Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004245.1 Hibiscus syriacus cultivar Beakdansim tig00009308_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: 199927
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:916 original size:3 final size:3
Alignment explanation
Indices: 908--953 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
898 GGTATAATTT
* *
908 ATA ATA ATA ATA AAA ATA AAA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
954 ACTCAATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:1390 original size:16 final size:15
Alignment explanation
Indices: 1369--1421 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 15
1359 TATCTTGGAG
1369 TTTATTTTTATAATTT
1 TTTATTTTTA-AATTT
*
1385 TTTATTTCTAAATTT
1 TTTATTTTTAAATTT
* *
1400 ATAATTTTTAAAATTT
1 TTTATTTTT-AAATTT
*
1416 TATATT
1 TTTATT
1422 CTCTACTATA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
15 11 0.38
16 18 0.62
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTATTTTTAAATTT
Found at i:6340 original size:33 final size:33
Alignment explanation
Indices: 6295--6365 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
6285 TCAATCATCA
*
6295 TTCACGATAATATCAATACCAAAACATTCATAT
1 TTCACGATAATATCAATACCAAAACATTCACAT
* *
6328 TTCAC-ATCAATATCGATACCAAAATATTCACAT
1 TTCACGAT-AATATCAATACCAAAACATTCACAT
6361 TTCAC
1 TTCAC
6366 TTATCTTTCT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 2 0.06
33 32 0.94
ACGTcount: A:0.42, C:0.24, G:0.03, T:0.31
Consensus pattern (33 bp):
TTCACGATAATATCAATACCAAAACATTCACAT
Found at i:7206 original size:29 final size:29
Alignment explanation
Indices: 7173--7231 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
7163 AGCACCGCGT
7173 ATTCAAGAGTATAAACATTCGTTGTCATA
1 ATTCAAGAGTATAAACATTCGTTGTCATA
7202 ATTCAAGAGTATAAACATTCGTTGTCATA
1 ATTCAAGAGTATAAACATTCGTTGTCATA
7231 A
1 A
7232 GATCGAGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.34
Consensus pattern (29 bp):
ATTCAAGAGTATAAACATTCGTTGTCATA
Found at i:7722 original size:16 final size:18
Alignment explanation
Indices: 7701--7735 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
7691 AATATCAAAC
7701 AATAAC-AAACTAA-AAA
1 AATAACAAAACTAATAAA
7717 AATAACAAAACTAATAAA
1 AATAACAAAACTAATAAA
7735 A
1 A
7736 CACCATACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 7 0.41
18 4 0.24
ACGTcount: A:0.74, C:0.11, G:0.00, T:0.14
Consensus pattern (18 bp):
AATAACAAAACTAATAAA
Found at i:8220 original size:31 final size:30
Alignment explanation
Indices: 8182--8268 Score: 102
Period size: 31 Copynumber: 2.8 Consensus size: 30
8172 GTATCAAAAG
*
8182 TTATAAAATAATCATTAAAATTCTTAAATAA
1 TTATAAAAT-ATCATTAAAATTATTAAATAA
** *
8213 TTATAAAATTATCATTAATTTTTATTAAATTA
1 TTATAAAA-TATCATTAA-AATTATTAAATAA
*
8245 TTATAAAATATCATTAAATTTATT
1 TTATAAAATATCATTAAAATTATT
8269 GAGCTATTAC
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
30 6 0.12
31 25 0.51
32 18 0.37
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (30 bp):
TTATAAAATATCATTAAAATTATTAAATAA
Found at i:8265 original size:32 final size:32
Alignment explanation
Indices: 8182--8265 Score: 102
Period size: 32 Copynumber: 2.7 Consensus size: 32
8172 GTATCAAAAG
* *
8182 TTATAAAATAATCATTAAA--ATTCTTAAATAA
1 TTATAAAAT-ATCATTAAATTTTTATTAAATAA
*
8213 TTATAAAATTATCATT-AATTTTTATTAAATTA
1 TTATAAAA-TATCATTAAATTTTTATTAAATAA
8245 TTATAAAATATCATTAAATTT
1 TTATAAAATATCATTAAATTT
8266 ATTGAGCTAT
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
30 2 0.04
31 21 0.46
32 23 0.50
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (32 bp):
TTATAAAATATCATTAAATTTTTATTAAATAA
Found at i:9669 original size:25 final size:26
Alignment explanation
Indices: 9641--9695 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 26
9631 TATTAAAAAA
*
9641 ATTTATAAAATTTTAA-AAAATATAT
1 ATTTATAAAATTTTAATAAAAAATAT
9666 ATTTATAAAATTTTAATAAAAAATAT
1 ATTTATAAAATTTTAATAAAAAATAT
9692 ATTT
1 ATTT
9696 CAACAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
25 16 0.57
26 12 0.43
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
ATTTATAAAATTTTAATAAAAAATAT
Found at i:9703 original size:28 final size:25
Alignment explanation
Indices: 9641--9713 Score: 74
Period size: 25 Copynumber: 2.8 Consensus size: 25
9631 TATTAAAAAA
* *
9641 ATTTATAAAATTTTAAAAAATATAT
1 ATTTACAAAATTTTAAAAAAAATAT
*
9666 ATTTATAAAATTTTAATAAAAAATAT
1 ATTTACAAAATTTTAA-AAAAAATAT
*
9692 ATTTCAACAAAATATATAAAAA
1 ATTT--ACAAAAT-TTTAAAAA
9714 TATTCTAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
25 16 0.39
26 12 0.29
28 9 0.22
29 4 0.10
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (25 bp):
ATTTACAAAATTTTAAAAAAAATAT
Found at i:13448 original size:24 final size:25
Alignment explanation
Indices: 13421--13472 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
13411 TCATTTAAAG
13421 TTTTTA-AAATA-TATTTTTTCATA
1 TTTTTATAAATAGTATTTTTTCATA
*
13444 TTTTTATTAATAGTATTTTTTCATA
1 TTTTTATAAATAGTATTTTTTCATA
13469 TTTT
1 TTTT
13473 CTATTCAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 6 0.23
24 4 0.15
25 16 0.62
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (25 bp):
TTTTTATAAATAGTATTTTTTCATA
Found at i:13466 original size:25 final size:25
Alignment explanation
Indices: 13428--13477 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
13418 AAGTTTTTAA
13428 AATATATTTTTTCATATTTT-TATT
1 AATATATTTTTTCATATTTTCTATT
13452 AATAGTATTTTTTCATATTTTCTATT
1 AATA-TATTTTTTCATATTTTCTATT
13478 CAAAATATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 4 0.17
25 16 0.67
26 4 0.17
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.64
Consensus pattern (25 bp):
AATATATTTTTTCATATTTTCTATT
Found at i:21992 original size:28 final size:28
Alignment explanation
Indices: 21947--22001 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
21937 CACACGTTGC
* * * *
21947 TTTCAAGCATTTGTTCGACGATATAATG
1 TTTCAAGCAATAGCTCGACGACATAATG
21975 TTTCAAGCAATAGCTCGACGACATAAT
1 TTTCAAGCAATAGCTCGACGACATAAT
22002 ATAAACTGAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (28 bp):
TTTCAAGCAATAGCTCGACGACATAATG
Found at i:40098 original size:21 final size:22
Alignment explanation
Indices: 40058--40112 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
40048 TTTTTTATAT
* **
40058 ATTATTTTTTTTCAATTAAATC
1 ATTATTTTTATTCAATTAAAAA
*
40080 ATTATTTTTATTGAA-TAAAAA
1 ATTATTTTTATTCAATTAAAAA
*
