Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008539.1 Hibiscus syriacus cultivar Beakdansim tig00111427_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: 6067759
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 31
Found at i:311474 original size:22 final size:23
Alignment explanation
Indices: 311434--311476 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
311424 TGGTGTGGCA
*
311434 TCCAATTAGCAGCTTCTAGAAGG
1 TCCAATCAGCAGCTTCTAGAAGG
311457 TCCAATCAGCA-CTTCTAGAA
1 TCCAATCAGCAGCTTCTAGAA
311477 TGACGATTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.26
Consensus pattern (23 bp):
TCCAATCAGCAGCTTCTAGAAGG
Found at i:313856 original size:43 final size:45
Alignment explanation
Indices: 313806--313921 Score: 141
Period size: 43 Copynumber: 2.6 Consensus size: 45
313796 TCAAACACCG
* *
313806 CTAAAGGTTATGCTTTTTAGTGGCGTTTATTTTACAAA-T-GCTA
1 CTAAAGGTTATGCTTTTTAGCGGCGTTTAGTTTACAAACTAGCTA
*
313849 CTAAAGGTTATGCTTTTTAGCGGCATTT-GTTTACAAACGTAGCTA
1 CTAAAGGTTATGCTTTTTAGCGGCGTTTAGTTTACAAAC-TAGCTA
* * *
313894 -AAAAGGTTATGATCTTTAGCGGCGTTTA
1 CTAAAGGTTATGCTTTTTAGCGGCGTTTA
313922 AAACGCCACT
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
42 8 0.13
43 26 0.42
44 24 0.39
45 4 0.06
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.40
Consensus pattern (45 bp):
CTAAAGGTTATGCTTTTTAGCGGCGTTTAGTTTACAAACTAGCTA
Found at i:318022 original size:41 final size:41
Alignment explanation
Indices: 317963--318178 Score: 150
Period size: 41 Copynumber: 5.2 Consensus size: 41
317953 TATTGCAGCA
* *
317963 TTGTTTAAAAAACACCACTAAAGAACGATTATATTGCGGTGT
1 TTGTTT-AAAAACGCCACTAAAGAACGATTCTATTGCGGTGT
* * * * *
318005 TTGTTTAGAAACGCCACTATAGTACTAGGTTGTA--GCGGTGT
1 TTGTTTAAAAACGCCACTAAAGAAC--GATTCTATTGCGGTGT
* * *** * *
318046 TTGTCTAAAAACGCCAC-AATATATTTACTCTATTGCGGCGT
1 TTGTTTAAAAACGCCACTAA-AGAACGATTCTATTGCGGTGT
* **
318087 TTGTTTAAAAATGCCACTAAAGAACGATTCTATTGTTGTGT
1 TTGTTTAAAAACGCCACTAAAGAACGATTCTATTGCGGTGT
* * * * * ***
318128 TTATTTAGAAACGCCACTAAAGTAGGATTCTATGGCGCCAT
1 TTGTTTAAAAACGCCACTAAAGAACGATTCTATTGCGGTGT
318169 TTGTTTAAAA
1 TTGTTTAAAA
318179 CCGTCATTAA
Statistics
Matches: 127, Mismatches: 41, Indels: 13
0.70 0.23 0.07
Matches are distributed among these distances:
39 3 0.02
40 1 0.01
41 110 0.87
42 8 0.06
43 5 0.04
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (41 bp):
TTGTTTAAAAACGCCACTAAAGAACGATTCTATTGCGGTGT
Found at i:322038 original size:24 final size:21
Alignment explanation
Indices: 321991--322041 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
321981 CATATATAAA
321991 AAATAATAATAAAACAAAATA
1 AAATAATAATAAAACAAAATA
* *
322012 AAATTATAATAATAATAATAATCA
1 AAATAATAATAA-AACAA-AAT-A
322036 AAATAA
1 AAATAA
322042 AAGAAATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 11 0.46
22 4 0.17
23 3 0.12
24 6 0.25
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (21 bp):
AAATAATAATAAAACAAAATA
Found at i:322049 original size:33 final size:33
Alignment explanation
Indices: 321985--322062 Score: 90
Period size: 33 Copynumber: 2.4 Consensus size: 33
321975 TTTAAACATA
321985 TATAA-AA-AATAATAATAAAACAAAATAAAAT
1 TATAATAATAATAATAATAAAACAAAATAAAAT
* *
322016 TATAATAATAATAATAATCAAAATAAAA-GAAAT
1 TATAATAATAATAATAAT-AAAACAAAATAAAAT
*
322049 TAAAAGTAATAATA
1 TATAA-TAATAATA
322063 TTAAATTGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
31 5 0.12
32 2 0.05
33 17 0.43
34 16 0.40
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.26
Consensus pattern (33 bp):
TATAATAATAATAATAATAAAACAAAATAAAAT
Found at i:322917 original size:20 final size:20
Alignment explanation
Indices: 322883--322959 Score: 127
Period size: 20 Copynumber: 3.9 Consensus size: 20
322873 TCGTCGTTTC
*
322883 TTGCTTTCTGTTCTCTTGGG
1 TTGCTCTCTGTTCTCTTGGG
* *
322903 TTACTCTCCGTTCTCTTGGG
1 TTGCTCTCTGTTCTCTTGGG
322923 TTGCTCTCTGTTCTCTTGGG
1 TTGCTCTCTGTTCTCTTGGG
322943 TTGCTCTCTGTTCTCTT
1 TTGCTCTCTGTTCTCTT
322960 CCTTTCGCAG
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.01, C:0.26, G:0.21, T:0.52
Consensus pattern (20 bp):
TTGCTCTCTGTTCTCTTGGG
Found at i:323413 original size:3 final size:3
Alignment explanation
Indices: 323405--323494 Score: 150
Period size: 3 Copynumber: 31.0 Consensus size: 3
323395 CCTGTTTGTT
323405 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
323452 ATA A-A ATA ATA ATA ATA ATA GTA A-A ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
323495 TTATTATTAT
Statistics
Matches: 82, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
2 6 0.07
3 76 0.93
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:323439 original size:20 final size:20
Alignment explanation
Indices: 323405--323495 Score: 146
Period size: 20 Copynumber: 4.5 Consensus size: 20
323395 CCTGTTTGTT
323405 ATAATAATAATAATAATAATA
1 ATAATAAT-ATAATAATAATA
323426 ATAATAATATAATAATAATA
1 ATAATAATATAATAATAATA
*
323446 ATAATAATAAAATAATAATA
1 ATAATAATATAATAATAATA
* *
323466 ATAATAGTAAAATAATAATA
1 ATAATAATATAATAATAATA
323486 ATAATAATAT
1 ATAATAATAT
323496 TATTATTATT
Statistics
Matches: 66, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
20 58 0.88
21 8 0.12
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (20 bp):
ATAATAATATAATAATAATA
Found at i:323774 original size:17 final size:17
Alignment explanation
Indices: 323752--323811 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
323742 GTTGAACAAA
323752 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
** *
323769 TTCTTCTTTTTCA-GATGAG
1 TTCTTCTCATT-ATGA--AC
323788 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
*
323805 TCCTTCT
1 TTCTTCT
323812 GGAAATGTCG
Statistics
Matches: 32, Mismatches: 7, Indels: 8
0.68 0.15 0.17
Matches are distributed among these distances:
17 18 0.56
18 2 0.06
19 12 0.38
ACGTcount: A:0.18, C:0.23, G:0.08, T:0.50
Consensus pattern (17 bp):
TTCTTCTCATTATGAAC
Found at i:324006 original size:121 final size:113
Alignment explanation
Indices: 323873--324193 Score: 357
Period size: 121 Copynumber: 2.8 Consensus size: 113
323863 GAATTAAGGC
323873 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-TCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * *
323937 TGAACACT-TCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGAT-AGAGTC-ATGC-A
66 TGAACTCTATCTGGAAATGTTGATGC--ATCGA---------GTGATGA-AGTCGA-ACAA
* * *
323994 AAGGTTGAACAAGTGCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTATTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * * *
324058 TGAACTTTCTCTGGAAAAGTTGATGCATCGAGTGATGAATTCGAACAA
66 TGAACTCTATCTGGAAATGTTGATGCATCGAGTGATGAAGTCGAACAA
* * *
324106 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCATTCTTTAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
*
324171 TGAACTCTATCTGGAAATATTGA
66 TGAACTCTATCTGGAAATGTTGA
324194 AAGCATTATG
Statistics
Matches: 175, Mismatches: 19, Indels: 20
0.82 0.09 0.09
Matches are distributed among these distances:
111 9 0.05
112 40 0.23
113 40 0.23
120 4 0.02
121 63 0.36
122 19 0.11
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.39
Consensus pattern (113 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
TGAACTCTATCTGGAAATGTTGATGCATCGAGTGATGAAGTCGAACAA
Found at i:325170 original size:13 final size:13
Alignment explanation
Indices: 325152--325177 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
325142 TTCCTTGGAC
325152 CATATCATGTCAA
1 CATATCATGTCAA
325165 CATATCATGTCAA
1 CATATCATGTCAA
325178 GATGCTTAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (13 bp):
CATATCATGTCAA
Found at i:326295 original size:75 final size:75
Alignment explanation
Indices: 326172--326329 Score: 289
Period size: 75 Copynumber: 2.1 Consensus size: 75
326162 CACTGCTTCT
*
326172 CCAACATTGGCTAATACAAACATTCAAAATATATCAATATTCCTGATTCTGATTGAAATGGGCTT
1 CCAACATTGGCTAATACAAACATTCAAAATACATCAATATTCCTGATTCTGATTGAAATGGGCTT
*
326237 TCAGTATGCC
66 TCAGCATGCC
326247 CCAACATTGGCTAATACAAACATTCAAAATACATCAATATTCCTGATTCTGATTGAAATGGGCTT
1 CCAACATTGGCTAATACAAACATTCAAAATACATCAATATTCCTGATTCTGATTGAAATGGGCTT
326312 TCAGCATGCC
66 TCAGCATGCC
*
326322 CCATCATT
1 CCAACATT
326330 TGCTTTTTGT
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
75 80 1.00
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.31
Consensus pattern (75 bp):
CCAACATTGGCTAATACAAACATTCAAAATACATCAATATTCCTGATTCTGATTGAAATGGGCTT
TCAGCATGCC
Found at i:329357 original size:9 final size:9
Alignment explanation
Indices: 329343--329415 Score: 89
Period size: 9 Copynumber: 8.4 Consensus size: 9
329333 CTTGACTCAA
*
329343 TTTTTCCCT
1 TTTTTCACT
329352 TTTTT--CT
1 TTTTTCACT
**
329359 TTTTTTTCT
1 TTTTTCACT
329368 -TTTTCACT
1 TTTTTCACT
*
329376 CTTTTCACT
1 TTTTTCACT
329385 TTTTTCACT
1 TTTTTCACT
329394 TTTTTCACT
1 TTTTTCACT
329403 TTTTTCACT
1 TTTTTCACT
329412 TTTT
1 TTTT
329416 GTTGAATGAG
Statistics
Matches: 58, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
7 7 0.12
8 6 0.10
9 45 0.78
ACGTcount: A:0.07, C:0.22, G:0.00, T:0.71
Consensus pattern (9 bp):
TTTTTCACT
Found at i:331477 original size:21 final size:21
Alignment explanation
Indices: 331451--331492 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
331441 CCAGAATGGG
*
331451 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
331472 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
331493 ATAGTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:331637 original size:19 final size:19
Alignment explanation
Indices: 331597--331639 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
331587 GAGCCTCGGG
**
331597 TTACTGTTCAAACAGTGCT
1 TTACTGTTCAAACAGTAAT
*
331616 TTACTGTTCAAATAGTAAT
1 TTACTGTTCAAACAGTAAT
331635 TTACT
1 TTACT
331640 ATTTGAACAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.42
Consensus pattern (19 bp):
