0.91
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.22
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGGTCAAGT
Found at i:433842 original size:24 final size:24
Alignment explanation
Indices: 433783--433898 Score: 146
Period size: 24 Copynumber: 4.8 Consensus size: 24
433773 CATAAATCAG
* *
433783 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCATATCAGAATCCAA
* *
433807 GTCAAGTGTCAGATCAGAATCCAA
1 GTCAAGTATCATATCAGAATCCAA
*
433831 GTCAAGTATCAGATCAGAATCCATA
1 GTCAAGTATCATATCAGAATCCA-A
*
433856 -TC-AGATATCATATCAGAATCCAT
1 GTCAAG-TATCATATCAGAATCCAA
433879 GTCAAGTATCATATCAGAAT
1 GTCAAGTATCATATCAGAAT
433899 TCAAATCGAA
Statistics
Matches: 81, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
23 2 0.02
24 76 0.94
25 3 0.04
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.26
Consensus pattern (24 bp):
GTCAAGTATCATATCAGAATCCAA
Found at i:433860 original size:12 final size:11
Alignment explanation
Indices: 433838--433898 Score: 59
Period size: 12 Copynumber: 5.2 Consensus size: 11
433828 CAAGTCAAGT
*
433838 ATCAGATCAGA
1 ATCATATCAGA
433849 ATCCATATCAGA
1 AT-CATATCAGA
433861 TATCATATCAGA
1 -ATCATATCAGA
* *
433873 ATCCATGTCAAGT
1 AT-CATATC-AGA
433886 ATCATATCAGA
1 ATCATATCAGA
433897 AT
1 AT
433899 TCAAATCGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
11 8 0.20
12 27 0.66
13 6 0.15
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.28
Consensus pattern (11 bp):
ATCATATCAGA
Found at i:436990 original size:2 final size:2
Alignment explanation
Indices: 436983--437007 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
436973 TTTTTAAAAC
436983 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
437008 CCCCCATCCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:437232 original size:19 final size:20
Alignment explanation
Indices: 437210--437302 Score: 53
Period size: 24 Copynumber: 4.1 Consensus size: 20
437200 AAAATCAAAA
437210 CATAAAT-CAGGTCAAGTAT
1 CATAAATCCAGGTCAAGTAT
437229 CATATCAAAATCCAGGTCAAGTAT
1 C--AT--AAATCCAGGTCAAGTAT
*
437253 CATATCAGAATCCAAGTCAAGTAT
1 C--AT-A-AATCCAGGTCAAGTAT
*
437277 CAGATCAAAATCCAAGTCAAGTAT
1 C--AT--AAATCCAGGTCAAGTAT
437301 CA
1 CA
437303 GATCAGAATC
Statistics
Matches: 63, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
19 1 0.02
21 2 0.03
22 1 0.02
23 5 0.08
24 53 0.84
25 1 0.02
ACGTcount: A:0.43, C:0.20, G:0.13, T:0.24
Consensus pattern (20 bp):
CATAAATCCAGGTCAAGTAT
Found at i:437288 original size:48 final size:48
Alignment explanation
Indices: 437220--437382 Score: 197
Period size: 48 Copynumber: 3.4 Consensus size: 48
437210 CATAAATCAG
* * *
437220 GTCAAGTATCATATCAAAATCCAGGTCAAGTATCATATCAGAATCCAA
1 GTCAAGTATCAGATCAAAATCCAAGTCAAGTATCAGATCAGAATCCAA
*
437268 GTCAAGTATCAGATCAAAATCCAAGTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAAAATCCAAGTCAAGTATCAGATCAGAATCCAA
* * *
437316 GTC-AGATATCAGATCAGAATCCATGTCAAGTATCAGA-CAAGAATTCAA
1 GTCAAG-TATCAGATCAAAATCCAAGTCAAGTATCAGATC-AGAATCCAA
* **
437364 ATCAAAAATCAGAT-AAAAT
1 GTCAAGTATCAGATCAAAAT
437383 ATTCATGTGA
Statistics
Matches: 100, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
47 7 0.07
48 92 0.92
49 1 0.01
ACGTcount: A:0.44, C:0.19, G:0.13, T:0.23
Consensus pattern (48 bp):
GTCAAGTATCAGATCAAAATCCAAGTCAAGTATCAGATCAGAATCCAA
Found at i:437368 original size:24 final size:24
Alignment explanation
Indices: 437220--437352 Score: 187
Period size: 24 Copynumber: 5.5 Consensus size: 24
437210 CATAAATCAG
* * *
437220 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAA
*
437244 GTCAAGTATCATATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAA
*
437268 GTCAAGTATCAGATCAAAATCCAA
1 GTCAAGTATCAGATCAGAATCCAA
*
437292 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAA
*
437316 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAA
437340 GTCAAGTATCAGA
1 GTCAAGTATCAGA
437353 CAAGAATTCA
Statistics
Matches: 101, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
23 2 0.02
24 97 0.96
25 2 0.02
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAA
Found at i:437375 original size:72 final size:72
Alignment explanation
Indices: 437227--437382 Score: 192
Period size: 72 Copynumber: 2.2 Consensus size: 72
437217 CAGGTCAAGT
* *
437227 ATCATATCAAAATCCAGGTCAAGTATCATATCAGAATCCAAGTCAAGTATCAGATCAAAATCCAA
1 ATCAGATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAGTCAAGTATCAGATCAAAATCCAA
* **
437292 GTCAAGT
66 ATCAAAA
* * * *
437299 ATCAGATCAGAATCCATGTC-AGATATCAGATCAGAATCCATGTCAAGTATCAGA-CAAGAATTC
1 ATCAGATCAAAATCCAGGTCAAG-TATCAGATCAGAATCCAAGTCAAGTATCAGATCAA-AATCC
437362 AAATCAAAA
64 AAATCAAAA
437371 ATCAGAT-AAAAT
1 ATCAGATCAAAAT
437383 ATTCATGTGA
Statistics
Matches: 72, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
71 9 0.12
72 63 0.88
ACGTcount: A:0.45, C:0.19, G:0.13, T:0.23
Consensus pattern (72 bp):
ATCAGATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAGTCAAGTATCAGATCAAAATCCAA
ATCAAAA
Found at i:438509 original size:17 final size:17
