Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002881.1 Hibiscus syriacus cultivar Beakdansim tig00005939_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: 1746118
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 9
Found at i:245669 original size:22 final size:22
Alignment explanation
Indices: 245633--245676 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
245623 ATATAAAACG
*
245633 TCGATTCATCGTCGATCGATCA
1 TCGATTCATCATCGATCGATCA
* *
245655 TCGATTCATTATCGATTGATCA
1 TCGATTCATCATCGATCGATCA
245677 CAATTTCATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (22 bp):
TCGATTCATCATCGATCGATCA
Found at i:246074 original size:2 final size:2
Alignment explanation
Indices: 246069--246098 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
246059 TCTCTCTCTC
246069 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
246099 AAGTTTTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:247121 original size:26 final size:26
Alignment explanation
Indices: 247085--247137 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
247075 AGTTATTGAA
247085 CCATCTGCTTTACTTATTTGCTTCAC
1 CCATCTGCTTTACTTATTTGCTTCAC
247111 CCATCTGCTTTACTTATTTGCTTCAC
1 CCATCTGCTTTACTTATTTGCTTCAC
247137 C
1 C
247138 TTCACAGAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.15, C:0.32, G:0.08, T:0.45
Consensus pattern (26 bp):
CCATCTGCTTTACTTATTTGCTTCAC
Found at i:247132 original size:13 final size:13
Alignment explanation
Indices: 247090--247133 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
247080 TTGAACCATC
247090 TGCTTTACTTATT
1 TGCTTTACTTATT
* ** *
247103 TGCTTCACCCATC
1 TGCTTTACTTATT
247116 TGCTTTACTTATT
1 TGCTTTACTTATT
247129 TGCTT
1 TGCTT
247134 CACCTTCACA
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.14, C:0.25, G:0.09, T:0.52
Consensus pattern (13 bp):
TGCTTTACTTATT
Found at i:247565 original size:22 final size:22
Alignment explanation
Indices: 247523--247565 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
247513 AATGATGCTG
* *
247523 GTGGCAGTGATGAATTTGAGAA
1 GTGGCAGAGATGAATTAGAGAA
247545 GTGGCAGAGA-GAGATTAGAGA
1 GTGGCAGAGATGA-ATTAGAGA
247566 GGCTGAGGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.35, C:0.05, G:0.40, T:0.21
Consensus pattern (22 bp):
GTGGCAGAGATGAATTAGAGAA
Found at i:255235 original size:29 final size:29
Alignment explanation
Indices: 255179--255236 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
255169 CCATCTGGGC
** **
255179 AAAATTCATGAGATAATGCTTTTGGAAAA
1 AAAATTCATGAGATAATGCAATCCGAAAA
*
255208 AAAATTCATGAGATATTGCAATCCGAAAA
1 AAAATTCATGAGATAATGCAATCCGAAAA
255237 TTATTTGCTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.47, C:0.10, G:0.16, T:0.28
Consensus pattern (29 bp):
AAAATTCATGAGATAATGCAATCCGAAAA
Found at i:255612 original size:15 final size:15
Alignment explanation
Indices: 255591--255659 Score: 77
Period size: 15 Copynumber: 4.5 Consensus size: 15
255581 GTTCGGTTGT
*
255591 AAGAAGAAGGAAAGG
1 AAGAAGAAAGAAAGG
*
255606 GAGAAGAAAGAAAGG
1 AAGAAGAAAGAAAGG
* *
255621 GAGAAGAAAGAAAGAA
1 AAGAAGAAAGAAAG-G
255637 AAGGAAG-AAGAAAGG
1 AA-GAAGAAAGAAAGG
255652 AAGAAGAA
1 AAGAAGAA
255660 GGAGGGCCCA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
14 4 0.09
15 30 0.65
16 8 0.17
17 4 0.09
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (15 bp):
AAGAAGAAAGAAAGG
Found at i:255627 original size:11 final size:11
Alignment explanation
Indices: 255608--255659 Score: 63
Period size: 11 Copynumber: 4.8 Consensus size: 11
255598 AGGAAAGGGA
255608 GAAGAAAGAAAG
1 GAAG-AAGAAAG
*
255620 GGAGAAGAAAG
1 GAAGAAGAAAG
*
255631 AAAG-A-AAAG
1 GAAGAAGAAAG
255640 GAAGAAGAAAG
1 GAAGAAGAAAG
255651 GAAGAAGAA
1 GAAGAAGAA
255660 GGAGGGCCCA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
9 7 0.21
10 2 0.06
11 22 0.65
12 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (11 bp):
GAAGAAGAAAG
Found at i:255639 original size:20 final size:20
Alignment explanation
Indices: 255609--255662 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
255599 GGAAAGGGAG
*
255609 AAGAAAG-AAAGGGAGAAGA
1 AAGAAAGAAAAGGAAGAAGA
255628 AAGAAAGAAAAGGAAGAAGA
1 AAGAAAGAAAAGGAAGAAGA
*
255648 AAGGAAGAAGAAGGA
1 AAGAAAGAA-AAGGA
255663 GGGCCCATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.23
20 19 0.61
21 5 0.16
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (20 bp):
AAGAAAGAAAAGGAAGAAGA
Found at i:255985 original size:50 final size:49
Alignment explanation
Indices: 255927--256030 Score: 122
Period size: 50 Copynumber: 2.1 Consensus size: 49
255917 TTTAATTTAT
* * *
255927 ATTAGTTTTTGTTTGTTT-GTTGAAGTTATATTAT-ATAAAAAATTAGTTA
1 ATTAGGTTTT-TTAGTTTAGTT-AAGTTATATTATAATAAAAAAATAGTTA
* *
255976 ATTAGGTTTTTTAGTTTAAGTTAAGTTGTATTATAATAAAAAAATAGTTT
1 ATTAGGTTTTTTAGTTT-AGTTAAGTTATATTATAATAAAAAAATAGTTA
256026 ATTAG
1 ATTAG
256031 TTTAAGTTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
48 6 0.13
49 20 0.43
50 21 0.45
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (49 bp):
ATTAGGTTTTTTAGTTTAGTTAAGTTATATTATAATAAAAAAATAGTTA
Found at i:259292 original size:18 final size:18
Alignment explanation
Indices: 259269--259303 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
259259 ATTGTATATT
*
259269 TGTCCCGAAGGACCACTA
1 TGTCCCAAAGGACCACTA
*
259287 TGTCCCAAATGACCACT
1 TGTCCCAAAGGACCACT
259304 CCTTAAGAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.34, G:0.17, T:0.20
Consensus pattern (18 bp):
TGTCCCAAAGGACCACTA
Found at i:259919 original size:20 final size:20
Alignment explanation
Indices: 259894--259937 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
259884 ATATATATAT
259894 ATATATATATATGGATGGATGG
1 ATATAT-TA-ATGGATGGATGG
*
259916 ATATATTAATGGGTGGATGG
1 ATATATTAATGGATGGATGG
259936 AT
1 AT
259938 GTTGTGGGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.62
21 2 0.10
22 6 0.29
ACGTcount: A:0.34, C:0.00, G:0.30, T:0.36
Consensus pattern (20 bp):
ATATATTAATGGATGGATGG
Found at i:259921 original size:2 final size:2
Alignment explanation
Indices: 259880--259905 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
259870 TATTTTTTTA
259880 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
259906 GGATGGATGG
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:262089 original size:20 final size:20
Alignment explanation
Indices: 262066--262123 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
262056 AAATTTCAAT
262066 TTAAAATAAGCTTAAATATG
1 TTAAAATAAGCTTAAATATG
*
262086 TTAAAAT----TT-CA-AT-
1 TTAAAATAAGCTTAAATATG
262099 TTAAAATAAGCTTAAATATG
1 TTAAAATAAGCTTAAATATG
262119 TTAAA
1 TTAAA
262124 TATTATTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 14
0.64 0.04 0.31
Matches are distributed among these distances:
13 7 0.24
14 2 0.07
15 1 0.03
16 2 0.07
17 2 0.07
18 1 0.03
19 2 0.07
20 12 0.41
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (20 bp):
TTAAAATAAGCTTAAATATG
Found at i:262093 original size:33 final size:33
Alignment explanation
Indices: 262056--262123 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
262046 TTAAAAACTT
262056 AAATTTCAATTTAAAATAAGCTTAAATATGTTA
1 AAATTTCAATTTAAAATAAGCTTAAATATGTTA
262089 AAATTTCAATTTAAAATAAGCTTAAATATGTTA
1 AAATTTCAATTTAAAATAAGCTTAAATATGTTA
262122 AA
1 AA
262124 TATTATTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (33 bp):
AAATTTCAATTTAAAATAAGCTTAAATATGTTA
Found at i:262141 original size:17 final size:15
Alignment explanation
Indices: 262119--262158 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 15
262109 CTTAAATATG
262119 TTAAATATTATTAAAA
1 TTAAATATTA-TAAAA
*
262135 CTTAAATATTATAATA
1 -TTAAATATTATAAAA
262151 TTAAATAT
1 TTAAATAT
262159 GCATGCCTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 4 0.18
17 10 0.45
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAAATATTATAAAA
Found at i:262214 original size:22 final size:22
Alignment explanation
Indices: 262187--262230 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
262177 TATAAAAAGA
*
262187 ATAAATTAGATTATTTATAAAT
1 ATAAATTAGACTATTTATAAAT
*
262209 ATAAATTTGACTATTTATAAAT
1 ATAAATTAGACTATTTATAAAT
262231 TTTAACTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (22 bp):
ATAAATTAGACTATTTATAAAT
Found at i:262240 original size:17 final size:17
Alignment explanation
Indices: 262208--262248 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
262198 TATTTATAAA
*
262208 TATAAA-TTTGACTATT
1 TATAAATTTTAACTATT
262224 TATAAATTTTAACTATT
1 TATAAATTTTAACTATT
262241 TATAAATT
1 TATAAATT
262249 CGATTTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 6 0.26
17 17 0.74
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.51
Consensus pattern (17 bp):
TATAAATTTTAACTATT
Found at i:262267 original size:20 final size:20
Alignment explanation
Indices: 262242--262279 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
262232 TTAACTATTT
262242 ATAAATTCGATTTAAATAGA
1 ATAAATTCGATTTAAATAGA
*
262262 ATAAATTCTATTTAAATA
1 ATAAATTCGATTTAAATA
262280 TTTAATCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.39
Consensus pattern (20 bp):
ATAAATTCGATTTAAATAGA
Found at i:262292 original size:11 final size:11
Alignment explanation
Indices: 262278--262373 Score: 59
Period size: 11 Copynumber: 8.2 Consensus size: 11
262268 TCTATTTAAA
262278 TATTTAATCAT
1 TATTTAATCAT
* *
262289 TATTAAATAAT
1 TATTTAATCAT
262300 TATTAGTAATCAT
1 TATT--TAATCAT
*
262313 TATTAAATCAT
1 TATTTAATCAT
* *
262324 TA-TTAGTAAT
1 TATTTAATCAT
262334 TATTATAATTTCAT
