Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008884.1 Hibiscus syriacus cultivar Beakdansim tig00112130_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: 397847
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:271835 original size:13 final size:13
Alignment explanation
Indices: 271792--271846 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
271782 TTGGAAGTAT
271792 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
271805 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
271819 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
271832 TTAAGTATTTGAA
1 TTAAGTATTTCAA
271845 TT
1 TT
271847 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:272268 original size:15 final size:15
Alignment explanation
Indices: 272243--272298 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
272233 ATCTGGAATA
*
272243 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
272258 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
*
272273 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
272290 TTAAAACCG
1 TTAAAACCG
272299 AAACCGGTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 21 0.62
17 13 0.38
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:272307 original size:21 final size:18
Alignment explanation
Indices: 272262--272295 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
272252 GTTTTTTTAT
272262 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
272279 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
272296 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:272415 original size:15 final size:17
Alignment explanation
Indices: 272389--272420 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
272379 TTCTATGGGA
272389 AAAAACCAGAT-CGGAT
1 AAAAACCAGATCCGGAT
272405 AAAAACC-GATCCGGAT
1 AAAAACCAGATCCGGAT
272421 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (17 bp):
AAAAACCAGATCCGGAT
Found at i:277149 original size:21 final size:21
Alignment explanation
Indices: 277120--277166 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
277110 ATTCTGACTA
*
277120 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCAATTTCCCAAAT
* * *
277141 TCGCGTTGCAATTTTCCTAAT
1 TCGCATTGCAATTTCCCAAAT
277162 TCGCA
1 TCGCA
277167 ATGCGAATAC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.21, C:0.28, G:0.15, T:0.36
Consensus pattern (21 bp):
TCGCATTGCAATTTCCCAAAT
Found at i:277187 original size:20 final size:20
Alignment explanation
Indices: 277162--277234 Score: 137
Period size: 20 Copynumber: 3.6 Consensus size: 20
277152 TTTTCCTAAT
277162 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
277182 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
277202 TCGCAATGCGAATACATAAA
1 TCGCAATGCGAATACGTAAA
277222 TCGCAATGCGAAT
1 TCGCAATGCGAAT
277235 CTGACTATCG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:277848 original size:21 final size:20
Alignment explanation
Indices: 277787--277881 Score: 108
Period size: 20 Copynumber: 4.8 Consensus size: 20
277777 TTCTAAACTT
277787 AAAATCGCAACATGA-AAATG
1 AAAATCGCAACA-GAGAAATG
277807 AAAATCGCAACAG-GAAAATG
1 AAAATCGCAACAGAG-AAATG
**
277827 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAAC-AGAGAAATG
*
277848 AAAATCGCAAC-GCGAAATG
1 AAAATCGCAACAGAGAAATG
277867 AAAATCGCAAC-GAGA
1 AAAATCGCAACAGAGA
277882 TAATCGCAAC
Statistics
Matches: 65, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
19 22 0.34
20 26 0.40
21 16 0.25
22 1 0.02
ACGTcount: A:0.51, C:0.18, G:0.20, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACAGAGAAATG
Found at i:277866 original size:40 final size:40
Alignment explanation
Indices: 277787--277881 Score: 124
Period size: 40 Copynumber: 2.4 Consensus size: 40
277777 TTCTAAACTT
277787 AAAATCGCAAC-ATGAAAATGAAAATCGCAACAGGAAAATG
1 AAAATCGCAACGA-GAAAATGAAAATCGCAACAGGAAAATG
**
277827 ACTATCGCAACGAGAGAAATGAAAATCGCAAC-GCG-AAATG
1 AAAATCGCAACGAGA-AAATGAAAATCGCAACAG-GAAAATG
277867 AAAATCGCAACGAGA
1 AAAATCGCAACGAGA
277882 TAATCGCAAC
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
40 30 0.62
41 18 0.38
ACGTcount: A:0.51, C:0.18, G:0.20, T:0.12
Consensus pattern (40 bp):
AAAATCGCAACGAGAAAATGAAAATCGCAACAGGAAAATG
Found at i:277949 original size:14 final size:14
Alignment explanation
Indices: 277926--278028 Score: 89
Period size: 14 Copynumber: 6.6 Consensus size: 14
277916 TTTCATTTAG
*
277926 CGTTGTGATTCTCT
1 CGTTGCGATTCTCT
*
277940 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
277959 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
277973 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
277990 CGCATTGCGATTCTCT
1 CG--TTGCGATTCTCT
278006 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
278020 CGTTGCGAT
1 CGTTGCGAT
278029 AGTCATTTCC
Statistics
Matches: 74, Mismatches: 5, Indels: 20
0.75 0.05 0.20
Matches are distributed among these distances:
14 38 0.51
16 10 0.14
17 10 0.14
19 16 0.22
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:277951 original size:33 final size:33
Alignment explanation
Indices: 277909--278015 Score: 187
Period size: 33 Copynumber: 3.2 Consensus size: 33
277899 TAAAATCGCA
* *
277909 TTGCGATTTTCATTTAGCGTTGTGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
277942 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
277975 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
278008 TTGCGATT
1 TTGCGATT
278016 CTCTCGTTGC
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 71 1.00
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:278013 original size:47 final size:48
Alignment explanation
Indices: 277959--278049 Score: 148
Period size: 47 Copynumber: 1.9 Consensus size: 48
277949 TTTCATTTCG
**
277959 CGTTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTCTCT
1 CGTTGCGATTCTCTCGTTGCGATAGTCATTTCCGCATTGCGATTCTCT
*
278006 CGTTGCGATTCTCTCGTTGCGATAGTCATTTCCGCGTTGCGATT
1 CGTTGCGATTCTCTCGTTGCGATAGTCATTTCCGCATTGCGATT
278050 TTCATTCTCT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
47 29 0.73
48 11 0.28
ACGTcount: A:0.11, C:0.25, G:0.22, T:0.42
