Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr11
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: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 102 of 205
Found at i:30052076 original size:50 final size:50
Alignment explanation
Indices: 30052014--30052194 Score: 222
Period size: 50 Copynumber: 3.7 Consensus size: 50
30052004 CAATGTCATA
* ** * * * *
30052014 TCCCAGATATGGTCTTACATGGGAGTTCCCATATAGGTGCCCATGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTAGGTGCCAACGCCATG
* ** * *
30052064 TCCCAGATATGGTCTTACGGGGGACCTCTCATCTCGATGCCAACGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTAGGTGCCAACGCCATG
* *
30052114 TCCCAGACATGGTCTTACATAGGACCTCTCATCTTGGTGCCAACGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTAGGTGCCAACGCCATG
30052164 TCCCAGACATGGTCTTACATGGGA--TCTCATC
1 TCCCAGACATGGTCTTACATGGGACCTCTCATC
30052195 CTCTTAATGT
Statistics
Matches: 114, Mismatches: 17, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
48 7 0.06
50 107 0.94
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.27
Consensus pattern (50 bp):
TCCCAGACATGGTCTTACATGGGACCTCTCATCTAGGTGCCAACGCCATG
Found at i:30054268 original size:4 final size:4
Alignment explanation
Indices: 30054259--30055230 Score: 1872
Period size: 4 Copynumber: 243.0 Consensus size: 4
30054249 TATTAAATCA
* * *
30054259 GTAT GTAT GTAT GCAT GTAT GTAC GTAT GCAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* * *
30054307 GGAT GTAT GTAC GTAT GTAT GTAC GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
30054355 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
30054403 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
30054451 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
30054499 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
30054547 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
30054595 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
30054643 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
30054691 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
30054739 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
30054787 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
30054835 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
30054883 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
30054931 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
30054979 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
30055027 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
30055075 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
30055123 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* *
30055171 GTAT GTAT GTAT GTAT GCAT GCAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
30055219 GTAT GTAT GTAT
1 GTAT GTAT GTAT
30055231 ATTTTATTTT
Statistics
Matches: 954, Mismatches: 14, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
4 954 1.00
ACGTcount: A:0.25, C:0.01, G:0.25, T:0.49
Consensus pattern (4 bp):
GTAT
Found at i:30056215 original size:42 final size:42
Alignment explanation
Indices: 30056168--30056339 Score: 202
Period size: 42 Copynumber: 4.1 Consensus size: 42
30056158 AGTGCCTGGT
* *
30056168 AGGCTTATTGCCAGTGAAACAATATCAGACTTTACGTCCAGC
1 AGGCTTAATGCCAGTGAAACAATATCAGACTTTACGTCTAGC
* * * *
30056210 AGGCTTAATGTCGGTGAAATAATTTCAGACTTTACGTCTAGC
1 AGGCTTAATGCCAGTGAAACAATATCAGACTTTACGTCTAGC
** * *
30056252 AGGCTTAATGCTGGTGAAACAATATCAGACTTTACATCTAGT
1 AGGCTTAATGCCAGTGAAACAATATCAGACTTTACGTCTAGC
* * * * *
30056294 TGGCTTAATGCCAGTGAAAC-ATTTCAGACTATATGTTTAGC
1 AGGCTTAATGCCAGTGAAACAATATCAGACTTTACGTCTAGC
30056335 AGGCT
1 AGGCT
30056340 AAGTGCCGGT
Statistics
Matches: 108, Mismatches: 22, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
41 19 0.18
42 89 0.82
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (42 bp):
AGGCTTAATGCCAGTGAAACAATATCAGACTTTACGTCTAGC
Found at i:30072557 original size:3 final size:3
Alignment explanation
Indices: 30072549--30072583 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
30072539 TTATATAACT
30072549 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
30072584 TTCTTTGAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:30074985 original size:3 final size:3
Alignment explanation
Indices: 30074971--30075050 Score: 81
Period size: 3 Copynumber: 26.7 Consensus size: 3
30074961 CTCTACAGCC
* * * *
30074971 ATT ATC ATT ATT ATT ATT ATT ATT ATT ATA ATT ATT CTT ATT CTT -TAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
* * *
30075019 CTT ATT CTT ATT ATT CTT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
30075051 CTTCTTTGAA
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
2 1 0.02
3 61 0.97
4 1 0.02
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:30083141 original size:18 final size:19
Alignment explanation
Indices: 30083114--30083149 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
30083104 TTTGATTAAA
30083114 AATTAACCGAATT-AATCG
1 AATTAACCGAATTGAATCG
*
30083132 AATTACCCGAATTGAATC
1 AATTAACCGAATTGAATC
30083150 ACTACATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.42, C:0.19, G:0.11, T:0.28
Consensus pattern (19 bp):
AATTAACCGAATTGAATCG
Found at i:30083174 original size:17 final size:17
Alignment explanation
Indices: 30083152--30083215 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 17
30083142 ATTGAATCAC
30083152 TACATAATTAAAAATAT
1 TACATAATTAAAAATAT
*** *
30083169 TACATAAGTCTTTGAATCAC
1 TACATAA-T-TAAAAAT-AT
*
30083189 TACATAATTAAAAACAT
1 TACATAATTAAAAATAT
30083206 TACATAATTA
1 TACATAATTA
30083216 TTGAAATTAA
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
17 18 0.51
18 4 0.11
19 5 0.14
20 8 0.23
ACGTcount: A:0.50, C:0.12, G:0.03, T:0.34
Consensus pattern (17 bp):
TACATAATTAAAAATAT
Found at i:30083391 original size:38 final size:39
Alignment explanation
Indices: 30083347--30083424 Score: 131
Period size: 38 Copynumber: 2.0 Consensus size: 39
30083337 TACTAAGAGT
*
30083347 TAGACTTTAGTTTTATTTTTATTGGGTT-GCTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGCTAATTGGG
*
30083385 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGCTAATTGGG
30083424 T
1 T
30083425 TGGGTTGGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
38 27 0.73
39 10 0.27
ACGTcount: A:0.18, C:0.04, G:0.27, T:0.51
Consensus pattern (39 bp):
TAGACTTTAGTTTTAGTTTTATTGGGTTGGCTAATTGGG
Found at i:30083423 original size:13 final size:13
Alignment explanation
Indices: 30083405--30083429 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30083395 TTTTAGTTTT
30083405 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
30083418 ATTGGGTTGGGT
1 ATTGGGTTGGGT
30083430 TGGATAATTT
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:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:30086948 original size:37 final size:37
Alignment explanation
Indices: 30086898--30086976 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
30086888 TTTTAACGAA
* * *
30086898 GTCTTACCCGGACATAATCTCCACACGA-AGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACAC-ATAGTCATCGG
30086935 GTCTTACCCGGACAAAATCCCCACACATAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACATAGTCATCGG
30086972 GTCTT
1 GTCTT
30086977 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 1 0.03
37 37 0.97
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACATAGTCATCGG
Found at i:30087232 original size:37 final size:37
Alignment explanation
Indices: 30087182--30087260 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
30087172 TTTTAACGAA
* * *
30087182 GTCTTACCCGGACATAATCTCCACACGA-AGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACAC-ATAGTCATCGG
30087219 GTCTTACCCGGACAAAATCCCCACACATAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACATAGTCATCGG
30087256 GTCTT
1 GTCTT
30087261 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 1 0.03
37 37 0.97
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACATAGTCATCGG
Found at i:30087372 original size:284 final size:284
Alignment explanation
Indices: 30086862--30087416 Score: 1110
Period size: 284 Copynumber: 2.0 Consensus size: 284
30086852 TTAACCTTTC
30086862 GCATTGAATATATTTATAAGCAATTCTTTTAACGAAGTCTTACCCGGACATAATCTCCACACGAA
1 GCATTGAATATATTTATAAGCAATTCTTTTAACGAAGTCTTACCCGGACATAATCTCCACACGAA
30086927 GTTATCGGGTCTTACCCGGACAAAATCCCCACACATAGTCATCGGGTCTTTAGAGCTCGGATATA
66 GTTATCGGGTCTTACCCGGACAAAATCCCCACACATAGTCATCGGGTCTTTAGAGCTCGGATATA
30086992 GTACGAGCACGAAGCTTACGGACATTAATCAGTGATAATATTCTCGCATAAAGCCTGCGGGGTTT
131 GTACGAGCACGAAGCTTACGGACATTAATCAGTGATAATATTCTCGCATAAAGCCTGCGGGGTTT
30087057 TAACCCGGATATAGTACTGACACAAATGCCCTTCGGGACTTATCACATTTATACACTTTCACATC
196 TAACCCGGATATAGTACTGACACAAATGCCCTTCGGGACTTATCACATTTATACACTTTCACATC
30087122 CATCACGTTGGCCACTCGGCCCTG
261 CATCACGTTGGCCACTCGGCCCTG
30087146 GCATTGAATATATTTATAAGCAATTCTTTTAACGAAGTCTTACCCGGACATAATCTCCACACGAA
1 GCATTGAATATATTTATAAGCAATTCTTTTAACGAAGTCTTACCCGGACATAATCTCCACACGAA
30087211 GTTATCGGGTCTTACCCGGACAAAATCCCCACACATAGTCATCGGGTCTTTAGAGCTCGGATATA
66 GTTATCGGGTCTTACCCGGACAAAATCCCCACACATAGTCATCGGGTCTTTAGAGCTCGGATATA
30087276 GTACGAGCACGAAGCTTACGGACATTAATCAGTGATAATATTCTCGCATAAAGCCTGCGGGGTTT
131 GTACGAGCACGAAGCTTACGGACATTAATCAGTGATAATATTCTCGCATAAAGCCTGCGGGGTTT
30087341 TAACCCGGATATAGTACTGACACAAATGCCCTTCGGGACTTATCACATTTATACACTTTCACATC
196 TAACCCGGATATAGTACTGACACAAATGCCCTTCGGGACTTATCACATTTATACACTTTCACATC
30087406 CATCACGTTGG
261 CATCACGTTGG
30087417 ATTAGGCCTT
Statistics
Matches: 271, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
284 271 1.00
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (284 bp):
GCATTGAATATATTTATAAGCAATTCTTTTAACGAAGTCTTACCCGGACATAATCTCCACACGAA
GTTATCGGGTCTTACCCGGACAAAATCCCCACACATAGTCATCGGGTCTTTAGAGCTCGGATATA
GTACGAGCACGAAGCTTACGGACATTAATCAGTGATAATATTCTCGCATAAAGCCTGCGGGGTTT
TAACCCGGATATAGTACTGACACAAATGCCCTTCGGGACTTATCACATTTATACACTTTCACATC
CATCACGTTGGCCACTCGGCCCTG
Found at i:30087499 original size:47 final size:45
Alignment explanation
Indices: 30087379--30087499 Score: 170
Period size: 47 Copynumber: 2.6 Consensus size: 45
30087369 CCCTTCGGGA
* * * *
30087379 CTTATCACATTTATACACTTTCACATCCATCACGTTGGATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGATTAGGC
30087424 CTTATCACATATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGG--ATTAGGC
30087473 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
30087500 TACACACTGT
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
45 8 0.12
47 45 0.66
49 15 0.22
ACGTcount: A:0.30, C:0.26, G:0.07, T:0.36
Consensus pattern (45 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGATTAGGC
Found at i:30090128 original size:26 final size:26
Alignment explanation
Indices: 30090088--30090137 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
30090078 AAAATATTAT
* *
30090088 CCAAAGTTCCTAAATCAAAATCCAAA
1 CCAAAGTCCCAAAATCAAAATCCAAA
* *
30090114 CCAAAGTCCCAAAATTAAAGTCCA
1 CCAAAGTCCCAAAATCAAAATCCA
30090138 TATAGCATGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.48, C:0.28, G:0.06, T:0.18
Consensus pattern (26 bp):
CCAAAGTCCCAAAATCAAAATCCAAA
Found at i:30090280 original size:18 final size:18
Alignment explanation
Indices: 30090257--30090293 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
30090247 AAATCAAAGT
30090257 TTGAGGGCGTGAGCTTAA
1 TTGAGGGCGTGAGCTTAA
*
30090275 TTGAGGGGGTGAGCTTAA
1 TTGAGGGCGTGAGCTTAA
30090293 T
1 T
30090294 AAGCTCAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.08, G:0.41, T:0.30
Consensus pattern (18 bp):
TTGAGGGCGTGAGCTTAA
Found at i:30098510 original size:54 final size:54
Alignment explanation
Indices: 30098452--30098576 Score: 144
Period size: 54 Copynumber: 2.3 Consensus size: 54
30098442 TCTTAAACCG
* * * *
30098452 TGTAACTCACTGATTTAG-GTCACACAATCGTGTCACAAACCGTGTGCTAGACCA
