Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008092.1 Hibiscus syriacus cultivar Beakdansim tig00110607_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: 2324158
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 12
Found at i:315352 original size:98 final size:98
Alignment explanation
Indices: 315179--315375 Score: 385
Period size: 98 Copynumber: 2.0 Consensus size: 98
315169 AATTGAGAGA
315179 GGAGCTTAATCAAATCAGGCCGTGGAGAACAAAGAGCCTCCAATGGCATAGCCTTGGACAAAGTT
1 GGAGCTTAATCAAATCAGGCCGTGGAGAACAAAGAGCCTCCAATGGCATAGCCTTGGACAAAGTT
*
315244 GGTCCGGTACCTGGTCTCATATCTACAGTATCT
66 GGTCCAGTACCTGGTCTCATATCTACAGTATCT
315277 GGAGCTTAATCAAATCAGGCCGTGGAGAACAAAGAGCCTCCAATGGCATAGCCTTGGACAAAGTT
1 GGAGCTTAATCAAATCAGGCCGTGGAGAACAAAGAGCCTCCAATGGCATAGCCTTGGACAAAGTT
315342 GGTCCAGTACCTGGTCTCATATCTACAGTATCT
66 GGTCCAGTACCTGGTCTCATATCTACAGTATCT
315375 G
1 G
315376 ACCCTACATT
Statistics
Matches: 98, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
98 98 1.00
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.23
Consensus pattern (98 bp):
GGAGCTTAATCAAATCAGGCCGTGGAGAACAAAGAGCCTCCAATGGCATAGCCTTGGACAAAGTT
GGTCCAGTACCTGGTCTCATATCTACAGTATCT
Found at i:324541 original size:53 final size:51
Alignment explanation
Indices: 324453--324568 Score: 180
Period size: 53 Copynumber: 2.2 Consensus size: 51
324443 TAACTAGATA
324453 TTTTATTCTGTTAGTTATTAGATAGGATCTATTTTAATTAGATAGAATCAG
1 TTTTATTCTGTTAGTTATTAGATAGGATCTATTTTAATTAGATAGAATCAG
* *
324504 TTTTTTATTCTGTTAGTTATTAGATATGAT-TAGTTTTAATTAGATATAATCAG
1 --TTTTATTCTGTTAGTTATTAGATAGGATCTA-TTTTAATTAGATAGAATCAG
324557 TTTTATTCTGTT
1 TTTTATTCTGTT
324569 GCTAATTTTA
Statistics
Matches: 60, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
51 12 0.20
52 2 0.03
53 46 0.77
ACGTcount: A:0.28, C:0.05, G:0.14, T:0.53
Consensus pattern (51 bp):
TTTTATTCTGTTAGTTATTAGATAGGATCTATTTTAATTAGATAGAATCAG
Found at i:324547 original size:20 final size:20
Alignment explanation
Indices: 324522--324561 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
324512 TCTGTTAGTT
* *
324522 ATTAGATATGATTAGTTTTA
1 ATTAGATATAATCAGTTTTA
324542 ATTAGATATAATCAGTTTTA
1 ATTAGATATAATCAGTTTTA
324562 TTCTGTTGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (20 bp):
ATTAGATATAATCAGTTTTA
Found at i:329163 original size:20 final size:20
Alignment explanation
Indices: 329138--329177 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
329128 TCTGTTAGTT
*
329138 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
329158 ATTAGATAGAATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
329178 TTCTGTTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.17, T:0.40
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:339210 original size:176 final size:176
Alignment explanation
Indices: 338916--339447 Score: 1064
Period size: 176 Copynumber: 3.0 Consensus size: 176
338906 TTGATCAACA
338916 ACAATGACTAAAGGAGTTGACATCTTTTTGTAGAAAAACAAGAAAGAAACAGTCACCTCATCATG
1 ACAATGACTAAAGGAGTTGACATCTTTTTGTAGAAAAACAAGAAAGAAACAGTCACCTCATCATG
338981 TCATTAACGACTTAATGTGTCGTTAATGTCACAATGCATGCCCTAATTAAACTTAAAACTCAAAT
66 TCATTAACGACTTAATGTGTCGTTAATGTCACAATGCATGCCCTAATTAAACTTAAAACTCAAAT
339046 TTAGCGCTTATATTAAAATGTTTTAAAATCCAACGCTAAAATCAAT
131 TTAGCGCTTATATTAAAATGTTTTAAAATCCAACGCTAAAATCAAT
339092 ACAATGACTAAAGGAGTTGACATCTTTTTGTAGAAAAACAAGAAAGAAACAGTCACCTCATCATG
1 ACAATGACTAAAGGAGTTGACATCTTTTTGTAGAAAAACAAGAAAGAAACAGTCACCTCATCATG
339157 TCATTAACGACTTAATGTGTCGTTAATGTCACAATGCATGCCCTAATTAAACTTAAAACTCAAAT
66 TCATTAACGACTTAATGTGTCGTTAATGTCACAATGCATGCCCTAATTAAACTTAAAACTCAAAT
339222 TTAGCGCTTATATTAAAATGTTTTAAAATCCAACGCTAAAATCAAT
131 TTAGCGCTTATATTAAAATGTTTTAAAATCCAACGCTAAAATCAAT
339268 ACAATGACTAAAGGAGTTGACATCTTTTTGTAGAAAAACAAGAAAGAAACAGTCACCTCATCATG
1 ACAATGACTAAAGGAGTTGACATCTTTTTGTAGAAAAACAAGAAAGAAACAGTCACCTCATCATG
339333 TCATTAACGACTTAATGTGTCGTTAATGTCACAATGCATGCCCTAATTAAACTTAAAACTCAAAT
66 TCATTAACGACTTAATGTGTCGTTAATGTCACAATGCATGCCCTAATTAAACTTAAAACTCAAAT
339398 TTAGCGCTTATATTAAAATGTTTTAAAATCCAACGCTAAAATCAAT
131 TTAGCGCTTATATTAAAATGTTTTAAAATCCAACGCTAAAATCAAT
339444 ACAA
1 ACAA
339448 AGTCTAAAAT
Statistics
Matches: 356, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
176 356 1.00
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (176 bp):
ACAATGACTAAAGGAGTTGACATCTTTTTGTAGAAAAACAAGAAAGAAACAGTCACCTCATCATG
TCATTAACGACTTAATGTGTCGTTAATGTCACAATGCATGCCCTAATTAAACTTAAAACTCAAAT
TTAGCGCTTATATTAAAATGTTTTAAAATCCAACGCTAAAATCAAT
Found at i:341594 original size:33 final size:32
Alignment explanation
Indices: 341557--341623 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
341547 AATTTCGGGA
** *
341557 TCGGGCCGGGTCGGGTTTTTTTAAGTTTGATAT
1 TCGGGCCGGGTC-AATTTTTTTAAGTGTGATAT
*
341590 TCGGGTCGGGTCAATTTTTTTAAGTGTGATAT
1 TCGGGCCGGGTCAATTTTTTTAAGTGTGATAT
341622 TC
1 TC
341624 AGATCGGGTC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 19 0.63
33 11 0.37
ACGTcount: A:0.15, C:0.12, G:0.30, T:0.43
Consensus pattern (32 bp):
TCGGGCCGGGTCAATTTTTTTAAGTGTGATAT
Found at i:341608 original size:32 final size:32
Alignment explanation
Indices: 341572--341633 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
341562 CCGGGTCGGG
* * *
341572 TTTTTTTAAGTTTGATATTCGGGTCGGGTCAA
1 TTTTTTTAAGTGTGATATTCAGATCGGGTCAA
341604 TTTTTTTAAGTGTGATATTCAGATCGGGTC
1 TTTTTTTAAGTGTGATATTCAGATCGGGTC
341634 GGTGTCGGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.19, C:0.10, G:0.24, T:0.47
Consensus pattern (32 bp):
TTTTTTTAAGTGTGATATTCAGATCGGGTCAA
Found at i:342184 original size:17 final size:17
Alignment explanation
Indices: 342162--342210 Score: 89
Period size: 17 Copynumber: 2.9 Consensus size: 17
342152 GTTTCAGATT
342162 CATATTTCAATTCCTAA
1 CATATTTCAATTCCTAA
342179 CATATTTCAATTCCTAA
1 CATATTTCAATTCCTAA
*
342196 CATATTCCAATTCCT
1 CATATTTCAATTCCT
342211 TCACAGATTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.33, C:0.27, G:0.00, T:0.41
Consensus pattern (17 bp):
CATATTTCAATTCCTAA
Found at i:342222 original size:18 final size:17
Alignment explanation
Indices: 342169--342227 Score: 73
Period size: 17 Copynumber: 3.4 Consensus size: 17
342159 ATTCATATTT
* *
342169 CAATTCCTAACATATTT
1 CAATTCCTAACAGATTC
*
342186 CAATTCCTAACATATTC
1 CAATTCCTAACAGATTC
*
342203 CAATTCCTTCACAGATTC
1 CAATTCC-TAACAGATTC
342221 CAATTCC
1 CAATTCC
342228 CTCATAAACA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
17 23 0.61
18 15 0.39
ACGTcount: A:0.32, C:0.31, G:0.02, T:0.36
Consensus pattern (17 bp):
CAATTCCTAACAGATTC
Found at i:343511 original size:18 final size:17
Alignment explanation
Indices: 343477--343515 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
343467 GAAAAGGAAG
* *
343477 AAAAAAATAGACTAAAT
1 AAAAAAATAAACAAAAT
343494 AAAAAATATAAACAAAAT
1 AAAAAA-ATAAACAAAAT
343512 AAAA
1 AAAA
343516 CATAAATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.77, C:0.05, G:0.03, T:0.15
Consensus pattern (17 bp):
AAAAAAATAAACAAAAT
Found at i:343730 original size:28 final size:29
Alignment explanation
Indices: 343664--343739 Score: 93
Period size: 28 Copynumber: 2.7 Consensus size: 29
343654 AAAGTAATAA
* *
343664 AAAACAAACAAAATAAAGATAGTCAAAAT
1 AAAACAAATAAAATAAAAATAGTCAAAAT
343693 AAAACAAATAAAA-AAAAATAGTCAAAAT
1 AAAACAAATAAAATAAAAATAGTCAAAAT
* *
343721 ATATAC-AATAATATAAAAA
1 A-AAACAAATAAAATAAAAA
343740 GGATAAATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
28 21 0.51
29 20 0.49
ACGTcount: A:0.71, C:0.08, G:0.04, T:0.17
Consensus pattern (29 bp):
AAAACAAATAAAATAAAAATAGTCAAAAT
Found at i:344931 original size:19 final size:17
Alignment explanation
Indices: 344903--344973 Score: 53
Period size: 19 Copynumber: 4.2 Consensus size: 17
344893 GAAAAAAATG
344903 TAAATAAATATACTATATA
1 TAAATAAATATA-TA-ATA
*
344922 TAAATGAATATATAATA
1 TAAATAAATATATAATA
344939 T-AAT---T-TATAATA
1 TAAATAAATATATAATA
344951 TAAATAGATATTATATAATA
1 TAAATA-A-A-TATATAATA
344971 TAA
1 TAA
344974 GGACGAAATT
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
12 8 0.19
13 4 0.09
16 3 0.07
17 4 0.09
18 2 0.05
19 12 0.28
20 10 0.23
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.39