Consensus pattern (48 bp):
CGTTGCGATTCTCTCGTTGCGATAGTCATTTCCGCATTGCGATTCTCT
Found at i:278074 original size:21 final size:20
Alignment explanation
Indices: 277933--278076 Score: 81
Period size: 20 Copynumber: 7.2 Consensus size: 20
277923 TAGCGTTGTG
277933 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
277953 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
277966 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
* *
277986 ATT-TCGCATTGCGATTCTCTCGTTGC
1 ATTCTCTCGTTGCGA---T-T--TT-C
**
278012 GATTCTCTCGTTGCGATAGTC
1 -ATTCTCTCGTTGCGATTTTC
*
278033 ATT-TCCGCGTTGCGATTTTC
1 ATTCT-CTCGTTGCGATTTTC
278053 ATTCTCTCGTTGCGATTTTTC
1 ATTCTCTCGTTGCGA-TTTTC
278074 ATT
1 ATT
278077 TCAACCAAAA
Statistics
Matches: 93, Mismatches: 12, Indels: 37
0.65 0.08 0.26
Matches are distributed among these distances:
13 3 0.03
14 9 0.10
19 19 0.20
20 33 0.35
21 10 0.11
22 2 0.02
23 1 0.01
25 3 0.03
26 1 0.01
27 3 0.03
28 9 0.10
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.46
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:279944 original size:94 final size:93
Alignment explanation
Indices: 279753--280128 Score: 535
Period size: 94 Copynumber: 4.1 Consensus size: 93
279743 TAGATTGCTT
* * * *
279753 AGTAAATTTATTTGGTTGCTGTCAATACTGCTAAAC--TGT-TTA-TTAACACTGTTAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTATTTAACACTGTGAAGTTAGT
*
279814 TTTTGTCTTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGA
* * *
279843 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTATTTATTATTTAATACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTATTTAACACTGTGAAGTTAGT
*
279908 ATTTGTCTTTGTTTTATCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * *
279937 AGTAAATTTGTTCGGTTGCTGTCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTATTTAACACTGTGAAGTTAGT
280002 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * * * *
280031 AGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTATTTAACACTGTGAAGTTAGT
*
280096 ATTTGTCTTTGTTTTGTCTTTTAGTTGA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
280124 AGTAA
1 AGTAA
280129 TGCAATCCAT
Statistics
Matches: 261, Mismatches: 20, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
90 33 0.13
92 2 0.01
93 28 0.11
94 198 0.76
ACGTcount: A:0.22, C:0.11, G:0.18, T:0.49
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTATTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:280262 original size:20 final size:20
Alignment explanation
Indices: 280239--280276 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
280229 TCGCAACGAC
280239 AAAATCGCAACGCGAAACCA
1 AAAATCGCAACGCGAAACCA
*
280259 AAAATCGCAACGTGAAAC
1 AAAATCGCAACGCGAAAC
280277 TATAATCGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.26, G:0.16, T:0.08
Consensus pattern (20 bp):
AAAATCGCAACGCGAAACCA
Found at i:280325 original size:14 final size:14
Alignment explanation
Indices: 280306--280360 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
280296 TCATTTCGCA
280306 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
280320 TTGCGATTTTCATTTCGCG
1 TTGCGA--TTC---TCTCG
280339 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
280353 TTGCGATT
1 TTGCGATT
280361 TTCGTTTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.24, G:0.22, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:280327 original size:33 final size:33
Alignment explanation
Indices: 280285--280417 Score: 185
Period size: 33 Copynumber: 3.8 Consensus size: 33
280275 ACTATAATCG
*
280285 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
280318 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
*
280351 CGTTGCGATTTTCGTTTCGCGTTGCGATTTTCATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCG------ATTCTCT
*
280390 CGTTGCGATTTTTATTTCGCGTTGCGAT
1 CGTTGCGATTTTCATTTCGCGTTGCGAT
280418 AGTCATTTTT
Statistics
Matches: 90, Mismatches: 4, Indels: 12
0.85 0.04 0.11
Matches are distributed among these distances:
33 59 0.66
39 31 0.34
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.47
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:280425 original size:19 final size:19
Alignment explanation
Indices: 280282--280417 Score: 139
Period size: 19 Copynumber: 7.6 Consensus size: 19
280272 GAAACTATAA
280282 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
280301 TCGCATTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
280315 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
280334 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
280348 TCTCGTTGCGATTTTCGTT
1 TCGCGTTGCGATTTTCATT
280367 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
280386 CTCTCGTTGCGATTTTTATT
1 -TCGCGTTGCGATTTTCATT
280406 TCGCGTTGCGAT
1 TCGCGTTGCGAT
280418 AGTCATTTTT
Statistics
Matches: 96, Mismatches: 10, Indels: 22
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.20
16 6 0.06
17 6 0.06
19 48 0.50
20 17 0.18
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:280442 original size:39 final size:38
Alignment explanation
Indices: 280285--280442 Score: 124
Period size: 33 Copynumber: 4.3 Consensus size: 38
280275 ACTATAATCG
*
280285 CGTTGCGATTTTCATTTCGCATTGCGAT--TC--TCT--
1 CGTTGCGATTTT-ATTTCGCGTTGCGATAGTCATTCTCA
280318 CGTTGCGATTTTCATTTCGCGTTGCGAT--TC--TCT--
1 CGTTGCGATTTT-ATTTCGCGTTGCGATAGTCATTCTCA
* ** *
280351 CGTTGCGATTTTCGTTTCGCGTTGCGATTTTCATTCTCT
1 CGTTGCGATTTT-ATTTCGCGTTGCGATAGTCATTCTCA
*
280390 CGTTGCGATTTTTATTTCGCGTTGCGATAGTCATTTTTCA
1 CGTTGCGA-TTTTATTTCGCGTTGCGATAGTCA-TTCTCA
*
280430 CGTTACGATTTTA
1 CGTTGCGATTTTA
280443 AGTTCCAGAA
Statistics
Matches: 109, Mismatches: 8, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
33 59 0.54
35 2 0.02
37 3 0.03
39 30 0.28
40 15 0.14
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.47
Consensus pattern (38 bp):
CGTTGCGATTTTATTTCGCGTTGCGATAGTCATTCTCA
Found at i:280959 original size:21 final size:21
Alignment explanation
Indices: 280902--280960 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
280892 CGAGAGTCCC
280902 CTCCCACCGTTCAAGAGGCCA
1 CTCCCACCGTTCAAGAGGCCA