1 TGTAACTCACTGACTT-GCGACACACAACCATGTCACAAACCGTGTGCTAGACCA
** * **
30098506 TGTAACTCTTTGACTTGCGACACACAACCATGTCGCATGCCGTGTGCTAGACCA
1 TGTAACTCACTGACTTGCGACACACAACCATGTCACAAACCGTGTGCTAGACCA
*
30098560 TGTAACTCATTGACTTG
1 TGTAACTCACTGACTTG
30098577 AAATAATAAG
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
53 1 0.02
54 59 0.98
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.28
Consensus pattern (54 bp):
TGTAACTCACTGACTTGCGACACACAACCATGTCACAAACCGTGTGCTAGACCA
Found at i:30102429 original size:30 final size:31
Alignment explanation
Indices: 30102390--30102449 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
30102380 GGAGGTGGGA
30102390 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
30102421 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
30102450 TAAAAGGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 23 0.85
31 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:30102614 original size:30 final size:31
Alignment explanation
Indices: 30102554--30102614 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
30102544 GGGTTGGGAG
* *
30102554 GGGAGAGGAGTAAAAGTTTTGGGGAGAAAGT
1 GGGAGAGGAATAAAAGTTTTAGGGAGAAAGT
30102585 GGGA-AGGAATAAAAGTTTTAAGGGA-AAAGT
1 GGGAGAGGAATAAAAGTTTT-AGGGAGAAAGT
30102615 AAAAAAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 19 0.70
31 8 0.30
ACGTcount: A:0.41, C:0.00, G:0.39, T:0.20
Consensus pattern (31 bp):
GGGAGAGGAATAAAAGTTTTAGGGAGAAAGT
Found at i:30102677 original size:9 final size:9
Alignment explanation
Indices: 30102663--30102699 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
30102653 TATAGTTTGA
30102663 TATTCGAAT
1 TATTCGAAT
30102672 TATTCGAAT
1 TATTCGAAT
*
30102681 TATTCGAGT
1 TATTCGAAT
30102690 TATTCGAAT
1 TATTCGAAT
30102699 T
1 T
30102700 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:30107558 original size:15 final size:14
Alignment explanation
Indices: 30107527--30107555 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
30107517 ATTAATGAAA
30107527 TATTAAAAATAAAT
1 TATTAAAAATAAAT
30107541 TATTAAAAATAAAT
1 TATTAAAAATAAAT
30107555 T
1 T
30107556 TATATTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TATTAAAAATAAAT
Found at i:30110883 original size:36 final size:37
Alignment explanation
Indices: 30110802--30110884 Score: 98
Period size: 36 Copynumber: 2.3 Consensus size: 37
30110792 ACATTATAAA
* * *
30110802 CACTTTCACATGGCATGAATAATATACCCACATATAT
1 CACTTTCACATGGCATGAACAACACACCCACATATAT
* * *
30110839 -ACTGTCACATGGGATGAACAACACACCCTCATAT-T
1 CACTTTCACATGGCATGAACAACACACCCACATATAT
30110874 CACTTTCACAT
1 CACTTTCACAT
30110885 CAGTCATCAT
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
35 1 0.03
36 37 0.97
ACGTcount: A:0.35, C:0.28, G:0.10, T:0.28
Consensus pattern (37 bp):
CACTTTCACATGGCATGAACAACACACCCACATATAT
Found at i:30114782 original size:2 final size:2
Alignment explanation
Indices: 30114777--30114806 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
30114767 TTATCAAAAA
*
30114777 AG AG AG AG AG AG AG AG AG CG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
30114807 TTAGTTTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.03, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:30115081 original size:11 final size:11
Alignment explanation
Indices: 30115065--30115094 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
30115055 TTGATTAATG
*
30115065 AAATATATTTA
1 AAATATATTAA
30115076 AAATATATTAA
1 AAATATATTAA
30115087 AAATATAT
1 AAATATAT
30115095 ATTGAGTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AAATATATTAA
Found at i:30117783 original size:22 final size:22
Alignment explanation
Indices: 30117758--30117799 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
30117748 TTGAATTTAA
30117758 AATTTATTACACA-TATTAATCC
1 AATTTATTA-ACATTATTAATCC
30117780 AATTTATTAACATTATTAAT
1 AATTTATTAACATTATTAAT
30117800 TTTTTAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.45
Consensus pattern (22 bp):
AATTTATTAACATTATTAATCC
Found at i:30117972 original size:23 final size:22
Alignment explanation
Indices: 30117942--30117995 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 22
30117932 GTTGATTNCG
30117942 TACATAATAAAAATATATACTAA
1 TACATAATAAAAATA-ATACTAA
* *
30117965 TACATAATAATAATAATAGTAA
1 TACATAATAAAAATAATACTAA
30117987 TAC-TAATAA
1 TACATAATAA
30117996 TACTAATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 6 0.21
22 9 0.31
23 14 0.48
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.31
Consensus pattern (22 bp):
TACATAATAAAAATAATACTAA
Found at i:30117976 original size:3 final size:3
Alignment explanation
Indices: 30117945--30118015 Score: 63
Period size: 3 Copynumber: 23.3 Consensus size: 3
30117935 GATTNCGTAC
* * * *
30117945 ATA ATA AAA ATA TATA CTA ATA CATA ATA ATA ATA ATA GTA ATA CTA
1 ATA ATA ATA ATA -ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
* *
30117992 ATA ATA CTA ATA AT- ATA AAA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
30118016 CAAGGATATT
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
2 2 0.04
3 45 0.85
4 6 0.11
ACGTcount: A:0.62, C:0.06, G:0.01, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:30118501 original size:11 final size:12
Alignment explanation
Indices: 30118481--30118518 Score: 60
Period size: 11 Copynumber: 3.2 Consensus size: 12
30118471 AGAAAAAAAA
30118481 GAAGAGAGAGAGG
1 GAAGAGAGA-AGG
30118494 GAAGAGAGAAGG
1 GAAGAGAGAAGG
30118506 G-AGAGAGAAGG
1 GAAGAGAGAAGG
30118517 GA
1 GA
30118519 GGGGGAAGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.46
12 4 0.17
13 9 0.38
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (12 bp):
GAAGAGAGAAGG
Found at i:30130362 original size:22 final size:22
Alignment explanation
Indices: 30130337--30130381 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
30130327 AACAAGTTCC
* *
30130337 AATGGAGACTTGGGTTGAGTTA
1 AATGGACACTTCGGTTGAGTTA
30130359 AATGGACACTTCGGTTGAGTTA
1 AATGGACACTTCGGTTGAGTTA
30130381 A
1 A
30130382 GAAGAATGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.29, C:0.09, G:0.31, T:0.31
Consensus pattern (22 bp):
AATGGACACTTCGGTTGAGTTA
Found at i:30130920 original size:27 final size:28
Alignment explanation
Indices: 30130867--30130921 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
30130857 CATGTATGGA
* *
30130867 AAACATGAAGTCTTGTGGTCAAAGTATG
1 AAACATGAAGCCTTGAGGTCAAAGTATG
* *
30130895 AAACATGAA-CCTTGAGGTTAAGGTATG
1 AAACATGAAGCCTTGAGGTCAAAGTATG
30130922 CTTGTGTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 14 0.61
28 9 0.39
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.27
Consensus pattern (28 bp):
AAACATGAAGCCTTGAGGTCAAAGTATG
Found at i:30131397 original size:32 final size:32
Alignment explanation
Indices: 30131358--30131434 Score: 118
Period size: 32 Copynumber: 2.4 Consensus size: 32
30131348 TAGATAGGAA
*
30131358 AGCCTTTGTGGCAAGTACTGGATATAAAGGAT
1 AGCCTTTGTGGCAAGTACTGGATATAAAGAAT
* *
30131390 AGTCTTTGTGGCCAGTACTGGATATAAAGAAT
1 AGCCTTTGTGGCAAGTACTGGATATAAAGAAT
*
30131422 AGCCTTTATGGCA
1 AGCCTTTGTGGCA
30131435 CAACTCTGGA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (32 bp):
AGCCTTTGTGGCAAGTACTGGATATAAAGAAT
Found at i:30131490 original size:93 final size:93
Alignment explanation
Indices: 30131318--30131490 Score: 211
Period size: 93 Copynumber: 1.9 Consensus size: 93
30131308 TGAGTACCTA
* * * * **
30131318 ATATAAAGGATAGCCCTTGTGGAACAACTCTAGATAGGAAAGCCTTTGTGGCAAGTACTGGATAT
1 ATATAAAGAATAGCCCTTATGGAACAACTCTAGACAAGAAAGCCTTTGTGGCAAGTACTAAATAT
* **
30131383 AAAGGATAGTCTTTGTGGCCAGTACTGG
66 AAAGGACAACCTTTGTGGCCAGTACTGG
* * * * *
30131411 ATATAAAGAATAGCCTTTATGGCACAACTCTGGACAAGAAAGCCTTTGTGGCGAGTACTAAATGT
1 ATATAAAGAATAGCCCTTATGGAACAACTCTAGACAAGAAAGCCTTTGTGGCAAGTACTAAATAT
*
30131476 AAAGGCCAACCTTTG
66 AAAGGACAACCTTTG
30131491 CGGAAAAACT
Statistics
Matches: 65, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
93 65 1.00
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (93 bp):
ATATAAAGAATAGCCCTTATGGAACAACTCTAGACAAGAAAGCCTTTGTGGCAAGTACTAAATAT
AAAGGACAACCTTTGTGGCCAGTACTGG
Found at i:30131574 original size:29 final size:28
Alignment explanation
Indices: 30131512--30131581 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 28
30131502 TAGACAAGAT
*
30131512 AGCCTTTGTGGCAAATCTTTGAAAGGAA
1 AGCCTTTGTGGCAAATCTTTCAAAGGAA
*
30131540 ATGCCTTTGTGGC-GATCTCTGTCAAAGGAA
1 A-GCCTTTGTGGCAAATCT-T-TCAAAGGAA
*
30131570 AGCCTCTGTGGC
1 AGCCTTTGTGGC
30131582 TACCTTCGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 5 0.14
29 22 0.61
30 9 0.25
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (28 bp):
AGCCTTTGTGGCAAATCTTTCAAAGGAA
Found at i:30139157 original size:43 final size:43
Alignment explanation
Indices: 30139100--30139212 Score: 126
Period size: 41 Copynumber: 2.7 Consensus size: 43
30139090 AGCTCGTACA
* * *
30139100 ATGCCATATCCTAGATATGGTCTTACATGTTATAAT-ATAT-CG
1 ATGCCATGTCCTAGACATGGTCTTACATGCTA-AATCATATACG
*
30139142 ATGCCATTGTCCTAGACAGGGTCTTACA--CTAAATCATATACG
1 ATGCCA-TGTCCTAGACATGGTCTTACATGCTAAATCATATACG
* *
30139184 ATGCAATGTCCCAGACATGGTCTTACATG
1 ATGCCATGTCCTAGACATGGTCTTACATG
30139213 AAATCACACC
Statistics
Matches: 59, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
40 3 0.05
41 25 0.42
42 13 0.22
43 18 0.31
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (43 bp):
ATGCCATGTCCTAGACATGGTCTTACATGCTAAATCATATACG
Found at i:30145182 original size:104 final size:104
Alignment explanation
Indices: 30145002--30145477 Score: 855
Period size: 104 Copynumber: 4.6 Consensus size: 104
30144992 TAACCGTTAT
* ** *
30145002 TGGTGGATCTCGCACTTAGCACCACCGCTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
30145067 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
30145106 TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
30145171 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
30145210 TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
30145275 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
30145314 TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
30145379 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCC-TTTCACATTTCAAAGATA
* * **
30145419 TGGTGGATCA-CGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCT
30145478 TTATATACAA
Statistics
Matches: 362, Mismatches: 8, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
104 290 0.80
105 71 0.20
106 1 0.00
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (104 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
Found at i:30164097 original size:10 final size:10
Alignment explanation
Indices: 30164074--30164119 Score: 65
Period size: 10 Copynumber: 4.5 Consensus size: 10
30164064 TATATTCCAA
30164074 CACATATCAAT
1 CACATAT-AAT
30164085 CACATATAAT
1 CACATATAAT
30164095 CACATATAAT
1 CACATATAAT
* *
30164105 TACATATAAC
1 CACATATAAT
30164115 CACAT
1 CACAT
30164120 TTAGTCACAG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
10 25 0.78
11 7 0.22
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (10 bp):
CACATATAAT
Found at i:30166443 original size:70 final size:71
Alignment explanation
Indices: 30166360--30166500 Score: 266
Period size: 70 Copynumber: 2.0 Consensus size: 71
30166350 TTGTTTGTAG
*
30166360 GGGAAAGCTGTAAATGGTGGTTTTTATTGGTGTTCAACTTTGGCTATTGCATTTAAGTTGCTTT-
1 GGGAAAGCTGTAAATGGTGGTTATTATTGGTGTTCAACTTTGGCTATTGCATTTAAGTTGCTTTG
30166424 TTTTTT
66 TTTTTT
30166430 GGGAAAGCTGTAAATGGTGGTTATTATTGGTGTTCAACTTTGGCTATTGCATTTAAGTTGCTTTG
1 GGGAAAGCTGTAAATGGTGGTTATTATTGGTGTTCAACTTTGGCTATTGCATTTAAGTTGCTTTG
30166495 TTTTTT
66 TTTTTT
30166501 TGCCCTGTAT
Statistics
Matches: 69, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
70 63 0.91
71 6 0.09