40101 AATATTTTTATT
1 ATTATTTTTATT
40113 ATTATTTCAG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 15 0.54
22 13 0.46
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (22 bp):
ATTATTTTTATTCAATTAAAAA
Found at i:43536 original size:2 final size:2
Alignment explanation
Indices: 43529--43557 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
43519 AAAACCCTTA
43529 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
43558 AAGAAAAGGG
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:47268 original size:14 final size:15
Alignment explanation
Indices: 47246--47274 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
47236 ATCTTTTGTC
47246 AATTATTTTTTTTAT
1 AATTATTTTTTTTAT
47261 AATT-TTTTTTTTAT
1 AATTATTTTTTTTAT
47275 TTTTATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
AATTATTTTTTTTAT
Found at i:50312 original size:28 final size:27
Alignment explanation
Indices: 50276--50328 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
50266 AAAATTTAAT
* *
50276 TTCTTTTCAAATTTAAAATATATATTAG
1 TTCTATTCAAATAT-AAATATATATTAG
*
50304 TTCTATTCATATATAAATATATATT
1 TTCTATTCAAATATAAATATATATT
50329 TGGGATGGGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 11 0.50
28 11 0.50
ACGTcount: A:0.40, C:0.08, G:0.02, T:0.51
Consensus pattern (27 bp):
TTCTATTCAAATATAAATATATATTAG
Found at i:56823 original size:2 final size:2
Alignment explanation
Indices: 56818--56843 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
56808 TTCCCTTCAA
56818 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
56844 GAACAGTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59554 original size:17 final size:16
Alignment explanation
Indices: 59528--59559 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
59518 AAACCTTAGC
59528 TTTTCAACAAAAATAT
1 TTTTCAACAAAAATAT
59544 TTTTACAACAAAAATA
1 TTTT-CAACAAAAATA
59560 CGCTACTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.34
Consensus pattern (16 bp):
TTTTCAACAAAAATAT
Found at i:60295 original size:60 final size:60
Alignment explanation
Indices: 60202--60323 Score: 226
Period size: 60 Copynumber: 2.0 Consensus size: 60
60192 TAATGGACTG
*
60202 ATTAATTAATATGTTTGATTTGATCCATTAAATACTTTTATGGAAATGTAATAATAATTT
1 ATTAATTAATATGTTTGATTTGATCCATTAAATACTTTTATGGAAATGCAATAATAATTT
*
60262 ATTAATTAATATGTTTGATTTGATCCATTAAATACTTTTATGGAAATGCAATACTAATTT
1 ATTAATTAATATGTTTGATTTGATCCATTAAATACTTTTATGGAAATGCAATAATAATTT
60322 AT
1 AT
60324 AAAATATTAT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.46
Consensus pattern (60 bp):
ATTAATTAATATGTTTGATTTGATCCATTAAATACTTTTATGGAAATGCAATAATAATTT
Found at i:60411 original size:12 final size:13
Alignment explanation
Indices: 60386--60410 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
60376 TTGTAATAAT
60386 TATGATTAAAAAA
1 TATGATTAAAAAA
60399 TATGATTAAAAA
1 TATGATTAAAAA
60411 TTCAATAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (13 bp):
TATGATTAAAAAA
Found at i:65869 original size:2 final size:2
Alignment explanation
Indices: 65862--65900 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
65852 GTACATTAAG
65862 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
65901 AATAAAATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:90900 original size:4 final size:4
Alignment explanation
Indices: 90884--90965 Score: 85
Period size: 4 Copynumber: 20.5 Consensus size: 4
90874 ATTATGCAAG
* * * * * *
90884 TCTA TCTA CCTA TCTA TCTA TCCA TCCA TCCA T-TCA TCCA TTTA TCTA
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCT-A TCTA TCTA TCTA
*
90932 TCTA TCTA TCTA TCTA TCTA CCTA TCTA TCTA TC
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TC
90966 CATCCCTTGA
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
4 66 1.00
ACGTcount: A:0.24, C:0.32, G:0.00, T:0.44
Consensus pattern (4 bp):
TCTA
Found at i:100271 original size:2 final size:2
Alignment explanation
Indices: 100264--100292 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
100254 TTGGTCTTAA
100264 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
100293 ATGCATTCGA
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:104736 original size:6 final size:6
Alignment explanation
Indices: 104725--104759 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
104715 GGGAATGTTA
104725 GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG GAAGA
1 GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG GAAGA
104760 AGGGGTTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (6 bp):
GAAGAG
Found at i:114038 original size:15 final size:16
Alignment explanation
Indices: 114006--114038 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
113996 AAAATCTTTC
114006 TTTCCCGTTCTAGATT
1 TTTCCCGTTCTAGATT
*
114022 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTAGATT
114037 TT
1 TT
114039 GATCTGCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.09, C:0.24, G:0.15, T:0.52
Consensus pattern (16 bp):
TTTCCCGTTCTAGATT
Found at i:114815 original size:16 final size:17
Alignment explanation
Indices: 114788--114822 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
114778 TATCGCCGAC
114788 CGAAATTTCACTATTCA
1 CGAAATTTCACTATTCA
114805 CGAAA-TTCACTATTCA
1 CGAAATTTCACTATTCA
114821 CG
1 CG
114823 TGAATAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.34, C:0.26, G:0.09, T:0.31
Consensus pattern (17 bp):
CGAAATTTCACTATTCA
Found at i:116408 original size:16 final size:15
Alignment explanation
Indices: 116376--116430 Score: 57
Period size: 14 Copynumber: 3.9 Consensus size: 15
116366 ATTGAACTAG
*
116376 AATATAAAAATTAAT
1 AATATAAATATTAAT
116391 -ATAT-AAT-TTACAT
1 AATATAAATATTA-AT
116404 AATATAAATATTAAT
1 AATATAAATATTAAT
116419 AATA-AAA-ATTAA
1 AATATAAATATTAA
116431 CATATCTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
12 3 0.09
13 9 0.26
14 11 0.31
15 9 0.26
16 3 0.09
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (15 bp):
AATATAAATATTAAT
Found at i:117230 original size:18 final size:19
Alignment explanation
Indices: 117197--117232 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
117187 CGATAAATCA
117197 TTTTATAAATATATTTAAT
1 TTTTATAAATATATTTAAT
*
117216 TTTTTTAAATA-ATTTAA
1 TTTTATAAATATATTTAA
117233 GGTGATTACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTTATAAATATATTTAAT
Found at i:125705 original size:36 final size:36
Alignment explanation
