Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008296.1 Hibiscus syriacus cultivar Beakdansim tig00110963_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: 1205179
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 3 of 7
Found at i:384534 original size:45 final size:45
Alignment explanation
Indices: 384478--384576 Score: 155
Period size: 46 Copynumber: 2.2 Consensus size: 45
384468 CAGATAATAC
*
384478 TTTATAATCGCTCT-AATTATTAAAAGAATATAAATAGAAAATGGG
1 TTTATAATCGCTCTAAATTATTAAAAGAATATAAAGAGAAAAT-GG
*
384523 TTTATAATCGCTCTAAATTATTAAAAGAATATAAAGAGGAAATGG
1 TTTATAATCGCTCTAAATTATTAAAAGAATATAAAGAGAAAATGG
384568 TTTAGTAAT
1 TTTA-TAAT
384577 TCTTTAAACT
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
45 20 0.40
46 30 0.60
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.34
Consensus pattern (45 bp):
TTTATAATCGCTCTAAATTATTAAAAGAATATAAAGAGAAAATGG
Found at i:389176 original size:48 final size:47
Alignment explanation
Indices: 389124--389223 Score: 105
Period size: 48 Copynumber: 2.1 Consensus size: 47
389114 ATAAAATATC
* * *
389124 TATTT-TAATTACTAT-ATTTATAGATTACTATATTTTAATTATTTATTA
1 TATTTATAATTAATATCATTAAT-GATTA-T-TATTATAATTATTTATTA
* *
389172 TATTTAATAATTAATATCATTAATTATTATTATTATATTTATTTATTA
1 TATTT-ATAATTAATATCATTAATGATTATTATTATAATTATTTATTA
389220 TATT
1 TATT
389224 CATTTAACTT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
48 25 0.57
49 1 0.02
50 13 0.30
51 5 0.11
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (47 bp):
TATTTATAATTAATATCATTAATGATTATTATTATAATTATTTATTA
Found at i:389217 original size:16 final size:16
Alignment explanation
Indices: 389131--389220 Score: 54
Period size: 16 Copynumber: 5.3 Consensus size: 16
389121 ATCTATTTTA
* **
389131 ATTACTATATTTATAG
1 ATTATTATATTTATTT
* *
389147 ATTACTATATTTTAATT
1 ATTATTATA-TTTATTT
* *
389164 ATTTATTATATTTAATA
1 A-TTATTATATTTATTT
* *
389181 ATTAATATCATTAATTATT
1 ATTATTAT-ATTTA-T-TT
389200 ATTATTATATTTATTT
1 ATTATTATATTTATTT
389216 ATTAT
1 ATTAT
389221 ATTCATTTAA
Statistics
Matches: 58, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
16 22 0.38
17 17 0.29
18 11 0.19
19 8 0.14
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (16 bp):
ATTATTATATTTATTT
Found at i:390706 original size:64 final size:64
Alignment explanation
Indices: 390622--390778 Score: 160
Period size: 64 Copynumber: 2.5 Consensus size: 64
390612 TTGAAGGTGT
* * * * *
390622 ATCGATGCACAGGTAGTGCATCGATGCA-CTCT-TTTAAAATAGAAACATCGAATGCA-ATTAGT
1 ATCGATGCATAAGCAGTGCATCGATGCATC-CTAATAAAAATA-AAACATCGAATGCATATTA-T
390684 GC
63 GC
* * *
390686 ATCGATGCATAAGGCA-TGCATCGATGCATCCTAATAAAAATACAACATCGAATGTATTTTATGC
1 ATCGATGCATAA-GCAGTGCATCGATGCATCCTAATAAAAATAAAACATCGAATGCATATTATGC
* *
390750 ATCGATGCATCAGTAGTGCATCGATGCAT
1 ATCGATGCATAAGCAGTGCATCGATGCAT
390779 ACCCTTATTG
Statistics
Matches: 78, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
63 2 0.03
64 63 0.81
65 13 0.17
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.27
Consensus pattern (64 bp):
ATCGATGCATAAGCAGTGCATCGATGCATCCTAATAAAAATAAAACATCGAATGCATATTATGC
Found at i:391977 original size:31 final size:31
Alignment explanation
Indices: 391888--392014 Score: 114
Period size: 31 Copynumber: 4.1 Consensus size: 31
391878 AGAGTCGAGG
* *
391888 GTATTCCTATGTTCTACGGAACATTTGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* * * *
391919 GAATTACCTATG-TCTTTC-GAGATATATGGGCA
1 GTA-TACCTATGTTC-TACGGA-ACATATGGACA
*
391951 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* * * *
391982 GTTTACCTAGGTTCTTCGGAACCTATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
392013 GT
1 GT
392015 TGCCGAGGAT
Statistics
Matches: 75, Mismatches: 16, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
31 52 0.69
32 23 0.31
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (31 bp):
GTATACCTATGTTCTACGGAACATATGGACA
Found at i:392053 original size:30 final size:30
Alignment explanation
Indices: 392002--392073 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
391992 GTTCTTCGGA
* * *
392002 ACCTATGGACAGTTGCCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
392032 ACCTCTGGATAGTTACCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
392062 ACCTCTGGATAG
1 ACCTCTGGATAG
392074 GTCCTTCAGG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.31
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCGAGGATCTTTATG
Found at i:396522 original size:31 final size:31
Alignment explanation
Indices: 396448--396575 Score: 111
Period size: 31 Copynumber: 4.1 Consensus size: 31
396438 AAGAGTCGAG
396448 AGTATACCTATGTTCTACG-GAACATATGGAC
1 AGTATACCTATGTTCTACGAG-ACATATGGAC
*
396479 A-TAATTACCTATG-TCTTTCGAGACATATGGAC
1 AGT-A-TACCTATGTTC-TACGAGACATATGGAC
*
396511 AGTATACCTATGTTCTAAG-GAACATATGGAC
1 AGTATACCTATGTTCTACGAG-ACATATGGAC
* * * * * *
396542 AATTTACCTAGGTTCTTCGAAACCTATGGAC
1 AGTATACCTATGTTCTACGAGACATATGGAC
396573 AGT
1 AGT
396576 TGCCGAGGAT
Statistics
Matches: 78, Mismatches: 11, Indels: 16
0.74 0.10 0.15
Matches are distributed among these distances:
30 2 0.03
31 49 0.63
32 25 0.32
33 2 0.03
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (31 bp):
AGTATACCTATGTTCTACGAGACATATGGAC
Found at i:396526 original size:63 final size:62
Alignment explanation
Indices: 396448--396575 Score: 186
Period size: 63 Copynumber: 2.0 Consensus size: 62
396438 AAGAGTCGAG
* * *
396448 AGTATACCTATGTTCTACGGAACATATGGACATAATTACCTATG-TCTTTCGAGACATATGGAC
1 AGTATACCTATGTTCTAAGGAACATATGGACA-AATTACCTAGGTTC-TTCGAAACATATGGAC
* *
396511 AGTATACCTATGTTCTAAGGAACATATGGACAATTTACCTAGGTTCTTCGAAACCTATGGAC
1 AGTATACCTATGTTCTAAGGAACATATGGACAAATTACCTAGGTTCTTCGAAACATATGGAC
396573 AGT
1 AGT
396576 TGCCGAGGAT
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
62 26 0.44
63 33 0.56
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (62 bp):
AGTATACCTATGTTCTAAGGAACATATGGACAAATTACCTAGGTTCTTCGAAACATATGGAC
Found at i:396614 original size:30 final size:30
Alignment explanation
Indices: 396563--396634 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
396553 GTTCTTCGAA
* * *
396563 ACCTATGGACAGTTGCCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
396593 ACCTCTGGATAGTTACCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATG
396623 ACCTCTGGATAG
1 ACCTCTGGATAG
396635 GTCCTTCGGA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.31
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCGAGGATCTTTATG
Found at i:397296 original size:19 final size:19
Alignment explanation
Indices: 397272--397311 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
397262 GGGTGTTACA
397272 CCATAGGTCGCCAAGTGCT
1 CCATAGGTCGCCAAGTGCT
397291 CCATAGGTCGCCAAGTGCT
1 CCATAGGTCGCCAAGTGCT
397310 CC
1 CC
397312 TTGCGACAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.20, C:0.35, G:0.25, T:0.20
Consensus pattern (19 bp):
CCATAGGTCGCCAAGTGCT
Found at i:397410 original size:30 final size:30
Alignment explanation
Indices: 397374--397440 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
397364 GCAGCTCCAT
* * * *
397374 AGGTCGCCGTGTGCTTCTGGAGACCTATGG
1 AGGTCGCCATATGCTCCTGGAGACATATGG
397404 AGGTCGCCATATGCTCCTGGAGACATATGG
1 AGGTCGCCATATGCTCCTGGAGACATATGG
*
397434 TGGTCGC
1 AGGTCGC
397441 AATCACCCTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.16, C:0.24, G:0.34, T:0.25
Consensus pattern (30 bp):
AGGTCGCCATATGCTCCTGGAGACATATGG
Found at i:400152 original size:40 final size:39
Alignment explanation
Indices: 400095--400178 Score: 100
Period size: 40 Copynumber: 2.1 Consensus size: 39
400085 AGTTGACAAG
*
400095 TTGGTTGGTGACCAACTTGTACACATTG-GAAAATTCATCT
1 TTGGTAGGTGACCAACTTGTACACA-TGAG-AAATTCATCT
* *
400135 TTGGTAGGTG-CCAAACTTGTTCACATGAGAATTTCATCT
1 TTGGTAGGTGACC-AACTTGTACACATGAGAAATTCATCT
400174 TTGGT
1 TTGGT
400179 CCCTAAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
39 18 0.46
40 21 0.54
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37
Consensus pattern (39 bp):
TTGGTAGGTGACCAACTTGTACACATGAGAAATTCATCT
Found at i:404757 original size:40 final size:40
Alignment explanation
Indices: 404702--404826 Score: 182
Period size: 40 Copynumber: 3.1 Consensus size: 40
404692 AGTTGACAAG
* *
404702 TTGGTTGGTGACCAACTTGTACACATTGGAAAATTCATCT
1 TTGGTAGGTGGCCAACTTGTACACATTGGAAAATTCATCT
404742 TTGGTAGGTGGCCAACTTGTACACATTGGAAAATTCATCT
1 TTGGTAGGTGGCCAACTTGTACACATTGGAAAATTCATCT
* *
404782 TTGGTAGGTGGCCAAACTTGTGCACA-T-GAGAATTTCATCT
1 TTGGTAGGTGGCC-AACTTGTACACATTGGA-AAATTCATCT
404822 TTGGT
1 TTGGT
404827 CCATAAAATA
Statistics
Matches: 79, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
39 2 0.03
40 66 0.84
41 11 0.14
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (40 bp):
TTGGTAGGTGGCCAACTTGTACACATTGGAAAATTCATCT
Found at i:405307 original size:21 final size:22
Alignment explanation
Indices: 405281--405321 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
405271 AAAAGTCAAA
405281 GGGGGCACCAGC-TTGCTTGGT
1 GGGGGCACCAGCTTTGCTTGGT
*
405302 GGGGGCACCGGCTTTGCTTG
1 GGGGGCACCAGCTTTGCTTG
405322 ATATTTTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.07, C:0.24, G:0.44, T:0.24
Consensus pattern (22 bp):
GGGGGCACCAGCTTTGCTTGGT
Found at i:409890 original size:21 final size:22
Alignment explanation
Indices: 409864--409904 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
409854 AAAGTCAAAG
409864 GGGGGCACCAGC-TTGCTTGGT
1 GGGGGCACCAGCTTTGCTTGGT
*
409885 GGGGGCACCGGCTTTGCTTG
1 GGGGGCACCAGCTTTGCTTG
409905 ATATTTTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.07, C:0.24, G:0.44, T:0.24
Consensus pattern (22 bp):
GGGGGCACCAGCTTTGCTTGGT
Found at i:417469 original size:2 final size:2
Alignment explanation
Indices: 417462--417490 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
417452 AGGAAAAATG
417462 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 A
417491 GGAAGATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:417993 original size:23 final size:23
Alignment explanation
Indices: 417959--418022 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
417949 TAACCTTATA
417959 TGGCACTTCGGTGAATTTCTACG
1 TGGCACTTCGGTGAATTTCTACG
* *
417982 TGGCACTACGGTGCAA-TTCTATG
1 TGGCACTTCGGTG-AATTTCTACG
*
418005 TGGCACTTCGGTGCATTT
1 TGGCACTTCGGTGAATTT
418023 ATACAAGCTG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
22 1 0.03
23 32 0.91
24 2 0.06
ACGTcount: A:0.17, C:0.22, G:0.27, T:0.34
Consensus pattern (23 bp):
TGGCACTTCGGTGAATTTCTACG
Found at i:424373 original size:3 final size:3
Alignment explanation
Indices: 424365--424401 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
424355 TGCTCTTTGT
424365 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
424402 GTTTGTCAGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:425853 original size:23 final size:23
Alignment explanation
Indices: 425818--425864 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
425808 GAGCTTCAGA
425818 ACTTGACTCGTTCAACATTCTCC
1 ACTTGACTCGTTCAACATTCTCC
* *
425841 ACTTGGCTGGTTCAACATTCTCC
1 ACTTGACTCGTTCAACATTCTCC
425864 A
1 A
425865 AACTGTTTGA