ACGTcount: A:0.19, C:0.09, G:0.25, T:0.48
Consensus pattern (71 bp):
GGGAAAGCTGTAAATGGTGGTTATTATTGGTGTTCAACTTTGGCTATTGCATTTAAGTTGCTTTG
TTTTTT
Found at i:30168671 original size:9 final size:9
Alignment explanation
Indices: 30168659--30168736 Score: 79
Period size: 9 Copynumber: 8.7 Consensus size: 9
30168649 TTCAATTCAA
*
30168659 TTAATTCCG
1 TTAATTCGG
30168668 TTAATTCTGG
1 TTAATTC-GG
*
30168678 -TAATTCAG
1 TTAATTCGG
30168686 TTAATTCGG
1 TTAATTCGG
* * *
30168695 ATAATCCAG
1 TTAATTCGG
30168704 TTAATTCGG
1 TTAATTCGG
30168713 TTAATTCAGG
1 TTAATTC-GG
30168723 -TAATTCGG
1 TTAATTCGG
30168731 TTAATT
1 TTAATT
30168737 TTTAACCAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
8 3 0.05
9 50 0.89
10 3 0.05
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.42
Consensus pattern (9 bp):
TTAATTCGG
Found at i:30168707 original size:36 final size:36
Alignment explanation
Indices: 30168667--30168735 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
30168657 AATTAATTCC
*
30168667 GTTAATTCTGG-TAATTCAGTTAATTCGGATAATCCA
1 GTTAATTC-GGTTAATTCAGGTAATTCGGATAATCCA
*
30168703 GTTAATTCGGTTAATTCAGGTAATTCGGTTAAT
1 GTTAATTCGGTTAATTCAGGTAATTCGGATAAT
30168736 TTTTAACCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 2 0.07
36 28 0.93
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.41
Consensus pattern (36 bp):
GTTAATTCGGTTAATTCAGGTAATTCGGATAATCCA
Found at i:30179443 original size:55 final size:56
Alignment explanation
Indices: 30179351--30179502 Score: 193
Period size: 55 Copynumber: 2.7 Consensus size: 56
30179341 TTATTAAGTC
* * *
30179351 CGCACACTCAGTGCTATATAATC-AACTCGCACACTTAGTGCTACGTAATCAA-AT
1 CGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTACATAATCAAGAT
* *
30179405 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTACATAATCAAGAT
* * *
30179461 CGCACACTTAGTGCTGTACA-ATTTAAACCCGCACACTTAGTG
1 CGCACACTTAGTGC--TACATAATCAAACTCGCACACTTAGTG
30179503 TCAATCTCAT
Statistics
Matches: 86, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
54 20 0.23
55 28 0.33
56 15 0.17
57 19 0.22
58 4 0.05
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.26
Consensus pattern (56 bp):
CGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTACATAATCAAGAT
Found at i:30179444 original size:28 final size:28
Alignment explanation
Indices: 30179351--30179502 Score: 193
Period size: 27 Copynumber: 5.5 Consensus size: 28
30179341 TTATTAAGTC
* *
30179351 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
30179378 CGCACACTTAGTGCTACGTAATCAAA-T
1 CGCACACTTAGTGCTACATAATCAAACT
*
30179405 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
30179433 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAACT
* * *
30179461 CGCACACTTAGTGCTGTACA-ATTTAAACC
1 CGCACACTTAGTGC--TACATAATCAAACT
30179490 CGCACACTTAGTG
1 CGCACACTTAGTG
30179503 TCAATCTCAT
Statistics
Matches: 110, Mismatches: 11, Indels: 6
0.87 0.09 0.05
Matches are distributed among these distances:
27 45 0.41
28 43 0.39
29 18 0.16
30 4 0.04
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAATCAAACT
Found at i:30181293 original size:15 final size:15
Alignment explanation
Indices: 30181273--30181303 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
30181263 AAGTTTAATG
30181273 AAGAATTTAACTCAA
1 AAGAATTTAACTCAA
30181288 AAGAATTTAACTCAA
1 AAGAATTTAACTCAA
30181303 A
1 A
30181304 CTAGAACTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.13, G:0.06, T:0.26
Consensus pattern (15 bp):
AAGAATTTAACTCAA
Found at i:30194095 original size:18 final size:19
Alignment explanation
Indices: 30194059--30194097 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
30194049 CCAAAATTTT
*
30194059 ATTTTAATATTTTTTATAC
1 ATTTTAATATTTATTATAC
30194078 ATTTTAAT-TTTATTATAC
1 ATTTTAATATTTATTATAC
30194096 AT
1 AT
30194098 GTTTTATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTTTAATATTTATTATAC
Found at i:30198655 original size:103 final size:104
Alignment explanation
Indices: 30198449--30198645 Score: 299
Period size: 104 Copynumber: 1.9 Consensus size: 104
30198439 GTGCTAGTGC
* *
30198449 AGTGTTTACACCACGTTATAATTTAGGGGATGTAGGACTTAGATTAAGGGCTAGTTAGTAATTCT
1 AGTGCTTACACCACGTTATAATTTAGGGGATGGAGGACTTAGATTAAGGGCTAGTTAGTAATTCT
30198514 TTTGATAAGTGATTTTGAGAAGAATGTTTCTTAAAAGTT
66 TTTGATAAGTGATTTTGAGAAGAATGTTTCTTAAAAGTT
* * * * *
30198553 AGTGCTTACACCACTTTATAATTTAGTGGATGGATGACTTAGATTAA-GGTTAGTTAG-CATTGC
1 AGTGCTTACACCACGTTATAATTTAGGGGATGGAGGACTTAGATTAAGGGCTAGTTAGTAATT-C
*
30198616 TTTTGATAGGTGATTTTGAGAAGAATGTTT
65 TTTTGATAAGTGATTTTGAGAAGAATGTTT
30198646 TTGTAAAGTT
Statistics
Matches: 84, Mismatches: 8, Indels: 3
0.88 0.08 0.03
Matches are distributed among these distances:
102 3 0.04
103 39 0.46
104 42 0.50
ACGTcount: A:0.29, C:0.08, G:0.23, T:0.39
Consensus pattern (104 bp):
AGTGCTTACACCACGTTATAATTTAGGGGATGGAGGACTTAGATTAAGGGCTAGTTAGTAATTCT
TTTGATAAGTGATTTTGAGAAGAATGTTTCTTAAAAGTT
Found at i:30199606 original size:22 final size:22
Alignment explanation
Indices: 30199581--30199624 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
30199571 AAATTGTAAA
30199581 GATGTGAATAGTTTTAAGACTC
1 GATGTGAATAGTTTTAAGACTC
30199603 GATGTGAATAGTTTTAAGACTC
1 GATGTGAATAGTTTTAAGACTC
30199625 AAGTATAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.09, G:0.23, T:0.36
Consensus pattern (22 bp):
GATGTGAATAGTTTTAAGACTC
Found at i:30199932 original size:14 final size:11
Alignment explanation
Indices: 30199900--30199931 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
30199890 GTGCTAGCTT
30199900 TTATTATTATG
1 TTATTATTATG
30199911 TTATTATTATG
1 TTATTATTATG
30199922 TTATTATTAT
1 TTATTATTAT
30199932 TTGAATATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (11 bp):
TTATTATTATG
Found at i:30202514 original size:13 final size:13
Alignment explanation
Indices: 30202496--30202547 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
30202486 TGGCAGCTAG
*
30202496 GAAAAATAGAGAA
1 GAAAAATAAAGAA
30202509 GAAAAATAAAGAA
1 GAAAAATAAAGAA
* * *
30202522 TAAATAGAAAGAA
1 GAAAAATAAAGAA
30202535 CGAAAAA-AAAGAA
1 -GAAAAATAAAGAA
30202548 ACGTGAATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
13 28 0.88
14 4 0.12
ACGTcount: A:0.73, C:0.02, G:0.17, T:0.08
Consensus pattern (13 bp):
GAAAAATAAAGAA
Found at i:30209814 original size:27 final size:27
Alignment explanation
Indices: 30209784--30209961 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 27
30209774 ATATTGAGTC
* *
30209784 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
30209811 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
30209838 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
30209866 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
30209893 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * * *
30209920 AGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
30209947 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
30209962 GTACAATTTA
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 103 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:30218567 original size:190 final size:190
Alignment explanation
Indices: 30218240--30218611 Score: 568
Period size: 190 Copynumber: 2.0 Consensus size: 190
30218230 CTATACTTGC
* *
30218240 CATTATATCAAAAGTTATTTTACTAATTATACCAAGGTGAGCTATAGGATAGTGTGATCTTGCTC
1 CATTATACCAAAAGTAATTTTACTAATTATACCAAGGTGAGCTATAGGATAGTGTGATCTTGCTC
* * *
30218305 CGAGCCGCTTCCAACCTTTACAAGCTTCCGAGTACTATAAAACAGAGGAAAGAAAAAACGAGCAA
66 CAACCCGCTTCCAACCTTTACAAGCTTCCGAGTACTATAAAACAAAGGAAAGAAAAAACGAGCAA
*
30218370 ACATTTAATGCTTAGTGAGTTCGTATAACAG-AAATTAACTTACCATTCATATCGAGTAAG
131 ACATTTAATGCTTAGTAAGTTCGTAT-ACAGAAAATTAACTTACCATTCATATCGAGTAAG
30218430 CATTATACCAAAAGTAATTTTACTAATTATACCAAGGTGAGCTGA-AGGATAGTGTGATCTTGCT
1 CATTATACCAAAAGTAATTTTACTAATTATACCAAGGTGAGCT-ATAGGATAGTGTGATCTTGCT
* * * * ** *
30218494 CCAACCCGCTTCTAACCTTTACGAGCTTCCGAGTATTATAAAATAAAGGAAAGAAAAATTGAGTA
65 CCAACCCGCTTCCAACCTTTACAAGCTTCCGAGTACTATAAAACAAAGGAAAGAAAAAACGAGCA
* **
30218559 AGCATTTAATGCTTAGTAAGTTCGTATATTGAAAATTAACTTACCATTCATAT
130 AACATTTAATGCTTAGTAAGTTCGTATACAGAAAATTAACTTACCATTCATAT
30218612 TCATCTACAA
Statistics
Matches: 164, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
189 2 0.01
190 161 0.98
191 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (190 bp):
CATTATACCAAAAGTAATTTTACTAATTATACCAAGGTGAGCTATAGGATAGTGTGATCTTGCTC
CAACCCGCTTCCAACCTTTACAAGCTTCCGAGTACTATAAAACAAAGGAAAGAAAAAACGAGCAA
ACATTTAATGCTTAGTAAGTTCGTATACAGAAAATTAACTTACCATTCATATCGAGTAAG
Found at i:30242735 original size:42 final size:42
Alignment explanation
Indices: 30242682--30243582 Score: 1497
Period size: 42 Copynumber: 20.9 Consensus size: 42
30242672 AATTCTAAAT
30242682 TGTG-ATAAGGCCTAATGGCCGATGTGATGAATGTGAATATA
1 TGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAATATA
30242723 TGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAATATA
1 TGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAATATA
30242765 TGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAATATA
1 TGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAATATA
30242807 TGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAATATA
1 TGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAATATA
30242849 TGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAATATA
1 TGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAATATA
30242891 TGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAATATA
1 TGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAATATA
30242933 TGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAATATA
1 TGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAATATA
30242975 TGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAATATA
1 TGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAATATA
30243017 TGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAATATA
1 TGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAATATA
30243059 TGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAATATA
1 TGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAATATA
30243101 TGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAATATA
1 TGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAATATA
30243143 TGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAATATA
1 TGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAATATA
30243185 TGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAATATA
1 TGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAATATA
30243227 TGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAATATA
1 TGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAATATA
30243269 TGGTG-ATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 T-GTGAATAAGGCCTAATGGCCGATGTGATGAATGTG--A----ATATA
30243317 TGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAATATA
1 TGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAATATA
30243359 TGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGAATAAGGCCTAATGGCCGATGTGATGAATGTG--A----ATATA
*
30243407 TGTG-ATAAGGCCTAATGGCCGAGGTGATGAATGTGAAAGTGTATATA
1 TGTGAATAAGGCCTAATGGCCGATGTGATGAATGTG--A----ATATA
30243454 TGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAATAATA
1 TGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAAT-ATA
30243497 TGTG-ATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TGTGAATAAGGCCTAATGGCCGATGTGATGAA--T----GTG-A-ATATA
*
30243546 TGTG-ATAAGGCCTAATGGCCGATGTGATAAATGTGAA
1 TGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAA
30243583 AGTGTATATA
Statistics
Matches: 832, Mismatches: 3, Indels: 50
0.94 0.00 0.06
Matches are distributed among these distances:
41 5 0.01
42 644 0.77
43 13 0.02
44 3 0.00
46 2 0.00
47 50 0.06
48 79 0.09
49 34 0.04
50 2 0.00
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (42 bp):
TGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAATATA
Found at i:30243824 original size:38 final size:37
Alignment explanation
Indices: 30243767--30243845 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 37
30243757 CTGAGCTCTA
* *
30243767 AAGACCCGATGACTACGTGTGG-GAATTTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-A-TTATGTCCGGGT
*
30243805 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
30243842 AAGA
1 AAGA
30243846 TTTCGTAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
37 15 0.41
38 21 0.57
39 1 0.03
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:30247386 original size:17 final size:16
Alignment explanation
Indices: 30247359--30247390 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
30247349 TGATAGGTCT
30247359 CTGATGAGCTTCCAAA
1 CTGATGAGCTTCCAAA
30247375 CTGATCGAGCTTCCAA
1 CTGAT-GAGCTTCCAA
30247391 TAATCTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (16 bp):
CTGATGAGCTTCCAAA
Found at i:30247908 original size:11 final size:11
Alignment explanation
Indices: 30247892--30247922 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
30247882 TCAACATCCA
30247892 TCATTTGCATG
1 TCATTTGCATG
30247903 TCATTTGCATG
1 TCATTTGCATG
30247914 TCATTTGCA
1 TCATTTGCA
30247923 AGACCAGCAC
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:0.19, C:0.19, G:0.16, T:0.45
Consensus pattern (11 bp):
TCATTTGCATG
Found at i:30255194 original size:14 final size:14
Alignment explanation
Indices: 30255175--30255205 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
30255165 TGGTCAAAAC
30255175 ATCAAAAACTACTG
1 ATCAAAAACTACTG
30255189 ATCAAAAACTACTG
1 ATCAAAAACTACTG
30255203 ATC
1 ATC
30255206 TTCGACGAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.48, C:0.23, G:0.06, T:0.23
Consensus pattern (14 bp):
ATCAAAAACTACTG
Found at i:30256083 original size:25 final size:26
Alignment explanation
Indices: 30256042--30256092 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
30256032 AAATATATAA
*
30256042 ATTCAATTCATTAAATACTTC-TATT
1 ATTCAATTCAGTAAATACTTCATATT
* *
30256067 ATTCAATTCAGTCAATATTTCATATT
1 ATTCAATTCAGTAAATACTTCATATT
30256093 TTTGCAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.35, C:0.16, G:0.02, T:0.47
Consensus pattern (26 bp):
ATTCAATTCAGTAAATACTTCATATT
Found at i:30258547 original size:19 final size:20
Alignment explanation
Indices: 30258510--30258552 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
30258500 ATATATGAAA
30258510 ATTTAGAATTTTTATAAA-T
1 ATTTAGAATTTTTATAAATT
30258529 ATTTAGAATTTTTGA-AAATT
1 ATTTAGAATTTTT-ATAAATT
30258549 ATTT
1 ATTT
30258553 TAATTATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (20 bp):
ATTTAGAATTTTTATAAATT
Found at i:30259722 original size:19 final size:18
Alignment explanation
Indices: 30259698--30259734 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
30259688 AATCAGTCGG
30259698 ATTAAAAAATTATTAAAAA
1 ATTAAAAAATT-TTAAAAA
30259717 ATTAAAAAATTTTAAAAA
1 ATTAAAAAATTTTAAAAA
30259735 TCCTGATTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
ATTAAAAAATTTTAAAAA
Found at i:30271889 original size:27 final size:27
Alignment explanation
Indices: 30271859--30271916 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
30271849 AGTAAACACA
*
30271859 GGGTAGTCCATTAGGAAAATAAACATG
1 GGGTAATCCATTAGGAAAATAAACATG
* * * *
30271886 GGGTAATTCATTGGGACAATAATCATG
1 GGGTAATCCATTAGGAAAATAAACATG
30271913 GGGT
1 GGGT
30271917 TACTTTGGGG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.34, C:0.10, G:0.29, T:0.26
Consensus pattern (27 bp):
GGGTAATCCATTAGGAAAATAAACATG
Found at i:30281420 original size:13 final size:13
Alignment explanation
Indices: 30281404--30281435 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
30281394 ACACATATTT
30281404 AAAACATAACTTG
1 AAAACATAACTTG
*
30281417 AAAACATATCTTG
1 AAAACATAACTTG
30281430 AAAACA
1 AAAACA
30281436 GAGTATCAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.16, G:0.06, T:0.22
Consensus pattern (13 bp):
AAAACATAACTTG
Found at i:30283813 original size:50 final size:52
Alignment explanation
Indices: 30283688--30283818 Score: 151
Period size: 50 Copynumber: 2.6 Consensus size: 52
30283678 TGAACAAAAG
* * *
30283688 AGTTACTTAATGCA-AGACTTAATTTAATGATGCAGACTTAAACTAACATGGG
1 AGTTACATAATGCATA-ACTTTATTTAATGATGCAGACTTAAACTAACATGGA
** * * *
30283740 AGTTACATAATGCATGTCATTATTT-ATGATGCATACTT-AACTAGCATGGA
1 AGTTACATAATGCATAACTTTATTTAATGATGCAGACTTAAACTAACATGGA
*
30283790 AGTTACATAATGCATAACTTTATTAAATG
1 AGTTACATAATGCATAACTTTATTTAATG
30283819 TAAAACACAC
Statistics
Matches: 65, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
50 31 0.48
51 15 0.23
52 19 0.29
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.34
Consensus pattern (52 bp):
AGTTACATAATGCATAACTTTATTTAATGATGCAGACTTAAACTAACATGGA
Found at i:30287927 original size:20 final size:21
Alignment explanation
Indices: 30287883--30287952 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 21
30287873 AAATGATAAA
* * *
30287883 AATAAAAATCAATGAAAGTTT
1 AATAAAAATTATTTAAAGTTT
*
30287904 --TAAAAATTA-TTAAATTTT
1 AATAAAAATTATTTAAAGTTT
30287922 AATAAAAA-TATTTAAAGTTT
1 AATAAAAATTATTTAAAGTTT
*
30287942 ATTAAAAATTA
1 AATAAAAATTA
30287953 GAAAAAATTA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
18 7 0.17
19 10 0.25
20 21 0.52
21 2 0.05
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.39
Consensus pattern (21 bp):
AATAAAAATTATTTAAAGTTT
Found at i:30287967 original size:9 final size:9
Alignment explanation
Indices: 30287944--30288090 Score: 59
Period size: 9 Copynumber: 15.1 Consensus size: 9
30287934 TAAAGTTTAT
30287944 TAAAAATTA
1 TAAAAATTA
*
30287953 GAAAAAATTA
1 -TAAAAATTA
30287963 TAAAAATCGTA
1 TAAAAAT--TA
*
30287974 AAAAAATTA
1 TAAAAATTA
30287983 T-AAAATATA
1 TAAAAAT-TA
*
30287992 TAGAAATATA
1 TAAAAAT-TA
*
30288002 GAAATAAATTA
1 -TAA-AAATTA
*
30288013 T-AAAATTT
1 TAAAAATTA
*
30288021 TATATAATCGTA
1 TA-AAAAT--TA
30288033 -AGAAAATTA
1 TA-AAAATTA
*
30288042 TAAAAAATA
1 TAAAAATTA
*
30288051 TAAAGAAATA
1 TAAA-AATTA
30288061 T-AAAATTCA
1 TAAAAATT-A
30288070 TAAAAAAATTA
1 T--AAAAATTA
30288081 TAAAAATTA
1 TAAAAATTA
30288090 T
1 T
30288091 GGTACCAAAA
Statistics
Matches: 106, Mismatches: 15, Indels: 33
0.69 0.10 0.21
Matches are distributed among these distances:
8 14 0.13
9 37 0.35
10 26 0.25
11 18 0.17
12 11 0.10
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (9 bp):
TAAAAATTA
Found at i:30287979 original size:30 final size:29
Alignment explanation
Indices: 30287945--30288054 Score: 98
Period size: 30 Copynumber: 3.7 Consensus size: 29
30287935 AAAGTTTATT
*
30287945 AAAAATTAGAAAAAATTATAAAAATCGTAA
1 AAAAATTATAAAAAA-TATAAAAATCGTAA
* *
30287975 AAAAATTATAAAATATATAGAAATATAG-AA
1 AAAAATTATAAAAAATATA-AAA-ATCGTAA
* * * *
30288005 ATAAATTAT-AAAATTTTATATAATCGTAA
1 AAAAATTATAAAAAATATA-AAAATCGTAA
*
30288034 GAAAATTATAAAAAATATAAA
1 AAAAATTATAAAAAATATAAA
30288055 GAAATATAAA
Statistics
Matches: 61, Mismatches: 15, Indels: 9
0.72 0.18 0.11
Matches are distributed among these distances:
28 3 0.05
29 22 0.36
30 33 0.54
31 3 0.05
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (29 bp):
AAAAATTATAAAAAATATAAAAATCGTAA
Found at i:30287987 original size:10 final size:10
Alignment explanation
Indices: 30287940--30288090 Score: 63
Period size: 10 Copynumber: 15.4 Consensus size: 10
30287930 TATTTAAAGT
*
30287940 TTATTAAAAA
1 TTATAAAAAA
*
30287950 TTAGAAAAAA
1 TTATAAAAAA
30287960 TTAT-AAAAA
1 TTATAAAAAA
30287969 TCGTA-AAAAAA
1 T--TATAAAAAA
*
30287980 TTATAAAATA
1 TTATAAAAAA
*
30287990 -TAT-AGAAA
1 TTATAAAAAA
*
30287998 TATAGAAATAAA
1 T-TATAAA-AAA
30288010 TTAT--AAAA
1 TTATAAAAAA
* * *
30288018 TTTTATATAA
1 TTATAAAAAA
**
30288028 TCGTAAGAAAA
1 TTATAA-AAAA
30288039 TTATAAAAAA
1 TTATAAAAAA
30288049 -TATAAAGAAA
1 TTATAAA-AAA
30288059 -TAT--AAAA
1 TTATAAAAAA
30288066 TTCATAAAAAAA
1 TT-AT-AAAAAA
30288078 TTAT-AAAAA
1 TTATAAAAAA
30288087 TTAT
1 TTAT
30288091 GGTACCAAAA
Statistics
Matches: 107, Mismatches: 17, Indels: 35
0.67 0.11 0.22
Matches are distributed among these distances:
7 3 0.03
8 11 0.10
9 29 0.27
10 34 0.32
11 20 0.19
12 10 0.09
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (10 bp):
TTATAAAAAA
Found at i:30288084 original size:20 final size:19
Alignment explanation
Indices: 30287954--30288085 Score: 74
Period size: 20 Copynumber: 6.7 Consensus size: 19
30287944 TAAAAATTAG
*
30287954 AAAAAATTATAAAAATCGTA
1 AAAAAATTAT-AAAATCATA
30287974 AAAAAATTATAAAAT-ATA
1 AAAAAATTATAAAATCATA
* * *
30287992 TAGAAA-TATAGAAATAAATTA
1 AAAAAATTATA-AAAT-CA-TA
** * *
30288013 TAAAATTTTATATAATCGTA
1 -AAAAAATTATAAAATCATA
*
30288033 AGAAAATTATAAAAAAT-ATA
1 AAAAAATTAT--AAAATCATA
*
30288053 AAGAAA-TATAAAATTCATA
1 AAAAAATTATAAAA-TCATA
30288072 AAAAAATTATAAAA
1 AAAAAATTATAAAA
30288086 ATTATGGTAC
Statistics
Matches: 83, Mismatches: 18, Indels: 22
0.67 0.15 0.18
Matches are distributed among these distances:
17 8 0.10
18 11 0.13
19 23 0.28
20 26 0.31
21 6 0.07
22 5 0.06
23 4 0.05
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (19 bp):
AAAAAATTATAAAATCATA
Found at i:30292393 original size:16 final size:17
Alignment explanation
Indices: 30292361--30292394 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
30292351 GGGGATAGCG
30292361 TTTGTTTGATATTTATT
1 TTTGTTTGATATTTATT
*
30292378 TTTGTTTG-TTTTTATT
1 TTTGTTTGATATTTATT
30292394 T
1 T
30292395 CATAATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (17 bp):
TTTGTTTGATATTTATT
Found at i:30303516 original size:104 final size:104
Alignment explanation
Indices: 30303326--30303546 Score: 307
Period size: 104 Copynumber: 2.1 Consensus size: 104
30303316 GTTAGTTTCC
* * * *
30303326 ATTATTAAGGCTCGCTGATTTAAGATAGCAACCTTCGATTATTTGAGTTAGCTGATTTAATACCC
1 ATTATTAAGGCTCGCTAATTTAAGATAGCAACCTCCGATTATTTGAGTTAGCTGATCTAAGACCC
* * *
30303391 CAACTCCTAACAGCTCACTGACGTACGTTCACAACGAAT
66 CAACTCCTAACAACTCACTGACCTACATTCACAACGAAT
* * * *
30303430 ATTACTAAGGCTCGCTAATTTAAGATCGCAACCTCCGATTATTTGAGTTAGCTGATCTAAGATCG
1 ATTATTAAGGCTCGCTAATTTAAGATAGCAACCTCCGATTATTTGAGTTAGCTGATCTAAGACCC
* * *
30303495 CAACTCCTAACAACTCGCTGACCTACATTCACAGCTAAT
66 CAACTCCTAACAACTCACTGACCTACATTCACAACGAAT
*
30303534 GTTATTAAGGCTC
1 ATTATTAAGGCTC
30303547 ATTGACCTAC
Statistics
Matches: 101, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
104 101 1.00
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.30
Consensus pattern (104 bp):
ATTATTAAGGCTCGCTAATTTAAGATAGCAACCTCCGATTATTTGAGTTAGCTGATCTAAGACCC
CAACTCCTAACAACTCACTGACCTACATTCACAACGAAT
Found at i:30303560 original size:36 final size:36
Alignment explanation
Indices: 30303513--30303587 Score: 105
Period size: 36 Copynumber: 2.1 Consensus size: 36
30303503 AACAACTCGC
* *
30303513 TGACCTACATTCACAGCTAATGTTATTAAGGCTCAT
1 TGACCTACATTCACAACTAATGTTACTAAGGCTCAT
* * *
30303549 TGACCTACATTCACAACTGATTTTACTAAGGCTCGT
1 TGACCTACATTCACAACTAATGTTACTAAGGCTCAT
30303585 TGA
1 TGA
30303588 TTTAAGATCG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (36 bp):
TGACCTACATTCACAACTAATGTTACTAAGGCTCAT
Found at i:30306893 original size:21 final size:20
Alignment explanation
Indices: 30306869--30306908 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
30306859 AAAGTATCAA
30306869 TAATATTATATACTTTTGAAG
1 TAATATTATA-ACTTTTGAAG
* *
30306890 TAATTTTATAATTTTTGAA
1 TAATATTATAACTTTTGAA
30306909 AATTTTATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.53
Consensus pattern (20 bp):
TAATATTATAACTTTTGAAG
Found at i:30306975 original size:20 final size:21
Alignment explanation
Indices: 30306950--30306995 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
30306940 ATTTTAATAA
*
30306950 ATTTTTAATTTTTATATT-TAT
1 ATTTTAAATTTTTA-ATTATAT