Alignment explanation
Indices: 438476--438527 Score: 77
Period size: 17 Copynumber: 3.0 Consensus size: 17
438466 TCCATTCTGT
*
438476 CTTATTATTTAATTCCAG
1 CTTATCATTT-ATTCCAG
*
438494 CTTATCATTTATTCCAA
1 CTTATCATTTATTCCAG
438511 CTTATCATTTATTCCAG
1 CTTATCATTTATTCCAG
438528 ACATTTCAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
17 22 0.71
18 9 0.29
ACGTcount: A:0.27, C:0.21, G:0.04, T:0.48
Consensus pattern (17 bp):
CTTATCATTTATTCCAG
Found at i:439850 original size:18 final size:18
Alignment explanation
Indices: 439810--439850 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
439800 CACAAGTCAA
*
439810 CGGGTCAACGGGTCGAGT
1 CGGGTAAACGGGTCGAGT
* *
439828 GGGGTAAACGGGTCGGGT
1 CGGGTAAACGGGTCGAGT
439846 CGGGT
1 CGGGT
439851 TGAAACCGGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.15, C:0.17, G:0.51, T:0.17
Consensus pattern (18 bp):
CGGGTAAACGGGTCGAGT
Found at i:443414 original size:23 final size:21
Alignment explanation
Indices: 443384--443441 Score: 75
Period size: 23 Copynumber: 2.8 Consensus size: 21
443374 ACGACCTGTG
443384 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTTCCCC-TC-AA
443407 GGGGGAATCGGTT-CCCTCAA
1 GGGGGAATCGGTTCCCCTCAA
*
443427 GGGGG-ATCGATTCCC
1 GGGGGAATCGGTTCCC
443442 TCTGTACCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
19 6 0.18
20 9 0.27
21 2 0.06
22 3 0.09
23 13 0.39
ACGTcount: A:0.19, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCCTCAA
Found at i:451320 original size:2 final size:2
Alignment explanation
Indices: 451313--451337 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
451303 TTTGTAAAAC
451313 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
451338 CCCCTATCCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:451560 original size:24 final size:24
Alignment explanation
Indices: 451533--451584 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
451523 TATATAAAAA
451533 ATCAAAACATAAAT-CAGGTCAAGT
1 ATCAAAACA-AAATCCAGGTCAAGT
* *
451557 ATCATATCAAAATCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
451581 ATCA
1 ATCA
451585 GATTTGAGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 4 0.16
24 21 0.84
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.23
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGGTCAAGT
Found at i:451620 original size:24 final size:24
Alignment explanation
Indices: 451550--451683 Score: 119
Period size: 24 Copynumber: 5.6 Consensus size: 24
451540 CATAAATCAG
* * *
451550 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAA
** *
451574 GTCAAGTATCAGATTTGAGTCCAA
1 GTCAAGTATCAGATCAGAATCCAA
*
451598 GTTAAGTATCAGATCAGAATCCATA
1 GTCAAGTATCAGATCAGAATCCA-A
* *
451623 -T-TAGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAA
*
451646 GTCAAGTATCAGATCAGAATTCAA
1 GTCAAGTATCAGATCAGAATCCAA
* **
451670 ATCAAAAATCAGAT
1 GTCAAGTATCAGAT
451684 AAAATATTCA
Statistics
Matches: 88, Mismatches: 18, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
23 2 0.02
24 83 0.94
25 3 0.03
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.27
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAA
Found at i:452806 original size:17 final size:18
Alignment explanation
Indices: 452773--452807 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
452763 TCCATTCTGT
*
452773 CTTATTATTTAATTCCAA
1 CTTATCATTTAATTCCAA
452791 CTTATCATTT-ATTCCAA
1 CTTATCATTTAATTCCAA
452808 ATCTTTCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.31, C:0.20, G:0.00, T:0.49
Consensus pattern (18 bp):
CTTATCATTTAATTCCAA
Found at i:455612 original size:88 final size:88
Alignment explanation
Indices: 455333--455617 Score: 434
Period size: 87 Copynumber: 3.3 Consensus size: 88
455323 AGTGGAGGTT
* * *
455333 CTAATTATTAA-CCTAACTAATTATGTT-AAATGAATATCTAATTAAAAA-CTAAAAGACTAAAT
1 CTAATTATTAACCCTAATTAATTATGTTAAAAT-AGTATCTAATTAAAAAGCTTAAAGACTAAAT
455395 TGTGAAGAATCTAAAATTGAGGCA
65 TGTGAAGAATCTAAAATTGAGGCA
* *
455419 CTAATTATTAACCCTAATTAATTATGTTAAAAGAGTATCTAATT-AAAAGCTTAAGGACTAAATT
1 CTAATTATTAACCCTAATTAATTATGTTAAAATAGTATCTAATTAAAAAGCTTAAAGACTAAATT
*
455483 GCGAAGAATCTAAAATTGAGGCA
66 GTGAAGAATCTAAAATTGAGGCA
* * *
455506 CTAATTATTAACCCTAATTAATTGTTTTAAAATAGTATCTAATTAAAAAGCTTAAAGACTTAATT
1 CTAATTATTAACCCTAATTAATTATGTTAAAATAGTATCTAATTAAAAAGCTTAAAGACTAAATT
* *
455571 GTGAAGAATCTAAAATTAAGGAA
66 GTGAAGAATCTAAAATTGAGGCA
455594 CTAATTATTAACCCTAATTAATTA
1 CTAATTATTAACCCTAATTAATTA
455618 ACTAATTATG
Statistics
Matches: 180, Mismatches: 15, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
86 15 0.08
87 101 0.56
88 64 0.36
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (88 bp):
CTAATTATTAACCCTAATTAATTATGTTAAAATAGTATCTAATTAAAAAGCTTAAAGACTAAATT
GTGAAGAATCTAAAATTGAGGCA
Found at i:456208 original size:180 final size:175
Alignment explanation
Indices: 455910--456269 Score: 621
Period size: 180 Copynumber: 2.0 Consensus size: 175
455900 AAAAATTTCC
* *
455910 AAATAAAATTATTAAAAAAAATTTTTAGGCCTAATTAATATAAGGACTAATTAAAACATTCATAA