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:0.21, C:0.32, G:0.13, T:0.34
Consensus pattern (23 bp):
ACTTGACTCGTTCAACATTCTCC
Found at i:431021 original size:20 final size:20
Alignment explanation
Indices: 430998--431058 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
430988 TTGAAAATCG
430998 CATTGCGATAGTACTGTTTA
1 CATTGCGATAGTACTGTTTA
* *
431018 CATTACGATAGTATTGTTTA
1 CATTGCGATAGTACTGTTTA
* *
431038 CATTGTGATAGTACTATTTA
1 CATTGCGATAGTACTGTTTA
431058 C
1 C
431059 CTATATCGGT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.43
Consensus pattern (20 bp):
CATTGCGATAGTACTGTTTA
Found at i:431101 original size:77 final size:77
Alignment explanation
Indices: 431018--431383 Score: 598
Period size: 77 Copynumber: 4.8 Consensus size: 77
431008 GTACTGTTTA
* * *
431018 CATTACGATAGTATTGTTTACATTGTGATAGTACTATTTACCTATATCGGTAATTAGCGTTGCGA
1 CATTACGATAGTACTGTTTACATTGCGATAGTACTATTTACCTATATCGGTAATTAACGTTGCGA
431083 ATTTGAAAATCG
66 ATTTGAAAATCG
431095 CATTACGATAGTACTGTTTACATTGCGATAGTACTATTTACCTATATCGGTAATTAACGTTGCGA
1 CATTACGATAGTACTGTTTACATTGCGATAGTACTATTTACCTATATCGGTAATTAACGTTGCGA
431160 ATTTGAAAATCG
66 ATTTGAAAATCG
* * * *
431172 CATTGCGATAGTACTGTTTACATTGCGATAGTATTGTTTATCTATATCGGTAATTAACGTTGCGA
1 CATTACGATAGTACTGTTTACATTGCGATAGTACTATTTACCTATATCGGTAATTAACGTTGCGA
431237 ATTTGAAAATCG
66 ATTTGAAAATCG
* *
431249 CATTGCGATAGTACTGTTTACATTGCGATAGTACTGTTTACCTATATCGGTAATTAACGTTGCGA
1 CATTACGATAGTACTGTTTACATTGCGATAGTACTATTTACCTATATCGGTAATTAACGTTGCGA
431314 ATTTGAAAATCG
66 ATTTGAAAATCG
* *
431326 C---A--ATAGTACTGTTTACATTGCGATAGTATTATTTACCTATATCGGTAATTAGCGTTGC
1 CATTACGATAGTACTGTTTACATTGCGATAGTACTATTTACCTATATCGGTAATTAACGTTGC
431384 ACATTTTCAA
Statistics
Matches: 276, Mismatches: 13, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
72 53 0.19
77 223 0.81
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.38
Consensus pattern (77 bp):
CATTACGATAGTACTGTTTACATTGCGATAGTACTATTTACCTATATCGGTAATTAACGTTGCGA
ATTTGAAAATCG
Found at i:431123 original size:20 final size:20
Alignment explanation
Indices: 431095--431135 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
431085 TTGAAAATCG
*
431095 CATTACGATAGTACTGTTTA
1 CATTACGATAGTACTATTTA
*
431115 CATTGCGATAGTACTATTTA
1 CATTACGATAGTACTATTTA
431135 C
1 C
431136 CTATATCGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (20 bp):
CATTACGATAGTACTATTTA
Found at i:431135 original size:97 final size:97
Alignment explanation
Indices: 430957--431135 Score: 313
Period size: 97 Copynumber: 1.8 Consensus size: 97
430947 GATAGTTGTG
*
430957 TTTACCTATATCGGTAATTAGAGTTGCGAATTTGAAAATCGCATTGCGATAGTACTGTTTACATT
1 TTTACCTATATCGGTAATTAGAGTTGCGAATTTGAAAATCGCATTACGATAGTACTGTTTACATT
* *
431022 ACGATAGTATTGTTTACATTGTGATAGTACTA
66 ACGATAGTACTATTTACATTGTGATAGTACTA
*
431054 TTTACCTATATCGGTAATTAGCGTTGCGAATTTGAAAATCGCATTACGATAGTACTGTTTACATT
1 TTTACCTATATCGGTAATTAGAGTTGCGAATTTGAAAATCGCATTACGATAGTACTGTTTACATT
*
431119 GCGATAGTACTATTTAC
66 ACGATAGTACTATTTAC
431136 CTATATCGGT
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
97 77 1.00
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.39
Consensus pattern (97 bp):
TTTACCTATATCGGTAATTAGAGTTGCGAATTTGAAAATCGCATTACGATAGTACTGTTTACATT
ACGATAGTACTATTTACATTGTGATAGTACTA
Found at i:431195 original size:20 final size:20
Alignment explanation
Indices: 431172--431211 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
431162 TTGAAAATCG
431172 CATTGCGATAGTACTGTTTA
1 CATTGCGATAGTACTGTTTA
*
431192 CATTGCGATAGTATTGTTTA
1 CATTGCGATAGTACTGTTTA
431212 TCTATATCGG
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:0.25, C:0.12, G:0.20, T:0.42
Consensus pattern (20 bp):
CATTGCGATAGTACTGTTTA
Found at i:431272 original size:20 final size:20
Alignment explanation
Indices: 431249--431289 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
431239 TTGAAAATCG
431249 CATTGCGATAGTACTGTTTA
1 CATTGCGATAGTACTGTTTA
431269 CATTGCGATAGTACTGTTTA
1 CATTGCGATAGTACTGTTTA
431289 C
1 C
431290 CTATATCGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (20 bp):
CATTGCGATAGTACTGTTTA
Found at i:434772 original size:15 final size:15
Alignment explanation
Indices: 434752--434801 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
434742 CTGCAAAGAA
*
434752 AATAATACTAATACT
1 AATAATACTAATAAT
434767 AATAATACTAATAAT
1 AATAATACTAATAAT
* *
434782 AATAATAATAAGAAT
1 AATAATACTAATAAT
434797 AATAA
1 AATAA
434802 AATGTGTATG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.30
Consensus pattern (15 bp):
AATAATACTAATAAT
Found at i:434792 original size:6 final size:6
Alignment explanation
Indices: 434752--434801 Score: 64
Period size: 6 Copynumber: 8.3 Consensus size: 6
434742 CTGCAAAGAA
* * * *
434752 AATAAT ACTAAT ACTAAT AATACT AATAAT AATAAT AATAAG AATAAT
1 AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT AATAAT
434800 AA
1 AA
434802 AATGTGTATG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.30
Consensus pattern (6 bp):
AATAAT
Found at i:434792 original size:9 final size:9
Alignment explanation
Indices: 434752--434801 Score: 64
Period size: 9 Copynumber: 5.6 Consensus size: 9
434742 CTGCAAAGAA
*
434752 AATAATACT
1 AATAATAAT
*
434761 AATACTAAT
1 AATAATAAT
*
434770 AATACTAAT
1 AATAATAAT
434779 AATAATAAT
1 AATAATAAT
*
434788 AATAAGAAT
1 AATAATAAT
434797 AATAA
1 AATAA
434802 AATGTGTATG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.30
Consensus pattern (9 bp):
AATAATAAT
Found at i:435825 original size:20 final size:22
Alignment explanation
Indices: 435802--435850 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 22
435792 GATGGAGCCG
435802 TTGACCAATTGACT-TTGA-TT
1 TTGACCAATTGACTGTTGACTT
**
435822 TTGACCCGTTGACTGTTGACTT
1 TTGACCAATTGACTGTTGACTT
435844 TT-ACCAA
1 TTGACCAA
435851 AAAGTCAACT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 12 0.52
21 7 0.30
22 4 0.17
ACGTcount: A:0.22, C:0.20, G:0.16, T:0.41
Consensus pattern (22 bp):
TTGACCAATTGACTGTTGACTT
Found at i:438933 original size:111 final size:112
Alignment explanation
Indices: 438726--438949 Score: 398
Period size: 111 Copynumber: 2.0 Consensus size: 112
438716 CCGAGTGATG
*
438726 ATGATGTTATCAGTGATTGCTCTGCTTGGAACAAAACACGTTCGGTTAGTCGACACCCATTCTGG
1 ATGATGTTATCAGTGATTGCTCTGCTTGGAACAAAACAAGTTCGGTTAGTCGACACCCATTCTGG
*
438791 CAAAACCGGTTTAAGTTTGTTGACAATGATTTTGGTGATTATCTTAT
66 CAAAACCGGTTTAAGTCTGTTGACAATGATTTTGGTGATTATCTTAT
*
438838 ATGATGTTATCGGTGATTGCTCTGCTTGGAACAAAACAAGTTCGG-TATGTC-ACACCCATTCTG
1 ATGATGTTATCAGTGATTGCTCTGCTTGGAACAAAACAAGTTCGGTTA-GTCGACACCCATTCTG
438901 GCAAAACCGGTTTAAGTCTGTTGACAATGATTTTGGTGATTATCTTAT
65 GCAAAACCGGTTTAAGTCTGTTGACAATGATTTTGGTGATTATCTTAT
438949 A
1 A
438950 ACACATTACA
Statistics
Matches: 108, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
111 62 0.57
112 46 0.43
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.35
Consensus pattern (112 bp):
ATGATGTTATCAGTGATTGCTCTGCTTGGAACAAAACAAGTTCGGTTAGTCGACACCCATTCTGG
CAAAACCGGTTTAAGTCTGTTGACAATGATTTTGGTGATTATCTTAT
Found at i:445111 original size:17 final size:16
Alignment explanation
Indices: 445078--445111 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
445068 GACAAAATAT
*
445078 TTTACTATTCATGAAA
1 TTTACTATTCACGAAA
445094 TTTACTATTCACGTAAA
1 TTTACTATTCACG-AAA
445111 T
1 T
445112 AGTAATGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44
Consensus pattern (16 bp):
TTTACTATTCACGAAA
Found at i:446738 original size:13 final size:13
Alignment explanation
Indices: 446701--446740 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
446691 CAAATACCTA
446701 AAAATAAATA-TT
1 AAAATAAATATTT
*
446713 AAAATAATTTATTT
1 AAAATAA-ATATTT
446727 AAAATAAATATTT
1 AAAATAAATATTT
446740 A
1 A
446741 TTTATTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 7 0.29
13 8 0.33
14 9 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATAAATATTT
Found at i:447961 original size:44 final size:44
Alignment explanation
Indices: 447911--448013 Score: 197
Period size: 44 Copynumber: 2.3 Consensus size: 44
447901 GGCACTGGCA
*
447911 GCAGAGGCGGCTGGAAGCTGGACCGTTGGCTGAGGCGGTTGGAG
1 GCAGAGGCGGCTGGAAGCTGGACCGTTGGCTGAGGCAGTTGGAG
447955 GCAGAGGCGGCTGGAAGCTGGACCGTTGGCTGAGGCAGTTGGAG
1 GCAGAGGCGGCTGGAAGCTGGACCGTTGGCTGAGGCAGTTGGAG
447999 GCAGAGGCGGCTGGA
1 GCAGAGGCGGCTGGA
448014 GGCAGAGGCG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 58 1.00
ACGTcount: A:0.17, C:0.18, G:0.50, T:0.15
Consensus pattern (44 bp):
GCAGAGGCGGCTGGAAGCTGGACCGTTGGCTGAGGCAGTTGGAG
Found at i:447963 original size:16 final size:16
Alignment explanation
Indices: 447942--448024 Score: 66
Period size: 16 Copynumber: 5.4 Consensus size: 16
447932 ACCGTTGGCT
447942 GAGGCGGTTGGAGGCA
1 GAGGCGGTTGGAGGCA
* * *
447958 GAGGCGGCTGGAAGCT
1 GAGGCGGTTGGAGGCA
* * *
447974 G-GACCGTT---GGCT
1 GAGGCGGTTGGAGGCA
*
447986 GAGGCAGTTGGAGGCA
1 GAGGCGGTTGGAGGCA
*
448002 GAGGCGGCTGGAGGCA
1 GAGGCGGTTGGAGGCA
448018 GAGGCGG
1 GAGGCGG
448025 CTAGGGTTAG
Statistics
Matches: 51, Mismatches: 12, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
12 4 0.08
13 5 0.10
15 4 0.08
16 38 0.75
ACGTcount: A:0.18, C:0.17, G:0.53, T:0.12
Consensus pattern (16 bp):
GAGGCGGTTGGAGGCA
Found at i:448147 original size:3 final size:3
Alignment explanation
Indices: 448139--448260 Score: 129
Period size: 3 Copynumber: 41.0 Consensus size: 3
448129 TATATATATT
* * *
448139 TAA TAA TAA TAA TAA TAA TAT TTA TAA TAA TAA TAA TAA TAA TAA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
448187 TTA TAG TAA TAA TAA TAA TAA TAA TAT TTA TAG TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
448235 TTA TTA TTA TTA T-A TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
448261 ATAAATCAAA
Statistics
Matches: 101, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
2 2 0.02
3 99 0.98
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:448177 original size:27 final size:27
Alignment explanation
Indices: 448139--448260 Score: 185
Period size: 27 Copynumber: 4.6 Consensus size: 27
448129 TATATATATT
448139 TAATAATAATAATAATAATATTTATAA
1 TAATAATAATAATAATAATATTTATAA
*
448166 TAATAATAATAATAATAATATTTATAG
1 TAATAATAATAATAATAATATTTATAA
*
448193 TAATAATAATAATAATAATATTTATAG
1 TAATAATAATAATAATAATATTTATAA
* *
448220 TAATAATAATAATAATTAT-TATTATTA
1 TAATAATAATAATAATAATAT-TTATAA
448247 T-ATAATAATAATAA
1 TAATAATAATAATAA
448261 ATAAATCAAA
Statistics
Matches: 90, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
26 14 0.16
27 76 0.84
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (27 bp):
TAATAATAATAATAATAATATTTATAA
Found at i:448871 original size:24 final size:23
Alignment explanation
Indices: 448834--448880 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
448824 GTTGAACAAA
448834 TTCTTCTTATTATGAACTTCTTCT
1 TTCTTCTTATTATG-ACTTCTTCT
*
448858 TTCTTCTTCA-TATGAGTTCTTCT
1 TTCTTCTT-ATTATGACTTCTTCT
448881 CATTATGAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 8 0.38
24 12 0.57
25 1 0.05
ACGTcount: A:0.15, C:0.21, G:0.06, T:0.57
Consensus pattern (23 bp):
TTCTTCTTATTATGACTTCTTCT