Indices: 125665--125768 Score: 145
Period size: 36 Copynumber: 2.9 Consensus size: 36
125655 TGAGGAGGAG
*
125665 GTTGAAACTGCTGCAAATCAAATGCAACAACACACA
1 GTTGAAACTGCTGCAGATCAAATGCAACAACACACA
* *
125701 GTTGAAACTGCTGCAGATCAAATGCAGCAACATACA
1 GTTGAAACTGCTGCAGATCAAATGCAACAACACACA
* * * *
125737 GTTGTAACTACTGCAGATCAAGTTCAACAACA
1 GTTGAAACTGCTGCAGATCAAATGCAACAACA
125769 AGCGCCGCCT
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 60 1.00
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.20
Consensus pattern (36 bp):
GTTGAAACTGCTGCAGATCAAATGCAACAACACACA
Found at i:129211 original size:3 final size:3
Alignment explanation
Indices: 129199--129227 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
129189 CCAAATTCGC
129199 TCT T-T TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
129228 GCAATGAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TCT
Found at i:136954 original size:22 final size:22
Alignment explanation
Indices: 136929--137026 Score: 92
Period size: 22 Copynumber: 4.5 Consensus size: 22
136919 TTAAAATAAA
*
136929 TTATTATAAAATATGGATTGAT
1 TTATTTTAAAATATGGATTGAT
** * *
136951 TTATTTTAAAATAATTTATTTTAA
1 TTATTTTAAAAT-ATGGA-TTGAT
* * *
136975 ATAATTT--AGTATGGATTGAT
1 TTATTTTAAAATATGGATTGAT
136995 TTATTTTAAAATATGGATTGAT
1 TTATTTTAAAATATGGATTGAT
137017 TTATTTTAAA
1 TTATTTTAAA
137027 TAATTTATTA
Statistics
Matches: 57, Mismatches: 15, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
20 8 0.14
21 3 0.05
22 35 0.61
23 3 0.05
24 8 0.14
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (22 bp):
TTATTTTAAAATATGGATTGAT
Found at i:136962 original size:37 final size:40
Alignment explanation
Indices: 136912--137007 Score: 117
Period size: 44 Copynumber: 2.4 Consensus size: 40
136902 TTATAAAATA
136912 ATTTATTTTAAAATAAATTA-TT-ATAA-AATATGGATTG
1 ATTTATTTTAAAATAAATTATTTAATAATAATATGGATTG
* *
136949 ATTTATTTTAAAATAATTTATTTTAAATAATTTAGTATGGATTG
1 ATTTATTTTAAAATAAATTA-TTT-AATAA--TAATATGGATTG
136993 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
137008 TGGATTGATT
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
37 19 0.38
39 2 0.04
41 4 0.08
44 25 0.50
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (40 bp):
ATTTATTTTAAAATAAATTATTTAATAATAATATGGATTG
Found at i:136978 original size:14 final size:15
Alignment explanation
Indices: 136867--136982 Score: 126
Period size: 15 Copynumber: 7.3 Consensus size: 15
136857 TAATAAAGTT
136867 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
136882 ATTTATTCTAAAATA
1 ATTTATTTTAAAATA
*
136897 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
136912 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
136927 AATTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
136946 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
136964 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
136978 ATTTA
1 ATTTA
136983 GTATGGATTG
Statistics
Matches: 87, Mismatches: 7, Indels: 15
0.80 0.06 0.14
Matches are distributed among these distances:
14 10 0.11
15 57 0.66
16 4 0.05
17 2 0.02
18 1 0.01
19 1 0.01
20 2 0.02
21 4 0.05
22 6 0.07
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.50
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:137006 original size:66 final size:67
Alignment explanation
Indices: 136882--137036 Score: 206
Period size: 66 Copynumber: 2.3 Consensus size: 67
136872 TTTTAAAATA
* * *
136882 ATTTATTCTAAAATAATTTATTATAAAATAATTTATTTTAAAATAAATTATTATAAAATATGGAT
1 ATTTATTTTAAAATAATTTATTATAAAATAATTTAGTATAAAATAAATTATTATAAAATATGGAT
136947 TG
66 TG
* ** * * * *
136949 ATTTATTTTAAAATAATTTATT-TTAAATAATTTAGTATGGATTGATTTATTTTAAAATATGGAT
1 ATTTATTTTAAAATAATTTATTATAAAATAATTTAGTATAAAATAAATTATTATAAAATATGGAT
137013 TG
66 TG
137015 ATTTATTTT-AAATAATTTATTA
1 ATTTATTTTAAAATAATTTATTA
137037 GTATGGATTG
Statistics
Matches: 77, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
65 12 0.16
66 44 0.57
67 21 0.27
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.50
Consensus pattern (67 bp):
ATTTATTTTAAAATAATTTATTATAAAATAATTTAGTATAAAATAAATTATTATAAAATATGGAT
TG
Found at i:137044 original size:32 final size:32
Alignment explanation
Indices: 137006--137412 Score: 200
Period size: 32 Copynumber: 13.7 Consensus size: 32
136996 TATTTTAAAA
137006 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
137038 TATGGATTGATTTA-TTT---TAA---A--A-
1 TATGGATTGATTTATTTTAAATAATTTATTAG
137060 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
137092 TATGGATTGATTTATTTT--A-AA---A-TA-
1 TATGGATTGATTTATTTTAAATAATTTATTAG
* *
137116 TA--GATTGGTTTATTTTAAATAATTTATTTG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
**
137146 TATGGATTGATTTATTTTAAA-ATATGGATT-G
1 TATGGATTGATTTATTTTAAATA-ATTTATTAG
** * *
137177 -ATTTATT-ATTGTAGTTTTATGGATTGATTTATT--
1 TATGGATTGATT-TA-TTTTA---AATAATTTATTAG
* * * * * *
137210 T-T-AAATAATTTATTTGTATGGATGATTTATTTAAAA
1 TATGGATTGATTTATTT-TA--AATAATTTA-TT--AG
** *
137246 TATAAATTGATTTA--TT--AT--TGTAGTT-G
1 TATGGATTGATTTATTTTAAATAATTTA-TTAG
*
137272 TATAGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
*
137304 TATGTATTGATTTATTTTAAA-AATTTATT-G
1 TATGGATTGATTTATTTTAAATAATTTATTAG
*
137334 TATGGATTGATTTA--TT--AT--TGTAGTT-G
1 TATGGATTGATTTATTTTAAATAATTTA-TTAG
137360 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
137392 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
137413 ATATGGATTG
Statistics
Matches: 294, Mismatches: 28, Indels: 106
0.69 0.07 0.25
Matches are distributed among these distances:
22 27 0.09
23 4 0.01
24 3 0.01
25 8 0.03
26 35 0.12
28 10 0.03
29 12 0.04
30 28 0.10
31 36 0.12
32 109 0.37
33 4 0.01
34 6 0.02
35 1 0.00
36 2 0.01
37 1 0.00
38 8 0.03
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (32 bp):
TATGGATTGATTTATTTTAAATAATTTATTAG
Found at i:137052 original size:54 final size:54
Alignment explanation
Indices: 136964--137183 Score: 392
Period size: 54 Copynumber: 4.1 Consensus size: 54
136954 TTTTAAAATA
136964 ATTTATTTTAAATAA--T-TTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
137015 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
137069 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* *
137123 GTTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
137177 ATTTATT
1 ATTTATT
137184 ATTGTAGTTT
Statistics
Matches: 161, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
51 15 0.09
53 1 0.01
54 145 0.90