Consensus pattern (17 bp):
TAAATAAATATATAATA
Found at i:344964 original size:18 final size:17
Alignment explanation
Indices: 344931--344973 Score: 50
Period size: 20 Copynumber: 2.4 Consensus size: 17
344921 ATAAATGAAT
344931 ATATAATATAATTTATA
1 ATATAATATAATTTATA
*
344948 ATATAAATAGATATTATATA
1 ATAT-AATATA-ATT-TATA
344968 ATATAA
1 ATATAA
344974 GGACGAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 4 0.18
18 5 0.23
19 5 0.23
20 8 0.36
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
ATATAATATAATTTATA
Found at i:346951 original size:6 final size:6
Alignment explanation
Indices: 346936--346968 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
346926 CCCACCTTAT
*
346936 TTTTTC TTTTTG TTTTTG TTTTTG TTTTT- TTTT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTT
346969 CCTCTCTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.00, C:0.03, G:0.09, T:0.88
Consensus pattern (6 bp):
TTTTTG
Found at i:352879 original size:21 final size:21
Alignment explanation
Indices: 352853--352897 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
352843 GATTTCTGGG
* *
352853 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
352874 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
352895 CAA
1 CAA
352898 ATGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:354270 original size:32 final size:32
Alignment explanation
Indices: 354229--354325 Score: 119
Period size: 32 Copynumber: 3.1 Consensus size: 32
354219 GAGTCGAGGG
*
354229 TTTACCTATGTTCTACGGAACATATAGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
*
354261 TTTACCTATG-TCTTTC-GAGACATATGGACAG-
1 TTTACCTATGTTC-TACGGA-ACATATGGACAGT
* *
354292 TATACCTATGTTCTAAGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
354324 TT
1 TT
354326 ACCGAGGATC
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
31 26 0.48
32 28 0.52
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.35
Consensus pattern (32 bp):
TTTACCTATGTTCTACGGAACATATGGACAGT
Found at i:354301 original size:31 final size:31
Alignment explanation
Indices: 354228--354328 Score: 116
Period size: 31 Copynumber: 3.2 Consensus size: 31
354218 AGAGTCGAGG
*
354228 GTTTACCTATGTTCT-ACGGAACATATAGACA
1 GTTTACCTATGTTCTAAC-GAACATATGGACA
**
354259 GTTTTACCTATG-TCTTTCGAGACATATGGACA
1 G-TTTACCTATGTTCTAACGA-ACATATGGACA
* *
354291 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTAACGAACATATGGACA
354322 GTTTACC
1 GTTTACC
354329 GAGGATCTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
31 32 0.54
32 27 0.46
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTAACGAACATATGGACA
Found at i:354360 original size:30 final size:30
Alignment explanation
Indices: 354316--354389 Score: 130
Period size: 30 Copynumber: 2.4 Consensus size: 30
354306 AAGGAACATA
354316 TGGACAGTTTACCGAGGATCTTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
354347 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
*
354377 TGGATAGTTACCG
1 TGGACAGTTACCG
354390 GGGTATGTGT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
30 35 0.83
31 7 0.17
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:354410 original size:29 final size:30
Alignment explanation
Indices: 354324--354412 Score: 108
Period size: 30 Copynumber: 3.0 Consensus size: 30
354314 TATGGACAGT
* * *
354324 TTACCGAGGATCTTTATGACCTCTGGACAG
1 TTACCGAGGATATGTATGACCTCTGGATAG
* *
354354 TTACCGAGGATCTTTATGACCTCTGGATAG
1 TTACCGAGGATATGTATGACCTCTGGATAG
* *
354384 TTACCG-GGGTATGTGTGACCTCTGGATAG
1 TTACCGAGGATATGTATGACCTCTGGATAG
354413 GTCCTTCGGG
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 19 0.35
30 35 0.65
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.31
Consensus pattern (30 bp):
TTACCGAGGATATGTATGACCTCTGGATAG
Found at i:357133 original size:21 final size:21
Alignment explanation
Indices: 357107--357151 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
357097 GATTTCTGGG
* *
357107 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
357128 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
357149 CAA
1 CAA
357152 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:358522 original size:32 final size:32
Alignment explanation
Indices: 358481--358577 Score: 119
Period size: 32 Copynumber: 3.1 Consensus size: 32
358471 GAGTCGAGGG
*
358481 TTTACCTATGTTCTACGGAACATATAGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
*
358513 TTTACCTATG-TCTTTC-GAGACATATGGACAG-
1 TTTACCTATGTTC-TACGGA-ACATATGGACAGT
* *
358544 TATACCTATGTTCTAAGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
358576 TT
1 TT
358578 ACCGAGGATC
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
31 26 0.48
32 28 0.52
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.35
Consensus pattern (32 bp):
TTTACCTATGTTCTACGGAACATATGGACAGT
Found at i:358553 original size:31 final size:31
Alignment explanation
Indices: 358480--358580 Score: 116
Period size: 31 Copynumber: 3.2 Consensus size: 31
358470 AGAGTCGAGG
*
358480 GTTTACCTATGTTCT-ACGGAACATATAGACA
1 GTTTACCTATGTTCTAAC-GAACATATGGACA
**
358511 GTTTTACCTATG-TCTTTCGAGACATATGGACA
1 G-TTTACCTATGTTCTAACGA-ACATATGGACA
* *
358543 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTAACGAACATATGGACA
358574 GTTTACC
1 GTTTACC
358581 GAGGATCTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
31 32 0.54
32 27 0.46
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTAACGAACATATGGACA
Found at i:358612 original size:30 final size:30
Alignment explanation
Indices: 358568--358661 Score: 127
Period size: 30 Copynumber: 3.1 Consensus size: 30
358558 AAGGAACATA
358568 TGGACAGTTTACCGAGGATCTTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
358599 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * * * *
358629 TGGATAGTTATCG-GGGTCTGTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
358658 TGGA
1 TGGA
358662 TAGGTCCTTC
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
29 17 0.29
30 34 0.59
31 7 0.12
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.32
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:364614 original size:27 final size:28
Alignment explanation
Indices: 364569--364626 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
364559 AGGGGTGCAC
*
364569 AAAAAATCCGAATATCCGATTTTGCGAA
1 AAAAAATCCGAATATCCGAATTTGCGAA
*
364597 AAAAATATCCGAA-A-CCGAATTTGGGAA
1 AAAAA-ATCCGAATATCCGAATTTGCGAA
364624 AAA
1 AAA
364627 CCGATTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 14 0.52
28 6 0.22
29 7 0.26
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.21
Consensus pattern (28 bp):
AAAAAATCCGAATATCCGAATTTGCGAA
Found at i:364673 original size:13 final size:13
Alignment explanation
Indices: 364655--364679 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
364645 ATCTGATTTG
364655 TTTTAACCGGTTA
1 TTTTAACCGGTTA
364668 TTTTAACCGGTT
1 TTTTAACCGGTT
364680 TGGAGAAAAA
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:0.20, C:0.16, G:0.16, T:0.48
Consensus pattern (13 bp):
TTTTAACCGGTTA
Found at i:367056 original size:21 final size:21
Alignment explanation
Indices: 367032--367073 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
367022 AGTTTATTTT
367032 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
367053 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
367074 AACTTGAAGT
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:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:367122 original size:33 final size:32
Alignment explanation
Indices: 367068--367166 Score: 153
Period size: 33 Copynumber: 3.0 Consensus size: 32
367058 TTTGTTTCAA
367068 TTATCGAACTTGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGAAGTTTTTAAGTATTTGAAT
367100 TTATCGAACTTGAAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTG-AAGTTTTTAAGTATTTGAAT
* * *
367133 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
367166 T
1 T
367167 ATGTTGAGTT
Statistics
Matches: 62, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
32 12 0.19
33 49 0.79
34 1 0.02
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.45
Consensus pattern (32 bp):
TTATCGAACTTGAAGTTTTTAAGTATTTGAAT
Found at i:367195 original size:13 final size:13