30306971 ATTTTGAAATTTTTAATTATAT
1 ATTTT-AAATTTTTAATTATAT
30306993 ATT
1 ATT
30306996 GATAAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (21 bp):
ATTTTAAATTTTTAATTATAT
Found at i:30306997 original size:20 final size:22
Alignment explanation
Indices: 30306956--30306997 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
30306946 ATAAATTTTT
*
30306956 AATTTTTATATTTATATTTTGA
1 AATTTTTATATTTATATATTGA
30306978 AATTTTTA-A-TTATATATTGA
1 AATTTTTATATTTATATATTGA
30306998 TAAATTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 1 0.05
22 8 0.42
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (22 bp):
AATTTTTATATTTATATATTGA
Found at i:30307002 original size:22 final size:21
Alignment explanation
Indices: 30306956--30307013 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 21
30306946 ATAAATTTTT
*
30306956 AATTTTTATATTTATATTTTGA
1 AATTTTTA-ATTTATATTATGA
30306978 AATTTTTAATTATATATTGAT-A
1 AATTTTTAATT-TATATT-ATGA
30307000 AATTATTTGAATTT
1 AATT-TTT-AATTT
30307014 TTAGAATCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
21 3 0.10
22 19 0.61
23 5 0.16
24 4 0.13
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (21 bp):
AATTTTTAATTTATATTATGA
Found at i:30311343 original size:44 final size:43
Alignment explanation
Indices: 30311283--30311489 Score: 177
Period size: 43 Copynumber: 4.8 Consensus size: 43
30311273 GCGTCGCTAA
* * *
30311283 CTTTAGTGGCGTTTTTTCCCAAAAACGCCGCTATAGACCATGAC
1 CTTTAGCGGCGCTTTTT-CCAAAAACGCCGCTAAAGACCATGAC
* *
30311327 CTTTAGCGGTGCTTTTTCCGAAAACGCCGCTAAAGACCATGAC
1 CTTTAGCGGCGCTTTTTCCAAAAACGCCGCTAAAGACCATGAC
* * * * * * *
30311370 TTTTAGCGACGCTTTTTTCACAAATGCCGCTAAAGATCATGAAG
1 CTTTAGCGGCGCTTTTTCCAAAAACGCCGCTAAAGACCATG-AC
* * * *** *
30311414 CTTTAGCGGCGCTGTTAT-CACAAACGCCACTAAAG-GTTTGTC
1 CTTTAGCGGCGCT-TTTTCCAAAAACGCCGCTAAAGACCATGAC
*
30311456 CTTTAGCGGCGC-TTCTCACAAAAACGCCGCTAAA
1 CTTTAGCGGCGCTTTTTC-CAAAAACGCCGCTAAA
30311490 AATATAACCT
Statistics
Matches: 132, Mismatches: 27, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
40 3 0.02
42 26 0.20
43 59 0.45
44 41 0.31
45 3 0.02
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.28
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTTCCAAAAACGCCGCTAAAGACCATGAC
Found at i:30314208 original size:21 final size:20
Alignment explanation
Indices: 30314166--30314210 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
30314156 TCTTGGATGT
*
30314166 GGGAAATTAGGGATTTTAGG
1 GGGAAATTAGGGATTTCAGG
* *
30314186 GGGAAAGTTGGGGATTTCGGG
1 GGGAAA-TTAGGGATTTCAGG
30314207 GGGA
1 GGGA
30314211 GGGGGTGGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.24, C:0.02, G:0.49, T:0.24
Consensus pattern (20 bp):
GGGAAATTAGGGATTTCAGG
Found at i:30314577 original size:143 final size:142
Alignment explanation
Indices: 30314220--30314746 Score: 697
Period size: 143 Copynumber: 3.7 Consensus size: 142
30314210 AGGGGGTGGG
* *
30314220 GAATTTAAAAAAATGGTGCTATTTTTTTAAAAGTAAATTTTATTTTGTAGCGTTTTTTTATAAAA
1 GAATTTAAAAAAATGGCGCTATTTTTTTAAAAGTAAATTTTATTTTGTGGCG-TTTTTTATAAAA
** * * * *
30314285 ACGCCGCTATTTTTTATCTATTGCTGTGTTTTTTATACAAATGCCGTAAAAAATTATTTTATTTG
65 ACGCCGCTATTGCTTATCTATTGCGGCGTTTTTTATACAAACGCCGCAAAAAATTATTTTATTTG
*
30314350 GAAT-AAACGAGA
130 GAATAAAACGAGT
*** *
30314362 GAATTTAAAAAAATGATTCTATTTTTTTAAAAGTAAATTTTATTTTGTGGCATTTTTTATAAAAA
1 GAATTTAAAAAAATGGCGCTATTTTTTTAAAAGTAAATTTTATTTTGTGGCGTTTTTTATAAAAA
* *
30314427 CGCCGCTATTGCTTATCTATTGTGGCGTTTTTTACACAAACGCCGCAAAAAATTATTTTATTTGG
66 CGCCGCTATTGCTTATCTATTGCGGCGTTTTTTATACAAACGCCGCAAAAAATTATTTTATTTGG
30314492 AATAAAACGAGT
131 AATAAAACGAGT
30314504 GAATTTAAAAAAAATGGCGCTATTTTTTTAAAAGTAAATTTTATTTTGTGGCGTTTTTTATAAAA
1 GAATTT-AAAAAAATGGCGCTATTTTTTTAAAAGTAAATTTTATTTTGTGGCGTTTTTTATAAAA
* *
30314569 ACGCCGCTATTGCTTATCTATTGCGGCGTTTTTTTTATAAAAACGCGGCAAAAAATTATTTTATT
65 ACGCCGCTATTGCTTATCTATTGCGGCG--TTTTTTATACAAACGCCGCAAAAAATTATTTTATT
*
30314634 TGGAATAAAACGACACT
128 TGGAATAAAACG--AGT
** * *
30314651 GTTTTGCTATATAAAATGGCGCTA--TTTTTAAAA-TAAA-ATTATTTTTGTGGCGTTTTTTA-A
1 GAATT--TA-AAAAAATGGCGCTATTTTTTTAAAAGTAAATTTTA-TTTTGTGGCGTTTTTTATA
* * *
30314711 AAAACGTCGCTATTGCTTACCTTTTGCGGCGTTTTT
62 AAAACGCCGCTATTGCTTATCTATTGCGGCGTTTTT
30314747 CATTTGGAAT
Statistics
Matches: 346, Mismatches: 29, Indels: 19
0.88 0.07 0.05
Matches are distributed among these distances:
141 73 0.21
142 61 0.18
143 86 0.25
145 76 0.22
146 21 0.06
147 14 0.04
148 1 0.00
149 14 0.04
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.42
Consensus pattern (142 bp):
GAATTTAAAAAAATGGCGCTATTTTTTTAAAAGTAAATTTTATTTTGTGGCGTTTTTTATAAAAA
CGCCGCTATTGCTTATCTATTGCGGCGTTTTTTATACAAACGCCGCAAAAAATTATTTTATTTGG
AATAAAACGAGT
Found at i:30315171 original size:46 final size:46
Alignment explanation
Indices: 30315080--30315580 Score: 206
Period size: 46 Copynumber: 11.2 Consensus size: 46
30315070 CCACTGTAGT
* * ** * * *
30315080 CAGGGAGGTAAGATCTGCCATCTTTGATCTGCTT-CGCTGCCAAATA
1 CAGGGAGGCAAGATCTGCAATCTTCAATCT-ATTCCACTGCTAAATA
*
30315126 CAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCTAAATA
1 CAGGGAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCTAAATA
* ** * * * *
30315172 CAGGGA-G-ATAGAAT-TATC-GGCTTCTATGTACTCCACTG-T-AGT-
1 CAGGGAGGCA-AG-ATCT-GCAATCTTCAATCTATTCCACTGCTAAATA
* * * ** * * *
30315214 CAGGGAGGGAAAATCTGCCATCTTTGATCTGCTT-CGCTGCCAAATA
1 CAGGGAGGCAAGATCTGCAATCTTCAATCT-ATTCCACTGCTAAATA
*
30315260 CAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCTAAATA
1 CAGGGAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCTAAATA
* ** * * * *
30315306 CAGGGA-G-ATAGAAT-TATC-GGCTTCTATGTACTCCACTG-T-AGT-
1 CAGGGAGGCA-AG-ATCT-GCAATCTTCAATCTATTCCACTGCTAAATA
* * * ** * * *
30315348 CAGGGAGGGAAAATCTGCCATCTTTGATCTGCTT-CGCTGCCAAATA
1 CAGGGAGGCAAGATCTGCAATCTTCAATCT-ATTCCACTGCTAAATA
* *
30315394 CAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAATA
1 CAGGGAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCTAAATA
* ** * *
30315440 CAGGGA-G-ATAGAAT-TATC-GGCTTCAATGTATTCCACTG-T-AGT-
1 CAGGGAGGCA-AG-ATCT-GCAATCTTCAATCTATTCCACTGCTAAATA
* * * * ** * * *
30315482 CAGGGAGGTAAAACCTGCCATCTTTGATCTGCTT-CGCTGCCAAATA
1 CAGGGAGGCAAGATCTGCAATCTTCAATCT-ATTCCACTGCTAAATA
*
30315528 CAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCTAAATA
1 CAGGGAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCTAAATA
30315574 CAGGGAG
1 CAGGGAG
30315581 ATAGAATTAT
Statistics
Matches: 323, Mismatches: 95, Indels: 74
0.66 0.19 0.15
Matches are distributed among these distances:
42 26 0.08
43 45 0.14
44 12 0.04
45 73 0.23
46 167 0.52
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (46 bp):
CAGGGAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCTAAATA
Found at i:30315688 original size:134 final size:134
Alignment explanation
Indices: 30315004--30315677 Score: 1224
Period size: 134 Copynumber: 5.0 Consensus size: 134
30314994 AAAATCTGCC
*
30315004 ATCTGCAATCTTCAATCTATTCCACTGGC-AAATGCAGGGAGATAGAATTATCGGCTTCAATGTA
1 ATCTGCAATCTTCAATCTATTCCACT-GCTAAATACAGGGAGATAGAATTATCGGCTTCAATGTA
*
30315068 CTCCACTGTAGTCAGGGAGGTAAGATCTGCCATCTTTGATCTGCTTCGCTGCCAAATACAGGAAG
65 CTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGCTGCCAAATACAGGAAG
30315133 GCAAG
130 GCAAG
*
30315138 ATCTGCAATCTTCAATCTATTCCACTGCTAAATACAGGGAGATAGAATTATCGGCTTCTATGTAC
1 ATCTGCAATCTTCAATCTATTCCACTGCTAAATACAGGGAGATAGAATTATCGGCTTCAATGTAC
*
30315203 TCCACTGTAGTCAGGGAGGGAAAATCTGCCATCTTTGATCTGCTTCGCTGCCAAATACAGGAAGG
66 TCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGCTGCCAAATACAGGAAGG
30315268 CAAG
131 CAAG
*
30315272 ATCTGCAATCTTCAATCTATTCCACTGCTAAATACAGGGAGATAGAATTATCGGCTTCTATGTAC
1 ATCTGCAATCTTCAATCTATTCCACTGCTAAATACAGGGAGATAGAATTATCGGCTTCAATGTAC
*
30315337 TCCACTGTAGTCAGGGAGGGAAAATCTGCCATCTTTGATCTGCTTCGCTGCCAAATACAGGAAGG
66 TCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGCTGCCAAATACAGGAAGG
30315402 CAAG
131 CAAG
* *
30315406 ATCTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAATTATCGGCTTCAATGTAT
1 ATCTGCAATCTTCAATCTATTCCACTGCTAAATACAGGGAGATAGAATTATCGGCTTCAATGTAC
*
30315471 TCCACTGTAGTCAGGGAGGTAAAACCTGCCATCTTTGATCTGCTTCGCTGCCAAATACAGGAAGG
66 TCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGCTGCCAAATACAGGAAGG
30315536 CAAG
131 CAAG
*
30315540 ATCTGCAATCTTCAATCTATTCCACTGCTAAATACAGGGAGATAGAATTATCAGCTTCAATGTAC
1 ATCTGCAATCTTCAATCTATTCCACTGCTAAATACAGGGAGATAGAATTATCGGCTTCAATGTAC
* *
30315605 TCCACTGTAGTCAGGGAGGTAAAATCTTCTATCTTTGATCTGCTTCGCTGCCAAATACAGGAAGG
66 TCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGCTGCCAAATACAGGAAGG
30315670 CAAG
131 CAAG
30315674 ATCT
1 ATCT
30315678 ATTATCTTCA
Statistics
Matches: 524, Mismatches: 15, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
133 2 0.00
134 522 1.00
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.28
Consensus pattern (134 bp):
ATCTGCAATCTTCAATCTATTCCACTGCTAAATACAGGGAGATAGAATTATCGGCTTCAATGTAC
TCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGCTGCCAAATACAGGAAGG
CAAG
Found at i:30321058 original size:21 final size:21
Alignment explanation
Indices: 30321017--30321058 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
30321007 TCGGGTCACC
*
30321017 TAGAAATTTGGGTTGTTTTAA
1 TAGAAATTTGGGTTGTATTAA
*
30321038 TAGAACATTTTGGTT-TATTAA
1 TAGAA-ATTTGGGTTGTATTAA
30321059 AACAATGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.31, C:0.02, G:0.19, T:0.48
Consensus pattern (21 bp):
TAGAAATTTGGGTTGTATTAA
Found at i:30324064 original size:21 final size:21
Alignment explanation
Indices: 30324038--30324083 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
30324028 TCTTGGATGT
30324038 GGGAAA-TTAGGGATTTTAGGG
1 GGGAAAGTTAGGGA-TTTAGGG
* *
30324059 GGGAAAGTTGGGGATTTCGGG
1 GGGAAAGTTAGGGATTTAGGG
30324080 GGGA
1 GGGA
30324084 GGGGGGAGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.24, C:0.02, G:0.50, T:0.24
Consensus pattern (21 bp):
GGGAAAGTTAGGGATTTAGGG
Found at i:30325219 original size:21 final size:21
Alignment explanation
Indices: 30325178--30325220 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
30325168 GACCCCGAAT
*
30325178 CTCTAAACCCTAAATCACTAA
1 CTCTAAACCCCAAATCACTAA
*
30325199 CTCTTAACCCCAAACTC-CTAA
1 CTCTAAACCCCAAA-TCACTAA
30325220 C
1 C
30325221 CACTAACCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.37, C:0.40, G:0.00, T:0.23
Consensus pattern (21 bp):
CTCTAAACCCCAAATCACTAA
Found at i:30325295 original size:7 final size:7
Alignment explanation
Indices: 30325280--30325378 Score: 57
Period size: 7 Copynumber: 14.7 Consensus size: 7
30325270 ATCTAAATCA
*
30325280 TAAATCC
1 TAAACCC
30325287 TAAACCC
1 TAAACCC
30325294 T-AA--C
1 TAAACCC
*
30325298 TCAACCC
1 TAAACCC
30325305 TAAATCCC
1 TAAA-CCC
* **
30325313 TAATCTT
1 TAAACCC
30325320 TAAACCC
1 TAAACCC
30325327 TAAACCC
1 TAAACCC
*
30325334 TAAACTC
1 TAAACCC
*
30325341 TAAACTC
1 TAAACCC
30325348 T-AACCC
1 TAAACCC
30325354 --AACCC
1 TAAACCC
*
30325359 CAAATCCC
1 TAAA-CCC
*
30325367 TAACCCC
1 TAAACCC
30325374 TAAAC
1 TAAAC
30325379 ATTATTTAAT
Statistics
Matches: 72, Mismatches: 13, Indels: 14
0.73 0.13 0.14
Matches are distributed among these distances:
4 2 0.03
5 7 0.10
6 6 0.08
7 46 0.64
8 11 0.15
ACGTcount: A:0.39, C:0.39, G:0.00, T:0.21
Consensus pattern (7 bp):
TAAACCC
Found at i:30326367 original size:40 final size:41
Alignment explanation
Indices: 30326307--30326506 Score: 287
Period size: 41 Copynumber: 4.9 Consensus size: 41
30326297 TTTTATTATT
30326307 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGC
* *
30326348 ATTA-CGGCGCTTTTTCAAAAATGCCGCTAAAGGCCAGAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGC
* * **
30326388 ATTAGCGACACTTTTTCAAAAACGCCGCTAAAGGCTAGAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGC
*