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.53
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
Found at i:137063 original size:22 final size:22
Alignment explanation
Indices: 137038--137080 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
137028 AATTTATTAG
137038 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
137060 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
137081 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:137106 original size:108 final size:105
Alignment explanation
Indices: 136964--137214 Score: 393
Period size: 108 Copynumber: 2.4 Consensus size: 105
136954 TTTTAAAATA
*
136964 ATTTATTTTAAATAATTTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATA
1 ATTTATTTTAAATAATTTAGTATGGATTGATTTATTTTAAAATATAGATTGATTTATTTTAAATA
137029 ATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
66 ATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
137069 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTGGTTTATTTTAA
1 ATTTATTTTAAATAA--T-TTAGTATGGATTGATTTATTTTAAAATATAGATTGATTTATTTTAA
*
137134 ATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTG
63 ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* *
137177 ATTTATTATT--GTAGTTT--TATGGATTGATTTATTTTAAA
1 ATTTATT-TTAAATAATTTAGTATGGATTGATTTATTTTAAA
137215 TAATTTATTT
Statistics
Matches: 137, Mismatches: 5, Indels: 11
0.90 0.03 0.07
Matches are distributed among these distances:
102 21 0.15
104 2 0.01
105 16 0.12
107 3 0.02
108 93 0.68
109 2 0.01
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (105 bp):
ATTTATTTTAAATAATTTAGTATGGATTGATTTATTTTAAAATATAGATTGATTTATTTTAAATA
ATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
Found at i:137372 original size:166 final size:160
Alignment explanation
Indices: 137114--137429 Score: 483
Period size: 166 Copynumber: 1.9 Consensus size: 160
137104 TATTTTAAAA
* *
137114 TATAGATTGGTTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
* *
137179 TTATTATTGTAGTTTTATGGATTGATTTATTTTAAATAATTTATTTGTATGGA-TGATTTA-TTT
66 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT
137242 AAAATATAAATTGATTTATTATTGTAGTTG
131 AAAATATAAATTGATTTATTATTGTAGTTG
*
137272 TATAGATTGATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAAAATTTATTGTAT
1 TATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT--AAA---A---TAT
137337 GGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGA
58 GGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGA
**
137402 TTTATTTTAAAATATGGATTGATTTATT
123 TTTATTTTAAAATATAAATTGATTTATT
137430 TTAAAATATG
Statistics
Matches: 141, Mismatches: 7, Indels: 10
0.89 0.04 0.06
Matches are distributed among these distances:
158 47 0.33
160 3 0.02
163 1 0.01
166 62 0.44
167 7 0.05
168 21 0.15
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (160 bp):
TATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT
AAAATATAAATTGATTTATTATTGTAGTTG
Found at i:137406 original size:18 final size:18
Alignment explanation
Indices: 137383--137504 Score: 54
Period size: 22 Copynumber: 6.4 Consensus size: 18
137373 ATTTTAAATA
137383 ATTTATTAGTATGGATTG
1 ATTTATTAGTATGGATTG
*
137401 ATTTATTTTAAAATATGGATTG
1 ATTTA--TT--AGTATGGATTG
*
137423 ATTTATTTTAAAATATGGATTG
1 ATTTA--TT--AGTATGGATTG
**
137445 ATTTATTATTGTAATAAATTG
1 ATTTATTA--GT-ATGGATTG
* * *
137466 ATTTATT--T-T-AAATA
1 ATTTATTAGTATGGATTG
137480 ATTTATTAGTATGGATTG
1 ATTTATTAGTATGGATTG
137498 ATTTATT
1 ATTTATT
137505 TTAAAATATA
Statistics
Matches: 84, Mismatches: 9, Indels: 22
0.73 0.08 0.19
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 1 0.01
17 2 0.02
18 15 0.18
20 5 0.06
21 13 0.15
22 37 0.44
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.52
Consensus pattern (18 bp):
ATTTATTAGTATGGATTG
Found at i:137417 original size:22 final size:22
Alignment explanation
Indices: 137392--137477 Score: 122
Period size: 22 Copynumber: 4.0 Consensus size: 22
137382 AATTTATTAG
137392 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
137414 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
**
137436 TATGGATTGATTTATTATTGTAA
1 TATGGATTGATTTATT-TTAAAA
*
137459 TA--AATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
137478 TAATTTATTA
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
20 3 0.05
21 11 0.19
22 38 0.66
23 6 0.10
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:137530 original size:21 final size:22
Alignment explanation
Indices: 137396--137533 Score: 111
Period size: 22 Copynumber: 5.9 Consensus size: 22
137386 TATTAGTATG
*
137396 GATTGATTTATTTTAAAATATG
1 GATTGATTTATTTTAAAATATA
*
137418 GATTGATTTATTTTAAAATATG
1 GATTGATTTATTTTAAAATATA
**
137440 GATTGATTTATTATTGTAATA-A
1 GATTGATTTATT-TTAAAATATA
137462 -ATTGATTTATTTTAAATAATTTATTA
1 GATTGATTTATTTT-AA-AA--TA-TA
*
137488 GTATGGATTGATTTATTTTAAAATATA
1 G-ATTGA-T---TTATTTTAAAATATA
137515 GATTGATTTA-TTTAAAATA
1 GATTGATTTATTTTAAAATA
137534 ATTTATTATT
Statistics
Matches: 96, Mismatches: 7, Indels: 27
0.74 0.05 0.21
Matches are distributed among these distances:
20 2 0.02
21 20 0.21
22 39 0.41
23 6 0.06
24 2 0.02
25 1 0.01
26 5 0.05
27 3 0.03
28 6 0.06
29 1 0.01
30 2 0.02
31 2 0.02
32 7 0.07
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
GATTGATTTATTTTAAAATATA
Found at i:137538 original size:54 final size:53
Alignment explanation
Indices: 137309--137541 Score: 202
Period size: 54 Copynumber: 4.5 Consensus size: 53
137299 ATTAGTATGT
* ** **
137309 ATTGATTTATTTTAAA-AATTTATT-GTATGGATTGATTTATTATTGTAGTTGTATGG
1 ATTGATTTATTTAAAATAATTTATTAGTATGGATTGATTTATTA-T-TA---AAATAA
*
137365 ATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATT-TTAAAAT--
1 ATTGATTTATTTAAAATAATTTATTAGTATGGATTGATTTATTATTAAAATAA
* * * * **
137415 ATGGATTGATTT---AT--TTTA-AAATATGGATTGATTTATTATTGTAATAA
1 ATTGATTTATTTAAAATAATTTATTAGTATGGATTGATTTATTATTAAAATAA
*
137462 ATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATT-TTAAAATATA
1 ATTGATTTATTTAAAATAATTTATTAGTATGGATTGATTTATTATTAAAATA-A
137515 GATTGATTTATTTAAAATAATTTATTA
1 -ATTGATTTATTTAAAATAATTTATTA
137542 TTGTAGTTGT
Statistics
Matches: 149, Mismatches: 15, Indels: 28
0.78 0.08 0.15
Matches are distributed among these distances:
44 17 0.11
45 9 0.06
47 12 0.08
50 12 0.08
52 12 0.08
53 18 0.12
54 25 0.17
55 2 0.01
56 17 0.11
57 8 0.05
58 17 0.11
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.52
