Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011868.1 Kokia drynarioides strain JFW-HI SEQ_126865, 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: 310627
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 32 characters in sequence are not A, C, G, or T
Found at i:537 original size:59 final size:59
Alignment explanation
Indices: 405--712 Score: 430
Period size: 59 Copynumber: 5.2 Consensus size: 59
395 GGAGGTCCCT
405 AAACTATCCAAAAA-TCTCATTTTTACCCTCGAACTTCCAAAAA-CCCA-TTTTGACCCCA
1 AAACT-TCCAAAAATTC-CATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCA
*
463 AAACTTTCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCA
*
522 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAATAATCCCA-TTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCA
* * * **
580 AAACTTCTAAAAAATCCCATTTTTAACCTTAAAACTTCCAAAAATCCCATTTTT-ACCCCA
1 AAACTTC-CAAAAATTCCATTTTT-ACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCA
* * *
640 AAACTTCCAAAAATCCCATTTTTGACCCT-AAAATATCCAAAAATCCCATTTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTT-ACCCTCGAACT-TCCAAAAATCCCATTTTTGACCCCA
700 AAACTTCCAAAAA
1 AAACTTCCAAAAA
713 ATACTATTTT
Statistics
Matches: 229, Mismatches: 13, Indels: 14
0.89 0.05 0.05
Matches are distributed among these distances:
57 33 0.14
58 33 0.14
59 107 0.47
60 52 0.23
61 4 0.02
ACGTcount: A:0.37, C:0.31, G:0.03, T:0.30
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCA
Found at i:727 original size:29 final size:30
Alignment explanation
Indices: 405--712 Score: 368
Period size: 30 Copynumber: 10.4 Consensus size: 30
395 GGAGGTCCCT
*
405 AAACTATCCAAAAATCTCATTTTT-ACCCTC-
1 AAACT-TCCAAAAATCCCATTTTTGACCC-CA
*
435 GAACTTCCAAAAA-CCCA-TTTTGACCCCA
1 AAACTTCCAAAAATCCCATTTTTGACCCCA
* *
463 AAACTTTCAAAAATTCCATTTTT-ACCCTC-
1 AAACTTCCAAAAATCCCATTTTTGACCC-CA
*
492 GAACTTCCAAAAATCCCATTTTTGACCCCA
1 AAACTTCCAAAAATCCCATTTTTGACCCCA
*
522 AAACTTCCAAAAATTCCATTTTT-ACCCTC-
1 AAACTTCCAAAAATCCCATTTTTGACCC-CA
* *
551 GAACTTCCAATAATCCCA-TTTTGACCCCA
1 AAACTTCCAAAAATCCCATTTTTGACCCCA
* * **
580 AAACTTCTAAAAAATCCCATTTTTAACCTTA
1 AAACTTC-CAAAAATCCCATTTTTGACCCCA
611 AAACTTCCAAAAATCCCATTTTT-ACCCCA
1 AAACTTCCAAAAATCCCATTTTTGACCCCA
*
640 AAACTTCCAAAAATCCCATTTTTGACCCTA
1 AAACTTCCAAAAATCCCATTTTTGACCCCA
670 AAA-TATCCAAAAATCCCATTTTTGACCCCA
1 AAACT-TCCAAAAATCCCATTTTTGACCCCA
700 AAACTTCCAAAAA
1 AAACTTCCAAAAA
713 ATACTATTTT
Statistics
Matches: 239, Mismatches: 24, Indels: 30
0.82 0.08 0.10
Matches are distributed among these distances:
27 5 0.02
28 23 0.10
29 93 0.39
30 102 0.43
31 16 0.07
ACGTcount: A:0.37, C:0.31, G:0.03, T:0.30
Consensus pattern (30 bp):
AAACTTCCAAAAATCCCATTTTTGACCCCA
Found at i:8518 original size:22 final size:22
Alignment explanation
Indices: 8493--8552 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 22
8483 ACAATAAAGT
8493 TTCTTATTTAGATTATTTAGAG
