Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007746.1 Hibiscus syriacus cultivar Beakdansim tig00110009_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3674400
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 15
Found at i:809424 original size:22 final size:22
Alignment explanation
Indices: 809396--809438 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
809386 AATTTATTAG
809396 TATGGATTGATTTAATTTAAAA
1 TATGGATTGATTTAATTTAAAA
*
809418 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTAATTTAAA
809439 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (22 bp):
TATGGATTGATTTAATTTAAAA
Found at i:809491 original size:21 final size:22
Alignment explanation
Indices: 809450--809494 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
809440 AATTTATTAG
809450 TATGGATTGATTTATTTTTAAA
1 TATGGATTGATTTATTTTTAAA
809472 TATGGATTGATTTA-TTTTAAA
1 TATGGATTGATTTATTTTTAAA
809493 TA
1 TA
809495 ATTTATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.53
Consensus pattern (22 bp):
TATGGATTGATTTATTTTTAAA
Found at i:809552 original size:31 final size:31
Alignment explanation
Indices: 809517--809575 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
809507 AGTTGTATGG
* * *
809517 ATTATTTAAATTTCTGTATTGTAAAACTAAA
1 ATTATTTAAATATCAGTATTGCAAAACTAAA
809548 ATTATTTAAATATCAGTATTGCAAAACT
1 ATTATTTAAATATCAGTATTGCAAAACT
809576 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATATCAGTATTGCAAAACTAAA
Found at i:811888 original size:13 final size:13
Alignment explanation
Indices: 811865--811911 Score: 67
Period size: 13 Copynumber: 3.5 Consensus size: 13
811855 ATAAAATAAT
811865 AAAGAAAATGAGAA
1 AAAG-AAATGAGAA
*
811879 AAATAAATGAGAA
1 AAAGAAATGAGAA
*
811892 AAAGAAATTAGAA
1 AAAGAAATGAGAA
811905 AAAGAAA
1 AAAGAAA
811912 AAAAGAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
13 27 0.90
14 3 0.10
ACGTcount: A:0.72, C:0.00, G:0.17, T:0.11
Consensus pattern (13 bp):
AAAGAAATGAGAA
Found at i:814192 original size:102 final size:100
Alignment explanation
Indices: 814015--814632 Score: 688
Period size: 102 Copynumber: 6.1 Consensus size: 100
814005 TGCGAAGAAT
* * * * * *
814015 TTTATCTCACTTGAAATTGTCTTTTCTTAAAA-CAATTTTCATCTCGCTCGAGACAGTTTCCTTT
1 TTTATCTCACTTGAGATTGT-TTTCCTTAAAACCAA-TTTCGTCTCGCTTGAGAGA-TTTCCCTT
* * *
814079 GAAACACAAATTTTGGAATTGTTTCATTCGAAATAAATA
63 GAAACACAAATTTTGAAATTGTTTCACTCGAAACAAA-A
* *
814118 TTTATCTCACTTAAGATTGTTTTCCTTAAAACAAATTTCGTCTCGCTTGAGATGATTTCCCTTGA
1 TTTATCTCACTTGAGATTGTTTTCCTTAAAACCAATTTCGTCTCGCTTGAGA-GATTTCCCTTGA
* * *
814183 AACACAAATTTGGAAATTGTTTCATTCAAAACAAAGA
65 AACACAAATTTTGAAATTGTTTCACTCGAAACAAA-A
* * *
814220 CTTATCTTACTTGAGATTGTTTTCCTTAAAACCAATTTCGTCTCTCTTGAGATGATTTCCCTTGA
1 TTTATCTCACTTGAGATTGTTTTCCTTAAAACCAATTTCGTCTCGCTTGAGA-GATTTCCCTTGA
* * *
814285 AACACAAATTTTAAAATTGTTTCATTCGAAACAAAGG
65 AACACAAATTTTGAAATTGTTTCACTCGAAACAAA-A
* * * *
814322 CTTATCTCACTTGAGAGTGTTTTCCTTAAAACCAATTTTGTCTCGCTTGAGACAGTTTCCCTTGA
1 TTTATCTCACTTGAGATTGTTTTCCTTAAAACCAATTTCGTCTCGCTTGAGAGA-TTTCCCTTGA
* *
814387 AACACAAACTTTGAAATTGTTTCACTCGAAACAAAGT
65 AACACAAATTTTGAAATTGTTTCACTCGAAACAAA-A
* * * ** * * * **
814424 TTTATCTCACTTGGGTTTGTTTTTCTTAAAACCAATTTTATCTCGTTTAAGACAATTTCTGTTGA
1 TTTATCTCACTTGAGATTGTTTTCCTTAAAACCAATTTCGTCTCGCTTGAGA-GATTTCCCTTGA
*
814489 AACACAAATTTTGAAATTATTTCACTCGAAACAAAA
65 AACACAAATTTTGAAATTGTTTCACTCGAAACAAAA
* * * *
814525 TTTTATCTCACTTG-GGTT-TTTTTCTTAAAA-CAATTTTGTCTCGCTTGAGACGGTTTCCCTTG
1 -TTTATCTCACTTGAGATTGTTTTCCTTAAAACCAATTTCGTCTCGCTTGAGA-GATTTCCCTTG
*
814587 AAACACTAAA-TTTGAAATTTTTTCACTCGAAACAAAA
64 AAACAC-AAATTTTGAAATTGTTTCACTCGAAACAAAA
814624 TTTTATCTC
1 -TTTATCTC
814633 TCATAAGACG
Statistics
Matches: 455, Mismatches: 54, Indels: 16
0.87 0.10 0.03
Matches are distributed among these distances:
99 66 0.15
100 15 0.03
101 4 0.01
102 348 0.76
103 22 0.05
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.40
Consensus pattern (100 bp):
TTTATCTCACTTGAGATTGTTTTCCTTAAAACCAATTTCGTCTCGCTTGAGAGATTTCCCTTGAA
ACACAAATTTTGAAATTGTTTCACTCGAAACAAAA
Found at i:815320 original size:15 final size:14
Alignment explanation
Indices: 815300--815339 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 14
815290 TGTAGTTGAT
815300 AAGAAAAAATGGAAA
1 AAGAAAAAAT-GAAA
815315 AAGAAAAAAATGAAA
1 AAG-AAAAAATGAAA
815330 AATGAAAAAA
1 AA-GAAAAAA
815340 AATTAATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (14 bp):
AAGAAAAAATGAAA
Found at i:815322 original size:7 final size:7
Alignment explanation
Indices: 815300--815382 Score: 51
Period size: 7 Copynumber: 11.0 Consensus size: 7
815290 TGTAGTTGAT
815300 AAGAAAA
1 AAGAAAA
*
815307 AATGGAAA
1 AA-GAAAA
815315 AAGAAAAA
1 AAG-AAAA
815323 AATGAAAA
1 AA-GAAAA
*
815331 ATGAAAA
1 AAGAAAA
*
815338 AA-AATTA
1 AAGAA-AA
*
815345 ATGAAAA
1 AAGAAAA
815352 AAGAAAA
1 AAGAAAA
815359 AAGAGAGAA
1 AAGA-A-AA
*
815368 AATTAAAA
1 AA-GAAAA
815376 AAGAAAA
1 AAGAAAA
815383 TAAATATATG
Statistics
Matches: 58, Mismatches: 10, Indels: 16
0.69 0.12 0.19
Matches are distributed among these distances:
6 2 0.03
7 26 0.45
8 23 0.40
9 6 0.10
10 1 0.02
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (7 bp):
AAGAAAA
Found at i:815324 original size:16 final size:16
Alignment explanation
Indices: 815303--815340 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
815293 AGTTGATAAG
815303 AAAAAATGGAAAAA-GA
1 AAAAAAT-GAAAAATGA
815319 AAAAAATGAAAAATGA
1 AAAAAATGAAAAATGA
815335 AAAAAA
1 AAAAAA
815341 ATTAATGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (16 bp):
AAAAAATGAAAAATGA
Found at i:815347 original size:21 final size:21
Alignment explanation
Indices: 815304--815360 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
815294 GTTGATAAGA
815304 AAAAATGGAAAAAGAAAAAAATG
1 AAAAAT-GAAAAA-AAAAAAATG
**
815327 AAAAATGAAAAAAAATTAATG
1 AAAAATGAAAAAAAAAAAATG
*
815348 AAAAAAGAAAAAA
1 AAAAATGAAAAAA
815361 GAGAGAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 19 0.61
22 6 0.19
23 6 0.19
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.11
Consensus pattern (21 bp):
AAAAATGAAAAAAAAAAAATG
Found at i:815369 original size:28 final size:29
Alignment explanation
Indices: 815319--815373 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
815309 TGGAAAAAGA
*
815319 AAAAAATGAAAAATGAAAAAAAATTAATG
1 AAAAAATGAAAAAAGAAAAAAAATTAATG
* *
815348 AAAAAA-GAAAAAAGAGAGAAAATTAA
1 AAAAAATGAAAAAAGAAAAAAAATTAA
815374 AAAAGAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 17 0.74
29 6 0.26
ACGTcount: A:0.75, C:0.00, G:0.13, T:0.13
Consensus pattern (29 bp):
AAAAAATGAAAAAAGAAAAAAAATTAATG
Found at i:815370 original size:45 final size:45
Alignment explanation
Indices: 815302--815387 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
815292 TAGTTGATAA
* *
815302 GAAAAAATGGAAAAAGAAAAAAATGAAAAATGAAAAAAAATTAAT
1 GAAAAAATGAAAAAAGAAAAAAATGAAAAAAGAAAAAAAATTAAT
* * *
815347 GAAAAAA-GAAAAAAGAGAGAAAATTAAAAAAGAAAATAAAT
1 GAAAAAATGAAAAAAGA-AAAAAATGAAAAAAGAAAAAAAAT
815388 ATATGACAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 8 0.23
45 27 0.77
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.12
Consensus pattern (45 bp):
GAAAAAATGAAAAAAGAAAAAAATGAAAAAAGAAAAAAAATTAAT
Found at i:815988 original size:19 final size:18
Alignment explanation
Indices: 815964--816002 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
815954 GTGACCATTA
*
815964 CAATATCTAAACCTATTTT
1 CAATATC-AAACCCATTTT
*
815983 CAATATCGAACCCATTTT
1 CAATATCAAACCCATTTT
816001 CA
1 CA
816003 TTTTATTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.36
Consensus pattern (18 bp):
CAATATCAAACCCATTTT
Found at i:826157 original size:25 final size:25
Alignment explanation
Indices: 826123--826177 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
826113 TATGGTGGAG
* *
826123 CATTCTGAGAATGTATTGTTAGAAA
1 CATTCAGAGAATGTATTGATAGAAA
826148 CATTCAGAGAATGTATTGATAGAAA
1 CATTCAGAGAATGTATTGATAGAAA
826173 CATTC
1 CATTC
826178 GAATGTACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (25 bp):
CATTCAGAGAATGTATTGATAGAAA
Found at i:826457 original size:13 final size:14
Alignment explanation
Indices: 826431--826462 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
826421 AGTTAACTAA
826431 ATTATTTAATTTAT
1 ATTATTTAATTTAT
826445 ATTATTTAA-TTAT
1 ATTATTTAATTTAT
826458 ATTAT
1 ATTAT
826463 ACATTTGTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
ATTATTTAATTTAT
Found at i:826560 original size:160 final size:160
Alignment explanation
Indices: 826379--826682 Score: 608
Period size: 160 Copynumber: 1.9 Consensus size: 160
826369 TTTGGTACTC
826379 CACAAGCACAAAGAGTTTGGAAACAAATGAATTCGGGTAAATAGTTAACTAAATTATTTAATTTA
1 CACAAGCACAAAGAGTTTGGAAACAAATGAATTCGGGTAAATAGTTAACTAAATTATTTAATTTA
826444 TATTATTTAATTATATTATACATTTGTCGTAGCCGTCTTTCAAGTGGGCTCGGAATTGGGCTTCG
66 TATTATTTAATTATATTATACATTTGTCGTAGCCGTCTTTCAAGTGGGCTCGGAATTGGGCTTCG
826509 ACTTGAATAAAATGAAACATGATCATTTTT
131 ACTTGAATAAAATGAAACATGATCATTTTT
826539 CACAAGCACAAAGAGTTTGGAAACAAATGAATTCGGGTAAATAGTTAACTAAATTATTTAATTTA
1 CACAAGCACAAAGAGTTTGGAAACAAATGAATTCGGGTAAATAGTTAACTAAATTATTTAATTTA
826604 TATTATTTAATTATATTATACATTTGTCGTAGCCGTCTTTCAAGTGGGCTCGGAATTGGGCTTCG
66 TATTATTTAATTATATTATACATTTGTCGTAGCCGTCTTTCAAGTGGGCTCGGAATTGGGCTTCG
826669 ACTTGAATAAAATG
131 ACTTGAATAAAATG
826683 GTTAGAGTCA
Statistics
Matches: 144, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
160 144 1.00
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (160 bp):
CACAAGCACAAAGAGTTTGGAAACAAATGAATTCGGGTAAATAGTTAACTAAATTATTTAATTTA
TATTATTTAATTATATTATACATTTGTCGTAGCCGTCTTTCAAGTGGGCTCGGAATTGGGCTTCG
ACTTGAATAAAATGAAACATGATCATTTTT
Found at i:826617 original size:13 final size:14
Alignment explanation
Indices: 826591--826622 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
826581 AGTTAACTAA
826591 ATTATTTAATTTAT
1 ATTATTTAATTTAT
826605 ATTATTTAA-TTAT
1 ATTATTTAATTTAT
826618 ATTAT
1 ATTAT
826623 ACATTTGTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
ATTATTTAATTTAT
Found at i:827156 original size:15 final size:15
Alignment explanation
Indices: 827136--827208 Score: 85
Period size: 15 Copynumber: 4.7 Consensus size: 15
827126 TAATCTCCAA
827136 AAAAATAAAATAAAGT
1 AAAAATAAAATAAA-T
*
827152 -GAAATAAAATAAAT
1 AAAAATAAAATAAAT
827166 AAAAATAAAATAAAT
1 AAAAATAAAATAAAT
827181 AAAAATAAATTAATAAAT
1 AAAAAT-AA--AATAAAT
*
827199 AAATATAAAA
1 AAAAATAAAA
827209 ATAAGGAAGA
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
14 1 0.02
15 33 0.66
16 2 0.04
17 2 0.04
18 12 0.24
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (15 bp):
AAAAATAAAATAAAT
Found at i:827158 original size:10 final size:9
Alignment explanation
Indices: 827134--827207 Score: 62
Period size: 10 Copynumber: 7.9 Consensus size: 9
827124 ACTAATCTCC
827134 AAAA-AAAT
1 AAAATAAAT
827142 AAAATAAAGT
1 AAAATAAA-T
*
827152 GAAATAAAAT
1 AAAAT-AAAT
*
827162 AAATAAAAAT
1 AAA-ATAAAT
827172 AAAATAAAT
1 AAAATAAAT
827181 AAAAATAAAT
1 -AAAATAAAT
*
827191 -TAATAAAT
1 AAAATAAAT
827199 AAATATAAA
1 AAA-ATAAA
827208 AATAAGGAAG
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
8 11 0.21
9 9 0.17
10 29 0.55
11 4 0.08
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.22
Consensus pattern (9 bp):
AAAATAAAT
Found at i:827197 original size:8 final size:8
Alignment explanation
Indices: 827138--827212 Score: 52
Period size: 8 Copynumber: 9.2 Consensus size: 8
827128 ATCTCCAAAA
827138 AAATAAAAT
1 AAAT-AAAT
827147 AAAGTGAAAT
1 AAA-T-AAAT
827157 AAAATAAAT
1 -AAATAAAT
827166 -AA-AAAT
1 AAATAAAT
827172 AAAATAAAT
1 -AAATAAAT
827181 -AA-AAAT
1 AAATAAAT
*
827187 AAATTAAT
1 AAATAAAT
827195 AAATAAAT
1 AAATAAAT
827203 ATAA-AAAT
1 A-AATAAAT
827211 AA
1 AA
827213 GGAAGAAATA
Statistics
Matches: 55, Mismatches: 3, Indels: 18
0.72 0.04 0.24
Matches are distributed among these distances:
6 8 0.15
7 7 0.13
8 18 0.33
9 13 0.24
10 6 0.11
11 3 0.05
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.23
Consensus pattern (8 bp):
AAATAAAT
Found at i:827221 original size:23 final size:21
Alignment explanation
Indices: 827203--827251 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 21
827193 ATAAATAAAT
827203 ATAAAAATAAGGAA-GAAATAAA
1 ATAAAAAT--GGAATGAAATAAA
*
827225 A-AATAATGGAATGAAATAAA
1 ATAAAAATGGAATGAAATAAA
827245 ATAAAAA
1 ATAAAAA
827252 AGAAACAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
19 4 0.17
20 9 0.39
21 9 0.39
22 1 0.04
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.16
Consensus pattern (21 bp):
ATAAAAATGGAATGAAATAAA
Found at i:827226 original size:18 final size:20
Alignment explanation
Indices: 827199--827245 Score: 71
Period size: 19 Copynumber: 2.4 Consensus size: 20
827189 ATTAATAAAT
827199 AAATATAAAAATAA-GGAA-G
1 AAATA-AAAAATAATGGAATG
827218 AAATAAAAAATAATGGAATG
1 AAATAAAAAATAATGGAATG
827238 AAATAAAA
1 AAATAAAA
827246 TAAAAAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.31
19 9 0.35
20 9 0.35
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (20 bp):
AAATAAAAAATAATGGAATG
Found at i:827227 original size:19 final size:21
Alignment explanation
Indices: 827199--827245 Score: 64
Period size: 18 Copynumber: 2.4 Consensus size: 21
827189 ATTAATAAAT
*
827199 AAATATAAAAATAA-GGAA-G
1 AAATAAAAAAATAATGGAATG
827218 AAAT-AAAAAATAATGGAATG
1 AAATAAAAAAATAATGGAATG
827238 AAATAAAA
1 AAATAAAA
827246 TAAAAAAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 8 0.33
19 8 0.33
20 5 0.21
21 3 0.12
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (21 bp):
AAATAAAAAAATAATGGAATG
Found at i:830528 original size:11 final size:11
Alignment explanation
Indices: 830509--830556 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
830499 ACCCACCTTA
*
830509 TTTTCTTTTCT
1 TTTTTTTTTCT
830520 TTTTTTTTTCT
1 TTTTTTTTTCT
* **
830531 TTGTTTTTTAA
1 TTTTTTTTTCT
*
830542 TTTTTTTCTCT
1 TTTTTTTTTCT
830553 TTTT
1 TTTT
830557 CCAATTTAGG
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.04, C:0.10, G:0.02, T:0.83
Consensus pattern (11 bp):
TTTTTTTTTCT
Found at i:841533 original size:27 final size:26
Alignment explanation
Indices: 841503--841567 Score: 62
Period size: 26 Copynumber: 2.5 Consensus size: 26
841493 AAAGAAAAAG
*
841503 AAAATCAAA-AAAGAAATTGAAGCACTC
1 AAAA-CAAAGAAAGAAA-TCAAGCACTC
* *
841530 AAAAGAAAGAAAGAAATCCAGCACTC
1 AAAACAAAGAAAGAAATCAAGCACTC
841556 AAAA-AGAAGAAA
1 AAAACA-AAGAAA
841568 AGCAAAGAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
25 1 0.03
26 21 0.64
27 11 0.33
ACGTcount: A:0.63, C:0.14, G:0.14, T:0.09
Consensus pattern (26 bp):
AAAACAAAGAAAGAAATCAAGCACTC
Found at i:844359 original size:11 final size:13
Alignment explanation
Indices: 844327--844356 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
844317 TGGCCAAAGA
844327 TGAAAAGGTATGT
1 TGAAAAGGTATGT
844340 TGAAAAGGTATG-
1 TGAAAAGGTATGT
844352 TGAAA
1 TGAAA
844357 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:853972 original size:5 final size:5
Alignment explanation
Indices: 853962--854011 Score: 75
Period size: 5 Copynumber: 10.2 Consensus size: 5
853952 AAAGGAAAAT
* *
853962 AATAA AATAA AAT-A AATAA AATAA AGTGA AATAA AATAA AATAA AATAA
1 AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA
854011 A
1 A
854012 TAAGGAAGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
4 4 0.10
5 36 0.90
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:854928 original size:22 final size:21
Alignment explanation
Indices: 854876--854930 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 21
854866 CTTTGGACTG
854876 GTTCGGGTTACAGCGTGGGTC
1 GTTCGGGTTACAGCGTGGGTC
*
854897 GATTCAGGTTACAGCGTGGGTC
1 G-TTCGGGTTACAGCGTGGGTC
854919 AGTTCGGGTTAC
1 -GTTCGGGTTAC
854931 TCCAAGATCT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 1 0.03
22 28 0.93
23 1 0.03
ACGTcount: A:0.15, C:0.18, G:0.38, T:0.29
Consensus pattern (21 bp):
GTTCGGGTTACAGCGTGGGTC
Found at i:857534 original size:42 final size:42
Alignment explanation
Indices: 857466--857591 Score: 148
Period size: 42 Copynumber: 3.0 Consensus size: 42
857456 AAGCCTAGAC
*
857466 TTACGATTGAATCAC-AGAGATCAAACTGAAACCTACATAATG
1 TTACGATTGAATCTCGA-AGATCAAACTGAAACCTACATAATG
* * * *
857508 TTATGATTGAATCTCGAAGATTAAACT-AGAATCTACAAAATG
1 TTACGATTGAATCTCGAAGATCAAACTGA-AACCTACATAATG
* * *
857550 TTACGATTGGATCTCGGAGATCAAACTGGAACCTACATAATG
1 TTACGATTGAATCTCGAAGATCAAACTGAAACCTACATAATG
857592 GTATTATAGA
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
41 1 0.01
42 67 0.97
43 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.27
Consensus pattern (42 bp):
TTACGATTGAATCTCGAAGATCAAACTGAAACCTACATAATG
Found at i:863808 original size:22 final size:21
Alignment explanation
Indices: 863765--863809 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
863755 TTCATATTTA
* *
863765 TTTTAATTAATTTTTAGTATC
1 TTTTAATTAATTTCTAGAATC
*
863786 TTTTAATTTTATTTCTAGAATC
1 TTTTAA-TTAATTTCTAGAATC
863808 TT
1 TT
863810 GTTTGCATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.27, C:0.07, G:0.04, T:0.62
Consensus pattern (21 bp):
TTTTAATTAATTTCTAGAATC
Found at i:865383 original size:40 final size:40
Alignment explanation
Indices: 865328--865406 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
865318 ACCGTTGCAT
**
865328 AATATACATTGGGAAGAAAAGAACAATTAATAACTAGCAG
1 AATATACACAGGGAAGAAAAGAACAATTAATAACTAGCAG
* *
865368 AATATACACAGGGAAGAAAAGAGCAATTAATAATTAGCA
1 AATATACACAGGGAAGAAAAGAACAATTAATAACTAGCA
865407 TGGGGAACAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.53, C:0.10, G:0.18, T:0.19
Consensus pattern (40 bp):
AATATACACAGGGAAGAAAAGAACAATTAATAACTAGCAG
Found at i:865413 original size:31 final size:31
Alignment explanation
Indices: 865378--865444 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
865368 AATATACACA
* *
865378 GGGAAGAAAAGAGCAATTAATAATTAGCATG
1 GGGAACAAAAGAGCAATTAATAATTAACATG
* *
865409 GGGAACAAAAGAGCAATTAGTAATTAACATT
1 GGGAACAAAAGAGCAATTAATAATTAACATG
865440 GGGAA
1 GGGAA
865445 TAAGATAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.48, C:0.07, G:0.25, T:0.19
Consensus pattern (31 bp):
GGGAACAAAAGAGCAATTAATAATTAACATG
Found at i:870097 original size:23 final size:23
Alignment explanation
Indices: 869971--870094 Score: 122
Period size: 23 Copynumber: 5.3 Consensus size: 23
869961 GAGTCGAAGG
* * *
869971 TTCTACGCGGTCTTTTGGGACAA
1 TTCTACGCGGTCCTTCGGGACAT
* * ** *
869994 TACTATGTTGTCATTCGGGACAT
1 TTCTACGCGGTCCTTCGGGACAT
* *
870017 ATTCTACGCAGTCCTTCGTGACAT
1 -TTCTACGCGGTCCTTCGGGACAT
*
870041 ATTCTACACGGTCCTTCGGGACAT
1 -TTCTACGCGGTCCTTCGGGACAT
*
870065 TTCTACGTGGTCCTTCGGGACAT
1 TTCTACGCGGTCCTTCGGGACAT
870088 TTCTACG
1 TTCTACG
870095 TGGCACTTCG
Statistics
Matches: 82, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
23 44 0.54
24 38 0.46
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.35
Consensus pattern (23 bp):
TTCTACGCGGTCCTTCGGGACAT
Found at i:878958 original size:45 final size:45
Alignment explanation
Indices: 878903--879189 Score: 423
Period size: 45 Copynumber: 6.4 Consensus size: 45
878893 GAATACCATG
* * *
878903 AGTGGAACCTTTTATGCCGATAATCCATCGTTATGCATTTTCATT
1 AGTGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATT
878948 AGTGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATTT
1 AGTGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCA-TT
*** *
878994 A-TGGCACCTTTTATATTGATAATGCACCATTATGCATTTTCATT
1 AGTGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATT
*
879038 AGTGGCACCTTTTATGCCGATAATGCACCGTTATCCATTTTCATT
1 AGTGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATT
* * *
879083 AGTGGCACCTTTTATGCCGATAATGCATCGTTGTTCATTTTCATT
1 AGTGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATT
* * *
879128 AGTGGCACCTTTTATGCCGATAATGCTCTGTTAAGCATTTTCATT
1 AGTGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATT
*
879173 AGTTGCACCTTTTATGC
1 AGTGGCACCTTTTATGC
879190 GATTTATAGA
Statistics
Matches: 218, Mismatches: 22, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
44 3 0.01
45 212 0.97
46 3 0.01
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.40
Consensus pattern (45 bp):
AGTGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATT
Found at i:878962 original size:26 final size:26
Alignment explanation
Indices: 878933--879054 Score: 76
Period size: 26 Copynumber: 5.2 Consensus size: 26
878923 TAATCCATCG
*
878933 TTATGCATTTTCATTAGTGGCACCTT
1 TTATGCATTTTCATTAATGGCACCTT
*
878959 TTATGC-----CGA-TAAT-GCACC-G
1 TTATGCATTTTC-ATTAATGGCACCTT
*
878978 TTATGCATTTTCATTTATGGCACCTT
1 TTATGCATTTTCATTAATGGCACCTT
* *
879004 TTAT--A--TTGA-TAAT-GCACC-A
1 TTATGCATTTTCATTAATGGCACCTT
*
879023 TTATGCATTTTCATTAGTGGCACCTT
1 TTATGCATTTTCATTAATGGCACCTT
879049 TTATGC
1 TTATGC
879055 CGATAATGCA
Statistics
Matches: 70, Mismatches: 10, Indels: 32
0.62 0.09 0.29
Matches are distributed among these distances:
19 10 0.14
20 10 0.14
21 8 0.11
22 4 0.06
23 4 0.06
24 8 0.11
25 10 0.14
26 16 0.23
ACGTcount: A:0.23, C:0.20, G:0.15, T:0.43
Consensus pattern (26 bp):
TTATGCATTTTCATTAATGGCACCTT
Found at i:889348 original size:13 final size:13
Alignment explanation
Indices: 889327--889391 Score: 67
Period size: 13 Copynumber: 5.0 Consensus size: 13
889317 AATGACGCTC
*
889327 AATGTGCGTCATA
1 AATGCGCGTCATA
* *
889340 AATGGGCGTTATA
1 AATGCGCGTCATA
* *
889353 AATGTGAGTCATA
1 AATGCGCGTCATA
* *
889366 AATGCGTGTCATC
1 AATGCGCGTCATA
889379 AATGCGCGTCATA
1 AATGCGCGTCATA
889392 GATTTATGAC
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 42 1.00
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:889382 original size:26 final size:26
Alignment explanation
Indices: 889325--889391 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 26
889315 TGAATGACGC
* *
889325 TCAATGTGCGTCATAAATGGGCGTTA
1 TCAATGTGCGTCATAAATGCGCGTCA
* * *
889351 TAAATGTGAGTCATAAATGCGTGTCA
1 TCAATGTGCGTCATAAATGCGCGTCA
*
889377 TCAATGCGCGTCATA
1 TCAATGTGCGTCATA
889392 GATTTATGAC
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (26 bp):
TCAATGTGCGTCATAAATGCGCGTCA
Found at i:889915 original size:60 final size:59
Alignment explanation
Indices: 889823--890040 Score: 276
Period size: 60 Copynumber: 3.7 Consensus size: 59
889813 GAATGTTTTC
* * *
889823 AACATTTCCTTTGCTTGATTCACAACACTTCGAATCAGCAACGCCCCATCAGAGGGGTT
1 AACATTTCATTTGCTCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTT
*
889882 AACATTTCATATTGCTCGATTCACAACACTTCGAATCAGTAACGCCCCACCAGAGGGGTT
1 AACATTTCAT-TTGCTCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTT
** * * * *
889942 AACATTTCATATTTATCGATTCACAATAATTTGAATCAGCAACGTCCCACCAGAGGGGTT
1 AACATTTCAT-TTGCTCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTT
* * * * *
890002 AACATTTGATTTGCTTGATTC-CCATACTTTGAATCAGCA
1 AACATTTCATTTGCTCGATTCACAACACTTCGAATCAGCA
890041 TAAGTCCTTC
Statistics
Matches: 141, Mismatches: 17, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
58 16 0.11
59 17 0.12
60 108 0.77
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (59 bp):
AACATTTCATTTGCTCGATTCACAACACTTCGAATCAGCAACGCCCCACCAGAGGGGTT
Found at i:891474 original size:139 final size:139
Alignment explanation
Indices: 891155--891645 Score: 651
Period size: 139 Copynumber: 3.6 Consensus size: 139
891145 GAAGATGAAC
* *
891155 GATCAACATTTCAAATTG-AGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTT
1 GATCAACATTTC-AAGTGAAGAGTTCATAATGAGAAGAACTCATCCGATA-AGGGAGAAGAAGTT
* * * *
891219 CATAATGAGAAGAA-TGTGTTCGACCTATA-CTCGATTCATGACAT-T----TCGAATCAGTGAC
64 CATAATGAGAAGAACT-TGTTCAACCT-TAGCTCGATTCATCACATATGGAGTTGAATCAGTAAC
* *
891277 ACCTCATTCTAGG
127 ACCTCACTCGAGG
* * * * *
891290 GATCAACATTTAAAGTAGATG-GTTCATATTGAGAAAAACTTATCCGATAAGGGAGAAGAAGTTC