** * * *
280923 CTGTCATCGTTGAAGAGGTCA
1 CTCCCACCGTTCAAGAGGCCA
*
280944 CTCCCACCATTCAAGAG
1 CTCCCACCGTTCAAGAG
280961 CCTGATTCAC
Statistics
Matches: 28, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.25, C:0.34, G:0.20, T:0.20
Consensus pattern (21 bp):
CTCCCACCGTTCAAGAGGCCA
Found at i:282296 original size:14 final size:14
Alignment explanation
Indices: 282254--282290 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
282244 GATTGTTTAA
*
282254 TTGATTTGTAAAAG
1 TTGATTTGTAAAAT
*
282268 ATGATTTGTAAAAT
1 TTGATTTGTAAAAT
282282 TTGATTTGT
1 TTGATTTGT
282291 TTAATTGATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAT
Found at i:282466 original size:19 final size:19
Alignment explanation
Indices: 282444--282552 Score: 85
Period size: 19 Copynumber: 6.2 Consensus size: 19
282434 ATTCGCGTTT
282444 CGATTTTCATTTCGCATTG
1 CGATTTTCATTTCGCATTG
**
282463 CGA--TTC-CCTCG--TTG
1 CGATTTTCATTTCGCATTG
282477 CGATTTTCATTTCGCATTG
1 CGATTTTCATTTCGCATTG
*
282496 CGA--TTC-TCTCG--TTG
1 CGATTTTCATTTCGCATTG
282510 CGATTTTCATTTCGCATTG
1 CGATTTTCATTTCGCATTG
** *
282529 CGATAGTCATTTCCGCGTTG
1 CGATTTTCATTT-CGCATTG
282549 CGAT
1 CGAT
282553 AGACATTAAG
Statistics
Matches: 70, Mismatches: 9, Indels: 21
0.70 0.09 0.21
Matches are distributed among these distances:
14 12 0.17
16 13 0.19
17 13 0.19
19 22 0.31
20 10 0.14
ACGTcount: A:0.14, C:0.25, G:0.19, T:0.42
Consensus pattern (19 bp):
CGATTTTCATTTCGCATTG
Found at i:282486 original size:33 final size:33
Alignment explanation
Indices: 282439--282532 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
282429 ACTAAATTCG
*
282439 CGTTTCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
282472 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
282505 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
282533 AGTCATTTCC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:282551 original size:20 final size:20
Alignment explanation
Indices: 282505--282598 Score: 68
Period size: 20 Copynumber: 4.7 Consensus size: 20
282495 GCGATTCTCT
**
282505 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATAGTCATTTCCG
*
282524 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* **
282544 CGTTGCGATAGACA-TTAAG
1 CGTTGCGATAGTCATTTCCG
*
282563 ATGATTGCGA-ACGTCATTTCCG
1 -CG-TTGCGATA-GTCATTTCCG
*
282585 TGTTGCGATAGTCA
1 CGTTGCGATAGTCA
282599 AATGAATGCC
Statistics
Matches: 58, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
19 17 0.29
20 26 0.45
21 12 0.21
22 3 0.05
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:286860 original size:108 final size:108
Alignment explanation
Indices: 286671--286886 Score: 423
Period size: 108 Copynumber: 2.0 Consensus size: 108
286661 TTGGAGTAAT
*
286671 GTTTTGATATTTGAATAGTTATATCGAATATACTTAGAAAATCATTTGGAAAATCTTAAAATCCA
1 GTTTTGATATTCGAATAGTTATATCGAATATACTTAGAAAATCATTTGGAAAATCTTAAAATCCA
286736 TTTAACTTAATTTGTTATATCGAAATATCAAAATGTTTCAACA
66 TTTAACTTAATTTGTTATATCGAAATATCAAAATGTTTCAACA
286779 GTTTTGATATTCGAATAGTTATATCGAATATACTTAGAAAATCATTTGGAAAATCTTAAAATCCA
1 GTTTTGATATTCGAATAGTTATATCGAATATACTTAGAAAATCATTTGGAAAATCTTAAAATCCA
286844 TTTAACTTAATTTGTTATATCGAAATATCAAAATGTTTCAACA
66 TTTAACTTAATTTGTTATATCGAAATATCAAAATGTTTCAACA
286887 ATCTCCCCCT
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
108 107 1.00
ACGTcount: A:0.40, C:0.11, G:0.10, T:0.39
Consensus pattern (108 bp):
GTTTTGATATTCGAATAGTTATATCGAATATACTTAGAAAATCATTTGGAAAATCTTAAAATCCA
TTTAACTTAATTTGTTATATCGAAATATCAAAATGTTTCAACA
Found at i:289310 original size:22 final size:24
Alignment explanation
Indices: 289259--289310 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
289249 GATTCCCCTG
289259 TGGGGGGGAATCGGTTCCCCTTCA
1 TGGGGGGGAATCGGTTCCCCTTCA
**
289283 -AAGGGGGAATCGGTT-CCC-TCA
1 TGGGGGGGAATCGGTTCCCCTTCA
289304 TGGGGGG
1 TGGGGGG
289311 ATCGATTCTC
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
21 3 0.13
22 7 0.30
23 13 0.57
ACGTcount: A:0.15, C:0.21, G:0.42, T:0.21
Consensus pattern (24 bp):
TGGGGGGGAATCGGTTCCCCTTCA
Found at i:293029 original size:108 final size:108
Alignment explanation
Indices: 292840--293055 Score: 432
Period size: 108 Copynumber: 2.0 Consensus size: 108
292830 TTGGAGTAAT
292840 GTTTTGATATTCGAATAGTTATATCGAATATACTTAGAAAATCATTTGGAAAATCTTAAAATCCA
1 GTTTTGATATTCGAATAGTTATATCGAATATACTTAGAAAATCATTTGGAAAATCTTAAAATCCA
292905 TTTAACTTAATTTGTTATATCGAAATATCAAAATGTTTCAACA
66 TTTAACTTAATTTGTTATATCGAAATATCAAAATGTTTCAACA
292948 GTTTTGATATTCGAATAGTTATATCGAATATACTTAGAAAATCATTTGGAAAATCTTAAAATCCA
1 GTTTTGATATTCGAATAGTTATATCGAATATACTTAGAAAATCATTTGGAAAATCTTAAAATCCA
293013 TTTAACTTAATTTGTTATATCGAAATATCAAAATGTTTCAACA
66 TTTAACTTAATTTGTTATATCGAAATATCAAAATGTTTCAACA
293056 CAAACGAGCT
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
108 108 1.00
ACGTcount: A:0.40, C:0.11, G:0.10, T:0.39
Consensus pattern (108 bp):
GTTTTGATATTCGAATAGTTATATCGAATATACTTAGAAAATCATTTGGAAAATCTTAAAATCCA
TTTAACTTAATTTGTTATATCGAAATATCAAAATGTTTCAACA
Found at i:293373 original size:21 final size:21
Alignment explanation
Indices: 293349--293388 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
293339 ATTCACATTG
293349 CGAATTAGGAAAATCGCAACA
1 CGAATTAGGAAAATCGCAACA
* *
293370 CGAATTTGGGAAATCGCAA
1 CGAATTAGGAAAATCGCAA
293389 TGCGATAGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.17
Consensus pattern (21 bp):
CGAATTAGGAAAATCGCAACA
Found at i:295368 original size:40 final size:40
Alignment explanation
Indices: 295313--295392 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
295303 AATAAGCATC
295313 CATGAATTATAATTAGGGGTGTTCATGGTCGGTTAAACTT
1 CATGAATTATAATTAGGGGTGTTCATGGTCGGTTAAACTT
*
295353 CATGAATTATAATTAGGGGTGTTCATGGTTGGTTAAACTT
1 CATGAATTATAATTAGGGGTGTTCATGGTCGGTTAAACTT
295393 ATCGTTTAGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.28, C:0.09, G:0.25, T:0.39
Consensus pattern (40 bp):
CATGAATTATAATTAGGGGTGTTCATGGTCGGTTAAACTT
Found at i:295658 original size:2 final size:2
Alignment explanation
Indices: 295594--295647 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
295584 AATTTACGAT