1 TTCTTATTTAGATTATTTAGAG
8515 TTC-TAGTTTA-ATTA---AGAG
1 TTCTTA-TTTAGATTATTTAGAG
8533 TT-TTATTTAGATTTATTTAG
1 TTCTTATTTAGA-TTATTTAG
8553 CTTGCCTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 14
0.69 0.00 0.31
Matches are distributed among these distances:
17 4 0.13
18 9 0.29
19 3 0.10
21 6 0.19
22 9 0.29
ACGTcount: A:0.28, C:0.03, G:0.13, T:0.55
Consensus pattern (22 bp):
TTCTTATTTAGATTATTTAGAG
Found at i:8656 original size:25 final size:24
Alignment explanation
Indices: 8620--8667 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
8610 AGTTAAAAAT
*
8620 AATTCTCTTTGAGTTTTTCTTTAAG
1 AATTCTCTTTGAGTTGTT-TTTAAG
8645 AATTGCTC-TTGAGTTGTTTTTAA
1 AATT-CTCTTTGAGTTGTTTTTAA
8668 AAGTTGTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
25 13 0.62
26 3 0.14
ACGTcount: A:0.21, C:0.10, G:0.15, T:0.54
Consensus pattern (24 bp):
AATTCTCTTTGAGTTGTTTTTAAG
Found at i:9556 original size:18 final size:18
Alignment explanation
Indices: 9529--9563 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
9519 AAAAGTGATC
9529 AAAAAGTAGAGAAAAAAG
1 AAAAAGTAGAGAAAAAAG
*
9547 AAAAATTAGAGAAAAAA
1 AAAAAGTAGAGAAAAAA
9564 AAATTTCGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (18 bp):
AAAAAGTAGAGAAAAAAG
Found at i:13138 original size:21 final size:20
Alignment explanation
Indices: 13114--13191 Score: 59
Period size: 21 Copynumber: 3.6 Consensus size: 20
13104 TATTTTTTTA
13114 ATTTTAAAATTTTTATAACTT
1 ATTTTAAAATTTTTATAA-TT
13135 ATTTTATAAATTTTGTTTATAATT
1 ATTTTA-AAA--TT-TTTATAATT
** * *
13159 -TTTTGTAATTTTTTTAAATA
1 ATTTTAAAATTTTTAT-AATT
13179 ATTTTAAAATTTT
1 ATTTTAAAATTTT
13192 AAAAGGGATT
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
19 4 0.09
20 5 0.11
21 16 0.36
22 5 0.11
23 4 0.09
24 4 0.09
25 7 0.16
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.62
Consensus pattern (20 bp):
ATTTTAAAATTTTTATAATT
Found at i:20395 original size:23 final size:23
Alignment explanation
Indices: 20369--20412 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
20359 AAAGAATATT
*
20369 TATATTAAAAATGTTATTATAAA
1 TATAATAAAAATGTTATTATAAA
* *
20392 TATAATAAACATTTTATTATA
1 TATAATAAAAATGTTATTATA
20413 TTAAAAAACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
TATAATAAAAATGTTATTATAAA
Found at i:20585 original size:26 final size:28
Alignment explanation
Indices: 20555--20613 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
20545 TGAGTTGATG
20555 ATTTA-ATATAAAAAT-ATATAATTATT
1 ATTTACATATAAAAATAATATAATTATT
* *
20581 ATTTAACATATATAATTAATATAATTATT
1 ATTT-ACATATAAAAATAATATAATTATT
20610 -TTTA
1 ATTTA
20614 TAACACATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
26 4 0.14
27 2 0.07
28 11 0.39
29 11 0.39
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (28 bp):
ATTTACATATAAAAATAATATAATTATT
Found at i:21982 original size:19 final size:19
Alignment explanation
