Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005766.1 Hibiscus syriacus cultivar Beakdansim tig00013498_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: 72949
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:5283 original size:335 final size:331
Alignment explanation
Indices: 4655--5652 Score: 1413
Period size: 335 Copynumber: 3.0 Consensus size: 331
4645 ATCCCTTTAA
* * *
4655 CTACAATCTATCCGTAATGTAGTGATAATTCTGATGTCTGTTTTGTTCATGTGCTACGAG-ATGA
1 CTACAATTTATCCGTAATGCAGTGATAATTCTGATGTCTGTTTTGTTCATGTGCTACGAGAAAG-
* * * *
4719 TAATTGTGTGGTGCATGCACTTACCAAATCTG-GAAGGACAAGATAAGAAGGTTCATGGCATTGT
65 TAATTGTGTGGTGAATGCACTTGCCAAATCTGAAAAGGACAA-ATAAGAAGGTTCATGGCATGGT
* * *
4783 CGTATTGTAAGAGTTTTTTTTTAATCTAGTGTGCAAAATAGTAAATATGTTTTTTTAAATGAGAT
129 CGTATTAT-A-AG--TTTTTTTAATCTAGTGTGTAAAATAGTAAATATGTTTTTTTTAATGAGAT
* * *
4848 TTAAAGTTCTGATATGATTTTTTAACCTTTTAAGTACATGAGCAACAACCTTAAACATATAAAGG
190 TTCAACTTCTGATATGATTTTTTAACCTTTTAAGTACATGAACAACAACCTTAAACATATAAAGG
* *
4913 AAGCTTCAAAAGCAGAAGAGTAAAGTGTTCATTAAGTTTAATATATTGATTGGGATAATAATTTA
255 AAGCTTCAAAAGCACAAGAGTAAATTGTTCATTAAGTTTAATATATTGATTGGGATAATAATTTA
4978 AGGCTTAATACC
320 AGGCTTAATACC
* * * *
4990 TCAAAAGTACAATTTATCCGTAAAGCAGTGATAATTCTAATGTCTGTTTTTTTCATGTGCTATGA
1 -C-----TACAATTTATCCGTAATGCAGTGATAATTCTGATGTCTGTTTTGTTCATGTGCTACGA
* *
5055 GAAAGTAATTGTGCGGTGAATGCGCTTGCCAAATCTGAAAAAGGACAAA-AAGAAGGTTCATGGC
60 GAAAGTAATTGTGTGGTGAATGCACTTGCCAAATCTG-AAAAGGACAAATAAGAAGGTTCATGGC
* * *
5119 AAGGTCATA-T-TAAGTTTTTTT-ATCTAATGTGTAAAATAGTAAATATGGTTTTTTTTAATGAG
124 ATGGTCGTATTATAAGTTTTTTTAATCTAGTGTGTAAAATAGTAAATAT-GTTTTTTTTAATGAG
*
5181 ATTTCAACTTCTGGTCA-GATTTTTTAACCTTTTAAGTACATGAACAACAACCTTAAACATATAA
188 ATTTCAACTTCTGAT-ATGATTTTTTAACCTTTTAAGTACATGAACAACAACCTTAAACATATAA
* * * *
5245 AGGAAGCATCAAAACCACAAGAGTAAATTGTACATTAAGTTTAATATGTTGATTGGGATAATAAT
252 AGGAAGCTTCAAAAGCACAAGAGTAAATTGTTCATTAAGTTTAATATATTGATTGGGATAATAAT
5310 TTAAGGCTTAATA-C
317 TTAAGGCTTAATACC
* * * *
5324 CTACAATTTATCCTTAATGCAGTGATAACTCTGATGTCTGTTTTGTTCATGTACTACGAGAAGGT
1 CTACAATTTATCCGTAATGCAGTGATAATTCTGATGTCTGTTTTGTTCATGTGCTACGAGAAAGT
*
5389 AATTGTGTGGTGAATGCACTTGCCAAATCTGAAAATGACAAAATAAGAAGGTTCATGGCATGGTC
66 AATTGTGTGGTGAATGCACTTGCCAAATCTGAAAAGGAC-AAATAAGAAGGTTCATGGCATGGTC
* *
5454 GTATTATAAGTTTTTTTAATCTAGTGTGTAAAATAGTATATATG-TTTTTTTAATGATATTTCAA
130 GTATTATAAGTTTTTTTAATCTAGTGTGTAAAATAGTAAATATGTTTTTTTTAATGAGATTTCAA
* *
5518 CTTCTGATATGATTTTTTAACCTTTTAAGTACATGAACAACAACCTTAAACATATACAGGATGCT
195 CTTCTGATATGATTTTTTAACCTTTTAAGTACATGAACAACAACCTTAAACATATAAAGGAAGCT
* * *
5583 TC-AAAGTACAATAGTAAATTGTTCATTAAGTTAAATATATTGATTGGGATAATAATTTAAGGCT
260 TCAAAAGCACAAGAGTAAATTGTTCATTAAGTTTAATATATTGATTGGGATAATAATTTAAGGCT
5647 TAATAC
325 TAATAC
5653 ATAGTTTAAT
Statistics
Matches: 591, Mismatches: 54, Indels: 40
0.86 0.08 0.06
Matches are distributed among these distances:
327 7 0.01
328 88 0.15
329 84 0.14
330 81 0.14
331 12 0.02
332 23 0.04
333 1 0.00
334 24 0.04
335 151 0.26
336 2 0.00
337 2 0.00
338 1 0.00
339 1 0.00
340 1 0.00
341 102 0.17
342 3 0.01
343 8 0.01
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (331 bp):
CTACAATTTATCCGTAATGCAGTGATAATTCTGATGTCTGTTTTGTTCATGTGCTACGAGAAAGT
AATTGTGTGGTGAATGCACTTGCCAAATCTGAAAAGGACAAATAAGAAGGTTCATGGCATGGTCG
TATTATAAGTTTTTTTAATCTAGTGTGTAAAATAGTAAATATGTTTTTTTTAATGAGATTTCAAC
TTCTGATATGATTTTTTAACCTTTTAAGTACATGAACAACAACCTTAAACATATAAAGGAAGCTT
CAAAAGCACAAGAGTAAATTGTTCATTAAGTTTAATATATTGATTGGGATAATAATTTAAGGCTT
AATACC
Found at i:7672 original size:21 final size:21
Alignment explanation
Indices: 7633--7672 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
7623 CATTCTAGAT
* *
7633 TATCATGTAAACTTTTTGAAC
1 TATCATGTAAACGTCTTGAAC
*
7654 TATCATGTAATCGTCTTGA
1 TATCATGTAAACGTCTTGA
7673 CGATTTGATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.42
Consensus pattern (21 bp):
TATCATGTAAACGTCTTGAAC
Found at i:8394 original size:42 final size:41
Alignment explanation
Indices: 8328--8440 Score: 124
Period size: 41 Copynumber: 2.8 Consensus size: 41
8318 TTTATATTAT
*
8328 TAAAATATATTCTTTAACTA-TTAAAAT-TATAAAAAACACTA
1 TAAAA-ATATTATTTAACTATTTAAAATATATAAAAAA-ACTA
* * * *
8369 TAAAAATATTATTTTAACCATTTAAAATATATTAAATAATTA
1 TAAAAATATTA-TTTAACTATTTAAAATATATAAAAAAACTA
*
8411 TAAACATATTATTTAACTATTTAAAA-ATAT
1 TAAAAATATTATTTAACTATTTAAAATATAT
8441 GAATATATTC
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
40 9 0.15
41 26 0.42
42 20 0.32