295594 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
295636 TA TA TA TA TA TA
1 TA TA TA TA TA TA
295648 ATGAGATATA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:298455 original size:8 final size:8
Alignment explanation
Indices: 298397--298461 Score: 51
Period size: 8 Copynumber: 7.8 Consensus size: 8
298387 TCTACAAAAA
298397 TATTTTAT
1 TATTTTAT
*
298405 TATATTA-
1 TATTTTAT
298412 TATATTTATT
1 TAT-TTTA-T
*
298422 TCTTCTTAT
1 TATT-TTAT
*
298431 TATTATTAA
1 TATT-TTAT
*
298440 TATATTAT
1 TATTTTAT
298448 TATTTTAT
1 TATTTTAT
298456 TATTTT
1 TATTTT
298462 TGTAAGCCCC
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
7 3 0.07
8 25 0.57
9 11 0.25
10 5 0.11
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (8 bp):
TATTTTAT
Found at i:298935 original size:37 final size:36
Alignment explanation
Indices: 298884--298980 Score: 103
Period size: 36 Copynumber: 2.7 Consensus size: 36
298874 TATTTTATCC
*
298884 TAATTTTA-ATATTATTTATTCTTTTACATTGTT-A-
1 TAATATTATATATTATTTATT-TTTTACATTGTTCAT
* *
298918 TATATATATATATATTATTTATTTTTTTCATTTTTCAT
1 TA-ATAT-TATATATTATTTATTTTTTACATTGTTCAT
*
298956 TAATATTATATATTA-ATATTTTTTA
1 TAATATTATATATTATTTATTTTTTA
298981 TTATCTTTCT
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
34 2 0.04
35 11 0.21
36 21 0.40
37 17 0.32
38 2 0.04
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.63
Consensus pattern (36 bp):
TAATATTATATATTATTTATTTTTTACATTGTTCAT
Found at i:302720 original size:110 final size:110
Alignment explanation
Indices: 302527--303182 Score: 1034
Period size: 110 Copynumber: 6.0 Consensus size: 110
302517 GATGGTGGTT
* **
302527 GCTCAACTTCACAGCGAAGGGGCGAATGAAGGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
* *
302592 AATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACAAAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
302637 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
302702 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* *
302747 GCTCAACTTCGCAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTTATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
* * *
302812 AATTTCAATTTCACAGGGAATGATATTGGACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* * * * *
302857 GCTCAACTTCACAACAAATGGGCAACTAACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
302922 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* *
302967 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCTTTCAAAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
* * *
303032 AATTTCAACTTTACAGCGAAGAATATTGGACTCGAGACAACACTA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* *
303077 GCTCAACTTCACAGCGAAGGGGCGGCT-AGCTGTCAACAAATAACTTTTCAG--T--TTCAGAGT
1 GCTCAACTTCACAGCGAAGGGGCGACTGA-CTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
* * * *
303137 CAATTTCAACTTCACGGCGAAGGATATTGGTCTCGAAACAGCACAA
65 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
303183 ATATTTGGAT
Statistics
Matches: 505, Mismatches: 40, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
106 46 0.09
108 1 0.00
109 1 0.00
110 457 0.90
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (110 bp):
GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
Found at i:303522 original size:84 final size:83
Alignment explanation
Indices: 303289--303891 Score: 637
Period size: 84 Copynumber: 7.3 Consensus size: 83
303279 AATCGTGCCC
* * * *
303289 ACCAAAGGCCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAACTTAAGT
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGG
* **
303354 CAAGAAGGGTTATCTGCAA
66 CTAGAAGGGTTATCTG-TG
* * * * * * *
303373 ACCGAAGACCCTT-GAGTTCTATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAA
1 ACCAAAGA-CCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTCAA
303437 GGCTAGAAGGGTTATCTGTG
64 GGCTAGAAGGGTTATCTGTG
* * *
303457 ACCAAAAGACCTTCGAATTCGACTACGCTCAGCTCCAAGGCACATCATTTACAACATAACTCAAG
1 ACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAG
303522 GCTAGAAGGGTTATCTGTG
65 GCTAGAAGGGTTATCTGTG
* *
303541 ACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAG
1 ACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAG
* ** * ***
303606 TCGGGAAGTGTTATCTACCA
65 GCTAGAAGGGTTATCT-GTG
* * * *
303626 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCATCATAGCTTAAGT
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGG
* *
303691 CGAAAAGGGTTATC--TG
66 CTAGAAGGGTTATCTGTG
* * * * * *
303707 -CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCAAGGGTACATCATTTAC-GACATAACTCAA
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAG-CATAACTCAA
* *
303770 GGTTAGAAGGGTTATCTGTC
64 GGCTAGAAGGGTTATCTGTG
* * * * * *
303790 AACAAAGACCTTCGAGTTCGACTCCACTCACCTCAAAGGCACCATCATTTGCAGCATAGCTCAAG
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCA-CATCATTTGCAGCATAACTCAAG
* *
303855 GCAAGAATGGTTATC--TG
65 GCTAGAAGGGTTATCTGTG
303872 -CCAAAGACCTTCGAGTTCGA
1 ACCAAAGACCTTCGAGTTCGA
303892 TTCCATTTAG
Statistics
Matches: 437, Mismatches: 70, Indels: 27
0.82 0.13 0.05
Matches are distributed among these distances:
80 32 0.07
81 51 0.12
82 1 0.00
83 4 0.01
84 279 0.64
85 70 0.16
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (83 bp):
ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGG
CTAGAAGGGTTATCTGTG
Found at i:304256 original size:3 final size:3
Alignment explanation
Indices: 304239--304304 Score: 77
Period size: 3 Copynumber: 22.7 Consensus size: 3
304229 CAAAAACATT
304239 TTA TT- TTA TTA -TA TTA TTTA TTTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA -TTA TTA TTA TTA TTA TTA TTA TTA
*
304284 ATA -TA TTA TTA TT- TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TT
304305 TTTACAGGCC
Statistics
Matches: 57, Mismatches: 1, Indels: 10
0.84 0.01 0.15
Matches are distributed among these distances:
2 8 0.14
3 42 0.74
4 7 0.12
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:304304 original size:8 final size:8
Alignment explanation
Indices: 304239--304306 Score: 66
Period size: 8 Copynumber: 7.9 Consensus size: 8
304229 CAAAAACATT
304239 TTATTTTA
1 TTATTTTA