Alignment explanation
Indices: 367152--367206 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
367142 TTGGAAGTAT
367152 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
367165 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
367179 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
367192 TTAAGTATTTGAA
1 TTAAGTATTTCAA
367205 TT
1 TT
367207 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:367909 original size:15 final size:15
Alignment explanation
Indices: 367882--367937 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
367872 TTTAATAATA
*
367882 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
367897 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
*
367912 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
367929 TTAAAACCG
1 TTAAAACCG
367938 AAACCGGTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 21 0.62
17 13 0.38
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:367946 original size:21 final size:18
Alignment explanation
Indices: 367901--367934 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
367891 GTTTTTTTAT
367901 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
367918 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
367935 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:377364 original size:146 final size:147
Alignment explanation
Indices: 377100--377394 Score: 574
Period size: 146 Copynumber: 2.0 Consensus size: 147
377090 GAAAAAAGCT
377100 TCCAGCCTGGGGTGATATTAATTATAGCCGCAACTGGAAACAAATAATATAAAAGCTACCAGCCA
1 TCCAGCCTGGGGTGATATTAATTATAGCCGCAACTGGAAACAAATAATATAAAAGCTACCAGCCA
377165 CGTAGTGACTTTTTTTACCGATGACATCATCCAATGTTTTCATGTGCTCCTTCGTGCTC-AAATA
66 CGTAGTGACTTTTTTTACCGATGACATCATCCAATGTTTTCATGTGCTCCTTCGTGCTCAAAATA
377229 TATGAACCGATGCTGCC
131 TATGAACCGATGCTGCC
377246 TCCAGCCTGGGGTGATATTAATTATAGCCGCAACTGGAAACAAATAATATAAAAGCTACCAGCCA
1 TCCAGCCTGGGGTGATATTAATTATAGCCGCAACTGGAAACAAATAATATAAAAGCTACCAGCCA
377311 CGTAGTGACTTTTTTTACCGATGACATCATCCAATGTTTTCATGTGCTCCTTCGTGCTCATAAAT
66 CGTAGTGACTTTTTTTACCGATGACATCATCCAATGTTTTCATGTGCTCCTTCGTGCTCA-AAAT
377376 ATATGAACCGATGCTGCC
130 ATATGAACCGATGCTGCC
377394 T
1 T
377395 GCGTCTATAA
Statistics
Matches: 147, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
146 124 0.84
148 23 0.16
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (147 bp):
TCCAGCCTGGGGTGATATTAATTATAGCCGCAACTGGAAACAAATAATATAAAAGCTACCAGCCA
CGTAGTGACTTTTTTTACCGATGACATCATCCAATGTTTTCATGTGCTCCTTCGTGCTCAAAATA
TATGAACCGATGCTGCC
Found at i:381568 original size:2 final size:2
Alignment explanation
Indices: 381561--381590 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
381551 CATTTTATTA
381561 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
381591 CAATTTATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:388435 original size:15 final size:16
Alignment explanation
Indices: 388403--388435 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
388393 AAAATCTTTC
388403 TTTCCCGTTCTAGATT
1 TTTCCCGTTCTAGATT
*
388419 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTAGATT
388434 TT
1 TT
388436 GATCTGCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.09, C:0.24, G:0.15, T:0.52
Consensus pattern (16 bp):
TTTCCCGTTCTAGATT
Found at i:389212 original size:16 final size:17
Alignment explanation
Indices: 389185--389219 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
389175 TATCGCCGAC
389185 CGAAATTTCACTATTCA
1 CGAAATTTCACTATTCA
389202 CGAAA-TTCACTATTCA
1 CGAAATTTCACTATTCA
389218 CG
1 CG
389220 TGAATAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.34, C:0.26, G:0.09, T:0.31
Consensus pattern (17 bp):
CGAAATTTCACTATTCA
Found at i:390528 original size:35 final size:35
Alignment explanation
Indices: 390487--390557 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
390477 AAGAAATAAG
* * *
390487 TTTATGGGCCCTACTTTTAATTTAGTTTATTAATA
1 TTTATGGACCATACTTTTAATTTAGTATATTAATA
*
390522 TTTATGGACCATGCTTTTAATTTAGTATATTAATA
1 TTTATGGACCATACTTTTAATTTAGTATATTAATA
390557 T
1 T
390558 AATTTTTAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.28, C:0.10, G:0.11, T:0.51
Consensus pattern (35 bp):
TTTATGGACCATACTTTTAATTTAGTATATTAATA
Found at i:396885 original size:36 final size:36
Alignment explanation
Indices: 396838--396908 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
396828 CACAAGAGAT
*
396838 AATAATAACATTAATACGATCAATGAAGGTTAAATC
1 AATAATAACATTAATACGATCAATGAAGATTAAATC
396874 AATAATAACATTAATACGATCAATGAAGATTAAAT
1 AATAATAACATTAATACGATCAATGAAGATTAAAT
396909 AAAGGACAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.28
Consensus pattern (36 bp):
AATAATAACATTAATACGATCAATGAAGATTAAATC
Found at i:400795 original size:22 final size:21
Alignment explanation
Indices: 400770--400811 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
400760 TTCTGCCAGG
*
400770 GAACCGATTCCCCTGCTACAGA
1 GAACCGA-TACCCTGCTACAGA
*
400792 GAACTGATACCCTGCTACAG
1 GAACCGATACCCTGCTACAG
400812 TACTGATACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.29, C:0.33, G:0.19, T:0.19
Consensus pattern (21 bp):
GAACCGATACCCTGCTACAGA
Found at i:400818 original size:19 final size:20
Alignment explanation
Indices: 400780--400820 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
400770 GAACCGATTC
400780 CCCTGCTACAGAGAACTGATA
1 CCCTGCTACA-AGAACTGATA
*
400801 CCCTGCTAC-AGTACTGATA
1 CCCTGCTACAAGAACTGATA
400820 C
1 C
400821 AGTACTACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 10 0.53
21 9 0.47
ACGTcount: A:0.29, C:0.32, G:0.17, T:0.22
Consensus pattern (20 bp):
CCCTGCTACAAGAACTGATA
Found at i:401611 original size:31 final size:31
Alignment explanation
Indices: 401570--401740 Score: 114
Period size: 31 Copynumber: 5.5 Consensus size: 31
401560 TAGATCCCGA
* *
401570 AGAACCTAGGTAAATTGTTCATATGTTCCTT
1 AGAACATAGGTAAATTGTCCATATGTTCCTT
* * **
401601 AGAACATAGGTATACTGTCCATATG-TCCCG
1 AGAACATAGGTAAATTGTCCATATGTTCCTT
* * *
401631 AAAGACATAGGTAATTTTGTCCATATGTT-TTGT
1 AGA-ACATAGGTAA-ATTGTCCATATGTTCCT-T
* * * * *
401664 AGAACATAGATATACTGTCCATAT-ATCCTG
1 AGAACATAGGTAAATTGTCCATATGTTCCTT
* *
401694 AAAGACATAGGTAATTATGTCCATATGTTCCTT
1 AGA-ACATAGGTAAAT-TGTCCATATGTTCCTT
* *
401727 AGAATATTGGTAAA
1 AGAACATAGGTAAA
401741 CCCTCGACTC
Statistics
Matches: 100, Mismatches: 32, Indels: 15
0.68 0.22 0.10
Matches are distributed among these distances:
30 8 0.08
31 48 0.48
32 35 0.35
33 9 0.09
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (31 bp):
AGAACATAGGTAAATTGTCCATATGTTCCTT
Found at i:401657 original size:32 final size:32
Alignment explanation
Indices: 401604--401721 Score: 111
Period size: 32 Copynumber: 3.8 Consensus size: 32
401594 GTTCCTTAGA
*
401604 ACATAGGT-A-TACTGTCCATATGTCCCGAAAG
1 ACATAGGTAATTA-TGTCCATATGTCCTGAAAG
* ** *
401635 ACATAGGTAATTTTGTCCATATGTTTTG-TAG
1 ACATAGGTAATTATGTCCATATGTCCTGAAAG
* *
401666 AACATAGAT-A-TACTGTCCATATATCCTGAAAG
1 -ACATAGGTAATTA-TGTCCATATGTCCTGAAAG
401698 ACATAGGTAATTATGTCCATATGT
1 ACATAGGTAATTATGTCCATATGT
401722 TCCTTAGAAT
Statistics
Matches: 67, Mismatches: 13, Indels: 13
0.72 0.14 0.14
Matches are distributed among these distances:
30 1 0.01
31 30 0.45
32 33 0.49
33 3 0.04
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (32 bp):
ACATAGGTAATTATGTCCATATGTCCTGAAAG
Found at i:401730 original size:63 final size:62
Alignment explanation
Indices: 401552--401730 Score: 227
Period size: 63 Copynumber: 2.9 Consensus size: 62
401542 AACTTCAGTA
* * * * * *
401552 ACTGTCAATAGATCCCG-AAGAACCTAGGTAAATTGTTCATATGTTCCTTAGAACATAGGTAT
1 ACTGTCCATATATCCCGAAAG-ACATAGGTAATTTGTCCATATGTTCCTTAGAACATAGATAT
* *
401614 ACTGTCCATATGTCCCGAAAGACATAGGTAATTTTGTCCATATGTT-TTGTAGAACATAGATAT
1 ACTGTCCATATATCCCGAAAGACATAGGTAA-TTTGTCCATATGTTCCT-TAGAACATAGATAT
*
401677 ACTGTCCATATATCCTGAAAGACATAGGTAATTATGTCCATATGTTCCTTAGAA
1 ACTGTCCATATATCCCGAAAGACATAGGTAATT-TGTCCATATGTTCCTTAGAA
401731 TATTGGTAAA
Statistics
Matches: 101, Mismatches: 11, Indels: 9
0.83 0.09 0.07
Matches are distributed among these distances:
62 26 0.26
63 74 0.73
64 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (62 bp):