43 7 0.11
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (41 bp):
TAAAAATATTATTTAACTATTTAAAATATATAAAAAAACTA
Found at i:8426 original size:23 final size:22
Alignment explanation
Indices: 8371--8426 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 22
8361 AAACACTATA
* *
8371 AAAATATTATTTTAACCATT-T
1 AAAATATTATTTAAACAATTAT
*
8392 AAAATA-TA-TTAAATAATTAT
1 AAAATATTATTTAAACAATTAT
8412 AAACATATTATTTAA
1 AAA-ATATTATTTAA
8427 CTATTTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 7 0.25
20 6 0.21
21 9 0.32
22 2 0.07
23 4 0.14
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (22 bp):
AAAATATTATTTAAACAATTAT
Found at i:10317 original size:15 final size:15
Alignment explanation
Indices: 10281--10313 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
10271 TTACCAACCC
10281 CTAACTTCTAATATG
1 CTAACTTCTAATATG
10296 CTAACTTCTAA-ATG
1 CTAACTTCTAATATG
10310 CTAA
1 CTAA
10314 ACTTTGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.36
Consensus pattern (15 bp):
CTAACTTCTAATATG
Found at i:10438 original size:29 final size:29
Alignment explanation
Indices: 10406--10468 Score: 74
Period size: 30 Copynumber: 2.2 Consensus size: 29
10396 TTTTATGCGC
*
10406 TTTA-ATTCATGCCCTTTAAATTTCTAGTA
1 TTTATATTCATGCCCTTTAAATTT-TAGCA
* * *
10435 TTTATATTTATGTCCTTTAGATTTTAGCA
1 TTTATATTCATGCCCTTTAAATTTTAGCA
10464 TTTAT
1 TTTAT
10469 TTTTCTGTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 13 0.45
30 16 0.55
ACGTcount: A:0.25, C:0.13, G:0.08, T:0.54
Consensus pattern (29 bp):
TTTATATTCATGCCCTTTAAATTTTAGCA
Found at i:15293 original size:116 final size:115
Alignment explanation
Indices: 14942--15298 Score: 412
Period size: 116 Copynumber: 3.1 Consensus size: 115
14932 GGATAAACCA
* * * **
14942 ATCAACATTTCCAA-TGGAAGGGTTCATAATGAGAATAACTTGTCCGATGAGGGAGAATAAGTTC
1 ATCAATATTT-CAAGTGAAAGGGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAATAAGTTC
* * **
15006 CTAATGATAAGAACTTGTTCGACCTTGGCTCATTTATAACATAAGGAGTTGG
65 CTAATGAGAAGAACTTGTTCGACCATGGCTCATCCAT-ACATAAGGAGTTGG
* * * * * * *
15058 ACCAACACTTCAAGTGGAAGGGTCCATAATGATAAGAACTCATCTGATGAGGGAGAATAAGTTCC
1 ATCAATATTTCAAGTGAAAGGGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAATAAGTTCC
* * * *
15123 TAATAAGAA-AAGGTTGTTCAACTATGGCTCATCCATATCATAAGGAGTTGG
66 TAATGAGAAGAA-CTTGTTCGACCATGGCTCATCCATA-CATAAGGAGTTGG
* * * * * *
15174 ATCAGTATTTCTAGTGAAAGGGTTTATAATAAGAAGAACTCATCCGATGAGGGATAAGAAGTTCC
1 ATCAATATTTCAAGTGAAAGGGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAATAAGTTCC
*
15239 TAATGAGAAGAACTTGTTCGACCATGGCTCATCCATCACATAAGGAGTTAG
66 TAATGAGAAGAACTTGTTCGACCATGGCTCATCCAT-ACATAAGGAGTTGG
15290 ATCAATATT
1 ATCAATATT
15299 CCCAATGAGG
Statistics
Matches: 201, Mismatches: 35, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
115 6 0.03
116 192 0.96
117 3 0.01
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.27
Consensus pattern (115 bp):
ATCAATATTTCAAGTGAAAGGGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAATAAGTTCC
TAATGAGAAGAACTTGTTCGACCATGGCTCATCCATACATAAGGAGTTGG
Found at i:19768 original size:80 final size:77
Alignment explanation
Indices: 19620--19769 Score: 219
Period size: 80 Copynumber: 1.9 Consensus size: 77
19610 TTCCATTACG
* *
19620 AAATGTCACTTTTGATCCAACATCCTAAATTTTACTATTCATTATAAATTGTGTTCTAAATTACT
1 AAATGTCACTTTTGATCCAACATCCTAAATTTTACTATTCATTATAAACTATGTTCTAAATTACT
19685 TGACTAGCCTAT
66 TGACTAGCCTAT
* * *
19697 AAATGTCACTTTTGATCCAACTTCCTAAATTATTTTACTATTCCTTATAAACTATGTTTTAAATT
1 AAATGTCACTTTTGATCCAACATCCT-AA--ATTTTACTATTCATTATAAACTATGTTCTAAATT
*
19762 ATTTGACT
63 ACTTGACT
19770 TGTCTCTTAT
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
77 25 0.39
78 2 0.03
80 37 0.58
ACGTcount: A:0.32, C:0.17, G:0.07, T:0.44
Consensus pattern (77 bp):
AAATGTCACTTTTGATCCAACATCCTAAATTTTACTATTCATTATAAACTATGTTCTAAATTACT
TGACTAGCCTAT
Found at i:20284 original size:2 final size:2
Alignment explanation
Indices: 20275--20305 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
20265 AAGAAATAAA
20275 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20306 TTGGATTTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:30688 original size:49 final size:48
Alignment explanation
Indices: 30629--30729 Score: 148
Period size: 49 Copynumber: 2.1 Consensus size: 48
30619 AACATACGAT
* *
30629 AATAACAACCTTCAATCTTGTTTGACACAAAATATATTTAACCTCTCAA
1 AATAAAAACCTTCAATCTTGTTTGACAC-AAATATATTCAACCTCTCAA
* * *