*
304247 TTATATTA
1 TTATTTTA
304255 TT-TATTTA
1 TTAT-TTTA
304263 TTATTATTA
1 TTATT-TTA
304272 TTATTATTA
1 TTATT-TTA
304281 TTAATATATTA
1 TT-AT-T-TTA
304292 TTATTTTA
1 TTATTTTA
304300 TTATTTT
1 TTATTTT
304307 TACAGGCCCC
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
7 1 0.02
8 25 0.47
9 16 0.30
10 4 0.08
11 7 0.13
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (8 bp):
TTATTTTA
Found at i:304400 original size:33 final size:33
Alignment explanation
Indices: 304358--304424 Score: 118
Period size: 33 Copynumber: 2.0 Consensus size: 33
304348 GAAAATAAAT
304358 CAACGTATTTGAG-TCTTATTGAAACACTAAAAC
1 CAACGTATTTGAGTTC-TATTGAAACACTAAAAC
304391 CAACGTATTTGAGTTCTATTGAAACACTAAAAC
1 CAACGTATTTGAGTTCTATTGAAACACTAAAAC
304424 C
1 C
304425 GAAGCATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 31 0.94
34 2 0.06
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.30
Consensus pattern (33 bp):
CAACGTATTTGAGTTCTATTGAAACACTAAAAC
Found at i:306922 original size:22 final size:23
Alignment explanation
Indices: 306888--306935 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
306878 GATTAAAATA
*
306888 TAAAAAAACATTTCTGAT-TTTT
1 TAAAAAAACATTTCTAATATTTT
306910 TAAAAATAA-ATTTCTAATATTTT
1 TAAAAA-AACATTTCTAATATTTT
306933 TAA
1 TAA
306936 CCACTTGTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (23 bp):
TAAAAAAACATTTCTAATATTTT
Found at i:309092 original size:179 final size:179
Alignment explanation
Indices: 308792--309142 Score: 666
Period size: 179 Copynumber: 2.0 Consensus size: 179
308782 ACATTCCACC
308792 ATCTATCATTGACCTCTGAACTTCACTAAGAACATTGGACTTCAAGAGGACCTTTTCTATGCAAA
1 ATCTATCATTGACCTCTGAACTTCACTAAGAACATTGGACTTCAAGAGGACCTTTTCTATGCAAA
* *
308857 TCCTATAAAATTTCAGTCAAATTTCTTAGTTGTCTAATAAGAAAGAAAATAAATGTTTTATATTC
66 TCCTATAAAATTTCAGTCAAATTTCTTAGTCGTCTAATAAGAAAGAAAATAAATGTTTTACATTC
308922 TACAAAAGAGCTAAAAGTGCTTTCACCAGTAAGCTATAGAGACAACCAA
131 TACAAAAGAGCTAAAAGTGCTTTCACCAGTAAGCTATAGAGACAACCAA
*
308971 ATCTATCATTGACCTCTGAACTTCACTAAGAACATTGGACTTCAAGAGGACCTTTTCTATGCGAA
1 ATCTATCATTGACCTCTGAACTTCACTAAGAACATTGGACTTCAAGAGGACCTTTTCTATGCAAA
*
309036 TCCTATAAAATTTCAGTCAAATTTCTTAGTCGTCTAATAAGGAAGAAAATAAATGTTTTACATTC
66 TCCTATAAAATTTCAGTCAAATTTCTTAGTCGTCTAATAAGAAAGAAAATAAATGTTTTACATTC
309101 TACAAAAGAGCTAAAAGTGCTTTCACCAGTAAGCTATAGAGA
131 TACAAAAGAGCTAAAAGTGCTTTCACCAGTAAGCTATAGAGA
309143 ACTAAGGTAT
Statistics
Matches: 168, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
179 168 1.00
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.31
Consensus pattern (179 bp):
ATCTATCATTGACCTCTGAACTTCACTAAGAACATTGGACTTCAAGAGGACCTTTTCTATGCAAA
TCCTATAAAATTTCAGTCAAATTTCTTAGTCGTCTAATAAGAAAGAAAATAAATGTTTTACATTC
TACAAAAGAGCTAAAAGTGCTTTCACCAGTAAGCTATAGAGACAACCAA
Found at i:313404 original size:28 final size:28
Alignment explanation
Indices: 313372--313426 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
313362 CTTCATTTAC
313372 ATTATATTGTCGAGCCAATACTTGAAAG
1 ATTATATTGTCGAGCCAATACTTGAAAG
* *
313400 ATTATATTGTCGAGTCAATGCTTGAAA
1 ATTATATTGTCGAGCCAATACTTGAAA
313427 CCAACAACAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.35
Consensus pattern (28 bp):
ATTATATTGTCGAGCCAATACTTGAAAG
Found at i:314210 original size:60 final size:60
Alignment explanation
Indices: 314031--314213 Score: 224
Period size: 60 Copynumber: 3.0 Consensus size: 60
314021 ATGAATGTAT
* * * * * *
314031 GGATGAAATTGAAAGATTTAGAAGTTTAGGGATCAATTTAGAATGAGAGTCATAGTTTGA
1 GGATGAAATTGAAATATTTAAAAGTTTAAGGATTAATTTAAAATGAGAGTCATAGTTTGG
* * * * * *
314091 CGATGAAATTGGAATGTTCAAATGTTTAAGGATTAATTTAAATTGAGTA-TCATAGTTTGG
1 GGATGAAATTGAAATATTTAAAAGTTTAAGGATTAATTTAAAATGAG-AGTCATAGTTTGG
* *
314151 GGATGAAATTAAAATATTTAAAAGTTTAAGGATTAATTTAAAATGAGGGTCATAGTTTGG
1 GGATGAAATTGAAATATTTAAAAGTTTAAGGATTAATTTAAAATGAGAGTCATAGTTTGG
314211 GGA
1 GGA
314214 CATATGATGG
Statistics
Matches: 101, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
60 100 0.99
61 1 0.01
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.34
Consensus pattern (60 bp):
GGATGAAATTGAAATATTTAAAAGTTTAAGGATTAATTTAAAATGAGAGTCATAGTTTGG
Found at i:314806 original size:15 final size:15
Alignment explanation
Indices: 314788--314831 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
314778 TATTCGCCTT
314788 GCATCAGCCCGCCCC
1 GCATCAGCCCGCCCC
*
314803 GCATCTGCCCGCCCC
1 GCATCAGCCCGCCCC
314818 GCATCTA-CCCGCCC
1 GCATC-AGCCCGCCC
314832 AATAAATACC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.11, C:0.59, G:0.18, T:0.11
Consensus pattern (15 bp):
GCATCAGCCCGCCCC
Found at i:317043 original size:12 final size:12
Alignment explanation
Indices: 317026--317057 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
317016 GATAATTAGC
317026 AATGGCAATGGA
1 AATGGCAATGGA
317038 AATGGCAATGGA
1 AATGGCAATGGA
*
317050 AACGGCAA
1 AATGGCAA
317058 CATCAGCAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.44, C:0.12, G:0.31, T:0.12
Consensus pattern (12 bp):
AATGGCAATGGA
Found at i:318082 original size:16 final size:16
Alignment explanation
Indices: 318063--318106 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
318053 TGGATGGCTA
318063 AATAGATGGATGAACC
1 AATAGATGGATGAACC
*
318079 AATAGATGGATGAATC
1 AATAGATGGATGAACC
* *
318095 AAAAGATAGATG
1 AATAGATGGATG
318107 GATGGATAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.48, C:0.07, G:0.25, T:0.20
Consensus pattern (16 bp):
AATAGATGGATGAACC
Found at i:319423 original size:2 final size:2
Alignment explanation
Indices: 319416--319446 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
319406 ATCAGCTTGT
319416 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
319447 TCGCATAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:321032 original size:16 final size:16
Alignment explanation
Indices: 321011--321041 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
321001 GTCACTTTCC
321011 GTTAAGTTACATATAG
1 GTTAAGTTACATATAG
321027 GTTAAGTTACATATA
1 GTTAAGTTACATATA
321042 TGACAATAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.06, G:0.16, T:0.39
Consensus pattern (16 bp):