ACTGTCCATATATCCCGAAAGACATAGGTAATTTGTCCATATGTTCCTTAGAACATAGATAT
Found at i:403006 original size:20 final size:23
Alignment explanation
Indices: 402942--403006 Score: 64
Period size: 24 Copynumber: 2.9 Consensus size: 23
402932 CATCAATGCA
*
402942 TAAGGAGTGCATCGATGCACATGT
1 TAAGGAATGCATCGATGCAC-TGT
* * *
402966 TAAGGGATGCATCGGTACACTG-
1 TAAGGAATGCATCGATGCACTGT
402988 T-A-GAATGCATCGATGCACT
1 TAAGGAATGCATCGATGCACT
403007 TCAAGGGGAA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
20 14 0.41
21 1 0.03
22 1 0.03
23 2 0.06
24 16 0.47
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.25
Consensus pattern (23 bp):
TAAGGAATGCATCGATGCACTGT
Found at i:403724 original size:31 final size:31
Alignment explanation
Indices: 403662--403726 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
403652 AGATTTGAGG
* *
403662 GTTTACCTATGTCTTTCGAGACATATGGACA
1 GTTTACCTAGGTCTTTCGAGACATATAGACA
* *
403693 GTTTACCTAGGT-TCTTCGGGACCTATAGACA
1 GTTTACCTAGGTCT-TTCGAGACATATAGACA
403724 GTT
1 GTT
403727 GTCGAGGTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 1 0.03
31 28 0.97
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (31 bp):
GTTTACCTAGGTCTTTCGAGACATATAGACA
Found at i:403746 original size:30 final size:29
Alignment explanation
Indices: 403712--403775 Score: 83
Period size: 30 Copynumber: 2.2 Consensus size: 29
403702 GGTTCTTCGG
403712 GACCTATAGACAGTTGTCGAGGTTCTTTAT
1 GACCTATAGACAGTTGTCGAGG-TCTTTAT
* * * *
403742 GACCTCTGGATAGTTGTCGAGGTCTTTGT
1 GACCTATAGACAGTTGTCGAGGTCTTTAT
403771 GACCT
1 GACCT
403776 CTGGATAGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 11 0.37
30 19 0.63
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.36
Consensus pattern (29 bp):
GACCTATAGACAGTTGTCGAGGTCTTTAT
Found at i:403776 original size:29 final size:30
Alignment explanation
Indices: 403723--403783 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 30
403713 ACCTATAGAC
403723 AGTTGTCGAGGTTCTTTATGACCTCTGGAT
1 AGTTGTCGAGGTTCTTTATGACCTCTGGAT
*
403753 AGTTGTCGAGG-TCTTTGTGACCTCTGGAT
1 AGTTGTCGAGGTTCTTTATGACCTCTGGAT
403782 AG
1 AG
403784 GTCCTTCGGG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 19 0.63
30 11 0.37
ACGTcount: A:0.16, C:0.16, G:0.30, T:0.38
Consensus pattern (30 bp):
AGTTGTCGAGGTTCTTTATGACCTCTGGAT
Found at i:411633 original size:20 final size:20
Alignment explanation
Indices: 411608--411647 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
411598 TTTTGGTGCA
411608 GAGGGAA-TCGATCCCCCCTT
1 GAGGGAACT-GATCCCCCCTT
*
411628 GAGGGAACTGATTCCCCCTT
1 GAGGGAACTGATCCCCCCTT
411648 TGAAGGGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.20, C:0.33, G:0.25, T:0.23
Consensus pattern (20 bp):
GAGGGAACTGATCCCCCCTT
Found at i:411645 original size:21 final size:23
Alignment explanation
Indices: 411610--411669 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
411600 TTGGTGCAGA
*
411610 GGGAATCGA-TCCCCCCTTG-A-
1 GGGAACCGATTCCCCCCTTGAAG
* *
411630 GGGAACTGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCCTTGAAG
411653 GGGAACCGATTCCCCCC
1 GGGAACCGATTCCCCCC
411670 ACAGGGGAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
20 7 0.22
21 9 0.28
22 1 0.03
23 15 0.47
ACGTcount: A:0.20, C:0.35, G:0.25, T:0.20
Consensus pattern (23 bp):
GGGAACCGATTCCCCCCTTGAAG
Found at i:411677 original size:21 final size:21
Alignment explanation
Indices: 411651--411690 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
411641 CCCCCTTTGA
*
411651 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
411672 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
411691 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:411873 original size:20 final size:20
Alignment explanation
Indices: 411848--411888 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
411838 ATCTTCTAAA
* * *
411848 CTTGCAATCATCATTAAAAT
1 CTTGCAAACAACATCAAAAT
411868 CTTGCAAACAACATCAAAAT
1 CTTGCAAACAACATCAAAAT
411888 C
1 C
411889 CACTCAATCT
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:0.44, C:0.24, G:0.05, T:0.27
Consensus pattern (20 bp):
CTTGCAAACAACATCAAAAT
Found at i:416958 original size:29 final size:29
Alignment explanation
Indices: 416888--416963 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
416878 ATGTCTTTCG
*
416888 AGACATATGGACAGTTTACCTAGGTTCTTT
1 AGACATATGGACAGTTTA-CGAGGTTCTTT
*
416918 AGTACCTATGGACAGTTT-CGAGGTTCTTT
1 AG-ACATATGGACAGTTTACGAGGTTCTTT
* *
416947 ATGACATCTGGATAGTT
1 A-GACATATGGACAGTT
416964 GCCGGGGTCT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
29 22 0.56
30 3 0.08
31 14 0.36
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (29 bp):
AGACATATGGACAGTTTACGAGGTTCTTT
Found at i:418614 original size:2 final size:2
Alignment explanation
Indices: 418607--418641 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
418597 CTTTTAAAAC
418607 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
418642 CCCCCTTCCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:418839 original size:24 final size:24
Alignment explanation
Indices: 418807--418894 Score: 70
Period size: 24 Copynumber: 3.7 Consensus size: 24
418797 GATATCAGAA
*
418807 ATCAAAACAGAATTCAGAACATAT
1 ATCAGAACAGAATTCAGAACATAT
* * * *
418831 ATCAGAACAGAATCCA-AATTAGAA
1 ATCAGAACAGAATTCAGAA-CATAT
* ** *
418855 ATCAGAACATAATTCAGGTCATGT
1 ATCAGAACAGAATTCAGAACATAT
*
418879 ATCATAACAGAATTCA
1 ATCAGAACAGAATTCA
418895 AGTCGAAAAT
Statistics
Matches: 47, Mismatches: 15, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
23 2 0.04
24 45 0.96
ACGTcount: A:0.49, C:0.17, G:0.11, T:0.23
Consensus pattern (24 bp):
ATCAGAACAGAATTCAGAACATAT
Found at i:420994 original size:23 final size:23
Alignment explanation
Indices: 420956--420999 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
420946 GGTCAACGTC
*
420956 GGTCAACGAGTTGGGTCGGGTCG
1 GGTCAACGAGTCGGGTCGGGTCG
* *
420979 GGTCAACGGGTCGGGTTGGGT
1 GGTCAACGAGTCGGGTCGGGT
421000 AAACGGGTCG
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:0.11, C:0.16, G:0.50, T:0.23
Consensus pattern (23 bp):
GGTCAACGAGTCGGGTCGGGTCG
Found at i:421013 original size:18 final size:18
Alignment explanation
Indices: 420968--421015 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
420958 TCAACGAGTT
* *
420968 GGGTCGGGTCGGGTCAAC
1 GGGTCGGGTTGGGTAAAC
420986 GGGTCGGGTTGGGTAAAC
1 GGGTCGGGTTGGGTAAAC
421004 GGGTCGGGTTGG
1 GGGTCGGGTTGG
421016 TTTGTAACTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.10, C:0.15, G:0.54, T:0.21
Consensus pattern (18 bp):
GGGTCGGGTTGGGTAAAC
Found at i:424453 original size:20 final size:20
Alignment explanation
Indices: 424417--424454 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
424407 ATCTTATTCT
**
424417 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
424437 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
424455 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:424705 original size:23 final size:23
Alignment explanation
Indices: 424677--424722 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
424667 TATGATTTTC
424677 AAATTTATATTCTATTCAACCAT
1 AAATTTATATTCTATTCAACCAT
424700 AAATTTATATTCTATTCAACCAT
1 AAATTTATATTCTATTCAACCAT
424723 TCAAATATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.00, T:0.43
Consensus pattern (23 bp):
AAATTTATATTCTATTCAACCAT
Found at i:426543 original size:21 final size:21
Alignment explanation
Indices: 426518--426559 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
426508 CCATTAAAAT
*
426518 TTGATTAATATTTAAATTGAA
1 TTGATTAATATTGAAATTGAA
* *
426539 TTGATTTATATTGAATTTGAA
1 TTGATTAATATTGAAATTGAA
426560 CTCGAATCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (21 bp):
TTGATTAATATTGAAATTGAA
Found at i:435073 original size:3 final size:3
Alignment explanation
Indices: 435067--435093 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
435057 ATCATCATAA
435067 TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT
435094 ACGGTTGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:438055 original size:21 final size:19
Alignment explanation
Indices: 438006--438061 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
437996 ATTAGAATAT