30678 AATAAAAACCTTTAATCTTGTTTGACACATATATGTTCAACCTCTCAA
1 AATAAAAACCTTCAATCTTGTTTGACACAAATATATTCAACCTCTCAA
30726 AATA
1 AATA
30730 TTCCTACCTC
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
48 21 0.45
49 26 0.55
ACGTcount: A:0.41, C:0.21, G:0.05, T:0.34
Consensus pattern (48 bp):
AATAAAAACCTTCAATCTTGTTTGACACAAATATATTCAACCTCTCAA
Found at i:32367 original size:24 final size:24
Alignment explanation
Indices: 32340--32414 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 24
32330 TAGGATTTGA
* **
32340 TTCAGTATGTTTAACAGTATTGGT
1 TTCAGTATGTTCAACAACATTGGT
*
32364 TTCAGTATGTTCAACAACATTTGT
1 TTCAGTATGTTCAACAACATTGGT
* *
32388 TTCAATATGTTCAACAACATTAGT
1 TTCAGTATGTTCAACAACATTGGT
32412 TTC
1 TTC
32415 CACTACTTCT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (24 bp):
TTCAGTATGTTCAACAACATTGGT
Found at i:36227 original size:21 final size:21
Alignment explanation
Indices: 36197--36361 Score: 144
Period size: 21 Copynumber: 8.0 Consensus size: 21
36187 GATTTACATA
*
36197 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
36218 TTCGCGTTGCGATAGTCAAAG
1 TTCGCGTTGCGATAGTCCAAG
** *
36239 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
*
36260 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
36279 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
* *
36302 TT--CGTTTCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
36321 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
36344 TT--CGTTGCGATAGTCCAA
1 TTCGCGTTGCGATAGTCCAA
36362 AATCGCAACG
Statistics
Matches: 114, Mismatches: 22, Indels: 18
0.74 0.14 0.12
Matches are distributed among these distances:
19 30 0.26
21 68 0.60
23 16 0.14
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.35
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:36249 original size:42 final size:41
Alignment explanation
Indices: 36222--36358 Score: 231
Period size: 42 Copynumber: 3.3 Consensus size: 41
36212 TCCAAGTTCG
*
36222 CGTTGCGATAGTCAAAGTTCGCGTTGCGATT-TTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTATTCCAAATT
36262 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TTATTCCAAATT
*
36304 CGTTTCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TTATTCCAAATT
36346 CGTTGCGATAGTC
1 CGTTGCGATAGTC
36359 CAAAATCGCA
Statistics
Matches: 92, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
40 28 0.30
41 2 0.02
42 62 0.67
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (41 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTATTCCAAATT
Found at i:36978 original size:5 final size:5
Alignment explanation
Indices: 36964--36995 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
36954 TCGCCGCCGC
36964 CGTC- CGTCT CGTCT CGTCT CGTCT CGTCT CGT
1 CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGT
36996 GGTCGTGGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.00, C:0.41, G:0.22, T:0.38
Consensus pattern (5 bp):
CGTCT
Found at i:37003 original size:6 final size:6
Alignment explanation
Indices: 36992--37022 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
36982 TCGTCTCGTC
36992 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
37023 AATACGTGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:37145 original size:21 final size:21
Alignment explanation
Indices: 37119--37291 Score: 141
Period size: 21 Copynumber: 8.4 Consensus size: 21
37109 ATTTTGGACT
37119 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* *
37140 ATCGCAACGCGAACTTGGACT--
1 ATCGCAA--CGAATTTGGAATAA
*
37161 ATCGCAACGAATTTTGAATAA
1 ATCGCAACGAATTTGGAATAA
37182 ATCGCAACGAATTT-GAA-AA
1 ATCGCAACGAATTTGGAATAA
* * *
37201 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAATTTGGAATAA
37222 ATCGCAACGAATTTGG-A-AA
1 ATCGCAACGAATTTGGAATAA
* * *
37241 ATCGCAATGCGAACTTCGACT--
1 ATCGCAA--CGAATTTGGAATAA
37262 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
37283 ATCGCAACG
1 ATCGCAACG
37292 CGAACTTGAA
Statistics
Matches: 120, Mismatches: 16, Indels: 32
0.71 0.10 0.19
Matches are distributed among these distances:
19 41 0.34
20 3 0.03
21 64 0.53
22 2 0.02
23 10 0.08
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (21 bp):
ATCGCAACGAATTTGGAATAA
Found at i:37213 original size:61 final size:61
Alignment explanation
Indices: 37119--37247 Score: 208
Period size: 61 Copynumber: 2.1 Consensus size: 61
37109 ATTTTGGACT
*
37119 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTTGAATAA
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAA-TTTGAA-AA