Found at i:449267 original size:113 final size:112
Alignment explanation
Indices: 448592--449268 Score: 1016
Period size: 113 Copynumber: 6.0 Consensus size: 112
448582 ATAGAATTAT
* * * * *
448592 GCAAAAAGTTGAACAAGTTCTTATTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTC
**
448657 ATTATGAAC-TTCTCTGGAAAAGCTGCTCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGG-AAAGCTAATCCATCAAGTGATGGATTTGA
* *
448704 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGACGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTC
* * **
448769 ATTATGAACTTTCTCTGGAAAGGCTGATCCATCAAGTGATGAATTCAA
66 ATTATGAACTTTCTCTGGAAA-GCTAATCCATCAAGTGATGGATTTGA
* * * *
448817 GCAAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTTCTTCTTCATATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTC
*
448882 ATTATGAACTTTCTCTGGCGAAGCTAATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGG-AAAGCTAATCCATCAAGTGATGGATTTGA
* * *
448930 ACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTT-ATTCATTCTTCAGATGAGTTCTTCT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCA-TCCTTCTTCAGATGAGTTCTTCT
448994 CATTATGAACTTTCTCTGGCAAAGCTAATCCATCAAGTGATGGATTTGA
65 CATTATGAACTTTCTCTGG-AAAGCTAATCCATCAAGTGATGGATTTGA
449043 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTC
* ** * *
449108 ATTATGAACTCTAACTGGAAAAGATAATCCATCAAGTGATAGATTTGA
66 ATTATGAACTTTCTCTGG-AAAGCTAATCCATCAAGTGATGGATTTGA
449156 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTC
* * *
449221 ATTATGAACTTCCTCTGGAAAGGCTGATCCATCAAATGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAA-GCTAATCCATCAAGTGATGGATTTGA
449269 ATCTTTGTTA
Statistics
Matches: 516, Mismatches: 43, Indels: 11
0.91 0.08 0.02
Matches are distributed among these distances:
112 75 0.15
113 438 0.85
114 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (112 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTCTGGAAAGCTAATCCATCAAGTGATGGATTTGA
Found at i:450307 original size:83 final size:83
Alignment explanation
Indices: 450040--450798 Score: 1263
Period size: 83 Copynumber: 9.0 Consensus size: 83
450030 CTTATTTCTA
*
450040 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACCCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
*
450105 GAACATTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* * *
450123 CTATTG-GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGCTAAACCA-ATCAGATAACCCAA
1 CTA-TGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAA
450186 AGAACACTTCCA-AAGATG
65 AGAACACTTCCAGAAGATG
450204 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
450269 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
450287 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
450352 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* *
450370 CTATGAGCAAATTCATCTTCCAAATTCAGTGATTGGTTCTGCTAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
*
450435 GAACACTTCCAGAAAGATA
66 GAACACTTCCAG-AAGATG
450454 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
450519 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
*
450537 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCTAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
450602 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
*
450620 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCTAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
450685 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
** * * *
450703 CTATGAGCAAATTCATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGACCAGA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGA------TT--GGTTC-TGCCAAACCAGATCAGA
450768 TAACTCAAAGAACACTTCCAGAAGATG
57 TAACTCAAAGAACACTTCCAGAAGATG
450795 CTAT
1 CTAT
450799 TGAGTCTTCT
Statistics
Matches: 643, Mismatches: 19, Indels: 19
0.94 0.03 0.03
Matches are distributed among these distances:
80 2 0.00
81 50 0.08
82 50 0.08
83 407 0.63
84 82 0.13
89 2 0.00
91 5 0.01
92 45 0.07
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.26
Consensus pattern (83 bp):
CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATG
Found at i:450586 original size:250 final size:250
Alignment explanation
Indices: 450040--450798 Score: 1285
Period size: 250 Copynumber: 3.0 Consensus size: 250
450030 CTTATTTCTA
*
450040 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACCCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
* *
450105 GAACATTTCCAGAAGATGCTATTG-GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGCTAAA
66 GAACACTTCCAGAAGATGCTA-TGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCTAAA
*
450169 CCA-ATCAGATAACCCAAAGAACACTTCC--AAAGATGCTATGAGCAAATTCATCTTCCAAATTC
130 CCAGATCAGATAACTCAAAGAACACTTCCAGAAAGATGCTATGAGCAAATTCATCTTCCAAATTC
450231 AATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
195 AATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
450287 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
*
450352 GAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAAATTCAGTGATTGGTTCTGCTAAAC
66 GAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCTAAAC
*
450417 CAGATCAGATAACTCAAAGAACACTTCCAGAAAGATACTATGAGCAAATTCATCTTCCAAATTCA
131 CAGATCAGATAACTCAAAGAACACTTCCAGAAAGATGCTATGAGCAAATTCATCTTCCAAATTCA
450482 ATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
196 ATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
*
450537 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCTAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
450602 GAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCTAAAC
66 GAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCTAAAC
** *
450667 CAGATCAGATAACTCAAAGAACACTTCCAG-AAGATGCTATGAGCAAATTCATCTTTTAAATCCA
131 CAGATCAGATAACTCAAAGAACACTTCCAGAAAGATGCTATGAGCAAATTCATCTTCCAAATTCA
* *
450731 ATGATTGGTTTTGGGGTTCATACCAAACCAGACCAGATAACTCAAAGAACACTTCCAGAAGATG
196 ATGA------TT--GGTTC-TGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
450795 CTAT
1 CTAT
450799 TGAGTCTTCT
Statistics
Matches: 485, Mismatches: 14, Indels: 15
0.94 0.03 0.03
Matches are distributed among these distances:
246 2 0.00
247 125 0.26
248 24 0.05
249 34 0.07
250 247 0.51
255 2 0.00
257 5 0.01
258 46 0.09
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.26
Consensus pattern (250 bp):
CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCTAAAC
CAGATCAGATAACTCAAAGAACACTTCCAGAAAGATGCTATGAGCAAATTCATCTTCCAAATTCA
ATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
Found at i:450643 original size:333 final size:329
Alignment explanation
Indices: 450040--450798 Score: 1257
Period size: 333 Copynumber: 2.3 Consensus size: 329
450030 CTTATTTCTA
* *
450040 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACCCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCTAAACCAGATCAGATAACTCAAA
* * *
450105 GAACATTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAATGATTGGTTCTGCTAAAC
66 GAACACTTCCAGAAGATGCTA-TGGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAAC
450170 CAATCAGATAACCCAAAGAACACTTCCAAAGATGCTATGAGCAAATTCATCTTCCAAATTCAATG
130 CAATCAGATAACCCAAAGAACACTTCCAAAGATGCTATGAGCAAATTCATCTTCCAAATTCAATG
450235 ATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATT
195 ATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATT
450300 CATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGA
260 CATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGA
450365 AGATG
325 AGATG
*
450370 CTATGAGCAAATTCATCTTCCAAATTCAGTGATTGGTTCTGCTAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCTAAACCAGATCAGATAACTCAAA
*
450435 GAACACTTCCAGAAAGATACTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAA
66 GAACACTTCCAG-AAGATGCTATG-GCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAA
*
450500 CCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAAATTCA
129 CCA-ATCAGATAACCCAAAGAACACTTCCA-AAGATGCTATGAGCAAATTCATCTTCCAAATTCA
*
450565 ATGATTGGTTCTGCTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAA
192 ATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAA
*
450630 ATTCATCTTCCAAATTCAATGATTGGTTCTGCTAAACCAGATCAGATAACTCAAAGAACACTTCC
257 ATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCC
450695 AGAAGATG
322 AGAAGATG
** * * *
450703 CTATGAGCAAATTCATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGACCAGA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCT---G--C-T---AAACCAGATCAGA
450768 TAACTCAAAGAACACTTCCAGAAGATGCTAT
57 TAACTCAAAGAACACTTCCAGAAGATGCTAT
450799 TGAGTCTTCT
Statistics
Matches: 399, Mismatches: 17, Indels: 15
0.93 0.04 0.03
Matches are distributed among these distances:
330 75 0.19
331 49 0.12
332 25 0.06
333 205 0.51
336 1 0.00
338 1 0.00
339 1 0.00
341 9 0.02
342 33 0.08
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.26
Consensus pattern (329 bp):
CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCTAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATGCTATGGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACC
AATCAGATAACCCAAAGAACACTTCCAAAGATGCTATGAGCAAATTCATCTTCCAAATTCAATGA
TTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTC
ATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAA
GATG
Found at i:453097 original size:10 final size:10
Alignment explanation
Indices: 453082--453110 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
453072 TCAATTTTCC
453082 TTTTTCTTTT
1 TTTTTCTTTT
453092 TTTTTCTTTT
1 TTTTTCTTTT
453102 TTTTTCTTT
1 TTTTTCTTT
453111 CTTTGCTGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:456410 original size:14 final size:14
Alignment explanation
Indices: 456376--456429 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
456366 TTGTGCAATA
* *
456376 CAAATGCAAAGATG
1 CAAATGTAAATATG
456390 CCAAATGTAAATATG
1 -CAAATGTAAATATG
*
456405 CAAATGTAAAAATG
1 CAAATGTAAATATG
*
456419 TAAATGTAAAT
1 CAAATGTAAAT
456430 TATTTAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (14 bp):
CAAATGTAAATATG
Found at i:458757 original size:13 final size:13
Alignment explanation
Indices: 458720--458759 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
458710 TCGATATTGA
458720 AAAATAAATA-TT
1 AAAATAAATATTT
*
458732 AAAATAATTTATTT
1 AAAATAA-ATATTT
458746 AAAATAAATATTT
1 AAAATAAATATTT
458759 A
1 A
458760 TTTATTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 7 0.29
13 8 0.33
14 9 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATAAATATTT
Found at i:459996 original size:16 final size:16
Alignment explanation
Indices: 459975--460015 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
459965 ACCGTTGGCT
*
459975 GAGGCGGTTGGAGGCA
1 GAGGCGGCTGGAGGCA
459991 GAGGCGGCTGGAGGCA
1 GAGGCGGCTGGAGGCA
460007 GAGGCGGCT
1 GAGGCGGCT
460016 AGGGTTAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.56, T:0.10
Consensus pattern (16 bp):
GAGGCGGCTGGAGGCA
Found at i:460140 original size:3 final size:3
Alignment explanation
Indices: 460132--460248 Score: 162
Period size: 3 Copynumber: 39.0 Consensus size: 3
460122 TATATATATT
* *
460132 TAA TAA TAA TAA TAA TAA TAT TTA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * *
460180 TAA TAT TTA TAG TAA TAA TAA TAA TAA TAA TAA TAT TTA TAG TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
460228 TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
460249 ATAAATCAAA
Statistics
Matches: 98, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 98 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:460168 original size:30 final size:30
Alignment explanation
Indices: 460132--460244 Score: 190
Period size: 30 Copynumber: 3.7 Consensus size: 30
460122 TATATATATT
*
460132 TAATAATAATAATAATAATATTTATAATAATAA
1 TAATAATAATAATAATAATA-TT-T-ATAGTAA
460165 TAATAATAATAATAATAATATTTATAGTAA
1 TAATAATAATAATAATAATATTTATAGTAA
460195 TAATAATAATAATAATAATATTTATAGTAA
1 TAATAATAATAATAATAATATTTATAGTAA
460225 TAATAATAATAATAATAATA
1 TAATAATAATAATAATAATA
460245 ATAAATAAAT
Statistics
Matches: 79, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
30 56 0.71
31 1 0.01
32 2 0.03
33 20 0.25
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (30 bp):
TAATAATAATAATAATAATATTTATAGTAA
Found at i:461126 original size:23 final size:22
Alignment explanation
Indices: 461099--461173 Score: 78
Period size: 23 Copynumber: 3.3 Consensus size: 22
461089 TATTTGGATA
*
461099 TTAAATTATAATTAAATATATTT
1 TTAAAATATAATT-AATATATTT
* *
461122 TTAAAATATAATTAATACAATAT
1 TTAAAATATAATTAATA-TATTT
* *
461145 TTAAAATAAAATTTAATTTATTT
1 TTAAAATATAA-TTAATATATTT
461168 TTAAAA
1 TTAAAA
461174 AATTAAATTT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
22 4 0.09
23 34 0.79
24 5 0.12
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (22 bp):
TTAAAATATAATTAATATATTT
Found at i:461201 original size:25 final size:24
Alignment explanation
Indices: 461147--461192 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
461137 TACAATATTT
461147 AAAATAAAATTTAATTTATTTTTAA
1 AAAATAAAATTTAA-TTATTTTTAA
*
461172 AAAATTAAATTTAA-TATTTTT
1 AAAATAAAATTTAATTATTTTT
461193 CATATAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 7 0.35
25 13 0.65
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
AAAATAAAATTTAATTATTTTTAA
Found at i:462003 original size:29 final size:29
Alignment explanation
Indices: 461961--462035 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 29
461951 AACCCAACCA
* **
461961 TAGGTCGCCGTGCACTCCCAGCGACCTCC
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
* * *
461990 TAGGTCGCCATGCACGCCCGGCGACCAAG
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
*
462019 GAGGTCGCCATGCACTC
1 TAGGTCGCCATGCACTC
462036 GGGGCGACCA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.17, C:0.40, G:0.28, T:0.15
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCCAGCGACCAAC
Found at i:462041 original size:29 final size:29
Alignment explanation
Indices: 461991--462049 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
461981 GCGACCTCCT
461991 AGGTCGCCATGCACGCCCGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
* **
462020 AGGTCGCCATGCACTCGGGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
462049 A
1 A
462050 TTCATGCATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.22, C:0.34, G:0.36, T:0.08
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGCGACCAAGG
Found at i:462301 original size:29 final size:29
Alignment explanation
Indices: 462266--462352 Score: 120
Period size: 29 Copynumber: 3.0 Consensus size: 29
462256 GTTGGCTGGT
*
462266 AGGTCGCAGGGCATGCATGGCGACCTACC
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
* ***
462295 AGGTCGCTGGGCGTGCATGGCGACCTGGT
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
*
462324 AGGTCGCCGGGCGTGCATGGCGACCTACC
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
462353 CCCGGTGCTG
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.15, C:0.30, G:0.39, T:0.16
Consensus pattern (29 bp):
AGGTCGCAGGGCGTGCATGGCGACCTACC
Found at i:464573 original size:194 final size:194
Alignment explanation
Indices: 464244--464602 Score: 459
Period size: 194 Copynumber: 1.9 Consensus size: 194
464234 GTATATCGTC
* * *
464244 ACCTAATAATAGAATGGATGACATTTATATATAACGTCACTATATAATTAATATTCAATGACAAC
1 ACCTAATAATAGAATGAATGACATTTATACATAACATCACTATATAATTAATATTCAATGACAAC
** ** * *
464309 TAATTATGTCACTAAATTATGTAAAATTTCGTTATTAATGATTTATATCGTCACGAATAATACAT
66 TAATTACATCACTAAATTAAATAAAATTTCGTTATTAATAATTTATATCGTCACAAATAATACAT
*
464374 TAAAATCAA-TCTATATATGACAAAAGAGCTATTGTCATATTTTTAGTGACATAATATAAATGTT
131 TAAAATCAACT-TATATATGACAAAAGAGATATTGTCATATTTTTAGTGACATAATATAAATGTT
** * * * * * **
464438 ACCTAATAATATTATGAATGACGTTTATGCATAACATCACTTTATAATTTATATTCTATGACAGT
1 ACCTAATAATAGAATGAATGACATTTATACATAACATCACTATATAATTAATATTCAATGACAAC
** * * * *
464503 TGGTTACATCACTAAATTAAATAAGATTTCGTTATTGATAATTTATATTGTCACAAATAATGCAT
66 TAATTACATCACTAAATTAAATAAAATTTCGTTATTAATAATTTATATCGTCACAAATAATACAT
* *
464568 TAAAATCAACTTATATCTGACGAAAGAGATATTGT
131 TAAAATCAACTTATATATGACAAAAGAGATATTGT
464603 AGCAAACACA
Statistics
Matches: 137, Mismatches: 27, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
194 136 0.99
195 1 0.01
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (194 bp):
ACCTAATAATAGAATGAATGACATTTATACATAACATCACTATATAATTAATATTCAATGACAAC
TAATTACATCACTAAATTAAATAAAATTTCGTTATTAATAATTTATATCGTCACAAATAATACAT
TAAAATCAACTTATATATGACAAAAGAGATATTGTCATATTTTTAGTGACATAATATAAATGTT
Found at i:466639 original size:37 final size:37
Alignment explanation
Indices: 466595--466669 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
466585 TGAAGTAAAT
466595 ACTATTTTTAACAATTTCATAATAAATAATTACTCCA
1 ACTATTTTTAACAATTTCATAATAAATAATTACTCCA
466632 ACTATTTTTAACAATTTCATAATAAATAATTACTCCA
1 ACTATTTTTAACAATTTCATAATAAATAATTACTCCA
466669 A
1 A
466670 TGCAAAGTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (37 bp):
ACTATTTTTAACAATTTCATAATAAATAATTACTCCA
Found at i:471104 original size:14 final size:13
Alignment explanation
Indices: 471048--471104 Score: 51
Period size: 14 Copynumber: 4.0 Consensus size: 13
471038 TTTTAATTAT
471048 ATATTAATAAAATA
1 ATATTAATAAAA-A
*
471062 ATAATAATAAAAA
1 ATATTAATAAAAA
*
471075 ATATTATGTCACAAAA
1 ATATTA-AT-A-AAAA
471091 ATTATTAATAAAAA
1 A-TATTAATAAAAA
471105 TAAATTATAG
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
13 6 0.17
14 16 0.46
15 2 0.06
16 6 0.17
17 5 0.14
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.32
Consensus pattern (13 bp):
ATATTAATAAAAA
Found at i:481365 original size:16 final size:16
Alignment explanation
Indices: 481344--481378 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
481334 TTCATTAAAC
481344 ATAAGAAATTACATAG
1 ATAAGAAATTACATAG
481360 ATAAGAAATTACATAG
1 ATAAGAAATTACATAG
481376 ATA
1 ATA
481379 CAACCAGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.57, C:0.06, G:0.11, T:0.26
Consensus pattern (16 bp):
ATAAGAAATTACATAG
Found at i:482397 original size:27 final size:27
Alignment explanation
Indices: 482367--482418 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
482357 TCTCCGCGTG
*
482367 TTCCAGCACTACCTCGTGTTCCACCGT
1 TTCCAACACTACCTCGTGTTCCACCGT
*
482394 TTCCAACACTTCCTCGTGTTCCACC
1 TTCCAACACTACCTCGTGTTCCACC
482419 ACTTCCTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.15, C:0.42, G:0.12, T:0.31
Consensus pattern (27 bp):
TTCCAACACTACCTCGTGTTCCACCGT
Found at i:482424 original size:27 final size:27
Alignment explanation
Indices: 482367--482424 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
482357 TCTCCGCGTG
* **
482367 TTCCAGCACTACCTCGTGTTCCACCGT
1 TTCCAACACTACCTCGTGTTCCACCAC
*
482394 TTCCAACACTTCCTCGTGTTCCACCAC
1 TTCCAACACTACCTCGTGTTCCACCAC
482421 TTCC
1 TTCC
482425 TTGATTTGCG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.16, C:0.43, G:0.10, T:0.31
Consensus pattern (27 bp):
TTCCAACACTACCTCGTGTTCCACCAC
Found at i:489843 original size:18 final size:18
Alignment explanation
Indices: 489820--489862 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
489810 CTTTAATTTG
489820 TTTATTTAATTATTT-TCC
1 TTTATTTAATT-TTTATCC
*
489838 TTTATTTAATTTTTATCT
1 TTTATTTAATTTTTATCC
489856 TTTATTT
1 TTTATTT
489863 TTTTAAAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 3 0.13
18 20 0.87
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTAATTTTTATCC
Found at i:489921 original size:28 final size:28
Alignment explanation
Indices: 489891--489952 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
489881 CAAAACCTCT
*
489891 TTTTA-TATTTACTACTATTATTTATTA
1 TTTTATTATTTACCACTATTATTTATTA
* *
489918 TTTTATTATTTTCCATTATTATTTATT-
1 TTTTATTATTTACCACTATTATTTATTA
489945 TTATTATT
1 TT-TTATT
489953 TTTCTTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 7 0.23
28 23 0.77
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (28 bp):
TTTTATTATTTACCACTATTATTTATTA
Found at i:489935 original size:25 final size:25
Alignment explanation
Indices: 489907--489954 Score: 80
Period size: 25 Copynumber: 1.9 Consensus size: 25
489897 ATTTACTACT
489907 ATTATT-TATTATTTTATTATTTTCC
1 ATTATTAT-TTATTTTATTATTTTCC
489932 ATTATTATTTATTTTATTATTTT
1 ATTATTATTTATTTTATTATTTT
489955 TCTTTTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 21 0.95
26 1 0.05
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (25 bp):
ATTATTATTTATTTTATTATTTTCC
Found at i:491132 original size:21 final size:21
Alignment explanation
Indices: 491090--491132 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
491080 TTTCTGGGCT
* * *
491090 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
491111 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
491132 A
1 A
491133 ACAAACCAGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:492764 original size:23 final size:23
Alignment explanation
Indices: 492730--492797 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
492720 ATTATTATAT
492730 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
*
492753 GGCACT-CTGGTGCAATTCTACGT
1 GGCACTAC-GGTGCAATTCTACGC
* * *
492776 GGCACTTCGGTGTAATTATACG
1 GGCACTACGGTGCAATTCTACG
492798 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
22 1 0.03
23 38 0.95
24 1 0.03
ACGTcount: A:0.21, C:0.25, G:0.26, T:0.28
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:496404 original size:21 final size:21
Alignment explanation
Indices: 496362--496404 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
496352 TTTCTGGGCT
* * *
496362 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
496383 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
496404 A
1 A
496405 ACGAACCAGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:498035 original size:23 final size:23
Alignment explanation
Indices: 498002--498069 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
497992 ATTATTATAT
498002 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* * *
498025 GGCACTCCGGTGTAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* *
498048 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
498070 AGTTGTGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:506326 original size:20 final size:20
Alignment explanation
Indices: 506301--506339 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