Consensus pattern (53 bp):
ATTGATTTATTTAAAATAATTTATTAGTATGGATTGATTTATTATTAAAATAA
Found at i:137591 original size:30 final size:30
Alignment explanation
Indices: 137555--137611 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
137545 TAGTTGTATG
* *
137555 AATTATTTAAATTTCAGTATTGTAAAATAA
1 AATTATTTAAATCTCAGTATTGCAAAATAA
137585 AATTATTTAAATCTCAGTATTGCAAAA
1 AATTATTTAAATCTCAGTATTGCAAAA
137612 CTCTTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.40
Consensus pattern (30 bp):
AATTATTTAAATCTCAGTATTGCAAAATAA
Found at i:138262 original size:47 final size:47
Alignment explanation
Indices: 138186--138280 Score: 172
Period size: 47 Copynumber: 2.0 Consensus size: 47
138176 AGCGGTGTGT
*
138186 GGGGCATTGTTGGCTGGTTCCAGAGATGACGAGGTAGAAAGGTTGAG
1 GGGGCATTGTTGGCTGGTTCCAAAGATGACGAGGTAGAAAGGTTGAG
*
138233 GGGGCATTGTTGGCTGGTTCCAAATATGACGAGGTAGAAAGGTTGAG
1 GGGGCATTGTTGGCTGGTTCCAAAGATGACGAGGTAGAAAGGTTGAG
138280 G
1 G
138281 AGATACGGTC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.24, C:0.11, G:0.41, T:0.24
Consensus pattern (47 bp):
GGGGCATTGTTGGCTGGTTCCAAAGATGACGAGGTAGAAAGGTTGAG
Found at i:141052 original size:2 final size:2
Alignment explanation
Indices: 141045--141069 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
141035 TGTTCAGTGC
141045 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 A
141070 GGAAACATTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:142694 original size:133 final size:135
Alignment explanation
Indices: 142378--142862 Score: 716
Period size: 133 Copynumber: 3.6 Consensus size: 135
142368 TTGTTAGATT
* * * *
142378 GAACAAGTTCTTCGCA-TATGAACTTCTTCTCTCT-TTTGGATGAGTTTTTCTCATTATGAACTC
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTTGGATGAGTTCTTCTCATTATGAACTC
** * * * * *
142441 TTTACTGAAAATGTTGATCCCTCAAGCGAGGCGTCCCTGACTCGAAATG-CTGTGAATCGAGTGA
66 TCCATTGAAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTC-ATGAATCGAGTGA
142505 TAGGTC
130 TAGGTC
*
142511 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTC
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTTGGATGAGTTCTTCTCATTATGAACTC
142576 TCCATTGAAAATGTTGATCCCTC-AGCGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGAT
66 TCCATTGAAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGAT
142640 A-GTC
131 AGGTC
*
142644 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTTTTTCGGATGA-TTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTT-GGATGAGTTCTTCTCATTATGAACT
* ** *
142708 CTCCATTGGAAATGTCAATTCCTCAAGCGA-GTGTCACTGATTCGAAATGTCATGAATCGAGTGA
65 CTCCATTGAAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGA
142772 TAGGTC
130 TAGGTC
*
142778 GAACAAGCTC-TCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCT-TTGGATGAGTTCTTCTCATTATGAACT
*
142842 CTCCATTGAAAATGCTGATCC
65 CTCCATTGAAAATGTTGATCC
142863 ACCTCTTTTT
Statistics
Matches: 319, Mismatches: 25, Indels: 15
0.89 0.07 0.04
Matches are distributed among these distances:
133 159 0.50
134 112 0.35
135 48 0.15
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.35
Consensus pattern (135 bp):
GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTTGGATGAGTTCTTCTCATTATGAACTC
TCCATTGAAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGAT
AGGTC
Found at i:142852 original size:267 final size:266
Alignment explanation
Indices: 142378--142862 Score: 744
Period size: 267 Copynumber: 1.8 Consensus size: 266
142368 TTGTTAGATT
* * * *
142378 GAACAAGTTCTTCGCATATGAACTTCTTCTCTCTTTTGGATGAGTTTTTCTCATTATGAACTCTT
1 GAACAAGCTCTTCGCATATGAACTTCTTCTCCCTTTTGGATGAGTTCTTCTCATTATGAACTCTC
* ** * *
142443 TACTGAAAATGTTGATCCCTCAAGCGAGGCGTCCCTGACTCGAAATGCTGTGAATCGAGTGATAG
66 CACTGAAAATGTCAATCCCTCAAGCGAGGCGTCACTGACTCGAAATGCTATGAATCGAGTGATAG
*
142508 GTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
131 GTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTCGGATGAGTTCTTCTCATTATGAA
*
142573 CTCTCCATTGAAAATGTTGATCCCTCAGCGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTG
196 CTCTCCATTGAAAATGCTGATCCCTCAGCGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTG
142638 ATAGTC
261 ATAGTC
*
142644 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTTTTTCGGATGA-TTCTTCTCATTATGAACT
1 GAACAAGCTCTTCGCA-TATGAACTTCTTCTCCC-TTTT-GGATGAGTTCTTCTCATTATGAACT
* * * * *
142708 CTCCATTGGAAATGTCAATTCCTCAAGCGA-GTGTCACTGATTCGAAATG-TCATGAATCGAGTG
63 CTCCACTGAAAATGTCAATCCCTCAAGCGAGGCGTCACTGACTCGAAATGCT-ATGAATCGAGTG
142771 ATAGGTCGAACAAGCTC-TCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATT
127 ATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTC-GTCGGATGAGTTCTTCTCATT
142835 ATGAACTCTCCATTGAAAATGCTGATCC
191 ATGAACTCTCCATTGAAAATGCTGATCC
142863 ACCTCTTTTT
Statistics
Matches: 197, Mismatches: 17, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
266 40 0.20
267 107 0.54
268 44 0.22
269 6 0.03
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.35
Consensus pattern (266 bp):
GAACAAGCTCTTCGCATATGAACTTCTTCTCCCTTTTGGATGAGTTCTTCTCATTATGAACTCTC
CACTGAAAATGTCAATCCCTCAAGCGAGGCGTCACTGACTCGAAATGCTATGAATCGAGTGATAG
GTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTCGGATGAGTTCTTCTCATTATGAA
CTCTCCATTGAAAATGCTGATCCCTCAGCGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTG
ATAGTC
Found at i:143848 original size:14 final size:13
Alignment explanation
Indices: 143829--143876 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
143819 TCCTTCTTCA
*
143829 TTTTTTCTTTCTT
1 TTTTTTTTTTCTT
143842 TTTTTTTTCTTCTT
1 TTTTTTTT-TTCTT
* *
143856 TTTATTTTTTCAT
1 TTTTTTTTTTCTT
143869 TTTTTTTT
1 TTTTTTTT
143877 CTTCAAGCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
13 18 0.60
14 12 0.40
ACGTcount: A:0.04, C:0.10, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTTTTTTCTT
Found at i:143881 original size:14 final size:14
Alignment explanation
Indices: 143822--143881 Score: 67
Period size: 14 Copynumber: 4.5 Consensus size: 14
143812 CGAACCCTCC
143822 TTCTTCATTTTTTCT
1 TTCTTCATTTTTT-T
143837 TTC-T--TTTTTTT
1 TTCTTCATTTTTTT
143848 TTCTTC-TTTTTATT
1 TTCTTCATTTTT-TT
143862 TT-TTCATTTTTTT
1 TTCTTCATTTTTTT
143875 TTCTTCA
1 TTCTTCA
143882 AGCATAGTAC
Statistics
Matches: 40, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
11 4 0.10
12 7 0.17
13 12 0.30
14 14 0.35
15 3 0.08
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (14 bp):
TTCTTCATTTTTTT
Found at i:149689 original size:150 final size:149