TTACTGTTCAAACAGTAAT
Found at i:331784 original size:21 final size:21
Alignment explanation
Indices: 331758--331799 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
331748 ATTTGAATAT
*
331758 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
331779 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
331800 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:331861 original size:21 final size:21
Alignment explanation
Indices: 331828--331867 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
331818 TTTTTGCAGA
*
331828 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
331850 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
331868 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:334194 original size:7 final size:7
Alignment explanation
Indices: 334159--334199 Score: 59
Period size: 6 Copynumber: 6.0 Consensus size: 7
334149 AGCAAACAAG
334159 AAATGCA
1 AAATGCA
334166 AAATG-A
1 AAATGCA
334172 AAATGCA
1 AAATGCA
334179 AAGATGCA
1 AA-ATGCA
334187 AAATGC-
1 AAATGCA
334193 AAATGCA
1 AAATGCA
334200 TGTATGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
6 12 0.39
7 12 0.39
8 7 0.23
ACGTcount: A:0.56, C:0.12, G:0.17, T:0.15
Consensus pattern (7 bp):
AAATGCA
Found at i:334325 original size:43 final size:45
Alignment explanation
Indices: 334262--334346 Score: 138
Period size: 43 Copynumber: 1.9 Consensus size: 45
334252 ACACAAAAGT
334262 TTCTATGCTTCAAACAAAACTTTACATATAGGGGACAACTTTTAG
1 TTCTATGCTTCAAACAAAACTTTACATATAGGGGACAACTTTTAG
* *
334307 TTCTAT-CTTC-AACAAAACTTTTCATATAGGGGATAACTTT
1 TTCTATGCTTCAAACAAAACTTTACATATAGGGGACAACTTT
334347 CCCATTTTCT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
43 28 0.74
44 4 0.11
45 6 0.16
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (45 bp):
TTCTATGCTTCAAACAAAACTTTACATATAGGGGACAACTTTTAG
Found at i:336547 original size:13 final size:14
Alignment explanation
Indices: 336529--336558 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
336519 TATTTTAATA
336529 AAAATT-AATTTAT
1 AAAATTAAATTTAT
336542 AAAATTAAATTTAT
1 AAAATTAAATTTAT
336556 AAA
1 AAA
336559 TAGGATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AAAATTAAATTTAT
Found at i:336640 original size:12 final size:11
Alignment explanation
Indices: 336623--336735 Score: 90
Period size: 12 Copynumber: 9.9 Consensus size: 11
336613 GACTTGAGAT
336623 AATAATAATGAA
1 AATAATAAT-AA
336635 AATAATAATTTAA
1 AATAATAA--TAA
336648 ACATATATAA-AA
1 A-ATA-ATAATAA
336660 AATAATAATAA
1 AATAATAATAA
*
336671 AACAA-AATAA
1 AATAATAATAA
*
336681 AATTATAATAA
1 AATAATAATAA
336692 TAATAATAATCAA
1 -AATAATAAT-AA
*
336705 AATAAAAATAA
1 AATAATAATAA
*
336716 AA-AA-ATTAA
1 AATAATAATAA
336725 AAGTAATAATA
1 AA-TAATAATA
336736 TTAAATTGAA
Statistics
Matches: 83, Mismatches: 7, Indels: 22
0.74 0.06 0.20
Matches are distributed among these distances:
9 6 0.07
10 14 0.17
11 20 0.24
12 30 0.36
13 5 0.06
14 4 0.05
15 4 0.05
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.27
Consensus pattern (11 bp):
AATAATAATAA
Found at i:336673 original size:24 final size:23
Alignment explanation
Indices: 336633--336712 Score: 70
Period size: 25 Copynumber: 3.1 Consensus size: 23
336623 AATAATAATG
* *
336633 AAAATAATAATTTAAACATATATAA
1 AAAATAATAA-TAAAACA-AAATAA
336658 AAAATAATAATAAAACAAAATAAA
1 AAAATAATAATAAAACAAAAT-AA
336682 ATTATAATAATAATAATAATCAAAATAA
1 A--A-AATAATAATAA-AA-CAAAATAA
336710 AAA
1 AAA
336713 TAAAAAAATT
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
23 3 0.06
24 9 0.19
25 11 0.23
26 2 0.04
27 11 0.23
28 5 0.11
29 6 0.13
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (23 bp):
AAAATAATAATAAAACAAAATAA
Found at i:336715 original size:24 final size:21
Alignment explanation
Indices: 336658--336735 Score: 77
Period size: 21 Copynumber: 3.6 Consensus size: 21
336648 ACATATATAA
336658 AAAATAATAATAAAACAAAAT
1 AAAATAATAATAAAACAAAAT
* *
336679 AAAATTATAATAATAATAATAAT
1 AAAATAATAATAA-AACAA-AAT
* *
336702 CAAAATAAAAATAAAA-AAATT
1 -AAAATAATAATAAAACAAAAT
336723 AAAAGTAATAATA
1 AAAA-TAATAATA
336736 TTAAATTGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
20 4 0.09
21 21 0.45
22 6 0.13
23 5 0.11
24 11 0.23
ACGTcount: A:0.72, C:0.03, G:0.01, T:0.24
Consensus pattern (21 bp):
AAAATAATAATAAAACAAAAT
Found at i:336735 original size:3 final size:3
Alignment explanation
Indices: 336621--336715 Score: 55
Period size: 3 Copynumber: 33.3 Consensus size: 3
336611 ATGACTTGAG
*
336621 ATA ATA ATA ATGA A-A ATA ATA AT- TTA A-A CATA TATA A-A A-A ATA
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA -ATA -ATA ATA ATA ATA
* *
336664 ATA ATA A-A ACA A-A ATA A-A ATT ATA ATA ATA ATA ATA ATCA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA
*
336706 ATA AAA ATA A
1 ATA ATA ATA A
336716 AAAAATTAAA
Statistics
Matches: 74, Mismatches: 7, Indels: 22
0.72 0.07 0.21
Matches are distributed among these distances:
2 16 0.22
3 50 0.68
4 8 0.11
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:338044 original size:3 final size:3
Alignment explanation
Indices: 338036--338120 Score: 113
Period size: 3 Copynumber: 29.3 Consensus size: 3
338026 CATGTTTTTT
*
338036 ATA ATA ATA TTA ATA ATA ATA ATA ATA ATA AT- ATA ATA A-A ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
338082 ATA ATA ATA GTA A-A ATA ATA ATA ATA TTA ATA AAA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
338121 AAAACAAATG
Statistics
Matches: 71, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
2 6 0.08
3 65 0.92
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:343940 original size:20 final size:20
Alignment explanation
Indices: 343901--343941 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
343891 CATTGCAGGA
*
343901 ATTTATGGCCTCTACGAAAG
1 ATTTATGGCCTCCACGAAAG
343921 ATTTCATGGCCTCCAC-AAAG
1 ATTT-ATGGCCTCCACGAAAG
343941 A
1 A
343942 CCTTAATGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (20 bp):
ATTTATGGCCTCCACGAAAG
Found at i:346179 original size:22 final size:22
Alignment explanation
Indices: 346148--346202 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
346138 AAGATTTTTT
* *
346148 ATGAATAGTGATAAACAGTACC
1 ATGAACAGTGATAAACAATACC
* *
346170 ATGAACAGTGATGAACAATATC
1 ATGAACAGTGATAAACAATACC
*
346192 GTGAACAGTGA
1 ATGAACAGTGA
346203 AAAATGTAAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.44, C:0.13, G:0.22, T:0.22
Consensus pattern (22 bp):
ATGAACAGTGATAAACAATACC
Found at i:346920 original size:40 final size:40
Alignment explanation
Indices: 346876--347016 Score: 246
Period size: 40 Copynumber: 3.5 Consensus size: 40
346866 ACCGTAGTGC
346876 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
346916 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* *
346956 TACACATAAGGTCGTGCCCACCGTATACACAGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
346996 TACACATAAGGCCGTGCCCAC
1 TACACATAAGGTCGTGCCCAC
347017 TATGTAAACT
Statistics
Matches: 96, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 96 1.00
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.21
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:364498 original size:16 final size:16
Alignment explanation
Indices: 364479--364518 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
364469 CTTTATTATC
364479 TTATTTTATCTTCCGT
1 TTATTTTATCTTCCGT
**
364495 TTA-TTTATCTTTTGT
1 TTATTTTATCTTCCGT
364510 TTATTTTAT
1 TTATTTTAT
364519 TCTAATCTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.70
Consensus pattern (16 bp):
TTATTTTATCTTCCGT
Found at i:364538 original size:322 final size:322
Alignment explanation
Indices: 363948--364587 Score: 1208
Period size: 322 Copynumber: 2.0 Consensus size: 322
363938 TTCAAGTTCT
363948 TGTGAGGGAGATTAATCTTCACACTCCAATTTGCCTTTTCATCACGACTAGGAGGGTTGGTTAGA
1 TGTGAGGGAGATTAATCTTCACACTCCAATTTGCCTTTTCATCACGACTAGGAGGGTTGGTTAGA
*
364013 GCCATTTATCGTGTTTTCCTTTTCATTACGACTAGGAGGGCTCGATAGGACACTTATCCATCTAT
66 GCCATTTATCGTGTTTTCCTTTTCATTACAACTAGGAGGGCTCGATAGGACACTTATCCATCTAT
364078 TATCCACAAATCCATTCGCACCATCAATCATCTTTACCGTTCACCTTCATAAGGGAGATCTTCTG
131 TATCCACAAATCCATTCGCACCATCAATCATCTTTACCGTTCACCTTCATAAGGGAGATCTTCTG
364143 ATTTCTTTATTATCTTATTTCATCTTCCGTTTATTTATCTTTTGTTTATTTTATTCTAATCTTAT
196 ATTTCTTTATTATCTTATTTCATCTTCCGTTTATTTATCTTTTGTTTATTTTATTCTAATCTTAT
364208 TGCCTTGATTCCAGCACATAAAAGAAACCCTAAAGAATCCTAACTACTGCCGCCACCTATCG
261 TGCCTTGATTCCAGCACATAAAAGAAACCCTAAAGAATCCTAACTACTGCCGCCACCTATCG
*
364270 TGTGAGGGAGATTAATCTTCACACTCCAATTTGCCTTTTCATCATGACTAGGAGGGTTGGTTAGA
1 TGTGAGGGAGATTAATCTTCACACTCCAATTTGCCTTTTCATCACGACTAGGAGGGTTGGTTAGA
*
364335 GCCATTTATCGTGTTTTCCTTTTCATTGCAACTAGGAGGGCTCGATAGGACACTTATCCATCTAT
66 GCCATTTATCGTGTTTTCCTTTTCATTACAACTAGGAGGGCTCGATAGGACACTTATCCATCTAT
*
364400 TATCCACAAATCCATTCGCACCATCAATCATCTTTACCGTTCACCTTTATAAGGGAGATCTTCTG
131 TATCCACAAATCCATTCGCACCATCAATCATCTTTACCGTTCACCTTCATAAGGGAGATCTTCTG
*
364465 ATTTCTTTATTATCTTATTTTATCTTCCGTTTATTTATCTTTTGTTTATTTTATTCTAATCTTAT
196 ATTTCTTTATTATCTTATTTCATCTTCCGTTTATTTATCTTTTGTTTATTTTATTCTAATCTTAT
* * *
364530 TTCCTTGATTCCAGCACATAAAAGAAACCCTAAAGAATCCTAGCTGCTGCCGCCACCT
261 TGCCTTGATTCCAGCACATAAAAGAAACCCTAAAGAATCCTAACTACTGCCGCCACCT
364588 TCCCCTATTC
Statistics
Matches: 310, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
322 310 1.00
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (322 bp):
TGTGAGGGAGATTAATCTTCACACTCCAATTTGCCTTTTCATCACGACTAGGAGGGTTGGTTAGA
GCCATTTATCGTGTTTTCCTTTTCATTACAACTAGGAGGGCTCGATAGGACACTTATCCATCTAT
TATCCACAAATCCATTCGCACCATCAATCATCTTTACCGTTCACCTTCATAAGGGAGATCTTCTG
ATTTCTTTATTATCTTATTTCATCTTCCGTTTATTTATCTTTTGTTTATTTTATTCTAATCTTAT
TGCCTTGATTCCAGCACATAAAAGAAACCCTAAAGAATCCTAACTACTGCCGCCACCTATCG
Found at i:366432 original size:21 final size:21
Alignment explanation