1 GATCAACATTTCAAGT-GAAGAGTTCATAATGAGAAGAACTCATCCGATAAGGGAGAAGAAGTTC
* * *
891354 ATAATGAGAAGAACTTGTTCAACCTTAGTTTGATTCATCACATATGGAGTTGAATTAGTAACACC
65 ATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGTAACACC
891419 TCACTCGAGG
130 TCACTCGAGG
*
891429 GATCAACATTTCCAGTGAAGAGTTCATAATGAGAAGAACTCATCCGATGAA-GGAGAAGAAGTTC
1 GATCAACATTTCAAGTGAAGAGTTCATAATGAGAAGAACTCATCCGAT-AAGGGAGAAGAAGTTC
*
891493 ATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACC
65 ATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGTAACACC
891558 TCACTCGAGG
130 TCACTCGAGG
* * * * *
891568 GATCAACCTTTCCAGTGGAGAGTTCATAATGAGAAGAGCTCATCCGATAAGAGAGAAGAAGTTCA
1 GATCAACATTTCAAGTGAAGAGTTCATAATGAGAAGAACTCATCCGATAAGGGAGAAGAAGTTCA
891633 TAATGAGAAGAAC
66 TAATGAGAAGAAC
891646 ATTAGCTTGT
Statistics
Matches: 314, Mismatches: 30, Indels: 20
0.86 0.08 0.05
Matches are distributed among these distances:
133 2 0.01
134 52 0.17
135 38 0.12
136 1 0.00
138 5 0.02
139 214 0.68
140 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.25
Consensus pattern (139 bp):
GATCAACATTTCAAGTGAAGAGTTCATAATGAGAAGAACTCATCCGATAAGGGAGAAGAAGTTCA
TAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGTAACACCT
CACTCGAGG
Found at i:891512 original size:20 final size:19
Alignment explanation
Indices: 891450--891513 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 19
891440 CCAGTGAAGA
891450 GTTCATAATGAGAAGAACT
1 GTTCATAATGAGAAGAACT
* * *
891469 CATCCGATGAAGGAGAAGAA--
1 -GTTC-AT-AATGAGAAGAACT
891489 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAAC-T
891509 GTTCA
1 GTTCA
891514 ACCTTAGCTC
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
17 10 0.30
18 2 0.06
19 2 0.06
20 7 0.21
21 2 0.06
22 10 0.30
ACGTcount: A:0.41, C:0.12, G:0.23, T:0.23
Consensus pattern (19 bp):
GTTCATAATGAGAAGAACT
Found at i:891753 original size:42 final size:42
Alignment explanation
Indices: 891698--891806 Score: 209
Period size: 42 Copynumber: 2.6 Consensus size: 42
891688 CTTTTGCTCT
891698 TCCATCACATAAGGAGTTGGATCAGCATCATCATTTCGCTAA
1 TCCATCACATAAGGAGTTGGATCAGCATCATCATTTCGCTAA
*
891740 TCCATCACATAAGGAGTTGGATCAGCATCATCATTTCGCTAG
1 TCCATCACATAAGGAGTTGGATCAGCATCATCATTTCGCTAA
891782 TCCATCACATAAGGAGTTGGATCAG
1 TCCATCACATAAGGAGTTGGATCAG
891807 TATTACCTTA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 66 1.00
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (42 bp):
TCCATCACATAAGGAGTTGGATCAGCATCATCATTTCGCTAA
Found at i:894437 original size:23 final size:23
Alignment explanation
Indices: 894403--894489 Score: 124
Period size: 23 Copynumber: 3.8 Consensus size: 23
894393 GGGATATGCA
894403 CCGAAGTG-CCACATA-AATTTGTC
1 CCGAAG-GACCACATAGAA-TTGTC
894426 CCGAAGGACCACATAGAATTGTC
1 CCGAAGGACCACATAGAATTGTC
894449 CCGAAGGACCACATAGAATTGTC
1 CCGAAGGACCACATAGAATTGTC
* *
894472 CCGAAGAACCACGTAGAA
1 CCGAAGGACCACATAGAA
894490 CCCTAAACTC
Statistics
Matches: 60, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
22 1 0.02
23 57 0.95
24 2 0.03
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.17
Consensus pattern (23 bp):
CCGAAGGACCACATAGAATTGTC
Found at i:904175 original size:25 final size:24
Alignment explanation
Indices: 904147--904198 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
904137 TGAAATAATT
*
904147 AAAACAAAAGATAATAA-AAACATTA
1 AAAACAAAAAATAA-AATAAACA-TA
*
904172 AAAATAAAAAATAAAATAAACATA
1 AAAACAAAAAATAAAATAAACATA
904196 AAA
1 AAA
904199 TAAAGACCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.77, C:0.06, G:0.02, T:0.15
Consensus pattern (24 bp):
AAAACAAAAAATAAAATAAACATA
Found at i:905564 original size:91 final size:90
Alignment explanation
Indices: 905410--906122 Score: 1025
Period size: 91 Copynumber: 7.9 Consensus size: 90
905400 GAGCCAGAAG
* * ** *
905410 GAACAAGTTCTTCTCATTATGAATTTCTCCTCTTTCA-TGGATGAGTTATTCTCATTATGAACTC
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAACTC
* ** *
905474 TTCGTTGGAAATACT-AAGCTAAGGTT
66 TCCACTGGAAAT-CTGAA-CCAAGGTT
905500 GAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAACTC
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAACTC
905565 TCCACTGGAAATCTTGAACCAAGGTT
66 TCCACTGGAAATC-TGAACCAAGGTT
*
905591 GAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAGCTC
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAACTC
*
905656 TCCACTGGAAATCTTGAACCAATGTT
66 TCCACTGGAAATC-TGAACCAAGGTT
* * *
905682 GAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCGTAGGATGAGTTCTTCTCATTATGAACTC
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAACTC
*
905747 TCCACTGGAAATATTGAACCAAGGTT
66 TCCACTGGAAAT-CTGAACCAAGGTT
* * *
905773 GAACAAATTCTTCTTATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTC
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAACTC
** * *
905838 TCCGTTGGAAATACTGAGCTAAGGTT
66 TCCACTGGAAAT-CTGAACCAAGGTT
* *
905864 GAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTATTCTCATTATAAACTC
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAACTC
* * *
905929 TCCACTGGAAATGTTGAGCTAAGGTT
66 TCCACTGGAAAT-CTGAACCAAGGTT
* *
905955 GAACAAGTTCTTCTCATTATGAACTTCTTCCCCCTCGTTGGATGAGTTCTTCTCATTATGAACTC
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAACTC
906020 TCCACTGGAAATCTTGAACCAAGGTT
66 TCCACTGGAAATC-TGAACCAAGGTT
* * * *
906046 GAACAAGTTCTTCTCATTATGAACTTGTTCTCCCTCGTTGGACGAGTTCTTCTAATTATGAACTC
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAACTC
* *
906111 TCCGCTAGAAAT
66 TCCACTGGAAAT
906123 GTTGATCGGT
Statistics
Matches: 570, Mismatches: 48, Indels: 9
0.91 0.08 0.01
Matches are distributed among these distances:
90 34 0.06
91 534 0.94
92 2 0.00
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.37
Consensus pattern (90 bp):
GAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAACTC
TCCACTGGAAATCTGAACCAAGGTT
Found at i:906659 original size:36 final size:36
Alignment explanation
Indices: 906602--906793 Score: 97
Period size: 36 Copynumber: 5.6 Consensus size: 36
906592 AAAGATCAAT
* * *
906602 GTTTCAAGGAAAACTATCTCAAGAGAGACAAAACTC
1 GTTTCAAGGGAAACGACCTCAAGAGAGACAAAACTC
****
906638 GTTTCAAGGGAAACGACCTC-A-A-AGATTTTA-T-
1 GTTTCAAGGGAAACGACCTCAAGAGAGACAAAACTC
* * *
906669 GTTTCAAGAGAAACTG-TCTCAAG-GAATACAAAACTC
1 GTTTCAAGGGAAAC-GACCTCAAGAG-AGACAAAACTC
****
906705 GTTTCAAGGGAAACGACCTC-A-A-AGATTTTA-T-
1 GTTTCAAGGGAAACGACCTCAAGAGAGACAAAACTC
* * *
906736 GTTTCAAGAGAAACTG-TCTCAAG-GAATACAAAACTC
1 GTTTCAAGGGAAAC-GACCTCAAGAG-AGACAAAACTC
906772 GTTTCAAGGGAAACGACCTCAA
1 GTTTCAAGGGAAACGACCTCAA
906794 AGATTTTATG
Statistics
Matches: 109, Mismatches: 30, Indels: 34
0.63 0.17 0.20
Matches are distributed among these distances:
31 32 0.29
32 6 0.06
33 7 0.06
34 7 0.06
35 6 0.06
36 51 0.47
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.23
Consensus pattern (36 bp):
GTTTCAAGGGAAACGACCTCAAGAGAGACAAAACTC
Found at i:906673 original size:31 final size:31
Alignment explanation
Indices: 906638--906815 Score: 117
Period size: 31 Copynumber: 5.4 Consensus size: 31
906628 GACAAAACTC
*
906638 GTTTCAAGGGAAACGACCTCAAAGATTTTAT
1 GTTTCAAGAGAAACGACCTCAAAGATTTTAT
* * ***
906669 GTTTCAAGAGAAACTG-TCTCAAGGAATACAAAACT
1 GTTTCAAGAGAAAC-GACCTCAAAG-AT--TTTA-T
*
906704 CGTTTCAAGGGAAACGACCTCAAAGATTTTAT
1 -GTTTCAAGAGAAACGACCTCAAAGATTTTAT
* * ***
906736 GTTTCAAGAGAAACTG-TCTCAAGGAATACAAAACT
1 GTTTCAAGAGAAAC-GACCTCAAAG-AT--TTTA-T
*
906771 CGTTTCAAGGGAAACGACCTCAAAGATTTTAT
1 -GTTTCAAGAGAAACGACCTCAAAGATTTTAT
906803 GTTTCAAGAGAAA
1 GTTTCAAGAGAAA
906816 ATGTCCCAAG
Statistics
Matches: 108, Mismatches: 25, Indels: 28
0.67 0.16 0.17
Matches are distributed among these distances:
31 50 0.46
32 8 0.07
33 2 0.02
34 2 0.02
35 8 0.07
36 38 0.35
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.26
Consensus pattern (31 bp):
GTTTCAAGAGAAACGACCTCAAAGATTTTAT
Found at i:906861 original size:134 final size:136
Alignment explanation
Indices: 906600--906916 Score: 403
Period size: 134 Copynumber: 2.3 Consensus size: 136
906590 TCAAAGATCA
906600 ATGTTTCAAG-GAAAACTATCTCAA-GAGAGACAAAACTCGTTTCAAGGGAAACGACCTCAAAGA
1 ATGTTTCAAGAG-AAACTATCTCAAGGAGAGACAAAACTCGTTTCAAGGGAAACGACCTCAAAGA
* * * * *
906663 TTTTATGTTTCAAGAGAAACTGTCTCAAGGAATACAAAACTCGTTTCAAGGGAAACGACCTCAAA
65 TTTTATGTTTCAAGAGAAAATGTCCCAAGGAAGACAAAACTCGTTTCAAGAGAAACGAACTCAAA
906728 GA-TTTT
130 GATTTTT
* *
906734 ATGTTTCAAGAGAAACTGTCTCAAGGA-ATACAAAACTCGTTTCAAGGGAAACGACCTCAAAGAT
1 ATGTTTCAAGAGAAACTATCTCAAGGAGAGACAAAACTCGTTTCAAGGGAAACGACCTCAAAGAT
* * * * *
906798 TTTATGTTTCAAGAGAAAATGTCCCAAGGAAGAGAAAATTTGTTTCAAGAGAAA-TATATTCAAA
66 TTTATGTTTCAAGAGAAAATGTCCCAAGGAAGACAAAACTCGTTTCAAGAGAAACGA-ACTCAAA
906862 GATTTTTTT
130 GA--TTTTT
* * * * *
906871 TTGTTTCAAAAGAAACTATCTCAA-GCGAGACAAAATTTGTTTCAAG
1 ATGTTTCAAGAGAAACTATCTCAAGGAGAGACAAAACTCGTTTCAAG
906917 TGAATATGTC
Statistics
Matches: 157, Mismatches: 19, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
133 1 0.01
134 111 0.71
135 3 0.02
136 1 0.01
137 41 0.26
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.27
Consensus pattern (136 bp):
ATGTTTCAAGAGAAACTATCTCAAGGAGAGACAAAACTCGTTTCAAGGGAAACGACCTCAAAGAT
TTTATGTTTCAAGAGAAAATGTCCCAAGGAAGACAAAACTCGTTTCAAGAGAAACGAACTCAAAG
ATTTTT
Found at i:906867 original size:67 final size:67
Alignment explanation
Indices: 906574--906851 Score: 400
Period size: 67 Copynumber: 4.2 Consensus size: 67
906564 CAAAATTCAG
* * ** *
906574 TTCAAGGGAAACAATCTCAAAGA-TCAATGTTTCAAG-GAAAACTATCTCAA-GAGAGACAAAAC
1 TTCAAGGGAAACGACCTCAAAGATTTTATGTTTCAAGAG-AAACTGTCTCAAGGA-AGACAAAAC
906636 TCGT
64 TCGT
*
906640 TTCAAGGGAAACGACCTCAAAGATTTTATGTTTCAAGAGAAACTGTCTCAAGGAATACAAAACTC
1 TTCAAGGGAAACGACCTCAAAGATTTTATGTTTCAAGAGAAACTGTCTCAAGGAAGACAAAACTC
906705 GT
66 GT
*
906707 TTCAAGGGAAACGACCTCAAAGATTTTATGTTTCAAGAGAAACTGTCTCAAGGAATACAAAACTC
1 TTCAAGGGAAACGACCTCAAAGATTTTATGTTTCAAGAGAAACTGTCTCAAGGAAGACAAAACTC
906772 GT
66 GT
* * * * *
906774 TTCAAGGGAAACGACCTCAAAGATTTTATGTTTCAAGAGAAAATGTCCCAAGGAAGAGAAAATTT
1 TTCAAGGGAAACGACCTCAAAGATTTTATGTTTCAAGAGAAACTGTCTCAAGGAAGACAAAACTC
906839 GT
66 GT
*
906841 TTCAAGAGAAA
1 TTCAAGGGAAA
906852 TATATTCAAA
Statistics
Matches: 196, Mismatches: 13, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
66 21 0.11
67 172 0.88
68 3 0.02
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.24
Consensus pattern (67 bp):
TTCAAGGGAAACGACCTCAAAGATTTTATGTTTCAAGAGAAACTGTCTCAAGGAAGACAAAACTC
GT
Found at i:906913 original size:36 final size:36
Alignment explanation
Indices: 906870--906966 Score: 115
Period size: 36 Copynumber: 2.7 Consensus size: 36
906860 AAGATTTTTT
*
906870 TTTGTTTCAAAAGAAACTATCTCAAGCGAGACAAAA
1 TTTGTTTCAAGAGAAACTATCTCAAGCGAGACAAAA
* * *
906906 TTTGTTTCAAGTGAATA-TGTCTCAAGCGAGACCAAA
1 TTTGTTTCAAGAGAA-ACTATCTCAAGCGAGACAAAA
* * *
906942 TTTATTCCAAGAGAAACAATCTCAA
1 TTTGTTTCAAGAGAAACTATCTCAA
906967 AGGTTGATGC
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
35 1 0.02
36 48 0.96
37 1 0.02
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTATCTCAAGCGAGACAAAA
Found at i:907125 original size:37 final size:34
Alignment explanation
Indices: 907040--907125 Score: 102
Period size: 34 Copynumber: 2.4 Consensus size: 34
907030 AAATATTTTG
* *
907040 TGTTTCAAGAGAAACTATCTCAAGAGAGAAAATT
1 TGTTTCAAGAGAAACTATATCAAGAGACAAAATT
*
907074 TGTTTCAA-AGGAAACTGTATCAAGATAGACAAAACTT
1 TGTTTCAAGA-GAAACTATATCAAG--AGACAAAA-TT
907111 TGTTTCAAGAGAAAC
1 TGTTTCAAGAGAAAC
907126 AAACTCAGGC
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
33 1 0.02
34 20 0.45
36 7 0.16
37 15 0.34
38 1 0.02
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (34 bp):
TGTTTCAAGAGAAACTATATCAAGAGACAAAATT
Found at i:907159 original size:166 final size:166
Alignment explanation
Indices: 906867--907172 Score: 370
Period size: 166 Copynumber: 1.8 Consensus size: 166
906857 TCAAAGATTT
* *
906867 TTTTTTGTTTCAAAAGAAACTATCTCAAGCGAGACAAAATTTGTTTCAAGTGAATATGTCTCAAG