Alignment explanation
Indices: 149408--149709 Score: 552
Period size: 150 Copynumber: 2.0 Consensus size: 149
149398 ATTTACAATA
149408 TGTTTTGGACTTAATTGAATTTATTCAAAGTTTTAAAAGGTTTCAAAATAATTCAAAGTCAATTA
1 TGTTTTGGACTTAATTGAATTTATTCAAAGTTTTAAAAGGTTTCAAAATAATTCAAAGTCAATTA
149473 AAATTCTGATTTGAGCCAAAATATTTTAAGGGGTTTCAAGATTGCCCAGGGGTACAGATTCCCCC
66 AAATTCTGATTTGAGCCAAAATATTTTAAGGGGTTTCAAGATTGCCCAGGGGTACAGATT-CCCC
149538 CCCAGGGGGTACAGATACCC
130 CCCAGGGGGTACAGATACCC
149558 TGTTTTGGACTTAATTGAATTTATTCAAAGTTTT-AAAGGTTTCAAAAATAATTCAAAGTCAATT
1 TGTTTTGGACTTAATTGAATTTATTCAAAGTTTTAAAAGGTTTC-AAAATAATTCAAAGTCAATT
149622 AAAATTCTGATTTGAGCCAAAAATATTTTAAGGGGTTTCAAGATTGCCCAGGGGGTACAGATTCC
65 AAAATTCTGATTTGAGCC-AAAATATTTTAAGGGGTTTCAAGATTGCCCA-GGGGTACAGATT-C
149687 CCCCCCAGGGGGTACAGATACCC
127 CCCCCCAGGGGGTACAGATACCC
149710 CGGGTACAGA
Statistics
Matches: 149, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
149 9 0.06
150 72 0.48
151 31 0.21
152 37 0.25
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.32
Consensus pattern (149 bp):
TGTTTTGGACTTAATTGAATTTATTCAAAGTTTTAAAAGGTTTCAAAATAATTCAAAGTCAATTA
AAATTCTGATTTGAGCCAAAATATTTTAAGGGGTTTCAAGATTGCCCAGGGGTACAGATTCCCCC
CCAGGGGGTACAGATACCC
Found at i:149694 original size:22 final size:22
Alignment explanation
Indices: 149668--149749 Score: 88
Period size: 22 Copynumber: 4.0 Consensus size: 22
149658 TTCAAGATTG
149668 CCCAGGGGGTACAGATTCCCCC
1 CCCAGGGGGTACAGATTCCCCC
*
149690 CCCAGGGGGTACAGA-T---AC
1 CCCAGGGGGTACAGATTCCCCC
*
149708 CCC---GGGTACAGATACCCCC
1 CCCAGGGGGTACAGATTCCCCC
*
149727 CCCAGGGGGTACCGATTCCCCC
1 CCCAGGGGGTACAGATTCCCCC
149749 C
1 C
149750 TGTCTAAAGC
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
15 9 0.19
18 4 0.08
19 4 0.08
21 1 0.02
22 30 0.62
ACGTcount: A:0.20, C:0.41, G:0.27, T:0.12
Consensus pattern (22 bp):
CCCAGGGGGTACAGATTCCCCC
Found at i:149715 original size:37 final size:37
Alignment explanation
Indices: 149674--149747 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
149664 ATTGCCCAGG
*
149674 GGGTACAGATTCCCCCCCCAGGGGGTACAGATACCCC
1 GGGTACAGATACCCCCCCCAGGGGGTACAGATACCCC
* *
149711 GGGTACAGATACCCCCCCCAGGGGGTACCGATTCCCC
1 GGGTACAGATACCCCCCCCAGGGGGTACAGATACCCC
149748 CCTGTCTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.20, C:0.39, G:0.27, T:0.14
Consensus pattern (37 bp):
GGGTACAGATACCCCCCCCAGGGGGTACAGATACCCC
Found at i:149716 original size:15 final size:15
Alignment explanation
Indices: 149696--149725 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
149686 CCCCCCCAGG
149696 GGGTACAGATACCCC
1 GGGTACAGATACCCC
149711 GGGTACAGATACCCC
1 GGGTACAGATACCCC
149726 CCCCAGGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.33, G:0.27, T:0.13
Consensus pattern (15 bp):
GGGTACAGATACCCC
Found at i:151001 original size:19 final size:20
Alignment explanation
Indices: 150977--151024 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
150967 AATGATTTTC
*
150977 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
150996 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
151016 TTTTGAAAA
1 TTTTGAAAA
151025 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:152310 original size:34 final size:30
Alignment explanation
Indices: 152272--152340 Score: 77
Period size: 30 Copynumber: 2.2 Consensus size: 30
152262 TTGATATAAC
152272 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTA
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTA
* *
152306 AATTT-ACAATATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTA
152335 AATTTA
1 AATTTA
152341 TTCAAAGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
29 9 0.28
30 12 0.38
31 5 0.16
33 1 0.03
34 5 0.16
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.43
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTA
Found at i:152455 original size:21 final size:21
Alignment explanation
Indices: 152430--152508 Score: 89
Period size: 21 Copynumber: 4.0 Consensus size: 21
152420 TTCAAGATTG
152430 CCCAGGGGGTACAGATTCCCC
1 CCCAGGGGGTACAGATTCCCC
*
152451 CCCAGGGGGTACAGA-T--AC
1 CCCAGGGGGTACAGATTCCCC
*
152469 CCC---GGGTACAGATACCCC
1 CCCAGGGGGTACAGATTCCCC
*
152487 CCCAGGGGGTACCGATTCCCC
1 CCCAGGGGGTACAGATTCCCC
152508 C
1 C
152509 TGTCTAAAGC
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
15 9 0.19
18 8 0.17
20 1 0.02
21 29 0.62
ACGTcount: A:0.20, C:0.39, G:0.28, T:0.13
Consensus pattern (21 bp):
CCCAGGGGGTACAGATTCCCC
Found at i:152476 original size:36 final size:36
Alignment explanation
Indices: 152436--152507 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
152426 ATTGCCCAGG
*
152436 GGGTACAGATTCCCCCCCAGGGGGTACAGATACCCC
1 GGGTACAGATACCCCCCCAGGGGGTACAGATACCCC
* *
152472 GGGTACAGATACCCCCCCAGGGGGTACCGATTCCCC
1 GGGTACAGATACCCCCCCAGGGGGTACAGATACCCC
152508 CTGTCTAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.21, C:0.38, G:0.28, T:0.14
Consensus pattern (36 bp):
GGGTACAGATACCCCCCCAGGGGGTACAGATACCCC
Found at i:152477 original size:15 final size:15
Alignment explanation
Indices: 152457--152486 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
152447 CCCCCCCAGG
152457 GGGTACAGATACCCC
1 GGGTACAGATACCCC
152472 GGGTACAGATACCCC
1 GGGTACAGATACCCC
152487 CCCAGGGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.33, G:0.27, T:0.13
Consensus pattern (15 bp):
GGGTACAGATACCCC
Found at i:152573 original size:19 final size:20
Alignment explanation
Indices: 152534--152575 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
152524 AACAGAATGT
152534 CCAGGGGGTACCGATTCCCC
1 CCAGGGGGTACCGATTCCCC
152554 CCAGGGGGTACCGATTCCCC
1 CCAGGGGGTACCGATTCCCC
152574 CC
1 CC
152576 CTGTTCAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.43, G:0.29, T:0.14
Consensus pattern (20 bp):
CCAGGGGGTACCGATTCCCC
Found at i:152638 original size:21 final size:21
Alignment explanation
Indices: 152612--152653 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
152602 ATTTGAATAT
*
152612 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
152633 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
152654 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:152975 original size:34 final size:32
Alignment explanation
Indices: 152936--153005 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
152926 TTTTGTAAAG
*
152936 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