*
438006 GGGTTTAGAAACTAAGTAA
1 GGGTTTAGAAACCAAGTAA
* *
438025 GGGTTAAGAAACCAAGTACG
1 GGGTTTAGAAACCAAGTA-A
438045 GTGGTTTAGAAA-CAAGT
1 G-GGTTTAGAAACCAAGT
438062 TGAGGGTTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 16 0.52
20 6 0.19
21 9 0.29
ACGTcount: A:0.39, C:0.09, G:0.29, T:0.23
Consensus pattern (19 bp):
GGGTTTAGAAACCAAGTAA
Found at i:438853 original size:19 final size:19
Alignment explanation
Indices: 438831--438879 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
438821 TAAGAAAAAA
*
438831 ATAAAGTTATAATTTACTC
1 ATAAAATTATAATTTACTC
* *
438850 ATAAATTTTATAATTTATTC
1 ATAAA-ATTATAATTTACTC
438870 ATAAAATTAT
1 ATAAAATTAT
438880 TGTTGGTCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (19 bp):
ATAAAATTATAATTTACTC
Found at i:438862 original size:20 final size:20
Alignment explanation
Indices: 438837--438874 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
438827 AAAAATAAAG
438837 TTATAATTTACTCATAAATT
1 TTATAATTTACTCATAAATT
*
438857 TTATAATTTATTCATAAA
1 TTATAATTTACTCATAAA
438875 ATTATTGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (20 bp):
TTATAATTTACTCATAAATT
Found at i:440628 original size:11 final size:12
Alignment explanation
Indices: 440612--440644 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
440602 ATATATTCTC
440612 TTAATTTAATA-
1 TTAATTTAATAT
440623 TTAATTTAA-AT
1 TTAATTTAATAT
440634 TTAATTTAATA
1 TTAATTTAATA
440645 AATTAATCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 18 0.90
12 1 0.05
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TTAATTTAATAT
Found at i:458108 original size:39 final size:40
Alignment explanation
Indices: 458065--458140 Score: 111
Period size: 39 Copynumber: 1.9 Consensus size: 40
458055 GGTCAACTAT
*
458065 TCTACTTTAGCCG-ATAAATTTAATATGTTTT-TCAGGGAC
1 TCTACTTTAACCGCA-AAATTTAATATGTTTTATCAGGGAC
*
458104 TCTACTTTAACTGCAAAATTTAATATGTTTTATCAGG
1 TCTACTTTAACCGCAAAATTTAATATGTTTTATCAGG
458141 TCTGCTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
39 27 0.82
40 6 0.18
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.42
Consensus pattern (40 bp):
TCTACTTTAACCGCAAAATTTAATATGTTTTATCAGGGAC
Found at i:458494 original size:7 final size:7
Alignment explanation
Indices: 458482--458514 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
458472 TTTCAAGAAT
458482 CCTTCGC
1 CCTTCGC
458489 CCTTCGC
1 CCTTCGC
458496 CCTTCGC
1 CCTTCGC
458503 CCTTCGC
1 CCTTCGC
458510 CCTTC
1 CCTTC
458515 TCACTTGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.00, C:0.58, G:0.12, T:0.30
Consensus pattern (7 bp):
CCTTCGC
Found at i:461951 original size:7 final size:7
Alignment explanation
Indices: 461939--461964 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
461929 ACCCTAGAGT
461939 TTAAACC
1 TTAAACC
461946 TTAAACC
1 TTAAACC
461953 TTAAACC
1 TTAAACC
461960 TTAAA
1 TTAAA
461965 TGTAACATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (7 bp):
TTAAACC
Found at i:466073 original size:19 final size:17
Alignment explanation
Indices: 466051--466085 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
466041 TTTGAGAGAA
466051 GAGGAAGACAAATGAAGAT
1 GAGGAA-ACAAA-GAAGAT
466070 GAGGAAACAAAGAAGA
1 GAGGAAACAAAGAAGA
466086 GTTCTCAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 5 0.31
19 6 0.38
ACGTcount: A:0.57, C:0.06, G:0.31, T:0.06
Consensus pattern (17 bp):
GAGGAAACAAAGAAGAT
Found at i:468037 original size:6 final size:6
Alignment explanation
Indices: 468026--468051 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
468016 TGACAATCAC
468026 CAGCTA CAGCTA CAGCTA CAGCTA CA
1 CAGCTA CAGCTA CAGCTA CAGCTA CA
468052 AATCCATTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.35, G:0.15, T:0.15
Consensus pattern (6 bp):
CAGCTA
Found at i:471177 original size:19 final size:19
Alignment explanation
Indices: 471131--471188 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 19
471121 CTCATATAAA
*
471131 TTATATTTTTATTATAATT
1 TTATATTTTAATTATAATT
* * * *
471150 ATATTTTTTAATTGTATTT
1 TTATATTTTAATTATAATT
*
471169 TTATATTTTTATTATAATT
1 TTATATTTTAATTATAATT
471188 T
1 T
471189 AAATTTATAT
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (19 bp):
TTATATTTTAATTATAATT
Found at i:475599 original size:37 final size:37
Alignment explanation
Indices: 475525--475599 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 37
475515 TAATATAATT
* **
475525 AATTTATATATATTTTTTAAAAAATTTAAATTTATAA
1 AATTTATATATATTTTTTAAAAAATTGAAATAGATAA
* *
475562 AATTTATATAATTTTTTTTACAAAATTGAAA-AGATAA
1 AATTTATAT-ATATTTTTTAAAAAATTGAAATAGATAA
475599 A
1 A
475600 TAGGTTTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
37 14 0.44
38 18 0.56
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (37 bp):
AATTTATATATATTTTTTAAAAAATTGAAATAGATAA
Found at i:479488 original size:18 final size:18
Alignment explanation
Indices: 479459--479515 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
479449 AAATCCAGGG
*
479459 AAACAAACAAAAAATCAA
1 AAACAAAAAAAAAATCAA
*
479477 AAGCAAAAAAAAAATCAA
1 AAACAAAAAAAAAATCAA
*
479495 AAACATAACAAAAAAAACAA
1 AAACA-AA-AAAAAAATCAA
479515 A
1 A
479516 CAAATAAGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
18 20 0.61
19 2 0.06
20 11 0.33
ACGTcount: A:0.79, C:0.14, G:0.02, T:0.05
Consensus pattern (18 bp):
AAACAAAAAAAAAATCAA
Found at i:483177 original size:22 final size:22
Alignment explanation
Indices: 483152--483215 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
483142 ATTAAATTAA
*
483152 TAATAGAATATATTTAATAAGT
1 TAATAAAATATATTTAATAAGT
* *
483174 TAATATAAAAATATTT-TTAAGT
1 TAATA-AAATATATTTAATAAGT
* *
483196 TAATATATATATATATAATA
1 TAATA-AAATATATTTAATA
483216 GTATGAATTT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
22 23 0.70
23 10 0.30
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.44
Consensus pattern (22 bp):
TAATAAAATATATTTAATAAGT
Found at i:485191 original size:2 final size:2
Alignment explanation
Indices: 485184--485229 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
485174 ATACACCCTT
485184 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
485225 TA TA T
1 TA TA T
485230 TAATGAAAGC
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:485721 original size:23 final size:23
Alignment explanation
Indices: 485704--485749 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
485694 AGAAAGTGTG
* *
485704 CCATAAAGGCATATGAAAACGTA
1 CCATAAAGGAAGATGAAAACGTA
485727 CCATAAAGGAAGATGAAAACGTA
1 CCATAAAGGAAGATGAAAACGTA
485750 GGAGCATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.50, C:0.15, G:0.20, T:0.15
Consensus pattern (23 bp):
CCATAAAGGAAGATGAAAACGTA
Found at i:495965 original size:20 final size:20
Alignment explanation
Indices: 495940--495982 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
495930 TCTAAGAGCC
**
495940 CATTTAGGATTATATAGATG
1 CATTTAGGAGCATATAGATG
*
495960 CATTTAGGAGCATATAGTTG
1 CATTTAGGAGCATATAGATG
495980 CAT
1 CAT
495983 GTGGTGGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.37
Consensus pattern (20 bp):
CATTTAGGAGCATATAGATG
Found at i:498109 original size:21 final size:21
Alignment explanation
Indices: 498080--498126 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
498070 ATTCTGACTA
498080 TCGCATTGCGATTTTCCA-AAT
1 TCGCATTGCGATTTT-CAGAAT
*
498101 TCGCGTTGCGATTTTCAGAAT
1 TCGCATTGCGATTTTCAGAAT
498122 TCGCA
1 TCGCA
498127 ATGTGATAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCAGAAT
Found at i:498155 original size:21 final size:21
Alignment explanation
Indices: 498079--498156 Score: 59
Period size: 21 Copynumber: 3.7 Consensus size: 21
498069 GATTCTGACT
**
498079 ATCGCATTGCGATTTTCCAAA
1 ATCGCATTGCGATAGTCCAAA
* * * *
498100 TTCGCGTTGCGAT-TTTCAGAA
1 ATCGCATTGCGATAGTCCA-AA
* * *
498121 TTCGCAATGTGATAGTCCAAA
1 ATCGCATTGCGATAGTCCAAA
498142 ATCGCATTGCGATAG
1 ATCGCATTGCGATAG
498157 CACTGTTCAC
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
20 4 0.09
21 37 0.84
22 3 0.07
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.32
Consensus pattern (21 bp):
ATCGCATTGCGATAGTCCAAA
Found at i:498175 original size:21 final size:21
Alignment explanation