30326429 ATTAGCGGCGCTTTTTCAAAAACGCCACTAAAGGCCCGAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGC
* * *
30326470 ACTAGTGGCGCTTTTTCAAAAAC-CTCGCTAAATGCCC
1 ATTAGCGGCGCTTTTTCAAAAACGC-CGCTAAAGGCCC
30326507 CCAAAACTCA
Statistics
Matches: 142, Mismatches: 15, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
40 39 0.27
41 103 0.73
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (41 bp):
ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGC
Found at i:30327021 original size:114 final size:114
Alignment explanation
Indices: 30326840--30327275 Score: 734
Period size: 114 Copynumber: 3.8 Consensus size: 114
30326830 CGCCGCAAAA
* * * * * * * *
30326840 TCTCCTATCCAAAACACAACG-TTTTCGTCTTTATGTATGCAAGAATTAGTGGCGCTTCAAAAAA
1 TCTCCTAACCAAAACGCATCGTTTTTAGTGTTGATGTATCCTAGAATTAGTGGCGCTTCAAAAAA
30326904 CACGCCGCTAAAGTGTCTTAGCGGTGTTTTACAACAACGCGTCATAATT
66 CACGCCGCTAAAGTGTCTTAGCGGTGTTTTACAACAACGCGTCATAATT
30326953 TCTCCTAACCAAAACGCATCGTTTTTAGTGTTGATGTATCCTAGAATTAGTGGCGCTTCAAAAAA
1 TCTCCTAACCAAAACGCATCGTTTTTAGTGTTGATGTATCCTAGAATTAGTGGCGCTTCAAAAAA
30327018 CACGCCGCTAAAGTGTCTTAGCGGTGTTTTACAACAACGCGTCATAATT
66 CACGCCGCTAAAGTGTCTTAGCGGTGTTTTACAACAACGCGTCATAATT
30327067 TCTCCTAACCAAAACGCATCGTTTTTAGTGTTGATGTATCCTAGAATTAGTGGCGCTTCAAAAAA
1 TCTCCTAACCAAAACGCATCGTTTTTAGTGTTGATGTATCCTAGAATTAGTGGCGCTTCAAAAAA
30327132 CACGCCGCTAAAGTGTCTTAGCGGTGTTTTACAACAACGCGTCATAATT
66 CACGCCGCTAAAGTGTCTTAGCGGTGTTTTACAACAACGCGTCATAATT
30327181 TCTCCTAACCAAAACGCATCGTTTTTAGTGTTGATGTATCCTAGAATTAGTGGCGCTTCTCAAAA
1 TCTCCTAACCAAAACGCATCGTTTTTAGTGTTGATGTATCCTAGAATTAGTGGCGC-T-TCAAAA
* * *
30327246 AACA--CCGCAAAAGCGTCTTAGCGGCGTTTT
64 AACACGCCGCTAAAGTGTCTTAGCGGTGTTTT
30327276 GTGATATGCA
Statistics
Matches: 309, Mismatches: 11, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
113 18 0.06
114 280 0.91
115 1 0.00
116 10 0.03
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (114 bp):
TCTCCTAACCAAAACGCATCGTTTTTAGTGTTGATGTATCCTAGAATTAGTGGCGCTTCAAAAAA
CACGCCGCTAAAGTGTCTTAGCGGTGTTTTACAACAACGCGTCATAATT
Found at i:30328004 original size:266 final size:266
Alignment explanation
Indices: 30327318--30328124 Score: 1294
Period size: 266 Copynumber: 3.1 Consensus size: 266
30327308 GCGTTTCGTA
*
30327318 AAAAGCGCCGC-AAAATATCTTTACTAAAACGCGTAGTTTTAATTTTGATGTATACTTATATTAG
1 AAAA-CGCCGCAAAAATATCTTAACTAAAACGCGTAGTTTTAATTTTGATGTATACTTATATTAG
* *
30327382 TGGCGCTTACTAGAAAACACCGTTAAAGAATAGATTTAGCGGCGCTTGAGCCAAAGCGCCGCAAC
65 TGGCGCTTACTAGAAAACGCCGTTAAAGAATAGCTTTAGCGGCGCTTGAGCCAAAGCGCCGCAAC
30327447 GTATCTTAACAAAACGCAGTGTTTGGTCTTAAGCTATGTTACATTTAGTGGCGCTTATAGGAAAA
130 GTATCTTAACAAAACGCAGTGTTTGGTCTTAAGCTATGTTACATTTAGTGGCGCTTATAGGAAAA
* * *
30327512 TGCCGTAAAAAATCTGAACCAAAACGCACCGTTTTGGTCTCGATGTATACTTTCAATTAGTGGCG
195 CGCCGCAAAATATCTGAACCAAAACGCACCGTTTTGGTCTCGATGTATA-TTTCAATTAGTGGCG
30327577 CTGACGTT
259 CTGACGTT
* *
30327585 AAAACGCCGCAAAAATATCTTAACTAAAACACATAGTTTTAA-TTT--TG---A-TTATATTAGT
1 AAAACGCCGCAAAAATATCTTAACTAAAACGCGTAGTTTTAATTTTGATGTATACTTATATTAGT
* * *
30327643 GGCGCTTACTAGAAAACGCCGTTAAAGAATAGCATTAGCGGCGCTTGAGCCAAAGTGCCGCAAAG
66 GGCGCTTACTAGAAAACGCCGTTAAAGAATAGCTTTAGCGGCGCTTGAGCCAAAGCGCCGCAACG
*
30327708 TATCTTAACAAAACACAGTGTTTGGTCTTAAGCTATGTTACATTTAGTGGCG-TGTATAGGAAAA
131 TATCTTAACAAAACGCAGTGTTTGGTCTTAAGCTATGTTACATTTAGTGGCGCT-TATAGGAAAA
*
30327772 CGCCGCAAAATATCTGAAGCAAAACGCACCGTTTTGGTCTCGATGTATATTTCAATTAGTGGCGC
195 CGCCGCAAAATATCTGAACCAAAACGCACCGTTTTGGTCTCGATGTATATTTCAATTAGTGGCGC
30327837 TGACGTT
260 TGACGTT
* *
30327844 GAAACGCCGCAAAAATATCTTAACTAAAGCGCGTAGTTTTAATTTTGATGTATACTTATATTAGT
1 AAAACGCCGCAAAAATATCTTAACTAAAACGCGTAGTTTTAATTTTGATGTATACTTATATTAGT
*
30327909 GGCGCTTACTAGAAAACGCCGTTAAAGAATAGCTTTAGCGGCGCTTTG-GATC-AAGCGCCGCAA
66 GGCGCTTACTAGAAAACGCCGTTAAAGAATAGCTTTAGCGGCGC-TTGAG-CCAAAGCGCCGCAA
* * *
30327972 CGTTTCTTAACAAAACGCAGTGTTTTGTCTTAAGCTATGCTACATTTAGTGGCGCTTATAGGAAA
129 CGTATCTTAACAAAACGCAGTGTTTGGTCTTAAGCTATGTTACATTTAGTGGCGCTTATAGGAAA
* *
30328037 ACGCCGCAAAATATCTGAACCAAAATGCACCGTTTTGGTCTCGATGTATACTTCAATTAGTGGCG
194 ACGCCGCAAAATATCTGAACCAAAACGCACCGTTTTGGTCTCGATGTATATTTCAATTAGTGGCG
30328102 CTGACGTT
259 CTGACGTT
*
30328110 AAAACGCCGTAAAAA
1 AAAACGCCGCAAAAA
30328125 AGCAAAATAC
Statistics
Matches: 498, Mismatches: 30, Indels: 25
0.90 0.05 0.05
Matches are distributed among these distances:
259 62 0.12
260 179 0.36
261 1 0.00
262 2 0.00
264 2 0.00
265 1 0.00
266 214 0.43
267 37 0.07
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (266 bp):
AAAACGCCGCAAAAATATCTTAACTAAAACGCGTAGTTTTAATTTTGATGTATACTTATATTAGT
GGCGCTTACTAGAAAACGCCGTTAAAGAATAGCTTTAGCGGCGCTTGAGCCAAAGCGCCGCAACG
TATCTTAACAAAACGCAGTGTTTGGTCTTAAGCTATGTTACATTTAGTGGCGCTTATAGGAAAAC
GCCGCAAAATATCTGAACCAAAACGCACCGTTTTGGTCTCGATGTATATTTCAATTAGTGGCGCT
GACGTT
Found at i:30328452 original size:110 final size:110
Alignment explanation
Indices: 30328334--30328685 Score: 695
Period size: 110 Copynumber: 3.2 Consensus size: 110
30328324 ATTTTTAGAT
30328334 TATAGTTTAGGGTTTAAGGTCTACGTTGTAGGTTTAGTGTTTTCAGTTTAGGGTTTGAGAGTTTG
1 TATAGTTTAGGGTTTAAGGTCTACGTTGTAGGTTTAGTGTTTTCAGTTTAGGGTTTGAGAGTTTG
30328399 ATGATTAAGGTTCAGTGATTATTATAAGTTAAAAATTTTATCGTA
66 ATGATTAAGGTTCAGTGATTATTATAAGTTAAAAATTTTATCGTA
30328444 TATAGTTTAGGGTTTAAGGTCTACGTTGTAGGTTTAGTGTTTTCAGTTTAGGGTTTGAGAGTTTG
1 TATAGTTTAGGGTTTAAGGTCTACGTTGTAGGTTTAGTGTTTTCAGTTTAGGGTTTGAGAGTTTG
30328509 ATGATTAAGGTTCAGTGATTATTATAAGTTAAAAATTTTATCGTA
66 ATGATTAAGGTTCAGTGATTATTATAAGTTAAAAATTTTATCGTA
30328554 TATAGTTTAGGGTTTAAGGTCTACGTTGTAGGTTTAGTGTTTTCAGTTTAGGGTTTGAGAGTTTG
1 TATAGTTTAGGGTTTAAGGTCTACGTTGTAGGTTTAGTGTTTTCAGTTTAGGGTTTGAGAGTTTG
30328619 ATGATTAAGGTTCAGTGATTATTATAAGTTAAAAATTTTATCGTA
66 ATGATTAAGGTTCAGTGATTATTATAAGTTAAAAATTTTATCGTA
30328664 TATAGTTTAGGGTTTTAAGGTC
1 TATAGTTTAGGG-TTTAAGGTC
30328686 AATCATTGTA
Statistics
Matches: 241, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
110 232 0.96
111 9 0.04
ACGTcount: A:0.26, C:0.05, G:0.25, T:0.45
Consensus pattern (110 bp):
TATAGTTTAGGGTTTAAGGTCTACGTTGTAGGTTTAGTGTTTTCAGTTTAGGGTTTGAGAGTTTG
ATGATTAAGGTTCAGTGATTATTATAAGTTAAAAATTTTATCGTA
Found at i:30328943 original size:15 final size:14
Alignment explanation
Indices: 30328923--30328972 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
30328913 TAAGGTTTGT
30328923 AGTTTAGGGTTTAA
1 AGTTTAGGGTTTAA
**
30328937 GAGTTTAAAGTTTAA
1 -AGTTTAGGGTTTAA
*
30328952 AGGTTACGGGTTTAA
1 AGTTTA-GGGTTTAA
30328967 AGTTTA
1 AGTTTA
30328973 AAGGTTACGG
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
14 5 0.18
15 23 0.82
ACGTcount: A:0.32, C:0.02, G:0.26, T:0.40
Consensus pattern (14 bp):
AGTTTAGGGTTTAA
Found at i:30328948 original size:22 final size:21
Alignment explanation
Indices: 30328923--30328979 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
30328913 TAAGGTTTGT
*
30328923 AGTTTAGGGTTTAAGAGTTTAA
1 AGTTTAAGG-TTAAGAGTTTAA
* *
30328945 AGTTTAAAGGTTACGGGTTTAA
1 AGTTT-AAGGTTAAGAGTTTAA
30328967 AGTTTAAAGGTTA
1 AGTTT-AAGGTTA
30328980 CGGGTTAAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
22 28 0.90
23 3 0.10
ACGTcount: A:0.33, C:0.02, G:0.26, T:0.39
Consensus pattern (21 bp):
AGTTTAAGGTTAAGAGTTTAA
Found at i:30328949 original size:29 final size:30
Alignment explanation
Indices: 30328893--30328975 Score: 91
Period size: 29 Copynumber: 2.9 Consensus size: 30
30328883 TTTTGAGTGT
* * * *
30328893 AAGGTTACAGGTTT-AGAGTGTAAGGTTTG
1 AAGGTTACGGGTTTAAGAGTTTAAAGTTTA
* *
30328922 TAGTTTA-GGGTTTAAGAGTTTAAAGTTTA
1 AAGGTTACGGGTTTAAGAGTTTAAAGTTTA
30328951 AAGGTTACGGGTTTAA-AGTTTAAAG
1 AAGGTTACGGGTTTAAGAGTTTAAAG
30328976 GTTACGGGTT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
28 5 0.11
29 31 0.70
30 8 0.18
ACGTcount: A:0.31, C:0.02, G:0.29, T:0.37
Consensus pattern (30 bp):
AAGGTTACGGGTTTAAGAGTTTAAAGTTTA
Found at i:30328978 original size:15 final size:15
Alignment explanation
Indices: 30328930--30328978 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
30328920 TGTAGTTTAG
30328930 GGTTTAAGAGTTTAAA
1 GGTTTAA-AGTTTAAA
* **
30328946 -GTTTAAAGGTTACG
1 GGTTTAAAGTTTAAA
30328960 GGTTTAAAGTTTAAA
1 GGTTTAAAGTTTAAA
30328975 GGTT
1 GGTT
30328979 ACGGGTTAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
14 5 0.19
15 21 0.81
ACGTcount: A:0.33, C:0.02, G:0.27, T:0.39
Consensus pattern (15 bp):
GGTTTAAAGTTTAAA
Found at i:30328980 original size:22 final size:22
Alignment explanation
Indices: 30328939--30328991 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
30328929 GGGTTTAAGA
30328939 GTTTAAAGTTTAAAGGTTACGG
1 GTTTAAAGTTTAAAGGTTACGG
30328961 GTTTAAAGTTTAAAGGTTACGG
1 GTTTAAAGTTTAAAGGTTACGG
30328983 G-TTAAAGTT
1 GTTTAAAGTT
30328992 AGGGGCCTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 8 0.26
22 23 0.74
ACGTcount: A:0.32, C:0.04, G:0.26, T:0.38
Consensus pattern (22 bp):
GTTTAAAGTTTAAAGGTTACGG
Found at i:30329585 original size:39 final size:40
Alignment explanation
Indices: 30329530--30329608 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 40
30329520 TCCCTAATTT
* * *
30329530 CCCATTTCGTATTCCCCCA-ATTCCCCGATTTCATTTCCC
1 CCCAATTCCTATTCCCCCAGATTCCCCGATTTAATTTCCC
*
30329569 CCCAATTCCTATTCCCCCAGTTTCCCCGATTTAATTTCCC
1 CCCAATTCCTATTCCCCCAGATTCCCCGATTTAATTTCCC
30329609 TAAATCCCCA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
39 17 0.49
40 18 0.51
ACGTcount: A:0.16, C:0.43, G:0.05, T:0.35
Consensus pattern (40 bp):
CCCAATTCCTATTCCCCCAGATTCCCCGATTTAATTTCCC
Found at i:30331618 original size:15 final size:15
Alignment explanation
Indices: 30331594--30331626 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
30331584 AAGGTTTCTA
*
30331594 TATTAGTATTAAATT
1 TATTACTATTAAATT
30331609 TATTACTATTAAATT
1 TATTACTATTAAATT
30331624 TAT
1 TAT
30331627 AAAATTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (15 bp):
TATTACTATTAAATT
Found at i:30331829 original size:24 final size:26
Alignment explanation
Indices: 30331802--30331856 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 26
30331792 TATATATCTT
* *
30331802 ACATAATACATAAC-TACATAACAA-
1 ACATAATAAAGAACTTACATAACAAC
*
30331826 ACATAATAAAGAACTTACATAATAAC
1 ACATAATAAAGAACTTACATAACAAC
30331852 ACATA
1 ACATA
30331857 CCGTACATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 12 0.46
25 9 0.35
26 5 0.19
ACGTcount: A:0.58, C:0.18, G:0.02, T:0.22
Consensus pattern (26 bp):
ACATAATAAAGAACTTACATAACAAC
Found at i:30331978 original size:9 final size:9
Alignment explanation
Indices: 30331946--30332196 Score: 158
Period size: 9 Copynumber: 29.8 Consensus size: 9
30331936 TACATAATAA
30331946 TACAT-ACT
1 TACATAACT
*
30331954 TACATAAAT
1 TACATAACT
* *
30331963 TAAATAAGT
1 TACATAACT
30331972 TACATAA--
1 TACATAACT
* *
30331979 TACACAAAT
1 TACATAACT
30331988 TACATAACT
1 TACATAACT
30331997 TACATAA--
1 TACATAACT
*
30332004 TACATAATT
1 TACATAACT
30332013 TACATAA--
1 TACATAACT
*
30332020 TACACAACT
1 TACATAACT
*
30332029 GACATAACT
1 TACATAACT
30332038 TACATAA--
1 TACATAACT
**
30332045 TACATATTT
1 TACATAACT
*
30332054 TACATCACT
1 TACATAACT
30332063 TACATAA--
1 TACATAACT
*
30332070 GACATAACT
1 TACATAACT
*
30332079 TACATAAGT
1 TACATAACT
*
30332088 TTCATAA--
1 TACATAACT
*
30332095 TACACAACT
1 TACATAACT
*
30332104 GACATAACT
1 TACATAACT
30332113 TACATAA--
1 TACATAACT
*
30332120 TACACAACT
1 TACATAACT
*
30332129 TACATAAGT
1 TACATAACT
**
30332138 TTGATAA--
1 TACATAACT
*
30332145 TACACAACT
1 TACATAACT
* *
30332154 TACACAGCT
1 TACATAACT
30332163 TACATAACT
1 TACATAACT
* *
30332172 TACACAAGT
1 TACATAACT
30332181 TACATAACT
1 TACATAACT
30332190 TACATAA
1 TACATAA
30332197 TAAATAACTT
Statistics
Matches: 186, Mismatches: 40, Indels: 33
0.72 0.15 0.13
Matches are distributed among these distances:
7 46 0.25
8 5 0.03
9 135 0.73
ACGTcount: A:0.47, C:0.20, G:0.04, T:0.30