1 AAATAAAATTATTAAAAAAAAATTTTAGGCCTAATTAATATAAGGACTAATTAAAACATACATAA
*
455975 TAAATTAGAGACTATTTTGAATTGAGTACCAATTTTAAAAATGATGACTAAATTGAATATTAGTT
66 TAAATTAGAGACTATTTTAAATTGAGTACCAATTTTAAAAATGATGACTAAATTGAATATTAGTT
456040 AAAATCAAACATGCAATCGGAGAATTAAAATCGTGACCCAAGTGGT
131 AAAATCAAACATGCAATCGGAGAATTAAAATCGTGACCCAAGT-GT
* *
456086 AAATAAAATTATTAAAAAAAAACAAATTTTAGGGCTAATTAATCTAAGGACTAATTAAAACATAC
1 AAATAAAATTATT---AAAAAA-AAATTTTAGGCCTAATTAATATAAGGACTAATTAAAACATAC
456151 ATAATAAATTAGAGACTATTTTAAATTGAGTACCAATTTTAAAAATGATGACTAAATTGAATATT
62 ATAATAAATTAGAGACTATTTTAAATTGAGTACCAATTTTAAAAATGATGACTAAATTGAATATT
*
456216 AGTTAAAATCAAACATGCAATCTGAGAATTAAAATCGTGACCCAAGTGT
127 AGTTAAAATCAAACATGCAATCGGAGAATTAAAATCGTGACCCAAGTGT
456265 AAATA
1 AAATA
456270 GGCGCAAAAA
Statistics
Matches: 174, Mismatches: 6, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
176 13 0.07
179 13 0.07
180 148 0.85
ACGTcount: A:0.48, C:0.10, G:0.12, T:0.31
Consensus pattern (175 bp):
AAATAAAATTATTAAAAAAAAATTTTAGGCCTAATTAATATAAGGACTAATTAAAACATACATAA
TAAATTAGAGACTATTTTAAATTGAGTACCAATTTTAAAAATGATGACTAAATTGAATATTAGTT
AAAATCAAACATGCAATCGGAGAATTAAAATCGTGACCCAAGTGT
Found at i:456864 original size:21 final size:22
Alignment explanation
Indices: 456824--456883 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 22
456814 AAACTCGAAA
* * *
456824 TAATAAAAATATTATTTTTATT
1 TAATAAAAATAATATATTTAAT
456846 TAATAAAAATAATA-ATTTAAT
1 TAATAAAAATAATATATTTAAT
*
456867 TAAAAAAAATAATATAT
1 TAATAAAAATAATATAT
456884 AAAAAAATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 18 0.55
22 15 0.45
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TAATAAAAATAATATATTTAAT
Found at i:456865 original size:17 final size:16
Alignment explanation
Indices: 456843--456892 Score: 57
Period size: 15 Copynumber: 3.0 Consensus size: 16
456833 TATTATTTTT
456843 ATTTAATAAAAATAATA
1 ATTTAATAAAAA-AATA
456860 ATTTAATTAAAAAAAATA
1 ATTTAA-T-AAAAAAATA
*
456878 ATAT-ATAAAAAAATA
1 ATTTAATAAAAAAATA
456893 TTATTATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
15 9 0.30
16 1 0.03
17 7 0.23
18 8 0.27
19 5 0.17
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
ATTTAATAAAAAAATA
Found at i:456872 original size:18 final size:17
Alignment explanation
Indices: 456843--456890 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
456833 TATTATTTTT
*
456843 ATTTAATAAAAATAATA
1 ATTTAATAAAAAAAATA
456860 ATTTAATTAAAAAAAATA
1 ATTTAA-TAAAAAAAATA
*
456878 ATAT-ATAAAAAAA
1 ATTTAATAAAAAAA
456891 TATTATTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 8 0.29
17 7 0.25
18 13 0.46
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
ATTTAATAAAAAAAATA
Found at i:456900 original size:16 final size:16
Alignment explanation
Indices: 456865--456901 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
456855 TAATAATTTA
456865 ATTA-AAAAAAATAAT
1 ATTATAAAAAAATAAT
*
456880 A-TATAAAAAAATATT
1 ATTATAAAAAAATAAT
456895 ATTATAA
1 ATTATAA
456902 TTATTTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 2 0.11
15 12 0.63
16 5 0.26
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
ATTATAAAAAAATAAT
Found at i:457999 original size:27 final size:27
Alignment explanation
Indices: 457961--458014 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
457951 GTGTATCCTA
*
457961 TACGTGTGATGATCGGTTGTTGCATTT
1 TACGTGTGATGATCGGCTGTTGCATTT
457988 TACGTGTGATGATCGGCTGTTGCATTT
1 TACGTGTGATGATCGGCTGTTGCATTT
458015 CCTAGTTGCG
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:0.15, C:0.13, G:0.30, T:0.43
Consensus pattern (27 bp):
TACGTGTGATGATCGGCTGTTGCATTT
Found at i:458610 original size:2 final size:2
Alignment explanation
Indices: 458603--458627 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
458593 ACTATTTTCA
458603 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
458628 CACTGTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:458720 original size:21 final size:22
Alignment explanation
Indices: 458665--458721 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
458655 ACTATATATA
* *
458665 TATATATACTATATTTTCAAAAT
1 TATAT-TACTATTTTTTCAAAAC
* *
458688 TATATAATTATTTTTTCAAAAC
1 TATATTACTATTTTTTCAAAAC
458710 TAT-TTACTATTT
1 TATATTACTATTT
458722 ACAAAAATAT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
21 7 0.25
22 16 0.57
23 5 0.18
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.53
Consensus pattern (22 bp):
TATATTACTATTTTTTCAAAAC
Found at i:459882 original size:26 final size:26
Alignment explanation
Indices: 459825--459876 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
459815 AAGTGCAGTA
459825 GAAATATAGGTTAATATAATAAAGAC
1 GAAATATAGGTTAATATAATAAAGAC
459851 GAAATATAGGTTAATATAATAAAGAC
1 GAAATATAGGTTAATATAATAAAGAC
459877 TTAATAGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.54, C:0.04, G:0.15, T:0.27
Consensus pattern (26 bp):
GAAATATAGGTTAATATAATAAAGAC
Found at i:460768 original size:18 final size:18
Alignment explanation