*
37182 ATCGCAACGAATTT-GAA-AAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGAAAA
37241 ATCGCAA
1 ATCGCAA
37248 TGCGAACTTC
Statistics
Matches: 64, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
59 9 0.14
60 5 0.08
61 33 0.52
62 3 0.05
63 14 0.22
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.22
Consensus pattern (61 bp):
ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGAAAA
Found at i:37226 original size:40 final size:40
Alignment explanation
Indices: 37182--37298 Score: 198
Period size: 40 Copynumber: 2.9 Consensus size: 40
37172 TTTTGAATAA
37182 ATCGCAACGAATTTGAAAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAATTTGAAAAATCGCAACGCGAACTTCGACT
* *
37222 ATCGCAACGAATTTGGAAAATCGCAATGCGAACTTCGACT
1 ATCGCAACGAATTTGAAAAATCGCAACGCGAACTTCGACT
37262 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTT
1 ATCGCAACGAATTT-GAA-AAATCGCAACGCGAACTT
37299 GAACCATCGC
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
40 52 0.73
41 2 0.03
42 17 0.24
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (40 bp):
ATCGCAACGAATTTGAAAAATCGCAACGCGAACTTCGACT
Found at i:37307 original size:21 final size:21
Alignment explanation
Indices: 37139--37316 Score: 88
Period size: 21 Copynumber: 8.6 Consensus size: 21
37129 ATTTGGAATA
*
37139 AATCGCAACGCGAACTT-GGAC
1 AATCGCAA-GCGAACTTCGAAC
* * * *
37160 TATCGCAA-CGAATTTTGAATA
1 AATCGCAAGCGAACTTCGAA-C
* *
37181 AATCGCAA-CGAA-TTTGAAA
1 AATCGCAAGCGAACTTCGAAC
37200 AATCGCAACGCGAACTTCG-AC
1 AATCGCAA-GCGAACTTCGAAC
* * *
37221 TATCGCAA-CGAATTTGGAA-
1 AATCGCAAGCGAACTTCGAAC
37240 AATCGCAATGCGAACTTCG-AC
1 AATCGCAA-GCGAACTTCGAAC
* * * *
37261 TATCGCAA-CGAATTTGGAATA
1 AATCGCAAGCGAACTTCGAA-C
37282 AATCGCAACGCGAACTT-GAAC
1 AATCGCAA-GCGAACTTCGAAC
*
37303 CATCGCAATGCGAA
1 AATCGCAA-GCGAA
37317 TATGTAAATC
Statistics
Matches: 122, Mismatches: 22, Indels: 26
0.72 0.13 0.15
Matches are distributed among these distances:
19 36 0.30
20 11 0.09
21 63 0.52
22 6 0.05
23 6 0.05
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (21 bp):
AATCGCAAGCGAACTTCGAAC
Found at i:37354 original size:21 final size:22
Alignment explanation
Indices: 37325--37377 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
37315 AATATGTAAA
*
37325 TCGCATTGCGA-TAGTCCAAGT
1 TCGCGTTGCGACTAGTCCAAGT
**
37346 TCGCGTTGC-ACTAGTTGAAGT
1 TCGCGTTGCGACTAGTCCAAGT
37367 TCGCGTTGCGA
1 TCGCGTTGCGA
37378 ATCTAGAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 1 0.04
21 25 0.93
22 1 0.04
ACGTcount: A:0.19, C:0.23, G:0.28, T:0.30
Consensus pattern (22 bp):
TCGCGTTGCGACTAGTCCAAGT
Found at i:42623 original size:22 final size:22
Alignment explanation
Indices: 42598--42665 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 22
42588 TATATATGAA
42598 ATGTTTTTGAGTTAACTAATAT
1 ATGTTTTTGAGTTAACTAATAT
** *
42620 ATG-TTTAAAGTGT--TTAA-A-
1 ATGTTTTTGAGT-TAACTAATAT
42638 ATGTTTTTGAGTTAACTAATAT
1 ATGTTTTTGAGTTAACTAATAT
42660 ATGTTT
1 ATGTTT
42666 AAAGTGTTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 12
0.65 0.12 0.23
Matches are distributed among these distances:
18 4 0.12
19 7 0.21
20 6 0.18
21 7 0.21
22 10 0.29
ACGTcount: A:0.32, C:0.03, G:0.15, T:0.50
Consensus pattern (22 bp):
ATGTTTTTGAGTTAACTAATAT
Found at i:42641 original size:40 final size:40
Alignment explanation
Indices: 42596--42685 Score: 180
Period size: 40 Copynumber: 2.2 Consensus size: 40
42586 AATATATATG
42596 AAATGTTTTTGAGTTAACTAATATATGTTTAAAGTGTTTA
1 AAATGTTTTTGAGTTAACTAATATATGTTTAAAGTGTTTA
42636 AAATGTTTTTGAGTTAACTAATATATGTTTAAAGTGTTTA
1 AAATGTTTTTGAGTTAACTAATATATGTTTAAAGTGTTTA
42676 AAATGTTTTT
1 AAATGTTTTT
42686 AAAGCTTTTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.34, C:0.02, G:0.14, T:0.49
Consensus pattern (40 bp):
AAATGTTTTTGAGTTAACTAATATATGTTTAAAGTGTTTA
Found at i:42688 original size:20 final size:19
Alignment explanation
Indices: 42623--42699 Score: 57
Period size: 20 Copynumber: 3.8 Consensus size: 19
42613 CTAATATATG
42623 TTTAAAGTGTTTAAAATGTT
1 TTTAAAGT-TTTAAAATGTT
* * * * *
42643 TTT-GAGTTAACTAATATATG
1 TTTAAAGTT--TTAAAATGTT
42663 TTTAAAGTGTTTAAAATGTT
1 TTTAAAGT-TTTAAAATGTT
42683 TTTAAAGCTTTTAAAAT
1 TTTAAAG-TTTTAAAAT
42700 ATGAAAAAAC
Statistics
Matches: 42, Mismatches: 10, Indels: 10
0.68 0.16 0.16
Matches are distributed among these distances:
18 1 0.02
19 3 0.07
20 33 0.79
21 4 0.10
22 1 0.02
ACGTcount: A:0.36, C:0.03, G:0.13, T:0.48
Consensus pattern (19 bp):