1 TATT-TAA--TCAT
262348 TATTAGTAATCAT
1 TATT--TAATCAT
* *
262361 TACTAAATCAT
1 TATTTAATCAT
262372 TA
1 TA
262374 GTATCAAATC
Statistics
Matches: 65, Mismatches: 13, Indels: 14
0.71 0.14 0.15
Matches are distributed among these distances:
10 7 0.11
11 30 0.46
12 2 0.03
13 16 0.25
14 7 0.11
15 3 0.05
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.48
Consensus pattern (11 bp):
TATTTAATCAT
Found at i:262309 original size:24 final size:24
Alignment explanation
Indices: 262282--262373 Score: 132
Period size: 24 Copynumber: 3.8 Consensus size: 24
262272 TTTAAATATT
*
262282 TAATCATTATTAAATAATTATTAG
1 TAATCATTATTAAATCATTATTAG
262306 TAATCATTATTAAATCATTATTAG
1 TAATCATTATTAAATCATTATTAG
* *
262330 TAATTATTA-TAATTTCATTATTAG
1 TAATCATTATTAA-ATCATTATTAG
*
262354 TAATCATTACTAAATCATTA
1 TAATCATTATTAAATCATTA
262374 GTATCAAATC
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
23 3 0.05
24 55 0.90
25 3 0.05
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (24 bp):
TAATCATTATTAAATCATTATTAG
Found at i:262325 original size:21 final size:22
Alignment explanation
Indices: 262282--262376 Score: 68
Period size: 21 Copynumber: 4.1 Consensus size: 22
262272 TTTAAATATT
*
262282 TAATCATTATTAAATAATTATTAG
1 TAATCATTATT--ATAATCATTAG
*
262306 TAATCATTATTA-AATCATTAT
1 TAATCATTATTATAATCATTAG
* *
262327 TAGTAATTATTATAATTTCATTATTAG
1 TAATCATTATTATAA--TC---ATTAG
*
262354 TAATCATTACTA-AATCATTAG
1 TAATCATTATTATAATCATTAG
262375 TA
1 TA
262377 TCAAATCATT
Statistics
Matches: 57, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
21 24 0.42
22 3 0.05
24 15 0.26
26 2 0.04
27 13 0.23
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.46
Consensus pattern (22 bp):
TAATCATTATTATAATCATTAG
Found at i:262394 original size:21 final size:21
Alignment explanation
Indices: 262379--262453 Score: 98
Period size: 21 Copynumber: 3.4 Consensus size: 21
262369 CATTAGTATC
262379 AAATCATTAAATATTAATAAT
1 AAATCATTAAATATTAATAAT
*
262400 AAATCATT-ATTATTAATCATTACT
1 AAATCATTAAATATTAAT-A--A-T
262424 AAATCATTAAATATTAATAAT
1 AAATCATTAAATATTAATAAT
262445 AAATCATTA
1 AAATCATTA
262454 GTAGTATCGG
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
20 8 0.17
21 19 0.40
22 1 0.02
23 1 0.02
24 10 0.21
25 8 0.17
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (21 bp):
AAATCATTAAATATTAATAAT
Found at i:263110 original size:21 final size:20
Alignment explanation
Indices: 263081--263123 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
263071 AAAAAATATA
263081 TAAATAAATCAAT-TTAAAAT
1 TAAATAAAT-AATATTAAAAT
*
263101 TAAATTAAATATTATTAAAAT
1 TAAA-TAAATAATATTAAAAT
263122 TA
1 TA
263124 CTATAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAATAAATAATATTAAAAT
Found at i:264483 original size:64 final size:64
Alignment explanation
Indices: 264415--264557 Score: 173
Period size: 64 Copynumber: 2.2 Consensus size: 64
264405 TTTGTTTAAG
* *
264415 GTGCATCGATGCAT-GAATTTAAATAGAAAACATCGAATAGGATTTATGCATCGATG-AAGAAGG
1 GTGCATCGATGCATCCAA-TTAAATA-AAAACATCGAAAAGGATTTATGCATCGATGCAAGAAGG
264478 A
64 A
* * * ** *
264479 GTGCATCGATGCATCCCCATTAAATACAAACATCGAAAAGGATTTATGCATCGATGCATGGTGTA
1 GTGCATCGATGCAT-CCAATTAAATAAAAACATCGAAAAGGATTTATGCATCGATGCAAGAAGGA
264544 GTGCATCGATGCAT
1 GTGCATCGATGCAT
264558 ACCTTCATTA
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
64 42 0.62
65 25 0.37
66 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (64 bp):
GTGCATCGATGCATCCAATTAAATAAAAACATCGAAAAGGATTTATGCATCGATGCAAGAAGGA
Found at i:264557 original size:65 final size:65
Alignment explanation
Indices: 264433--264557 Score: 180
Period size: 64 Copynumber: 1.9 Consensus size: 65
264423 ATGCATGAAT
*
264433 TTAAATAGAAAACATCGAATAGGATTTATGCATCGATGAAGAAGGAGTGCATCGATGCATCCCCA
1 TTAAATAGAAAACATCGAAAAGGATTTATGCATCGATGAAGAAGGAGTGCATCGATGCATCCCCA
* * ** *
264498 TTAAATA-CAAACATCGAAAAGGATTTATGCATCGATGCATGGTGTAGTGCATCGATGCAT
1 TTAAATAGAAAACATCGAAAAGGATTTATGCATCGATG-AAGAAGGAGTGCATCGATGCAT
264558 ACCTTCATTA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
64 28 0.53
65 25 0.47
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.26
Consensus pattern (65 bp):
TTAAATAGAAAACATCGAAAAGGATTTATGCATCGATGAAGAAGGAGTGCATCGATGCATCCCCA
Found at i:265072 original size:18 final size:18
Alignment explanation
Indices: 265049--265083 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
265039 CTAGGAGATT
265049 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
265067 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
265084 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:265424 original size:2 final size:2
Alignment explanation
Indices: 265417--265482 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
265407 GAACATGTGA
265417 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
265459 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
265483 GTCTAAGAGA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:266204 original size:147 final size:148
Alignment explanation
Indices: 266032--266344 Score: 531
Period size: 149 Copynumber: 2.1 Consensus size: 148
266022 GAGTCGAGGG
* * ** *
266032 TCTACGCGGTCCTTCAGGATATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACATAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACAT
266097 A-TGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTAT
66 ACTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTAT
266161 ATGGCACTACGGTGCAAT
131 ATGGCACTACGGTGCAAT
*
266179 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
266244 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
66 AC-TGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
266309 TATGGCACTACGGTGCAAT
130 TATGGCACTACGGTGCAAT
266328 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
266345 TGCAATTATA
Statistics
Matches: 156, Mismatches: 7, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
147 60 0.38
148 1 0.01
149 95 0.61
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.35
Consensus pattern (148 bp):
TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTAT
ATGGCACTACGGTGCAAT
Found at i:266345 original size:23 final size:23
Alignment explanation
Indices: 266312--266356 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
266302 ATTATTATAT
*
266312 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
266335 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
266357 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:269555 original size:64 final size:63
Alignment explanation
Indices: 269487--269648 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 63
269477 TTGTTTAAGG
*
269487 TGCATCGATGTACATGCAGTGCATCGATGCATGAAT-TTAAATAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCACATGCAGTGCATCGATGCAT-AATATTAAATA-AAAACATCGAATAGGATTTA
* * * ** *
269551 TGCATCGATGCATAAGGAGTGCATCGATGCATCCTCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCACATGCAGTGCATCGATGCATAAT-ATTAAATAAAAACATCGAATAGGATTTA
** *
269615 TGCATCGATGCATGGTGTAGTGCATCGATGCATA
1 TGCATCGATGCA-CATGCAGTGCATCGATGCATA
269649 CCTTCATTAA
Statistics
Matches: 83, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
63 1 0.01
64 59 0.71
65 23 0.28
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.28
Consensus pattern (63 bp):
TGCATCGATGCACATGCAGTGCATCGATGCATAATATTAAATAAAAACATCGAATAGGATTTA
Found at i:269647 original size:65 final size:67
Alignment explanation
Indices: 269523--269659 Score: 210
Period size: 64 Copynumber: 2.1 Consensus size: 67
269513 ATGCATGAAT
269523 TTAAATAGAAAACATCGAATAGGATTTATGCATCGATGCATAAGGAGTGCATCGATGCAT-CC-T
1 TTAAATAGAAAACATCGAATAGGATTTATGCATCGATGCATAAGGAGTGCATCGATGCATACCTT
269586 CA
66 CA
* *
269588 TTAAATA-CAAACATCGAATAGGATTTATGCATCGATGCAT-GGTGTAGTGCATCGATGCATACC
1 TTAAATAGAAAACATCGAATAGGATTTATGCATCGATGCATAAG-G-AGTGCATCGATGCATACC
269651 TTCA
64 TTCA
269655 TTAAA
1 TTAAA
269660 AGATGAAATT
Statistics
Matches: 66, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
63 1 0.02
64 33 0.50
65 22 0.33
66 2 0.03
67 8 0.12
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (67 bp):
TTAAATAGAAAACATCGAATAGGATTTATGCATCGATGCATAAGGAGTGCATCGATGCATACCTT
CA
Found at i:270159 original size:18 final size:18
Alignment explanation
Indices: 270136--270170 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
270126 CTAGGAGATT
270136 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
270154 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
270171 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:271239 original size:149 final size:149
Alignment explanation
Indices: 271068--271382 Score: 535
Period size: 149 Copynumber: 2.1 Consensus size: 149
271058 GAGTCGAGGG
* **
271068 TCTACGCGGTCCTTCGGGATATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACAT
271133 A-TATGATCCCTAGCATATGTATATGATTATTAAGGAATTCTATGTGGTCCTTATGGACATCATT
66 ACT-TGATCCCTAGCATATGTATATGATTATTAAGGAATTCTATGTGGTCCTTATGGACATCATT
271197 ATATGGCACTACGGTGCAAT
130 ATATGGCACTACGGTGCAAT
*
271217 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACAT
* *
271282 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTATTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
*
271347 TATGGCACTACGGTGTAAT
131 TATGGCACTACGGTGCAAT
271366 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
271383 TGCAATTATA
Statistics
Matches: 157, Mismatches: 7, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
148 1 0.01
149 155 0.99