Indices: 460745--460786 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
460735 TCTAGACTCG
460745 AGCCCAAGCAAAAACCCT
1 AGCCCAAGCAAAAACCCT
*
460763 AGCCC-AGGAAAAACCCT
1 AGCCCAAGCAAAAACCCT
*
460780 AACCCAA
1 AGCCCAA
460787 CTGGAGCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.45, C:0.38, G:0.12, T:0.05
Consensus pattern (18 bp):
AGCCCAAGCAAAAACCCT
Found at i:461950 original size:108 final size:108
Alignment explanation
Indices: 461722--461927 Score: 254
Period size: 108 Copynumber: 1.9 Consensus size: 108
461712 CCTAACTTAA
* * * * *
461722 GCGTGTTTTGCATGTTAGTCACCTATAAGGTCCGAATTTACTATTTACCCATTTTTATGCATGCT
1 GCGT-TTTTACATGTTAGTCACCTATAAGGACCGAAGTTACTATTTACACATTTTTATGCATGAT
461787 ATATATTTTTTGGGATATTTGCTTCTTAGTCCCCATAGTTTAGT
65 ATATATTTTTTGGGATATTTGCTTCTTAGTCCCCATAGTTTAGT
* * * * ** *
461831 GTGTTTTTACATGTTGGTCACCTATAGGGACTGAAGTTGTTATTTACACATTTTTATGCATGATG
1 GCGTTTTTACATGTTAGTCACCTATAAGGACCGAAGTTACTATTTACACATTTTTATGCATGATA
* *
461896 TGTA-TTTTTGGGATATTTG-TTGTTTAGTCCCC
66 TATATTTTTTGGGATATTTGCTT-CTTAGTCCCC
461928 CTTATTTAGG
Statistics
Matches: 82, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
106 2 0.02
107 24 0.29
108 53 0.65
109 3 0.04
ACGTcount: A:0.20, C:0.15, G:0.19, T:0.46
Consensus pattern (108 bp):
GCGTTTTTACATGTTAGTCACCTATAAGGACCGAAGTTACTATTTACACATTTTTATGCATGATA
TATATTTTTTGGGATATTTGCTTCTTAGTCCCCATAGTTTAGT
Found at i:463039 original size:131 final size:131
Alignment explanation
Indices: 462792--463315 Score: 603
Period size: 131 Copynumber: 4.0 Consensus size: 131
462782 AGTAACACTT
* * * * * *
462792 GAATCAATAATGA-TTTTAGGATGAAATAATAATATCTTTTCATTTCGGTTGGAGTAATATATGA
1 GAATCAATAATGATTTTTAAGACGAAA-AATGATATCTCTTCATTTCGATTGGAGTAATAAATGA
* * * * *
462856 CTGCTCTAAGGCATGAGAGGTCATTTATTCTC-TATTGGAAATAATTAGATATTATCGTTTTCTC
65 ATGCTTTAAGGCATAAGAGGTCATTTATTATCAGATTGGAAATAATTAGATATTATCGTTTTCTC
462920 TC
130 TC
* *
462922 GAATCAATATTGATTTTTAAGACGAAAAAGTGATATCTCTTCGTTTCGATTGGAGTAATAAATGA
1 GAATCAATAATGATTTTTAAGACGAAAAA-TGATATCTCTTCATTTCGATTGGAGTAATAAATGA
** *
462987 ATGCTTTAAGGCATGTGAGGTCATTCATTATCAG-TTGGAAATAATTAGATATTATCGTTTTCTC
65 ATGCTTTAAGGCATAAGAGGTCATTTATTATCAGATTGGAAATAATTAGATATTATCGTTTTCTC
463051 TC
130 TC
** * * * *
463053 GAATCAATTTTGATTTTTAAGATGAAATAGTGACATCTCTTCATTTCGATTGGAGTAACAAATGA
1 GAATCAATAATGATTTTTAAGACGAAA-AATGATATCTCTTCATTTCGATTGGAGTAATAAATGA
* * * * *
463118 ATGCTTTAAGGTATAAGAGATCATTTATTCT-TGATTGGAAATAATTAGATATTATTGTTTTCTC
65 ATGCTTTAAGGCATAAGAGGTCATTTATTATCAGATTGGAAATAATTAGATATTATCGTTTTCTC
463182 TC
130 TC
* * * *
463184 -AGATCGATAATGAATTTTAGGACGAGATAATGATATCTCTTCACTTT-GATTGGAGTAATAAAT
1 GA-ATCAATAATGATTTTTAAGACGA-AAAATGATATCTCTTCA-TTTCGATTGGAGTAATAAAT
* * * * * *
463247 GATTTGCTTTATGACATAAGATGTCATTTATTATC-GATTGAAAATAATTAGATATTATCATTTT
63 GA-ATGCTTTAAGGCATAAGAGGTCATTTATTATCAGATTGGAAATAATTAGATATTATCGTTTT
463311 CTCTC
127 CTCTC
463316 TTAAAATCCA
Statistics
Matches: 336, Mismatches: 48, Indels: 18
0.84 0.12 0.04
Matches are distributed among these distances:
130 16 0.05
131 260 0.77
132 60 0.18
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.40
Consensus pattern (131 bp):
GAATCAATAATGATTTTTAAGACGAAAAATGATATCTCTTCATTTCGATTGGAGTAATAAATGAA
TGCTTTAAGGCATAAGAGGTCATTTATTATCAGATTGGAAATAATTAGATATTATCGTTTTCTCT
C
Found at i:473838 original size:7 final size:7
Alignment explanation
Indices: 473826--473904 Score: 99
Period size: 8 Copynumber: 11.0 Consensus size: 7
473816 TCGCTTGAAG
473826 AAAGAAA
1 AAAGAAA
473833 AAAGAAA
1 AAAGAAA
473840 AAAGAAAA
1 AAAG-AAA
473848 AAATGAAA
1 AAA-GAAA
473856 AAATGAAA
1 AAA-GAAA
473864 AAAG-AA
1 AAAGAAA
473870 AAAG-AA
1 AAAGAAA
473876 AAAGAAA
1 AAAGAAA
*
473883 AATGAAA
1 AAAGAAA
473890 AAAGAGAA
1 AAAGA-AA
473898 AAAGAAA
1 AAAGAAA
473905 GAAAAATGGG
Statistics
Matches: 66, Mismatches: 2, Indels: 8
0.87 0.03 0.11
Matches are distributed among these distances:
6 12 0.18
7 26 0.39
8 27 0.41
9 1 0.02
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (7 bp):
AAAGAAA
Found at i:473847 original size:6 final size:6
Alignment explanation
Indices: 473826--473910 Score: 59
Period size: 6 Copynumber: 13.5 Consensus size: 6
473816 TCGCTTGAAG
* *
473826 AAAGAAA AAAGAAA AAAGAA AAA-AA TGAA-AA AATGAAA AAAGAA AAAGAA
1 AAAG-AA AAAG-AA AAAGAA AAAGAA -AAAGAA AAAG-AA AAAGAA AAAGAA
*
473876 AAAGAA AAATGAAA AAAGAGA AAA-AG AAAGAA AAA
1 AAAGAA AAA-G-AA AAAGA-A AAAGAA AAAGAA AAA
473911 TGGGTTCAAG
Statistics
Matches: 65, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
5 6 0.09
6 32 0.49
7 22 0.34
8 5 0.08
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (6 bp):
AAAGAA
Found at i:473883 original size:26 final size:25
Alignment explanation
Indices: 473826--473912 Score: 113
Period size: 26 Copynumber: 3.4 Consensus size: 25
473816 TCGCTTGAAG
*
473826 AAAGAAAAAAGAAAAAAGAAAAAAA
1 AAAGAAAAATGAAAAAAGAAAAAAA
**
473851 TGA-AAAAATGAAAAAAGAAAAAGAA
1 AAAGAAAAATGAAAAAAGAAAAA-AA
*
473876 AAAGAAAAATGAAAAAAGAGAAAAAG
1 AAAGAAAAATGAAAAAAGA-AAAAAA
473902 AAAGAAAAATG
1 AAAGAAAAATG