GTTAAGTTACATATAG
Found at i:330859 original size:40 final size:39
Alignment explanation
Indices: 330778--330860 Score: 98
Period size: 40 Copynumber: 2.1 Consensus size: 39
330768 TGATAACAAA
* *
330778 TTTTCTATTTTTTCAATGTAGTCTCTCAATTTTGTATAT
1 TTTTCTATTTATTCAATGTAGTCTCTCAATTTTGTACAT
*
330817 TTTTCGTATTTATTCAATTTA-TC-CTCAATTTTAAGTACAT
1 TTTTC-TATTTATTCAATGTAGTCTCTCAATTTT--GTACAT
330857 TTTT
1 TTTT
330861 GACGAAATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
38 9 0.24
39 7 0.18
40 22 0.58
ACGTcount: A:0.23, C:0.13, G:0.06, T:0.58
Consensus pattern (39 bp):
TTTTCTATTTATTCAATGTAGTCTCTCAATTTTGTACAT
Found at i:331572 original size:2 final size:2
Alignment explanation
Indices: 331565--331618 Score: 90
Period size: 2 Copynumber: 26.5 Consensus size: 2
331555 TTAATATTAA
*
331565 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT
331608 AT AT AT AT AT A
1 AT AT AT AT AT A
331619 ATTGTATTTA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 48 0.98
3 1 0.02
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:336109 original size:15 final size:15
Alignment explanation
Indices: 336091--336123 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
336081 ATATAAAATA
*
336091 TTAATTGATATAATT
1 TTAATTAATATAATT
336106 TTAATTAATATAATT
1 TTAATTAATATAATT
336121 TTA
1 TTA
336124 CAGAAATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
TTAATTAATATAATT
Found at i:341046 original size:18 final size:18
Alignment explanation
Indices: 341025--341157 Score: 187
Period size: 18 Copynumber: 7.4 Consensus size: 18
341015 TTTATCCCAT
341025 AGGACCACTATGTCCCGA
1 AGGACCACTATGTCCCGA
*
341043 AGGACCACTGTGTCCCGA
1 AGGACCACTATGTCCCGA
* *
341061 AGAACCATTATGTCCCGA
1 AGGACCACTATGTCCCGA
*
341079 AGGACCATTATGTCCCGA
1 AGGACCACTATGTCCCGA
*
341097 AGGACCAC-GTGTCCCGA
1 AGGACCACTATGTCCCGA
*
341114 AGGACCATTATGTCCCGA
1 AGGACCACTATGTCCCGA
* *
341132 AGGACCACTATATCTCGA
1 AGGACCACTATGTCCCGA
341150 AGGACCAC
1 AGGACCAC
341158 GTAGACCCTC
Statistics
Matches: 102, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
17 15 0.15
18 87 0.85
ACGTcount: A:0.29, C:0.31, G:0.23, T:0.18
Consensus pattern (18 bp):
AGGACCACTATGTCCCGA
Found at i:341130 original size:53 final size:53
Alignment explanation
Indices: 341025--341159 Score: 225
Period size: 53 Copynumber: 2.5 Consensus size: 53
341015 TTTATCCCAT
341025 AGGACCACTATGTCCCGAAGGACCACTGTGTCCCGAAGAACCATTATGTCCCGA
1 AGGACCACTATGTCCCGAAGGACCAC-GTGTCCCGAAGAACCATTATGTCCCGA
* *
341079 AGGACCATTATGTCCCGAAGGACCACGTGTCCCGAAGGACCATTATGTCCCGA
1 AGGACCACTATGTCCCGAAGGACCACGTGTCCCGAAGAACCATTATGTCCCGA
* *
341132 AGGACCACTATATCTCGAAGGACCACGT
1 AGGACCACTATGTCCCGAAGGACCACGT
341160 AGACCCTCGA
Statistics
Matches: 76, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
53 51 0.67
54 25 0.33
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.19
Consensus pattern (53 bp):
AGGACCACTATGTCCCGAAGGACCACGTGTCCCGAAGAACCATTATGTCCCGA
Found at i:341550 original size:24 final size:24
Alignment explanation
Indices: 341493--341552 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
341483 CCCCTTGAAG
*
341493 TGCATCGATGCATTCTTTAACATG
1 TGCATCGATGCATTCTTTAACATA
*
341517 TACATCGATGCATTCTTTAACATA
1 TGCATCGATGCATTCTTTAACATA
*
341541 TGCATTGATGCA
1 TGCATCGATGCA
341553 CTACCCATAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (24 bp):
TGCATCGATGCATTCTTTAACATA
Found at i:344534 original size:2 final size:2
Alignment explanation
Indices: 344527--344570 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
344517 ATTGATATTC
*
344527 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
344569 AT
1 AT
344571 TCATATACAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:344845 original size:18 final size:18
Alignment explanation
Indices: 344816--344939 Score: 176
Period size: 18 Copynumber: 6.9 Consensus size: 18
344806 GTGTAGAATT
*
344816 TGTCCCGTAGGACCACTA
1 TGTCCCGAAGGACCACTA
* *
344834 TGTCTCGAAGGACCACTG
1 TGTCCCGAAGGACCACTA
* *
344852 TGTCCCGAAGAACCATTA
1 TGTCCCGAAGGACCACTA
344870 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
344888 TGTCCCGAAGGACCACTG
1 TGTCCCGAAGGACCACTA
*
344906 TGTCCCGAAGGACCATTA
1 TGTCCCGAAGGACCACTA
*
344924 TGTCCCGAATGACCAC
1 TGTCCCGAAGGACCAC
344940 GTAGACCCTC
Statistics
Matches: 92, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 92 1.00
ACGTcount: A:0.26, C:0.31, G:0.23, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:344882 original size:54 final size:54
Alignment explanation
Indices: 344816--344939 Score: 212
Period size: 54 Copynumber: 2.3 Consensus size: 54
344806 GTGTAGAATT
* *
344816 TGTCCCGTAGGACCACTATGTCTCGAAGGACCACTGTGTCCCGAAGAACCATTA
1 TGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGTGTCCCGAAGAACCATTA
*
344870 TGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGTGTCCCGAAGGACCATTA
1 TGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGTGTCCCGAAGAACCATTA
*
344924 TGTCCCGAATGACCAC
1 TGTCCCGAAGGACCAC
344940 GTAGACCCTC
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 66 1.00
ACGTcount: A:0.26, C:0.31, G:0.23, T:0.20
Consensus pattern (54 bp):
TGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGTGTCCCGAAGAACCATTA
Found at i:345699 original size:20 final size:22
Alignment explanation
Indices: 345674--345730 Score: 91
Period size: 20 Copynumber: 2.6 Consensus size: 22
345664 TTCCCCTTGA
345674 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
345694 AGTGCATCGATGCATTCTTAAC
1 AGTGCATCGATGCATTCTTAAC
345716 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
345731 CTACCCATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
20 17 0.50
21 1 0.03
22 3 0.09
23 13 0.38
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:345855 original size:63 final size:63
Alignment explanation
Indices: 345719--345857 Score: 158
Period size: 63 Copynumber: 2.2 Consensus size: 63
345709 TCTTAACATG
* * * *
345719 TGCATCGATGCACTACC-CATGCATCGATACAAAAATTACCTTCGATGTTTCATTTTAAGGGGA
1 TGCATCGATGCACT-CCTTATGCATCGATACAAAAATTACATTCGATGTTTCATTTTAAAGAGA