150 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTATTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:271383 original size:23 final size:23
Alignment explanation
Indices: 271350--271394 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
271340 ATTATTATAT
* *
271350 GGCACTACGGTGTAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
271373 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
271395 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:272458 original size:21 final size:21
Alignment explanation
Indices: 272428--272474 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
272418 TTGGGCAAGG
*
272428 TGTACCGGTACCCTATGAACA
1 TGTACAGGTACCCTATGAACA
272449 TGTACAGGTACCCTATGAACA
1 TGTACAGGTACCCTATGAACA
272470 TGTAC
1 TGTAC
272475 TGATATCCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (21 bp):
TGTACAGGTACCCTATGAACA
Found at i:272484 original size:21 final size:21
Alignment explanation
Indices: 272436--272484 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
272426 GGTGTACCGG
*
272436 TACCCTATGAACATGTACAGG
1 TACCCTATGAACATGTACAGA
*
272457 TACCCTATGAACATGTACTGA
1 TACCCTATGAACATGTACAGA
*
272478 TATCCTA
1 TACCCTA
272485 AGACCAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (21 bp):
TACCCTATGAACATGTACAGA
Found at i:273467 original size:18 final size:18
Alignment explanation
Indices: 273444--273486 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
273434 GTTATTAAGG
273444 AGTGGTCATTCGGGACAT
1 AGTGGTCATTCGGGACAT
*
273462 AGTGGTCTTTCGGGACAT
1 AGTGGTCATTCGGGACAT
273480 AGTGGTC
1 AGTGGTC
273487 CTTTTGGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.19, C:0.16, G:0.35, T:0.30
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:284207 original size:18 final size:17
Alignment explanation
Indices: 284153--284201 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
284143 TTGGACCCTT
* *
284153 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
284171 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
284189 AGTGCATTCGATG
1 AGTGCA-TCGATG
284202 TTTCAACATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:284371 original size:65 final size:64
Alignment explanation
Indices: 284173--284382 Score: 232
Period size: 65 Copynumber: 3.2 Consensus size: 64
284163 TGCACTAAGA
* * * *
284173 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAACATAGC-CAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATATCTCAG-GTGCATCGATGCATGGTTG
* *
284237 GTGCATCGATGCATCAAATGCATTCGATGTTTTC-ATAAAATCCTCA-GTGCATCGGTGCATGGT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCAAT-ATAT-CTCAGGTGCATCGATGCATGGT
284300 AT-
63 -TG
* * *
284302 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTATTTCATGGTGCATCGATGCATGGATT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATATCTCA-GGTGCATCGATGCATGG-TT
284366 G
64 G
*
284367 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
284383 CTCTGAAAAA
Statistics
Matches: 123, Mismatches: 13, Indels: 19
0.79 0.08 0.12
Matches are distributed among these distances:
62 3 0.02
63 5 0.04
64 47 0.38
65 64 0.52
66 2 0.02
67 2 0.02
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATATCTCAGGTGCATCGATGCATGGTTG
Found at i:286286 original size:2 final size:2
Alignment explanation
Indices: 286279--286329 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
286269 TTATAAAAAC
* *
286279 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT AG
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
286321 AT AT AT AT A
1 AT AT AT AT A
286330 CGCACATCAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (2 bp):
AT
Found at i:288139 original size:20 final size:20
Alignment explanation
Indices: 288101--288142 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
288091 CAAATGTAAA
*
288101 ATATAATTATTAATAATAAT
1 ATATAATTAATAATAATAAT
* *
288121 ATATAATTAATAGTTATAAT
1 ATATAATTAATAATAATAAT
288141 AT
1 AT
288143 TTTTTAATCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
ATATAATTAATAATAATAAT
Found at i:288376 original size:55 final size:54
Alignment explanation
Indices: 288317--288926 Score: 510
Period size: 55 Copynumber: 11.5 Consensus size: 54
288307 CGACCAGTAG
*
288317 GTTCGCTCCCTCTTGCTTTAGGGAGTATAGAACTCGAACAATCTTCTGCCAACA
1 GTTCGCTCCCTCTTGCTTCAGGGAGTATAGAACTCGAACAATCTTCTGCCAACA
*
288371 TGTTCGCTCCCTCTTGCTTTAGGGAGTATAGAACTCGAACAATCTTCTGCCAACA
1 -GTTCGCTCCCTCTTGCTTCAGGGAGTATAGAACTCGAACAATCTTCTGCCAACA
* * *
288426 TGTTCGCTCCCTCTTGCTTCAGAGAGTAT-GAAACTCGAAC-ATCTTCTGCTAACGG
1 -GTTCGCTCCCTCTTGCTTCAGGGAGTATAG-AACTCGAACAATCTTCTGCCAAC-A
* * * * * * *
288481 GTTCGTTCCCTCTTGTTTTAAGGAGTATGGAATTCGAACAATCTTCTGTCAACGA
1 GTTCGCTCCCTCTTGCTTCAGGGAGTATAGAACTCGAACAATCTTCTGCCAAC-A
* * * * * * **
288536 GTTCGCTCCCTCTTGCTTCAGTGAGTATAAAACTCGAACATTCTTTTACGAATGG
1 GTTCGCTCCCTCTTGCTTCAGGGAGTATAGAACTCGAACAATCTTCTGCCAA-CA
* * * * * ** **
288591 GTTCGCTTCCTTTTGCTTCAGGGAGTATGGAATTTGAACAATCTTCTGAAAATGG
1 GTTCGCTCCCTCTTGCTTCAGGGAGTATAGAACTCGAACAATCTTCTGCCAA-CA
* * * * * * * * *
288646 GTTTGCTCCCTATCGCTTCAGGGAGTAT--AATTCGAACAA-ATGCTACCTACGG
1 GTTCGCTCCCTCTTGCTTCAGGGAGTATAGAACTCGAACAATCTTCTGCCAAC-A
* *
288698 GTTCGCTTCCTCTTGCTTCAGGGAG--TAGAACTCGAACAATCTTCTGCCTACGA
1 GTTCGCTCCCTCTTGCTTCAGGGAGTATAGAACTCGAACAATCTTCTGCCAAC-A
* *
288751 GTTCGCTCCCTCTTGCTTCAGGGAG--TAGAACTCGAACAATCTTCTGCCTACGG
1 GTTCGCTCCCTCTTGCTTCAGGGAGTATAGAACTCGAACAATCTTCTGCCAAC-A
** * * *
288804 GTTCGCTTTCTCTTG---CAGGGAG--T--AACTCGAACAATCTTATGTCTACGA
1 GTTCGCTCCCTCTTGCTTCAGGGAGTATAGAACTCGAACAATCTTCTGCCAAC-A
*
288852 GTTCG--CCCTCTTGCTTCAGGGAG--TAGAACTCGAACAATCTT-TGCCTACGA
1 GTTCGCTCCCTCTTGCTTCAGGGAGTATAGAACTCGAACAATCTTCTGCCAAC-A
*
288902 GTTCACT-CC-CTTGCTTCAGGGAGTA
1 GTTCGCTCCCTCTTGCTTCAGGGAGTA
288927 CAACTCGAAA
Statistics
Matches: 465, Mismatches: 72, Indels: 39
0.81 0.12 0.07
Matches are distributed among these distances:
46 6 0.01
48 27 0.06
49 8 0.02
50 35 0.08
51 17 0.04
52 36 0.08
53 83 0.18
54 44 0.09
55 209 0.45
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.32
Consensus pattern (54 bp):
GTTCGCTCCCTCTTGCTTCAGGGAGTATAGAACTCGAACAATCTTCTGCCAACA
Found at i:288597 original size:164 final size:163
Alignment explanation
Indices: 288316--288935 Score: 638
Period size: 164 Copynumber: 3.9 Consensus size: 163
288306 TCGACCAGTA
*
288316 GGTTCGCTCCCTCTTGCTTTAGGGAGTATAGAACTCGAACAATCTTCTGCCAAC-ATGTTCGCTC
1 GGTTCGCTCCCTCTTGCTTTAGGGAGTAT-GAATTCGAACAATCTTCTGCCAACGA-GTTCGCTC
*
288380 CCTCTTGCTTTAGGGAGTATAGAACTCGAACAATCTTCTGCCAAC-ATGTTCGCTCCCTCTTGCT
64 CCTCTTGCTTCAGGGAGTATAGAACTCGAACAATCTTCTGCCAACGA-GTTCGCTCCCTCTTGCT
*
288444 TCAGAGAGTATGAAACTCGAAC-ATCTTCTGCTAACG
128 TCAGGGAGTATG-AACTCGAACAATCTTCTGCTAACG
* * * *
288480 GGTTCGTTCCCTCTTGTTTTAAGGAGTATGGAATTCGAACAATCTTCTGTCAACGAGTTCGCTCC
1 GGTTCGCTCCCTCTTGCTTTAGGGAGTAT-GAATTCGAACAATCTTCTGCCAACGAGTTCGCTCC
* * * * * * * * * *
288545 CTCTTGCTTCAGTGAGTATAAAACTCGAACATTCTTTTACGAATGGGTTCGCTTCCTTTTGCTTC
65 CTCTTGCTTCAGGGAGTATAGAACTCGAACAATCTTCTGCCAACGAGTTCGCTCCCTCTTGCTTC
* * ** *
288610 AGGGAGTATGGAATTTGAACAATCTTCTGAAAATG
130 AGGGAGTAT-GAACTCGAACAATCTTCTGCTAACG
* * * * * * * * * *
288645 GGTTTGCTCCCTATCGCTTCAGGGAGTAT-AATTCGAACAA-ATGCTACCTACGGGTTCGCTTCC
1 GGTTCGCTCCCTCTTGCTTTAGGGAGTATGAATTCGAACAATCTTCTGCCAACGAGTTCGCTCCC
*
288708 TCTTGCTTCAGGGAG--TAGAACTCGAACAATCTTCTGCCTACGAGTTCGCTCCCTCTTGCTTCA
66 TCTTGCTTCAGGGAGTATAGAACTCGAACAATCTTCTGCCAACGAGTTCGCTCCCTCTTGCTTCA
288771 GGGAGTA-GAACTCGAACAATCTTCTGCCT-ACG
131 GGGAGTATGAACTCGAACAATCTTCTG-CTAACG
** * * * *
288803 GGTTCGCTTTCTCTTGC---AGGGAG--T-AACTCGAACAATCTTATGTCTACGAGTTCG--CCC
1 GGTTCGCTCCCTCTTGCTTTAGGGAGTATGAATTCGAACAATCTTCTGCCAACGAGTTCGCTCCC
* *
288860 TCTTGCTTCAGGGAG--TAGAACTCGAACAATCTT-TGCCTACGAGTTCACT-CC-CTTGCTTCA
66 TCTTGCTTCAGGGAGTATAGAACTCGAACAATCTTCTGCCAACGAGTTCGCTCCCTCTTGCTTCA
*
288920 GGGAGTA-CAACTCGAA
131 GGGAGTATGAACTCGAA
288936 AATTCTTGGG
Statistics
Matches: 382, Mismatches: 68, Indels: 27
0.80 0.14 0.06
Matches are distributed among these distances:
149 24 0.06
150 2 0.01
151 15 0.04
152 35 0.09
153 11 0.03
154 12 0.03
155 6 0.02
158 31 0.08
160 45 0.12
162 30 0.08
163 11 0.03
164 125 0.33
165 35 0.09
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.31
Consensus pattern (163 bp):
GGTTCGCTCCCTCTTGCTTTAGGGAGTATGAATTCGAACAATCTTCTGCCAACGAGTTCGCTCCC
TCTTGCTTCAGGGAGTATAGAACTCGAACAATCTTCTGCCAACGAGTTCGCTCCCTCTTGCTTCA
GGGAGTATGAACTCGAACAATCTTCTGCTAACG
Found at i:289000 original size:27 final size:28
Alignment explanation
Indices: 288970--289024 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
288960 TCAGAGTAGA
*
288970 ACTCGAACAA-CTTCTG-CTAACGGGTTC
1 ACTCCAACAATCTTCTGCCT-ACGGGTTC
288997 ACTCCAACAATCTTCTGCCTACGGGTTC
1 ACTCCAACAATCTTCTGCCTACGGGTTC
289025 GCTTTCTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 9 0.36
28 14 0.56
29 2 0.08
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.27
Consensus pattern (28 bp):
ACTCCAACAATCTTCTGCCTACGGGTTC
Found at i:289087 original size:53 final size:53
Alignment explanation
Indices: 288997--289385 Score: 539
Period size: 53 Copynumber: 7.3 Consensus size: 53
288987 TAACGGGTTC
* **
288997 ACTCCAACAATCTTCTGCCTACGGGTTCGCTTTCTCTTGCTTCAGGGAGTAGA
1 ACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGA
* * *
289050 ACTCGAACAATCTTATGTCTACGAGTTCGCTCCCTCTTGCTTCAGGGAGTAGA
1 ACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGA
* * *
289103 ACTCGAACAATCTTCTGCCTACGAGTTCACTCCCTCTTGCTTCAGGGAGTACA
1 ACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGA
* * * *