Indices: 498151--498208 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
498141 AATCGCATTG
*
498151 CGATAGCACTGTTCACCGTTT
1 CGATAGCACTGTTCACCGTTA
498172 CGATAGCACTGTTCACCGTTA
1 CGATAGCACTGTTCACCGTTA
*
498193 CGATAGCATTGTTCAC
1 CGATAGCACTGTTCAC
498209 ATTGCGAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.22, C:0.28, G:0.19, T:0.31
Consensus pattern (21 bp):
CGATAGCACTGTTCACCGTTA
Found at i:498915 original size:21 final size:21
Alignment explanation
Indices: 498889--498941 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
498879 ATTTTGATCA
498889 CTATCGCAATGGTGAACAGTG
1 CTATCGCAATGGTGAACAGTG
*
498910 CTATCGCAACGGTGAACAGTG
1 CTATCGCAATGGTGAACAGTG
498931 CTATCGCAATG
1 CTATCGCAATG
498942 CGATTTTGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (21 bp):
CTATCGCAATGGTGAACAGTG
Found at i:498955 original size:21 final size:21
Alignment explanation
Indices: 498931--498987 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
498921 GTGAACAGTG
*
498931 CTATCGCAATGCGATTTTGGA
1 CTATCGCAATGCGATTTTGAA
* *
498952 CTATCGCATTGCGAATTTGAA
1 CTATCGCAATGCGATTTTGAA
**
498973 AAATCGCAATGCGAT
1 CTATCGCAATGCGAT
498988 AGTCAGAATC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (21 bp):
CTATCGCAATGCGATTTTGAA
Found at i:511814 original size:28 final size:28
Alignment explanation
Indices: 511782--511837 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
511772 TGCTTGCCAT
* *
511782 GCCACGTTGGCAATAGCTGTTAAGAGGA
1 GCCACGTTGACAATAGCTGCTAAGAGGA
511810 GCCACGTTGACAATAGCTGCTAAGAGGA
1 GCCACGTTGACAATAGCTGCTAAGAGGA
511838 AGATAAGAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (28 bp):
GCCACGTTGACAATAGCTGCTAAGAGGA
Found at i:514697 original size:18 final size:18
Alignment explanation
Indices: 514671--514707 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
514661 AGCCAGTTGT
*
514671 TAATGTTCTTGAACCCTC
1 TAATATTCTTGAACCCTC
514689 TAATATTCTTGAACCCTC
1 TAATATTCTTGAACCCTC
514707 T
1 T
514708 GAACCTATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.27, G:0.08, T:0.41
Consensus pattern (18 bp):
TAATATTCTTGAACCCTC
Found at i:519455 original size:2 final size:2
Alignment explanation
Indices: 519448--519474 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
519438 CTTTTAAAAC
519448 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
519475 CCCCCATCCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:519717 original size:24 final size:24
Alignment explanation
Indices: 519690--519804 Score: 160
Period size: 24 Copynumber: 4.8 Consensus size: 24
519680 CATTATTCAC
* * * *
519690 GTCAAATATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAT
*
519714 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
*
519738 GTCAAGTATCATATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
519762 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
519786 GTCAAGTATCAGATCAGAA
1 GTCAAGTATCAGATCAGAA
519805 ATCAAATCGA
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
23 2 0.02
24 78 0.95
25 2 0.02
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:519821 original size:48 final size:48
Alignment explanation
Indices: 519721--519821 Score: 125
Period size: 48 Copynumber: 2.1 Consensus size: 48
519711 CAGGTCAAGT
* ** *
519721 ATCAGATCAGAATCCAAGTCAAGTATCATATCAGAATCCATGTCAGAT
1 ATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAGAA
*
519769 ATCAGATCAGAATCCATGTCAAGTATCAGATCAGAAAT-CAAATC-GAAA
1 ATCAGATCAGAATCCAAGTCAAGTATCAGATCAG-AATCCAAATCAG-AA
519817 ATCAG
1 ATCAG
519822 GTAAAATATT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
47 1 0.02
48 42 0.91
49 3 0.07
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.23
Consensus pattern (48 bp):
ATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAGAA
Found at i:523721 original size:168 final size:171
Alignment explanation
Indices: 523443--523782 Score: 641
Period size: 168 Copynumber: 2.0 Consensus size: 171
523433 TTAATAACCA
523443 TTCATGTAGTTCACCATGAAAAATAAAAAGGTTAACAAGGTATTAAACGAGTTGTTAATGAGCAT
1 TTCATGTAGTTCACCATGAAAAATAAAAAGGTTAACAAGGTATTAAACGAGTTGTTAATGAGCAT
523508 AATCGAGCTTATAAATTAGCTTCTAAACGAGTTTGTTCGTGAACATAAACAACTTGAAC-ATATA
66 AATCGAGCTTATAAATTAGCTTCTAAACGAGTTTGTTCGTGAACATAAACAACTTGAACAATATA
*
523572 TATTCGTGTTCGTTTGTTTA-TAACTGAAC-TAAAATGTTT
131 TATTCGTGTTCGTTTGTTTATTAAATGAACGTAAAATGTTT
523611 TTCATGTAGTTCACCATGAAAAATAAAAAGGTTAACAAGGTATTAAACGAGTTGTTAATGAGCAT
1 TTCATGTAGTTCACCATGAAAAATAAAAAGGTTAACAAGGTATTAAACGAGTTGTTAATGAGCAT
523676 AATCGAGCTTATAAATTAGCTTCTAAACGAGTTTGTTCGTGAACATAAACAACTTGAACATATAT
66 AATCGAGCTTATAAATTAGCTTCTAAACGAGTTTGTTCGTGAACATAAACAACTTGAACA-ATAT
523741 ATATTCGTGTTCGTTTGTTTATTAAATGAACGTAAAATGTTT
130 ATATTCGTGTTCGTTTGTTTATTAAATGAACGTAAAATGTTT
523783 ATTTATATTT
Statistics
Matches: 167, Mismatches: 1, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
168 124 0.74
170 25 0.15
171 8 0.05
172 10 0.06
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (171 bp):
TTCATGTAGTTCACCATGAAAAATAAAAAGGTTAACAAGGTATTAAACGAGTTGTTAATGAGCAT
AATCGAGCTTATAAATTAGCTTCTAAACGAGTTTGTTCGTGAACATAAACAACTTGAACAATATA
TATTCGTGTTCGTTTGTTTATTAAATGAACGTAAAATGTTT
Found at i:525026 original size:46 final size:46
Alignment explanation
Indices: 524975--525084 Score: 138
Period size: 46 Copynumber: 2.4 Consensus size: 46
524965 AATATAAAAT
524975 ATATTAAAAAAATATTATA-TAC-ATCTTAACTTAAATTCACAT-ATTA
1 ATATTAAAAAAATATTATACT-CTATCTTAAC-TAAATTCACATCA-TA
*
525021 ATATT-AAAAAATATTATACTCTTATGTTAACTAAATTCACATCATA
1 ATATTAAAAAAATATTATACTC-TATCTTAACTAAATTCACATCATA
525067 ATATTAAAAAATATATTA
1 ATATTAAAAAA-ATATTA
525085 AAAATATTTT
Statistics
Matches: 57, Mismatches: 1, Indels: 10
0.84 0.01 0.15
Matches are distributed among these distances:
45 14 0.25
46 24 0.42
47 13 0.23
48 6 0.11
ACGTcount: A:0.50, C:0.10, G:0.01, T:0.39
Consensus pattern (46 bp):
ATATTAAAAAAATATTATACTCTATCTTAACTAAATTCACATCATA
Found at i:525808 original size:24 final size:23
Alignment explanation
Indices: 525780--525853 Score: 94
Period size: 23 Copynumber: 3.2 Consensus size: 23
525770 TTTAAACGAT
525780 AAACGAACATAAACGAACACAAAC
1 AAACGAACATAAACGAACA-AAAC
* *
525804 AAACGAACATAAACGAACATAAT
1 AAACGAACATAAACGAACAAAAC
** *
525827 AAATAAACATAAACGAACAACAC
1 AAACGAACATAAACGAACAAAAC
525850 AAAC
1 AAAC
525854 ACAAAAAACA
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 23 0.55
24 19 0.45
ACGTcount: A:0.64, C:0.22, G:0.07, T:0.08
Consensus pattern (23 bp):
AAACGAACATAAACGAACAAAAC
Found at i:525845 original size:10 final size:10
Alignment explanation
Indices: 525778--525825 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
525768 CCTTTAAACG
525778 ATAAACGAAC
1 ATAAACGAAC
525788 ATAAACGAACAC
1 ATAAACG-A-AC
*
525800 AAACAAACGAAC
1 --ATAAACGAAC
525812 ATAAACGAAC
1 ATAAACGAAC
525822 ATAA
1 ATAA
525826 TAAATAAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
10 20 0.62
11 1 0.03
12 4 0.12
13 1 0.03
14 6 0.19
ACGTcount: A:0.62, C:0.21, G:0.08, T:0.08
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:526128 original size:14 final size:14
Alignment explanation
Indices: 526109--526146 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
526099 GCCTTCTGTT
526109 CGAACATAAATGAA
1 CGAACATAAATGAA
526123 CGAACATAAATGAA
1 CGAACATAAATGAA
526137 CGAACATAAA
1 CGAACATAAA
526147 CAAACATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.58, C:0.16, G:0.13, T:0.13
Consensus pattern (14 bp):
CGAACATAAATGAA
Found at i:527071 original size:21 final size:21
Alignment explanation
Indices: 527047--527088 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
527037 TTAATAAAAA
*
527047 ATTATTAAAAATATTATTATT
1 ATTATCAAAAATATTATTATT
*
527068 ATTATCGAAAATATTATTATT
1 ATTATCAAAAATATTATTATT
527089 GGACGTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (21 bp):
ATTATCAAAAATATTATTATT
Found at i:530043 original size:21 final size:21
Alignment explanation
Indices: 529992--530044 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
529982 ATTATGACTA
529992 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
530013 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
530034 TCGCAATGCGA
1 TCGCAATGCGA