1 TTTTGTGTTTCAAAAGAAACTATCTCAA-CGAGACAAAATTTGTTTCAAGTGAATATGTATCAAG
* * * **
906932 CGAGACCAAATTTATTCCAAGAGAAACAATCTCAAAGGTTGATGCTTCAAGAGAACTGTCTCAGG
65 AGAGACAAAATTTATTCCAAGAGAAACAAACTC-AAGGTTGATGCTTCAAGAGAACTGTCTCAAA
906997 AGAGACAAAAAATGTTTCAAGGGAAACCATCGCAAATA
129 AGAGACAAAAAATGTTTCAAGGGAAACCATCGCAAATA
* *
907035 TTTTGTGTTTCAAGAGAAACTATCTCAA-GAGAGAAAATTTGTTTCAAAG-GAA-ACTGTATCAA
1 TTTTGTGTTTCAAAAGAAACTATCTCAACGAGACAAAATTTGTTTC-AAGTGAATA-TGTATCAA
* * * * * **
907097 GATAGACAAAACTTTGTTTCAAGAGAAACAAACTC-AGGCTT-TTGTTTTGAGAGAAACTGTCTC
64 GAGAGACAAAA-TTTATTCCAAGAGAAACAAACTCAAGG-TTGATGCTTCAAGAG-AACTGTCTC
907160 AAAAGAGACAAAA
126 AAAAGAGACAAAA
907173 CTTGTTATGA
Statistics
Matches: 117, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
165 12 0.10
166 56 0.48
167 23 0.20
168 26 0.22
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (166 bp):
TTTTGTGTTTCAAAAGAAACTATCTCAACGAGACAAAATTTGTTTCAAGTGAATATGTATCAAGA
GAGACAAAATTTATTCCAAGAGAAACAAACTCAAGGTTGATGCTTCAAGAGAACTGTCTCAAAAG
AGACAAAAAATGTTTCAAGGGAAACCATCGCAAATA
Found at i:907413 original size:90 final size:90
Alignment explanation
Indices: 907260--907475 Score: 324
Period size: 90 Copynumber: 2.4 Consensus size: 90
907250 TGAAAATCAT
*
907260 GCTTAGTTTCTAAAAACTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGAAGGA
1 GCTTAGTTTCTAAAAACTCATTTGAAAACATCATGCACTGAAGGTCTTATGGATGGCCCGAAGGA
* * *
907325 ATTATAAATCAAGAAACCCTCGAAG
66 ATTACAAATCAAGAAACCCCCGAAA
* *
907350 GCTTAGTTTTTAAAATCTCATTTGAAAACATCATGCACTGAAGGTCTTATGGATGGCCCGAAGGA
1 GCTTAGTTTCTAAAAACTCATTTGAAAACATCATGCACTGAAGGTCTTATGGATGGCCCGAAGGA
*
907415 CTTACAAATCAAGAAACCCCCGAAA
66 ATTACAAATCAAGAAACCCCCGAAA
* * * *
907440 GCTTAGTATCCTAAAAAATCTTTTGAAAATATCATG
1 GCTTAGT-TTCTAAAAACTCATTTGAAAACATCATG
907476 TTGTTTGTGT
Statistics
Matches: 112, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
90 90 0.80
91 22 0.20
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.27
Consensus pattern (90 bp):
GCTTAGTTTCTAAAAACTCATTTGAAAACATCATGCACTGAAGGTCTTATGGATGGCCCGAAGGA
ATTACAAATCAAGAAACCCCCGAAA
Found at i:909404 original size:17 final size:19
Alignment explanation
Indices: 909377--909411 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
909367 CTATTCTCTT
909377 CTTTCTTCTTCT-TTTTTC
1 CTTTCTTCTTCTATTTTTC
909395 CTTT-TTCTTCTATTTTT
1 CTTTCTTCTTCTATTTTT
909412 TCTTCTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74
Consensus pattern (19 bp):
CTTTCTTCTTCTATTTTTC
Found at i:909420 original size:10 final size:10
Alignment explanation
Indices: 909373--909422 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
909363 CTGTCTATTC
*
909373 TCTTCTTTCT
1 TCTTCTTTTT
909383 TCTTCTTTTT
1 TCTTCTTTTT
909393 TC--C-TTTT
1 TCTTCTTTTT
909400 TCTTCTATTTTT
1 TCTTC--TTTTT
909412 TCTTCTTTTT
1 TCTTCTTTTT
909422 T
1 T
909423 TTTTGTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
7 6 0.18
8 1 0.03
9 1 0.03
10 17 0.50
12 9 0.26
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (10 bp):
TCTTCTTTTT
Found at i:909432 original size:22 final size:21
Alignment explanation
Indices: 909407--909449 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
909397 TTTTCTTCTA
*
909407 TTTTTTCTTCTTTTTTTTTTGT
1 TTTTTTC-TCTTATTTTTTTGT
909429 TTTTTTCTCTTATTTTTTTGT
1 TTTTTTCTCTTATTTTTTTGT
909450 GTGTGTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.02, C:0.09, G:0.05, T:0.84
Consensus pattern (21 bp):
TTTTTTCTCTTATTTTTTTGT
Found at i:909446 original size:12 final size:11
Alignment explanation
Indices: 909378--909445 Score: 61
Period size: 11 Copynumber: 6.3 Consensus size: 11
909368 TATTCTCTTC
*
909378 TTTCTTCTTCT
1 TTTCTTCTTTT
*
909389 TTT-TTC-CTT
1 TTTCTTCTTTT
909398 TTTCTTCTATTT
1 TTTCTTCT-TTT
909410 TTTCTTCTTTT
1 TTTCTTCTTTT
* *
909421 TTTTTTGTTTT
1 TTTCTTCTTTT
909432 TTTC-TCTTATT
1 TTTCTTCTT-TT
909443 TTT
1 TTT
909446 TTGTGTGTGT
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
9 4 0.09
10 9 0.20
11 23 0.50
12 10 0.22
ACGTcount: A:0.03, C:0.16, G:0.01, T:0.79
Consensus pattern (11 bp):
TTTCTTCTTTT
Found at i:909447 original size:24 final size:26
Alignment explanation
Indices: 909407--909462 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 26
909397 TTTTCTTCTA
* *
909407 TTTTT-TCTTCTTTTTTT-TTTGT-T
1 TTTTTCTCTTATTTTTTTGTGTGTGT
909430 TTTTTCTCTTATTTTTTTGTGTGTGT
1 TTTTTCTCTTATTTTTTTGTGTGTGT
909456 TTTTTCT
1 TTTTTCT
909463 ATATCTCTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 5 0.18
24 11 0.39
25 4 0.14
26 8 0.29
ACGTcount: A:0.02, C:0.09, G:0.09, T:0.80
Consensus pattern (26 bp):
TTTTTCTCTTATTTTTTTGTGTGTGT
Found at i:910467 original size:19 final size:19
Alignment explanation
Indices: 910440--910481 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
910430 TGATGCTTCA
*
910440 ATCTTCATTGCTTCATGTT
1 ATCTCCATTGCTTCATGTT
910459 ATCTCCATTGCTTCATGTT
1 ATCTCCATTGCTTCATGTT
910478 ATCT
1 ATCT
910482 TTGAATAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.17, C:0.24, G:0.10, T:0.50
Consensus pattern (19 bp):
ATCTCCATTGCTTCATGTT
Found at i:919715 original size:28 final size:29
Alignment explanation
Indices: 919641--919715 Score: 70
Period size: 28 Copynumber: 2.7 Consensus size: 29
919631 ACTTTTATAC
919641 TTTATTTTATTTTAATTTTGACATGATGT
1 TTTATTTTATTTTAATTTTGACATGATGT
* *
919670 TTTGA--TTA-TTTATGTTTTAGTCAT-AT-T
1 TTT-ATTTTATTTTA-ATTTT-GACATGATGT
919697 TTTATTTTATTTTAATTTT
1 TTTATTTTATTTTAATTTT
919716 TTCATGGTGC
Statistics
Matches: 37, Mismatches: 3, Indels: 13
0.70 0.06 0.25
Matches are distributed among these distances:
26 1 0.03
27 8 0.22
28 16 0.43
29 11 0.30
30 1 0.03
ACGTcount: A:0.23, C:0.03, G:0.08, T:0.67
Consensus pattern (29 bp):
TTTATTTTATTTTAATTTTGACATGATGT
Found at i:920489 original size:130 final size:130
Alignment explanation
Indices: 920204--920532 Score: 329
Period size: 130 Copynumber: 2.6 Consensus size: 130
920194 TTTCATTTGG
* * * * * *
920204 ATGGAGTAATAAATTATTGTTTTAAGGCATGAGAGGTCATTTATTCTCTATTGGAA--A-T--A-
1 ATGGAGCAATAAATGATTATTTTAAGGTATGAGAGGTCATTTATTCTCGATTGAAATCATTAGAT
* * * *
920263 A-T-TCGA-TTTCTCTTGAATTAATATTGATTTTTAAGATAAAATAGTGATATCTCTTAATTTCG
66 ATTATC-ATTTTCACTTGAATCAATATTGAATTTTAAGATAAAATAGTGATATCTATTAATTTCG
920325 A
130 A
* * * *
920326 ATGGAGCATTAAATGATTGTTTTAAGGTGTGAGAGGTCATTTATTCTCGATTAGAAATCATTAGT
1 ATGGAGCAATAAATGATTATTTTAAGGTATGAGAGGTCATTTATTCTCGATT-GAAATCATTAGA
* * * * *
920391 TATTATCGTTTTCACTTGAATCGATATTGAATTTTAAGACT-GAATAG-GATATCTATTCATTTT
65 TATTATCATTTTCACTTGAATCAATATTGAATTTTAAGA-TAAAATAGTGATATCTATTAATTTC
920454 GA
129 GA
* * * * * *
920456 TTGGAGTAATAAATTATTATTTTAAGGTATGAGAGGTCATTTATTTTTGATTGGAATCATTAGAT
1 ATGGAGCAATAAATGATTATTTTAAGGTATGAGAGGTCATTTATTCTCGATTGAAATCATTAGAT
920521 ATTATCATTTTC
66 ATTATCATTTTC
920533 TCTCTTAAAA
Statistics
Matches: 168, Mismatches: 28, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
122 46 0.27
123 3 0.02
125 1 0.01
126 1 0.01
129 23 0.14
130 60 0.36
131 33 0.20
132 1 0.01
ACGTcount: A:0.32, C:0.08, G:0.17, T:0.43
Consensus pattern (130 bp):
ATGGAGCAATAAATGATTATTTTAAGGTATGAGAGGTCATTTATTCTCGATTGAAATCATTAGAT
ATTATCATTTTCACTTGAATCAATATTGAATTTTAAGATAAAATAGTGATATCTATTAATTTCGA
Found at i:922376 original size:13 final size:13
Alignment explanation
Indices: 922358--922401 Score: 70
Period size: 13 Copynumber: 3.4 Consensus size: 13
922348 GTCATAAATC
*
922358 TATGACGCACATT
1 TATGACACACATT
*
922371 TATGACACGCATT
1 TATGACACACATT
922384 TATGACACACATT
1 TATGACACACATT
922397 TATGA
1 TATGA
922402 TGTGCATTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (13 bp):
TATGACACACATT
Found at i:922573 original size:2 final size:2
Alignment explanation
Indices: 922566--922592 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
922556 TGTCATAAAT
922566 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
922593 TGTAGATTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:927191 original size:42 final size:42
Alignment explanation
Indices: 927144--927223 Score: 151
Period size: 42 Copynumber: 1.9 Consensus size: 42
927134 TTTGTTTCTC
927144 GAGTTAATGGTTCTTTACCTAGAGAGTTCAACCCTAGTTGGG
1 GAGTTAATGGTTCTTTACCTAGAGAGTTCAACCCTAGTTGGG
*
927186 GAGTTAATGGTTCTTTACCTAGAGAGTTCAACCTTAGT
1 GAGTTAATGGTTCTTTACCTAGAGAGTTCAACCCTAGT
927224 CGAGGTCTCC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (42 bp):
GAGTTAATGGTTCTTTACCTAGAGAGTTCAACCCTAGTTGGG
Found at i:929454 original size:2 final size:2
Alignment explanation
Indices: 929447--929473 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
929437 TATCTAATAC
929447 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
929474 CTTAGTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:930644 original size:22 final size:22
Alignment explanation
Indices: 930617--930660 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
930607 TCCATTTCAA
*
930617 CATCAACACCATTAACATCTTC
1 CATCAACACCATCAACATCTTC
**
930639 CATCAAGGCCATCAACATCTTC
1 CATCAACACCATCAACATCTTC
930661 ATAATTCCAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.34, C:0.36, G:0.05, T:0.25
Consensus pattern (22 bp):
CATCAACACCATCAACATCTTC
Found at i:935028 original size:28 final size:27
Alignment explanation
Indices: 934983--935063 Score: 74
Period size: 29 Copynumber: 2.8 Consensus size: 27
934973 AAAAATAAAA
*
934983 AATAAAA-AATAAACTAAATATTAAAATAG
1 AATAAAAGAA-AAA-TAAATATCAAAAT-G
*
935012 AATAAAAGAAAAATAAAGATCAAAATG
1 AATAAAAGAAAAATAAATATCAAAATG
*
935039 AATGAAAGCAAAAAATAAGATATCA
1 AATAAAAG--AAAAATAA-ATATCA
935064 CAACACCCTT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
27 8 0.18
28 11 0.25
29 18 0.41
30 7 0.16
ACGTcount: A:0.68, C:0.05, G:0.09, T:0.19
Consensus pattern (27 bp):
AATAAAAGAAAAATAAATATCAAAATG
Found at i:937121 original size:13 final size:13
Alignment explanation
Indices: 937103--937129 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
937093 TCATAAATTA
937103 ATTAAAATGTATT
1 ATTAAAATGTATT
937116 ATTAAAATGTATT
1 ATTAAAATGTATT
937129 A
1 A
937130 AGTAATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (13 bp):
ATTAAAATGTATT
Found at i:937195 original size:2 final size:2
Alignment explanation
Indices: 937134--937180 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
937124 GTATTAAGTA
937134 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
937176 AT AT A
1 AT AT A
937181 CACACACAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:938893 original size:29 final size:29
Alignment explanation
Indices: 938841--938899 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
938831 TGGTGGAGTG
*
938841 GGTGGAAAGAAATATGATAATGGAAGCTT
1 GGTGGAAAGAAATAGGATAATGGAAGCTT
* **
938870 GGTGGAAAGAAATGGGATGGTGGAAGCTT
1 GGTGGAAAGAAATAGGATAATGGAAGCTT
938899 G
1 G
938900 ATTGAGGATG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.36, C:0.03, G:0.39, T:0.22
Consensus pattern (29 bp):
GGTGGAAAGAAATAGGATAATGGAAGCTT
Found at i:939213 original size:117 final size:111
Alignment explanation
Indices: 939063--939320 Score: 301
Period size: 117 Copynumber: 2.3 Consensus size: 111
939053 ATGTTGATAT
* * *
939063 AAGGTTGAACAAGTTCTTCACATTATGAACTTCTTC-TCCATCATTGAATGAGTTCTTCTTATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCATTGAATGAGTTATTCTCATTA
*
939127 T-ACTCTCCTTTGGAAATGTTGATGCCACCTCTTTCTGCAGTGAACTTGAAA
65 TAACTCT--TTTGGAAATGTTGAT-CCACCTCCTTCTGCAGTGAACTTG--A
* *
939178 CCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCGTTGGATGAGTTATTCTCATT
1 --AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTGAATGAGTTATTCTCATT
* * ** *
939243 ATGAACTCTTTTGGAAATGTTGGTTCACCTCCTTCTGTGGTGAATTTGA
64 AT-AACTCTTTTGGAAATGTTGATCCACCTCCTTCTGCAGTGAACTTGA
939292 AA-G--GAACAAGTTCTTCTCATTATGAACTT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTT
939321 TCTCTTTTAG
Statistics
Matches: 127, Mismatches: 11, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
109 26 0.20