289156 ACTCGAACAATATTCTGCCAATGGGTTTGCTCCCTCTTGCTTCAGGGAGTAGA
1 ACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGA
*
289209 ACTCGAACAATCTTCTG-CTAACGGGTTCCCTCCCTCTTGCTTCAGGGAGTAGA
1 ACTCGAACAATCTTCTGCCT-ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGA
* * * * *
289262 ATTCGAACAATCATCTGTCAACGGGTTCGCTTCCTCTTGCTTCAGGGAGTATAGA
1 ACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAG--TAGA
* *
289317 ACTCGAAC-ATCTTCTGCCAACGAGTTCGCTCCCTCTTGCTTCAGGGAGTAGA
1 ACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGA
*
289369 ACTTGAACAATCTTCTG
1 ACTCGAACAATCTTCTG
289386 GTGTGATTCT
Statistics
Matches: 298, Mismatches: 33, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
52 12 0.04
53 238 0.80
54 37 0.12
55 11 0.04
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (53 bp):
ACTCGAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGA
Found at i:290228 original size:79 final size:79
Alignment explanation
Indices: 290097--290243 Score: 258
Period size: 79 Copynumber: 1.9 Consensus size: 79
290087 ATCATGCTCG
* **
290097 AAAGAATTACTGATGGCACTTACTGATGGATTTGCTTCACTACTCTTCCGTGAAGGTTTACAAAT
1 AAAGAATTACTGATGACACTTACTGATGGATTTGCTTCACTACTCTTCCGTGAAGACTTACAAAT
290162 TACCCGAAGGATTT
66 TACCCGAAGGATTT
*
290176 AAAGACTTACTGATGACACTTACTGATGGATTTGCTTCACTACTCTTCCGTGAAGACTTACAAAT
1 AAAGAATTACTGATGACACTTACTGATGGATTTGCTTCACTACTCTTCCGTGAAGACTTACAAAT
290241 TAC
66 TAC
290244 TAAAATTATT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 64 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (79 bp):
AAAGAATTACTGATGACACTTACTGATGGATTTGCTTCACTACTCTTCCGTGAAGACTTACAAAT
TACCCGAAGGATTT
Found at i:290373 original size:37 final size:37
Alignment explanation
Indices: 290322--290468 Score: 187
Period size: 37 Copynumber: 4.1 Consensus size: 37
290312 AAGACTTACT
* * * *
290322 GATGGATTTTCTTCACTACTCTTCGGTGAAGGCATAA
1 GATGTATTTGCTTCACTACTCTTCAGTGAAGGCTTAA
* * *
290359 GATGTATTTGCTTCACTACTCTTCGGTGAAGGTTTAG
1 GATGTATTTGCTTCACTACTCTTCAGTGAAGGCTTAA
290396 GATGTATTTGCTTCACTACTCTTCAGTGAAGGCTTAA
1 GATGTATTTGCTTCACTACTCTTCAGTGAAGGCTTAA
*
290433 GATG-----GATTCACTACTCTTCAGTGAAGGCTTAA
1 GATGTATTTGCTTCACTACTCTTCAGTGAAGGCTTAA
290465 GATG
1 GATG
290469 GATTCACTTC
Statistics
Matches: 101, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
32 31 0.31
37 70 0.69
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (37 bp):
GATGTATTTGCTTCACTACTCTTCAGTGAAGGCTTAA
Found at i:290448 original size:32 final size:32
Alignment explanation
Indices: 290407--290476 Score: 140
Period size: 32 Copynumber: 2.2 Consensus size: 32
290397 ATGTATTTGC
290407 TTCACTACTCTTCAGTGAAGGCTTAAGATGGA
1 TTCACTACTCTTCAGTGAAGGCTTAAGATGGA
290439 TTCACTACTCTTCAGTGAAGGCTTAAGATGGA
1 TTCACTACTCTTCAGTGAAGGCTTAAGATGGA
290471 TTCACT
1 TTCACT
290477 TCTTCATACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (32 bp):
TTCACTACTCTTCAGTGAAGGCTTAAGATGGA
Found at i:293788 original size:20 final size:20
Alignment explanation
Indices: 293751--293789 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
293741 AGATTGAGTG
* * *
293751 GATTTTGATGTTGTTTGCAT
1 GATTTTAATGATGATTGCAT
293771 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
293790 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.05, G:0.23, T:0.49
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAT
Found at i:294023 original size:20 final size:21
Alignment explanation
Indices: 293969--294031 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
293959 GATTCCCCTG
293969 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
293993 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
294013 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
294032 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:300761 original size:26 final size:26
Alignment explanation
Indices: 300707--300764 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
300697 AATTTACACC
* *
300707 AATGATTTAATAATTATTATTAATAT
1 AATGATTTAATAATTATAATGAATAT
300733 AATGATTTAAT-ATT-TAATGAATTAGT
1 AATGATTTAATAATTATAATGAA-TA-T
300759 AATGAT
1 AATGAT
300765 ATGATTTAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 5 0.18
25 5 0.18
26 18 0.64
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.47
Consensus pattern (26 bp):
AATGATTTAATAATTATAATGAATAT
Found at i:300773 original size:16 final size:16
Alignment explanation
Indices: 300749--300780 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
300739 TTAATATTTA
300749 ATGAATTAGTAATGAT
1 ATGAATTAGTAATGAT
*
300765 ATGATTTAGTAATGAT
1 ATGAATTAGTAATGAT
300781 TACTAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (16 bp):
ATGAATTAGTAATGAT
Found at i:301401 original size:207 final size:199
Alignment explanation
Indices: 301030--301418 Score: 548
Period size: 207 Copynumber: 1.9 Consensus size: 199
301020 TTAAACAATT
*
301030 AATATAAACTAACTAACTAACTAATTTACACATACATACACAACAACAACAAATAACAAATTACC
1 AATATAAACTAACTAACTAACTAATTTA-ACATACATACACAACAACAAAAAATAACAAATTACC
*
301095 CGCGTATTTATGTATTCTTACTTTCCTTTCTTTTTTCTTTCTTCAAATCAATATGTAGGTGGGCA
65 CGCGTATTTATGTATTCTTACTTTCCCTTCTTTTTTCTTTCTTCAAATCAATATGTAGGTGGGCA
*
301160 AAAGTTGTGGAATAATGCCCTGTAGGTCTAAACAAAATATTTTTTTAAACAAATTAATTTTATAT
130 AAAGTTGTGGAATAATGCCATGTAGGTCTAAACAAAATATTTTTTTAAACAAATTAATTTTATAT
301225 AATCA
195 AATCA
* *
301230 AATATAAACTAACTAACTAACT-GTTT-ACATACATACACAACAACAAAAAATAACAATTTACCC
1 AATATAAACTAACTAACTAACTAATTTAACATACATACACAACAACAAAAAATAACAAATTACCC
* * * * *
301293 GTGTATTTATGCCTTCTTCCTTTCCTTTCTTTTCCCTTCTTTTTTCTTTCTTCAAATCAATCTTT
66 GCGTATTTATG------T--ATT-CTTAC-TTTCCCTTCTTTTTTCTTTCTTCAAATCAATATGT
* * *
301358 ATGTGGGCAAAAGTTGTGGAATAATGTCATGTAGGTGTAAACAAAATATTTTTTTAAACAA
121 AGGTGGGCAAAAGTTGTGGAATAATGCCATGTAGGTCTAAACAAAATATTTTTTTAAACAA
301419 CAATAAATTA
Statistics
Matches: 166, Mismatches: 13, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
197 45 0.27
199 3 0.02
200 22 0.13
203 1 0.01
205 2 0.01
206 4 0.02
207 89 0.54
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.37
Consensus pattern (199 bp):
AATATAAACTAACTAACTAACTAATTTAACATACATACACAACAACAAAAAATAACAAATTACCC
GCGTATTTATGTATTCTTACTTTCCCTTCTTTTTTCTTTCTTCAAATCAATATGTAGGTGGGCAA
AAGTTGTGGAATAATGCCATGTAGGTCTAAACAAAATATTTTTTTAAACAAATTAATTTTATATA
ATCA
Found at i:301754 original size:21 final size:21
Alignment explanation
Indices: 301725--301765 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
301715 CTAATATATT
301725 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
*
301746 ATAATTTAAACTAACAAACT
1 ATAACTTAAACTAACAAACT
301766 TTTACTCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.56, C:0.17, G:0.00, T:0.27
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:301815 original size:19 final size:15
Alignment explanation
Indices: 301782--301833 Score: 95
Period size: 15 Copynumber: 3.5 Consensus size: 15
301772 CAATCTCTTC
*
301782 TTCTTCTTCCTTTCT
1 TTCTTCTCCCTTTCT
301797 TTCTTCTCCCTTTCT
1 TTCTTCTCCCTTTCT
301812 TTCTTCTCCCTTTCT
1 TTCTTCTCCCTTTCT
301827 TTCTTCT
1 TTCTTCT
301834 TAACCGTACT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (15 bp):
TTCTTCTCCCTTTCT
Found at i:301996 original size:26 final size:26
Alignment explanation
Indices: 301967--302023 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 26
301957 TGCAAATCAT
* *
301967 GCAGGGCTGCTATATGCATGAGGGGA
1 GCAGGGCTGCTACATGCATAAGGGGA
* *
301993 GCAGGGGTTGCTGCATGCATAAGGGGA
1 GCA-GGGCTGCTACATGCATAAGGGGA
302020 GCAG
1 GCAG
302024 AGATCACGGG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 4 0.15
27 22 0.85
ACGTcount: A:0.23, C:0.16, G:0.44, T:0.18
Consensus pattern (26 bp):
GCAGGGCTGCTACATGCATAAGGGGA
Found at i:302098 original size:29 final size:29
Alignment explanation
Indices: 302034--302100 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
302024 AGATCACGGG
* *
302034 GCTTGGTCGCAGGGTGTGCATGGTGACCT
1 GCTTGGTCGCAGGCTGTGCATGGCGACCT
***
302063 AAGTGGTCGCATGGCT-TGCATGGCGACCT
1 GCTTGGTCGCA-GGCTGTGCATGGCGACCT
302092 GCTTGGTCG
1 GCTTGGTCG
302101 TTCTGATTGC
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
29 26 0.90
30 3 0.10
ACGTcount: A:0.12, C:0.22, G:0.39, T:0.27
Consensus pattern (29 bp):
GCTTGGTCGCAGGCTGTGCATGGCGACCT
Found at i:302851 original size:11 final size:11
Alignment explanation
Indices: 302835--302865 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
302825 TTCTAAGATT
302835 TTTTTTTTTCA
1 TTTTTTTTTCA
302846 TTTTTTTTTCA
1 TTTTTTTTTCA
302857 TTTTTTTTT
1 TTTTTTTTT
302866 AACTCTCCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.06, C:0.06, G:0.00, T:0.87
Consensus pattern (11 bp):
TTTTTTTTTCA
Found at i:313161 original size:20 final size:21
Alignment explanation
Indices: 313124--313171 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
313114 AAATACTTAA
**
313124 AAAAATAAATGTAGAATTATT
1 AAAAATAAAAATAGAATTATT
313145 AAAAATAAAAATA-AATTATT
1 AAAAATAAAAATAGAATTATT
313165 AAAAATA
1 AAAAATA
313172 CTATTAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (21 bp):
AAAAATAAAAATAGAATTATT
Found at i:315037 original size:22 final size:23
Alignment explanation
Indices: 315012--315072 Score: 106
Period size: 23 Copynumber: 2.7 Consensus size: 23
315002 ACAAAAAAAA
315012 TAAAAAAGGTAAAGTG-TTTTTT
1 TAAAAAAGGTAAAGTGTTTTTTT
315034 TAAAAAAGGTAAAGTGTTTTTTT
1 TAAAAAAGGTAAAGTGTTTTTTT
*
315057 TTAAAAAGGTAAAGTG
1 TAAAAAAGGTAAAGTG
315073 CTTCAAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
22 16 0.43
23 21 0.57