152970 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
153002 GGGA
1 GGGA
153006 GTTGTAAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:159793 original size:2 final size:2
Alignment explanation
Indices: 159786--159814 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
159776 TGTTCAGTGC
159786 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
159815 GGAAACATTA
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:161802 original size:3 final size:3
Alignment explanation
Indices: 161794--161823 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
161784 TCGTAAATCC
161794 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
161824 TTGAGTAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:164347 original size:15 final size:15
Alignment explanation
Indices: 164327--164359 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
164317 GAAAGCTTTG
164327 TATGTATAATTAAAT
1 TATGTATAATTAAAT
164342 TATGTATAATTAAAT
1 TATGTATAATTAAAT
164357 TAT
1 TAT
164360 AGGATAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (15 bp):
TATGTATAATTAAAT
Found at i:164838 original size:15 final size:15
Alignment explanation
Indices: 164818--164847 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
164808 TCGGCCTATA
164818 ATCAAGGGATGATTT
1 ATCAAGGGATGATTT
164833 ATCAAGGGATGATTT
1 ATCAAGGGATGATTT
164848 TGTAACTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.27, T:0.33
Consensus pattern (15 bp):
ATCAAGGGATGATTT
Found at i:172013 original size:2 final size:2
Alignment explanation
Indices: 172008--172034 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
171998 TCTCTGTCCG
172008 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
172035 TTCTTTCTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:177395 original size:76 final size:77
Alignment explanation
Indices: 177306--177458 Score: 272
Period size: 77 Copynumber: 2.0 Consensus size: 77
177296 GCTGCCAAAC
*
177306 TCTTAAAATTGATATTTATTTTGTTTAATTTCGTCGA-TTTTGAGAGGTAGCTAAAAAGTTTATC
1 TCTTAAAACTGATATTTATTTTGTTTAATTTCGTCGATTTTTGAGAGGTAGCTAAAAAGTTTATC
177370 GCATAAAAGTGA
66 GCATAAAAGTGA
* *
177382 TCTTAAAACTGATATTTGTTTTGTTTAATTTCGTCGATTTTTGAGAGGTGGCTAAAAAGTTTATC
1 TCTTAAAACTGATATTTATTTTGTTTAATTTCGTCGATTTTTGAGAGGTAGCTAAAAAGTTTATC
177447 GCATAAAAGTGA
66 GCATAAAAGTGA
177459 ATCATTTAAA
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
76 35 0.48
77 38 0.52
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.42
Consensus pattern (77 bp):
TCTTAAAACTGATATTTATTTTGTTTAATTTCGTCGATTTTTGAGAGGTAGCTAAAAAGTTTATC
GCATAAAAGTGA
Found at i:177532 original size:12 final size:12
Alignment explanation
Indices: 177515--177542 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
177505 GTTTAAAGCA
177515 ACATCGTTTTGG
1 ACATCGTTTTGG
177527 ACATCGTTTTGG
1 ACATCGTTTTGG
177539 ACAT
1 ACAT
177543 AAATAGTCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.39
Consensus pattern (12 bp):
ACATCGTTTTGG
Found at i:183254 original size:16 final size:15
Alignment explanation
Indices: 183214--183255 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
183204 AGAGAATTAG
183214 GATTTTAAAGATTTAT
1 GATTTTAAA-ATTTAT
*
183230 GA-GTTAAAATTCTAT
1 GATTTTAAAATT-TAT
183245 GATTTTAAAAT
1 GATTTTAAAAT
183256 GTTTTGTGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 3 0.14
15 10 0.45
16 9 0.41
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.45
Consensus pattern (15 bp):
GATTTTAAAATTTAT
Found at i:183563 original size:17 final size:17
Alignment explanation
Indices: 183541--183575 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
183531 TACGCTGACG
183541 AATGCCACGTGCAAACC
1 AATGCCACGTGCAAACC
183558 AATGCCACGTGCAAACC
1 AATGCCACGTGCAAACC
183575 A
1 A
183576 TAGTTGAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.34, G:0.17, T:0.11
Consensus pattern (17 bp):
AATGCCACGTGCAAACC
Found at i:187079 original size:30 final size:30
Alignment explanation
Indices: 187043--187111 Score: 122
Period size: 30 Copynumber: 2.3 Consensus size: 30
187033 TGTTGAGTAT
187043 TCTGATGATGAGGGT-TGGGAGGAAGATGAC
1 TCTGATGATGAGGGTGT-GGAGGAAGATGAC
187073 TCTGATGATGAGGGTGTGGAGGAAGATGAC
1 TCTGATGATGAGGGTGTGGAGGAAGATGAC
187103 TCTGATGAT
1 TCTGATGAT
187112 TATCTTGATG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
30 37 0.97
31 1 0.03
ACGTcount: A:0.26, C:0.07, G:0.41, T:0.26
Consensus pattern (30 bp):
TCTGATGATGAGGGTGTGGAGGAAGATGAC
Found at i:190082 original size:22 final size:22
Alignment explanation
Indices: 190054--190095 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
190044 TGTTTTTTGC
190054 TTTCGAATA-GAAAAGTAATAGT
1 TTTCGAATAGGAAAA-TAATAGT
190076 TTTCGAATAGGAAAATAATA
1 TTTCGAATAGGAAAATAATA
190096 CCTTTTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.48, C:0.05, G:0.17, T:0.31
Consensus pattern (22 bp):
TTTCGAATAGGAAAATAATAGT
Found at i:190101 original size:23 final size:22
Alignment explanation
Indices: 190054--190101 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
190044 TGTTTTTTGC
*
190054 TTTCGAATAGAAAAGTAATAGT
1 TTTCGAATAGAAAAGTAATACT
190076 TTTCGAATAGGAAAA-TAATACCT
1 TTTCGAATA-GAAAAGTAATA-CT
190099 TTT
1 TTT
190102 GAAAACTTGA
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:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (22 bp):
TTTCGAATAGAAAAGTAATACT
Found at i:191458 original size:29 final size:30
Alignment explanation
Indices: 191388--191446 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
191378 AATTTAAGGC
191388 AAAATGGTTTTTGGACTTGAATTGAATTTAA
1 AAAAT-GTTTTTGGACTTGAATTGAATTTAA
191419 AAAATGTTTTTGGACTT-AATTGAATTTA
1 AAAATGTTTTTGGACTTGAATTGAATTTA
191447 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 11 0.39
30 12 0.43
31 5 0.18
ACGTcount: A:0.36, C:0.03, G:0.17, T:0.44
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTGAATTTAA
Found at i:191582 original size:36 final size:36
Alignment explanation
Indices: 191542--191613 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
191532 ATTGCCCAGG
* * *
191542 GGGTATAGATTCCCCCTCAGGGGGTACAGATACCCC
1 GGGTACAGATACCCCCCCAGGGGGTACAGATACCCC
191578 GGGTACAGATACCCCCCCAGGGGGTACAGATACCCC
1 GGGTACAGATACCCCCCCAGGGGGTACAGATACCCC
191614 CCTGCAGGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.24, C:0.33, G:0.28, T:0.15
Consensus pattern (36 bp):
GGGTACAGATACCCCCCCAGGGGGTACAGATACCCC
Found at i:191583 original size:15 final size:15