Indices: 21958--21998 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
21948 TAAAAAAATT
21958 AAATAAAGATTATAAATAA
1 AAATAAAGATTATAAATAA
* *
21977 AAATAAATATTATATATAA
1 AAATAAAGATTATAAATAA
21996 AAA
1 AAA
21999 ATACGAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (19 bp):
AAATAAAGATTATAAATAA
Found at i:28121 original size:17 final size:17
Alignment explanation
Indices: 28099--28133 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
28089 CCTACGACTT
28099 AGTCAAATCCCCTTAGG
1 AGTCAAATCCCCTTAGG
*
28116 AGTCAAATCTCCTTAGG
1 AGTCAAATCCCCTTAGG
28133 A
1 A
28134 TTTAGTCTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (17 bp):
AGTCAAATCCCCTTAGG
Found at i:36124 original size:21 final size:23
Alignment explanation
Indices: 36082--36126 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
36072 TCTTAACAAT
*
36082 AATTTTAAAAATATATATTTAAA
1 AATTCTAAAAATATATATTTAAA
36105 AATTCTAAAAATAT-TA-TTAAA
1 AATTCTAAAAATATATATTTAAA
36126 A
1 A
36127 GTACTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.29
22 2 0.10
23 13 0.62
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
AATTCTAAAAATATATATTTAAA
Found at i:36135 original size:22 final size:24
Alignment explanation
Indices: 36086--36136 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
36076 AACAATAATT
*
36086 TTAAAAATATATATTTAAAAATTC
1 TTAAAAATATATATTTAAAAATAC
*
36110 -TAAAAATAT-TA-TTAAAAGTAC
1 TTAAAAATATATATTTAAAAATAC
36131 TTAAAA
1 TTAAAA
36137 TTTTAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 8 0.33
22 7 0.29
23 9 0.38
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (24 bp):
TTAAAAATATATATTTAAAAATAC
Found at i:36136 original size:21 final size:23
Alignment explanation
Indices: 36087--36137 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 23
36077 ACAATAATTT
*
36087 TAAAAATATATATTTAAAAATTC
1 TAAAAATATATATTTAAAAATAC
*
36110 TAAAAATAT-TA-TTAAAAGTAC
1 TAAAAATATATATTTAAAAATAC
*
36131 TTAAAAT
1 TAAAAAT
36138 TTTAAAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 14 0.56
22 2 0.08
23 9 0.36
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (23 bp):
TAAAAATATATATTTAAAAATAC
Found at i:37149 original size:23 final size:22
Alignment explanation
Indices: 37099--37171 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 22
37089 GATAGAAATT
**
37099 AAATTGTAATTTTTATAATAGTA
1 AAATTGTAA-TTTTATAATTTTA
*
37122 AAATTGTAATTTTATCATTTTA
1 AAATTGTAATTTTATAATTTTA
*
37144 ATAATT-TATATCTTTATAATTTTT
1 A-AATTGTA-AT-TTTATAATTTTA
37168 AAAT
1 AAAT
37172 GATTAAATCA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
22 13 0.31
23 18 0.43
24 11 0.26
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.53
Consensus pattern (22 bp):
AAATTGTAATTTTATAATTTTA
Found at i:41094 original size:30 final size:29
Alignment explanation
Indices: 41058--41200 Score: 142