473913 GGTTCAAGAT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
24 18 0.34
25 4 0.08
26 27 0.51
27 4 0.08
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (25 bp):
AAAGAAAAATGAAAAAAGAAAAAAA
Found at i:475530 original size:133 final size:132
Alignment explanation
Indices: 475288--475532 Score: 303
Period size: 133 Copynumber: 1.8 Consensus size: 132
475278 TCCTCTTCCT
* *
475288 TTTCCAGATTTGATATTCCTTAAGAACAGTGGAACAAGTCTACCTTGATTCAATCCTACCTGAAG
1 TTTCCAGATTTGATATTCCCTAAGAACAGTGGAACAAGTCTACCTCGATTCAATCCTACCTGAAG
* * * ** *
475353 AACAATGTAATTAATCGACGTCTCCAAATATGATTTTCCATGAAGAAACAATGGAACAGATCACC
66 AACAATGGAATGAATCAACGTCTCCAAATATGACCTACCATGAAGAAACAATGGAACAGATCACC
475418 TC
131 TC
* * * * * *
475420 TTTCCAGATTTGATCTTCCCTGAGTAGA-AGTGGAACAAGTCTGCCTCGATTTAATCTTCCCTGA
1 TTTCCAGATTTGATATTCCCTAAG-A-ACAGTGGAACAAGTCTACCTCGATTCAATCCTACCTGA
* * * *
475484 AGAACAATGGAATGAATCAACGTTTCCAGATCTGACCTACCTTGAAGAA
64 AGAACAATGGAATGAATCAACGTCTCCAAATATGACCTACCATGAAGAA
475533 GCAGGGAAGA
Statistics
Matches: 93, Mismatches: 18, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
132 21 0.23
133 71 0.76
134 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (132 bp):
TTTCCAGATTTGATATTCCCTAAGAACAGTGGAACAAGTCTACCTCGATTCAATCCTACCTGAAG
AACAATGGAATGAATCAACGTCTCCAAATATGACCTACCATGAAGAAACAATGGAACAGATCACC
TC
Found at i:476992 original size:109 final size:109
Alignment explanation
Indices: 476816--477021 Score: 306
Period size: 109 Copynumber: 1.9 Consensus size: 109
476806 TTAAGCGCAT
* *
476816 TTTTGCATGTTAGTCACATGTAAAGACCGAATTTGCTATTTACCCATTTTTATGCATGCTATATA
1 TTTTGCATGTTAGTCACATGTAAAGACCGAAGTTGCTATTTACCCATTTTTATGCATACTATATA
476881 TTTTTTGGGATATTTGTTATTTAGT-CCCTTATAGTTTAGCGTGG
66 -TTTTTGGGATATTTGTTATTTAGTCCCCTTATAGTTTAGCGTGG
* * * * * * *
476925 TTTTGCATGTTGGTCACCTGTAAGGACTGAAGTTGTTATTTATCCATTTTTATGCATACTATGTA
1 TTTTGCATGTTAGTCACATGTAAAGACCGAAGTTGCTATTTACCCATTTTTATGCATACTATATA
*
476990 TTTTTGGGATATTTGTTGTTTAGTCCCCTTAT
66 TTTTTGGGATATTTGTTATTTAGTCCCCTTAT
477022 TTAGGCGTAT
Statistics
Matches: 86, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
108 23 0.27
109 63 0.73
ACGTcount: A:0.21, C:0.14, G:0.18, T:0.47
Consensus pattern (109 bp):
TTTTGCATGTTAGTCACATGTAAAGACCGAAGTTGCTATTTACCCATTTTTATGCATACTATATA
TTTTTGGGATATTTGTTATTTAGTCCCCTTATAGTTTAGCGTGG
Found at i:478270 original size:131 final size:131
Alignment explanation
Indices: 477885--478406 Score: 639
Period size: 131 Copynumber: 4.0 Consensus size: 131
477875 AATAGTAACA
* * * * * * * *
477885 CTCGAATCAATAATGA-TTTTAGGACGAAATAATAATATATTTTCATTT-AAGTTGGAGTTATAA
1 CTCGAATCAATATTGATTTTTAAGACGAAATAGTGATATCTCTTCATTTCGA-TTGGAGTAATAA
* * * * **
477948 ATGATTGCTTTAATGCATGAGAGGTCA-TTATTCTTGATTGGAAAT--TAAGATATTATCAATTT
65 ATGACTGCTTTAAGGCATGAGAGTTCATTTATTCTCGATTGGAAATAATAAGATATTATCGTTTT
478010 CT
130 CT
* * *
478012 CTCAAATCAATATTGATTTTTAAAACGAAATAGTGATATCTCTTCTTTTCGATTGGAG-AATAAA
1 CTCGAATCAATATTGATTTTTAAGACGAAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAA
* *
478076 TGACTGCTTTAAGGCATGAGAGGTT-ATTTATTCTCGATTGGAAATAATTAGATATTATAGTTTT
66 TGACTGCTTTAAGGCATGAGA-GTTCATTTATTCTCGATTGGAAATAATAAGATATTATCGTTTT
478140 CT
130 CT
* * *
478142 CTCGAATTAATATTGATTTTTAAGATGAAATAGTGATATCTCTTAATTTCGATTGGAGTAATAAA
1 CTCGAATCAATATTGATTTTTAAGACGAAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAA
* * *
478207 TGACTGCTTTAAGACATAAGAGTTCATTTATTCTTGATTGGAAATAATAAGATATTATCGTTTTC
66 TGACTGCTTTAAGGCATGAGAGTTCATTTATTCTCGATTGGAAATAATAAGATATTATCGTTTTC
478272 T
131 T
* * * *
478273 TTCGAATCAATATTGAATTTTAAGACGAGATATAGTGATGTCTCTTCACTTCGATTGGAGTAATA
1 CTCGAATCAATATTGATTTTTAAGACGA-A-ATAGTGATATCTCTTCATTTCGATTGGAGTAATA
* * * * *
478338 AATGACTACTTTAAGGCATGAGAG-TAATTT-TTCTCGATTGAAAATAATTAGATGTTATCGTTT
64 AATGACTGCTTTAAGGCATGAGAGTTCATTTATTCTCGATTGGAAATAATAAGATATTATCGTTT
478401 TCT
129 TCT
478404 CTC
1 CTC
478407 TTAAAATCCA
Statistics
Matches: 339, Mismatches: 46, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
127 39 0.12
128 50 0.15
129 1 0.00
130 70 0.21
131 121 0.36
132 6 0.02
133 52 0.15
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (131 bp):
CTCGAATCAATATTGATTTTTAAGACGAAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAA
TGACTGCTTTAAGGCATGAGAGTTCATTTATTCTCGATTGGAAATAATAAGATATTATCGTTTTC
T
Found at i:480574 original size:10 final size:10
Alignment explanation
Indices: 480545--480578 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
480535 ATGTTTATAA
480545 ATTAAAAGAAT
1 ATTAAAA-AAT
480556 ATT-AAAAAT
1 ATTAAAAAAT
480565 ATTAAAAAAT
1 ATTAAAAAAT
480575 ATTA
1 ATTA
480579 TTATTTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 6 0.27
10 13 0.59
11 3 0.14
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (10 bp):
ATTAAAAAAT
Found at i:485096 original size:44 final size:44
Alignment explanation
Indices: 484958--485302 Score: 247
Period size: 44 Copynumber: 7.9 Consensus size: 44
484948 GTAACAAAAT
* * * * *
484958 TGATCCAACTCCTTATGCGATGGAATCAAGTG-AATCAATTG-TGC