TTTAAAGTTTTAAAATGTT
Found at i:57033 original size:3 final size:3
Alignment explanation
Indices: 57025--57061 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
57015 GGGTCAAAAA
*
57025 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
57062 TATTTATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:60513 original size:3 final size:3
Alignment explanation
Indices: 60505--60575 Score: 97
Period size: 3 Copynumber: 23.3 Consensus size: 3
60495 AGTGGTTTTA
* *
60505 AAT AAT AAT AAT AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
60553 AAT AAC AAT AAT ATTT AAT AAT A
1 AAT AAT AAT AAT A-AT AAT AAT A
60576 TTTTTTAACC
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
3 57 0.97
4 2 0.03
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:61078 original size:129 final size:129
Alignment explanation
Indices: 60726--61213 Score: 602
Period size: 129 Copynumber: 3.8 Consensus size: 129
60716 GATCGTCTAA
* * * * * * *
60726 GGGTTAACACGACTCCAACGTGATGAGTAGATTAGGTCGGGTGATGACACGGTTCCTACATAATG
1 GGGTTGACACGGCTCCTACGTGATGAGGAGATCAGGTCGGGTGATGACACGGTTCCTACGTGATG
* * * * * * *
60791 AGAACGACATGTCATCTAAGGGTGATAACACGGTTCTTACGTGATGAGGACAGTTGGTTATCTG
66 AGGACGGCAGGCCATCTAAGGGTGATAACACGATTCTTACGTGATGAGGACGGCTGGTTATCTG
* * * * * *
60855 AGGTTGACATGGCGCCTACGTTATGAGAAGATCAGGTC-GGTGATGACACGGTTCCTATGTGATG
1 GGGTTGACACGGCTCCTACGTGATGAGGAGATCAGGTCGGGTGATGACACGGTTCCTACGTGATG
* *
60919 AGGACGGCATGCCATCTAAGGGTGATAACACGATTCTTACGTGATGAGGATGGCTGGTTATCTG
66 AGGACGGCAGGCCATCTAAGGGTGATAACACGATTCTTACGTGATGAGGACGGCTGGTTATCTG
* * * * * *
60983 GGGTTCACACGGCTCCTATGTGATGAGGAGATCAAGTCGAGCGATGACACGGTTCCTATGTGATG
1 GGGTTGACACGGCTCCTACGTGATGAGGAGATCAGGTCGGGTGATGACACGGTTCCTACGTGATG
* * *
61048 AGGACGGTAGGCCATCTAAGGGTGATAACACTG-TTCTTACGTGATGAGGACGACTGGTTATCTT
66 AGGACGGCAGGCCATCTAAGGGTGATAACAC-GATTCTTACGTGATGAGGACGGCTGGTTATCTG
* * *
61112 GGGTTGACATGGCTCCTACGTGATGAGGAGATCATGTTGGGTGATGACACGGTTCCTACGTGATG
1 GGGTTGACACGGCTCCTACGTGATGAGGAGATCAGGTCGGGTGATGACACGGTTCCTACGTGATG
* * *
61177 AGGACGGCAGGCCGTCATTAGGGATGATAACCCGATT
66 AGGACGGCAGGCCATC-TAAGGG-TGATAACACGATT
61214 TCAAGAGAAA
Statistics
Matches: 308, Mismatches: 46, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
128 110 0.36
129 181 0.59
130 7 0.02
131 10 0.03
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (129 bp):
GGGTTGACACGGCTCCTACGTGATGAGGAGATCAGGTCGGGTGATGACACGGTTCCTACGTGATG
AGGACGGCAGGCCATCTAAGGGTGATAACACGATTCTTACGTGATGAGGACGGCTGGTTATCTG
Found at i:61171 original size:40 final size:42
Alignment explanation
Indices: 60764--61182 Score: 148
Period size: 46 Copynumber: 9.8 Consensus size: 42
60754 AGATTAGGTC
* * * *
60764 GGGTGATGACACGGTTCCTACATAATGAGAACGACATGTCATCTAA
1 GGGTGATGACACGGTTCCTACGTGATGAGGACG--A-GTCATCT-T
* * * *
60810 GGGTGATAACACGGTTCTTACGTGATGAGGACAGTTGGTTATC-T
1 GGGTGATGACACGGTTCCTACGTGATGAGGAC-G--AGTCATCTT
* ** * * **
60854 GAGGT--TGACATGGCGCCTACGTTATGA-GAAGA-TCA-GGT
1 G-GGTGATGACACGGTTCCTACGTGATGAGGACGAGTCATCTT
* * * *
60892 CGGTGATGACACGGTTCCTATGTGATGAGGACGGCATGCCATCTAA
1 GGGTGATGACACGGTTCCTACGTGATGAGGAC-G-A-GTCATCT-T
* * * *
60938 GGGTGATAACACGATTCTTACGTGATGAGGATGGCTG-GTTATC-T
1 GGGTGATGACACGGTTCCTACGTGATGAGGA---C-GAGTCATCTT
* * * * ** *
60982 GGG-GTTCACACGGCTCCTATGTGATGAGGA-GA-TCAAGTC
1 GGGTGATGACACGGTTCCTACGTGATGAGGACGAGTCATCTT
* * * * *
61021 GAGCGATGACACGGTTCCTATGTGATGAGGACGGTAGGCCATCTAA
1 GGGTGATGACACGGTTCCTACGTGATGAGGAC-G-A-GTCATCT-T
* * * *
61067 GGGTGATAACACTGTTCTTACGTGATGAGGACGACTGGTTATCTT
1 GGGTGATGACACGGTTCCTACGTGATGAGGACGA---GTCATCTT
* * *
61112 GGGT--TGACATGGCTCCTACGTGATGAGGA-GA-TCATGTT
1 GGGTGATGACACGGTTCCTACGTGATGAGGACGAGTCATCTT
61150 GGGTGATGACACGGTTCCTACGTGATGAGGACG
1 GGGTGATGACACGGTTCCTACGTGATGAGGACG
61183 GCAGGCCGTC
Statistics
Matches: 268, Mismatches: 76, Indels: 63
0.66 0.19 0.15
Matches are distributed among these distances:
37 3 0.01
38 15 0.06
39 19 0.07
40 49 0.18
41 3 0.01
42 6 0.02
43 58 0.22
44 7 0.03
45 11 0.04
46 94 0.35
47 1 0.00
49 2 0.01
ACGTcount: A:0.24, C:0.17, G:0.32, T:0.26
Consensus pattern (42 bp):
GGGTGATGACACGGTTCCTACGTGATGAGGACGAGTCATCTT
Found at i:61323 original size:28 final size:28
Alignment explanation
Indices: 61272--61325 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
61262 AAGAGATAAA
*
61272 ATATGTTTCAAGGGAAACGATCTCAAAG
1 ATATGTTTCAAGGAAAACGATCTCAAAG
*
61300 ATATGTTTCAAGAGAAAATG-TCTCAA
1 ATATGTTTCAAG-GAAAACGATCTCAA