Indices: 366406--366446 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
366396 AATTCCAGAA
*
366406 TGCTACAGGGGTACCGATACT
1 TGCTACAGGGGTACCAATACT
366427 TGCTACAGGGGTACCAATAC
1 TGCTACAGGGGTACCAATAC
366447 CATTACTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (21 bp):
TGCTACAGGGGTACCAATACT
Found at i:368363 original size:19 final size:20
Alignment explanation
Indices: 368326--368366 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
368316 TGAGACCATG
368326 AATTTCAAATATACAAAATT
1 AATTTCAAATATACAAAATT
368346 AATTTCAAA-ACT-CAAAATT
1 AATTTCAAATA-TACAAAATT
368365 AA
1 AA
368367 AGATAATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (20 bp):
AATTTCAAATATACAAAATT
Found at i:369551 original size:18 final size:17
Alignment explanation
Indices: 369528--369586 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 17
369518 CAACAATTGG
369528 TAACAATTAGTATCTTTT
1 TAACAATT-GTATCTTTT
369546 TAACAATTGATATTCTTTTGT
1 TAACAATTG-TA-TC-TTT-T
369567 TAACAAATTGGTATCTTTT
1 TAAC-AATT-GTATCTTTT
369586 T
1 T
369587 CATTAAACAT
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
17 1 0.03
18 10 0.29
19 4 0.11
20 6 0.17
21 7 0.20
22 6 0.17
23 1 0.03
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.51
Consensus pattern (17 bp):
TAACAATTGTATCTTTT
Found at i:369571 original size:21 final size:21
Alignment explanation
Indices: 369538--369585 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
369528 TAACAATTAG
369538 TATC-TTT-TTAAC-AATTGA
1 TATCTTTTGTTAACAAATTGA
*
369556 TATTCTTTTGTTAACAAATTGG
1 TA-TCTTTTGTTAACAAATTGA
369578 TATCTTTT
1 TATCTTTT
369586 TCATTAAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 2 0.08
19 2 0.08
20 3 0.12
21 11 0.44
22 7 0.28
ACGTcount: A:0.27, C:0.10, G:0.08, T:0.54
Consensus pattern (21 bp):
TATCTTTTGTTAACAAATTGA
Found at i:369929 original size:21 final size:21
Alignment explanation
Indices: 369903--369943 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
369893 AATTCCAGAA
369903 TGCTACACGGGTACCGATACC
1 TGCTACACGGGTACCGATACC
* *
369924 TGCTACAGGGGTACTGATAC
1 TGCTACACGGGTACCGATAC
369944 TGTTACTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (21 bp):
TGCTACACGGGTACCGATACC
Found at i:370022 original size:21 final size:21
Alignment explanation
Indices: 369996--370046 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
369986 TATGAAAGGA
369996 TATCGATACCTGCTACAGGGG
1 TATCGATACCTGCTACAGGGG
370017 TATCGATACCTGCTACAGGGG
1 TATCGATACCTGCTACAGGGG
*
370038 TACCGATAC
1 TATCGATAC
370047 TACCTATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.24
Consensus pattern (21 bp):
TATCGATACCTGCTACAGGGG
Found at i:381879 original size:20 final size:21
Alignment explanation
Indices: 381854--381903 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
381844 CATTCATTCA
*
381854 TTAGCTTATGTCATG-TTATC
1 TTAGCTTATGTCATGTTTACC
* **
381874 TTAGCTCATGTTGTGTTTACC
1 TTAGCTTATGTCATGTTTACC
381895 TTAGCTTAT
1 TTAGCTTAT
381904 TAGCTTTGCA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.18, C:0.16, G:0.16, T:0.50
Consensus pattern (21 bp):
TTAGCTTATGTCATGTTTACC
Found at i:382682 original size:21 final size:21
Alignment explanation
Indices: 382656--382698 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
382646 TTTCTGGGTT
* *
382656 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
382677 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
382698 A
1 A
382699 TGAAATGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:382799 original size:68 final size:68
Alignment explanation
Indices: 382678--382830 Score: 202
Period size: 68 Copynumber: 2.2 Consensus size: 68
382668 ACCCATTCAA
* * * *
382678 GGGGAACCGATACCCCTTCAATGAAATGAATTTCCAGAATGCTAGAGGGGAATCGGTACCCC-CA
1 GGGGAACCGATACCCCCTCAATGAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCTAA
382742 GGG
66 GGG
* * *
382745 GGGGAACCGATACCCCCTC-ATCGTATATGAAATTCCAGACTGCTTGAGGGGAATCGATACCCCT
1 GGGGAACCGATACCCCCTCAAT-G-AAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCT
382809 AAGGG
64 AAGGG
*
382814 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
382831 ATGAGAAAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
66 2 0.03
67 19 0.25
68 34 0.45
69 20 0.27
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.18
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAATGAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCTAA
GGG
Found at i:383543 original size:22 final size:22
Alignment explanation
Indices: 383469--383535 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
383459 TTATGGACAT
383469 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
383491 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
383513 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
383535 A
1 A
383536 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:389601 original size:21 final size:21
Alignment explanation
Indices: 389575--389617 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
389565 TTTCTGGGTT
* *
389575 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
389596 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
389617 A
1 A
389618 TGAAATGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:389702 original size:69 final size:68
Alignment explanation
Indices: 389597--389750 Score: 202
Period size: 69 Copynumber: 2.2 Consensus size: 68
389587 ACCCATTCAA
* * * *
389597 GGGGAACCGATACCCCTTCAATGAAATGAATTTCCAGAATGCTAGAGGGGAATCGGTACCCCCAG
1 GGGGAACCGATACCCCCTCAATGAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCAA
389662 GGG
66 GGG
* * * *
389665 GGGGAACCGATACCCCCTC-ATCGTATATGAAATTCCAGACTGCTTGAGGGGAATCGATACCCCT
1 GGGGAACCGATACCCCCTCAAT-G-AAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCC
389729 AAGGG
64 AAGGG
*
389734 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
389751 ATGAGAAAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
67 2 0.03
68 19 0.25
69 54 0.72
ACGTcount: A:0.27, C:0.27, G:0.28, T:0.18
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAATGAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCAA
GGG
Found at i:390463 original size:22 final size:22
Alignment explanation
Indices: 390389--390455 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
390379 TTATGGACAT
390389 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
390411 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
390433 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
390455 A
1 A
390456 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:393700 original size:16 final size:17
Alignment explanation
Indices: 393660--393702 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
393650 TAATTTAAAA
393660 ATTAATTTAAAGTGAATT
1 ATTAATTTAAAGT-AATT
*
393678 -CTAATTTAAAGT-ATT
1 ATTAATTTAAAGTAATT
393693 ATTAATTTAA
1 ATTAATTTAA
393703 GTTTAAAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 3 0.14
16 8 0.36
17 11 0.50
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (17 bp):
ATTAATTTAAAGTAATT
Found at i:394423 original size:21 final size:21
Alignment explanation
Indices: 394398--394468 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 21
394388 AAACTTGTAA
*
394398 TTAATTTAATTTACTAATAAT
1 TTAATTTAATTTAATAATAAT
* * *
394419 TTAATATAA-ATAATTACTAAT
1 TTAATTTAATTTAA-TAATAAT
*
394440 TTAATATTAATATTAATATTAAT
1 TTAAT-TTAAT-TTAATAATAAT
394463 ATTAAT
1 -TTAAT
394469 AGTCCTACTA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
20 2 0.05
21 19 0.50
22 3 0.08
23 6 0.16
24 8 0.21
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (21 bp):
TTAATTTAATTTAATAATAAT
Found at i:394449 original size:6 final size:6
Alignment explanation
Indices: 394397--394469 Score: 62
Period size: 6 Copynumber: 12.2 Consensus size: 6
394387 TAAACTTGTA
* * * *
394397 ATTAAT -TTAAT -TTACT AATAAT -TTAAT ATAAAT AATTACT AATTTAAT
1 ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT -ATTAAT -A-TTAAT
394445 ATTAAT ATTAAT ATTAAT ATTAAT A
1 ATTAAT ATTAAT ATTAAT ATTAAT A
394470 GTCCTACTAT
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
5 13 0.24
6 31 0.56
7 7 0.13
8 4 0.07
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (6 bp):
ATTAAT
Found at i:394457 original size:27 final size:24
Alignment explanation
Indices: 394397--394469 Score: 71
Period size: 24 Copynumber: 3.0 Consensus size: 24
394387 TAAACTTGTA
394397 ATTAAT-TTAAT-TTACTAATAAT
1 ATTAATATTAATATTACTAATAAT
*
394419 -TTAATATAAATAATTACTAATTTAAT
1 ATTAATATTAAT-ATTACTAA--TAAT
* *
394445 ATTAATATTAATATTAATATTAAT
1 ATTAATATTAATATTACTAATAAT
394469 A
1 A
394470 GTCCTACTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
21 5 0.12
22 4 0.10
24 12 0.29
26 10 0.24
27 10 0.24
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (24 bp):
ATTAATATTAATATTACTAATAAT
Found at i:395790 original size:16 final size:18
Alignment explanation
Indices: 395769--395802 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
395759 GCCTTCGGGC
395769 TTTATAA-ATA-ATAATA
1 TTTATAATATATATAATA
395785 TTTATAATATATATAATA
1 TTTATAATATATATAATA
395803 ACGTATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 3 0.19
18 6 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTATAATATATATAATA
Found at i:396340 original size:20 final size:20
Alignment explanation
Indices: 396305--396446 Score: 185
Period size: 20 Copynumber: 7.1 Consensus size: 20
396295 TCAAAGAATC
* *
396305 TACAAATTACCCGAAGGATT
1 TACAAATGACCCGAAGGCTT
* * *
396325 TTCAAATGACCTGAAGGATT
1 TACAAATGACCCGAAGGCTT
* *
396345 TACAAATAACCTGAAGGCTT
1 TACAAATGACCCGAAGGCTT
*
396365 TACAAATGACCTGAAGGCTT
1 TACAAATGACCCGAAGGCTT
396385 TACAAATGACCCGAAGGCTT
1 TACAAATGACCCGAAGGCTT
*
396405 TACATATGACCCGAAGGCTT
1 TACAAATGACCCGAAGGCTT
* *