Period size: 29 Copynumber: 4.8 Consensus size: 29
41048 TTCAAATTTG
41058 ACCCTTAAACTTTTTAAAATTTCATTTTTA
1 ACCCTTAAACTTTTTAAAATTTCA-TTTTA
* *
41088 ACCCTTAATCTTTCTAAAAATTTCATTTTA
1 ACCCTTAAACTTT-TTAAAATTTCATTTTA
* * * *
41118 ACCCTTAAAATTCTGAAAATTACATTTTA
1 ACCCTTAAACTTTTTAAAATTTCATTTTA
*
41147 ACCCTTAAACTTTTTAGAAAAATTGCATTTTA
1 ACCCTTAAACTTTTT---AAAATTTCATTTTA
* * **
41179 AACCTAAAACTTTCCAAAATTT
1 ACCCTTAAACTTTTTAAAATTT
41201 TGATTTTACC
Statistics
Matches: 93, Mismatches: 16, Indels: 9
0.79 0.14 0.08
Matches are distributed among these distances:
29 32 0.34
30 27 0.29
31 10 0.11
32 24 0.26
ACGTcount: A:0.38, C:0.18, G:0.02, T:0.42
Consensus pattern (29 bp):
ACCCTTAAACTTTTTAAAATTTCATTTTA
Found at i:41107 original size:60 final size:59
Alignment explanation
Indices: 41014--41159 Score: 161
Period size: 60 Copynumber: 2.5 Consensus size: 59
41004 GTTTTGTTTA
* * * * * * *
41014 AAAATTATATTTTAATCC-TAAACTTTCCCAAAAA-TTCAAATTTGACCCTTAAACTTTTT
1 AAAATTACATTTTAACCCTTAAACTTT-CTAAAAATTTC-AATTTAACCCTTAAAATTCTG
* * *
41073 AAAATTTCATTTTTAACCCTTAATCTTTCTAAAAATTTCATTTTAACCCTTAAAATTCTG
1 AAAATTACA-TTTTAACCCTTAAACTTTCTAAAAATTTCAATTTAACCCTTAAAATTCTG
41133 AAAATTACATTTTAACCCTTAAACTTT
1 AAAATTACATTTTAACCCTTAAACTTT
41160 TTAGAAAAAT
Statistics
Matches: 72, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
59 24 0.33
60 38 0.53
61 10 0.14
ACGTcount: A:0.38, C:0.18, G:0.01, T:0.42
Consensus pattern (59 bp):
AAAATTACATTTTAACCCTTAAACTTTCTAAAAATTTCAATTTAACCCTTAAAATTCTG
Found at i:44415 original size:19 final size:19
Alignment explanation
Indices: 44391--44428 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
44381 ATGCTACCAA
44391 GAGTTTCTCGGATATGGTT
1 GAGTTTCTCGGATATGGTT
44410 GAGTTTCTCGGATATGGTT
1 GAGTTTCTCGGATATGGTT
44429 ATGTCTGGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.16, C:0.11, G:0.32, T:0.42
Consensus pattern (19 bp):
GAGTTTCTCGGATATGGTT
Found at i:49382 original size:49 final size:49
Alignment explanation
Indices: 49326--49817 Score: 252
Period size: 49 Copynumber: 9.9 Consensus size: 49
49316 GTAACAGCGG
* *
49326 ATCTGGTACCATGAATATATGAATGGAAAGGTTAAGGCCGCAACGGAAA
1 ATCTGGTACCATGAAGATATGAATGGAAAGGTTAAGGCCGCAACGGAGA
* *
49375 ATCTGGTACCATGAAGATACGAAGGGAAAGGTTAAGGCCGCAACGGCA-A
1 ATCTGGTACCATGAAGATATGAATGGAAAGGTTAAGGCCGCAACGG-AGA
* * * * * * *
49424 ACCCGGTACCTTAGAAGATGTG-ATGGGAAGGATTGAGGCCGCAA-TGACGA
1 ATCTGGTACCAT-GAAGATATGAATGGAAAGG-TTAAGGCCGCAACGGA-GA
* * * * *
49474 ATTTGGTACCGTGAATATATGAAGGGAAAGGTTAAGGCCGCAACGGCGA
1 ATCTGGTACCATGAAGATATGAATGGAAAGGTTAAGGCCGCAACGGAGA
* ** * * * * * *
49523 ACCCAGTACCTTTGAAG-TA-GTTATGGGAAGGATTGAGGTCGCAACGGTGA
1 ATCTGGTACC-ATGAAGATATG-AATGGAAAGG-TTAAGGCCGCAACGGAGA
* * *
49573 ATCTGGTACCATGAAGATATGAAAGGAAAGGTTGAGGCCGTAAC-GACGA
1 ATCTGGTACCATGAAGATATGAATGGAAAGGTTAAGGCCGCAACGGA-GA
* * * * * * * * *
49622 A-CTCAGTACCTTAAAAGATGTG-ATGGGAAGGATTGAGGTCACAA-TGATGA