61326 GGGAGAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 18 0.78
29 5 0.22
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.28
Consensus pattern (28 bp):
ATATGTTTCAAGGAAAACGATCTCAAAG
Found at i:61347 original size:21 final size:21
Alignment explanation
Indices: 61322--61371 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
61312 AGAAAATGTC
61322 TCAAGGGAGAAAAAATTTGTT
1 TCAAGGGAGAAAAAATTTGTT
*
61343 TCAAGGGAGACAAAATTTGTT
1 TCAAGGGAGAAAAAATTTGTT
61364 TCAAGGGA
1 TCAAGGGA
61372 AATGTTTTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.40, C:0.08, G:0.26, T:0.26
Consensus pattern (21 bp):
TCAAGGGAGAAAAAATTTGTT
Found at i:61423 original size:86 final size:86
Alignment explanation
Indices: 61264--61437 Score: 242
Period size: 86 Copynumber: 2.0 Consensus size: 86
61254 TGTATCAAAA
* *
61264 GAGATAAAATATGTTTCAAGGGAAACGATCTCAAAGATATGTTTCAAGAGAAAATGTCTCAAGGG
1 GAGACAAAATATGTTTCAAGGGAAACGATCTCAAAGATATGTTTCAAGAGAAAATGTCTCAAGAG
*
61329 AGAAAAAA-TTTGTTTCAAGG
66 AGAAAAAATTTTGTTTAAAGG
* * * * * *
61349 GAGACAAAATTTGTTTCAAGGGAAATGTTTTCAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGA
1 GAGACAAAATATGTTTCAAGGGAAACGATCTCAAAG-ATATGTTTCAAGAGAAAATGTCTCAAGA
*
61414 GAGATAAAATTTTGTTTAAAGG
65 GAGAAAAAATTTTGTTTAAAGG
61436 GA
1 GA
61438 AACTATCTCA
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
85 31 0.40
86 33 0.43
87 13 0.17
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.29
Consensus pattern (86 bp):
GAGACAAAATATGTTTCAAGGGAAACGATCTCAAAGATATGTTTCAAGAGAAAATGTCTCAAGAG
AGAAAAAATTTTGTTTAAAGG
Found at i:61495 original size:72 final size:68
Alignment explanation
Indices: 61388--61647 Score: 276
Period size: 72 Copynumber: 3.8 Consensus size: 68
61378 TTCAAAGTTT
* * * *
61388 ATGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAATTTTGTTTAAAGGGAAACTATCTCAAGGAA
1 ATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAA-TTCGTTTCAAGGGAAACTATCTCAA-GAA
61453 GACAA
64 GACAA
* * * *
61458 ATCCGTTCCAAGGGAAACTATCTCAAGAAAGACAAAATTCGTTTCAAGGGAAACGT-TTTC-A-A
1 AT--GTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCGTTTCAAGGGAAAC-TATCTCAAGA
***
61520 AG-TTT
63 AGACAA
* * *
61525 ATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTGTTTTAAGGGAAACTATCTCAAGAGAG
1 ATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACTATCTCAAGA-AG
61590 ACAAA
65 AC-AA
*
61595 ATTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCGTTTCAAGGGAAA
1 A--TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCGTTTCAAGGGAAA
61648 TGTTATCAAA
Statistics
Matches: 154, Mismatches: 25, Indels: 20
0.77 0.13 0.10
Matches are distributed among these distances:
64 1 0.01
65 47 0.31
66 1 0.01
67 3 0.02
68 5 0.03
70 4 0.03
71 18 0.12
72 75 0.49
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.26
Consensus pattern (68 bp):
ATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACTATCTCAAGAAGA
CAA
Found at i:61576 original size:36 final size:36
Alignment explanation
Indices: 61526--61647 Score: 208
Period size: 36 Copynumber: 3.4 Consensus size: 36
61516 TCAAAGTTTA
* *
61526 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
*
61562 TGTTTTAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
61598 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
*
61634 CGTTTCAAGGGAAA
1 TGTTTCAAGGGAAA
61648 TGTTATCAAA
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 81 1.00
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.25
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
Found at i:61595 original size:101 final size:100
Alignment explanation
Indices: 61426--61612 Score: 284
Period size: 101 Copynumber: 1.9 Consensus size: 100
61416 GATAAAATTT
*
61426 TGTTTAAAGGGAAACTATCTCAAGGAAGACAAATCCGTTCCAAGGGAAACTATCTCAAGAAAGAC
1 TGTTTAAAGAGAAACTATCTCAAGGAAGACAAATCCGTTCCAAGGGAAACTATCTCAAGAAAGAC
61491 AAAATTCGTTTCAAGGGAAACGTTTTCAAAGTTTA
66 AAAATTCGTTTCAAGGGAAACGTTTTCAAAGTTTA
* * ** ** *
61526 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTGTTTTAAGGGAAACTATCTCAAGAGAGA
1 TGTTTAAAGAGAAACTATCTCAAGGAAGAC-AAATCCGTTCCAAGGGAAACTATCTCAAGAAAGA
*
61591 CAAAATTTGTTTCAAGGGAAAC
65 CAAAATTCGTTTCAAGGGAAAC
61613 TATCTCAAGA
Statistics
Matches: 77, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
100 27 0.35
101 50 0.65
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (100 bp):
TGTTTAAAGAGAAACTATCTCAAGGAAGACAAATCCGTTCCAAGGGAAACTATCTCAAGAAAGAC
AAAATTCGTTTCAAGGGAAACGTTTTCAAAGTTTA