506291 CGATTAACTT
*
506301 AAAAATCTAAATGTTGACCC
1 AAAAATCTAAAGGTTGACCC
506321 AAAAATCTAAAGGTTGACC
1 AAAAATCTAAAGGTTGACC
506340 TGAATTGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (20 bp):
AAAAATCTAAAGGTTGACCC
Found at i:508824 original size:21 final size:21
Alignment explanation
Indices: 508781--508824 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
508771 GTAATCTACA
*
508781 ATATTGATTTGACAGTTCACG
1 ATATTGATTTGACAGTACACG
*
508802 ATATT-ATTGTGACAGTACTCG
1 ATATTGATT-TGACAGTACACG
508823 AT
1 AT
508825 GGACGATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.39
Consensus pattern (21 bp):
ATATTGATTTGACAGTACACG
Found at i:509590 original size:18 final size:17
Alignment explanation
Indices: 509567--509600 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
509557 AATAGTAAGT
509567 TTATAAAATATATTTTTA
1 TTAT-AAATATATTTTTA
*
509585 TTATAATTATATTTTT
1 TTATAAATATATTTTT
509601 TATTTATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTATAAATATATTTTTA
Found at i:509601 original size:19 final size:20
Alignment explanation
Indices: 509574--509616 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
509564 AGTTTATAAA
*
509574 ATATATTTTTA-TTATAATT
1 ATATTTTTTTATTTATAATT
509593 ATA-TTTTTTATTTATAATT
1 ATATTTTTTTATTTATAATT
*
509612 TTATT
1 ATATT
509617 ATATTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 6 0.30
19 13 0.65
20 1 0.05
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
ATATTTTTTTATTTATAATT
Found at i:509618 original size:15 final size:16
Alignment explanation
Indices: 509575--509621 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
509565 GTTTATAAAA
*
509575 TATATTTTTATTATAAT
1 TATAATTTTATTAT-AT
509592 TAT-ATTTT-TTAT-T
1 TATAATTTTATTATAT
509605 TATAATTTTATTATAT
1 TATAATTTTATTATAT
509621 T
1 T
509622 TTAAATTGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
13 4 0.15
14 5 0.19
15 8 0.31
16 6 0.23
17 3 0.12
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TATAATTTTATTATAT
Found at i:510253 original size:20 final size:21
Alignment explanation
Indices: 510230--510272 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
510220 TGTAAATATT
*
510230 ATTTAAAATAT-ATATTTTTA
1 ATTTAAAATATAATATTTATA
*
510250 ATTTACAATATAATATTTATA
1 ATTTAAAATATAATATTTATA
510271 AT
1 AT
510273 CGACATTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTTAAAATATAATATTTATA
Found at i:511726 original size:229 final size:229
Alignment explanation
Indices: 511299--512016 Score: 1325
Period size: 228 Copynumber: 3.1 Consensus size: 229
511289 GTTATATTGT
* * *
511299 AAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGT-GAAAATATATTTATTATT
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
511363 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAA
66 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAA
*
511428 TAATTTTGTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
131 TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
*
511493 AAAAAATTGAAAAATAAATTACATAACTTTAAAA
196 AAAAAATTGAAACATAAATTACATAACTTTAAAA
* * *
511527 GAAGTATATATCATTTTTATAAAATTGTTCATACTTATTTCACTGTGGAAAACATATTTATTATT
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
511592 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAA
66 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAA
511657 TAATTTTTTGTGTAAA-GAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
131 TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
511721 AAAAAATTGAAACATAAATTACATAACTTTAAAA
196 AAAAAATTGAAACATAAATTACATAACTTTAAAA
511755 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
* *
511820 ATATTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAAAATCAAA
66 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAA
511885 TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-A
131 TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
511949 AAAAAATTGAAACATAAATTACATAACTTTAAAA
196 AAAAAATTGAAACATAAATTACATAACTTTAAAA
511983 AAAGTATATATCATTTTTATAAAAGTGTCCATAC
1 AAAGTATATATCATTTTTATAAAAGTGTCCATAC
512017 GTATAAAAGT
Statistics
Matches: 475, Mismatches: 13, Indels: 4
0.97 0.03 0.01
Matches are distributed among these distances:
228 332 0.70
229 143 0.30
ACGTcount: A:0.45, C:0.07, G:0.08, T:0.39
Consensus pattern (229 bp):
AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAA
TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
AAAAAATTGAAACATAAATTACATAACTTTAAAA
Found at i:512088 original size:20 final size:19
Alignment explanation
Indices: 512065--512111 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
512055 CGATATACCA
*
512065 GGTAAAAATTTGATAAAACC
1 GGTAAAAA-ATGATAAAACC
512085 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
512105 GGTAAAA
1 GGTAAAA
512112 CGTTACCGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 2 0.08
20 20 0.80
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:512269 original size:20 final size:19
Alignment explanation
Indices: 512246--512292 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
512236 CGATATAACA
512246 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
512266 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
512286 GGTAAAA
1 GGTAAAA
512293 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:512294 original size:17 final size:19
Alignment explanation
Indices: 512255--512297 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
512245 AGGTAAAAAT
512255 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
512275 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
512292 ATGATA
1 ATGATA
512298 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:514536 original size:21 final size:21
Alignment explanation
Indices: 514512--514555 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
514502 AAGACAATCA
*
514512 AGAGTTGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
514533 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
514554 AG
1 AG
514556 GCATAAGGGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.09, G:0.32, T:0.18
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:514631 original size:33 final size:33
Alignment explanation
Indices: 514589--514654 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
514579 AAATAGATGG
*
514589 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
514622 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
514655 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:516452 original size:19 final size:19
Alignment explanation
Indices: 516428--516477 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
516418 AATGTAGGGT
516428 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
516447 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
516466 TATTTTTGTATA
1 TAATTTTGTATA
516478 TGAATATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.32, C:0.02, G:0.10, T:0.56
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:517040 original size:198 final size:198
Alignment explanation
Indices: 516595--517948 Score: 2433
Period size: 198 Copynumber: 6.9 Consensus size: 198
516585 CAATATGGCC
* * * *
516595 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCAATCCCAAAAACATCGAAAA
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AAC
*
516660 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTTTACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
* *
516725 GAATATGTCTAAATAATGTGTCGACACTAATTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACT-TTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
516790 TGGAA
194 TGGAA
*
516795 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
* * *
516860 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGTTACAATTCTACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
516925 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATG
516990 GAA
196 GAA
* *
516993 AACAGGGTGCACACATAAAGTGTCGATCCATATATAAACAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
517058 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
517123 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATG
517188 GAA
196 GAA
517191 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
517256 CAAAAGTATAA--T-A-ATGTAATTTTTCAATCTAACCGGTAC-AGTATACCGG-TTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
* *
517315 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTGGTGTCGATATTTTTGGTCCAGAATAAATG
131 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATG
517380 GAA
196 GAA
517383 AACAGGGTGCACCCATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
517446 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTTCAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
*
517511 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTGGTGTCGATATTTTTGGTCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATG
517576 GAA
196 GAA
*
517579 AACAGGGTGCACCCATAAAGTGTCGATCC--ATATAAAAAGTGTCGATACCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
517642 C-AAAGTATAATGCAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
*
517706 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTGGTGTCGATATTTTTGGTCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATG
517771 GAA
196 GAA
517774 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
517839 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
517904 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGATA
131 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGATA
517949 CTAATTTAAA
Statistics
Matches: 1119, Mismatches: 26, Indels: 20
0.96 0.02 0.02
Matches are distributed among these distances:
190 45 0.04
192 106 0.09
193 11 0.01
194 51 0.05
195 169 0.15
196 141 0.13
197 34 0.03
198 411 0.37
199 92 0.08
200 59 0.05
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (198 bp):
AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATG
GAA
Found at i:519447 original size:3 final size:3
Alignment explanation
Indices: 519426--519470 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
519416 TGAAGCTGAC
* * *
519426 GAT GAA GAT GAT GAC GAT GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
519471 CCAAACAAGT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.38, C:0.02, G:0.33, T:0.27
Consensus pattern (3 bp):
GAT
Found at i:521242 original size:183 final size:182
Alignment explanation
Indices: 520967--521457 Score: 856
Period size: 183 Copynumber: 2.7 Consensus size: 182
520957 GCAATGCTAT
** *
520967 CGGTATAAATATAAAGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATCTT
1 CGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
* *
521032 GTGTTGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATTGTTAAAAAGTGTCGACA
66 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATT-TAAAAAAGTGTCGACA
* *
521097 TTTACACATCGTAACCCATAATTATAATGTAATAGATAATTTTATAATATAAC
130 TTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTATAATATAAC
521150 CGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
1 CGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
521215 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTGTCGACA
66 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATAC-ATTTAAAAAAGTGTCGACA
* *
521280 TTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATAAC
130 TTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTATAATATAAC
* *
521333 CGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTATAATATT
1 CGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
521398 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTGT
66 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATA-CATTTAAAAAAGTGT
521458 TGGTAATTTT
Statistics
Matches: 295, Mismatches: 11, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
183 291 0.99
184 4 0.01
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (182 bp):
CGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATTTAAAAAAGTGTCGACAT
TTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTATAATATAAC
Found at i:523954 original size:25 final size:25
Alignment explanation
Indices: 523926--523985 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
523916 TTATCATTAA
523926 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
523951 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
523976 ATTTAGGTAT
1 ATTTAGGTAT
523986 AACATCTTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.43
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:524316 original size:21 final size:22
Alignment explanation
Indices: 524270--524316 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
524260 AAATTACATA
524270 ACTTTTAAAAAAAGTATCGATC
1 ACTTTTAAAAAAAGTATCGATC
* *
524292 -CTTTTATAAAAAGTATGGA-C
1 ACTTTTAAAAAAAGTATCGATC
524312 ACTTT
1 ACTTT
524317 CAATATAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (22 bp):
ACTTTTAAAAAAAGTATCGATC
Found at i:524347 original size:20 final size:22
Alignment explanation
Indices: 524322--524397 Score: 68
Period size: 23 Copynumber: 3.5 Consensus size: 22
524312 ACTTTCAATA
*
524322 TAATAGGTA-AAC-ATATGATG
1 TAATAGGTAGAACTATATAATG
*
524342 TAATAGGTAGCACTTATATAATG
1 TAATAGGTAGAAC-TATATAATG
**
524365 TAATAGGTATCG-TTTATATAATG
1 TAATAGGTA--GAACTATATAATG
524388 TAATAGGTAG
1 TAATAGGTAG
524398 TGGTTATATT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
20 9 0.19
21 3 0.06
23 34 0.72
25 1 0.02
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.36
Consensus pattern (22 bp):
TAATAGGTAGAACTATATAATG
Found at i:524365 original size:23 final size:23
Alignment explanation
Indices: 524334--524397 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
524324 ATAGGTAAAC
*
524334 ATATGATGTAATAGGTAGCACTT
1 ATATAATGTAATAGGTAGCACTT
* **
524357 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCACTT
524380 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
524398 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.05, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCACTT
Found at i:524404 original size:23 final size:23
Alignment explanation
Indices: 524334--524406 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
524324 ATAGGTAAAC
* **
524334 ATATGATGTAATAGGTAGCACTT
1 ATATAATGTAATAGGTAGTGCTT
*
524357 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
524380 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
524403 ATAT
1 ATAT
524407 TGTAAAGTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:524849 original size:18 final size:18
Alignment explanation
Indices: 524828--524864 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
524818 GTAATTGGAG
524828 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
524846 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
524864 T
1 T
524865 ATATTTCGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:525163 original size:39 final size:39
Alignment explanation
Indices: 525120--525206 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
525110 TCCGATGCTC
*
525120 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
* *
525159 ATCAAAATTCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
525198 ATCAAAATC
1 ATCAAAATC
525207 TACAACTTGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.48, C:0.20, G:0.14, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:525652 original size:23 final size:23
Alignment explanation
Indices: 525621--525693 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
525611 ATAGGTAAAA
*
525621 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
525644 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
525667 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
525690 ATAT
1 ATAT
525694 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:526082 original size:23 final size:23
Alignment explanation
Indices: 526051--526123 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
526041 ATAGGTAAAA
*
526051 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* * *
526074 ATATAATGTAATAGATATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
526097 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
526120 ATAT
1 ATAT
526124 TGTAAAGTGT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:526513 original size:23 final size:23
Alignment explanation
Indices: 526482--526554 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
526472 ATAAGTAAAA
*
526482 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
526505 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
526528 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
526551 ATAT
1 ATAT
526555 TGTAAAATGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:526534 original size:431 final size:428
Alignment explanation
Indices: 525421--527752 Score: 4324
Period size: 426 Copynumber: 5.5 Consensus size: 428
525411 GTTAATGTTG
525421 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAATAATTTTTTGTGCAAA
1 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAATAATTTTTTGTGCAAA
525486 TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-AAAAAATTGAAACATAA
66 TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAA
525550 ATTACATAACTTTAAAAGAAGTATCGATCC-TTTTATAAAAAGTATGGACACTTTCAATATAATA
131 ATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATA
525614 GGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAAT
196 GGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAAT
*
525679 AGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTG
261 AGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTG
*
525744 GAAAACATTAATTTAAGGTTATCATTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCG
326 GAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCG
525809 TCTAATGATTTATTTTTTACGTTACGATATATATTATTA
391 TCTAATGATTTATTTTTTACGTTACGATATATA-TATTA
525848 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAATAATTTTTTGTGCAAA
1 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAATAATTTTTTGTGCAAA
525913 TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATA
66 TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-AAAAAAATTGAAACATA
*
525978 AATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAATATGGACACTTTCAATATAAT
130 AATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAAT
*
526043 AGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGATATCGTTTATATAATGTAA
195 AGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAA
* * *
526108 TAGGTAGTGGTTATATTGTAAAGTGTCTATCATTTTTTTAAAATTGTCCATACTTTTTTCACTGT
260 TAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGT
*
526173 GGAAAACATTAATTTAAGATTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGC
325 GGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGC
526238 GTCTAATGATTTATTTTTTACGTTACGATATATATTATTA
390 GTCTAATGATTTATTTTTTACGTTACGATATATA-TATTA
*
526278 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
1 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATC-AAATAATCAAATAATTTTTTGTGCAA
*
526343 ATGAAATTATTAAATTAATATTATAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACAT
65 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-AAAAAAATTGAAACAT
526408 AAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAA
129 AAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAA
*
526473 TAAGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTA
194 TAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTA
*
526538 ATAGGTAGTGGTTATATTGTAAAATGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTG
259 ATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTG
526603 TGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGG
324 TGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGG
526668 CGTCTAATGATTTATTTTTTACGTTACG--ATATATATTA
389 CGTCTAATGATTTATTTTTTACGTTACGATATATATATTA
526706 TTAAATTAAAAATTCTAAATAATA-TTTATAAAATATCAAATAATCAAATAATTTTTTGTGCAAA
1 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAATAATTTTTTGTGCAAA
526770 TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATA
66 TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-AAAAAAATTGAAACATA
526835 AATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAAT
130 AATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAAT
*
526900 AGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGATATCGTTTATATAATGTAA
195 AGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAA
* * *
526965 TAGGTAGTGGTTATATTGTAAAGTGTCTATCATTTTTTTAAAAGTGTCCATACTTTTTTTACTGT
260 TAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGT
**
527030 GGAAAACATTAATTTAAGACTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGC
325 GGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGC
527095 GTCTAATGATTTATTTTTTACGTTACGATATATATATTA
390 GTCTAATGATTTATTTTTTACGTTACGATATATATATTA
*
527134 TTAAATT-AAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
1 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATC-AAATAATCAAATAATTTTTTGTGCAA
*
527198 ATGAAATTATTAAATTAATATTATAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATA
65 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATA
*
527263 AATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAGGTATGGACACTTTCAATATAAT
130 AATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAAT
527328 AGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAA
195 AGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAA
*
527393 TAGGTAGTGGTTATATTGTAAAATGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGT
260 TAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGT
527458 GGAAAACATTAATTTAAGGTTATC-TTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGC
325 GGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGC
527522 GTCTAATGATTTATTTTTTACGTTACG--ATATATATTA
390 GTCTAATGATTTATTTTTTACGTTACGATATATATATTA
527559 TTAAATTAAAAATTCTAAATAATA-TTTATAAAATATCAAATAATCAAATAATTTTTTGTGCAAA
1 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAATAATTTTTTGTGCAAA
527623 TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAA
66 TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAA
*
527688 ATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACATTTTCAATATAATA
131 ATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATA
527753 TAATGTAATA
Statistics
Matches: 1854, Mismatches: 42, Indels: 21
0.97 0.02 0.01
Matches are distributed among these distances:
424 153 0.08
425 30 0.02
426 385 0.21
427 208 0.11
428 287 0.15
429 124 0.07
430 298 0.16
431 369 0.20
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (428 bp):
TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAATAATCAAATAATTTTTTGTGCAAA
TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAA
ATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATA
GGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAAT
AGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTG
GAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCG
TCTAATGATTTATTTTTTACGTTACGATATATATATTA
Found at i:526594 original size:21 final size:20
Alignment explanation
Indices: 526557--526596 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
526547 GGTTATATTG
* *
526557 TAAAATGTCTATCCTTTTTA
1 TAAAATGTCCATACTTTTTA
526577 TAAAAGTGTCCATACTTTTT
1 TAAAA-TGTCCATACTTTTT
526597 TCACTGTGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (20 bp):
TAAAATGTCCATACTTTTTA
Found at i:526939 original size:23 final size:23
Alignment explanation
Indices: 526908--526980 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
526898 ATAGGTAAAA
*
526908 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* * *
526931 ATATAATGTAATAGATATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
526954 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
526977 ATAT
1 ATAT
526981 TGTAAAGTGT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:527008 original size:21 final size:21
Alignment explanation
Indices: 526984--527025 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
526974 GTTATATTGT
*
526984 AAAGTGTCTAT-CATTTTTTTA
1 AAAGTGTCCATAC-TTTTTTTA
527005 AAAGTGTCCATACTTTTTTTA
1 AAAGTGTCCATACTTTTTTTA
527026 CTGTGGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.29, C:0.12, G:0.10, T:0.50
Consensus pattern (21 bp):
AAAGTGTCCATACTTTTTTTA
Found at i:527367 original size:23 final size:23
Alignment explanation
Indices: 527336--527408 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
527326 ATAGGTAAAA
*
527336 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
527359 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
527382 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
527405 ATAT
1 ATAT
527409 TGTAAAATGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:527448 original size:21 final size:20
Alignment explanation
Indices: 527411--527450 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
527401 GGTTATATTG
* *
527411 TAAAATGTCTATCCTTTTTA
1 TAAAATGTCCATACTTTTTA
527431 TAAAAGTGTCCATACTTTTT
1 TAAAA-TGTCCATACTTTTT
527451 TCACTGTGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (20 bp):
TAAAATGTCCATACTTTTTA
Found at i:527777 original size:857 final size:856
Alignment explanation
Indices: 525421--527752 Score: 4462
Period size: 857 Copynumber: 2.7 Consensus size: 856
525411 GTTAATGTTG
*
525421 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATC-AAATAATCAAATAATTTTTTGTGCAA
1 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
*
525485 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-AAAAAATTGAAACATA
66 ATGAAATTATTAAATTAATATTATAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATA
525549 AATTACATAACTTTAAAAGAAGTATCGATCC-TTTTATAAAAAGTATGGACACTTTCAATATAAT
131 AATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAAT
525613 AGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAA
196 AGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAA
* *
525678 TAGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGT
261 TAGGTAGTGGTTATATTGTAAAATGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGT
525743 GGAAAACATTAATTTAAGGTTATCATTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGC
326 GGAAAACATTAATTTAAGGTTATCATTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGC
525808 GTCTAATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTAAATAATAT
391 GTCTAATGATTTATTTTTTACGTTACG--ATATA-TATTATTAAATTAAAAATTCTAAATAATA-
525873 TTTATAAAATATCAAATAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAG
452 TTTATAAAATATCAAATAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAG
525938 GTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTAT
517 GTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTAT
*
526003 CGATCCTTTTTATAAAAAATATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTA
582 CGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTA
526068 GCGCTTATATAATGTAATAGATATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTG
647 GCGCTTATATAATGTAATAGATATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTG
* *
526133 TCTATCATTTTTTTAAAATTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGATTATCT
712 TCTATCATTTTTTTAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGACTATCT
526198 TTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTA
777 TTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTA
526263 CGATATATATTATTA
842 CGATATATATTATTA
526278 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
1 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
526343 ATGAAATTATTAAATTAATATTATAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACAT
66 ATGAAATTATTAAATTAATATTATAGGTGGAAAACATGAAACACTATT-AAAAAAATTGAAACAT
526408 AAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAA
130 AAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAA
*
526473 TAAGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTA
195 TAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTA
526538 ATAGGTAGTGGTTATATTGTAAAATGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTG
260 ATAGGTAGTGGTTATATTGTAAAATGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTG
*
526603 TGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGG
325 TGGAAAACATTAATTTAAGGTTATCATTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGG
526668 CGTCTAATGATTTATTTTTTACGTTACGATATATATTATTAAATTAAAAATTCTAAATAATATTT
390 CGTCTAATGATTTATTTTTTACGTTACGATATATATTATTAAATTAAAAATTCTAAATAATATTT
526733 ATAAAATATCAAATAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTG
455 ATAAAATATCAAATAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTG
526798 GAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGA
520 GAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGA
526863 TCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCG
585 TCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCG
526928 CTTATATAATGTAATAGATATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCT
650 CTTATATAATGTAATAGATATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCT
*
526993 ATCATTTTTTTAAAAGTGTCCATACTTTTTTTACTGTGGAAAACATTAATTTAAGACTATCTTTT
715 ATCATTTTTTTAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGACTATCTTTT
527058 GAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGA
780 GAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGA
527123 TATATA-TATTA
845 TATATATTATTA
527134 TTAAATT-AAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
1 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
527198 ATGAAATTATTAAATTAATATTATAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATA
66 ATGAAATTATTAAATTAATATTATAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATA
*
527263 AATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAGGTATGGACACTTTCAATATAAT
131 AATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAAT
527328 AGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAA
196 AGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAA
527393 TAGGTAGTGGTTATATTGTAAAATGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGT
261 TAGGTAGTGGTTATATTGTAAAATGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGT
527458 GGAAAACATTAATTTAAGGTTATC-TTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGC
326 GGAAAACATTAATTTAAGGTTATCATTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGC
527522 GTCTAATGATTTATTTTTTACGTTACGATATATATTATTAAATTAAAAATTCTAAATAATATTTA
391 GTCTAATGATTTATTTTTTACGTTACGATATATATTATTAAATTAAAAATTCTAAATAATATTTA
527587 TAAAATATCAAATAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGG
456 TAAAATATCAAATAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGG
527652 AAAACATGAAACACTATT-AAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGAT
521 AAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGAT
*
527716 CCTTTTTATAAAAAGTATGGACATTTTCAATATAATA
586 CCTTTTTATAAAAAGTATGGACACTTTCAATATAATA
527753 TAATGTAATA
Statistics
Matches: 1458, Mismatches: 13, Indels: 13
0.98 0.01 0.01
Matches are distributed among these distances:
852 82 0.06
853 188 0.13
854 234 0.16
855 105 0.07
856 12 0.01
857 433 0.30
858 101 0.07
859 5 0.00
860 47 0.03
861 251 0.17
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (856 bp):
TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
ATGAAATTATTAAATTAATATTATAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATA
AATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAAT
AGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAA
TAGGTAGTGGTTATATTGTAAAATGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGT
GGAAAACATTAATTTAAGGTTATCATTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGC
GTCTAATGATTTATTTTTTACGTTACGATATATATTATTAAATTAAAAATTCTAAATAATATTTA
TAAAATATCAAATAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGG
AAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAGTATCGAT
CCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGC
TTATATAATGTAATAGATATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTA
TCATTTTTTTAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGACTATCTTTTG
AGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGAT
ATATATTATTA
Found at i:527848 original size:23 final size:23
Alignment explanation
Indices: 527819--527866 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
527809 AAATAGGTAA
*
527819 ATATAAGCGTTACCTATTACATT
1 ATATAAGCGTTACCTAGTACATT
*
527842 ATATAAGCGTTACCTAGTATATT
1 ATATAAGCGTTACCTAGTACATT
527865 AT
1 AT
527867 TGTACTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (23 bp):
ATATAAGCGTTACCTAGTACATT
Found at i:528891 original size:18 final size:19
Alignment explanation
Indices: 528870--528908 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
528860 TAAAATTGAT
* *
528870 AATTTATTA-AAAATATTA
1 AATTTATAATAAAATAATA
528888 AATTTATAATAAAATAATA
1 AATTTATAATAAAATAATA
528907 AA
1 AA
528909 AAGTTTAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AATTTATAATAAAATAATA
Found at i:531493 original size:24 final size:23
Alignment explanation
Indices: 531478--531522 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
531468 AATTTATGTT
*
531478 TTTTCTTTTTTAAAAATATATAA
1 TTTTCTTTTTTAAAAATTTATAA
*
531501 TTTTCTTTTTTAAAATTTTATA
1 TTTTCTTTTTTAAAAATTTATA
531523 TAAATTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTTCTTTTTTAAAAATTTATAA
Found at i:537210 original size:91 final size:90
Alignment explanation