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.38
Consensus pattern (23 bp):
TAAAAAAGGTAAAGTGTTTTTTT
Found at i:315232 original size:37 final size:37
Alignment explanation
Indices: 315183--315286 Score: 136
Period size: 37 Copynumber: 2.8 Consensus size: 37
315173 ATGCTTGTGG
* * * *
315183 ATCATATCTTTAGGAGTTTAAATAATAGTATAACTCT
1 ATCATATTTTTAGGAGTTTGAATCATAGTAAAACTCT
* * * *
315220 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCATATTTTTAGGAGTTTGAATCATAGTAAAACTCT
315257 ATCATATTTTTAGGAGTTTGAATCATAGTA
1 ATCATATTTTTAGGAGTTTGAATCATAGTA
315287 GGACGAAAAT
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.41
Consensus pattern (37 bp):
ATCATATTTTTAGGAGTTTGAATCATAGTAAAACTCT
Found at i:316222 original size:106 final size:106
Alignment explanation
Indices: 316037--318029 Score: 3268
Period size: 106 Copynumber: 18.9 Consensus size: 106
316027 GCTTTGTTCT
* * * * *
316037 GAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAATCGGGAAATTATTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* * * *
316101 ACCAGTC-ATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 ACCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
316143 GAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
316208 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
316249 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
316314 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
316355 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTATGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
316420 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
316461 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
316526 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
316567 GAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAC
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
316632 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
316673 GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTAAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
316738 -C--C-GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
316775 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
316840 CCAGCGGTTCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
316881 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTATGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
316946 TCA---G-CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
316983 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
317048 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
317089 GAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAC
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
317154 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
317195 GAGTCCAATATCCTTTGATGTGAAGTTGAAATTGGCTCTAAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
317260 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
317301 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
317366 CCAGCGGTTCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
317407 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTATGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
317472 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
317513 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
317578 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
317619 GAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAC
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
317684 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
317725 GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTAAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
317790 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGCCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
317831 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
317896 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTTTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
317937 GAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTTTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
318002 CCAGCGGTCCCTTCGTCGTGAAGTTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAA
318030 TGTTGCGTAT
Statistics
Matches: 1776, Mismatches: 101, Indels: 20
0.94 0.05 0.01
Matches are distributed among these distances:
102 191 0.11
103 3 0.00
105 4 0.00
106 1577 0.89
107 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.33
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:318806 original size:24 final size:24
Alignment explanation
Indices: 318779--318828 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
318769 ATAAAAAACC
318779 AAAATAAA-CTTAAACATACCATTA
1 AAAATAAAGCTTAAACAT-CCATTA
*
318803 AAAATAAAGTTTAAACATCCATTA
1 AAAATAAAGCTTAAACATCCATTA
318827 AA
1 AA
318829 CCAACCACCG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAAGCTTAAACATCCATTA
Found at i:324421 original size:24 final size:24
Alignment explanation
Indices: 324394--324443 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
324384 ATAAAGAACC
324394 AAAATAAA-CTTAAACATACCATTA
1 AAAATAAAGCTTAAACAT-CCATTA
*
324418 AAAATAAAGTTTAAACATCCATTA
1 AAAATAAAGCTTAAACATCCATTA
324442 AA
1 AA
324444 CCAACCACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAAGCTTAAACATCCATTA
Found at i:325442 original size:106 final size:106
Alignment explanation
Indices: 325257--326159 Score: 1412
Period size: 106 Copynumber: 8.5 Consensus size: 106
325247 AGAGTAATCA
* * *
325257 TTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGATGTGAAGTTGAAATGGGCTCTGAAATTGG
1 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGG
325322 GAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
66 GAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
* *
325363 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATGGGCTCCGAAATTGG
1 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGG
* *
325428 GAAATTGTTTGTTGACACCCAGCGGTCCCTTCGTCGTGAAG
66 GAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
* *
325469 TTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGG
1 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGG
* *
325534 GAAGTTATTTGTTGACAACCAGCGGTCCCTTCATCGTGAAG
66 GAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
* *
325575 TTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA
1 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGG
325640 GAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
66 GAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
*
325681 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGG
1 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGG
* * * * * *
325746 AAAGTTATTTATTGAAAACCAGTGGTCCCTTCGTCATGAAG
66 GAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
**
325787 TTGAACTTGCGTTGTCAT-GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATTG
1 TTGAACTTGCGTTGTC-TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTG
* *
325851 GGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAG
65 GGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
* * *
325893 TTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTATGAAATTGA
1 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGG
*
325958 GAAGCTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
66 GAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
* * *
325999 TTGAACTTGCGTTGTCTAGAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGG
1 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGG
* *
326064 GAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAG
66 GAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
* * * * * *
326105 TTGAACTTGTGTTGTCTCGAGTGGCACGATATCCTCCGTCGTGGAGTTGAAATTG
1 TTGAACTTGCGTTGTCTGGAGT--C-CAATATCCTTCGTTGTGAAGTTGAAATTG
326160 CGGATAGCCA
Statistics
Matches: 733, Mismatches: 59, Indels: 7
0.92 0.07 0.01
Matches are distributed among these distances:
105 1 0.00
106 706 0.96
107 1 0.00
108 1 0.00
109 24 0.03
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (106 bp):
TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGG
GAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
Found at i:327113 original size:22 final size:22
Alignment explanation
Indices: 327087--327141 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
327077 TTGTGTTTGG
327087 TCAAAGGTTTGGAATTTGATGC
1 TCAAAGGTTTGGAATTTGATGC
*
327109 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGAATTTGATGC
327131 TCAAAGGTTTG
1 TCAAAGGTTTG
327142 ATGGGGTAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.25, C:0.11, G:0.27, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGAATTTGATGC
Found at i:327780 original size:7 final size:7
Alignment explanation
Indices: 327748--327828 Score: 58
Period size: 7 Copynumber: 11.6 Consensus size: 7
327738 TTTTTGTCCC
327748 TTTTTC-
1 TTTTTCT
**
327754 TTTTTGA
1 TTTTTCT
*
327761 TTTTTGT
1 TTTTTCT
*
327768 TCTTTCT
1 TTTTTCT
327775 TTTTTCT
1 TTTTTCT
*
327782 TTTAT-T
1 TTTTTCT
*
327788 TTATTCT
1 TTTTTCT
327795 TTTTTGCT
1 TTTTT-CT
*
327803 TCTTTTAT
1 T-TTTTCT
*
327811 TTTTTGT
1 TTTTTCT
327818 TTTTTCT
1 TTTTTCT
327825 TTTT
1 TTTT
327829 GTTCTGATTG
Statistics
Matches: 59, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
6 9 0.15
7 41 0.69
8 5 0.08
9 4 0.07
ACGTcount: A:0.05, C:0.10, G:0.05, T:0.80
Consensus pattern (7 bp):
TTTTTCT
Found at i:327784 original size:20 final size:20
Alignment explanation
Indices: 327750--327833 Score: 64