Consensus pattern (9 bp):
TACATAACT
Found at i:30332007 original size:16 final size:16
Alignment explanation
Indices: 30331988--30332135 Score: 115
Period size: 16 Copynumber: 9.0 Consensus size: 16
30331978 ATACACAAAT
30331988 TACATAACTTACATAA
1 TACATAACTTACATAA
*
30332004 TACATAATTTACATAA
1 TACATAACTTACATAA
* *
30332020 TACACAACTGACATAA
1 TACATAACTTACATAA
*
30332036 CTTACATAA--TACATATTT
1 --TACATAACTTACATA--A
*
30332054 TACATCACTTACATAA
1 TACATAACTTACATAA
*
30332070 GACATAACTTACATAA
1 TACATAACTTACATAA
* *
30332086 GTTTCATAA--TACACAA
1 --TACATAACTTACATAA
30332102 CTGACATAACTTACATAA
1 -T-ACATAACTTACATAA
*
30332120 TACACAACTTACATAA
1 TACATAACTTACATAA
30332136 GTTTGATAAT
Statistics
Matches: 103, Mismatches: 18, Indels: 22
0.72 0.13 0.15
Matches are distributed among these distances:
15 1 0.01
16 78 0.76
17 1 0.01
18 23 0.22
ACGTcount: A:0.47, C:0.20, G:0.03, T:0.30
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:30332021 original size:41 final size:41
Alignment explanation
Indices: 30331946--30332135 Score: 177
Period size: 41 Copynumber: 4.8 Consensus size: 41
30331936 TACATAATAA
* * *
30331946 TACAT-ACTTACATAAATTAAATAAGTTACATAATACACAAAT
1 TACATAACTTACAT-AA-TACATAATTTACATAATACACAACT
30331988 TACATAACTTACATAATACATAATTTACATAATACACAACT
1 TACATAACTTACATAATACATAATTTACATAATACACAACT
* *
30332029 GACATAACTTACATAATACATATTTTAC---AT---C-ACT
1 TACATAACTTACATAATACATAATTTACATAATACACAACT
*
30332063 TACATAA--GACATAACTTACATAAGTTT-CATAATACACAACT
1 TACATAACTTACATAA--TACATAA-TTTACATAATACACAACT
* * *
30332104 GACATAACTTACATAATACACAACTTACATAA
1 TACATAACTTACATAATACATAATTTACATAA
30332136 GTTTGATAAT
Statistics
Matches: 122, Mismatches: 12, Indels: 29
0.75 0.07 0.18
Matches are distributed among these distances:
32 6 0.05
34 16 0.13
35 4 0.03
37 2 0.02
38 2 0.02
40 3 0.02
41 68 0.56
42 7 0.06
43 14 0.11
ACGTcount: A:0.48, C:0.19, G:0.03, T:0.31
Consensus pattern (41 bp):
TACATAACTTACATAATACATAATTTACATAATACACAACT
Found at i:30332121 original size:25 final size:25
Alignment explanation
Indices: 30331899--30332207 Score: 225
Period size: 25 Copynumber: 12.2 Consensus size: 25
30331889 CCAAAAAAAA
*
30331899 AACTTACATAACTTAGATAATATC-C
1 AACTTACATAACTTACATAATA-CAC
* * * *
30331924 TACATA-ATAAATTACATAATAATAC
1 AACTTACATAACTTACATAAT-ACAC
* * *
30331949 ATACTTACATAAATTAAATAAGTTACAT
1 A-ACTTACATAACTTACATAA--TACAC
* * *
30331977 AA--TACACAAATTACATAACTTACAT
1 AACTTACATAACTTACATAA--TACAC
*
30332002 AA--TACATAATTTACATAATACAC
1 AACTTACATAACTTACATAATACAC
* *
30332025 AACTGACATAACTTACATAATACAT
1 AACTTACATAACTTACATAATACAC
** * * *
30332050 ATTTTACATCACTTACATAAGACAT
1 AACTTACATAACTTACATAATACAC
* *
30332075 AACTTACATAAGTTTCATAATACAC
1 AACTTACATAACTTACATAATACAC
*
30332100 AACTGACATAACTTACATAATACAC
1 AACTTACATAACTTACATAATACAC
* **
30332125 AACTTACATAAGTTTGATAATACAC
1 AACTTACATAACTTACATAATACAC
* *
30332150 AACTTACACAGCTTACATAACTTACAC
1 AACTTACATAACTTACATAA--TACAC
* * *
30332177 AAGTTACATAACTTACATAATAAAT
1 AACTTACATAACTTACATAATACAC
30332202 AACTTA
1 AACTTA
30332208 TTCCTAAATC
Statistics
Matches: 225, Mismatches: 49, Indels: 20
0.77 0.17 0.07
Matches are distributed among these distances:
23 6 0.03
24 12 0.05
25 164 0.73
26 4 0.02
27 35 0.16
28 3 0.01
29 1 0.00
ACGTcount: A:0.48, C:0.18, G:0.03, T:0.31
Consensus pattern (25 bp):
AACTTACATAACTTACATAATACAC
Found at i:30333435 original size:84 final size:84
Alignment explanation
Indices: 30333294--30333459 Score: 305
Period size: 84 Copynumber: 2.0 Consensus size: 84
30333284 GCTTTGCAAG
* * *
30333294 CGATCCTAGGAGTGTGAGGCTTGGGCTAGCATCTGATGGATTTAATCCTTTCAAGATCATGAGCA
1 CGATCCTAGAAGTGTGAGGCTTGGGCTAGCATATGATGGATTTAATCATTTCAAGATCATGAGCA
30333359 CTGCCTACAGTACTTGGAA
66 CTGCCTACAGTACTTGGAA
30333378 CGATCCTAGAAGTGTGAGGCTTGGGCTAGCATATGATGGATTTAATCATTTCAAGATCATGAGCA
1 CGATCCTAGAAGTGTGAGGCTTGGGCTAGCATATGATGGATTTAATCATTTCAAGATCATGAGCA
30333443 CTGCCTACAGTACTTGG
66 CTGCCTACAGTACTTGG
30333460 CCAGTAGTGC
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 79 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (84 bp):
CGATCCTAGAAGTGTGAGGCTTGGGCTAGCATATGATGGATTTAATCATTTCAAGATCATGAGCA
CTGCCTACAGTACTTGGAA
Found at i:30338309 original size:42 final size:42
Alignment explanation
Indices: 30338259--30338443 Score: 187
Period size: 42 Copynumber: 4.3 Consensus size: 42
30338249 TTTGTGAAAT
*
30338259 AAGCGCCGCTAAAGAACACT-ACTTTTAGCGGCGTTTTTGAAC-
1 AAGCGCCGCTAAAGAACA-TGACTTTTAGCGGCGTTTTT-TACG
* * * * * *
30338301 AAGCGCCGCTATAGAGCATTACTTTTAGAGGCGTTTTCCTCCG
1 AAGCGCCGCTAAAGAACATGACTTTTAGCGGCGTTTT-TTACG
* *
30338344 AAGCGCCGCTAAAGAACATGA-TCTTTAGCGGCGTTTTTTTCT
1 AAGCGCCGCTAAAGAACATGACT-TTTAGCGGCGTTTTTTACG
* *
30338386 AAGCGCCGCTAAAGAACATGATTTTTAGCGGCGTTTTTTTATG
1 AAGCGCCGCTAAAGAACATGACTTTTAGCGGCG-TTTTTTACG
*
30338429 TAAGCGCCGCAAAAG
1 -AAGCGCCGCTAAAG
30338444 TTAGCGACGT
Statistics
Matches: 119, Mismatches: 17, Indels: 12
0.80 0.11 0.08
Matches are distributed among these distances:
41 1 0.01
42 67 0.56
43 38 0.32
44 13 0.11
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (42 bp):
AAGCGCCGCTAAAGAACATGACTTTTAGCGGCGTTTTTTACG
Found at i:30338355 original size:85 final size:85
Alignment explanation
Indices: 30338259--30338422 Score: 217
Period size: 85 Copynumber: 1.9 Consensus size: 85
30338249 TTTGTGAAAT
* * *
30338259 AAGCGCCGCTAAAGAACACT-A-CTTTTAGCGGCGTTTTTGAAC-AAGCGCCGCTATAGAGCATT
1 AAGCGCCGCTAAAGAACA-TGATC-TTTAGCGGCGTTTTT-AACTAAGCGCCGCTAAAGAACATG
30338321 ACTTTTAGAGGCGTTTTCCTCCG
63 ACTTTTAGAGGCGTTTTCCTCCG
** *
30338344 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGATT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTAACTAAGCGCCGCTAAAGAACATGACT
*
30338409 TTTAGCGGCGTTTT
66 TTTAGAGGCGTTTT
30338423 TTTATGTAAG
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
84 2 0.03
85 66 0.96
86 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.30
Consensus pattern (85 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTAACTAAGCGCCGCTAAAGAACATGACT
TTTAGAGGCGTTTTCCTCCG
Found at i:30338538 original size:21 final size:21
Alignment explanation
Indices: 30338514--30338556 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
30338504 TTAGTGGCGT
* *
30338514 TAAAAAGCGCCGCTAAAGACC
1 TAAAAAACGCCGCTAAAAACC
30338535 TAAAAAACGCCGCTAAAAACC
1 TAAAAAACGCCGCTAAAAACC
30338556 T
1 T
30338557 GTTCTGTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.47, C:0.28, G:0.14, T:0.12
Consensus pattern (21 bp):
TAAAAAACGCCGCTAAAAACC
Found at i:30338581 original size:33 final size:33
Alignment explanation
Indices: 30338543--30338606 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
30338533 CCTAAAAAAC
*
30338543 GCCGCTAAAAACCTGTTCTGTTGTAGTGTAAAT
1 GCCGCTAAAAACCTGTTCTGGTGTAGTGTAAAT
* *
30338576 GCCGCTAAAAGCCTGTTTTGGTGTAGTGTAA
1 GCCGCTAAAAACCTGTTCTGGTGTAGTGTAA
30338607 GGTAACTCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (33 bp):
GCCGCTAAAAACCTGTTCTGGTGTAGTGTAAAT
Found at i:30343580 original size:48 final size:47
Alignment explanation
Indices: 30343522--30343815 Score: 453
Period size: 48 Copynumber: 6.2 Consensus size: 47
30343512 AATTCTAAAT
30343522 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
30343569 TGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTG-ATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
30343617 TGTGAATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTG-ATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
* *
30343665 TGTGAATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATG
1 TGTG-ATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
**
30343713 CATGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
* * * * * * * *
30343760 TGTGACAGGGCCGAGTGGCCAATGTGATGGATGTGAAAGTGCATAAA
1 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
30343807 TGTGATAAG
1 TGTGATAAG
30343816 TCCCGAAGGG
Statistics
Matches: 228, Mismatches: 18, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
47 89 0.39
48 139 0.61
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.28
Consensus pattern (47 bp):
TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
Found at i:30343990 original size:37 final size:37
Alignment explanation
Indices: 30343934--30344012 Score: 131
Period size: 37 Copynumber: 2.1 Consensus size: 37
30343924 CCGAGCTCTA
* *
30343934 AAGACCCGATGACTACGTGTGGAGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
30343971 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
30344008 AAGAC
1 AAGAC
30344013 TTCGTAATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:30344663 original size:23 final size:23
Alignment explanation
Indices: 30344633--30344676 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
30344623 TAGTACACAG
30344633 ATTGGGCAGTGTCTGGAAAATAA
1 ATTGGGCAGTGTCTGGAAAATAA
30344656 ATTGGGCAGTGTCTGGAAAAT
1 ATTGGGCAGTGTCTGGAAAAT
30344677 TATTTTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.32, C:0.09, G:0.32, T:0.27
Consensus pattern (23 bp):
ATTGGGCAGTGTCTGGAAAATAA
Found at i:30344818 original size:45 final size:45
Alignment explanation
Indices: 30344754--30345158 Score: 558
Period size: 45 Copynumber: 9.0 Consensus size: 45
30344744 GGGTGTTACA
*
30344754 ACTTCACTGCCAATACAGGAAGACAAGA-TCTACTATCTTCAGTCT
1 ACTTCACTGCCAATACAGGAAGACAAGACT-TGCTATCTTCAGTCT
* * *
30344799 ACTTCGCTGTCAATACAGGAAGACTAGACTTGCTATCTTC-GATCT
1 ACTTCACTGCCAATACAGGAAGACAAGACTTGCTATCTTCAG-TCT
* *
30344844 ACTTCACAGCCAATACAGGAAGATAAGA-TCTGCTATCTTCAGTCT
1 ACTTCACTGCCAATACAGGAAGACAAGACT-TGCTATCTTCAGTCT
* * *
30344889 ACTTCACTGTCAATACAGGAAGACTAGACTTGCTATCTTCAATCT
1 ACTTCACTGCCAATACAGGAAGACAAGACTTGCTATCTTCAGTCT
30344934 ACTTCACTGCCAATACAGGAAGACAAGACTTGCTATCTTC-GATCT
1 ACTTCACTGCCAATACAGGAAGACAAGACTTGCTATCTTCAG-TCT
*
30344979 ACTTCACTGCCAATACAGGAAGACAAGA-TCTACTATCTTCA-TCT
1 ACTTCACTGCCAATACAGGAAGACAAGACT-TGCTATCTTCAGTCT
**
30345023 ACTTTGCTGCCAATACAGGAAGACAAGACTTGCTATCTTC-GATCT
1 ACTTCACTGCCAATACAGGAAGACAAGACTTGCTATCTTCAG-TCT
30345068 ACTTCACTGCCAATACAGGAAGACAAGACTTGCTATCTTC-GATCT
1 ACTTCACTGCCAATACAGGAAGACAAGACTTGCTATCTTCAG-TCT
*
30345113 ACTTCACTGCCAATACAGGAAGATAAGA-TCTGCTATCTTCAGTCT
1 ACTTCACTGCCAATACAGGAAGACAAGACT-TGCTATCTTCAGTCT
30345158 A
1 A
30345159 ATTAATTACA
Statistics
Matches: 323, Mismatches: 24, Indels: 26
0.87 0.06 0.07
Matches are distributed among these distances:
44 42 0.13
45 277 0.86
46 4 0.01
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.28
Consensus pattern (45 bp):
ACTTCACTGCCAATACAGGAAGACAAGACTTGCTATCTTCAGTCT
Found at i:30345184 original size:134 final size:132
Alignment explanation
Indices: 30344764--30345162 Score: 604
Period size: 134 Copynumber: 3.0 Consensus size: 132
30344754 ACTTCACTGC
* * * *
30344764 CAATACAGGAAGACAAGA-TCTACTATCTTCAGTCTACTTCGCTGTCAATACAGGAAGACTAGAC
1 CAATACAGGAAGACAAGACT-TGCTATCTTCA-TCTACTTCACTGCCAATACAGGAAGACAAGAC
* *
30344828 TTGCTATCTTCGATCTACTTCACAGCCAATACAGGAAGATAAGATCTGCTATCTTCAGTCTACTT
64 TTGCTATCTTCGATCTACTTCACTGCCAATACAGGAAGATAAGATCTGCTATCTTCAGTCTAATT
30344893 CACTGT
129 -ACT-T
*
30344899 CAATACAGGAAGACTAGACTTGCTATCTTCAATCTACTTCACTGCCAATACAGGAAGACAAGACT
1 CAATACAGGAAGACAAGACTTGCTATCTTC-ATCTACTTCACTGCCAATACAGGAAGACAAGACT
* * *
30344964 TGCTATCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTACTATCTTCA-TCTACTTT
65 TGCTATCTTCGATCTACTTCACTGCCAATACAGGAAGATAAGATCTGCTATCTTCAGTCTA-ATT
* *
30345028 GCTGC
129 ACT-T
30345033 CAATACAGGAAGACAAGACTTGCTATCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGACT
1 CAATACAGGAAGACAAGACTTGCTATCTTC-ATCTACTTCACTGCCAATACAGGAAGACAAGACT
30345098 TGCTATCTTCGATCTACTTCACTGCCAATACAGGAAGATAAGATCTGCTATCTTCAGTCTAATTA
65 TGCTATCTTCGATCTACTTCACTGCCAATACAGGAAGATAAGATCTGCTATCTTCAGTCTAATTA
30345163 ATTACAGTGT
Statistics