111 1 0.01
112 2 0.02
114 1 0.01
116 19 0.15
117 70 0.55
118 3 0.02
119 5 0.04
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (111 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCATTGAATGAGTTATTCTCATTAT
AACTCTTTTGGAAATGTTGATCCACCTCCTTCTGCAGTGAACTTGA
Found at i:939819 original size:39 final size:39
Alignment explanation
Indices: 939668--941711 Score: 2908
Period size: 39 Copynumber: 52.7 Consensus size: 39
939658 GTTTTAAGAA
* * *
939668 AAACTATCTCAAGTGAGAT-ACAT-TTCTTGTTTCAAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTC-TGTTTCGAGGG
* * * * *
939706 AAACTGTCTCAAGAGAGACAAAA--TT-TGTTTCAAGCG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
* * * * **
939742 AAATTGTCTCAAGAGAG-TCAAAA-C-TC-ATTTAAAGGG
1 AAACTATCTCAAGCGAGAT-AAAATCTTCTGTTTCGAGGG
* * *
939778 AAAATATCTCAAGCGAGATAAAATCTTCTCTTTTGAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
* * *
939817 AAACTATCTCAAGCGAGATAAAATCTTTTGTTTCAATGG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
*
939856 AAACTATCTCAAGCGAGAAAAAATCTTCTGTTTCGAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
* *
939895 AAACTATCTCAAGCGAGAAAAAATGTTCTGTTTCGAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
* * * *
939934 AAACTATCTTAAGCGAGAAAAAATGTTCTGTTTCCAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
*
939973 AAACTATCTCAAGAGAGATAAAATCTTCTGTTTCGAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
* *
940012 AAACTACCTCAAGCGAGATAAAATCTTCTGTTTCGAGGT
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
*
940051 AAACTACCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
*
940090 AAACTACCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
940129 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
* *
940168 AAACTATCACAAGCGAGATAAAATCTTATGTTTCGAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
* *
940207 AAACTATCTCAAGCGAGATAAAATCTTATGTTTCAAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
* *
940246 AAACTATCTCAAGTGAGATAAAATCTTTTGTTTCGAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
* * * * *
940285 AAACTATCACAAGCGAGAAAAAATATTATGTTTCAAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
* *
940324 AAACTATCTCAAGCGAGATAAAATTTTCTGTTTCTAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
* * *
940363 AAACTATCTCAAGAGAGATAAAATCTTTTGATTCGAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
* *
940402 AAACTACCTCAAGCTAGATAAAATCTTCTGTTTCGAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
*
940441 AAACTACCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
940480 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
940519 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
* *
940558 AAACTATCACAAACGAGATAAAATCTTCTGTTTCGAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
* *
940597 AAACTATCTCATGCGAGATAAAATCTTCAGTTTCGAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
* **
940636 AAACTATCTCAGGCGAGATAAAATCTTCTGTTTCGAGTA
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
* * * * *
940675 AAACTATCTAAAGCGAGACAAAATATTTTGTTTCAAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
* * * *
940714 AAACTATCGCAAGCAAGATAAAATCTTTTATTTCGAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
*
940753 AAACTATCTCAAGAGAGATAAAATCTTCTGTTTCGAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
* *
940792 AAACTATCTCAAGTGAGATAAAATCTTCTGTTTCAAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
* *
940831 AAATTATCTCAAGCGAGATAAAATCTTATGTTTCGAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
940870 AAACTATCTCAAG-GAGATAAAATCTTCTGTTTCGAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
*
940908 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTGGAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
* *
940947 AAACTATCTCAAGCGAGACAAAATCTTATGTTTCGAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
940986 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
941025 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
*
941064 AAATTATCTCAAGCGAGATAAAATCTTC---TTCGAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
*
941100 AAACTATCTCAAGCGAGATAAAATCTTATGTTTCGAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
* * * * * *
941139 AAACTACCTGAAACGAGTTAAAATCTTTTGTTTCGAGAG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
* * *
941178 AAACTACCTCAATCGAGATAAAATCTTTTGTTTCGAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
* *
941217 AAACTATCTCAAGCGAGATAAAATCTTTTGTTTCGAGAG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
*
941256 AAACTATCTCAAGCGAGATAAAATCTTCAGTTTCGAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
941295 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
* * * *
941334 AAATTATCTCAAGCGAGACAAAATCTTATGTTTCGAGGT
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
* *
941373 AAACTATCTCAAGCGAGATAAAATCTTTTATTTCGAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
941412 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
* *
941451 AAACTATCTTAAGCGAGATAAAATCTTTTGTTTCGAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
*
941490 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTTGAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
* * * * * *
941529 AAACTATCTCGAGGGAGACAAAATATTTTGTTTTGAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
* * * * *
941568 AAACTTTCTCGAGCGAGACAAAATCTTTTGTTTTGAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
** ** * *
941607 AAACTATCTTGAGCGAGGCAAAATCTTTTGTTTTGAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
* *
941646 AAACTATCTCGAGCGAGATAAAATCTTTTGTTTCGAGGG
1 AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
**
941685 AAACTATCTCAAGTTAGATAAAATCTT
1 AAACTATCTCAAGCGAGATAAAATCTT
941712 ATTTAAAAAC
Statistics
Matches: 1827, Mismatches: 167, Indels: 23
0.91 0.08 0.01
Matches are distributed among these distances:
36 90 0.05
37 2 0.00
38 57 0.03
39 1678 0.92
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (39 bp):
AAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGG
Found at i:940605 original size:22 final size:22
Alignment explanation
Indices: 940580--940644 Score: 52
Period size: 22 Copynumber: 3.2 Consensus size: 22
940570 ACGAGATAAA
940580 ATCTTCTGTTTCGAGGGAAACT
1 ATCTTCTGTTTCGAGGGAAACT
**
940602 ATC-TCATG---CGAGATAAA--
1 ATCTTC-TGTTTCGAGGGAAACT
*
940619 ATCTTCAGTTTCGAGGGAAACT
1 ATCTTCTGTTTCGAGGGAAACT
940641 ATCT
1 ATCT
940645 CAGGCGAGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 14
0.62 0.10 0.28
Matches are distributed among these distances:
17 4 0.13
18 2 0.06
19 7 0.23
20 7 0.23
21 2 0.06
22 9 0.29
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.32
Consensus pattern (22 bp):
ATCTTCTGTTTCGAGGGAAACT
Found at i:941803 original size:76 final size:76
Alignment explanation
Indices: 941716--941894 Score: 324
Period size: 76 Copynumber: 2.4 Consensus size: 76
941706 AATCTTATTT
*
941716 AAAAACAATCTTGAGTGAAATGAAATATCTTCTTTCTAGTAAAAATTTTCTCAAGCGAGACAAAT
1 AAAAACAATCTTGAGTGAAATGAAATATCTTCTTTCGAGTAAAAATTTTCTCAAGCGAGACAAAT
941781 CTTATTTTAAG
66 CTTATTTTAAG
*
941792 AAAAACAATCTTGAGTGAAATGAAATTTCTTCTTTCGAGTAAAAATTTTCTCAAGCGAGACAAAT
1 AAAAACAATCTTGAGTGAAATGAAATATCTTCTTTCGAGTAAAAATTTTCTCAAGCGAGACAAAT
*
941857 CTTGTTTTAAG
66 CTTATTTTAAG
941868 AAAAACAATCTTGAGTGAAAT-AAATAT
1 AAAAACAATCTTGAGTGAAATGAAATAT
941895 TCTGTATTAA
Statistics
Matches: 99, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
75 5 0.05
76 94 0.95
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (76 bp):
AAAAACAATCTTGAGTGAAATGAAATATCTTCTTTCGAGTAAAAATTTTCTCAAGCGAGACAAAT
CTTATTTTAAG
Found at i:946787 original size:20 final size:20
Alignment explanation
Indices: 946737--946788 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
946727 AAATATATCG
*
946737 ATCAACAATGATATAACAGGT
1 ATCAA-AATGATAAAACAGGT
* *
946758 A-AAAATATGATAAAACTGGT
1 ATCAAA-ATGATAAAACAGGT
946778 ATCAAAATGAT
1 ATCAAAATGAT
946789 GAGACCGATA
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
19 1 0.04
20 20 0.80
21 4 0.16
ACGTcount: A:0.52, C:0.10, G:0.13, T:0.25
Consensus pattern (20 bp):
ATCAAAATGATAAAACAGGT
Found at i:946999 original size:182 final size:181
Alignment explanation
Indices: 946544--947016 Score: 648
Period size: 181 Copynumber: 2.6 Consensus size: 181
946534 GGTCCAAATT
* * * * **
946544 AAAAATGTATCGATCCACAACGATATAACAGGTAAAACTATGACAAAACC-AGTATTGAAATGAT
1 AAAAATGTATCGATCAACATCGATATAACAGGTAAAAATATGATAAAACCGA-TATCAAAATGAT
* * * *
946608 AAAACCGG-AAAAGCGGTACCGAATATATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACT
65 AAAACCGGTAAAA-CGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACT
* *
946672 TCGTTAATTTAAAAGAGAAACAGTTTAGCGCCTATAAAGTGTCGATACTTTCA
129 TCGTGAATTTAAAAGAGAAACAGTTTAGCGCCTATAAAGTGTCGATACTTTAA
* * *
946725 AAAAATATATCGATCAACAAT-GATATAACAGGTAAAAATATGATAAAACTGGTATCAAAATGAT
1 AAAAATGTATCGATCAAC-ATCGATATAACAGGTAAAAATATGATAAAACCGATATCAAAATGAT
* * * * * *
946789 GAGACCGATAAAACGCTACCGGATATATTGAAAGTGTCGAAACTTT-ATATAAGGATCGACACTT
65 AAAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTT
* * *
946853 TGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAATTGTCGATACTTTAA
130 CGTGAATTTAAAAGAGAAACAG-TTTAGCGCCTATAAAGTGTCGATACTTTAA
946906 AAAAATGTATCGATCAAACATCGATATAACAGGTAAAAATATGATAAAACCGATATCAAAATGAT
1 AAAAATGTATCGATC-AACATCGATATAACAGGTAAAAATATGATAAAACCGATATCAAAATGAT
*
946971 AAAACCGGTAAAATGATACCGGATATATTAAAAGTGTCGATACTTT
65 AAAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTT
947017 CGTAAGTACG
Statistics
Matches: 254, Mismatches: 32, Indels: 11
0.86 0.11 0.04
Matches are distributed among these distances:
180 37 0.15
181 129 0.51
182 88 0.35
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.26
Consensus pattern (181 bp):
AAAAATGTATCGATCAACATCGATATAACAGGTAAAAATATGATAAAACCGATATCAAAATGATA
AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAGAGAAACAGTTTAGCGCCTATAAAGTGTCGATACTTTAA
Found at i:949268 original size:21 final size:21
Alignment explanation
Indices: 949242--949282 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
949232 AAGACAATCA
949242 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAT
* *
949263 AGAGTCGAAGATACACTTGA
1 AGAGTCGAAGAGAAACTTGA
949283 GAGGCATAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.12, G:0.27, T:0.20
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAT
Found at i:949361 original size:33 final size:33
Alignment explanation
Indices: 949319--949384 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
949309 AAATAGATGG
*
949319 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
949352 AGTGGTGAAAGAGGTTGAGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
949385 TCTTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:949616 original size:33 final size:33
Alignment explanation
Indices: 949571--949636 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
949561 AAAATATGAA
949571 GAAGAAAAGAGGGAGGAGGAAGAAGAAGAGATG
1 GAAGAAAAGAGGGAGGAGGAAGAAGAAGAGATG
* *
949604 GAAGAAATGAGGGGGGAGGAAGAAGAAGAGATG
1 GAAGAAAAGAGGGAGGAGGAAGAAGAAGAGATG
949637 AAAAATTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.47, T:0.05
Consensus pattern (33 bp):
GAAGAAAAGAGGGAGGAGGAAGAAGAAGAGATG
Found at i:951160 original size:19 final size:20
Alignment explanation
Indices: 951136--951184 Score: 84
Period size: 19 Copynumber: 2.5 Consensus size: 20
951126 AATGTAGGGT
951136 TAATTTTGTATTA-GATTTA
1 TAATTTTGTATTATGATTTA
951155 TAATTTTGTA-TATGATTTA
1 TAATTTTGTATTATGATTTA
951174 TAATTTTGTAT
1 TAATTTTGTAT
951185 GTGAATGTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 2 0.07
19 26 0.93
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.59
Consensus pattern (20 bp):
TAATTTTGTATTATGATTTA
Found at i:951762 original size:200 final size:200
Alignment explanation
Indices: 951419--951806 Score: 668
Period size: 200 Copynumber: 1.9 Consensus size: 200