Period size: 20 Copynumber: 4.0 Consensus size: 20
327740 TTTGTCCCTT
**
327750 TTTCTTTTTGATTTTTGTTC
1 TTTCTTTTTTCTTTTTGTTC
327770 TTTCTTTTTTCTTTTAT-TT-
1 TTTCTTTTTTCTTTT-TGTTC
* *
327789 TATTCTTTTTTGCTTCTTTTATTT
1 T-TTCTTTTTT-C-T-TTTTGTTC
*
327813 TTTGTTTTTTCTTTTTGTTC
1 TTTCTTTTTTCTTTTTGTTC
327833 T
1 T
327834 GATTGAATCT
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
19 1 0.02
20 31 0.60
21 3 0.06
22 3 0.06
23 13 0.25
24 1 0.02
ACGTcount: A:0.05, C:0.11, G:0.06, T:0.79
Consensus pattern (20 bp):
TTTCTTTTTTCTTTTTGTTC
Found at i:327794 original size:24 final size:23
Alignment explanation
Indices: 327748--327822 Score: 71
Period size: 24 Copynumber: 3.1 Consensus size: 23
327738 TTTTTGTCCC
*
327748 TTTTTCTTTTTGATTTTTGTTCTTTCT
1 TTTTTC-TTTT-A-TTTTATTCTTT-T
327775 TTTTTCTTTTATTTTATTCTTTT
1 TTTTTCTTTTATTTTATTCTTTT
* *
327798 TTGCTTCTTTTATTTT-TTGTTTT
1 TT-TTTCTTTTATTTTATTCTTTT
327821 TT
1 TT
327823 CTTTTTGTTC
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
23 11 0.25
24 22 0.50
25 1 0.02
26 4 0.09
27 6 0.14
ACGTcount: A:0.05, C:0.09, G:0.05, T:0.80
Consensus pattern (23 bp):
TTTTTCTTTTATTTTATTCTTTT
Found at i:329563 original size:21 final size:21
Alignment explanation
Indices: 329521--329563 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
329511 TTTCTGGGCT
* *
329521 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
329542 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
329563 A
1 A
329564 ACGAACCAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:331087 original size:103 final size:103
Alignment explanation
Indices: 330908--331116 Score: 391
Period size: 103 Copynumber: 2.0 Consensus size: 103
330898 GGGTCTACGC
330908 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
* *
330973 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
331011 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
*
331076 CCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
331114 GGT
1 GGT
331117 TCTTATGGAC
Statistics
Matches: 103, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 103 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.36
Consensus pattern (103 bp):
GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
Found at i:331204 original size:23 final size:23
Alignment explanation
Indices: 331136--331188 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
331126 CATTATTATA
331136 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
331159 CGGCACTCCGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
331182 TGGCACT
1 TGGCACT
331189 TTGGTGTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.19, C:0.30, G:0.26, T:0.25
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:334785 original size:21 final size:21
Alignment explanation
Indices: 334744--334785 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
334734 TTCTGGGCTT
* *
334744 GGGGAATCGGTACCCATTCAA
1 GGGGAATCGATACCCACTCAA
*
334765 GGGGAATCGATACCCCCTCAA
1 GGGGAATCGATACCCACTCAA
334786 ACGAACCAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.17
Consensus pattern (21 bp):
GGGGAATCGATACCCACTCAA
Found at i:334858 original size:23 final size:22
Alignment explanation
Indices: 334814--334858 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
334804 AATCTCATAG
*
334814 GGGAACCGATTCCCCCACAGGA
1 GGGAACCGATTCCCCCAAAGGA
334836 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATTCCCCC-AAAGGA
334859 AAATGTGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.29, C:0.33, G:0.27, T:0.11
Consensus pattern (22 bp):
GGGAACCGATTCCCCCAAAGGA
Found at i:335733 original size:15 final size:15
Alignment explanation
Indices: 335709--335738 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
335699 CTATACAAAT
*
335709 TATATTAAAATATGA
1 TATATGAAAATATGA
335724 TATATGAAAATATGA
1 TATATGAAAATATGA
335739 ATAAGTTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.37
Consensus pattern (15 bp):
TATATGAAAATATGA
Found at i:338918 original size:18 final size:19
Alignment explanation
Indices: 338881--338918 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
338871 TGCAGATGAT
338881 GGAAATAAAATAAAAGAGA
1 GGAAATAAAATAAAAGAGA
338900 GGAAA-AAAATGAAAA-AGA
1 GGAAATAAAAT-AAAAGAGA
338918 G
1 G
338919 TTAGTAAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.68, C:0.00, G:0.24, T:0.08
Consensus pattern (19 bp):
GGAAATAAAATAAAAGAGA
Found at i:340096 original size:20 final size:19
Alignment explanation
Indices: 340046--340101 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
340036 AACCAATAAT
340046 AATAAACATAAAAT-AATTG
1 AATAAA-ATAAAATAAATTG
*
340065 GATGAAAA-AAAATGAAATTG
1 AAT-AAAATAAAAT-AAATTG
340085 AATAAAATAAAATAAAT
1 AATAAAATAAAATAAAT
340102 GAAGATAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
18 5 0.16
19 11 0.35
20 15 0.48
ACGTcount: A:0.66, C:0.02, G:0.09, T:0.23
Consensus pattern (19 bp):
AATAAAATAAAATAAATTG
Found at i:340263 original size:22 final size:21
Alignment explanation
Indices: 340188--340274 Score: 68
Period size: 22 Copynumber: 3.9 Consensus size: 21
340178 GAAATTGAAA
*
340188 ATATA-ATGAAAATAAATAAAT
1 ATATATATAAAAATAAA-AAAT
*
340209 AGTATAAATAAAATAATAAAAAAT
1 A-TATATAT-AAA-AATAAAAAAT
340233 ATATATATAAAAATATAAAAAT
1 ATATATATAAAAATA-AAAAAT
* *
340255 GTATGTATAATATAATAAAA
1 ATATATATAA-A-AATAAAA
340275 TATTAAATAG
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
21 5 0.09
22 21 0.38
23 12 0.22
24 11 0.20
25 6 0.11
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.30
Consensus pattern (21 bp):
ATATATATAAAAATAAAAAAT
Found at i:340553 original size:23 final size:22
Alignment explanation
Indices: 340508--340573 Score: 66
Period size: 23 Copynumber: 3.1 Consensus size: 22
340498 ACACAAAGAA
*
340508 AAATAAA-AAA-AAATTATAAT
1 AAATAAATAAATAAAATATAAT
340528 AAATAAATAAATAAAATATAATT
1 AAATAAATAAATAAAATATAA-T
* * *
340551 AAATATATACATATAA-ATAAT
1 AAATAAATAAATAAAATATAAT
340572 AA
1 AA
340574 GGGTTAAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
20 7 0.18
21 6 0.15
22 12 0.31
23 14 0.36
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.29
Consensus pattern (22 bp):
AAATAAATAAATAAAATATAAT
Found at i:341040 original size:37 final size:37
Alignment explanation
Indices: 340965--341065 Score: 105
Period size: 37 Copynumber: 2.8 Consensus size: 37
340955 ATGCTTGTGG
* * ** *
340965 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATACTAACAAAACTCT
* *
341002 ATCCTATTTTTAGGAGTTTAAATTCTAACAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATACTAACAAAACTCT
* * *
341039 ATCATA-TTTTAGGAATTTAAATCCTAA
1 ATCCTATTTTTAGGAGTTTAAATACTAA
341066 TAAGATGAAA
Statistics
Matches: 54, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
36 19 0.35
37 35 0.65
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATACTAACAAAACTCT
Found at i:342951 original size:20 final size:20
Alignment explanation
Indices: 342911--342949 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
342901 TACTGCAGGA
*
342911 ATTTATGGCTTGAACAAAAG
1 ATTTATGGCTTCAACAAAAG
342931 ATTTCATGGCTTCAACAAA
1 ATTT-ATGGCTTCAACAAA
342950 GACCTTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (20 bp):
ATTTATGGCTTCAACAAAAG
Found at i:345517 original size:10 final size:11
Alignment explanation
Indices: 345494--345554 Score: 51
Period size: 10 Copynumber: 5.8 Consensus size: 11
345484 AAATTAAATT
*
345494 ATAAATAGAC-
1 ATAAATAAACA
345504 ATAAA-AAACA
1 ATAAATAAACA
345514 ATAAATAAA-A
1 ATAAATAAACA
*
345524 TCATAAATAGAC-
1 --ATAAATAAACA
345536 ATAAA-AAACA
1 ATAAATAAACA
345546 ATAAATAAA
1 ATAAATAAA
345555 ATCAATACTT
Statistics
Matches: 41, Mismatches: 3, Indels: 13
0.72 0.05 0.23
Matches are distributed among these distances:
9 6 0.15
10 21 0.51
11 6 0.15
12 8 0.20
ACGTcount: A:0.70, C:0.08, G:0.03, T:0.18
Consensus pattern (11 bp):
ATAAATAAACA
Found at i:345533 original size:32 final size:32
Alignment explanation
Indices: 345484--345558 Score: 132
Period size: 32 Copynumber: 2.3 Consensus size: 32
345474 TCATATAAAA
* *
345484 AAATTAAATTATAAATAGACATAAAAAACAAT
1 AAATAAAATCATAAATAGACATAAAAAACAAT
345516 AAATAAAATCATAAATAGACATAAAAAACAAT
1 AAATAAAATCATAAATAGACATAAAAAACAAT
345548 AAATAAAATCA
1 AAATAAAATCA
345559 ATACTTCACA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.68, C:0.08, G:0.03, T:0.21
Consensus pattern (32 bp):
AAATAAAATCATAAATAGACATAAAAAACAAT
Found at i:349054 original size:23 final size:23
Alignment explanation
Indices: 349018--349086 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
349008 CACCACAGCT
* *
349018 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATACACCGAAGTGCCA
* * *
349041 CGTAGAATTACACCGTAGTGCCG
1 CGTAGAAATACACCGAAGTGCCA
*
349064 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATACACCGAAGTGCCA
349087 TATAAGGTTG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.32, C:0.26, G:0.25, T:0.17
Consensus pattern (23 bp):
CGTAGAAATACACCGAAGTGCCA
Found at i:349920 original size:20 final size:22
Alignment explanation
Indices: 349892--349949 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
349882 TTCCCCTTGA
*
349892 AGTGTATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
349912 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
349935 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
349950 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:350027 original size:45 final size:45
Alignment explanation
Indices: 349956--350057 Score: 118
Period size: 45 Copynumber: 2.3 Consensus size: 45