** * *
345782 TGCATCGATGCACTCCTTATGCATCGATACACCAATTGCATTCGATGTTTCTTCTTTAAAGAG-
1 TGCATCGATGCACTCCTTATGCATCGATACAAAAATTACATTCGATGTTTCAT-TTTAAAGAGA
345845 TGCA-CTGATGCAC
1 TGCATC-GATGCAC
345858 ATTGAATGTG
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
62 3 0.05
63 55 0.85
64 7 0.11
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (63 bp):
TGCATCGATGCACTCCTTATGCATCGATACAAAAATTACATTCGATGTTTCATTTTAAAGAGA
Found at i:352349 original size:2 final size:2
Alignment explanation
Indices: 352342--352366 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
352332 TTTTAAGTAT
352342 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
352367 CTTAATTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:353479 original size:38 final size:38
Alignment explanation
Indices: 353436--353508 Score: 112
Period size: 38 Copynumber: 1.9 Consensus size: 38
353426 TCTTATTGAT
*
353436 ATAAATATATATTA-TTTACATACATAATTGAAAATTCA
1 ATAAATACATATTATTTTA-ATACATAATTGAAAATTCA
*
353474 ATAAATACATATTATTTTAATATATAATTGAAAAT
1 ATAAATACATATTATTTTAATACATAATTGAAAAT
353509 ATGAACTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
38 28 0.88
39 4 0.12
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (38 bp):
ATAAATACATATTATTTTAATACATAATTGAAAATTCA
Found at i:357255 original size:4 final size:4
Alignment explanation
Indices: 357246--357272 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
357236 AAAGTCAACT
357246 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
357273 TGTGAGTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:357726 original size:30 final size:30
Alignment explanation
Indices: 357692--357764 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
357682 TTAGAATTGC
357692 GGGATCAAATAAACTTTTAATTACAACTGT
1 GGGATCAAATAAACTTTTAATTACAACTGT
*
357722 GGGATCAAATAAACTTTTAATTACAATTGT
1 GGGATCAAATAAACTTTTAATTACAACTGT
*
357752 TGGATCAAATAAA
1 GGGATCAAATAAA
357765 TTATTATTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (30 bp):
GGGATCAAATAAACTTTTAATTACAACTGT
Found at i:357818 original size:30 final size:31
Alignment explanation
Indices: 357767--357826 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
357757 CAAATAAATT
*
357767 ATTATTAATTTATTATT-AAAAATGAATAAAC
1 ATTATTAATCTATTATTAAAAAAT-AATAAAC
*
357798 ATTATTAA-CTATTGTTAAAAAATAATAAA
1 ATTATTAATCTATTATTAAAAAATAATAAA
357827 TAATGAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.40
Consensus pattern (31 bp):
ATTATTAATCTATTATTAAAAAATAATAAAC
Found at i:365122 original size:21 final size:21
Alignment explanation
Indices: 365092--365235 Score: 93
Period size: 21 Copynumber: 7.0 Consensus size: 21
365082 GATTTACATA
* *
365092 TTCGCATTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
** *
365113 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
365134 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* * * *
365153 TTCGGGTTGCGATTTATTACAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
365176 TT--CGTTGCGATAGTCCAGG
1 TTCGCGTTGCGATAGTCCAAG
* * *
365195 TTCGCGTTGCTATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
365218 TT--CGTTGCGATAGTCCAA
1 TTCGCGTTGCGATAGTCCAA
365236 AATCGCAACG
Statistics
Matches: 92, Mismatches: 23, Indels: 18
0.69 0.17 0.14
Matches are distributed among these distances:
19 30 0.33
21 46 0.50
23 16 0.17
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:365177 original size:42 final size:42
Alignment explanation
Indices: 365098--365235 Score: 217
Period size: 42 Copynumber: 3.3 Consensus size: 42
365088 CATATTCGCA
*
365098 TTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
* *
365138 TTGCGATAGTCCAAGTTCGGGTTGCGATTTATTACAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
* *
365180 TTGCGATAGTCCAGGTTCGCGTTGCTATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
365222 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
365236 AATCGCAACG
Statistics
Matches: 88, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
40 25 0.28
41 2 0.02
42 61 0.69
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.36
Consensus pattern (42 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:366081 original size:19 final size:19
Alignment explanation
Indices: 366057--366123 Score: 62
Period size: 19 Copynumber: 3.3 Consensus size: 19
366047 TCGTTGCGAT
*
366057 TTTGGACTATCGCAACTAA
1 TTTGGACTATCGCAACGAA
* *
366076 TTTGGAATAAATCGTAACGCGAA
1 TTTGGACT--ATCGCAA--CGAA
*
366099 CTTGGACTATCGCAACGAA
1 TTTGGACTATCGCAACGAA
366118 TTTGGA
1 TTTGGA
366124 AAATCGCGAT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
19 16 0.43
21 12 0.32
23 9 0.24
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (19 bp):
TTTGGACTATCGCAACGAA
Found at i:366129 original size:19 final size:19
Alignment explanation
Indices: 366065--366130 Score: 51
Period size: 19 Copynumber: 3.3 Consensus size: 19
366055 ATTTTGGACT
*
366065 ATCGCAACTAATTTGGAATAA
1 ATCGCAACGAATTTGG-A-AA
* * **
366086 ATCGTAACGCGAACTTGGACT
1 ATCGCAA--CGAATTTGGAAA
366107 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
366126 ATCGC
1 ATCGC
366131 GATAGTCGAA
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
19 14 0.41
21 12 0.35
22 1 0.03
23 7 0.21
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (19 bp):
ATCGCAACGAATTTGGAAA
Found at i:366153 original size:21 final size:21
Alignment explanation
Indices: 366129--366174 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
366119 TTGGAAAATC
*
366129 GCGATAGTCGAAGTTCGCGTT
1 GCGATAATCGAAGTTCGCGTT
*
366150 GCGATAATCGATGTTCGCGTT
1 GCGATAATCGAAGTTCGCGTT
366171 GCGA
1 GCGA
366175 ATCTGAAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.20, G:0.33, T:0.28
Consensus pattern (21 bp):
GCGATAATCGAAGTTCGCGTT
Found at i:366943 original size:26 final size:27
Alignment explanation
Indices: 366892--366945 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
366882 TTGTTTTCAA
* *
366892 TCCCAGCTTTGTAGTTTTTTTTGTAAT
1 TCCCAGCTTTCTAGTTTTTTATGTAAT
366919 TCCCAGCTTTCTAG-TTTTTATGTAAT
1 TCCCAGCTTTCTAGTTTTTTATGTAAT
366945 T
1 T