530045 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:530059 original size:20 final size:21
Alignment explanation
Indices: 530034--530085 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
530024 TTTTCCCAAT
*
530034 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
530054 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
530075 TCGCAATGCGA
1 TCGCAATGCGA
530086 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:530099 original size:20 final size:20
Alignment explanation
Indices: 530074--530168 Score: 84
Period size: 20 Copynumber: 4.7 Consensus size: 20
530064 AATTTGGAAA
*
530074 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
530094 ATCGCAAAGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
530115 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
530135 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* * *
530155 TTTGCAACGAGATA
1 ATCGCAACGCGATA
530169 ATTCATAATC
Statistics
Matches: 61, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
19 2 0.03
20 43 0.70
21 14 0.23
22 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:530383 original size:22 final size:22
Alignment explanation
Indices: 530355--530417 Score: 108
Period size: 22 Copynumber: 2.9 Consensus size: 22
530345 CACTCTCTCA
*
530355 CCCATCTCCGACGAAATTCGTC
1 CCCATCTCCGACGAAATCCGTC
530377 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
530399 CCCATCTCCGGCGAAATCC
1 CCCATCTCCGACGAAATCC
530418 ATCTATCTCC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.22, C:0.44, G:0.14, T:0.19
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:530724 original size:20 final size:20
Alignment explanation
Indices: 530685--530743 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
530675 TTTATTCTCT
**
530685 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
530705 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* * **
530725 TGATGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
530744 AGAAACTATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.41
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:532084 original size:18 final size:18
Alignment explanation
Indices: 532063--532110 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
532053 TCCACTTCGG
532063 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
* *
532081 GAGCTATCACCTCATCCA
1 GAGCCATCACCTCACCCA
532099 GAGCCATCACCT
1 GAGCCATCACCT
532111 GATCGACCCG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.27, C:0.44, G:0.12, T:0.17
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:532677 original size:20 final size:20
Alignment explanation
Indices: 532652--532697 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
532642 TAGTTTACTT
532652 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
532672 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
532692 TCGCAA
1 TCGCAA
532698 TGCGATTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:532746 original size:33 final size:33
Alignment explanation
Indices: 532709--532791 Score: 139
Period size: 33 Copynumber: 2.5 Consensus size: 33
532699 GCGATTTGTG
* * *
532709 TTTCGCGTTGTGATTTTGTCGTTGTGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
532742 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
532775 TTTCGCATTGCGATTTT
1 TTTCGCATTGCGATTTT
532792 CATTTCGCGT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.11, C:0.16, G:0.22, T:0.52
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:532758 original size:19 final size:19
Alignment explanation
Indices: 532728--532846 Score: 113
Period size: 19 Copynumber: 6.4 Consensus size: 19
532718 GTGATTTTGT
*
532728 CGTTGTGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* *
532747 CATTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
532761 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
532780 CATTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
**
532799 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
532819 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATTTTCA-TTTCG
532839 CGTTGCGA
1 CGTTGCGA
532847 AAGTAAGTTT
Statistics
Matches: 84, Mismatches: 9, Indels: 13
0.79 0.08 0.12
Matches are distributed among these distances:
14 7 0.08
15 3 0.04
16 2 0.02
17 2 0.02
18 3 0.04
19 38 0.45
20 26 0.31
21 3 0.04
ACGTcount: A:0.13, C:0.20, G:0.23, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:532822 original size:20 final size:19
Alignment explanation
Indices: 532761--532866 Score: 113
Period size: 20 Copynumber: 5.4 Consensus size: 19
532751 GCGATTTTGT
**
532761 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* **
532780 CATTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
532799 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
532819 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA-TTTCG
* *
532839 CGTTGCGAAAGTAAGTTTCG
1 CGTTGCGATAGTCA-TTTCG
*
532859 TGTTGCGA
1 CGTTGCGA
532867 AAGTAAACTA
Statistics
Matches: 77, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
19 32 0.42
20 42 0.55
21 3 0.04
ACGTcount: A:0.16, C:0.20, G:0.25, T:0.40
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:533303 original size:41 final size:42
Alignment explanation
Indices: 533213--533303 Score: 130
Period size: 41 Copynumber: 2.2 Consensus size: 42
533203 CCCGACTCAC
* * *
533213 CTGTCATCCCTCAAGAGTCCCCTCCAATCGTTTAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
* *
533255 CTATCATCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
533296 CTGTCATC
1 CTGTCATC
533304 GTTGAAGAGG
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 22 0.51
42 21 0.49
ACGTcount: A:0.22, C:0.41, G:0.15, T:0.22
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
Found at i:534746 original size:14 final size:14
Alignment explanation
Indices: 534712--534750 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
534702 TTGATTGTTT
534712 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
534726 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
534740 TGTTGATTTGT
1 AATTGATTTGT
534751 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:534914 original size:19 final size:19
Alignment explanation
Indices: 534890--534940 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
534880 GGAACGAGAG
534890 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
534909 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
534928 AATCGCAATGCGA
1 AATCGCAATGCGA
534941 TGTTCTCGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.16
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:534970 original size:20 final size:20
Alignment explanation
Indices: 534937--535015 Score: 131
Period size: 20 Copynumber: 4.0 Consensus size: 20
534927 AAATCGCAAT
* *
534937 GCGATGTTCTCGTTGCGATA
1 GCGATTTTCGCGTTGCGATA
534957 GCGATTTTCGCGTTGCGATA
1 GCGATTTTCGCGTTGCGATA
534977 GCGATTTTCGCGTTGCGATA
1 GCGATTTTCGCGTTGCGATA
*
534997 GCCATTTTCGCGTTGCGAT
1 GCGATTTTCGCGTTGCGAT
535016 TTCCCCGTTG
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.14, C:0.22, G:0.29, T:0.35
Consensus pattern (20 bp):
GCGATTTTCGCGTTGCGATA
Found at i:535015 original size:34 final size:36
Alignment explanation
Indices: 534936--535031 Score: 97
Period size: 40 Copynumber: 2.6 Consensus size: 36
534926 AAAATCGCAA
* * *
534936 TGCGATGTTCTCGTTGCGATAGCGATTTTCGCGTTGCG
1 TGCGATTTTCCCGTTGCGATAGCCATTTTCGCGTT--G
*
534974 ATAGCGATTTTCGCGTTGCGATAGCCATTTTCGCG-T-
1 -T-GCGATTTTCCCGTTGCGATAGCCATTTTCGCGTTG
*
535010 TGCGATTTCCCCGTTGCGATAG
1 TGCGATTTTCCCGTTGCGATAG
535032 TCAAATGAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
34 19 0.37
35 1 0.02
39 2 0.04
40 29 0.57
ACGTcount: A:0.14, C:0.23, G:0.28, T:0.35
Consensus pattern (36 bp):
TGCGATTTTCCCGTTGCGATAGCCATTTTCGCGTTG
Found at i:536923 original size:72 final size:72
Alignment explanation
Indices: 536806--536949 Score: 288
Period size: 72 Copynumber: 2.0 Consensus size: 72
536796 GATATACTAA
536806 TCTTGAACCGAGCATTCATGTCAGTCATAATTTCATGTCCCCGATATACCCTGCCATTCAAAAAC
1 TCTTGAACCGAGCATTCATGTCAGTCATAATTTCATGTCCCCGATATACCCTGCCATTCAAAAAC
536871 ATTAACT
66 ATTAACT