951409 AATTTACAAT
** *
951419 ATGGCAAACAGGGTGCAACCATAACTTGTCAATCCATATATAAAAGGTGTCGATCCCAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCAATCCATATAAAAAAGGTGTCGATCCCAGAAACAT
* * *
951484 CAAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAATCGGTATAAGTATACCATATTT
66 CAAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGATATAAGTATACCAGATTT
951549 ATGAGAGAATAGGTGTAATATATGTATCAACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
131 ATGAGAGAATAGGTGTAATATATGTATCAACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
951614 AATGA
196 AATGA
*
951619 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATAAAAAAGGTGTCGATCCCAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCAATCCATATAAAAAAGGTGTCGATCCCAGAAACAT
* * * *
951684 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAGTCTAACCGATATAAGTATATCGGATTT
66 CAAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGATATAAGTATACCAGATTT
*
951749 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATT
131 ATGAGAGAATAGGTGTAATATATGTATCAACACTTTTTAATTTTGTGTCGATACTATT
951807 TTTAAATATC
Statistics
Matches: 176, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
200 176 1.00
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.31
Consensus pattern (200 bp):
ATGGCAAACAGGGTGCAACCATAAAGTGTCAATCCATATAAAAAAGGTGTCGATCCCAGAAACAT
CAAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGATATAAGTATACCAGATTT
ATGAGAGAATAGGTGTAATATATGTATCAACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
AATGA
Found at i:953320 original size:12 final size:12
Alignment explanation
Indices: 953298--953337 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
953288 CAAGCGGTCA
*
953298 ATGAAGATGAAG
1 ATGACGATGAAG
*
953310 CTGACGATGAAG
1 ATGACGATGAAG
*
953322 ATGACGATGATG
1 ATGACGATGAAG
953334 ATGA
1 ATGA
953338 TGATCCAAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.40, C:0.07, G:0.33, T:0.20
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:953336 original size:18 final size:18
Alignment explanation
Indices: 953298--953337 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
953288 CAAGCGGTCA
*
953298 ATGAAGATGAAGCTGACG
1 ATGAAGATGAAGATGACG
* *
953316 ATGAAGATGACGATGATG
1 ATGAAGATGAAGATGACG
953334 ATGA
1 ATGA
953338 TGATCCAAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.40, C:0.07, G:0.33, T:0.20
Consensus pattern (18 bp):
ATGAAGATGAAGATGACG
Found at i:954963 original size:183 final size:184
Alignment explanation
Indices: 954624--954971 Score: 610
Period size: 183 Copynumber: 1.9 Consensus size: 184
954614 AAATTAGCAT
*
954624 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTA
1 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCACAATTATAATGTA
*
954689 ATAGGTAATTTTGTAATATAACCGGTATAGATATACCGGTTTTATGAGAGAATAGCTATACAACC
66 ATAGGTAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGAGAATAGCTATACAACC
*
954754 TATATCGACACTTTTTAATATTGTGTCGC-TACTTTATTTCCAGAATGGATTAAA
131 TATATCAACACTTTTTAATATTGTGTC-CATACTTTATTTCCAGAATGGATTAAA
* *
954808 AAAGTGTTGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCACAATTATAATTTA
1 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCACAATTATAATGTA
* *
954873 ATAGGTAATTTT-TAATATAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACC
66 ATAGGTAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGAGAATAGCTATACAACC
954937 TATATCAACACTTTTTAATATTGTGTCCATACTTT
131 TATATCAACACTTTTTAATATTGTGTCCATACTTT
954972 TAAGTAACGC
Statistics
Matches: 156, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
182 1 0.01
183 81 0.52
184 74 0.47
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (184 bp):
AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCACAATTATAATGTA
ATAGGTAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGAGAATAGCTATACAACC
TATATCAACACTTTTTAATATTGTGTCCATACTTTATTTCCAGAATGGATTAAA
Found at i:958199 original size:85 final size:86
Alignment explanation
Indices: 958094--958251 Score: 248
Period size: 85 Copynumber: 1.8 Consensus size: 86
958084 AAATAGGTCA
*
958094 ATATAAGCGCTACCTATTACATTATATAAGCGCTA-C-ATATGTTATTGTACTTAATAATATTTT
1 ATATAAGAGCTACCTATTACATTATATAAGCGCTACCAATATGTTATTGTACTTAATAATA-TTT
958157 CCGGTTAAATACCTATTTTATT
65 CCGGTTAAATACCTATTTTATT
* * *
958179 ATATAAGAGCTATCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGAGCTACCTATTACATTATATAAGCGCTACC-AATATGTTATTGTACTTAATAATATTT
958244 CCGGTTAA
65 CCGGTTAA
958252 TATAATAACG
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
85 32 0.48
86 1 0.02
87 11 0.17
88 22 0.33
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.42
Consensus pattern (86 bp):
ATATAAGAGCTACCTATTACATTATATAAGCGCTACCAATATGTTATTGTACTTAATAATATTTC
CGGTTAAATACCTATTTTATT
Found at i:959822 original size:29 final size:29
Alignment explanation
Indices: 959785--959841 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
959775 GGAGTGGGTA
*
959785 GAAAGAAATATGATAATGGAAGCTTGGTG
1 GAAAGAAATAGGATAATGGAAGCTTGGTG
* * **
959814 GAAATAAATGGGATGGTGGAAGCTTGGT
1 GAAAGAAATAGGATAATGGAAGCTTGGT
959842 TGAGGATGGG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.37, C:0.04, G:0.35, T:0.25
Consensus pattern (29 bp):
GAAAGAAATAGGATAATGGAAGCTTGGTG
Found at i:960383 original size:36 final size:36
Alignment explanation
Indices: 960327--960473 Score: 141
Period size: 36 Copynumber: 4.0 Consensus size: 36
960317 GATACATTTC
*
960327 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT
1 TTGTTTCAAGGGAAAATGTCTCAAGAGAGACAAAAT
* * *
960363 TTGTTTCAAGCGAAATTGTCTCAAGAGAGACAAAAC
1 TTGTTTCAAGGGAAAATGTCTCAAGAGAGACAAAAT
** * * *
960399 TCATTTCAAGGGAAAATATCTCAAGCGAGATAAAATCT
1 TTGTTTCAAGGGAAAATGTCTCAAGAGAGACAAAA--T
* * * * *
960437 TCTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAAT
1 T-TGTTTCAAGGGAAAATGTCTCAAGAGAGACAAAAT
960474 CTTCTATTTC
Statistics
Matches: 93, Mismatches: 15, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
36 61 0.66
37 1 0.01
38 1 0.01
39 30 0.32
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.26
Consensus pattern (36 bp):
TTGTTTCAAGGGAAAATGTCTCAAGAGAGACAAAAT
Found at i:960452 original size:39 final size:39
Alignment explanation
Indices: 960330--960589 Score: 273
Period size: 39 Copynumber: 6.8 Consensus size: 39
960320 ACATTTCTTG
* * * * *
960330 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAA--TT-TG
1 TTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCTA
* * * * * *
960366 TTTCAAGCGAAATTGTCTCAAGAGAGACAAAA-C-TC-A
1 TTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCTA
* * *
960402 TTTCAAGGGAAAATATCTCAAGCGAGATAAAATCTTCTG
1 TTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCTA
960441 TTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCTA
1 TTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCTA
* * *
960480 TTTCGAGGGAAACTATCTCAAACGTGATAAAATCTTCTG
1 TTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCTA
* * * * *
960519 TTTCAAGGGAATCTATCTGAAGCGAGAAAAAATCTTATA
1 TTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCTA
960558 TTTCGAGGGAAACTATCTCAAGCGAGA-AAAAT
1 TTTCGAGGGAAACTATCTCAAGCGAGATAAAAT
960590 GTTATGTTCG
Statistics
Matches: 193, Mismatches: 26, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
36 58 0.30
37 1 0.01
38 7 0.04
39 127 0.66
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (39 bp):
TTTCGAGGGAAACTATCTCAAGCGAGATAAAATCTTCTA
Found at i:960497 original size:78 final size:78
Alignment explanation
Indices: 960330--960624 Score: 311
Period size: 78 Copynumber: 3.9 Consensus size: 78
960320 ACATTTCTTG
* * * * * *
960330 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAA--TT-TGTTTCAAGCGAAATTGTCTCAAGAGAG
1 TTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCAAGGGAAACTATCTCAAGAGAG
*
960392 ACAAAA-C-TC-A
66 AAAAAATCTTCTA
* * *
960402 TTTCAAGGGAAAATATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAG
1 TTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCAAGGGAAACTATCTCAAGAGAG
*
960467 ATAAAATCTTCTA
66 AAAAAATCTTCTA
* * * * * *
960480 TTTCGAGGGAAACTATCTCAAACGTGATAAAATCTTCTGTTTCAAGGGAATCTATCTGAAGCGAG
1 TTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCAAGGGAAACTATCTCAAGAGAG
*
960545 AAAAAATCTTATA
66 AAAAAATCTTCTA
* * * **
960558 TTTCGAGGGAAACTATCTCAAGCGAGA-AAAATGTTATG-TTCGAA-ATAAACTATCTCAAGAGA
1 TTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTC-AAGGGAAACTATCTCAAGAGA
960620 GAAAA
65 GAAAA
960625 GGGAAACTAT
Statistics
Matches: 188, Mismatches: 28, Indels: 10
0.83 0.12 0.04
Matches are distributed among these distances:
72 28 0.15
74 2 0.01
75 28 0.15
76 22 0.12
77 13 0.07
78 95 0.51
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (78 bp):
TTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCAAGGGAAACTATCTCAAGAGAG
AAAAAATCTTCTA
Found at i:960667 original size:39 final size:39
Alignment explanation
Indices: 960624--962134 Score: 2123
Period size: 39 Copynumber: 38.8 Consensus size: 39
960614 AAGAGAGAAA
*
960624 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTATTTCG
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
* * *
960663 AGGGAAACTATCTCAAACGTGATAAAATCTTCTGTTTCA
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
* * * * *
960702 AGGGAATCTATCTGAAGCGAGAAAAAATCTTATATTTCG
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
* * *
960741 AGGGAAACTATCTCAAGCGAGAAAAAATGTTATGTTTCG
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
*** * *
960780 AAATAAACTATCTCAAGCGAGAAAAAATGTTCTGTTTCG
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
* * *
960819 AGGGAAACTATCTCAAGCGAGATAAAATTTTCTATTTCC
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
*
960858 AGGGAAACTATCTCAAGAGAGATAAAATCTTCTGTTTCG
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
* * * * *
960897 AGGGAAACAACCTTAAGCGAGATAAAATCTTTTTTTTCG
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
*
960936 AGGGAAACTACCTCAAGCGAGATAAAATCTTCTGTTTCG
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
960975 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
* *
961014 AGGGAAACTATCACAAGCAAGATAAAATCTTCTGTTTCG
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
* * *
961053 AGGGAAACTATCTCAAGTGAGATAAAATCTTTTGTTTCA
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
961092 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
961131 AGGGAAACTATCTCAA-CTGAGATAAAATCTTCTGTTTCG
1 AGGGAAACTATCTCAAGC-GAGATAAAATCTTCTGTTTCG
*
961170 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTATTTCG
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
* ** * * *
961209 AGGAAAACTATCAGAAGCTAGAGAAAATCTTCTATTTCG
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
*
961248 AGGGAAACTATCTCAAGCGAGATAAAATATTCTGTTTCG
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
*
961287 AGGGAAACTATCTAAAGCGAGATAAAATCTTCTGTTTCG
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
* * *
961326 AGGGAAACTATCACAAGCGAGATAAAATCTTCAGTTTGG
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
*
961365 AGGGAAACTATCTCAAGCGAGACAAAATCTTCTGTTTCG
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
*
961404 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTAG
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
961443 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
* *
961482 AGGGAAATTATCTCAAGCGAGATAAAATCTTC-G---AG
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
* *
961517 AGAGAAACTATCTCAAGCGAGATAAAATCTTATGTTTCG
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
* * ** * * *
961556 AGGGAAACTACCTGAAGCGATTTAAATTCTTATGTTTCA
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
* * * *
961595 AGAGAAACTACCTCAATCGAGATAAAATCTTTTGTTTCG
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
*
961634 AGGGAAACTATCTCAAGCGAGATAAAATCTTTTGTTTCG
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
*
961673 AGGGAAACTATCTCAAGCGAGATAAAATCTTTTGTTTCG