366946 TGAAAACCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 12 0.48
27 13 0.52
ACGTcount: A:0.17, C:0.17, G:0.13, T:0.54
Consensus pattern (27 bp):
TCCCAGCTTTCTAGTTTTTTATGTAAT
Found at i:370450 original size:17 final size:17
Alignment explanation
Indices: 370430--370472 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
370420 TGTGCTTGCA
370430 GGTCACGGGTGCGAGCT
1 GGTCACGGGTGCGAGCT
*
370447 GGTCACGAGTGCGAGCT
1 GGTCACGGGTGCGAGCT
370464 GGTCACGGG
1 GGTCACGGG
370473 CTTCAGGGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.14, C:0.23, G:0.47, T:0.16
Consensus pattern (17 bp):
GGTCACGGGTGCGAGCT
Found at i:371309 original size:55 final size:55
Alignment explanation
Indices: 371149--371889 Score: 1055
Period size: 55 Copynumber: 13.6 Consensus size: 55
371139 CTCCATAGTC
* * *
371149 CTTCAGAGAGTATAAGACCCGAACAATCTTTAACAATCGCGTCTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCTCCCTATTT
* * * * * * *
371204 CTTCAGAGAATATAAGAC-C-CACAATCCTCATCAATCACGTCTTCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCTCCCTATTT
* * *
371257 CTTCAGAGAGTATAAGACCCGAACAATCTTCAACAATCGTGTCGGCTCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCTCCCTATTT
* * * *
371312 CTGCAGAGAGTATAAGAC-C-CACAATCTTCATCAATCGCGTCTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCTCCCTATTT
* * *
371365 CGTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCTCCCTATTT
* * * *
371420 CTTCAGAGAGTATAAGAC-C-CACAATCTTCATCAATCGCGTCTTCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCTCCCTATTT
* * * *
371473 CTTCAGAGAGTAT-AGACCCGAACAATCTTCAACAATCGTGTCGGCTTCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCTCCCTATTT
* * ** * *
371527 CTGCATAGAGTACGAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATCT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCTCCCTATTT
* *
371582 CTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCTCCCTATTT
* *
371637 CTTCAGAGAGTATAAGACTCGAACAATTTTCAACAATCGTGTCTGCTCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCTCCCTATTT
371692 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCTCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCTCCCTATTT
* * *
371747 CTTCAGAGAGTATAAGACTCGAAAAATTTTCAACAATCGTGTCTGCTCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCTCCCTATTT
371802 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCTCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCTCCCTATTT
*
371857 CTTCAGAGAGTATAAGACTCGATCAATCTTCAA
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAA
371890 TTATCGTTGG
Statistics
Matches: 618, Mismatches: 61, Indels: 14
0.89 0.09 0.02
Matches are distributed among these distances:
52 4 0.01
53 134 0.22
54 42 0.07
55 438 0.71
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.29
Consensus pattern (55 bp):
CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCTCCCTATTT
Found at i:372902 original size:8 final size:8
Alignment explanation
Indices: 372889--372943 Score: 57
Period size: 8 Copynumber: 7.4 Consensus size: 8
372879 TGAACCGTCA
372889 TTTTTCAT
1 TTTTTCAT
372897 TTTTTCA-
1 TTTTTCAT
372904 ---TTCAT
1 TTTTTCAT
372909 TTTTT-ATT
1 TTTTTCA-T
*
372917 TTTTTTAT
1 TTTTTCAT
372925 TTTTTCAT
1 TTTTTCAT
372933 TTTTTCAT
1 TTTTTCAT
372941 TTT
1 TTT
372944 CACTCATTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
4 4 0.10
7 1 0.03
8 34 0.85
9 1 0.03
ACGTcount: A:0.13, C:0.09, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTTCAT
Found at i:372951 original size:42 final size:42
Alignment explanation
Indices: 372889--372971 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
372879 TGAACCGTCA
* *
372889 TTTTTCATTTTTTCATTCATTTTTTATTTTTTTTATTTTTTCAT
1 TTTTTCA-TTTTTCACTCATTTTTTATTCTTTTT-TTTTTTCAT
*
372933 TTTTTCA-TTTTCACTCATTTTTTCTTCTTTTTTTTTTTC
1 TTTTTCATTTTTCACTCATTTTTTATTCTTTTTTTTTTTC
372972 TTCAAGCAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
41 7 0.19
42 22 0.61
44 7 0.19
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (42 bp):
TTTTTCATTTTTCACTCATTTTTTATTCTTTTTTTTTTTCAT
Found at i:376462 original size:8 final size:8
Alignment explanation
Indices: 376449--376476 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
376439 GAAAAAGAAG
376449 ATATATAC
1 ATATATAC
376457 ATATATAC
1 ATATATAC
376465 ATATATAC
1 ATATATAC
376473 ATAT
1 ATAT
376477 GGAGAATCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATATAC
Found at i:385995 original size:17 final size:17
Alignment explanation
Indices: 385975--386017 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
385965 TGTGCTTGCA
385975 GGTCACGGGTGCGAGCT
1 GGTCACGGGTGCGAGCT
*
385992 GGTCACGAGTGCGAGCT
1 GGTCACGGGTGCGAGCT
386009 GGTCACGGG
1 GGTCACGGG
386018 CTTCAGGGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.14, C:0.23, G:0.47, T:0.16
Consensus pattern (17 bp):
GGTCACGGGTGCGAGCT
Found at i:386631 original size:21 final size:23
Alignment explanation
Indices: 386607--386656 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
386597 CGAAAATATT
* *
386607 CATTTTA-GGTAG-CAAAATTAA
1 CATTTTATGGTAGAAAAAAATAA
386628 CA-TTTATGGTAGAAAAAAATAA
1 CATTTTATGGTAGAAAAAAATAA
386650 CATTTTA
1 CATTTTA
386657 AGTAACGCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 4 0.17
21 7 0.29
22 9 0.38
23 4 0.17
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.34
Consensus pattern (23 bp):
CATTTTATGGTAGAAAAAAATAA
Found at i:387041 original size:12 final size:13
Alignment explanation
Indices: 387016--387053 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
387006 TTATTTTTAT
387016 TTAAATTAAAAAA
1 TTAAATTAAAAAA
387029 TTAAATT-AAAAA
1 TTAAATTAAAAAA
**
387041 TTATTTTAAAAAA
1 TTAAATTAAAAAA
387054 CACCCAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
TTAAATTAAAAAA
Found at i:393392 original size:18 final size:18
Alignment explanation
Indices: 393372--393407 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
393362 GATTTTTATA
393372 TTTAATTAAAATATAATAT
1 TTTAATT-AAATATAATAT
*
393391 TTTTATTAAATATAATA
1 TTTAATTAAATATAATA
393408 ATAAATTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTAATTAAATATAATAT
Done.