1 ATCT-GGTACCAT-GAAGATATGAATGGAAAGG-TTAAGGCCGCAACGGA-GA
* * * * *
49672 ATCTGGTACCATGAAGATATGAAGGGGAAGGTTAAGGTCGTAACGGCGA
1 ATCTGGTACCATGAAGATATGAATGGAAAGGTTAAGGCCGCAACGGAGA
* * * * * * **
49721 ACCTGATACCTTAGAAGATGTG-ATAAGAAAGATCGAGGCCGCAACGGTA-A
1 ATCTGGTACCAT-GAAGATATGAAT-GGAAAGGTTAAGGCCGCAACGG-AGA
* * * * *
49771 ATCTAGTACCATGAAAATATAAAGGGGAAA-GTCTAAGGCCCCAACGG
1 ATCTGGTACCATGAAGATATGAA-TGGAAAGGT-TAAGGCCGCAACGG
49818 CGAACCTTGT
Statistics
Matches: 326, Mismatches: 91, Indels: 51
0.70 0.19 0.11
Matches are distributed among these distances:
48 5 0.02
49 163 0.50
50 155 0.48
51 3 0.01
ACGTcount: A:0.35, C:0.16, G:0.30, T:0.20
Consensus pattern (49 bp):
ATCTGGTACCATGAAGATATGAATGGAAAGGTTAAGGCCGCAACGGAGA
Found at i:49481 original size:148 final size:148
Alignment explanation
Indices: 49212--49519 Score: 435
Period size: 148 Copynumber: 2.1 Consensus size: 148
49202 GGGAAGATTG
* *
49212 AGGCCGCAACGGCAAATCTGATACCCAGAAGATACAGAGGGAAAGGTTAAGGCCACAATGACAAA
1 AGGCCGCAACGGAAAATCTGATACCCAGAAGATACAGAGGGAAAGGTTAAGGCCACAACGACAAA
* * *
49277 TCCGGTACCTTAGAAGATGTGATGAGAAGGATTGAGCTCGTAACAGCGGATCTGGTACCATGAAT
66 CCCGGTACCTTAGAAGATGTGATGAGAAGGATTGAGCTCGCAACAGCGAATCTGGTACCATGAAT
*
49342 ATATGAATGGAAAGGTTA
131 ATATGAAGGGAAAGGTTA
* * *
49360 AGGCCGCAACGGAAAATCTGGTA-CCATGAAGATAC-GAAGGGAAAGGTTAAGGCCGCAACGGCA
1 AGGCCGCAACGGAAAATCTGATACCCA-GAAGATACAG-AGGGAAAGGTTAAGGCCACAACGACA
* * * *
49423 AACCCGGTACCTTAGAAGATGTGATGGGAAGGATTGAGGC-CGCAA-TGACGAATTTGGTACCGT
64 AACCCGGTACCTTAGAAGATGTGATGAGAAGGATTGA-GCTCGCAACAG-CGAATCTGGTACCAT
49486 GAATATATGAAGGGAAAGGTTA
127 GAATATATGAAGGGAAAGGTTA
49508 AGGCCGCAACGG
1 AGGCCGCAACGG
49520 CGAACCCAGT
Statistics
Matches: 143, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
147 5 0.03
148 136 0.95
149 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.30, T:0.18
Consensus pattern (148 bp):
AGGCCGCAACGGAAAATCTGATACCCAGAAGATACAGAGGGAAAGGTTAAGGCCACAACGACAAA
CCCGGTACCTTAGAAGATGTGATGAGAAGGATTGAGCTCGCAACAGCGAATCTGGTACCATGAAT
ATATGAAGGGAAAGGTTA
Found at i:49482 original size:99 final size:99
Alignment explanation
Indices: 49374--49823 Score: 528
Period size: 99 Copynumber: 4.5 Consensus size: 99
49364 CGCAACGGAA
* * *
49374 AATCTGGTACCATGAAGATACGAAGGGAAAGGTTAAGGCCGCAACGGCAAACCCGGTACCTTAGA
1 AATCTGGTACCATGAAGATATGAAGGGAAAGGTTAAGGCCGCAACGGCGAACCCAGTACCTTAGA
*
49439 AGATGTGATGGGAAGGATTGAGGCCGCAATGACG
66 AGATGTGATGGGAAGGATTGAGGCCGCAATGATG
* * * *
49473 AATTTGGTACCGTGAATATATGAAGGGAAAGGTTAAGGCCGCAACGGCGAACCCAGTACCTTTGA
1 AATCTGGTACCATGAAGATATGAAGGGAAAGGTTAAGGCCGCAACGGCGAACCCAGTACCTTAGA
* * * *
49538 AG-TAGTTATGGGAAGGATTGAGGTCGCAACGGTG
66 AGAT-GTGATGGGAAGGATTGAGGCCGCAATGATG
* * * * * *
49572 AATCTGGTACCATGAAGATATGAAAGGAAAGGTTGAGGCCGTAACGACGAACTCAGTACCTTAAA
1 AATCTGGTACCATGAAGATATGAAGGGAAAGGTTAAGGCCGCAACGGCGAACCCAGTACCTTAGA