Matches: 243, Mismatches: 17, Indels: 9
0.90 0.06 0.03
Matches are distributed among these distances:
134 126 0.52
135 115 0.47
136 2 0.01
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (132 bp):
CAATACAGGAAGACAAGACTTGCTATCTTCATCTACTTCACTGCCAATACAGGAAGACAAGACTT
GCTATCTTCGATCTACTTCACTGCCAATACAGGAAGATAAGATCTGCTATCTTCAGTCTAATTAC
TT
Found at i:30345509 original size:45 final size:45
Alignment explanation
Indices: 30345431--30345830 Score: 481
Period size: 45 Copynumber: 8.9 Consensus size: 45
30345421 GGCTGGTGCT
* * * *
30345431 TTCGATCTGCTTCACTGCCAGTATAGGAAGACAAGATCTGCTATC
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATC
* * *
30345476 TTCTG-TCTACTTCGCTGCCAATATAGGAAGACAAGA-CTTACTATG
1 TTC-GATCTACTTCGCTGCCAATACAGGAAGACAAGATC-TGCTATC
*
30345521 TTTGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATC
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATC
* * * *
30345566 TTCAATCCACTTTGCTGCCAATACAGGAAGACAAGGTCTGCTATC
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATC
* *
30345611 TTCGATCTACTTCGCTGCCAATACAAGAAGACAAGATCTACTATC
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATC
* * *
30345656 TTC-AGTCTACTTTGCTGCCAATATAGAAAGACAAGA-CTTGCTATC
1 TTCGA-TCTACTTCGCTGCCAATACAGGAAGACAAGATC-TGCTATC
* * *
30345701 TTCGATCTATTTCGCTGTCAA-ACAGGAAGACAAGATCTGTTATC
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATC
* *
30345745 TTC-AGTCTACTTTGCTGCCAATACAGGAAGACAAGA-CTTACTATC
1 TTCGA-TCTACTTCGCTGCCAATACAGGAAGACAAGATC-TGCTATC
*
30345790 TTCGATCTACTTCGCTGCCAAATACAGGAAGATAAGATCTG
1 TTCGATCTACTTCGCTGCC-AATACAGGAAGACAAGATCTG
30345831 TAATGTATAG
Statistics
Matches: 302, Mismatches: 39, Indels: 27
0.82 0.11 0.07
Matches are distributed among these distances:
43 1 0.00
44 39 0.13
45 240 0.79
46 21 0.07
47 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (45 bp):
TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATC
Found at i:30345557 original size:90 final size:90
Alignment explanation
Indices: 30345431--30345830 Score: 570
Period size: 90 Copynumber: 4.4 Consensus size: 90
30345421 GGCTGGTGCT
* * * * * *
30345431 TTCGATCTGCTTCACTGCCAGTATAGGAAGACAAGATCTGCTATCTTCTGTCTACTTCGCTGCCA
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTTGCTGCCA
* *
30345496 ATATAGGAAGACAAGACTTACTATG
66 ATACAGGAAGACAAGACTTACTATC
* * *
30345521 TTTGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAATCCACTTTGCTGCCA
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTTGCTGCCA
* *
30345586 ATACAGGAAGACAAG-GTCTGCTATC
66 ATACAGGAAGACAAGACT-TACTATC
* *
30345611 TTCGATCTACTTCGCTGCCAATACAAGAAGACAAGATCTACTATCTTCAGTCTACTTTGCTGCCA
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTTGCTGCCA
* * *
30345676 ATATAGAAAGACAAGACTTGCTATC
66 ATACAGGAAGACAAGACTTACTATC
* * *
30345701 TTCGATCTATTTCGCTGTCAA-ACAGGAAGACAAGATCTGTTATCTTCAGTCTACTTTGCTGCCA
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTTGCTGCCA
30345765 ATACAGGAAGACAAGACTTACTATC
66 ATACAGGAAGACAAGACTTACTATC
*
30345790 TTCGATCTACTTCGCTGCCAAATACAGGAAGATAAGATCTG
1 TTCGATCTACTTCGCTGCC-AATACAGGAAGACAAGATCTG
30345831 TAATGTATAG
Statistics
Matches: 274, Mismatches: 32, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
89 80 0.29
90 176 0.64
91 18 0.07
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (90 bp):
TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTTGCTGCCA
ATACAGGAAGACAAGACTTACTATC
Found at i:30346024 original size:100 final size:99
Alignment explanation
Indices: 30345850--30346223 Score: 426
Period size: 100 Copynumber: 3.7 Consensus size: 99
30345840 GCTTTAAAAT
* * * * * * * * * *
30345850 TTTTAAATTACGATGTCGGGGAAGCAAGATCCGCTATTGTAGCTTCAATCTGCCCCATTACACCA
1 TTTTAAATTGCAATGTCGGGGAAGCAAGATTCGCCATTGTAGCTTTAATCTGCTCCACTGCATCG
* *
30345915 CCA-GAGAAGTAAGATTCGTCGTTGCAGCCTCAATC
66 CCATG-GAAGTAAGATTCG-CGTTGCGGCTTCAATC
* * *
30345950 TTTTAATTTGCAATGTCAGGGAAGCAAGATTCGTCATTGTAGCTTTAATCTGCTCCACTGCATCG
1 TTTTAAATTGCAATGTCGGGGAAGCAAGATTCGCCATTGTAGCTTTAATCTGCTCCACTGCATCG
* *
30346015 GCATGGAAGTAAGATTCACCGTTGCGGCTTCAATC
66 CCATGGAAGTAAGATTC-GCGTTGCGGCTTCAATC
* * * * *
30346050 TTTTAAATTGCAATGTCGGGGAAGTAAGATTTGCCGTTGTAGTTTTAATCTGCTCCACTGTATCG
1 TTTTAAATTGCAATGTCGGGGAAGCAAGATTCGCCATTGTAGCTTTAATCTGCTCCACTGCATCG
30346115 CCATGGAAGTAAGATTCGCTGTTGCGGCTTCAATC
66 CCATGGAAGTAAGATTCGC-GTTGCGGCTTCAATC
* ** * * * * *
30346150 TTTTAAATTGCAATGTTGGAAAAGTAAGATTCACCGTTGTAGCTTTAATCTGTTCCACTGCATTG
1 TTTTAAATTGCAATGTCGGGGAAGCAAGATTCGCCATTGTAGCTTTAATCTGCTCCACTGCATCG
*
30346215 CCAGGGAAG
66 CCATGGAAG
30346224 GTAACTTCAT
Statistics
Matches: 234, Mismatches: 37, Indels: 6
0.84 0.13 0.02
Matches are distributed among these distances:
99 1 0.00
100 232 0.99
101 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (99 bp):
TTTTAAATTGCAATGTCGGGGAAGCAAGATTCGCCATTGTAGCTTTAATCTGCTCCACTGCATCG
CCATGGAAGTAAGATTCGCGTTGCGGCTTCAATC
Found at i:30346050 original size:50 final size:50
Alignment explanation
Indices: 30345991--30346150 Score: 142
Period size: 50 Copynumber: 3.2 Consensus size: 50
30345981 CGTCATTGTA
* * *
30345991 GCTTTAATCTGCTCCACTGCATCGGCATGGAAGTAAGATTCACCGTTGCG
1 GCTTCAATCTGCTCCACTGCATCGCCATGGAAGTAAGATTCGCCGTTGCG
** ** * * ** * **
30346041 GCTTCAATCTTTTAAATTGCAAT-GTCGGGGAAGTAAGATTTGCCGTTGTA
1 GCTTCAATCTGCTCCACTGC-ATCGCCATGGAAGTAAGATTCGCCGTTGCG
* * * *
30346091 GTTTTAATCTGCTCCACTGTATCGCCATGGAAGTAAGATTCGCTGTTGCG
1 GCTTCAATCTGCTCCACTGCATCGCCATGGAAGTAAGATTCGCCGTTGCG
30346141 GCTTCAATCT
1 GCTTCAATCT
30346151 TTTAAATTGC
Statistics
Matches: 78, Mismatches: 30, Indels: 4
0.70 0.27 0.04
Matches are distributed among these distances:
49 2 0.03
50 74 0.95
51 2 0.03
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (50 bp):
GCTTCAATCTGCTCCACTGCATCGCCATGGAAGTAAGATTCGCCGTTGCG
Found at i:30346200 original size:50 final size:48
Alignment explanation
Indices: 30346018--30346200 Score: 125
Period size: 50 Copynumber: 3.7 Consensus size: 48
30346008 TGCATCGGCA
*
30346018 TGGAAGTAAGATTCACCGTTGCGGCTTCAATCTTTTAAATTGCAATGT
1 TGGAAGTAAGATTCACCGTTGCAGCTTCAATCTTTTAAATTGCAATGT
* ** * * * ** ** * * *
30346066 CGGGGAAGTAAGATTTGCCGTTGTAGTTTTAATCTGCTCCACTG-TATCGCCA
1 --TGGAAGTAAGATTCACCGTTGCAGCTTCAATCTTTTAAATTGCAAT-G--T
* * *
30346118 TGGAAGTAAGATTCGCTGTTGCGGCTTCAATCTTTTAAATTGCAATGT
1 TGGAAGTAAGATTCACCGTTGCAGCTTCAATCTTTTAAATTGCAATGT
* *
30346166 TGGAAAAGTAAGATTCACCGTTGTAGCTTTAATCT
1 TGG--AAGTAAGATTCACCGTTGCAGCTTCAATCT
30346201 GTTCCACTGC
Statistics
Matches: 94, Mismatches: 33, Indels: 12
0.68 0.24 0.09
Matches are distributed among these distances:
48 3 0.03
49 2 0.02
50 87 0.93
51 2 0.02
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (48 bp):
TGGAAGTAAGATTCACCGTTGCAGCTTCAATCTTTTAAATTGCAATGT
Found at i:30347452 original size:17 final size:17
Alignment explanation
Indices: 30347411--30347453 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
30347401 TTGGCCTCTC
*
30347411 CTTTTTCTTTTTTCGTT
1 CTTTTTTTTTTTTCGTT
*
30347428 CTTCTTTTTTTTTCGTT
1 CTTTTTTTTTTTTCGTT
30347445 -TGTTTTTTT
1 CT-TTTTTTT
30347454 CAAGTGAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 1 0.05
17 21 0.95
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (17 bp):
CTTTTTTTTTTTTCGTT
Found at i:30347930 original size:20 final size:21
Alignment explanation
Indices: 30347895--30347940 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
30347885 AGGTTTTTTA
30347895 TTTTTTTGTCTCTTTT-GTTCT
1 TTTTTTTGTCTCTTTTGGTT-T
*
30347916 TTTTTTTGTGT-TTTTGGTTT
1 TTTTTTTGTCTCTTTTGGTTT
30347936 TTTTT
1 TTTTT
30347941 GCCTCCACTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.00, C:0.07, G:0.13, T:0.80
Consensus pattern (21 bp):
TTTTTTTGTCTCTTTTGGTTT
Found at i:30351554 original size:21 final size:23
Alignment explanation
Indices: 30351512--30351561 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 23
30351502 ACCTAAAAAC
**
30351512 TATATATGTATTTAAAAGAAATA
1 TATATATGTACATAAAAGAAATA
30351535 TATATATGTACAT-AAA-AAATA
1 TATATATGTACATAAAAGAAATA
30351556 TATATA
1 TATATA
30351562 AGTATGTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 11 0.44
22 3 0.12
23 11 0.44
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (23 bp):
TATATATGTACATAAAAGAAATA
Found at i:30351673 original size:27 final size:29
Alignment explanation
Indices: 30351621--30351674 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
30351611 ATGAGTACGT
*
30351621 ATGTATATATATATATATGAAAATAAAAA
1 ATGTATATAGATATATATGAAAATAAAAA
*
30351650 ATGTATATAGAT-TATA-GAATATAAA
1 ATGTATATAGATATATATGAAAATAAA
30351675 GAATATATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 8 0.35
28 4 0.17
29 11 0.48
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (29 bp):
ATGTATATAGATATATATGAAAATAAAAA
Found at i:30358328 original size:28 final size:28
Alignment explanation
Indices: 30358296--30358360 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
30358286 AATGGTGGAC
30358296 AGTGCAAGCCAAAATGGCAGATAGTCCA
1 AGTGCAAGCCAAAATGGCAGATAGTCCA
30358324 AGTGCAAGCCAAAATGGCAGATAGTCCA
1 AGTGCAAGCCAAAATGGCAGATAGTCCA
*
30358352 AGTACAAGC
1 AGTGCAAGC
30358361 TAAGTGGCGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.40, C:0.22, G:0.25, T:0.14
Consensus pattern (28 bp):
AGTGCAAGCCAAAATGGCAGATAGTCCA
Found at i:30360743 original size:13 final size:13
Alignment explanation
Indices: 30360725--30360755 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
30360715 TGACGAGATG
30360725 CAAAAGTACAAGA
1 CAAAAGTACAAGA
*
30360738 CAAAAGTACAAGC
1 CAAAAGTACAAGA
30360751 CAAAA
1 CAAAA
30360756 TAGCGGACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.61, C:0.19, G:0.13, T:0.06
Consensus pattern (13 bp):
CAAAAGTACAAGA
Found at i:30360848 original size:27 final size:28
Alignment explanation
Indices: 30360741--30360863 Score: 119
Period size: 27 Copynumber: 4.5 Consensus size: 28
30360731 TACAAGACAA
* * *
30360741 AAGTACAAGCCAAAATAGCGGACAGTCC
1 AAGTACAAGCCAAAGTGGAGGACAGTCC
* * *
30360769 AAGTGCAAGCC-AAGTGGCA-AACAATCC
1 AAGTACAAGCCAAAGTGG-AGGACAGTCC
**
30360796 AAGTACAAGCC-AAGTGTCGGACAGTCC
1 AAGTACAAGCCAAAGTGGAGGACAGTCC
*
30360823 AAGTACAAGCCAAAG-GGAGGATAGTCC
1 AAGTACAAGCCAAAGTGGAGGACAGTCC
*
30360850 AAGTGCAAGCCAAA
1 AAGTACAAGCCAAA
30360864 ATGGTGAACA
Statistics
Matches: 77, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
27 64 0.83
28 13 0.17
ACGTcount: A:0.41, C:0.24, G:0.24, T:0.11
Consensus pattern (28 bp):
AAGTACAAGCCAAAGTGGAGGACAGTCC
Found at i:30362542 original size:54 final size:54
Alignment explanation
Indices: 30362402--30362543 Score: 124
Period size: 54 Copynumber: 2.6 Consensus size: 54
30362392 ACTTTTGAAG
* * * * * * * *
30362402 TTGGGACACATGGCTGTGTCCCA-TCTCGTGTCTCTGCCCATGTAACTTACTTAC
1 TTGGGACACACGGCCGTGTCACAGAC-CGTGTCTCTACCCAGGTAACTCACTGAC
* * * * *
30362456 TTGGGACACACGGTCGTGTCTCAGCCCATGTCTCTACCCGGGTAACTCACTGAC
1 TTGGGACACACGGCCGTGTCACAGACCGTGTCTCTACCCAGGTAACTCACTGAC
* * *
30362510 TTGGGTCACACGGCCTTGTGACAGACCGTGTCTC
1 TTGGGACACACGGCCGTGTCACAGACCGTGTCTC
30362544 AGGTCGTGTG
Statistics
Matches: 69, Mismatches: 18, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
54 68 0.99
55 1 0.01
ACGTcount: A:0.17, C:0.31, G:0.24, T:0.28
Consensus pattern (54 bp):
TTGGGACACACGGCCGTGTCACAGACCGTGTCTCTACCCAGGTAACTCACTGAC
Found at i:30364241 original size:35 final size:35
Alignment explanation
Indices: 30364202--30364270 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
30364192 TTTAGCTCTC
30364202 TATTTTCAATTCTACCCCTTAATTTTGAAATTTTA
1 TATTTTCAATTCTACCCCTTAATTTTGAAATTTTA
* *
30364237 TATTTTCAATTCTACTCTTTAATTTTGAAATTTT
1 TATTTTCAATTCTACCCCTTAATTTTGAAATTTT
30364271 TACAATTTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.28, C:0.14, G:0.03, T:0.55
Consensus pattern (35 bp):
TATTTTCAATTCTACCCCTTAATTTTGAAATTTTA
Done.