396425 TCCAAATGACCCGAAGGTTT
1 TACAAATGACCCGAAGGCTT
396445 TA
1 TA
396447 ATTTTCTAGA
Statistics
Matches: 109, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 109 1.00
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.25
Consensus pattern (20 bp):
TACAAATGACCCGAAGGCTT
Found at i:403243 original size:21 final size:21
Alignment explanation
Indices: 403218--403279 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 21
403208 AAACTTTTAA
*
403218 TTAATTTAATTTACTAATAAT
1 TTAATTTAATTTAATAATAAT
* * *
403239 TTAATATAA-ATAATTACTAAT
1 TTAATTTAATTTAA-TAATAAT
403260 TTAATATTAATATTAATAAT
1 TTAAT-TTAAT-TTAATAAT
403280 CCTACTATAA
Statistics
Matches: 30, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
20 2 0.07
21 19 0.63
22 3 0.10
23 3 0.10
24 3 0.10
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (21 bp):
TTAATTTAATTTAATAATAAT
Found at i:403277 original size:27 final size:26
Alignment explanation
Indices: 403217--403302 Score: 78
Period size: 27 Copynumber: 3.4 Consensus size: 26
403207 TAAACTTTTA
403217 ATTAAT-TTAAT--TTACTAA-TAAT
1 ATTAATATTAATAATTACTAATTAAT
*
403239 -TTAATATAAATAATTACTAATTTAAT
1 ATTAATATTAATAATTACTAA-TTAAT
403265 ATTAATATTAATAATCCTACT-A-TAAT
1 ATTAATATTAATAAT--TACTAATTAAT
403291 ATTTAATATTAA
1 A-TTAATATTAA
403303 CATTATATGA
Statistics
Matches: 53, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
21 5 0.09
22 4 0.08
24 7 0.13
26 9 0.17
27 23 0.43
28 1 0.02
29 4 0.08
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.47
Consensus pattern (26 bp):
ATTAATATTAATAATTACTAATTAAT
Found at i:404581 original size:16 final size:16
Alignment explanation
Indices: 404548--404590 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
404538 CTTCGGGCTT
*
404548 TATAAATAATAATATA
1 TATAAATAATAACATA
* *
404564 TATATATAATAACGTA
1 TATAAATAATAACATA
404580 TATAAAATAAT
1 TAT-AAATAAT
404591 CGTCACTCGG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 16 0.73
17 6 0.27
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (16 bp):
TATAAATAATAACATA
Found at i:405384 original size:23 final size:23
Alignment explanation
Indices: 405353--405398 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
405343 TGTTCGTTTA
*
405353 TTTAGTGTTCACGAACATGTTCG
1 TTTAATGTTCACGAACATGTTCG
* *
405376 TTTAATGTTCGCGAACGTGTTCG
1 TTTAATGTTCACGAACATGTTCG
405399 CTTCATGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (23 bp):
TTTAATGTTCACGAACATGTTCG
Found at i:411534 original size:22 final size:22
Alignment explanation
Indices: 411508--411590 Score: 80
Period size: 23 Copynumber: 3.8 Consensus size: 22
411498 TTGGTGCAGA
*
411508 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATACCCCCTTGAAG
*
411530 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATACCCCC-TTGAAG
* * *
411553 GGGAACCAATTCCCCC--CACAG
1 GGGAACCGATACCCCCTTGA-AG
*
411574 GGGAATCGATACCCCCT
1 GGGAACCGATACCCCCT
411591 GAGGGTTCTG
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
20 1 0.02
21 15 0.29
22 14 0.27
23 21 0.41
ACGTcount: A:0.25, C:0.34, G:0.24, T:0.17
Consensus pattern (22 bp):
GGGAACCGATACCCCCTTGAAG
Found at i:411550 original size:23 final size:22
Alignment explanation
Indices: 411508--411568 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 22
411498 TTGGTGCAGA
* *
411508 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATTCCCCCTTGAAG
411530 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC-TTGAAG
*
411553 GGGAACCAATTCCCCC
1 GGGAACCGATTCCCCC
411569 CACAGGGGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 14 0.40
23 21 0.60
ACGTcount: A:0.25, C:0.33, G:0.25, T:0.18
Consensus pattern (22 bp):
GGGAACCGATTCCCCCTTGAAG
Found at i:413171 original size:18 final size:17
Alignment explanation
Indices: 413145--413190 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 17
413135 GAACCAGAAT
413145 AGCACGAGGAACAAGCAC
1 AGCA-GAGGAACAAGCAC
413163 GAGCAGAGGAACAAGCAC
1 -AGCAGAGGAACAAGCAC
413181 AGCCAGAGGA
1 AG-CAGAGGA
413191 TCAAATGCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 2 0.08
18 20 0.77
19 4 0.15
ACGTcount: A:0.43, C:0.24, G:0.33, T:0.00
Consensus pattern (17 bp):
AGCAGAGGAACAAGCAC
Found at i:413233 original size:20 final size:20
Alignment explanation
Indices: 413208--413253 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
413198 CCTCCATACT
413208 TTCGATCCTTTATGGAGACA
1 TTCGATCCTTTATGGAGACA
413228 TTCGATCCTTTATGGAGACA
1 TTCGATCCTTTATGGAGACA
413248 TTCGAT
1 TTCGAT
413254 TTCCGATATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.37
Consensus pattern (20 bp):
TTCGATCCTTTATGGAGACA
Found at i:413881 original size:23 final size:23
Alignment explanation
Indices: 413851--413897 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
413841 GAGAAGTGTT
*
413851 AGAGTAAGGGGGGGTAATTTCAA
1 AGAGTAAGGGGGAGTAATTTCAA
*
413874 AGAGTAAGGGGGAGTACTTTCAA
1 AGAGTAAGGGGGAGTAATTTCAA
413897 A
1 A
413898 CTTGATTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.36, C:0.06, G:0.36, T:0.21
Consensus pattern (23 bp):
AGAGTAAGGGGGAGTAATTTCAA
Found at i:413912 original size:16 final size:16
Alignment explanation
Indices: 413891--413921 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
413881 GGGGGAGTAC
413891 TTTCAAACTTGATTTA
1 TTTCAAACTTGATTTA
413907 TTTCAAACTTGATTT
1 TTTCAAACTTGATTT
413922 CAAAATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.13, G:0.06, T:0.52
Consensus pattern (16 bp):
TTTCAAACTTGATTTA
Found at i:414047 original size:13 final size:13
Alignment explanation
Indices: 414029--414053 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
414019 AATGAATTTT
414029 AAGATTTTCTAAA
1 AAGATTTTCTAAA
414042 AAGATTTTCTAA
1 AAGATTTTCTAA
414054 GTATATTCGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (13 bp):
AAGATTTTCTAAA
Found at i:423870 original size:12 final size:12
Alignment explanation
Indices: 423853--423877 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
423843 TCAATCTAAC
423853 AAGGAGAAAACA
1 AAGGAGAAAACA
423865 AAGGAGAAAACA
1 AAGGAGAAAACA
423877 A
1 A
423878 CTCTCAAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.08, G:0.24, T:0.00
Consensus pattern (12 bp):
AAGGAGAAAACA
Found at i:430021 original size:40 final size:40
Alignment explanation
Indices: 429957--430175 Score: 199
Period size: 40 Copynumber: 5.4 Consensus size: 40
429947 CAAAATGGTA
* * *
429957 ACTTTAGCGGCGCTTTTATACAAACACCGCAACAGAGTAGT
1 ACTTTAGCGGCG-TTTTTTACAAACGCCGCAATAGAGTAGT
* * * * *
429998 ACTTTAGTGGCGTTTTTTACAAACGCAGCTATAGACT-TT
1 ACTTTAGCGGCGTTTTTTACAAACGCCGCAATAGAGTAGT
* * * *
430037 ATCTATAGTGGCGTTTTTTCAACAAACGTCGTAATAGAGTAGT
1 A-CTTTAGCGGCGTTTTTT--ACAAACGCCGCAATAGAGTAGT
* * * *
430080 ACTTTAGCGGCGTTTTTTACAAATGTCGCTATAG-GCTATT
1 ACTTTAGCGGCGTTTTTTACAAACGCCGCAATAGAG-TAGT
* * *
430120 ACTTTAGTGGCGTTTTTATACAAATGCCGCAACAGAGTAGT
1 ACTTTAGCGGCGTTTTT-TACAAACGCCGCAATAGAGTAGT
430161 ACTTTAGCGGCGTTT
1 ACTTTAGCGGCGTTT
430176 GTAGACTTCA
Statistics
Matches: 144, Mismatches: 27, Indels: 14
0.78 0.15 0.08
Matches are distributed among these distances:
39 3 0.02
40 67 0.47
41 42 0.29
42 30 0.21
43 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (40 bp):
ACTTTAGCGGCGTTTTTTACAAACGCCGCAATAGAGTAGT
Found at i:430083 original size:82 final size:81
Alignment explanation
Indices: 429965--430175 Score: 275
Period size: 82 Copynumber: 2.6 Consensus size: 81
429955 TAACTTTAGC
* * *
429965 GGCGCTTTTATACAAACACCGCAACAGAGTAGTACTTTAGTGGCGTTTTTTACAAACG-CAGCTA
1 GGCGTTTTTATACAAACGCCGCAACAGAGTAGTACTTTAGCGGCGTTTTTTACAAACGTC-GCTA
430029 TAGACT-TTATCTATAGT
65 TAGACTATTA-CTATAGT
* * * *
430046 GGCGTTTTT-TCAACAAACGTCGTAATAGAGTAGTACTTTAGCGGCGTTTTTTACAAATGTCGCT
1 GGCGTTTTTAT--ACAAACGCCGCAACAGAGTAGTACTTTAGCGGCGTTTTTTACAAACGTCGCT
* *
430110 ATAGGCTATTACTTTAGT
64 ATAGACTATTACTATAGT
*
430128 GGCGTTTTTATACAAATGCCGCAACAGAGTAGTACTTTAGCGGCGTTT
1 GGCGTTTTTATACAAACGCCGCAACAGAGTAGTACTTTAGCGGCGTTT
430176 GTAGACTTCA
Statistics
Matches: 112, Mismatches: 13, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
80 1 0.01
81 41 0.37
82 65 0.58
83 5 0.04
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (81 bp):
GGCGTTTTTATACAAACGCCGCAACAGAGTAGTACTTTAGCGGCGTTTTTTACAAACGTCGCTAT
AGACTATTACTATAGT
Found at i:430302 original size:153 final size:148
Alignment explanation
Indices: 430029--430320 Score: 372
Period size: 153 Copynumber: 1.9 Consensus size: 148
430019 AACGCAGCTA
* * * *
430029 TAGACTTTATCTATAGTGGCGTTTTTTCAACAAACGTCGTAATAGAGTAGTACTTTAGCGGCGTT
1 TAGACTTCATCTATAGTGGCGTTTTTTCAACAAACGTCGCAATAAAGTAGTACTTTAGCGGCATT
* * * * *
430094 TTTTACAAATGTCGCTATAGGCTATTACTTTAGTGGCGTTTTTATACAAATGCCGCAACAGAGTA
66 TTTTACAAAGGTCGCTATAGACTATTACTTTAGTGACGTTTTTATACAAACGCCGCAACAGACTA
430159 GTACTTTAGCGGCGTTTG
131 GTACTTTAGCGGCGTTTG
*
430177 TAGACTTCATCTATAGTGGCG-TTTTTCAACAAACG-CTGCAATAAAGTAGTACTTTAGTGGCAT
1 TAGACTTCATCTATAGTGGCGTTTTTTCAACAAACGTC-GCAATAAAGTAGTACTTTAGCGGCAT
* * *
430240 GTTTTTACAAAAGGTCGCTATCTATAGATTGTTACTTTAGTGACGTTTTTATACAAACGCCGCTA
65 -TTTTTAC-AAAGGTCG----CTATAGACTATTACTTTAGTGACGTTTTTATACAAACGCCGCAA
* *
430305 TAGACTCGTACTTTAG
124 CAGACTAGTACTTTAG
430321 TGTCAATTTT
Statistics
Matches: 122, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
146 1 0.01
147 36 0.30
148 27 0.22
149 7 0.06
153 51 0.42
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (148 bp):
TAGACTTCATCTATAGTGGCGTTTTTTCAACAAACGTCGCAATAAAGTAGTACTTTAGCGGCATT
TTTTACAAAGGTCGCTATAGACTATTACTTTAGTGACGTTTTTATACAAACGCCGCAACAGACTA
GTACTTTAGCGGCGTTTG
Found at i:430308 original size:41 final size:41
Alignment explanation
Indices: 430272--430360 Score: 133
Period size: 41 Copynumber: 2.2 Consensus size: 41
430262 TATAGATTGT
** *
430272 TACTTTAGTGACGTTTTTATACAAACGCCGCTATAGACTCG
1 TACTTTAGTGACAATTTTATACAAACACCGCTATAGACTCG