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
*
961712 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCA
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
** * *
961751 AGGGAATTTATCTCAAGCGAGACAAAATCTTATGTTTCG
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
* * * *
961790 AGGTAAACTATCTAAAGCGAGATAAAATCTTTTATTTCG
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
961829 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
*
961868 AGGGAAACTATCTCAAGCGAGATAAAATCTTTTGTTTCG
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
* *
961907 AGGGAAACTATCTCAAGCGAGATAAAATATTCTGTTTTG
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
* * * * * * *
961946 AGAGAAACTATCTCGAGGGAGACAAAATCTTTTATTTTG
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
* * * *
961985 AGGGAAACTATCTCGAGCGAGACAAAATCTTTTGTTTTG
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
* ** * *
962024 AGGGAAACTATCTCGAGCGAGGCAAAATCTTTTGTTTTG
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
* * *
962063 AGGGAAACTATCTCGAGAGAGATAAAATCTTTTGTTTCG
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
*
962102 AGGGAAACTATCTCAAGTGAGATAAAATCTTCT
1 AGGGAAACTATCTCAAGCGAGATAAAATCTTCT
962135 TTAAAATAAT
Statistics
Matches: 1324, Mismatches: 142, Indels: 12
0.90 0.10 0.01
Matches are distributed among these distances:
35 30 0.02
36 1 0.00
38 2 0.00
39 1290 0.97
40 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.29
Consensus pattern (39 bp):
AGGGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCG
Found at i:961546 original size:17 final size:17
Alignment explanation
Indices: 961491--961546 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
961481 GAGGGAAATT
961491 ATCTCAAGCGAGATAAA
1 ATCTCAAGCGAGATAAA
* * *
961508 ATCTTCGAGAGAGA-AACT
1 ATC-TCAAGCGAGATAA-A
961526 ATCTCAAGCGAGATAAA
1 ATCTCAAGCGAGATAAA
961543 ATCT
1 ATCT
961547 TATGTTTCGA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
17 17 0.57
18 13 0.43
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.21
Consensus pattern (17 bp):
ATCTCAAGCGAGATAAA
Found at i:962232 original size:76 final size:76
Alignment explanation
Indices: 962137--962296 Score: 275
Period size: 76 Copynumber: 2.1 Consensus size: 76
962127 AATCTTCTTT
* *
962137 AAAATAATCTTGAGTGAAATGAAATGTCTTCTTTCGAGTAAAAATTTTCTCAAGCGAGATAAATC
1 AAAACAATCTTGAGTGAAATGAAATGTCTTCTTTCGAGTAAAAATTTTCTCAAGCGAGACAAATC
962202 TTATTTTAAGA
66 TTATTTTAAGA
* *
962213 AAAACAATCTTGAGTGAAATGAAATTTCTTCTTTCTAGTAAAAATTTTCTCAAGCGAGACAAATC
1 AAAACAATCTTGAGTGAAATGAAATGTCTTCTTTCGAGTAAAAATTTTCTCAAGCGAGACAAATC
*
962278 TTGTTTTAAGA
66 TTATTTTAAGA
962289 AAAACAAT
1 AAAACAAT
962297 GGTTGTCTCA
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
76 79 1.00
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.34
Consensus pattern (76 bp):
AAAACAATCTTGAGTGAAATGAAATGTCTTCTTTCGAGTAAAAATTTTCTCAAGCGAGACAAATC
TTATTTTAAGA
Found at i:964303 original size:27 final size:27
Alignment explanation
Indices: 964255--964316 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
964245 TGAAATGCAA
* * *
964255 ATGCAAAATTCAAAGGTACAAATGTAT
1 ATGCAAAATGCAAAGATACAAATGTAG
* *
964282 ATGCAAAATGCAAATATGCAAATGTAG
1 ATGCAAAATGCAAAGATACAAATGTAG
964309 ATGCAAAA
1 ATGCAAAA
964317 ATGTTGATCC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.50, C:0.11, G:0.16, T:0.23
Consensus pattern (27 bp):
ATGCAAAATGCAAAGATACAAATGTAG
Found at i:966580 original size:2 final size:2
Alignment explanation
Indices: 966573--966608 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
966563 CATTTTTGAG
966573 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
966609 AGGAAAATGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:967529 original size:182 final size:181
Alignment explanation
Indices: 967144--967617 Score: 637
Period size: 182 Copynumber: 2.6 Consensus size: 181
967134 GATCCAAATT
* * ** ** **
967144 AAAAATGTATCGATCCACAACGATATAACAGGTAAAACTATGGCAAAACCAATATTGAAATGATA
1 AAAAATGTATCGATCAACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * ** *
967209 AAACCGGTAAAGCAGTACCGAATATATTTAAAGTGTCGGTACTTTAATATAAGAATCGATACTTC
66 AAACCGGTAAAAC-GTACCGGATATATTGAAAGTGTCGAAACTTTAATATAAGAATCGACACTTC
* * *
967274 GTTAATTTAAAAGAGAACCAGTTTTAGCGCCTATAAAGTGTCGATACTTTCA
130 GTGAATTTAAAAGAGAACCAGTTTTAGCACCTATAAAGTGTCGATACTTTAA
* * *
967326 AAAAATATATCGATCAACAACGATATAACAGGTAAAAATATGATAAAACTGGTATCAAAATGATG
1 AAAAATGTATCGATCAACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * *
967391 AAACCGGTAAAACGCTACCGGATATATTGAAAGTGTTGAAACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACG-TACCGGATATATTGAAAGTGTCGAAACTTTAATATAAGAATCGACACTTC
*
967455 GTGAATTTAAAAGAGAAGCAGTTTTAGCACCTATAAAGTGTCGATACTTTAA
130 GTGAATTTAAAAGAGAACCAGTTTTAGCACCTATAAAGTGTCGATACTTTAA
967507 AAAAATGTATCGATCAAACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGAT
1 AAAAATGTATCGATC-AACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGAT
* * * *
967572 AAAACCAGTAAAATGATACCGGATATATTAAAAAG-GTCGATACTTT
65 AAAACCGGTAAAACG-TACCGGATATATT-GAAAGTGTCGAAACTTT
967618 CGTAAGTACG
Statistics
Matches: 256, Mismatches: 33, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
181 79 0.31
182 173 0.68
183 4 0.02
ACGTcount: A:0.44, C:0.14, G:0.16, T:0.26
Consensus pattern (181 bp):
AAAAATGTATCGATCAACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACCGGTAAAACGTACCGGATATATTGAAAGTGTCGAAACTTTAATATAAGAATCGACACTTCG
TGAATTTAAAAGAGAACCAGTTTTAGCACCTATAAAGTGTCGATACTTTAA
Found at i:967561 original size:20 final size:19
Alignment explanation
Indices: 967538--967584 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
967528 CGATATAACA
967538 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
967558 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
*
967578 AGTAAAA
1 GGTAAAA
967585 TGATACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.55, C:0.11, G:0.15, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:969744 original size:15 final size:15
Alignment explanation
Indices: 969724--969756 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
969714 TGGTTGTATT
*
969724 GGGGGATGACGGTGA
1 GGGGGACGACGGTGA
969739 GGGGGACGACGGTGA
1 GGGGGACGACGGTGA
969754 GGG
1 GGG
969757 AAAACAGAGT
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:0.18, C:0.09, G:0.64, T:0.09
Consensus pattern (15 bp):
GGGGGACGACGGTGA
Found at i:969865 original size:21 final size:21
Alignment explanation
Indices: 969839--969879 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
969829 AAGACAATCA
969839 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAT
* *
969860 AGAGTCGAAGATACACTTGA
1 AGAGTCGAAGAGAAACTTGA
969880 GAGGCATAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.12, G:0.27, T:0.20
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAT
Found at i:970224 original size:33 final size:33
Alignment explanation
Indices: 970181--970258 Score: 104
Period size: 33 Copynumber: 2.4 Consensus size: 33
970171 TATGAAGAAG
970181 AAAAGAGGGAGGAGAAAGAAGAAGAGATGGAAA
1 AAAAGAGGGAGGAGAAAGAAGAAGAGATGGAAA
* * * *
970214 AAAAGTGGGAGGAGGAGGAAGAAGAGATGGAAG
1 AAAAGAGGGAGGAGAAAGAAGAAGAGATGGAAA
*
970247 AAATGA-GGAGGA
1 AAAAGAGGGAGGA
970259 AGGAAGTCGA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
32 6 0.15
33 33 0.85
ACGTcount: A:0.51, C:0.00, G:0.44, T:0.05
Consensus pattern (33 bp):
AAAAGAGGGAGGAGAAAGAAGAAGAGATGGAAA
Found at i:971838 original size:19 final size:20
Alignment explanation
Indices: 971814--971862 Score: 84
Period size: 19 Copynumber: 2.5 Consensus size: 20
971804 AATGTAGGGT
971814 TAATTTTGTATTA-GATTTA
1 TAATTTTGTATTATGATTTA
971833 TAATTTTGTA-TATGATTTA
1 TAATTTTGTATTATGATTTA
971852 TAATTTTGTAT
1 TAATTTTGTAT
971863 GTGAATGTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 2 0.07
19 26 0.93
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.59
Consensus pattern (20 bp):
TAATTTTGTATTATGATTTA
Found at i:972455 original size:200 final size:200
Alignment explanation
Indices: 972097--972684 Score: 1095
Period size: 200 Copynumber: 2.9 Consensus size: 200
972087 AATTTACAAT
* *
972097 ATGGCAAATAGGGTACAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
*
972162 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCAGATTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGATTT
*
972227 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGAGTCGATACTATTGGTCCAG
131 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
972292 AATGA
196 AATGA
*
972297 ATGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
* *
972362 CGAAACCCATAAGTATAATGTAATAGGTAATTTGTCAATCTAACCGGTATAAGTATATCGGATTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGATTT
*
972427 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAT
131 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
972492 AATGA
196 AATGA
972497 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
*
972562 CAAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGATTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGATTT
972627 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATT
131 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATT
972685 TTTAAATAAC
Statistics
Matches: 376, Mismatches: 12, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
200 376 1.00
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.30
Consensus pattern (200 bp):
ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGATTT
ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
AATGA
Found at i:974190 original size:6 final size:6
Alignment explanation
Indices: 974179--974242 Score: 56
Period size: 6 Copynumber: 10.7 Consensus size: 6
974169 CAAGCATTCA
* * * * * *
974179 ATGAAG ATGAAG CTGACG ATGAAG ATGACG ATGAAT ATGATG ATGATG
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG
* *
974227 ATGATG ATGATG ATGA
1 ATGAAG ATGAAG ATGA
974243 TGATCCAAAC
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.39, C:0.05, G:0.31, T:0.25
Consensus pattern (6 bp):
ATGAAG
Found at i:974201 original size:12 final size:12
Alignment explanation
Indices: 974179--974242 Score: 65
Period size: 12 Copynumber: 5.3 Consensus size: 12
974169 CAAGCATTCA
*
974179 ATGAAGATGAAG
1 ATGACGATGAAG
*
974191 CTGACGATGAAG
1 ATGACGATGAAG
*
974203 ATGACGATGAAT
1 ATGACGATGAAG
* *
974215 ATGATGATGATG
1 ATGACGATGAAG
* *
974227 ATGATGATGATG
1 ATGACGATGAAG
974239 ATGA
1 ATGA
974243 TGATCCAAAC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 45 1.00
ACGTcount: A:0.39, C:0.05, G:0.31, T:0.25
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:974223 original size:3 final size:3
Alignment explanation
Indices: 974196--974246 Score: 68
Period size: 3 Copynumber: 17.0 Consensus size: 3
974186 TGAAGCTGAC
* *
974196 GAT GAA GAT GAC GAT GAAT -AT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT G-AT GAT GAT GAT GAT GAT GAT GAT GAT GAT
974241 GAT GAT
1 GAT GAT
974247 CCAAACAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 38 0.90
4 2 0.05
ACGTcount: A:0.37, C:0.02, G:0.31, T:0.29
Consensus pattern (3 bp):
GAT
Found at i:979020 original size:182 final size:182
Alignment explanation
Indices: 978556--979396 Score: 1429
Period size: 181 Copynumber: 4.6 Consensus size: 182
978546 ATTTTACCTT
** * * *
978556 TTTAAAAGAGAAGAAGTTATATAGTCAATAAAGTGTCGATACTTTATAAAAATGTATCAATTCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* *
978621 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTTGAAATAACAAAACAGGTAAAGCGCTAC
66 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
*
978686 CGGTTATGTTGAAAGTGTCGATAATTTATTATACA-TACCGACACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATA-AGTATCGACACTTTTGGAA
978738 TTTAAAAGAGAAG-AGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
**
978802 AACAATATAACATATAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