* *
49637 AGATGTGATGGGAAGGATTGAGGTCACAATGATG
66 AGATGTGATGGGAAGGATTGAGGCCGCAATGATG
* * * *
49671 AATCTGGTACCATGAAGATATGAAGGGGAAGGTTAAGGTCGTAACGGCGAA-CCTGATACCTTAG
1 AATCTGGTACCATGAAGATATGAAGGGAAAGGTTAAGGCCGCAACGGCGAACCCAG-TACCTTAG
** * * * * *
49735 AAGATGTGATAAGAAAGATCGAGGCCGCAACGGTA
65 AAGATGTGATGGGAAGGATTGAGGCCGCAATGATG
* * * *
49770 AATCTAGTACCATGAAAATATAAAGGGGAAA-GTCTAAGGCCCCAACGGCGAACC
1 AATCTGGTACCATGAAGATATGAA-GGGAAAGGT-TAAGGCCGCAACGGCGAACC
49824 TTGTACCCTA
Statistics
Matches: 295, Mismatches: 50, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
98 3 0.01
99 270 0.92
100 21 0.07
101 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.30, T:0.19
Consensus pattern (99 bp):
AATCTGGTACCATGAAGATATGAAGGGAAAGGTTAAGGCCGCAACGGCGAACCCAGTACCTTAGA
AGATGTGATGGGAAGGATTGAGGCCGCAATGATG
Found at i:49583 original size:198 final size:198
Alignment explanation
Indices: 49360--49823 Score: 583
Period size: 198 Copynumber: 2.3 Consensus size: 198
49350 GGAAAGGTTA
* * *
49360 AGGCCGCAACGGAAAATCTGGTACCATGAAGATACGAAGGGAAAGGTTAAGGCCGCAACGGCAAA
1 AGGCCGCAACGGTAAATCTGGTACCATGAAGATATGAAGGGAAAGGTTAAGGCCGCAACGGCGAA
* * * * * *
49425 CCCGGTACCTTAGAAGATGTGATGGGAAGGATTGAGGCCGCAATGACGAATTTGGTACCGTGAAT
66 CCCAGTACCTTAAAAGATGTGATGGGAAGGATTGAGGCCACAATGACGAATCTGGTACCATGAAG
* * ** *
49490 ATATGAAGGGAAAGGTTAAGGCCGCAACGGCGAACCCAG-TACCTTTGAAG-TAGTTATGGGAAG
131 ATATGAAGGGAAAGGTTAAGGCCGCAACGGCGAA-CCAGATACCTTAGAAGAT-GTGATAAGAAA
*
49553 GATTG
194 GATCG
* * * * * *
49558 AGGTCGCAACGGTGAATCTGGTACCATGAAGATATGAAAGGAAAGGTTGAGGCCGTAACGACGAA
1 AGGCCGCAACGGTAAATCTGGTACCATGAAGATATGAAGGGAAAGGTTAAGGCCGCAACGGCGAA
* * *
49623 CTCAGTACCTTAAAAGATGTGATGGGAAGGATTGAGGTCACAATGATGAATCTGGTACCATGAAG
66 CCCAGTACCTTAAAAGATGTGATGGGAAGGATTGAGGCCACAATGACGAATCTGGTACCATGAAG
* * * *
49688 ATATGAAGGGGAAGGTTAAGGTCGTAACGGCGAACCTGATACCTTAGAAGATGTGATAAGAAAGA
131 ATATGAAGGGAAAGGTTAAGGCCGCAACGGCGAACCAGATACCTTAGAAGATGTGATAAGAAAGA
49753 TCG
196 TCG
* * * *
49756 AGGCCGCAACGGTAAATCTAGTACCATGAAAATATAAAGGGGAAA-GTCTAAGGCCCCAACGGCG
1 AGGCCGCAACGGTAAATCTGGTACCATGAAGATATGAA-GGGAAAGGT-TAAGGCCGCAACGGCG
49820 AACC
64 AACC
49824 TTGTACCCTA
Statistics
Matches: 223, Mismatches: 39, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
197 3 0.01
198 199 0.89
199 21 0.09
ACGTcount: A:0.35, C:0.17, G:0.30, T:0.19
Consensus pattern (198 bp):
AGGCCGCAACGGTAAATCTGGTACCATGAAGATATGAAGGGAAAGGTTAAGGCCGCAACGGCGAA
CCCAGTACCTTAAAAGATGTGATGGGAAGGATTGAGGCCACAATGACGAATCTGGTACCATGAAG
ATATGAAGGGAAAGGTTAAGGCCGCAACGGCGAACCAGATACCTTAGAAGATGTGATAAGAAAGA
TCG
Found at i:49608 original size:148 final size:148
Alignment explanation
Indices: 49239--49622 Score: 345
Period size: 148 Copynumber: 2.6 Consensus size: 148
49229 CTGATACCCA
* * * * * * *
49239 GAAGATAC-AGAGGGAAAGGTTAAGGCCACAATGACAAATCCGGTACCTTAGAAGATGTG-ATGA