Alignment explanation
Indices: 191563--191592 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
191553 CCCCCTCAGG
191563 GGGTACAGATACCCC
1 GGGTACAGATACCCC
191578 GGGTACAGATACCCC
1 GGGTACAGATACCCC
191593 CCCAGGGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.33, G:0.27, T:0.13
Consensus pattern (15 bp):
GGGTACAGATACCCC
Found at i:191615 original size:21 final size:21
Alignment explanation
Indices: 191536--191615 Score: 91
Period size: 21 Copynumber: 4.1 Consensus size: 21
191526 TTCAAGATTG
* *
191536 CCCAGGGGGTATAGATTCCCC
1 CCCAGGGGGTACAGATACCCC
*
191557 CTCAGGGGGTACAGATA---C
1 CCCAGGGGGTACAGATACCCC
191575 CCC---GGGTACAGATACCCC
1 CCCAGGGGGTACAGATACCCC
191593 CCCAGGGGGTACAGATACCCC
1 CCCAGGGGGTACAGATACCCC
191614 CC
1 CC
191616 TGCAGGTTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
15 11 0.22
18 7 0.14
21 31 0.63
ACGTcount: A:0.23, C:0.36, G:0.28, T:0.14
Consensus pattern (21 bp):
CCCAGGGGGTACAGATACCCC
Found at i:191688 original size:19 final size:20
Alignment explanation
Indices: 191651--191690 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
191641 CAGAATGTCT
191651 AGGGGGTACCGATTCCCCCC
1 AGGGGGTACCGATTCCCCCC
191671 AGGGGGTACCGATTCCCCCC
1 AGGGGGTACCGATTCCCCCC
191691 TGTTCAACAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.40, G:0.30, T:0.15
Consensus pattern (20 bp):
AGGGGGTACCGATTCCCCCC
Found at i:191752 original size:21 final size:21
Alignment explanation
Indices: 191726--191768 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
191716 ATTTGAATAT
*
191726 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
191747 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
191768 T
1 T
191769 CTATTCTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:191834 original size:20 final size:22
Alignment explanation
Indices: 191796--191835 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
191786 TTTGAGTATA
191796 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
191818 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
191836 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:192031 original size:34 final size:32
Alignment explanation
Indices: 191992--192061 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
191982 TTTTGTAAAG
* *
191992 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
192026 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
192058 GGGA
1 GGGA
192062 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:194731 original size:29 final size:30
Alignment explanation
Indices: 194661--194719 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
194651 AATTTAAGGC
194661 AAAATGGTTTTTGGACTTGAATTGAATTTAA
1 AAAAT-GTTTTTGGACTTGAATTGAATTTAA
194692 AAAATGTTTTTGGACTT-AATTGAATTTA
1 AAAATGTTTTTGGACTTGAATTGAATTTA
194720 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 11 0.39
30 12 0.43
31 5 0.18
ACGTcount: A:0.36, C:0.03, G:0.17, T:0.44
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTGAATTTAA
Found at i:194834 original size:21 final size:21
Alignment explanation
Indices: 194809--194874 Score: 105
Period size: 21 Copynumber: 3.1 Consensus size: 21
194799 TTCAAGATTG
* *
194809 CCCAGGGGGTATAGATTCCCC
1 CCCAGGGGGTACAGATACCCC
194830 CCCAGGGGGTACAGATACCCCC
1 CCCAGGGGGTACAGATA-CCCC
194852 CCCAGGGGGTACAGATACCCC
1 CCCAGGGGGTACAGATACCCC
194873 CC
1 CC
194875 TGCAGGTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
21 21 0.50
22 21 0.50
ACGTcount: A:0.21, C:0.39, G:0.27, T:0.12
Consensus pattern (21 bp):
CCCAGGGGGTACAGATACCCC
Found at i:194851 original size:22 final size:22
Alignment explanation
Indices: 194809--194874 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
194799 TTCAAGATTG
* *
194809 CCCAGGGGGTATAGAT-TCCCC
1 CCCAGGGGGTACAGATACCCCC
194830 CCCAGGGGGTACAGATACCCCC
1 CCCAGGGGGTACAGATACCCCC
194852 CCCAGGGGGTACAGATACCCCC
1 CCCAGGGGGTACAGATACCCCC
194874 C
1 C
194875 TGCAGGTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
21 15 0.36
22 27 0.64
ACGTcount: A:0.21, C:0.39, G:0.27, T:0.12
Consensus pattern (22 bp):
CCCAGGGGGTACAGATACCCCC
Found at i:194936 original size:20 final size:20
Alignment explanation
Indices: 194911--194948 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
194901 AGAATGTCCA
194911 GGGGTACCGATTCCCCCCAG
1 GGGGTACCGATTCCCCCCAG
194931 GGGGTACCGATTCCCCCC
1 GGGGTACCGATTCCCCCC
194949 CTGTTCAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.42, G:0.29, T:0.16
Consensus pattern (20 bp):
GGGGTACCGATTCCCCCCAG
Found at i:195011 original size:21 final size:21
Alignment explanation
Indices: 194985--195027 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
194975 ATTTGAATAT
*
194985 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
195006 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
195027 T
1 T
195028 CTATTCTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:195328 original size:34 final size:32
Alignment explanation
Indices: 195285--195355 Score: 88
Period size: 34 Copynumber: 2.2 Consensus size: 32
195275 CCTTTTGTAA
* * *
195285 AGGGGAAGGTTCTAGCTTATCCCGTGTAAAAGCT
1 AGGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACT
*
195319 AGGGAAAGGTTCTAGTTTAGCCCGGAAAAACT
1 AGGGAAAGGTTCTAGCTTAGCCCGGAAAAACT
195351 AGGGA
1 AGGGA
195356 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.23
Consensus pattern (32 bp):
AGGGAAAGGTTCTAGCTTAGCCCGGAAAAACT
Found at i:197563 original size:44 final size:44
Alignment explanation
Indices: 197458--197674 Score: 240
Period size: 44 Copynumber: 4.9 Consensus size: 44
197448 GTCATATATT
* ** *
197458 TAGCGGCGTTTGTAT-CTGAAAAACGCCGCTAAATATTA-ACACTTT
1 TAGCGGCGTTTGTATCCT-AAAAACGCCGCTATATACCAGAC-C-TA
*
197503 TAACGGCGTTTGTATCCTAAAAACGCCGCTATATACCAGACCTA
1 TAGCGGCGTTTGTATCCTAAAAACGCCGCTATATACCAGACCTA
* *
197547 TTGCGGCGTTTGTATCCTAAAAACGCTGCTATATACCAGACCTA
1 TAGCGGCGTTTGTATCCTAAAAACGCCGCTATATACCAGACCTA
* ** * ** *
197591 TAGCGACACTTGTATCCTAAACACGGTGCTATATACCAGTCCTA
1 TAGCGGCGTTTGTATCCTAAAAACGCCGCTATATACCAGACCTA
* * *
197635 TAGCGGCGTTTGTACCCTGAAAACGCCGCTAAATACCAGA
1 TAGCGGCGTTTGTATCCTAAAAACGCCGCTATATACCAGA
197675 TATATGCGGT
Statistics
Matches: 145, Mismatches: 25, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
44 109 0.75
45 32 0.22
46 4 0.03
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (44 bp):
TAGCGGCGTTTGTATCCTAAAAACGCCGCTATATACCAGACCTA
Done.