Found at i:61607 original size:137 final size:136
Alignment explanation
Indices: 61350--61700 Score: 551
Period size: 137 Copynumber: 2.6 Consensus size: 136
61340 GTTTCAAGGG
* *
61350 AGACAAAATTTGTTTCAAGGGAAATGTTTTCAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGAG
1 AGACAAAATTCGTTTCAAGGGAAATGTTTTCAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGGG
61415 AGATAAAATTTTGTTTAAAGGGAAACTATCTCAAGGAAGACAAATCCGTTCCAAGGGAAACTATC
66 AGATAAAA-TTTGTTTAAAGGGAAACTATCTCAAGGAAGACAAATCCGTTCCAAGGGAAACTATC
61480 TCAAGAA
130 TCAAGAA
* *
61487 AGACAAAATTCGTTTCAAGGGAAACGTTTTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGGG
1 AGACAAAATTCGTTTCAAGGGAAATGTTTTCAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGGG
* * ** *
61552 AGACAAAATTTGTTTTAAGGGAAACTATCTCAA-GAGAGACAAAATTTGTTTCAAGGGAAACTAT
66 AGATAAAATTTGTTTAAAGGGAAACTATCTCAAGGA-AGAC-AAATCCGTTCCAAGGGAAACTAT
*
61616 CTCAAGAG
129 CTCAAGAA
* * *
61624 AGACAAAATTCGTTTCAAGGGAAATGTTATCAAAGTTTATGTTTTAAGAGAAACTGTCTTAAGGG
1 AGACAAAATTCGTTTCAAGGGAAATGTTTTCAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGGG
61689 AGATAAAATTTG
66 AGATAAAATTTG
61701 AAATCGTGGA
Statistics
Matches: 196, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
135 2 0.01
136 28 0.14
137 166 0.85
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.29
Consensus pattern (136 bp):
AGACAAAATTCGTTTCAAGGGAAATGTTTTCAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGGG
AGATAAAATTTGTTTAAAGGGAAACTATCTCAAGGAAGACAAATCCGTTCCAAGGGAAACTATCT
CAAGAA
Found at i:61884 original size:124 final size:119
Alignment explanation
Indices: 61698--62021 Score: 357
Period size: 124 Copynumber: 2.7 Consensus size: 119
61688 GAGATAAAAT
* * * *
61698 TTGAAATCGTGGATGGCCCCTTCCTCGTGAAG-TCAAGACTCGAATTGGATATCCTTCATCGTGA
1 TTGAAATCGTGGATGGCCCCTTCATCGTGAAGTTC-AGCCTTGAATTGGATATCCTTCGTCGTGA
* * *
61762 AGTTGAAATCCAATTTAAAG-ATGAATGTTGCTGATG-GATAAGATATCCTTCGTTGTGAAG
65 AGTTGAAATCCAATTT---GCAT---TGCTGCTGATGAG-CAAGATATCCTTCGTCGTGAAG
* * * *
61822 TTGAAATCATGGATGGCCCCTTCGTCGTGAAGTTCAGCCTTGAATTAGACATCCTTCGTCGTGAA
1 TTGAAATCGTGGATGGCCCCTTCATCGTGAAGTTCAGCCTTGAATTGGATATCCTTCGTCGTGAA
* * *
61887 GTTGAAATCCAAGGTTTGCATTGCTGCTGGTGAGCACGATATTCTTCGTCGTGAAG
66 GTTGAAATCCAA--TTTGCATTGCTGCTGATGAGCAAGATATCCTTCGTCGTGAAG
* * * *
61943 TTAAAATCGTGGATGGCCCCTTCATTGTGAATTTGAGCCTTGAAATTGGATATCCTTCGTCGTGA
1 TTGAAATCGTGGATGGCCCCTTCATCGTGAAGTTCAGCCTTG-AATTGGATATCCTTCGTCGTGA
*
62008 AGTTAAAATCCAAT
65 AGTTGAAATCCAAT
62022 GTAAGTTTCG
Statistics
Matches: 172, Mismatches: 22, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
120 1 0.01
121 63 0.37
122 33 0.19
123 1 0.01
124 69 0.40
125 2 0.01
126 3 0.02
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (119 bp):
TTGAAATCGTGGATGGCCCCTTCATCGTGAAGTTCAGCCTTGAATTGGATATCCTTCGTCGTGAA
GTTGAAATCCAATTTGCATTGCTGCTGATGAGCAAGATATCCTTCGTCGTGAAG
Found at i:62061 original size:121 final size:121
Alignment explanation
Indices: 61698--62325 Score: 407
Period size: 121 Copynumber: 5.1 Consensus size: 121
61688 GAGATAAAAT
* * * *
61698 TTGAAATCGTGGATGGCCCCTTCCTCGTGAAG-TCAAGACTCGAATTGGATATCCTTCATCGTGA
1 TTGAAATCGTGGATGGCCCCTTCATCGTGAAGTTC-AGCCTTGAATTGGATATCCTTCGTCGTGA
* * * * ** *
61762 AGTTGAAATCCAATTTAAAG-AT-GAATGTTGCTGATG-GATAAGATATCCTTCGTTGTGAAG
65 AGTTGAAATCCAATGT-AAGTTTCG-TTGTTTC-GA-GAG-CCA-ATATCCTTCGTCGTGAAG
* * * *
61822 TTGAAATCATGGATGGCCCCTTCGTCGTGAAGTTCAGCCTTGAATTAGACATCCTTCGTCGTGAA
1 TTGAAATCGTGGATGGCCCCTTCATCGTGAAGTTCAGCCTTGAATTGGATATCCTTCGTCGTGAA
* * * * * *
61887 GTTGAAATCCAA-G---GTTTGCATTGCTGCTGGTGAGCACGATATTCTTCGTCGTGAAG
66 GTTGAAATCCAATGTAAGTTT-CGTTG-T-TTCGAGAGC-CAATATCCTTCGTCGTGAAG
* * * *
61943 TTAAAATCGTGGATGGCCCCTTCATTGTGAATTTGAGCCTTGAAATTGGATATCCTTCGTCGTGA
1 TTGAAATCGTGGATGGCCCCTTCATCGTGAAGTTCAGCCTTG-AATTGGATATCCTTCGTCGTGA
* **
62008 AGTTAAAATCCAATGTAAGTTTCGTTGTTTCGAG-GCCAATATCCTTCACCGTGAAG
65 AGTTGAAATCCAATGTAAGTTTCGTTGTTTCGAGAGCCAATATCCTTCGTCGTGAAG
* * **** * * * * * ** * *
62064 TTGAAATTGACTCTGAAACTGGAAAGTTTATTGACAGACACTCCTTCTTTGAGTTGGATATCCTT
1 TTGAAA-T--C-GTG-GA-TGGCCCCTTCATCG--TGA-AGTTCAGCCTTGAATTGGATATCC-T
* * * * * * * * *
62129 TCTTCGTGAAGTTGAAATCCAATCTAGAG-ATGGATGTTTCTTGTGTGTACGAT-TCCGTTCGTC
56 TCGTCGTGAAGTTGAAATCCAATGTA-AGTTTCGTTGTTTC--GAGAG-CCAATATCC-TTCGTC
62192 GTGAAG
116 GTGAAG
* * * * *
62198 TTGAAACCGTGGATGGCCCCTTCGTCGTGAAGTTGAACCTTGAAATTGGATATCTTTCGTCGTGA
1 TTGAAATCGTGGATGGCCCCTTCATCGTGAAGTTCAGCCTTG-AATTGGATATCCTTCGTCGTGA