349946 TGCACTACCC
* * *
349956 ATGCATCGATACACAAATTACCTTCGATGTTTTCAT-TTTAAAGGG
1 ATGCATCGATGCACAAATTACATTCGATG-TTTCATCTTTAAAGAG
* * *
350001 ATGCATCGATGCACCAATTGCATTCGATGTTTCTTCTTTAAAGAG
1 ATGCATCGATGCACAAATTACATTCGATGTTTCATCTTTAAAGAG
*
350046 -TACATCGATGCA
1 ATGCATCGATGCA
350058 TATTGAATGT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
44 16 0.33
45 33 0.67
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (45 bp):
ATGCATCGATGCACAAATTACATTCGATGTTTCATCTTTAAAGAG
Found at i:351515 original size:24 final size:24
Alignment explanation
Indices: 351471--351518 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
351461 ATGTTCATTT
*
351471 TACATAACTTAGAAAGAAAAAAAA
1 TACATAACTTACAAAGAAAAAAAA
* *
351495 TACATAAC-TACAAATATAAAAAA
1 TACATAACTTACAAAGAAAAAAAA
351518 T
1 T
351519 TTATATCTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.65, C:0.10, G:0.04, T:0.21
Consensus pattern (24 bp):
TACATAACTTACAAAGAAAAAAAA
Found at i:352306 original size:11 final size:12
Alignment explanation
Indices: 352267--352317 Score: 54
Period size: 11 Copynumber: 4.4 Consensus size: 12
352257 ATATATTCCT
352267 TTATTT-TATT-
1 TTATTTATATTA
*
352277 TTATTTATAATA
1 TTATTTATATTA
352289 TTATTTAT-TTA
1 TTATTTATATTA
*
352300 TTCTTTATATTA
1 TTATTTATATTA
352312 TATATT
1 T-TATT
352318 AGATAAAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
10 6 0.18
11 12 0.36
12 12 0.36
13 3 0.09
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (12 bp):
TTATTTATATTA
Found at i:352400 original size:29 final size:29
Alignment explanation
Indices: 352367--352450 Score: 71
Period size: 29 Copynumber: 3.2 Consensus size: 29
352357 TTCATCTCTT
352367 ATATAAAATTTATATAATAATAAATAAAC
1 ATATAAAATTTATATAATAATAAATAAAC
*
352396 ATAT--AA-TTATGATACT--T-AAT----
1 ATATAAAATTTAT-ATAATAATAAATAAAC
*
352416 GTATAAAATTTATATAATAATAAATAAAC
1 ATATAAAATTTATATAATAATAAATAAAC
352445 ATATAA
1 ATATAA
352451 TTATGATACT
Statistics
Matches: 40, Mismatches: 4, Indels: 22
0.61 0.06 0.33
Matches are distributed among these distances:
20 3 0.08
22 6 0.15
23 4 0.10
24 4 0.10
25 4 0.10
26 4 0.10
27 6 0.15
29 9 0.22
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (29 bp):
ATATAAAATTTATATAATAATAAATAAAC
Found at i:352421 original size:28 final size:28
Alignment explanation
Indices: 352390--352466 Score: 78
Period size: 21 Copynumber: 3.0 Consensus size: 28
352380 ATAATAATAA
352390 ATAAACATATAATTATGATACTTAATGT
1 ATAAACATATAATTATGATACTTAATGT
* **
352418 AT-AA-A-AT--TTAT-ATA-ATAATAA
1 ATAAACATATAATTATGATACTTAATGT
352439 ATAAACATATAATTATGATACTTAATGT
1 ATAAACATATAATTATGATACTTAATGT
352467 TAATAAAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 14
0.64 0.11 0.25
Matches are distributed among these distances:
21 6 0.17
22 5 0.14
23 5 0.14
24 2 0.06
25 2 0.06
26 5 0.14
27 5 0.14
28 6 0.17
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39
Consensus pattern (28 bp):
ATAAACATATAATTATGATACTTAATGT
Found at i:352421 original size:49 final size:49
Alignment explanation
Indices: 352368--352466 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
352358 TCATCTCTTA
352368 TATAAAATTTATATAATAATAAATAAACATATAATTATGATACTTAATG
1 TATAAAATTTATATAATAATAAATAAACATATAATTATGATACTTAATG
352417 TATAAAATTTATATAATAATAAATAAACATATAATTATGATACTTAATG
1 TATAAAATTTATATAATAATAAATAAACATATAATTATGATACTTAATG
352466 T
1 T
352467 TAATAAAAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (49 bp):
TATAAAATTTATATAATAATAAATAAACATATAATTATGATACTTAATG
Found at i:352442 original size:21 final size:21
Alignment explanation
Indices: 352369--352443 Score: 60
Period size: 21 Copynumber: 3.2 Consensus size: 21
352359 CATCTCTTAT
352369 ATAAAATTTATATAATAATAA
1 ATAAAATTTATATAATAATAA
* **
352390 ATAAACATATAATTATGATACTTAATGT
1 AT-AA-A-AT--TTAT-ATA-ATAATAA
352418 ATAAAATTTATATAATAATAA
1 ATAAAATTTATATAATAATAA
352439 ATAAA
1 ATAAA
352444 CATATAATTA
Statistics
Matches: 41, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
21 11 0.27
22 5 0.12
23 5 0.12
24 2 0.05
25 2 0.05
26 5 0.12
27 5 0.12
28 6 0.15
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (21 bp):
ATAAAATTTATATAATAATAA
Found at i:352543 original size:16 final size:16
Alignment explanation
Indices: 352517--352556 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
352507 AGATATGAGA
352517 AAAATTAATTTAAATTT
1 AAAA-TAATTTAAATTT
*
352534 AAAATAATTTAATTTT
1 AAAATAATTTAAATTT
352550 AAAATAA
1 AAAATAA
352557 CATTAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AAAATAATTTAAATTT
Found at i:353518 original size:2 final size:2
Alignment explanation
Indices: 353507--353536 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
353497 CATGGTGTTT
353507 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
353537 TGTTTGATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:353799 original size:2 final size:2
Alignment explanation
Indices: 353792--353830 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
353782 TCAAATAATT
353792 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
353831 TTAATGCATA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:355011 original size:2 final size:2
Alignment explanation
Indices: 355000--355062 Score: 103
Period size: 2 Copynumber: 32.5 Consensus size: 2
354990 CTAAACTTTC
355000 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
355041 TA -A TA TA AA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
355063 CTCATGATTA
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
1 2 0.04
2 55 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:356372 original size:2 final size:2
Alignment explanation
Indices: 356365--356397 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
356355 GGAAAGATAA
356365 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
356398 TAATGTTCTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:362462 original size:17 final size:18
Alignment explanation
Indices: 362430--362463 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
362420 TTATATATTA
362430 TTAAATATAAAAAATAAT
1 TTAAATATAAAAAATAAT
*
362448 TTAAA-ATAAATAATAA
1 TTAAATATAAAAAATAA
362464 AATAATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
TTAAATATAAAAAATAAT
Found at i:367520 original size:29 final size:28
Alignment explanation
Indices: 367427--367525 Score: 74
Period size: 29 Copynumber: 3.4 Consensus size: 28
367417 ATTTAAGTAC
** **
367427 CTAAAGTATTTTTTTATCAAAATAAATAT
1 CTAAAGTATTTTTTGGTCAAAAT-AGGAT
* * *
367456 ATAAAGTTATCTCTTTGGTCAAACTAGG-T
1 CTAAAG-TAT-TTTTTGGTCAAAATAGGAT
367485 ACATAAAGTATTTTTTGGTCAAAATATGGAT
1 -C-TAAAGTATTTTTTGGTCAAAATA-GGAT
367516 CTAAAGTATT
1 CTAAAGTATT
367526 CAGTTGGTTT
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
29 28 0.52
30 10 0.19
31 16 0.30
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.40
Consensus pattern (28 bp):
CTAAAGTATTTTTTGGTCAAAATAGGAT
Found at i:367687 original size:31 final size:28
Alignment explanation
Indices: 367624--367713 Score: 90
Period size: 28 Copynumber: 3.1 Consensus size: 28
367614 TTTATGTATC
* * * *
367624 TATTTTAACATAAAATACTTTAGCTACC
1 TATTTTAACAAAAAATATTTTAGGTACT
*
367652 TATTTTAACAAAAAAAATAATTTTAGGTATT
1 TATTTTAAC--AAAAAAT-ATTTTAGGTACT
* *
367683 TATTTTGACCAAAAATATTTTAGGTACT
1 TATTTTAACAAAAAATATTTTAGGTACT
367711 TAT
1 TAT
367714 ATAAAAATAT
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
28 23 0.45
29 6 0.12
30 6 0.12
31 16 0.31
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.42
Consensus pattern (28 bp):
TATTTTAACAAAAAATATTTTAGGTACT
Found at i:367719 original size:23 final size:24
Alignment explanation
Indices: 367693--367738 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
367683 TATTTTGACC
*
367693 AAAAATAT-TTTAGGTACTTATAT
1 AAAAATATATTTAGATACTTATAT
367716 AAAAATATACTTTAGATACTTAT
1 AAAAATATA-TTTAGATACTTAT
367739 TTATGATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 8 0.40
25 12 0.60
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.41
Consensus pattern (24 bp):
AAAAATATATTTAGATACTTATAT
Found at i:368005 original size:11 final size:11
Alignment explanation
Indices: 367989--368017 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
367979 TAAAGATGTT
367989 CATGTTCAATA
1 CATGTTCAATA
368000 CATGTTCAATA
1 CATGTTCAATA
368011 CATGTTC
1 CATGTTC
368018 GTTTGTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (11 bp):
CATGTTCAATA
Found at i:371003 original size:22 final size:22
Alignment explanation
Indices: 370973--371018 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
370963 TGTATATTTT
*
370973 AATATTTTTTTAATTTTA-AAA
1 AATATTTTTATAATTTTATAAA
370994 AATATATTTTATAATTTTATAAA
1 AATAT-TTTTATAATTTTATAAA
371017 AA
1 AA
371019 AATTAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.23
22 12 0.55
23 5 0.23
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
AATATTTTTATAATTTTATAAA
Found at i:371876 original size:37 final size:37
Alignment explanation
Indices: 371830--371937 Score: 198
Period size: 37 Copynumber: 2.9 Consensus size: 37
371820 AACAAAACGT
*
371830 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATATGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATATGA
*
371867 TAGATTTTTACTATGATTCAAACTCCTAAAAATATGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATATGA
371904 TAGAGTTTTACTATGATTCAAACTCCTAAAAATA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATA
371938 GGATCTATAA
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 68 1.00