1 TGATCCAACTCCTTATGTGATGGATTCGAGCGAAAT--TTTGATGC
* * * * *
485002 TTA-CCAACTCCCTATGAGATAGAATT-GAGCGAAATTTTGATGA
1 TGATCCAACTCCTTATGTGAT-GGATTCGAGCGAAATTTTGATGC
* * **
485045 TGGTCCAATTCCTTATGTGATGGGCTCGAGCGAAATTTTGATGC
1 TGATCCAACTCCTTATGTGATGGATTCGAGCGAAATTTTGATGC
* *
485089 TGATCCAACTCCTTATGTGATGGATTCGAGTGAAATATTGATGC
1 TGATCCAACTCCTTATGTGATGGATTCGAGCGAAATTTTGATGC
* * * * *
485133 TGATTCAACT--TT-TATGATGGATTCGAACGAAATGTTGATAC
1 TGATCCAACTCCTTATGTGATGGATTCGAGCGAAATTTTGATGC
* * * * * *
485174 TGATCCAACTCCTTTTATGATGGATTCGATCAAAATATTGATGA
1 TGATCCAACTCCTTATGTGATGGATTCGAGCGAAATTTTGATGC
* * * ** * **
485218 TGATCTAGCTCCTTTTGTGATGGATTCGAGAAAAATGTTGATATT
1 TGATCCAACTCCTTATGTGATGGATTCGAGCGAAATTTTGAT-GC
* * * *
485263 TG-TCCAACTCATTATGTGATGGACTCAAGCGAAATGTTGA
1 TGATCCAACTCCTTATGTGATGGATTCGAGCGAAATTTTGA
485303 ATAAGTTCTT
Statistics
Matches: 240, Mismatches: 52, Indels: 18
0.77 0.17 0.06
Matches are distributed among these distances:
41 33 0.14
42 5 0.02
43 25 0.10
44 175 0.73
45 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (44 bp):
TGATCCAACTCCTTATGTGATGGATTCGAGCGAAATTTTGATGC
Found at i:485171 original size:85 final size:87
Alignment explanation
Indices: 485070--485285 Score: 244
Period size: 85 Copynumber: 2.5 Consensus size: 87
485060 TGTGATGGGC
* * * * *
485070 TCGAGCGAAATTTTGATGCTGATCCAACTCCTTATGTGATGGATTCGAGT-GAAATATTGATGCT
1 TCGAACGAAATGTTGATACTGATCCAACTCCTTATGTGATGGATTCGA-TCAAAATATTGATGAT
485134 GAT-T-CAACTTTTATGATGGAT
65 GATCTACAACTTTTATGATGGAT
* *
485155 TCGAACGAAATGTTGATACTGATCCAACTCCTTTTATGATGGATTCGATCAAAATATTGATGATG
1 TCGAACGAAATGTTGATACTGATCCAACTCCTTATGTGATGGATTCGATCAAAATATTGATGATG
** *
485220 ATCTAGCTCCTTTTGTGATGGAT
66 ATCTA-CAACTTTTATGATGGAT
* * *
485243 TCGAGA-AAAATGTTGATATTTG-TCCAACTCATTATGTGATGGA
1 TCGA-ACGAAATGTTGATA-CTGATCCAACTCCTTATGTGATGGA
485286 CTCAAGCGAA
Statistics
Matches: 110, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
84 1 0.01
85 58 0.53
86 1 0.01
88 47 0.43
89 3 0.03
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (87 bp):
TCGAACGAAATGTTGATACTGATCCAACTCCTTATGTGATGGATTCGATCAAAATATTGATGATG
ATCTACAACTTTTATGATGGAT
Found at i:485770 original size:21 final size:22
Alignment explanation
Indices: 485739--485779 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
485729 CTCCAAGTTT
485739 CTTTCCTTTTTTTTCCTTCTCC
1 CTTTCCTTTTTTTTCCTTCTCC
*
485761 CTTT-CTTTTTTTTTCTTCT
1 CTTTCCTTTTTTTTCCTTCT
485780 TTTATCATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (22 bp):
CTTTCCTTTTTTTTCCTTCTCC
Found at i:485770 original size:22 final size:21
Alignment explanation
Indices: 485739--485779 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
485729 CTCCAAGTTT
485739 CTTTCCTTTTTTTTCCTTCTCC
1 CTTTCCTTTTTTTT-CTTCTCC
*
485761 CTTTCTTTTTTTTTCTTCT
1 CTTTCCTTTTTTTTCTTCT
485780 TTTATCATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (21 bp):
CTTTCCTTTTTTTTCTTCTCC
Found at i:486464 original size:13 final size:14
Alignment explanation
Indices: 486448--486511 Score: 64
Period size: 13 Copynumber: 4.8 Consensus size: 14
486438 TATTTTCTTC
486448 TTTTTCTTTTAT-T
1 TTTTTCTTTTATAT
486461 TTTTTCTTTTATAT
1 TTTTTCTTTTATAT
*
486475 TTTCTTCTTTT-TCT
1 TTT-TTCTTTTATAT
*
486489 TCTTT-TTTTAT-T
1 TTTTTCTTTTATAT
*
486501 TTATTCTTTTA
1 TTTTTCTTTTA
486512 AGCGTAATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
12 8 0.19
13 20 0.47
14 8 0.19
15 7 0.16
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTTCTTTTATAT
Found at i:486470 original size:32 final size:30
Alignment explanation
Indices: 486434--486505 Score: 90
Period size: 34 Copynumber: 2.3 Consensus size: 30
486424 TCTTCAACCC
486434 CTTTTATTTTCTTCTTTTTCTTTTATTTTTTT
1 CTTTTATTTTCTTCTTTTTC--TTATTTTTTT
*
486466 CTTTTATATTTTCTTCTTTTTCTTCTTTTTTT
1 C-TTT-TATTTTCTTCTTTTTCTTATTTTTTT
*
486498 ATTTTATT
1 CTTTTATT
486506 CTTTTAAGCG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
30 4 0.11
31 3 0.08
32 10 0.28
33 3 0.08
34 16 0.44
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.79
Consensus pattern (30 bp):
CTTTTATTTTCTTCTTTTTCTTATTTTTTT
Found at i:486477 original size:12 final size:13
Alignment explanation
Indices: 486449--486502 Score: 51
Period size: 12 Copynumber: 4.3 Consensus size: 13
486439 ATTTTCTTCT
*
486449 TTTTCTTTTATTT
1 TTTTCTTTTATTA
486462 TTTTCTTTTA-TA
1 TTTTCTTTTATTA
486474 TTTTCTTCTT-TT-
1 TTTTCTT-TTATTA
* *
486486 TCTTCTTTTTTTA
1 TTTTCTTTTATTA
486499 TTTT
1 TTTT
486503 ATTCTTTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
11 2 0.06
12 16 0.47
13 16 0.47
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTCTTTTATTA
Found at i:486477 original size:15 final size:14
Alignment explanation
Indices: 486448--486510 Score: 56
Period size: 15 Copynumber: 4.3 Consensus size: 14
486438 TATTTTCTTC
486448 TTTTTC-TTTTATT
1 TTTTTCTTTTTATT
486461 TTTTTCTTTTATATT
1 TTTTTCTTTT-TATT
* *
486476 TTCTTCTTTTTCTT
1 TTTTTCTTTTTATT
*
486490 CTTTTTTTATTTTATT
1 -TTTTTCT-TTTTATT
486506 CTTTT
1 -TTTT