* *
430313 TACTTTAGTGTCAATTTTATACAAACACCGCTAAAGACTCG
1 TACTTTAGTGACAATTTTATACAAACACCGCTATAGACTCG
430354 TACTTTA
1 TACTTTA
430361 ATGGTATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.35
Consensus pattern (41 bp):
TACTTTAGTGACAATTTTATACAAACACCGCTATAGACTCG
Found at i:430372 original size:41 final size:41
Alignment explanation
Indices: 430285--430395 Score: 143
Period size: 41 Copynumber: 2.7 Consensus size: 41
430275 TTTAGTGACG
* *
430285 TTTTTATACAAACGCCGCTATAGACTCGTACTTTAGTGTCA
1 TTTTTATACAAACGCCGCTAAAGACTCGTACTTTAATGTCA
* *
430326 ATTTTATACAAACACCGCTAAAGACTCGTACTTTAATGGT-A
1 TTTTTATACAAACGCCGCTAAAGACTCGTACTTTAAT-GTCA
*
430367 TTTTTATTTACAAACGTCGCTAAAGACTC
1 TTTTTA--TACAAACGCCGCTAAAGACTC
430396 CTACGCAATT
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
41 39 0.65
42 2 0.03
43 19 0.32
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.35
Consensus pattern (41 bp):
TTTTTATACAAACGCCGCTAAAGACTCGTACTTTAATGTCA
Found at i:435679 original size:78 final size:79
Alignment explanation
Indices: 435587--435751 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
435577 GCAAAACTTG
* *
435587 ACTCGATTCGAAAAATCGA-TTTTTCAACTCGA-CTAAAAAAAGTTCAACTCGAATTGA-TTTCA
1 ACTCGACTCGAAAAATCGATTTTTTCAACTCGAGCTAAAAAAA-CTCAACTCGAATTGACTTT-A
*
435649 AGCTGTAATTTCGTAA
64 AGCTGTAATTTCATAA
* * * * *
435665 ACTCGACTGGAAAAATCGATTTTTTCTACTCGAGTTGAAAAAACTCAACTCGAATTGACTTTTAG
1 ACTCGACTCGAAAAATCGATTTTTTCAACTCGAGCTAAAAAAACTCAACTCGAATTGACTTTAAG
*
435730 TTGTAATTTCATAA
66 CTGTAATTTCATAA
435744 ACTCGACT
1 ACTCGACT
435752 TGACTCGAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
78 17 0.23
79 48 0.64
80 10 0.13
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.33
Consensus pattern (79 bp):
ACTCGACTCGAAAAATCGATTTTTTCAACTCGAGCTAAAAAAACTCAACTCGAATTGACTTTAAG
CTGTAATTTCATAA
Found at i:437030 original size:42 final size:43
Alignment explanation
Indices: 436984--437080 Score: 133
Period size: 44 Copynumber: 2.3 Consensus size: 43
436974 TAGATAATTT
436984 GCGACGTTTTT-CATACAAACGTCGCAAAAGGTTTGGTATATA
1 GCGACGTTTTTGCATACAAACGTCGCAAAAGGTTTGGTATATA
* * *
437026 GCGACGTTTTTTGGATGCAAATGTCGCAAAAGGTTTGGTATATA
1 GCGACG-TTTTTGCATACAAACGTCGCAAAAGGTTTGGTATATA
* *
437070 ACGGCGTTTTT
1 GCGACGTTTTT
437081 TGTTACAAAC
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
42 6 0.12
43 10 0.21
44 32 0.67
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (43 bp):
GCGACGTTTTTGCATACAAACGTCGCAAAAGGTTTGGTATATA
Found at i:437058 original size:44 final size:44
Alignment explanation
Indices: 436999--437082 Score: 141
Period size: 44 Copynumber: 1.9 Consensus size: 44
436989 GTTTTTCATA
*
436999 CAAACGTCGCAAAAGGTTTGGTATATAGCGACGTTTTTTGGATG
1 CAAACGTCGCAAAAGGTTTGGTATATAACGACGTTTTTTGGATG
* *
437043 CAAATGTCGCAAAAGGTTTGGTATATAACGGCGTTTTTTG
1 CAAACGTCGCAAAAGGTTTGGTATATAACGACGTTTTTTG
437083 TTACAAACGC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.27, C:0.13, G:0.26, T:0.33
Consensus pattern (44 bp):
CAAACGTCGCAAAAGGTTTGGTATATAACGACGTTTTTTGGATG
Found at i:437526 original size:21 final size:21
Alignment explanation
Indices: 437502--437547 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
437492 GCTGATATGT
437502 TGCTTCTCTCTGTGCTGT-CGC
1 TGCTTCTCTCTGTGCT-TCCGC
437523 TGCTTCTCTCTGTGCTTCCGC
1 TGCTTCTCTCTGTGCTTCCGC
437544 TGCT
1 TGCT
437548 GTTATCTCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.00, C:0.35, G:0.22, T:0.43
Consensus pattern (21 bp):
TGCTTCTCTCTGTGCTTCCGC
Found at i:437555 original size:23 final size:21
Alignment explanation
Indices: 437502--437557 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
437492 GCTGATATGT
*
437502 TGCTTCTCTCTGTGCTGTCGC
1 TGCTTATCTCTGTGCTGTCGC
*
437523 TGCTTCTCTCTGTGCT-TCCGC
1 TGCTTATCTCTGTGCTGT-CGC
437544 TGCTGTTATCTCTG
1 TGC--TTATCTCTG
437558 CTTCCCTCGC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 1 0.03
21 22 0.71
23 8 0.26
ACGTcount: A:0.02, C:0.32, G:0.21, T:0.45
Consensus pattern (21 bp):
TGCTTATCTCTGTGCTGTCGC
Found at i:441191 original size:22 final size:22
Alignment explanation
Indices: 441161--441205 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
441151 TCACAAGTCT
* *
441161 ACCTTATTTGTCCTTTTCTTTG
1 ACCTGATTTGTCATTTTCTTTG
441183 ACCTGATTTGTCATTTTCTTTG
1 ACCTGATTTGTCATTTTCTTTG
441205 A
1 A
441206 TCGTGTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.13, C:0.20, G:0.11, T:0.56
Consensus pattern (22 bp):
ACCTGATTTGTCATTTTCTTTG
Found at i:446141 original size:13 final size:13
Alignment explanation
Indices: 446123--446148 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
446113 CAATTTAATA
446123 CAAGGAACCGACG
1 CAAGGAACCGACG
446136 CAAGGAACCGACG
1 CAAGGAACCGACG
446149 GAGTGAATGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.31, G:0.31, T:0.00
Consensus pattern (13 bp):
CAAGGAACCGACG
Found at i:446195 original size:43 final size:43
Alignment explanation
Indices: 446131--446262 Score: 219
Period size: 43 Copynumber: 3.1 Consensus size: 43
446121 TACAAGGAAC
*
446131 CGACGCAAGGAACCGACGGAGTGAATGGTGGTGACTGAAGGCG
1 CGACGCAAGGAACCGACGGAGTGAATGGTGGCGACTGAAGGCG
*
446174 CGACGCAAGGAACCGAAGGAGTGAATGGTGGCGACTGAAGGCG
1 CGACGCAAGGAACCGACGGAGTGAATGGTGGCGACTGAAGGCG
* * *
446217 CGACGCAAGGAACCGACGGAGTGAATGCTGACGACTGAAGGTG
1 CGACGCAAGGAACCGACGGAGTGAATGGTGGCGACTGAAGGCG
446260 CGA
1 CGA
446263 TTTACTGAAG
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 83 1.00
ACGTcount: A:0.30, C:0.20, G:0.40, T:0.11
Consensus pattern (43 bp):
CGACGCAAGGAACCGACGGAGTGAATGGTGGCGACTGAAGGCG
Found at i:447786 original size:22 final size:22
Alignment explanation
Indices: 447758--447806 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
447748 CACGTTTTCA
447758 AAAGCTATTATTTTCCTATTCG
1 AAAGCTATTATTTTCCTATTCG
*
447780 AAAGCTATTATTTTCCTATTGG
1 AAAGCTATTATTTTCCTATTCG
447802 AAAGC
1 AAAGC
447807 AGAAAAATAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (22 bp):
AAAGCTATTATTTTCCTATTCG
Found at i:448404 original size:123 final size:123
Alignment explanation
Indices: 448269--448496 Score: 323
Period size: 123 Copynumber: 1.9 Consensus size: 123
448259 TTGTCTAAAA
* *
448269 ATGCCACTATAAACAACCCTATTACGATATTTTTCCTAAAAACACCGCTAAATTACTACTATATC
1 ATGCCACTATAAACAACCCTATTACGACATTTGTCCTAAAAACACCGCTAAATTACTACTATAT-
*
448334 ACGACA-TTTGTTGGAAAAACGCCACTATAAACAACACTATTGTGACGTTTATTAGAAC
65 ACGACATTTTGTTAGAAAAACGCCACTATAAACAACACTATTGTGACGTTTATTAGAAC
* * * * * *
448392 ATGCCACTATAAACAACCCTATTCCGACATTTGTGCTATAAATACCGCTAAATTACTACTCTATT
1 ATGCCACTATAAACAACCCTATTACGACATTTGTCCTAAAAACACCGCTAAATTACTACTATATA
* * * *
448457 CGACATTTTTTTAGAAAAATGCCCCTATAAACAACCCTAT
66 CGACATTTTGTTAGAAAAACGCCACTATAAACAACACTAT
448497 CTCGGTATTT
Statistics
Matches: 91, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
122 5 0.05
123 86 0.95
ACGTcount: A:0.37, C:0.24, G:0.09, T:0.30
Consensus pattern (123 bp):
ATGCCACTATAAACAACCCTATTACGACATTTGTCCTAAAAACACCGCTAAATTACTACTATATA
CGACATTTTGTTAGAAAAACGCCACTATAAACAACACTATTGTGACGTTTATTAGAAC
Found at i:456787 original size:13 final size:13
Alignment explanation
Indices: 456769--456798 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
456759 TTTATCTTTA
456769 TTTTTTTATGTTC
1 TTTTTTTATGTTC
456782 TTTTTTTATGTTC
1 TTTTTTTATGTTC
456795 TTTT
1 TTTT
456799 AATTTTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.07, C:0.07, G:0.07, T:0.80
Consensus pattern (13 bp):
TTTTTTTATGTTC
Found at i:460810 original size:12 final size:12
Alignment explanation
Indices: 460795--460828 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
460785 GGAGGAGGAC
* *
460795 GATGACGATGTT
1 GATGATGATGGT
460807 GATGATGATGGT
1 GATGATGATGGT
460819 GATGATGATG
1 GATGATGATG
460829 ACAACGAGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.26, C:0.03, G:0.38, T:0.32
Consensus pattern (12 bp):
GATGATGATGGT
Found at i:460996 original size:13 final size:13
Alignment explanation
Indices: 460954--460998 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
460944 ATTTAGTACT
*
460954 TTTTTTATTGTAG
1 TTTTTTATTGTAA
* * *
460967 TTGTTTATTGGAC
1 TTTTTTATTGTAA
460980 TTTTTTATTGTAA
1 TTTTTTATTGTAA
460993 TTTTTT
1 TTTTTT
460999 TATTATTTAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.16, C:0.02, G:0.13, T:0.69
Consensus pattern (13 bp):
TTTTTTATTGTAA
Found at i:464901 original size:14 final size:14
Alignment explanation
Indices: 464882--464911 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
464872 TCTAATCAAG
464882 AATATTAAATTAAA
1 AATATTAAATTAAA
464896 AATATTAAATTAAA
1 AATATTAAATTAAA
464910 AA
1 AA
464912 GATGATTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AATATTAAATTAAA
Found at i:467468 original size:18 final size:18
Alignment explanation
Indices: 467445--467481 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
467435 CCAGGACAAT
467445 AAGGTGGGGTATTAGTGC
1 AAGGTGGGGTATTAGTGC
467463 AAGGTGGGGTATTAGTGC
1 AAGGTGGGGTATTAGTGC
467481 A
1 A
467482 CTAATAGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.05, G:0.43, T:0.27
Consensus pattern (18 bp):
AAGGTGGGGTATTAGTGC
Found at i:470021 original size:13 final size:13
Alignment explanation
Indices: 470003--470029 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
469993 TTCTTTCATC
470003 TCTTTATTTTCTT
1 TCTTTATTTTCTT
470016 TCTTTATTTTCTT
1 TCTTTATTTTCTT
470029 T
1 T
470030 TCATTATGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (13 bp):
TCTTTATTTTCTT
Found at i:472452 original size:11 final size:11
Alignment explanation
Indices: 472436--472487 Score: 54
Period size: 11 Copynumber: 4.6 Consensus size: 11
472426 TCGAGACTCG
472436 AGCTCGATTGA
1 AGCTCGATTGA
472447 AGCTCGATTTTG-
1 AGCTCGA--TTGA
*
472459 AGCTCGATTCA
1 AGCTCGATTGA
472470 AGCTCGATT-A
1 AGCTCGATTGA