536878 TCTTGAACCGAGCATTCATGTCAGTCATAATTTCATGTCCCCGATATACCCTGCCATTCAAAAAC
1 TCTTGAACCGAGCATTCATGTCAGTCATAATTTCATGTCCCCGATATACCCTGCCATTCAAAAAC
536943 ATTAACT
66 ATTAACT
536950 CAGCCAGAAA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.31, C:0.28, G:0.11, T:0.31
Consensus pattern (72 bp):
TCTTGAACCGAGCATTCATGTCAGTCATAATTTCATGTCCCCGATATACCCTGCCATTCAAAAAC
ATTAACT
Found at i:537371 original size:12 final size:12
Alignment explanation
Indices: 537354--537378 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
537344 TCTTCGGGGA
537354 CTTTTTCTTCTT
1 CTTTTTCTTCTT
537366 CTTTTTCTTCTT
1 CTTTTTCTTCTT
537378 C
1 C
537379 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:537585 original size:24 final size:24
Alignment explanation
Indices: 537551--537604 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
537541 CTGAAACATC
*
537551 ATCAAAATCCGAG-TATTGACCAAT
1 ATCAAAATCCG-GTTATTGACCAAG
*
537575 ATCAAAGTCCGGTTATTGACCAAG
1 ATCAAAATCCGGTTATTGACCAAG
537599 ATCAAA
1 ATCAAA
537605 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 1 0.04
24 26 0.96
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGTTATTGACCAAG
Found at i:538372 original size:20 final size:20
Alignment explanation
Indices: 538360--538438 Score: 131
Period size: 20 Copynumber: 4.0 Consensus size: 20
538350 TCGTTGTGAT
* *
538360 AGTCATAATCTCGTTGCGAA
1 AGTCAGAATCGCGTTGCGAA
538380 AGTCAGAATCGCGTTGCGAA
1 AGTCAGAATCGCGTTGCGAA
538400 AGTCAGAATCGCGTTGCGAA
1 AGTCAGAATCGCGTTGCGAA
*
538420 AGTCAGTATCGCGTTGCGA
1 AGTCAGAATCGCGTTGCGA
538439 TTTTGTATTA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (20 bp):
AGTCAGAATCGCGTTGCGAA
Found at i:538472 original size:20 final size:20
Alignment explanation
Indices: 538346--538480 Score: 130
Period size: 20 Copynumber: 6.7 Consensus size: 20
538336 GATTCTGTAT
* *
538346 TATCTCGTTGTGATAGTCA-
1 TATCGCGTTGCGATAGTCAG
* *
538365 TAATCTCGTTGCGAAAGTCAG
1 T-ATCGCGTTGCGATAGTCAG
* *
538386 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
538406 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
538426 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
538447 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
538467 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
538481 TTTCCAAATT
Statistics
Matches: 100, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
19 4 0.04
20 80 0.80
21 14 0.14
22 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:538499 original size:41 final size:41
Alignment explanation
Indices: 538371--538501 Score: 122
Period size: 41 Copynumber: 3.2 Consensus size: 41
538361 GTCATAATCT
* * * *** *
538371 CGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGA-ATCG
1 CGTTGCGATAGTCAGTATCGCATTGCGATTTTCAAATATCG
* * ** *
538411 CGTTGCGAAAGTCAGTATCGCGTTGCGATTTTGTATTATCG
1 CGTTGCGATAGTCAGTATCGCATTGCGATTTTCAAATATCG
538452 CGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT-TCG
1 CGTTGCGATAGTCAGTATCGCATTGCGATTTT-CAAATATCG
*
538493 CATTGCGAT
1 CGTTGCGAT
538502 TTACTTATTC
Statistics
Matches: 75, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
40 28 0.37
41 45 0.60
42 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.31
Consensus pattern (41 bp):
CGTTGCGATAGTCAGTATCGCATTGCGATTTTCAAATATCG
Found at i:538513 original size:20 final size:21
Alignment explanation
Indices: 538469--538520 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
538459 ATAGTCAGTA
*
538469 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
538490 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
538510 TCGCATTGCGA
1 TCGCATTGCGA
538521 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:538562 original size:21 final size:22
Alignment explanation
Indices: 538510--538562 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
538500 ATTTACTTAT
538510 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
538531 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
538552 TCGCATTGCGA
1 TCGCATTGCGA
538563 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:539654 original size:60 final size:59
Alignment explanation
Indices: 539489--539643 Score: 179
Period size: 60 Copynumber: 2.6 Consensus size: 59
539479 AAGGAGCATA
* * * *
539489 AAGTGCGCCTTCGTGAGATTATG-TCAGAGTTGGCGCCACGGTGGAAAGACGCGGATCAT
1 AAGTGCGCCTTCGTGGGATTTTGTTC-GAGTTGGCGCCACGGTGGAAAGACACGAATCAT
* * *
539548 GAAGTGCTCCTTCGCGGGGTTCTT-TTCGAGTTGGCGCCACGGTGGAAAGACACGAATCAT
1 -AAGTGCGCCTTCGTGGGATT-TTGTTCGAGTTGGCGCCACGGTGGAAAGACACGAATCAT
* *
539608 AAGGTGCGCCTTTGTGGGATTTTGTTCGAGCTGGCG
1 AA-GTGCGCCTTCGTGGGATTTTGTTCGAGTTGGCG
539644 TCATGTTGGA
Statistics
Matches: 79, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
59 4 0.05
60 72 0.91
61 3 0.04
ACGTcount: A:0.19, C:0.21, G:0.34, T:0.26
Consensus pattern (59 bp):
AAGTGCGCCTTCGTGGGATTTTGTTCGAGTTGGCGCCACGGTGGAAAGACACGAATCAT
Found at i:543303 original size:24 final size:22
Alignment explanation
Indices: 543271--543337 Score: 75
Period size: 21 Copynumber: 3.0 Consensus size: 22
543261 AAGTAAAAAT
543271 TAAATAAAAATATTACAAACTAAA
1 TAAATAAAAATATTA-AAAC-AAA
* *
543295 TAAA-AAAAA-ATAAAAACAAT
1 TAAATAAAAATATTAAAACAAA
543315 TAAATAAAAATATTAAATACAAA
1 TAAATAAAAATATTAAA-ACAAA
543338 CGTTACAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
20 6 0.17
21 9 0.25
22 8 0.22
23 9 0.25
24 4 0.11
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (22 bp):
TAAATAAAAATATTAAAACAAA
Found at i:543411 original size:44 final size:44
Alignment explanation
Indices: 543363--543486 Score: 158
Period size: 48 Copynumber: 2.7 Consensus size: 44
543353 AATTAAAAAT
*
543363 TAAAAATATTAAGAAACAAAATAAATAAAAAGTCCATAATTAAA
1 TAAAAATATTAAGAAACAAAATAAATAAAAACTCCATAATTAAA
** * *
543407 TAAAAGCATTCAGAAAAAAATAAAATAAATAAAAACTCCATAATTAAA
1 TAAAA--A-T-ATTAAGAAACAAAATAAATAAAAACTCCATAATTAAA
*
543455 TAAAAACATTAAGAAACAAAATAAATAAAAAC
1 TAAAAATATTAAGAAACAAAATAAATAAAAAC
543487 AAGTTTGTCG
Statistics
Matches: 66, Mismatches: 10, Indels: 8
0.79 0.12 0.10
Matches are distributed among these distances:
44 26 0.39
46 2 0.03
47 1 0.02
48 37 0.56
ACGTcount: A:0.67, C:0.09, G:0.04, T:0.20
Consensus pattern (44 bp):
TAAAAATATTAAGAAACAAAATAAATAAAAACTCCATAATTAAA
Found at i:543447 original size:48 final size:49
Alignment explanation
Indices: 543380--543483 Score: 167
Period size: 48 Copynumber: 2.2 Consensus size: 49
543370 ATTAAGAAAC
* * *
543380 AAAATAAATAAAAAGTCCATAATTAAATAAAAGCATTCAGAAA-AAAAT
1 AAAATAAATAAAAACTCCATAATTAAATAAAAACATTAAGAAACAAAAT
543428 AAAATAAATAAAAACTCCATAATTAAATAAAAACATTAAGAAACAAAAT
1 AAAATAAATAAAAACTCCATAATTAAATAAAAACATTAAGAAACAAAAT
543477 -AAATAAA
1 AAAATAAA
543484 AACAAGTTTG
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
48 47 0.90
49 5 0.10
ACGTcount: A:0.67, C:0.09, G:0.04, T:0.20
Consensus pattern (49 bp):
AAAATAAATAAAAACTCCATAATTAAATAAAAACATTAAGAAACAAAAT
Found at i:544279 original size:11 final size:11
Alignment explanation
Indices: 544263--544291 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
544253 ACAAGCAACT
544263 AGAATCATGAG
1 AGAATCATGAG
544274 AGAATCATGAG
1 AGAATCATGAG
544285 AGAATCA
1 AGAATCA
544292 AAGAGAAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.48, C:0.10, G:0.24, T:0.17
Consensus pattern (11 bp):
AGAATCATGAG
Found at i:551011 original size:18 final size:19
Alignment explanation
Indices: 550985--551032 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
550975 GACTTCTCCG
* *
550985 ACGATGAACCAGAAC-AGC
1 ACGAGGAACAAGAACGAGC
*
551003 ACGAGGAACAAGCACGAGC
1 ACGAGGAACAAGAACGAGC
551022 A-GAGGAACAAG
1 ACGAGGAACAAG
551033 CACATCCAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 22 0.85
19 4 0.15
ACGTcount: A:0.46, C:0.23, G:0.29, T:0.02
Consensus pattern (19 bp):
ACGAGGAACAAGAACGAGC
Found at i:551033 original size:18 final size:19
Alignment explanation
Indices: 551000--551035 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
550990 GAACCAGAAC
551000 AGCACGAGGAACAAGCACG
1 AGCACGAGGAACAAGCACG
551019 AGCA-GAGGAACAAGCAC
1 AGCACGAGGAACAAGCAC
551036 ATCCAGAGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.44, C:0.25, G:0.31, T:0.00
Consensus pattern (19 bp):
AGCACGAGGAACAAGCACG
Done.