* *
978867 CGGTTATGTTGAAAGTGTCAATAATTTATTATACGTATCGACACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
978919 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* *
978984 AACAATATAACAGGTAATAATATGACAAAACCGGTCTCAAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
979049 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
*
979101 TTTAAAAGAG-AGAAGTTATAGCGCCAATAAAATGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
*
979165 AACAATATAACAGGTAAAAATATGACAAAACCAGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
*
979230 CGGATATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
*
979282 -TTAATAAGAGAAGAAGTTATAGCGCCAATAAAGTATCGATACTTTATAAAAATGTATCGATCCA
1 TTTAA-AAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCA
* * * **
979346 TAATAATATAACATGTAAAAATATGATAAAACCGGTCTATAAATGACAAAA
65 TAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAA
979397 GGTGAACGCG
Statistics
Matches: 624, Mismatches: 31, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
180 4 0.01
181 339 0.54
182 281 0.45
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.27
Consensus pattern (182 bp):
TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
Found at i:979221 original size:363 final size:362
Alignment explanation
Indices: 978556--979396 Score: 1427
Period size: 363 Copynumber: 2.3 Consensus size: 362
978546 ATTTTACCTT
** * * *
978556 TTTAAAAGAGAAGAAGTTATATAGTCAATAAAGTGTCGATACTTTATAAAAATGTATCAATTCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* *
978621 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTTGAAATAACAAAACAGGTAAAGCGCTAC
66 AACAATATAACAGGTAAAAATATGACAAAACCGGTC-TAAAATGACAAAACAGGTAAAGCGCTAC
978686 CGGTTATGTTGAAAGTGTCGATAATTTATTATACATACCGACACTTTTGGAATTTAAAAGAGAAG
130 CGGTTATGTTGAAAGTGTCGATAATTTATTATACATACCGACACTTTTGGAATTTAAAAGAGAAG
* *
978751 AGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATA
195 AGTTATAGCGCCAATAAAATGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGA
* *
978816 TAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAA
260 TAAAAATATGACAAAACCAGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGAAA
*
978881 GTGTCAATAATTTATTATACGTATCGACACTTTTGGAA
325 GTGTCAATAATTTATTATAAGTATCGACACTTTTGGAA
978919 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
*
978984 AACAATATAACAGGTAATAATATGACAAAACCGGTCTCAAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACAGGTAAAAATATGACAAAACCGGTCT-AAAATGACAAAACAGGTAAAGCGCTAC
*
979049 CGGTTATGTTGAAAGTGTCGATAATTTATTATA-AGTATCGACACTTTTGGAATTTAAAAGAG-A
130 CGGTTATGTTGAAAGTGTCGATAATTTATTATACA-TACCGACACTTTTGGAATTTAAAAGAGAA
979112 GAAGTTATAGCGCCAATAAAATGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACA
194 G-AGTTATAGCGCCAATAAAATGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACA
*
979177 GGTAAAAATATGACAAAACCAGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGA
258 GATAAAAATATGACAAAACCAGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGA
*
979242 AAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
323 AAGTGTCAATAATTTATTATAAGTATCGACACTTTTGGAA
*
979282 -TTAATAAGAGAAGAAGTTATAGCGCCAATAAAGTATCGATACTTTATAAAAATGTATCGATCCA
1 TTTAA-AAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCA
* * *
979346 TAATAATATAACATGTAAAAATATGATAAAACCGGTCTATAAATGACAAAA
65 TAACAATATAACAGGTAAAAATATGACAAAACCGGTCTA-AAATGACAAAA
979397 GGTGAACGCG
Statistics
Matches: 452, Mismatches: 21, Indels: 10
0.94 0.04 0.02
Matches are distributed among these distances:
362 9 0.02
363 443 0.98
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.27
Consensus pattern (362 bp):
TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
AACAATATAACAGGTAAAAATATGACAAAACCGGTCTAAAATGACAAAACAGGTAAAGCGCTACC
GGTTATGTTGAAAGTGTCGATAATTTATTATACATACCGACACTTTTGGAATTTAAAAGAGAAGA
GTTATAGCGCCAATAAAATGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGAT
AAAAATATGACAAAACCAGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGAAAG
TGTCAATAATTTATTATAAGTATCGACACTTTTGGAA
Found at i:979633 original size:87 final size:87
Alignment explanation
Indices: 979532--979694 Score: 317
Period size: 87 Copynumber: 1.9 Consensus size: 87
979522 AAATAGGTCA
979532 ATATAAGCGCTATCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTATCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
979597 CCGGTTAAATACCTATTTTATT
66 CCGGTTAAATACCTATTTTATT
*
979619 ATATAAGCGCTATCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTATCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
979684 CCGGTTAAATA
66 CCGGTTAAATA
979695 ATATAACATA
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 75 1.00
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (87 bp):
ATATAAGCGCTATCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
CCGGTTAAATACCTATTTTATT
Found at i:979666 original size:23 final size:23
Alignment explanation
Indices: 979616--979660 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
979606 TACCTATTTT
* *
979616 ATTATATAAGCGCTATCTATTAC
1 ATTATATAAGCGCTACCTAATAC
*
979639 ATTATATAAGCGTTACCTAATA
1 ATTATATAAGCGCTACCTAATA
979661 TGTTATTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:982428 original size:14 final size:14
Alignment explanation
Indices: 982409--982436 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
982399 ATTACTCCCC
982409 CTTACTTTAACACT
1 CTTACTTTAACACT
982423 CTTACTTTAACACT
1 CTTACTTTAACACT
982437 TCCTTCAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (14 bp):
CTTACTTTAACACT
Found at i:984300 original size:19 final size:20
Alignment explanation
Indices: 984256--984300 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
984246 TAGTTTTCAT
*
984256 AATAACAACATAATTTAATC
1 AATAACAACATAATTTAATA
984276 AA-AAC-ACAATAATTTAA-A
1 AATAACAAC-ATAATTTAATA
984294 AATAACA
1 AATAACA
984301 TTTTTTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 6
0.75 0.04 0.21
Matches are distributed among these distances:
18 4 0.19
19 15 0.71
20 2 0.10
ACGTcount: A:0.62, C:0.13, G:0.00, T:0.24
Consensus pattern (20 bp):
AATAACAACATAATTTAATA
Found at i:984727 original size:21 final size:21
Alignment explanation
Indices: 984701--984740 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
984691 CAGAACCCCA
*
984701 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
984722 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
984741 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:992056 original size:29 final size:29
Alignment explanation
Indices: 992012--992075 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
992002 GGATCTCAAA
992012 CAGAAATAGAACGGGGATATAATCCCATTG
1 CAGAAATAGAACGGGGATATAATCCC-TTG
* * *
992042 -AGAAATAGGATGGGGATATGATCCCTTG
1 CAGAAATAGAACGGGGATATAATCCCTTG
992070 CAGAAA
1 CAGAAA
992076 CATATATGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 3 0.10
29 27 0.90
ACGTcount: A:0.39, C:0.14, G:0.27, T:0.20
Consensus pattern (29 bp):
CAGAAATAGAACGGGGATATAATCCCTTG
Found at i:997843 original size:31 final size:31
Alignment explanation
Indices: 997803--997866 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
997793 AAAGTACAAA
997803 TAGGAACAACCCACTATGTAGAAGAAACACC
1 TAGGAACAACCCACTATGTAGAAGAAACACC
* *
997834 TAGGTACAACCCACTGTGTAGAAGAAACACC
1 TAGGAACAACCCACTATGTAGAAGAAACACC
997865 TA
1 TA
997867 TACTCTCTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.25, G:0.17, T:0.16
Consensus pattern (31 bp):
TAGGAACAACCCACTATGTAGAAGAAACACC
Found at i:999602 original size:29 final size:29
Alignment explanation
Indices: 999560--999633 Score: 85
Period size: 29 Copynumber: 2.6 Consensus size: 29
999550 TTTAATGTGG
* * * *
999560 ATCCCAAATAGAAATAGGACGGGGATATA
1 ATCCCATACAGAAACAGGACGGGAATATA
* * *
999589 ATCCTATACAGAAACAGGATGGGAATATG
1 ATCCCATACAGAAACAGGACGGGAATATA
999618 ATCCCATACAGAAACA
1 ATCCCATACAGAAACA
999634 TGTATGTATG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.45, C:0.18, G:0.20, T:0.18
Consensus pattern (29 bp):
ATCCCATACAGAAACAGGACGGGAATATA
Found at i:1001767 original size:20 final size:20
Alignment explanation
Indices: 1001744--1001791 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
1001734 ATGTGTGGGC
*
1001744 ATCGATACTACATGAACATT
1 ATCGATACTACATGAACAGT
*
1001764 ATCGATACTGCATGAACAGT
1 ATCGATACTACATGAACAGT
*
1001784 ATTGATAC
1 ATCGATAC
1001792 CATAAGGCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.29
Consensus pattern (20 bp):
ATCGATACTACATGAACAGT
Found at i:1002886 original size:30 final size:30
Alignment explanation
Indices: 1002852--1002914 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
1002842 ATAAATTATA
1002852 TGATTACATGATAA-TAAGATATAAGATATG
1 TGATTACATGA-AAGTAAGATATAAGATATG
* *
1002882 TGATTACATGAAAGTATGATATAAGCTATG
1 TGATTACATGAAAGTAAGATATAAGATATG
1002912 TGA
1 TGA
1002915 AAGTGATCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 2 0.07
30 28 0.93
ACGTcount: A:0.43, C:0.05, G:0.19, T:0.33
Consensus pattern (30 bp):
TGATTACATGAAAGTAAGATATAAGATATG
Found at i:1003090 original size:21 final size:19
Alignment explanation
Indices: 1003066--1003122 Score: 51
Period size: 21 Copynumber: 2.8 Consensus size: 19
1003056 ATATGTAATC
1003066 CTTTGGAACATATATACGGT
1 CTTTGGAACATATAT-CGGT
* *
1003086 ACTTTGGTACACATAGTCGGT
1 -CTTTGGAACATATA-TCGGT
*
1003107 CTATTGGAATATATAT
1 CT-TTGGAACATATAT
1003123 GTGGTCCTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
20 3 0.10
21 25 0.86
22 1 0.03
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (19 bp):
CTTTGGAACATATATCGGT
Found at i:1003168 original size:21 final size:21
Alignment explanation
Indices: 1003143--1003183 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1003133 TGGAGAAATC
*
1003143 TATGTTGTCATTCGGGACATA
1 TATGTGGTCATTCGGGACATA
*
1003164 TATGTGGTCCTTCGGGACAT
1 TATGTGGTCATTCGGGACAT
1003184 TTTATATGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.17, G:0.27, T:0.37
Consensus pattern (21 bp):
TATGTGGTCATTCGGGACATA
Found at i:1005827 original size:17 final size:18
Alignment explanation
Indices: 1005805--1005838 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1005795 AATCGAATGA
1005805 AATTTTTGAA-AAATATT
1 AATTTTTGAATAAATATT
*
1005822 AATTTTTTAATAAATAT
1 AATTTTTGAATAAATAT
1005839 GAAATAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
AATTTTTGAATAAATATT
Found at i:1005882 original size:21 final size:20
Alignment explanation
Indices: 1005841--1005884 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
1005831 ATAAATATGA
* *
1005841 AATAAATATTTTGTAAAAAT
1 AATAAATAATTTGAAAAAAT
*
1005861 AATAATTAATTTGAAAATAAT
1 AATAAATAATTTGAAAA-AAT
1005882 AAT
1 AAT
1005885 TATGATTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.39
Consensus pattern (20 bp):
AATAAATAATTTGAAAAAAT
Found at i:1006186 original size:35 final size:35
Alignment explanation
Indices: 1006141--1006224 Score: 141
Period size: 35 Copynumber: 2.4 Consensus size: 35
1006131 TTCATCAAAA
*
1006141 TTCTCTCAAATTTTCTCTCTTCTCCACCGAAAATT
1 TTCTCTCAAATTTCCTCTCTTCTCCACCGAAAATT
1006176 TTCTCTCAAATTTCCTCTCTTCTCCACCGAAAATT
1 TTCTCTCAAATTTCCTCTCTTCTCCACCGAAAATT
**
1006211 AACTCTCAAATTTC
1 TTCTCTCAAATTTC
1006225 TCGCAAATTC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 46 1.00
ACGTcount: A:0.25, C:0.32, G:0.02, T:0.40
Consensus pattern (35 bp):
TTCTCTCAAATTTCCTCTCTTCTCCACCGAAAATT
Found at i:1009984 original size:31 final size:31
Alignment explanation
Indices: 1009946--1010008 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
1009936 AAAGTACAAG
*
1009946 TAGGAACAACCCACTGTGTAGAAGAAACACC
1 TAGGAACAACCCACTATGTAGAAGAAACACC
*
1009977 TAGGAACAACCCACTATGTAGGAGAAACACC
1 TAGGAACAACCCACTATGTAGAAGAAACACC
1010008 T
1 T
1010009 CTACTCTCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.41, C:0.25, G:0.19, T:0.14
Consensus pattern (31 bp):
TAGGAACAACCCACTATGTAGAAGAAACACC
Done.