472480 TAGCTCGA
1 -AGCTCGA
472488 CGAGTTAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
10 3 0.08
11 23 0.64
12 7 0.19
13 3 0.08
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (11 bp):
AGCTCGATTGA
Found at i:472465 original size:23 final size:23
Alignment explanation
Indices: 472435--472487 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
472425 CTCGAGACTC
* *
472435 GAGCTCGATTGAAGCTCGATTTT
1 GAGCTCGATTCAAGCTCGATTAT
472458 GAGCTCGATTCAAGCTCGATTAT
1 GAGCTCGATTCAAGCTCGATTAT
472481 -AGCTCGA
1 GAGCTCGA
472488 CGAGTTAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
22 7 0.25
23 21 0.75
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (23 bp):
GAGCTCGATTCAAGCTCGATTAT
Found at i:473762 original size:24 final size:23
Alignment explanation
Indices: 473734--473786 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 23
473724 AATATTTTTA
*
473734 AATTTTTTCCCATCTAAATATATT
1 AATTTTTTCACAT-TAAATATATT
473758 AA---TTTCACATTAAATATATT
1 AATTTTTTCACATTAAATATATT
473778 AATATTTTT
1 AAT-TTTTT
473787 ATTAATATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 8
0.73 0.03 0.24
Matches are distributed among these distances:
20 12 0.50
21 7 0.29
24 5 0.21
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (23 bp):
AATTTTTTCACATTAAATATATT
Found at i:473784 original size:22 final size:21
Alignment explanation
Indices: 473739--473780 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
473729 TTTTAAATTT
*
473739 TTTCCCATCTAAATATATTAA
1 TTTCACATCTAAATATATTAA
473760 TTTCACAT-TAAATATATTAA
1 TTTCACATCTAAATATATTAA
473780 T
1 T
473781 ATTTTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.40, C:0.14, G:0.00, T:0.45
Consensus pattern (21 bp):
TTTCACATCTAAATATATTAA
Found at i:482898 original size:29 final size:29
Alignment explanation
Indices: 482866--483077 Score: 98
Period size: 29 Copynumber: 7.1 Consensus size: 29
482856 GAAGAGGAAC
*
482866 CAATCCTTGACTTCCTCGTGAAGAGAAGT
1 CAATCCTTGACTTCCTCGTAAAGAGAAGT
** * * *
482895 CAAT-CTTTTCTAT-TTC-TAAAGAGGATT
1 CAATCCTTGACT-TCCTCGTAAAGAGAAGT
* *
482922 CAATCATTGACTTCCTCATAAAGAGAAGT
1 CAATCCTTGACTTCCTCGTAAAGAGAAGT
* * *
482951 CAATCTTTGTTA-TTCCCGACTCCCTCATGAAGAGGAA-C
1 CAATCCTTG--ACTT--C--CT-CGT-A--AAGA-GAAGT
*
482989 CAATCCTTGACTTCATCGTAAAGAGAAGT
1 CAATCCTTGACTTCCTCGTAAAGAGAAGT
** * *
483018 CAAT-CTTTTCTAT--TCCTAAAGAGGAGT
1 CAATCCTTGACT-TCCTCGTAAAGAGAAGT
*
483045 CAATCCTTGACTTCCTCTTAAAGAGAAGT
1 CAATCCTTGACTTCCTCGTAAAGAGAAGT
483074 CAAT
1 CAAT
483078 ATTTGTTATT
Statistics
Matches: 135, Mismatches: 27, Indels: 42
0.66 0.13 0.21
Matches are distributed among these distances:
27 30 0.22
28 26 0.19
29 47 0.35
30 2 0.01
31 2 0.01
32 3 0.02
33 1 0.01
34 2 0.01
35 3 0.02
36 2 0.01
37 2 0.01
38 12 0.09
39 3 0.02
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (29 bp):
CAATCCTTGACTTCCTCGTAAAGAGAAGT
Found at i:482926 original size:56 final size:56
Alignment explanation
Indices: 482857--483271 Score: 267
Period size: 56 Copynumber: 6.8 Consensus size: 56
482847 CTCCCTCGTG
*
482857 AAGAGGAACCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTTCTATTTCTA
1 AAGAGGAACCAATCCTTGACTTCCTCGTAAAGAGAAGTCAATCTTTTCTATTTCTA
** * *
482913 AAGAGGATTCAATCATTGACTTCCTCATAAAGAGAAGTCAATCTTTGT-TATTCCCGACTCCCTC
1 AAGAGGAACCAATCCTTGACTTCCTCGTAAAGAGAAGTCAATCTTT-TCTATT------T--CT-
482977 A
56 A
* *
482978 TGAAGAGGAACCAATCCTTGACTTCATCGTAAAGAGAAGTCAATCTTTTCTATTCCTA
1 --AAGAGGAACCAATCCTTGACTTCCTCGTAAAGAGAAGTCAATCTTTTCTATTTCTA
** * *
483036 AAGAGGAGTCAATCCTTGACTTCCTCTTAAAGAGAAGTCAATATTTGT-TATTCCTAACTCCCTC
1 AAGAGGAACCAATCCTTGACTTCCTCGTAAAGAGAAGTCAATCTTT-TCTA-T--T---T--CT-
483100 A
56 A
* ** * *
483101 TGAAGAGGAACCAATCCTTGACTTCCTTGTAATTAGAAGTAAATCTTTGTTATTCCCGACTCTCT
1 --AAGAGGAACCAATCCTTGACTTCCTCGTAAAGAGAAGTCAATC----TT-TT--CTA-T-T-T
*
483166 CGTG
54 C-TA
* * * * *
483170 AAGAAGAACCAATCCTTGACTTCCTCGTGAAGACAAGTCAATCTTTACTATTCCTA
1 AAGAGGAACCAATCCTTGACTTCCTCGTAAAGAGAAGTCAATCTTTTCTATTTCTA
** * *
483226 AAGAGGAGTCAATCCTTGACTTTCTCGTAAATAGAAGTCAATCTTT
1 AAGAGGAACCAATCCTTGACTTCCTCGTAAAGAGAAGTCAATCTTT
483272 GTTATTCCTG
Statistics
Matches: 279, Mismatches: 46, Indels: 68
0.71 0.12 0.17
Matches are distributed among these distances:
56 128 0.46
57 4 0.01
58 2 0.01
59 4 0.01
60 2 0.01
62 2 0.01
63 2 0.01
64 4 0.01
65 2 0.01
66 1 0.00
67 116 0.42
69 1 0.00
70 1 0.00
71 5 0.02
72 1 0.00
73 2 0.01
74 2 0.01
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (56 bp):
AAGAGGAACCAATCCTTGACTTCCTCGTAAAGAGAAGTCAATCTTTTCTATTTCTA
Found at i:483021 original size:67 final size:67
Alignment explanation
Indices: 482913--483346 Score: 412
Period size: 67 Copynumber: 6.8 Consensus size: 67
482903 TCTATTTCTA
** * *
482913 AAGAGGATTCAATCATTGACTTCCTCATAAAGAGAAGTCAATCTTTGTTATTCCCGACTCCCTCA
1 AAGAGGAACCAATCCTTGACTTCCTCGTAAAGAGAAGTCAATCTTTGTTATTCCCGACTCCCTCA
482978 TG
66 TG
*
482980 AAGAGGAACCAATCCTTGACTTCATCGTAAAGAGAAGTCAATCTTT-TCTA-T------T-CCT-
1 AAGAGGAACCAATCCTTGACTTCCTCGTAAAGAGAAGTCAATCTTTGT-TATTCCCGACTCCCTC
483035 A--
65 ATG
** * * **
483036 AAGAGGAGTCAATCCTTGACTTCCTCTTAAAGAGAAGTCAATATTTGTTATTCCTAACTCCCTCA
1 AAGAGGAACCAATCCTTGACTTCCTCGTAAAGAGAAGTCAATCTTTGTTATTCCCGACTCCCTCA
483101 TG
66 TG
* ** * * *
483103 AAGAGGAACCAATCCTTGACTTCCTTGTAATTAGAAGTAAATCTTTGTTATTCCCGACTCTCTCG
1 AAGAGGAACCAATCCTTGACTTCCTCGTAAAGAGAAGTCAATCTTTGTTATTCCCGACTCCCTCA
483168 TG
66 TG
* * * * *
483170 AAGAAGAACCAATCCTTGACTTCCTCGTGAAGACAAGTCAATC--T-TTA----CTA-TTCCT-A
1 AAGAGGAACCAATCCTTGACTTCCTCGTAAAGAGAAGTCAATCTTTGTTATTCCCGACTCCCTCA
483226 --
66 TG
** * * * *
483226 AAGAGGAGTCAATCCTTGACTTTCTCGTAAATAGAAGTCAATCTTTGTTATTCCTGACTCTCTCA
1 AAGAGGAACCAATCCTTGACTTCCTCGTAAAGAGAAGTCAATCTTTGTTATTCCCGACTCCCTCA
483291 TG
66 TG
* *
483293 AAGA-GATACCAATCCTTGACTTCCTCATGAAGAGAAGTCAATCTTTGTTATTCC
1 AAGAGGA-ACCAATCCTTGACTTCCTCGTAAAGAGAAGTCAATCTTTGTTATTCC
483347 TGAAGAGGAG
Statistics
Matches: 292, Mismatches: 50, Indels: 50
0.74 0.13 0.13
Matches are distributed among these distances:
56 79 0.27
57 2 0.01
58 2 0.01
59 9 0.03
60 3 0.01
63 2 0.01
64 9 0.03
65 3 0.01
66 4 0.01
67 179 0.61
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (67 bp):
AAGAGGAACCAATCCTTGACTTCCTCGTAAAGAGAAGTCAATCTTTGTTATTCCCGACTCCCTCA
TG
Found at i:483067 original size:123 final size:123
Alignment explanation
Indices: 482844--483156 Score: 484
Period size: 123 Copynumber: 2.5 Consensus size: 123
482834 AGCTTCAACT
* *
482844 CGACTCCCTCGTGAAGAGGAACCAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTTCTATT
1 CGACTCCCTCATGAAGAGGAACCAATCCTTGACTTCCTCGTAAAGAGAAGTCAATCTTTTCTATT
* * *
482909 TCTAAAGAGGATTCAATCATTGACTTCCTCATAAAGAGAAGTCAATCTTTGTTATTCC
66 CCTAAAGAGGAGTCAATCATTGACTTCCTCATAAAGAGAAGTCAATATTTGTTATTCC
*
482967 CGACTCCCTCATGAAGAGGAACCAATCCTTGACTTCATCGTAAAGAGAAGTCAATCTTTTCTATT
1 CGACTCCCTCATGAAGAGGAACCAATCCTTGACTTCCTCGTAAAGAGAAGTCAATCTTTTCTATT
* *
483032 CCTAAAGAGGAGTCAATCCTTGACTTCCTCTTAAAGAGAAGTCAATATTTGTTATTCC
66 CCTAAAGAGGAGTCAATCATTGACTTCCTCATAAAGAGAAGTCAATATTTGTTATTCC
** * ** *
483090 TAACTCCCTCATGAAGAGGAACCAATCCTTGACTTCCTTGTAATTAGAAGTAAATCTTTGT-TAT
1 CGACTCCCTCATGAAGAGGAACCAATCCTTGACTTCCTCGTAAAGAGAAGTCAATCTTT-TCTAT
483154 TCC
65 TCC
483157 CGACTCTCTC
Statistics
Matches: 174, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
123 173 0.99
124 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (123 bp):
CGACTCCCTCATGAAGAGGAACCAATCCTTGACTTCCTCGTAAAGAGAAGTCAATCTTTTCTATT
CCTAAAGAGGAGTCAATCATTGACTTCCTCATAAAGAGAAGTCAATATTTGTTATTCC
Found at i:483211 original size:29 final size:28
Alignment explanation
Indices: 483179--483268 Score: 85
Period size: 29 Copynumber: 3.2 Consensus size: 28
483169 GAAGAAGAAC
* *
483179 CAATCCTTGACTTCCTCGTGAAGACAAGT
1 CAATCCTTGACTT-CTCGTAAAGAGAAGT
* * *
483208 CAAT-CTTTACTAT-TCCTAAAGAGGAGT
1 CAATCCTTGACT-TCTCGTAAAGAGAAGT
*
483235 CAATCCTTGACTTTCTCGTAAATAGAAGT
1 CAATCCTTGAC-TTCTCGTAAAGAGAAGT
483264 CAATC
1 CAATC
483269 TTTGTTATTC
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
27 14 0.29
28 12 0.25
29 22 0.46
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.31
Consensus pattern (28 bp):
CAATCCTTGACTTCTCGTAAAGAGAAGT
Found at i:483235 original size:27 final size:27
Alignment explanation
Indices: 483199--483280 Score: 76
Period size: 29 Copynumber: 3.0 Consensus size: 27
483189 CTTCCTCGTG
*
483199 AAGACAAGTCAATCTTTACTATTCCTA
1 AAGAGAAGTCAATCTTTACTATTCCTA
* *
483226 AAGAGGAGTCAATCCTTGACT-TTCTCGTA
1 AAGAGAAGTCAAT-CTTTACTATTC-C-TA
* **
483255 AATAGAAGTCAATCTTTGTTATTCCT
1 AAGAGAAGTCAATCTTTACTATTCCT
483281 GACTCTCTCA
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
27 15 0.35
28 12 0.28
29 16 0.37
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (27 bp):
AAGAGAAGTCAATCTTTACTATTCCTA
Found at i:483236 original size:190 final size:189
Alignment explanation
Indices: 482913--483346 Score: 629
Period size: 190 Copynumber: 2.3 Consensus size: 189
482903 TCTATTTCTA
** * **
482913 AAGAGGATTCAATCATTGACTTCCTCATAAAGAGAAGTCAATCTTTGTTATTCCCGACTCCCTCA
1 AAGAGGAACCAATCCTTGACTTCCTTGT-AAGAGAAGTCAATCTTTGTTATTCCCGACTCCCTCA
* * *
482978 TGAAGAGGAACCAATCCTTGACTTCATCGTAAAGAGAAGTCAATCTTTTCTATTCCTAAAGAGGA
65 TGAAGAAGAACCAATCCTTGACTTCATCGTAAAGACAAGTCAATCTTTACTATTCCTAAAGAGGA
*
483043 GTCAATCCTTGACTTCCTCTTAAAGAGAAGTCAATATTTGTTATTCCTAACTCCCTCATG
130 GTCAATCCTTGACTTCCTCGTAAAGAGAAGTCAATATTTGTTATTCCTAACTCCCTCATG
* * * *
483103 AAGAGGAACCAATCCTTGACTTCCTTGTAATTAGAAGTAAATCTTTGTTATTCCCGACTCTCTCG
1 AAGAGGAACCAATCCTTGACTTCCTTGTAA-GAGAAGTCAATCTTTGTTATTCCCGACTCCCTCA
* *
483168 TGAAGAAGAACCAATCCTTGACTTCCTCGTGAAGACAAGTCAATCTTTACTATTCCTAAAGAGGA
65 TGAAGAAGAACCAATCCTTGACTTCATCGTAAAGACAAGTCAATCTTTACTATTCCTAAAGAGGA
* * * * *
483233 GTCAATCCTTGACTTTCTCGTAAATAGAAGTCAATCTTTGTTATTCCTGACTCTCTCATG