Indices: 537048--537213 Score: 212
Period size: 91 Copynumber: 1.8 Consensus size: 90
537038 GGTGCACTAA
* *
537048 GAGTACATCGATGCATAAAATGCATTCGATGTTTTGAAAAAGCTTGAGTGCATCGATGCATGGTC
1 GAGTACATCGATGCATAAAATGCATTCGATGTTTT-AAAAACCATGAGTGCATCGATGCATGGTC
*
537113 TTGTGCATCGATGCATCAAATGCACT
65 TGGTGCATCGATGCATCAAATGCACT
* **
537139 GAGTGCATCGATGCATAAAATGCATTCGATGTTCAATT-AATTCCATG-GTGCATCGATGCATGG
1 GAGTACATCGATGCATAAAATGCATTCGATGTT---TTAAAAACCATGAGTGCATCGATGCATGG
537202 AT-TGGTGCATCG
63 -TCTGGTGCATCG
537214 GTGAATCACT
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
91 57 0.88
92 6 0.09
94 2 0.03
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.30
Consensus pattern (90 bp):
GAGTACATCGATGCATAAAATGCATTCGATGTTTTAAAAACCATGAGTGCATCGATGCATGGTCT
GGTGCATCGATGCATCAAATGCACT
Found at i:537954 original size:41 final size:38
Alignment explanation
Indices: 537881--537961 Score: 101
Period size: 41 Copynumber: 2.1 Consensus size: 38
537871 AAATAAATCG
*
537881 ATTTTGAAAGAAAAATTTGATTTGAAAAATCAAAATGAA
1 ATTTTGAAAGAAAAATTTGATTTCAAAAATCAAAAT-AA
*
537920 ATTTTGAAA-AATAATTTAGAGCTTTCAAAAATCAAAATAA
1 ATTTTGAAAGAAAAATTT-GA--TTTCAAAAATCAAAATAA
537960 AT
1 AT
537962 GATTTAGAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
38 7 0.19
39 11 0.30
40 4 0.11
41 15 0.41
ACGTcount: A:0.53, C:0.05, G:0.10, T:0.32
Consensus pattern (38 bp):
ATTTTGAAAGAAAAATTTGATTTCAAAAATCAAAATAA
Found at i:539306 original size:20 final size:19
Alignment explanation
Indices: 539264--539313 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 19
539254 ATAATGTTTT
* *
539264 TATGAATAGTATTGTACTG
1 TATGAATAGTATCGTACTA
*
539283 TATGAATATTATCGATACTA
1 TATGAATAGTATCG-TACTA
539303 TATGAATAGTA
1 TATGAATAGTA
539314 CCAATACTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.38, C:0.06, G:0.16, T:0.40
Consensus pattern (19 bp):
TATGAATAGTATCGTACTA
Found at i:539320 original size:20 final size:20
Alignment explanation
Indices: 539278--539321 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
539268 AATAGTATTG
* * * *
539278 TACTGTATGAATATTATCGA
1 TACTATATGAATAGTACCAA
539298 TACTATATGAATAGTACCAA
1 TACTATATGAATAGTACCAA
539318 TACT
1 TACT
539322 GTGTGAACAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (20 bp):
TACTATATGAATAGTACCAA
Found at i:541921 original size:22 final size:21
Alignment explanation
Indices: 541895--541979 Score: 78
Period size: 22 Copynumber: 4.3 Consensus size: 21
541885 TTATAAAATA
541895 TATATTTTAATTACTATATTAT
1 TATATTTTAATTA-TATATTAT
*
541917 TATATTTTAATTATGTATTA-
1 TATATTTTAATTATATATTAT
*
541937 TAT-TTAATAATTA-ATATTAT
1 TATATT-TTAATTATATATTAT
541957 TA-A--TT-ATTAT-TATTAT
1 TATATTTTAATTATATATTAT
541973 TATATTT
1 TATATTT
541980 ATTTATTATA
Statistics
Matches: 52, Mismatches: 4, Indels: 17
0.71 0.05 0.23
Matches are distributed among these distances:
16 12 0.23
17 2 0.04
19 8 0.15
20 11 0.21
21 6 0.12
22 13 0.25
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (21 bp):
TATATTTTAATTATATATTAT
Found at i:541929 original size:11 final size:11
Alignment explanation
Indices: 541866--541930 Score: 51
Period size: 11 Copynumber: 5.5 Consensus size: 11
541856 AAAACTTACA
**
541866 AATTATATTAG
1 AATTATATTTT
541877 AATTATATTTAT
1 AATTATATTT-T
541889 AAAATATATATTTT
1 --AAT-TATATTTT
*
541903 AATTACTATATT
1 AATTA-TATTTT
541915 -ATTATATTTT
1 AATTATATTTT
541925 AATTAT
1 AATTAT
541931 GTATTATATT
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
10 5 0.11
11 20 0.45
12 8 0.18
14 4 0.09
15 7 0.16
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (11 bp):
AATTATATTTT
Found at i:541965 original size:16 final size:16
Alignment explanation
Indices: 541912--541974 Score: 60
Period size: 16 Copynumber: 4.0 Consensus size: 16
541902 TAATTACTAT
541912 ATTATT-ATATT-TTA
1 ATTATTAATATTATTA
*
541926 ATTATGTATTA-TATTTA
1 ATTAT-TAATATTA-TTA
*
541943 ATAATTAATATTATTA
1 ATTATTAATATTATTA
*
541959 ATTATTATTATTATTA
1 ATTATTAATATTATTA
541975 TATTTATTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
14 5 0.13
15 2 0.05
16 23 0.59
17 9 0.23
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (16 bp):
ATTATTAATATTATTA
Found at i:541985 original size:16 final size:16
Alignment explanation
Indices: 541911--541991 Score: 74
Period size: 18 Copynumber: 4.8 Consensus size: 16
541901 TTAATTACTA
541911 TATTATTATATTTTAAT
1 TATTATTATA-TTTAAT
541928 TATGTATTATATTTAAT
1 TAT-TATTATATTTAAT
* *
541945 AATTAATAT-TATTAAT
1 TATTATTATAT-TTAAT
*
541961 TATTATTATTATTATATT
1 TATTATTA-TATT-TAAT
541979 TATTTATTATATT
1 TA-TTATTATATT
541992 CATTTAATTT
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
15 1 0.02
16 16 0.30
17 13 0.25
18 17 0.32
19 6 0.11
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (16 bp):
TATTATTATATTTAAT
Found at i:550733 original size:13 final size:14
Alignment explanation
Indices: 550715--550744 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
550705 ACTTCGTGGT
550715 TTTCCC-AGTAAGA
1 TTTCCCTAGTAAGA
550728 TTTCCCTAGTAAGA
1 TTTCCCTAGTAAGA
550742 TTT
1 TTT
550745 ATCCTCCACT
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:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (14 bp):
TTTCCCTAGTAAGA
Found at i:558055 original size:23 final size:23
Alignment explanation
Indices: 558026--558071 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
558016 TTTTATCTTT
*
558026 TAAATTTTATAAAAAATTATATA
1 TAAATTTTATAAAAAAGTATATA
*
558049 TAAATTTTATTAAAAAGTATATA
1 TAAATTTTATAAAAAAGTATATA
558072 AATTTAAAAT
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:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
TAAATTTTATAAAAAAGTATATA
Found at i:558250 original size:26 final size:26
Alignment explanation
Indices: 558216--558275 Score: 111
Period size: 26 Copynumber: 2.3 Consensus size: 26
558206 ATTCCTTCAA
*
558216 CCAAACAATGTAATCTTACATTCATG
1 CCAAACAATGTAATCTTACATTAATG
558242 CCAAACAATGTAATCTTACATTAATG
1 CCAAACAATGTAATCTTACATTAATG
558268 CCAAACAA
1 CCAAACAA
558276 ACCAAACACA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.43, C:0.23, G:0.07, T:0.27
Consensus pattern (26 bp):
CCAAACAATGTAATCTTACATTAATG
Found at i:558800 original size:55 final size:56
Alignment explanation
Indices: 558626--558809 Score: 203
Period size: 56 Copynumber: 3.3 Consensus size: 56
558616 CTCTATTTTC
* * * *
558626 TAGATATATTCGATTCCGGGGCCCTTATTTTTATGCTTCTTAATGGCAACATCTGA
1 TAGATATATTCGATTTCGGGCCCCCTATTTTTATGCTTCTTAATGGCAACAACTGA
* * * *
558682 TAGATATATTCGATTTCGGGGCTCCTATTTTTATGTTTCTTAATGGCAACAACTAA
1 TAGATATATTCGATTTCGGGCCCCCTATTTTTATGCTTCTTAATGGCAACAACTGA
* * * * *
558738 TAAATATACTT-GATTT-TGGCCCCCTATTTTTAAGCTTAC-TAATGGTAACAACGGA
1 TAGATATA-TTCGATTTCGGGCCCCCTATTTTTATGCTT-CTTAATGGCAACAACTGA
*
558793 TAGATATAATCGATTTC
1 TAGATATATTCGATTTC
558810 CGAACCCCTA
Statistics
Matches: 107, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
54 1 0.01
55 41 0.38
56 63 0.59
57 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (56 bp):
TAGATATATTCGATTTCGGGCCCCCTATTTTTATGCTTCTTAATGGCAACAACTGA
Found at i:561806 original size:34 final size:37
Alignment explanation
Indices: 561763--561864 Score: 158
Period size: 34 Copynumber: 2.8 Consensus size: 37
561753 TTTCGTCCTA
*
561763 TTAGGATTCAAACTCTTAAAAATAGGATAGA-A-TT-
1 TTAGGATTCAAACTCCTAAAAATAGGATAGACATTTG
561797 TTAGGATTCAAACTCCTAAAAATAGGATA-ACATTTTG
1 TTAGGATTCAAACTCCTAAAAATAGGATAGACA-TTTG
561834 TTAGGATTCAAACTCCTAAAAATAGGATAGA
1 TTAGGATTCAAACTCCTAAAAATAGGATAGA
561865 GTTCTACTAA
Statistics
Matches: 62, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
33 1 0.02
34 29 0.47
36 2 0.03
37 29 0.47
38 1 0.02
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.30
Consensus pattern (37 bp):
TTAGGATTCAAACTCCTAAAAATAGGATAGACATTTG
Found at i:562451 original size:16 final size:18
Alignment explanation
Indices: 562430--562468 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
562420 TTTACTCATT
562430 TATTTAT-CTAT-TTTTA
1 TATTTATCCTATATTTTA
562446 TATTTATCCTATATTTTA
1 TATTTATCCTATATTTTA
562464 TATTT
1 TATTT
562469 TTATATTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 7 0.33
17 4 0.19
18 10 0.48
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.67
Consensus pattern (18 bp):
TATTTATCCTATATTTTA
Found at i:566362 original size:18 final size:17
Alignment explanation
Indices: 566348--566404 Score: 51
Period size: 20 Copynumber: 3.0 Consensus size: 17
566338 AATAAAAAGG
566348 GCAAAAAGAAAAAAAAA
1 GCAAAAAGAAAAAAAAA
*
566365 GCAAAAAAAAAGCAAAAAAA
1 GC-AAAAAGAA--AAAAAAA
566385 GAACAAAAAGAAAAAGAAAA
1 G--CAAAAAGAAAAA-AAAA
566405 AGGGACAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
17 2 0.06
18 7 0.22
19 3 0.09
20 12 0.38
21 7 0.22
22 1 0.03
ACGTcount: A:0.81, C:0.07, G:0.12, T:0.00
Consensus pattern (17 bp):
GCAAAAAGAAAAAAAAA
Found at i:566370 original size:11 final size:11
Alignment explanation
Indices: 566350--566398 Score: 66
Period size: 11 Copynumber: 4.5 Consensus size: 11
566340 TAAAAAGGGC
566350 AAAAAG-AAAA
1 AAAAAGCAAAA
566360 AAAAAGCAAAA
1 AAAAAGCAAAA
566371 AAAAAGCAAAA
1 AAAAAGCAAAA
566382 AAAGAA-CAAAA
1 AAA-AAGCAAAA
566393 AGAAAA
1 A-AAAA
566399 AGAAAAAGGG
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
10 6 0.17
11 26 0.72
12 4 0.11
ACGTcount: A:0.84, C:0.06, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAGCAAAA
Found at i:566373 original size:12 final size:12
Alignment explanation
Indices: 566356--566405 Score: 61
Period size: 11 Copynumber: 4.3 Consensus size: 12
566346 GGGCAAAAAG
566356 AAAAAAAAAGC-
1 AAAAAAAAAGCA
566367 AAAAAAAAAGCA
1 AAAAAAAAAGCA
*
566379 AAAAAAGAA-CA
1 AAAAAAAAAGCA
566390 AAAAGAAAAAG-A
1 AAAA-AAAAAGCA
566402 AAAA
1 AAAA
566406 GGGACAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
11 17 0.50
12 17 0.50
ACGTcount: A:0.84, C:0.06, G:0.10, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGCA
Found at i:566375 original size:30 final size:32
Alignment explanation
Indices: 566341--566415 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 32
566331 TAATCAGAAT
*
566341 AAAAAGGGCAAAAAGAA-AA-AAAAAGCAAAA-
1 AAAAAGGGCAAAAA-AAGAACAAAAAGAAAAAG
566371 AAAAA--GCAAAAAAAGAACAAAAAGAAAAAG
1 AAAAAGGGCAAAAAAAGAACAAAAAGAAAAAG
566401 AAAAAGGGACAAAAA
1 AAAAAGGG-CAAAAA
566416 CACATGCAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
27 2 0.05
28 9 0.24
29 10 0.26
30 10 0.26
32 1 0.03
33 6 0.16
ACGTcount: A:0.77, C:0.07, G:0.16, T:0.00
Consensus pattern (32 bp):
AAAAAGGGCAAAAAAAGAACAAAAAGAAAAAG
Found at i:566404 original size:11 final size:10
Alignment explanation
Indices: 566350--566404 Score: 60
Period size: 9 Copynumber: 5.5 Consensus size: 10
566340 TAAAAAGGGC
566350 AAAAAGAAAA
1 AAAAAGAAAA
566360 AAAAAGCAAAA
1 AAAAAG-AAAA
*
566371 AAAAAG-CAA
1 AAAAAGAAAA
*
566380 AAAAAG-AAC
1 AAAAAGAAAA
566389 AAAAAGAAAA
1 AAAAAGAAAA
566399 AGAAAA
1 A-AAAA
566405 AGGGACAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
9 15 0.39
10 9 0.24
11 14 0.37
ACGTcount: A:0.84, C:0.05, G:0.11, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Done.