486511 AAGCGTAATA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
13 6 0.15
14 6 0.15
15 18 0.44
16 11 0.27
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTTCTTTTTATT
Found at i:486495 original size:25 final size:24
Alignment explanation
Indices: 486449--486510 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 24
486439 ATTTTCTTCT
* *
486449 TTTTCTTTTATTTTTTTCTTTTATA
1 TTTTCTTCT-TTTTCTTCTTTTATA
*
486474 TTTTCTTCTTTTTCTTCTTTTTTTA
1 TTTTCTTCTTTTTCTTC-TTTTATA
*
486499 TTTTATTCTTTT
1 TTTTCTTCTTTT
486511 AAGCGTAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 7 0.22
25 25 0.78
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.81
Consensus pattern (24 bp):
TTTTCTTCTTTTTCTTCTTTTATA
Found at i:498970 original size:23 final size:23
Alignment explanation
Indices: 498944--498997 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
498934 CAACCTAGGT
498944 TTGGGTTCTAGTTTCACTATATG
1 TTGGGTTCTAGTTTCACTATATG
498967 TTGGGTTCTAGTTTCACTATATG
1 TTGGGTTCTAGTTTCACTATATG
498990 TTGGGTTC
1 TTGGGTTC
498998 GACTCTAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.15, C:0.13, G:0.24, T:0.48
Consensus pattern (23 bp):
TTGGGTTCTAGTTTCACTATATG
Found at i:507298 original size:20 final size:20
Alignment explanation
Indices: 507273--507311 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
507263 CATATTGACT
507273 TTATTATCTTTCAGTTTATG
1 TTATTATCTTTCAGTTTATG
*
507293 TTATTATGTTTCAGTTTAT
1 TTATTATCTTTCAGTTTAT
507312 ATTTAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.08, G:0.10, T:0.62
Consensus pattern (20 bp):
TTATTATCTTTCAGTTTATG
Found at i:508457 original size:25 final size:24
Alignment explanation
Indices: 508429--508495 Score: 57
Period size: 25 Copynumber: 2.8 Consensus size: 24
508419 TAATTACCCT
*
508429 AATTATATTTTTAATATAAAT-TCA
1 AATTATATTTATAAT-TAAATATCA
* *
508453 GAATTTTATGTATAATTAAATATCA
1 -AATTATATTTATAATTAAATATCA
*
508478 AATATATATTAAT-ATTAA
1 AAT-TATATTTATAATTAA
508496 TTATACATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
24 13 0.38
25 21 0.62
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (24 bp):
AATTATATTTATAATTAAATATCA
Found at i:515867 original size:2 final size:2
Alignment explanation
Indices: 515860--515912 Score: 97
Period size: 2 Copynumber: 26.0 Consensus size: 2
515850 TGTATTGTTA
515860 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
515902 AT GAT AT AT AT
1 AT -AT AT AT AT
515913 GGCGTGTAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 48 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:517936 original size:31 final size:31
Alignment explanation
Indices: 517901--517962 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
517891 GAAAATTTAA
517901 GATGTGATATAGTAAGGGGGAGTAAGTTTTT
1 GATGTGATATAGTAAGGGGGAGTAAGTTTTT
* *
517932 GATGTGCTATATTAAGGGGGAGTAAGTTTTT
1 GATGTGATATAGTAAGGGGGAGTAAGTTTTT
517963 CAAAAATCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.27, C:0.02, G:0.34, T:0.37
Consensus pattern (31 bp):
GATGTGATATAGTAAGGGGGAGTAAGTTTTT
Found at i:517986 original size:12 final size:13
Alignment explanation
Indices: 517960--517988 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
517950 GGAGTAAGTT
517960 TTTCAAAAATCAA
1 TTTCAAAAATCAA
517973 TTTCAAAAAT-AA
1 TTTCAAAAATCAA
517985 TTTC
1 TTTC
517989 TTAAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (13 bp):
TTTCAAAAATCAA
Found at i:525791 original size:21 final size:21
Alignment explanation
Indices: 525749--525792 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
525739 ACCCCGGGAA
*
525749 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
525770 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
525791 CT
1 CT
525793 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:526441 original size:31 final size:31
Alignment explanation
Indices: 526370--526449 Score: 115
Period size: 31 Copynumber: 2.6 Consensus size: 31
526360 ATTTAACAAA
* * **
526370 AAGGGGGAGAAAATTTAAGATGTGCTATAGT
1 AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
*
526401 AAGGGGGAGTAAGTTTTTGATGTGCTATATT
1 AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
526432 AAGGGGGAGTAAGTTTTT
1 AAGGGGGAGTAAGTTTTT
526450 CAAAAATCAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.31, C:0.03, G:0.34, T:0.33
Consensus pattern (31 bp):
AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
Found at i:526473 original size:12 final size:13
Alignment explanation
Indices: 526447--526475 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
526437 GGAGTAAGTT
526447 TTTCAAAAATCAA
1 TTTCAAAAATCAA
526460 TTTCAAAAAT-AA
1 TTTCAAAAATCAA
526472 TTTC
1 TTTC
526476 TTAAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (13 bp):
TTTCAAAAATCAA
Found at i:531855 original size:2 final size:2
Alignment explanation
Indices: 531848--531877 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
531838 ACCATATACA
*
531848 AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