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35
Consensus pattern (37 bp):
TAGAGTTTTACTATGATTCAAACTCCTAAAAATATGA
Found at i:373556 original size:3 final size:3
Alignment explanation
Indices: 373550--373616 Score: 75
Period size: 3 Copynumber: 22.3 Consensus size: 3
373540 TGAAATCACC
* *
373550 ATT ATT ATC ATT ATT ATT ATT ATT ATT ATT ATT ATT GA-T ATT GTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT
*
373595 ATT -TT CATC ATT ATT ATT ATT A
1 ATT ATT -ATT ATT ATT ATT ATT A
373617 AACAAAGGGT
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
2 3 0.06
3 49 0.91
4 2 0.04
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:375057 original size:23 final size:23
Alignment explanation
Indices: 375021--375089 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 23
375011 CACCACAGCT
* *
375021 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATACACCGAAGTGCCA
* ** * *
375044 CGTAGAATTACACCCTAGTACCG
1 CGTAGAAATACACCGAAGTGCCA
*
375067 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATACACCGAAGTGCCA
375090 TATAAGGTTG
Statistics
Matches: 33, Mismatches: 13, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.33, C:0.28, G:0.22, T:0.17
Consensus pattern (23 bp):
CGTAGAAATACACCGAAGTGCCA
Found at i:382618 original size:21 final size:21
Alignment explanation
Indices: 382593--382637 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
382583 ACACTTTAGT
382593 AAGGATTAAAATGAACTTTGA
1 AAGGATTAAAATGAACTTTGA
382614 AAGGATTAAAATGAACTTTGA
1 AAGGATTAAAATGAACTTTGA
382635 AAG
1 AAG
382638 ACTTGGAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.49, C:0.04, G:0.20, T:0.27
Consensus pattern (21 bp):
AAGGATTAAAATGAACTTTGA
Found at i:386722 original size:18 final size:19
Alignment explanation
Indices: 386689--386733 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
386679 ACTTTAATAT
386689 ATATCTAAACTTAAATTCAA-
1 ATAT-TAAACTTAAATT-AAC
386709 ATATTAAA-TTAAATTAAC
1 ATATTAAACTTAAATTAAC
386727 ATATTAA
1 ATATTAA
386734 TTTTAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 2 0.08
18 14 0.58
19 4 0.17
20 4 0.17
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (19 bp):
ATATTAAACTTAAATTAAC
Found at i:386800 original size:29 final size:30
Alignment explanation
Indices: 386740--386896 Score: 139
Period size: 29 Copynumber: 5.3 Consensus size: 30
386730 TTAATTTTAA
* *
386740 AAAATATATATTTTATTTTTATCTTGT--TTT
1 AAAA-ATATATTTTAGTTTTATCTT-TAACTT
*
386770 AAAAATATATTTCA-TTTTATCTTTAACTT
1 AAAAATATATTTTAGTTTTATCTTTAACTT
*
386799 AAAAATATATATTA-TTCTTAT-TTTAACTT
1 AAAAATATATTTTAGTT-TTATCTTTAACTT
* * *
386828 AAAAATATATTTTAGTCTTA-ATTTAACTA
1 AAAAATATATTTTAGTTTTATCTTTAACTT
* *
386857 AAATAATATATTTTATTTTTATC-TTAACCT
1 AAA-AATATATTTTAGTTTTATCTTTAACTT
*
386887 AAAAAAATAT
1 AAAAATATAT
386897 ATGTTGTTCT
Statistics
Matches: 107, Mismatches: 13, Indels: 15
0.79 0.10 0.11
Matches are distributed among these distances:
27 1 0.01
28 9 0.08
29 65 0.61
30 32 0.30
ACGTcount: A:0.41, C:0.07, G:0.01, T:0.51
Consensus pattern (30 bp):
AAAAATATATTTTAGTTTTATCTTTAACTT
Found at i:386890 original size:59 final size:59
Alignment explanation
Indices: 386740--386896 Score: 176
Period size: 58 Copynumber: 2.7 Consensus size: 59
386730 TTAATTTTAA
*** * *
386740 AAAAT-ATATATTTTATTTTTATCTTGTTTTAAAAATATATTTCATTTTATCTTTAACT
1 AAAATAATATATTTTATTTTTATCTTAACTTAAAAATATATTTCATCTTATATTTAACT
* * * * *
386798 TAAA-AATATATATTATTCTTATTTTAACTTAAAAATATATTTTAGTCTTA-ATTTAACT
1 AAAATAATATATTTTATTTTTATCTTAACTTAAAAATATATTTCA-TCTTATATTTAACT
* *
386856 AAAATAATATATTTTATTTTTATCTTAACCTAAAAAAATAT
1 AAAATAATATATTTTATTTTTATCTTAACTTAAAAATATAT
386897 ATGTTGTTCT
Statistics
Matches: 80, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
58 45 0.56
59 35 0.44
ACGTcount: A:0.41, C:0.07, G:0.01, T:0.51
Consensus pattern (59 bp):
AAAATAATATATTTTATTTTTATCTTAACTTAAAAATATATTTCATCTTATATTTAACT
Found at i:386938 original size:88 final size:86
Alignment explanation
Indices: 386773--386941 Score: 200
Period size: 88 Copynumber: 1.9 Consensus size: 86
386763 TTGTTTTAAA
*
386773 AATATATTTCATTTTATCTTTAACTTAAAAATATATATTATTCTTATTTTAACTTAAAAATATAT
1 AATATATTTCATTTTATCTTTAACTAAAAAATATATATTATTCTTATTTT-A-TTAAAAATATAT
*
386838 TTTAGTCTTAATTTAACTAAAAT
64 TTTAGTCATAATTTAACTAAAAT
* * * *
386861 AATATATTTTATTTTTATC-TTAACCTAAAAAAATATATGTTGTTCTTATTTT-TTAAAATATTT
1 AATATATTTCA-TTTTATCTTTAA-CT-AAAAAATATATATTATTCTTATTTTATTAAAA-A-TA
386924 TATTTTA-TCATAATTTAA
61 TATTTTAGTCATAATTTAA
386942 AAGTACCCAA
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
87 6 0.09
88 25 0.36
89 17 0.24
90 22 0.31
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (86 bp):
AATATATTTCATTTTATCTTTAACTAAAAAATATATATTATTCTTATTTTATTAAAAATATATTT
TAGTCATAATTTAACTAAAAT
Found at i:387936 original size:29 final size:29
Alignment explanation
Indices: 387904--388015 Score: 138
Period size: 29 Copynumber: 3.9 Consensus size: 29
387894 TTTAATTTAA
* *
387904 AAATATATATTTTGTTATTATCTTAACTT
1 AAATATATATTTTATTCTTATCTTAACTT
*
387933 AAATATATATTTTATTCTTATTTTAACTT
1 AAATATATATTTTATTCTTATCTTAACTT
* * *
387962 AAATATATATTTCATTCTTATTTTAATTTT
1 AAATATATATTTTATTCTTATCTTAA-CTT
*
387992 AAA-ATATA-TTTATTTTTATCTTAA
1 AAATATATATTTTATTCTTATCTTAA
388016 TTTATAAATT
Statistics
Matches: 74, Mismatches: 8, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
28 13 0.18
29 56 0.76
30 5 0.07
ACGTcount: A:0.36, C:0.06, G:0.01, T:0.57
Consensus pattern (29 bp):
AAATATATATTTTATTCTTATCTTAACTT
Found at i:388023 original size:29 final size:28
Alignment explanation
Indices: 387885--388024 Score: 127
Period size: 29 Copynumber: 4.8 Consensus size: 28
387875 TTAATTTAAG
387885 ATTTTTATTTTTAATTTAAAAATATATATT
1 ATTTTTA-TTTTAATTTAAAAATATAT-TT
* * * *
387915 TTGTTATTATCTTAACTTAAATATATATTTT
1 AT-TT-TTATTTTAATTTAAAAATATA-TTT
* * *
387946 ATTCTTATTTTAACTTAAATATATATTT
1 ATTTTTATTTTAATTTAAAAATATATTT
* *
387974 CATTCTTATTTTAATTTTAAAATATATTT
1 -ATTTTTATTTTAATTTAAAAATATATTT
* *
388003 ATTTTTATCTTAATTTATAAAT
1 ATTTTTATTTTAATTTAAAAAT
388025 TTTTTAAAAT
Statistics
Matches: 92, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
28 21 0.23
29 45 0.49
30 2 0.02
31 20 0.22
32 4 0.04
ACGTcount: A:0.36, C:0.05, G:0.01, T:0.59
Consensus pattern (28 bp):
ATTTTTATTTTAATTTAAAAATATATTT
Found at i:388139 original size:19 final size:20
Alignment explanation
Indices: 388108--388147 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
388098 ATAAGTTAAG
388108 ATAAAAAATATATATTTTTA
1 ATAAAAAATATATATTTTTA
388128 ATAAAAAA-ATATATTTTTA
1 ATAAAAAATATATATTTTTA
388147 A
1 A
388148 AGATATATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
ATAAAAAATATATATTTTTA
Found at i:390759 original size:22 final size:22
Alignment explanation
Indices: 390734--390795 Score: 124
Period size: 22 Copynumber: 2.8 Consensus size: 22
390724 GCAATTTGTT
390734 TCAATTTACAACCTACAATCTA
1 TCAATTTACAACCTACAATCTA
390756 TCAATTTACAACCTACAATCTA
1 TCAATTTACAACCTACAATCTA
390778 TCAATTTACAACCTACAA
1 TCAATTTACAACCTACAA
390796 CTTACACCGC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.42, C:0.27, G:0.00, T:0.31
Consensus pattern (22 bp):
TCAATTTACAACCTACAATCTA
Found at i:392660 original size:28 final size:28
Alignment explanation
Indices: 392618--392674 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
392608 ACCAGTGAGT
*
392618 TTGGAGGAGGTAAGGAAGACTACTGGTC
1 TTGGAGGAGGCAAGGAAGACTACTGGTC
392646 TTGGAGGAGGCAAGGAAGACTACTGGTC
1 TTGGAGGAGGCAAGGAAGACTACTGGTC
392674 T
1 T
392675 AGAAAAAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.28, C:0.12, G:0.39, T:0.21
Consensus pattern (28 bp):
TTGGAGGAGGCAAGGAAGACTACTGGTC
Found at i:392835 original size:81 final size:81
Alignment explanation
Indices: 392695--392855 Score: 207
Period size: 81 Copynumber: 2.0 Consensus size: 81
392685 AGAGTTGTTT
* *
392695 TGGAAAAAGTATTTCTAAATTAGAGTAAGGCTTCTTGTCTAGAGGTAATGATGCAGTAGGATTAG
1 TGGAAAAAGTATTTCTAAATTAGAGGAAGGCTTCTGGTCTAGAGGTAATGATGCAGTAGGATTAG
392760 CTGATTAGGAAGGTTC
66 CTGATTAGGAAGGTTC
* ** * * * *
392776 TGGAAAAAGTATTTTTGGATTAGAGGAAGG-TTGCTGGTTTGGAGGTAATGATGCTGTAGGATTG
1 TGGAAAAAGTATTTCTAAATTAGAGGAAGGCTT-CTGGTCTAGAGGTAATGATGCAGTAGGATTA
* *
392840 GCTGGTTGGGAAGGTT
65 GCTGATTAGGAAGGTT
392856 GTTGGTTTGG
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
80 2 0.03
81 66 0.97
ACGTcount: A:0.28, C:0.06, G:0.33, T:0.33
Consensus pattern (81 bp):
TGGAAAAAGTATTTCTAAATTAGAGGAAGGCTTCTGGTCTAGAGGTAATGATGCAGTAGGATTAG
CTGATTAGGAAGGTTC
Found at i:396367 original size:45 final size:45
Alignment explanation
Indices: 396303--396394 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
396293 CACCACTATA
396303 CTAGGGGCAGTTGAAGTTATTGTTATGTGGTCTGAGTCAGGTTTC
1 CTAGGGGCAGTTGAAGTTATTGTTATGTGGTCTGAGTCAGGTTTC
396348 CTAGGGGCAGTTGAAGTTATTGTTATGTGGTCTGAGTCAGGTTTC
1 CTAGGGGCAGTTGAAGTTATTGTTATGTGGTCTGAGTCAGGTTTC
396393 CT
1 CT
396395 TCGTCCTTAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.17, C:0.12, G:0.33, T:0.38
Consensus pattern (45 bp):
CTAGGGGCAGTTGAAGTTATTGTTATGTGGTCTGAGTCAGGTTTC
Found at i:397355 original size:20 final size:21
Alignment explanation
Indices: 397325--397365 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
397315 ACTAATAGAA
*
397325 TAAAAATTGATTCTATCTAAT
1 TAAAAATTGATCCTATCTAAT
397346 TAAAAA-TGATCCTATCTAAT
1 TAAAAATTGATCCTATCTAAT
397366 ATTTAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.39
Consensus pattern (21 bp):
TAAAAATTGATCCTATCTAAT
Done.