130 GTCAATCCTTGACTTCCTCGTAAAGAGAAGTCAATATTTGTTATTCCTAACTCCCTCATG
483293 AAGA-GATACCAATCCTTGACTTCCTCATG-AAGAGAAGTCAATCTTTGTTATTCC
1 AAGAGGA-ACCAATCCTTGACTTCCT--TGTAAGAGAAGTCAATCTTTGTTATTCC
483347 TGAAGAGGAG
Statistics
Matches: 218, Mismatches: 22, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
189 4 0.02
190 210 0.96
191 2 0.01
192 2 0.01
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (189 bp):
AAGAGGAACCAATCCTTGACTTCCTTGTAAGAGAAGTCAATCTTTGTTATTCCCGACTCCCTCAT
GAAGAAGAACCAATCCTTGACTTCATCGTAAAGACAAGTCAATCTTTACTATTCCTAAAGAGGAG
TCAATCCTTGACTTCCTCGTAAAGAGAAGTCAATATTTGTTATTCCTAACTCCCTCATG
Found at i:483278 original size:56 final size:56
Alignment explanation
Indices: 483179--483362 Score: 179
Period size: 56 Copynumber: 3.1 Consensus size: 56
483169 GAAGAAGAAC
* **
483179 CAATCCTTGACTTCCTCGTGAAGACAAGTCAATCTTTACTATTCCTAAAGAGGAGT
1 CAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCCTAAAGAGGAGT
* * * * *
483235 CAATCCTTGACTTTCTCGTAAATAGAAGTCAATCTTTGTTATTCCTGACTCTCTCATGAAGAGAT
1 CAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCCT-A-------AAGAGGAG-T
* *
483300 ACCAATCCTTGACTTCCTCATGAAGAGAAGTCAATCTTTGTTATTCCTGAAGAGGAGT
1 --CAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCCTAAAGAGGAGT
483358 CAATC
1 CAATC
483363 TATCAGATTT
Statistics
Matches: 102, Mismatches: 15, Indels: 22
0.73 0.11 0.16
Matches are distributed among these distances:
56 45 0.44
57 1 0.01
58 1 0.01
59 6 0.06
64 6 0.06
65 1 0.01
67 42 0.41
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (56 bp):
CAATCCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCCTAAAGAGGAGT
Found at i:483356 original size:123 final size:123
Alignment explanation
Indices: 483101--483362 Score: 391
Period size: 123 Copynumber: 2.1 Consensus size: 123
483091 AACTCCCTCA
** * *
483101 TGAAGAGGAACCAATCCTTGACTTCCTTGTAATTAGAAGTAAATCTTTGTTATTCCCGACTCTCT
1 TGAAGAGGAGTCAATCCTTGACTTCCTCGTAAATAGAAGTAAATCTTTGTTATTCCCGACTCTCT
* *
483166 CGTGAAGAAGAACCAATCCTTGACTTCCTCGTGAAGACAAGTCAATCTTTACTATTCC
66 CATGAAGAAGAACCAATCCTTGACTTCCTCATGAAGACAAGTCAATCTTTACTATTCC
* * * *
483224 TAAAGAGGAGTCAATCCTTGACTTTCTCGTAAATAGAAGTCAATCTTTGTTATTCCTGACTCTCT
1 TGAAGAGGAGTCAATCCTTGACTTCCTCGTAAATAGAAGTAAATCTTTGTTATTCCCGACTCTCT
* **
483289 CATGAAG-AGATACCAATCCTTGACTTCCTCATGAAGAGAAGTCAATCTTTGTTATTCC
66 CATGAAGAAGA-ACCAATCCTTGACTTCCTCATGAAGACAAGTCAATCTTTACTATTCC
483347 TGAAGAGGAGTCAATC
1 TGAAGAGGAGTCAATC
483363 TATCAGATTT
Statistics
Matches: 124, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
122 3 0.02
123 121 0.98
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (123 bp):
TGAAGAGGAGTCAATCCTTGACTTCCTCGTAAATAGAAGTAAATCTTTGTTATTCCCGACTCTCT
CATGAAGAAGAACCAATCCTTGACTTCCTCATGAAGACAAGTCAATCTTTACTATTCC
Found at i:483667 original size:89 final size:89
Alignment explanation
Indices: 483365--483656 Score: 439
Period size: 86 Copynumber: 3.3 Consensus size: 89
483355 AGTCAATCTA
* * * * *
483365 TCAGATTTGGTCTTCCTGAAGAAGCAGCGAAGTAAATCAATTTCAAGTCTGAT-TTCCTGGAAGA
1 TCAGATTTGGTCTTCCTGAAGAAGCAGCGAAGCAAATCAATCTCGAGTCTGATCTCCCCGGAAGA
*
483429 GTAGTGGAGCATATTCTTCTTATT
66 GTAGTGGAGCATATTCTTATTATT
*
483453 TCAGATTTGGTCTTCCTGAAGAAGCAGCGAAGCAAATCAATCTCGAGTCTGATCTCCCGGGAAGA
1 TCAGATTTGGTCTTCCTGAAGAAGCAGCGAAGCAAATCAATCTCGAGTCTGATCTCCCCGGAAGA
*
483518 GTAGT---GCATATTCTTTTTATT
66 GTAGTGGAGCATATTCTTATTATT
* * *
483539 TTAGATTTGGTCTTCCTGAAGAAGCAGCGAAGCAAATCAACCTCGAGTCTGATCTCCCCGAAAGA
1 TCAGATTTGGTCTTCCTGAAGAAGCAGCGAAGCAAATCAATCTCGAGTCTGATCTCCCCGGAAGA
*
483604 GTAGTGGAGCAGATTCTTATTATT
66 GTAGTGGAGCATATTCTTATTATT
*
483628 TCAGATTTGGTATTCCTGAAGAAGCAGCG
1 TCAGATTTGGTCTTCCTGAAGAAGCAGCG
483657 GAGTGAATCA
Statistics
Matches: 186, Mismatches: 14, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
86 81 0.44
88 50 0.27
89 55 0.30
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (89 bp):
TCAGATTTGGTCTTCCTGAAGAAGCAGCGAAGCAAATCAATCTCGAGTCTGATCTCCCCGGAAGA
GTAGTGGAGCATATTCTTATTATT
Found at i:483999 original size:3 final size:3
Alignment explanation
Indices: 483991--484045 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
483981 GTCCATATAT
483991 TTA 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 TTA
484039 TTA TTA T
1 TTA TTA T
484046 CACTATAATT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:492716 original size:183 final size:181
Alignment explanation
Indices: 492408--492775 Score: 657
Period size: 180 Copynumber: 2.0 Consensus size: 181
492398 CTTATAATAA
492408 TCAAACTTAAAAATTAGCATAAACAATTAATTTCAAAGATACATCACATGTAAATCATGCAATAC
1 TCAAACTTAAAAATTAGCATAAACAATTAATTTCAAAGATACATCACATGTAAATCATGCAATAC
492473 TACGAAAAAATCTTCTAAGAAAAATCTAACCAAAAACATCAACAAAACTAAGCAAAAAAAAAAAA
66 TACGAAAAAATCTTCTAAGAAAAATCTAACCAAAAACATCAACAAAACTAAGC--AAAAAAAAAA
* * *
492538 AAATCAGAATTAGCAAAAAAATAAAGGCAATCAGAATAGACAACAGATGAATC
129 AAATCAGAATTAACAAAAAAAGAAAGGCAATCAGAATAGACAACAGACGAATC
492591 TCAAACTTAAAAATTAGCATAAACAATTAATTTCAAAGATACATCACATGTAAATCATGC-ATAC
1 TCAAACTTAAAAATTAGCATAAACAATTAATTTCAAAGATACATCACATGTAAATCATGCAATAC
* * *
492655 TACGAAAAACTCTTCTAAGAAAAATCTAACCAAAAATATCAACAAAACTAAGCAAAAAAAAATAA
66 TACGAAAAAATCTTCTAAGAAAAATCTAACCAAAAACATCAACAAAACTAAGCAAAAAAAAAAAA
492720 ATCAGAATTAACAAAAAAAGAAAGGCAATCAGAATAGACAACAGACGAATC
131 ATCAGAATTAACAAAAAAAGAAAGGCAATCAGAATAGACAACAGACGAATC
492771 TCAAA
1 TCAAA
492776 TTACCGATAT
Statistics
Matches: 179, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
180 64 0.36
182 55 0.31
183 60 0.34
ACGTcount: A:0.56, C:0.16, G:0.08, T:0.19
Consensus pattern (181 bp):
TCAAACTTAAAAATTAGCATAAACAATTAATTTCAAAGATACATCACATGTAAATCATGCAATAC
TACGAAAAAATCTTCTAAGAAAAATCTAACCAAAAACATCAACAAAACTAAGCAAAAAAAAAAAA
ATCAGAATTAACAAAAAAAGAAAGGCAATCAGAATAGACAACAGACGAATC
Found at i:493619 original size:41 final size:41
Alignment explanation
Indices: 493574--493677 Score: 104
Period size: 42 Copynumber: 2.5 Consensus size: 41
493564 TGTTGCGGTG
* ** *
493574 TTTGTATAAAAACACCACTAAAGTAT-AGCTTTGTTATGGCA
1 TTTGTATAAAAACACCACTAAAG-ATGAACCCTATTATGGCA
** *
493615 TTTGT-TGAATAAATGCCACTATAGATGAACCCTATTATGGCA
1 TTTGTAT-AA-AAACACCACTAAAGATGAACCCTATTATGGCA
493657 TTTGTATAAAAACACCACTAA
1 TTTGTATAAAAACACCACTAA
493678 CATACTACTC
Statistics
Matches: 49, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
40 1 0.02
41 18 0.37
42 29 0.59
43 1 0.02
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (41 bp):
TTTGTATAAAAACACCACTAAAGATGAACCCTATTATGGCA
Found at i:493751 original size:83 final size:83
Alignment explanation
Indices: 493574--493802 Score: 257
Period size: 82 Copynumber: 2.8 Consensus size: 83
493564 TGTTGCGGTG
* **
493574 TTTGTATAAAAACACCACTAAAGTA-TAGCTTTGTTATGGCATTTGTTGAATAAATGCCACTATA
1 TTTGTATAAAAACACCACTAAAGTACTA-CTCTGTTACAGCATTTGTTGAATAAATGCCACTATA
493638 GATGAACCCTATTATGGCA
65 GATGAACCCTATTATGGCA
* * *
493657 TTTGTATAAAAACACCACTAACA-TACTACTCTGTTACAGCGTTTGTTTAA-AAATGCCATTATA
1 TTTGTATAAAAACACCACTAA-AGTACTACTCTGTTACAGCATTTGTTGAATAAATGCCACTATA
* *
493720 GATTAACCCTATTGTGGCA
65 GATGAACCCTATTATGGCA
* * * * * *** * *
493739 TTTATGTAAAAAAACAACTAAAGTACTATTCTGTTGTGGCATTTCTTGAAAAAATGCCACTATA
1 TTTGTATAAAAACACCACTAAAGTACTACTCTGTTACAGCATTTGTTGAATAAATGCCACTATA
493803 TTGTGACATT
Statistics
Matches: 122, Mismatches: 20, Indels: 8
0.81 0.13 0.05
Matches are distributed among these distances:
81 1 0.01
82 66 0.54
83 52 0.43
84 3 0.02
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.34
Consensus pattern (83 bp):
TTTGTATAAAAACACCACTAAAGTACTACTCTGTTACAGCATTTGTTGAATAAATGCCACTATAG
ATGAACCCTATTATGGCA
Found at i:495688 original size:22 final size:21
Alignment explanation
Indices: 495638--495688 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
495628 TAAAGGATTG
495638 ATCATTTTTCAAAAGGGATCA
1 ATCATTTTTCAAAAGGGATCA
*
495659 ATCATTTTTCAAAATGGATCA
1 ATCATTTTTCAAAAGGGATCA
*
495680 ATCCTTTTT
1 ATCATTTTT
495689 ATGGAAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (21 bp):
ATCATTTTTCAAAAGGGATCA
Found at i:499813 original size:23 final size:24
Alignment explanation
Indices: 499788--499833 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
499778 AACGACTTTA
*
499788 TTTTCATTAAAAAATAAAACAAAT
1 TTTTCACTAAAAAATAAAACAAAT
*
499812 TTTTTACTAAAAAATAAAACAA
1 TTTTCACTAAAAAATAAAACAA
499834 GTTAATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.33
Consensus pattern (24 bp):
TTTTCACTAAAAAATAAAACAAAT
Found at i:500090 original size:40 final size:40
Alignment explanation
Indices: 500002--500083 Score: 137
Period size: 40 Copynumber: 2.0 Consensus size: 40
499992 AATATATTAA
*
500002 TGGATTATTATAAGAGTTTAAGTGTGAAGAATATTTTTAT
1 TGGATTATGATAAGAGTTTAAGTGTGAAGAATATTTTTAT
* *
500042 TGGATTATGATATGAGTTTAAGTGTGAATAATATTTTTAT
1 TGGATTATGATAAGAGTTTAAGTGTGAAGAATATTTTTAT
500082 TG
1 TG
500084 ATTTATGTAG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (40 bp):
TGGATTATGATAAGAGTTTAAGTGTGAAGAATATTTTTAT
Found at i:500737 original size:18 final size:18
Alignment explanation
Indices: 500714--500756 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
500704 CTTTAGATTA
*
500714 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTATCT
*
500732 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
500750 TTTATTT
1 TTTATTT
500757 TAAAAAACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:504690 original size:86 final size:87
Alignment explanation
Indices: 504576--504774 Score: 280
Period size: 86 Copynumber: 2.3 Consensus size: 87
504566 AGGAACATCT
* * *
504576 CACATGACTTTCCCATG-AAGGGGAGTCATCCAAAGATCATCTCACCTGGTTCAGACCTGCGAAG
1 CACATGACTTTCCCGTGAAAGGGGAGTCATCCAAAGATCATATCACCTGGTTCAGACCCGCGAAG
*
504640 GGGAACCACCTGAAGAATATAC
66 GCGAACCACCTGAAGAATATAC
* * * *
504662 TACATGACTTTCCCGTGAAAGGGG-GTCATTCAAAGATCATATCACTTGGTTTAGACCCGCGAAG