1 GAAGATACGA-AGGGAAAGGTTAAGGCCGCAACGGCAAACCCGGTACCATAGAAGATATGAAGGA
* * * *
49302 GAAGGATTGA-GCTCGTAAC-AGCGGATCTGGTACCATGAATATATGAATGGAAAGGTTAAGGCC
65 -AAGGATTGAGGC-CGCAACGA-CGAATTTGGTACCATGAATATATGAAGGGAAAGGTTAAGGCC
* **
49365 GCAACGGAAAATCTGGTACCAT
127 GCAACGGAAAACCCAGTACCAT
* * * *
49387 GAAGATACGAAGGGAAAGGTTAAGGCCGCAACGGCAAACCCGGTACCTTAGAAGATGTGATGGGA
1 GAAGATACGAAGGGAAAGGTTAAGGCCGCAACGGCAAACCCGGTACCATAGAAGATATGAAGGAA
* *
49452 AGGATTGAGGCCGCAATGACGAATTTGGTACCGTGAATATATGAAGGGAAAGGTTAAGGCCGCAA
66 AGGATTGAGGCCGCAACGACGAATTTGGTACCATGAATATATGAAGGGAAAGGTTAAGGCCGCAA
** *
49517 CGGCGAACCCAGTACCTTT
131 CGGAAAACCCAGTACC-AT
* * * ** * *
49536 GAAG-TA-GTTATGGG-AAGGATTGAGGTCGCAACGGTGAATCTGGTACCAT-GAAGATATGAAA
1 GAAGATACG--AAGGGAAAGG-TTAAGGCCGCAACGGCAAACCCGGTACCATAGAAGATATG-AA
*
49597 GGAAAGG-TTGAGGCCGTAACGACGAA
62 GGAAAGGATTGAGGCCGCAACGACGAA
49623 CTCAGTACCT
Statistics
Matches: 195, Mismatches: 32, Indels: 18
0.80 0.13 0.07
Matches are distributed among these distances:
147 1 0.01
148 150 0.77
149 44 0.23
ACGTcount: A:0.35, C:0.16, G:0.31, T:0.19
Consensus pattern (148 bp):
GAAGATACGAAGGGAAAGGTTAAGGCCGCAACGGCAAACCCGGTACCATAGAAGATATGAAGGAA
AGGATTGAGGCCGCAACGACGAATTTGGTACCATGAATATATGAAGGGAAAGGTTAAGGCCGCAA
CGGAAAACCCAGTACCAT
Found at i:50265 original size:38 final size:38
Alignment explanation
Indices: 50211--50387 Score: 142
Period size: 38 Copynumber: 4.5 Consensus size: 38
50201 TGTTGCCCCG
* *
50211 ATCATGGGGCAAATTGAAGCATCCAATCCTTTACCCTA
1 ATCAAGGGGCAGATTGAAGCATCCAATCCTTTACCCTA
* * * *
50249 ATCAGGGGGTAGATTGAAGCATTCAATCTTTTACCCTA
1 ATCAAGGGGCAGATTGAAGCATCCAATCCTTTACCCTA
* **
50287 ATCAAAGGGCAGATTGAAGGCATCATCCAAT-CTCTTACCCCG
1 ATCAAGGGGCAGATTGAA-G---CATCCAATCCT-TTACCCTA
* * * *
50329 ATCATGGGACAGATTGAAGCGTCCAATCTTTTACCAC-A
1 ATCAAGGGGCAGATTGAAGCATCCAATCCTTTACC-CTA
* *
50367 ACCATGGGGCAGATTTGAAGC
1 ATCAAGGGGCAGA-TTGAAGC
50388 TATCATCCTA
Statistics
Matches: 111, Mismatches: 20, Indels: 15
0.76 0.14 0.10
Matches are distributed among these distances:
38 71 0.64
39 10 0.09
41 2 0.02
42 28 0.25
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (38 bp):
ATCAAGGGGCAGATTGAAGCATCCAATCCTTTACCCTA
Found at i:50354 original size:118 final size:116
Alignment explanation
Indices: 50128--50363 Score: 296
Period size: 116 Copynumber: 2.0 Consensus size: 116
50118 AATCTCTTAC
* *
50128 CCCTGATCAAGGGGTAAATTAAAGCATCTAATCTTTTATCCAAATCAGAAGGCAAATTGAAGACA
1 CCCTAATCAAGGGGTAAATTAAAGCATCTAATCTTTTACCCAAATCAGAAGGCAAATTGAAGACA
* * *
50193 CACCAATCTGTTGCCCCGATCATGGGGCAAATTGAAGCATCCAATCCTTTA
66 CACCAATCTCTTACCCCGATCATGGGACAAATTGAAGCATCCAATCCTTTA
* * * * * *
50244 CCCTAATCAGGGGGTAGATTGAAGCAT-TCAATCTTTTACCCTAATCA-AAGGGCAGATTGAAGG
1 CCCTAATCAAGGGGTAAATTAAAGCATCT-AATCTTTTACCCAAATCAGAA-GGCAAATTGAAGA
* * *
50307 CATCATCCAATCTCTTACCCCGATCATGGGACAGATTGAAGCGTCCAATCTTTTA
64 CA-CA-CCAATCTCTTACCCCGATCATGGGACAAATTGAAGCATCCAATCCTTTA