62263 AGTTGAAATCCAATGTAAGTTTCGTTGTTTCGAG-GCCAATATCCTTCGTCGTGAAG
65 AGTTGAAATCCAATGTAAGTTTCGTTGTTTCGAGAGCCAATATCCTTCGTCGTGAAG
62319 TTGAAAT
1 TTGAAAT
62326 TGACTTTGAA
Statistics
Matches: 380, Mismatches: 92, Indels: 67
0.71 0.17 0.12
Matches are distributed among these distances:
119 1 0.00
120 1 0.00
121 97 0.26
122 42 0.11
123 6 0.02
124 71 0.19
125 47 0.12
126 17 0.04
127 9 0.02
128 7 0.02
129 14 0.04
130 40 0.11
131 3 0.01
132 2 0.01
133 4 0.01
134 19 0.05
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.33
Consensus pattern (121 bp):
TTGAAATCGTGGATGGCCCCTTCATCGTGAAGTTCAGCCTTGAATTGGATATCCTTCGTCGTGAA
GTTGAAATCCAATGTAAGTTTCGTTGTTTCGAGAGCCAATATCCTTCGTCGTGAAG
Found at i:62241 original size:255 final size:254
Alignment explanation
Indices: 61930--62455 Score: 872
Period size: 255 Copynumber: 2.1 Consensus size: 254
61920 GCACGATATT
* * * * *
61930 CTTCGTCGTGAAGTTAAAATCGTGGATGGCCCCTTCATTGTGAATTTGAGCCTTGAAATTGGATA
1 CTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCATCGTGAAGTTGAACCTTGAAATTGGATA
61995 TCCTTCGTCGTGAAGTTAAAATCCAATGTAAGTTTCGTTGTTTCGAGGCCAATATCCTTCACCGT
66 TCCTTCGTCGTGAAGTTAAAATCCAATGTAAGTTTCGTTGTTTCGAGGCCAATATCCTTCACCGT
*
62060 GAAGTTGAAATTGACTCTGAAACTGGAAAGTTTATTGACAGACACTCCTTCTTTGAGTTGGATAT
131 GAAGTTGAAATTGACTCTGAAACTGGAAAGTTTATTGACAAACACTCCTTCTTTGAGTTGGATAT
* * *
62125 CCTTTCTTCGTGAAGTTGAAATCCAATCTAGAGATGGATGTTTCTTGTGTGTACGATTCC
196 CC-TTCATCGTGAAGTTGAAATCCAATCTAGAGATGGATGCTGCTTGTGTGTACGATTCC
* *
62185 GTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCGTCGTGAAGTTGAACCTTGAAATTGGATA
1 CTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCATCGTGAAGTTGAACCTTGAAATTGGATA
* * **
62250 TCTTTCGTCGTGAAGTTGAAATCCAATGTAAGTTTCGTTGTTTCGAGGCCAATATCCTTCGTCGT
66 TCCTTCGTCGTGAAGTTAAAATCCAATGTAAGTTTCGTTGTTTCGAGGCCAATATCCTTCACCGT
* *
62315 GAAGTTGAAATTGACTTTGAAATTGGAAAGTTTATTGACAAACACTCCTTCTTTGAGTTGGATAT
131 GAAGTTGAAATTGACTCTGAAACTGGAAAGTTTATTGACAAACACTCCTTCTTTGAGTTGGATAT
* *
62380 CCTTCATCGTGAAGTTGAAATCCAATCTATAGATGGATGCTGCTTGTGTTTACGATTCC
196 CCTTCATCGTGAAGTTGAAATCCAATCTAGAGATGGATGCTGCTTGTGTGTACGATTCC
62439 CTTCGTCGTGAAGTTGA
1 CTTCGTCGTGAAGTTGA
62456 GCCTTGACTT
Statistics
Matches: 251, Mismatches: 20, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
254 68 0.27
255 183 0.73
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (254 bp):
CTTCGTCGTGAAGTTGAAACCGTGGATGGCCCCTTCATCGTGAAGTTGAACCTTGAAATTGGATA
TCCTTCGTCGTGAAGTTAAAATCCAATGTAAGTTTCGTTGTTTCGAGGCCAATATCCTTCACCGT
GAAGTTGAAATTGACTCTGAAACTGGAAAGTTTATTGACAAACACTCCTTCTTTGAGTTGGATAT
CCTTCATCGTGAAGTTGAAATCCAATCTAGAGATGGATGCTGCTTGTGTGTACGATTCC
Found at i:63096 original size:32 final size:32
Alignment explanation
Indices: 63055--63128 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
63045 TTGAATTCCT
* * *
63055 AAAGATGCCCCGATATTAGATGTTTAATC-TC
1 AAAGATGCCCCAACATTAGATGTTGAATCTTC
*
63086 AAAAGATGCCCCAACATTTGATGTTGAATCTTC
1 -AAAGATGCCCCAACATTAGATGTTGAATCTTC
63119 AAAGATGCCC
1 AAAGATGCCC
63129 TCTATTGCTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
32 35 0.95
33 2 0.05
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (32 bp):
AAAGATGCCCCAACATTAGATGTTGAATCTTC
Found at i:64906 original size:19 final size:19
Alignment explanation
Indices: 64882--64918 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
64872 ACCACTTGGG
64882 GGGGATCTATACCCCCTGC
1 GGGGATCTATACCCCCTGC
*
64901 GGGGATCTGTACCCCCTG
1 GGGGATCTATACCCCCTG
64919 GACAATCTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.14, C:0.35, G:0.30, T:0.22
Consensus pattern (19 bp):
GGGGATCTATACCCCCTGC
Found at i:66229 original size:24 final size:24
Alignment explanation
Indices: 66197--66244 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
66187 TAGCATGTGC
66197 ATGGCCTTGGCATTAAGTTGAGCT
1 ATGGCCTTGGCATTAAGTTGAGCT
66221 ATGGCCTTGGCATTAAGTTGAGCT
1 ATGGCCTTGGCATTAAGTTGAGCT
66245 TTCTTTTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.17, G:0.29, T:0.33
Consensus pattern (24 bp):
ATGGCCTTGGCATTAAGTTGAGCT
Found at i:67204 original size:20 final size:20
Alignment explanation
Indices: 67179--67219 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
67169 CCGTTAGACA
67179 GGGGGAATCGGTACCCCCTG
1 GGGGGAATCGGTACCCCCTG
67199 GGGGGAATCGGTACCCCCTG
1 GGGGGAATCGGTACCCCCTG
67219 G
1 G
67220 ACAATCTGAT
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:0.15, C:0.29, G:0.41, T:0.15
Consensus pattern (20 bp):
GGGGGAATCGGTACCCCCTG
Done.