1 CACATGACTTTCCCGTGAAAGGGGAGTCATCCAAAGATCATATCACCTGGTTCAGACCCGCGAAG
504726 GCGAACCACCTGAAGAATATAC
66 GCGAACCACCTGAAGAATATAC
* *
504748 CACTTGGC-TTCCCGT-AAAGGGGAGTCA
1 CACATGACTTTCCCGTGAAAGGGGAGTCA
504775 ACTAAAGAAT
Statistics
Matches: 100, Mismatches: 11, Indels: 5
0.86 0.09 0.04
Matches are distributed among these distances:
84 7 0.07
85 11 0.11
86 76 0.76
87 6 0.06
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.22
Consensus pattern (87 bp):
CACATGACTTTCCCGTGAAAGGGGAGTCATCCAAAGATCATATCACCTGGTTCAGACCCGCGAAG
GCGAACCACCTGAAGAATATAC
Found at i:505185 original size:200 final size:200
Alignment explanation
Indices: 504837--505524 Score: 1018
Period size: 200 Copynumber: 3.4 Consensus size: 200
504827 AGAGGAACCG
* * *
504837 TTTACAACATAGCTCAAGGTGAGAAGGGCTATATATCAACAAAACTTTCGAGTTTGATTCCATTC
1 TTTACAACATAGCTCAAGGCGAGAAGGGCTATCTATCAACAAAACTTTCGAGTTCGATTCCATTC
*
504902 AGCTCGAAGGCATATCAACCGCATGGTAGCAACGATGAACTACTTTTCGGTTGAAGTTTAAACCG
66 AGCTCGAAGGCATATCAACCGCATGGTAGCAACGAGGAACTACTTTTCGGTTGAAGTTTAAACCG
* * *
504967 AGGTCTTTAAGTCAAGAAGAAGACCTAGGTTGACTGCGATTTAGCAACAAGGAACTATCTCCCAT
131 AGGTCTTTAAGTCAAGAAGAAGACCTAGGTTGGCTGCGATTTACCAACAAGGAACTATCTCCCAG
*
505032 CTGAG
196 CTGAA
* * * * * * * * *
505037 TTTACAGCATAGCTCAAGGCAAGAATGGCTATCTGTCAACAAAACTTTCGCGTTTGGTACCATTT
1 TTTACAACATAGCTCAAGGCGAGAAGGGCTATCTATCAACAAAACTTTCGAGTTCGATTCCATTC
* * * * *
505102 AGCTCAAAAGCATATCAACCGTATGGTAGCAACGAGGAACTATTTTTCGGTTAAAGTTTAAACCG
66 AGCTCGAAGGCATATCAACCGCATGGTAGCAACGAGGAACTACTTTTCGGTTGAAGTTTAAACCG
* *
505167 AGGTCTTTAAGCCAAGAAGAAGACCTAGGTTGGCTGCGATTTACCAACAATGAACTATCTCCCAG
131 AGGTCTTTAAGTCAAGAAGAAGACCTAGGTTGGCTGCGATTTACCAACAAGGAACTATCTCCCAG
*
505232 CCGAA
196 CTGAA
* * * *
505237 TTTACAACATATCTTAAGGCGAGACGGGCTATCTGTCAACAAAACTTTCGAGTTCGATTCCATTC
1 TTTACAACATAGCTCAAGGCGAGAAGGGCTATCTATCAACAAAACTTTCGAGTTCGATTCCATTC
* *
505302 AGCTCGAAGGTATATCAACCGCATGGTAGCAACGAGGAACTACTTTCCGGTTGAAGTTTAAACCG
66 AGCTCGAAGGCATATCAACCGCATGGTAGCAACGAGGAACTACTTTTCGGTTGAAGTTTAAACCG
* * ** **
505367 AGGTCTTTAAATTAAGAAGAAGGTCTAGGTTGGCTGCGATTTATTAACAAGGAACTATCTCCCAG
131 AGGTCTTTAAGTCAAGAAGAAGACCTAGGTTGGCTGCGATTTACCAACAAGGAACTATCTCCCAG
505432 CTGAA
196 CTGAA
* *
505437 TTTACAGCATAGCTCAAGACGAGAAGGG-TATCTATCAACAAAACTTTCGAGTTCGATTCCATTC
1 TTTACAACATAGCTCAAGGCGAGAAGGGCTATCTATCAACAAAACTTTCGAGTTCGATTCCATTC
505501 AGCTCGAAGGCATATCAACCGCAT
66 AGCTCGAAGGCATATCAACCGCAT
505525 AGGTTGGATG
Statistics
Matches: 431, Mismatches: 57, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
199 58 0.13
200 373 0.87
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.26
Consensus pattern (200 bp):
TTTACAACATAGCTCAAGGCGAGAAGGGCTATCTATCAACAAAACTTTCGAGTTCGATTCCATTC
AGCTCGAAGGCATATCAACCGCATGGTAGCAACGAGGAACTACTTTTCGGTTGAAGTTTAAACCG
AGGTCTTTAAGTCAAGAAGAAGACCTAGGTTGGCTGCGATTTACCAACAAGGAACTATCTCCCAG
CTGAA
Found at i:506635 original size:18 final size:18
Alignment explanation
Indices: 506612--506651 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
506602 TAGATTATTT
*
506612 ATTTAATTATTTTCTTTC
1 ATTTAATTATTATCTTTC
* *
506630 ATTTAATTCTTATCTTTT
1 ATTTAATTATTATCTTTC
506648 ATTT
1 ATTT
506652 TAAAAACAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.68
Consensus pattern (18 bp):
ATTTAATTATTATCTTTC
Found at i:506842 original size:84 final size:83
Alignment explanation
Indices: 506733--506895 Score: 195
Period size: 84 Copynumber: 2.0 Consensus size: 83
506723 ATTTTCTTTA
** * ** * * *
506733 AAATTTAACATTTCTTTTTTTATTTT-ATTTTGTTTT-ATTTTTATTTTTTAACATTTTTTATAT
1 AAATTTAACATTTCTTCATTTATTTTAATTTTCTTTTAACATTT-TTATATAACATTTTTTA-AA
*
506796 TTTATTATTTTTCTTTTCTG
64 TTTAATATTTTTCTTTTCTG
*
506816 AAATTTAATATTTTCTTCATTTATTTTAATTTTCTTTTAACATTTTTATATAACATTTTTTAAAT
1 AAATTTAACA-TTTCTTCATTTATTTTAATTTTCTTTTAACATTTTTATATAACATTTTTTAAAT
506881 TTAATATTTTTCTTT
65 TTAATATTTTTCTTT
506896 GATTTTTTTT
Statistics
Matches: 67, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
83 9 0.13
84 30 0.45
85 24 0.36
86 4 0.06
ACGTcount: A:0.25, C:0.07, G:0.01, T:0.67
Consensus pattern (83 bp):
AAATTTAACATTTCTTCATTTATTTTAATTTTCTTTTAACATTTTTATATAACATTTTTTAAATT
TAATATTTTTCTTTTCTG
Found at i:506890 original size:29 final size:29
Alignment explanation
Indices: 506851--506914 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
506841 TTAATTTTCT
*
506851 TTTAACATTTTTATATAACATTTTTTAAA
1 TTTAATATTTTTATATAACATTTTTTAAA
* * * **
506880 TTTAATATTTTTCTTTGATTTTTTTTAAA
1 TTTAATATTTTTATATAACATTTTTTAAA
506909 TTTAAT
1 TTTAAT
506915 TTGATATTTC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (29 bp):
TTTAATATTTTTATATAACATTTTTTAAA
Found at i:507261 original size:20 final size:20
Alignment explanation
Indices: 507232--507270 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
507222 AGAGCTCATA
*
507232 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
507252 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
507271 GTGGTAGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:509496 original size:15 final size:15
Alignment explanation
Indices: 509447--509490 Score: 79
Period size: 15 Copynumber: 2.9 Consensus size: 15
509437 AACTATGTGG
509447 GCAACTACAATCGAC
1 GCAACTACAATCGAC
509462 GCAACTACAATCGAC
1 GCAACTACAATCGAC
*
509477 GCAACTATAATCGA
1 GCAACTACAATCGA
509491 TACAACAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.41, C:0.30, G:0.14, T:0.16
Consensus pattern (15 bp):
GCAACTACAATCGAC
Found at i:512996 original size:14 final size:14
Alignment explanation
Indices: 512977--513003 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
512967 ATTAAATAAA
512977 AAAAGAAAAAAAAG
1 AAAAGAAAAAAAAG
512991 AAAAGAAAAAAAA
1 AAAAGAAAAAAAA
513004 TACGGGAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAAAAG
Found at i:516910 original size:31 final size:31
Alignment explanation
Indices: 516875--516953 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
516865 TCAACATCCT
*
516875 AGTGATCAAAATGTTATAAATCAATAATATC
1 AGTGATCAAAATGTTATAAATCAATAACATC
** * *
516906 AGTGATCAAAACATTATAAATCGATAACATT
1 AGTGATCAAAATGTTATAAATCAATAACATC
*
516937 AGTTATCAAAATGTTAT
1 AGTGATCAAAATGTTAT
516954 TTTTTAACAT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.33
Consensus pattern (31 bp):
AGTGATCAAAATGTTATAAATCAATAACATC
Found at i:517560 original size:15 final size:16
Alignment explanation
Indices: 517521--517552 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
517511 TTTAACTTAT
*
517521 ATTAATTATAATAAAA
1 ATTAAATATAATAAAA
517537 ATTAAATATAATAAAA
1 ATTAAATATAATAAAA
517553 TTTCATATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
ATTAAATATAATAAAA
Found at i:525769 original size:21 final size:20
Alignment explanation
Indices: 525745--525799 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 20
525735 ACTTATTGTT
525745 TATTATGATTATTTGAAAAAA
1 TATTAT-ATTATTTGAAAAAA
525766 TATTATACTAATTATTTGAAAAAA
1 TA-T-TA-T-ATTATTTGAAAAAA
525790 TATTATATTA
1 TATTATATTA
525800 ATTATTTTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 4 0.13
21 3 0.10
22 3 0.10
23 3 0.10
24 17 0.57
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.45
Consensus pattern (20 bp):
TATTATATTATTTGAAAAAA
Found at i:525779 original size:24 final size:24
Alignment explanation
Indices: 525752--525806 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
525742 GTTTATTATG
525752 ATTATTTGAAAAAATATTATACTA
1 ATTATTTGAAAAAATATTATACTA
*
525776 ATTATTTGAAAAAATATTATATTA
1 ATTATTTGAAAAAATATTATACTA
525800 ATTATTT
1 ATTATTT
525807 TCAATTAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (24 bp):
ATTATTTGAAAAAATATTATACTA
Found at i:531522 original size:17 final size:18
Alignment explanation
Indices: 531481--531519 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
531471 ATTATATAAG
531481 TAAAATA-TTAAATAAAT
1 TAAAATACTTAAATAAAT
531498 TAAAATACTTAAATAAAT
1 TAAAATACTTAAATAAAT
531516 TAAA
1 TAAA
531520 TACAAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAATACTTAAATAAAT
Found at i:532263 original size:16 final size:16
Alignment explanation
Indices: 532242--532273 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
532232 TTATTAATTA
*
532242 AATTTTTTAATATAAT
1 AATTTTTTAAGATAAT
532258 AATTTTTTAAGATAAT
1 AATTTTTTAAGATAAT
532274 TATTAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
AATTTTTTAAGATAAT
Found at i:534292 original size:34 final size:32
Alignment explanation
Indices: 534253--534344 Score: 87
Period size: 33 Copynumber: 2.8 Consensus size: 32
534243 AATTAATAAT
534253 TATAAATAAATAATAATTATATAAATATTATTTTAA
1 TATAAA-AAATAATAATTATATAAATA-TA--TTAA
* * *
534289 TA-AAAATATAATATTTACATAAATATATTAA
1 TATAAAAAATAATAATTATATAAATATATTAA
* *
534320 TATAAAAAAATAATAACTATTTAAA
1 TAT-AAAAAATAATAATTATATAAA
534345 AAAATACTAA
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
31 6 0.13
33 18 0.39
34 17 0.37
35 3 0.07
36 2 0.04
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (32 bp):
TATAAAAAATAATAATTATATAAATATATTAA
Found at i:534310 original size:19 final size:18
Alignment explanation
Indices: 534240--534350 Score: 69
Period size: 17 Copynumber: 6.4 Consensus size: 18
534230 AATTAGCAAA
*
534240 AAAAAT-TAATAATT-AT
1 AAAAATATAATATTTAAT
*
534256 AAATAA-ATAATAATT-AT
1 AAA-AATATAATATTTAAT
* *
534273 ATAAATATTAT-TTTAAT
1 AAAAATATAATATTTAAT
534290 AAAAATATAATATTTACAT
1 AAAAATATAATATTTA-AT
*
534309 AAATATATTAATA--TAA-
1 AAAAATA-TAATATTTAAT
534325 AAAAATAATAACTATTTAA-
1 AAAAAT-ATAA-TATTTAAT
534344 AAAAATA
1 AAAAATA
534351 CTAACATAAA
Statistics
Matches: 77, Mismatches: 7, Indels: 20
0.74 0.07 0.19
Matches are distributed among these distances:
16 15 0.19
17 33 0.43
18 7 0.09
19 17 0.22
20 5 0.06
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (18 bp):
AAAAATATAATATTTAAT
Done.