531878 GTGTATGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:531882 original size:12 final size:12
Alignment explanation
Indices: 531848--531883 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
531838 ACCATATACA
*
531848 ATATATATATAT
1 ATATATATGTAT
531860 ATATATATGTAT
1 ATATATATGTAT
*
531872 ATATATGTGTAT
1 ATATATATGTAT
531884 GTGTGTGTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
ATATATATGTAT
Found at i:532495 original size:17 final size:17
Alignment explanation
Indices: 532483--532553 Score: 67
Period size: 17 Copynumber: 4.4 Consensus size: 17
532473 AGTATTGATT
532483 CTACAATAGTATTAGTA
1 CTACAATAGTATTAGTA
* *
532500 CTACAATAGTATCAATA
1 CTACAATAGTATTAGTA
* **
532517 CTACAACAGTATCGGTA
1 CTACAATAGTATTAGTA
*
532534 CTAC--TA-TATTGGTA
1 CTACAATAGTATTAGTA
532548 CTACAA
1 CTACAA
532554 CAATATTGAT
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
17 33 0.73
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.31
Consensus pattern (17 bp):
CTACAATAGTATTAGTA
Found at i:532553 original size:31 final size:31
Alignment explanation
Indices: 532515--532584 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
532505 ATAGTATCAA
* *
532515 TACTACAACAGTATCGGTACTAC-TATATTGG
1 TACTACAACAATATCGATACTACAT-TATTGG
* *
532546 TACTACAACAATATTGATTCTACATTATTGG
1 TACTACAACAATATCGATACTACATTATTGG
532577 TACTACAA
1 TACTACAA
532585 GAACATTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 33 0.97
32 1 0.03
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.34
Consensus pattern (31 bp):
TACTACAACAATATCGATACTACATTATTGG
Found at i:532592 original size:20 final size:20
Alignment explanation
Indices: 532567--532624 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
532557 TATTGATTCT
*
532567 ACATTATTGGTACTACAAGA
1 ACATTATTGATACTACAAGA
*
532587 ACATTAATGATACTACAAGA
1 ACATTATTGATACTACAAGA
* *
532607 ACAATATAGATACTACAA
1 ACATTATTGATACTACAA
532625 CTGAGAAAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.48, C:0.16, G:0.10, T:0.26
Consensus pattern (20 bp):
ACATTATTGATACTACAAGA
Found at i:533136 original size:17 final size:17
Alignment explanation
Indices: 533116--533179 Score: 53
Period size: 17 Copynumber: 3.9 Consensus size: 17
533106 ACTACAATTG
533116 TATTGGTACTACAACAA
1 TATTGGTACTACAACAA
* * *
533133 TA-T--TAATCCTACAA
1 TATTGGTACTACAACAA
* *
533147 TATTCGTACTACAATAA
1 TATTGGTACTACAACAA
*
533164 TTTTGGTACTACAACA
1 TATTGGTACTACAACA
533180 GTATCGGTTC
Statistics
Matches: 34, Mismatches: 10, Indels: 6
0.68 0.20 0.12
Matches are distributed among these distances:
14 10 0.29
15 1 0.03
16 1 0.03
17 22 0.65
ACGTcount: A:0.39, C:0.19, G:0.08, T:0.34
Consensus pattern (17 bp):
TATTGGTACTACAACAA
Found at i:533230 original size:20 final size:20
Alignment explanation
Indices: 533207--533248 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
533197 TTTGTAATAT
* *
533207 AAGAATAATATCGATACTAC
1 AAGAACAATATAGATACTAC
533227 AAGAACAATATAGATACTAC
1 AAGAACAATATAGATACTAC
533247 AA
1 AA
533249 CAAAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.14, G:0.10, T:0.21
Consensus pattern (20 bp):
AAGAACAATATAGATACTAC
Found at i:533774 original size:20 final size:21
Alignment explanation
Indices: 533727--533768 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
533717 TGAGATGAAG
* *
533727 AATGGAGAAGAAAACTAAAGA
1 AATGAAGAAGAAAACAAAAGA
533748 AATGAAGAAGAAAA-AAAAGA
1 AATGAAGAAGAAAACAAAAGA
533768 A
1 A
533769 GAGAAGGCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.69, C:0.02, G:0.21, T:0.07
Consensus pattern (21 bp):
AATGAAGAAGAAAACAAAAGA
Found at i:535116 original size:14 final size:14
Alignment explanation
Indices: 535097--535125 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
535087 GAATAGGAGC
535097 ATGCATCAACTTCT
1 ATGCATCAACTTCT
535111 ATGCATCAACTTCT
1 ATGCATCAACTTCT
535125 A
1 A
535126 ATTTAGGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.28, G:0.07, T:0.34
Consensus pattern (14 bp):
ATGCATCAACTTCT
Found at i:535316 original size:29 final size:30
Alignment explanation
Indices: 535270--535326 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
535260 GACCTATGTT
535270 CCCTTAAAATTTAAAAAAT-TATAATTTAA
1 CCCTTAAAATTTAAAAAATATATAATTTAA
* *
535299 CCCTTAAAAGTTT-TAAAATATTTAATTT
1 CCCTTAAAA-TTTAAAAAATATATAATTT
535327 GGCCCTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 14 0.58
30 10 0.42
ACGTcount: A:0.46, C:0.11, G:0.02, T:0.42
Consensus pattern (30 bp):
CCCTTAAAATTTAAAAAATATATAATTTAA
Found at i:535333 original size:30 final size:29
Alignment explanation
Indices: 535270--535326 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 29
535260 GACCTATGTT
535270 CCCTTAAAATTTAAAAAATTATAATTTAA
1 CCCTTAAAATTTAAAAAATTATAATTTAA
*
535299 CCCTTAAAAGTTTTAAAATATT-TAATTT
1 CCCTTAAAA--TTTAAAAAATTATAATTT
535327 GGCCCTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 9 0.36
30 6 0.24
31 10 0.40
ACGTcount: A:0.46, C:0.11, G:0.02, T:0.42
Consensus pattern (29 bp):
CCCTTAAAATTTAAAAAATTATAATTTAA
Done.