50362 CC
1 CC
50364 ACAACCATGG
Statistics
Matches: 102, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
115 3 0.03
116 52 0.51
117 2 0.02
118 45 0.44
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (116 bp):
CCCTAATCAAGGGGTAAATTAAAGCATCTAATCTTTTACCCAAATCAGAAGGCAAATTGAAGACA
CACCAATCTCTTACCCCGATCATGGGACAAATTGAAGCATCCAATCCTTTA
Found at i:50381 original size:118 final size:117
Alignment explanation
Indices: 50149--50387 Score: 288
Period size: 118 Copynumber: 2.0 Consensus size: 117
50139 GGGTAAATTA
* * *
50149 AAGCATCTAATCTTTTATCCAAATCAGAAGGCAAATTGAAGACACACCAATCTGTTGCCCCGATC
1 AAGCATCTAATCTTTTACCCAAATCAGAAGGCAAATTGAAGACACACCAATCTCTTACCCCGATC
* * *
50214 ATGGGGCAAATTGAAGCATCCAATCCTTTACCCTAATCAGGGGGTAGA-TTG
66 ATGGGACAAATTGAAGCATCCAATCCTTTACCCTAACCAGGGGGCAGATTTG
* * *
50265 AAGCAT-TCAATCTTTTACCCTAATCA-AAGGGCAGATTGAAGGCATCATCCAATCTCTTACCCC
1 AAGCATCT-AATCTTTTACCCAAATCAGAA-GGCAAATTGAAGACA-CA-CCAATCTCTTACCCC
* * * *
50328 GATCATGGGACAGATTGAAGCGTCCAATCTTTTACCAC-AACCATGGGGCAGATTTG
62 GATCATGGGACAAATTGAAGCATCCAATCCTTTACC-CTAACCAGGGGGCAGATTTG
50384 AAGC
1 AAGC
50388 TATCATCCTA
Statistics
Matches: 104, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
115 3 0.03
116 35 0.34
117 2 0.02
118 56 0.54
119 8 0.08
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (117 bp):
AAGCATCTAATCTTTTACCCAAATCAGAAGGCAAATTGAAGACACACCAATCTCTTACCCCGATC
ATGGGACAAATTGAAGCATCCAATCCTTTACCCTAACCAGGGGGCAGATTTG
Found at i:50488 original size:49 final size:49
Alignment explanation
Indices: 50416--50585 Score: 225
Period size: 49 Copynumber: 3.4 Consensus size: 49
50406 AATCTCAACC
* * *
50416 TCCTGAAGTTGCAGCGAAATGGAGTGATGGTTC-ACACCAAATCCTATCT
1 TCCT-AAGTTGCAGTGAAATGGAGTGAAGCTTCAACACCAAATCCTATCT
* *
50465 TCCTGAAGTTGCAGTGAAATGGAGTGAAACTTCAATACCAAATCCTATCT
1 TCCT-AAGTTGCAGTGAAATGGAGTGAAGCTTCAACACCAAATCCTATCT
* *
50515 TCCTAAGTTGCAATGAAATGGAGTGAAGCTTCAACACCAAATTCTATCT
1 TCCTAAGTTGCAGTGAAATGGAGTGAAGCTTCAACACCAAATCCTATCT
* * *
50564 TCCTAAGTGGTAGTGAAGTGGA
1 TCCTAAGTTGCAGTGAAATGGA
50586 TGCAGTGCAT
Statistics
Matches: 107, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
49 88 0.82
50 19 0.18
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (49 bp):
TCCTAAGTTGCAGTGAAATGGAGTGAAGCTTCAACACCAAATCCTATCT
Found at i:52468 original size:30 final size:29
Alignment explanation
Indices: 52432--52619 Score: 166
Period size: 30 Copynumber: 6.3 Consensus size: 29
52422 AAAATCAAAC
52432 TTGACCCCTAAACTTTCT-AAAATTTCATTT
1 TTGA-CCCTAAACTTTCTAAAAATTTCA-TT
* * *
52462 TTGACCCTAATCTTTCCAAAATTTTCATT
1 TTGACCCTAAACTTTCTAAAAATTTCATT
*
52491 TTGACCCCTAAACTTTCTAAAAAATTCATT
1 TTGA-CCCTAAACTTTCTAAAAATTTCATT
*
52521 TTGACCCTAAACTTTCTAAAAATTACATT
1 TTGACCCTAAACTTTCTAAAAATTTCATT
* * ** *
52550 TTCACCCTCGAACTTTAAGGAAAAATTACATT
1 TTGACCCT-AAACTTT--CTAAAAATTTCATT
* * *
52582 TTAACCCTAAAACTTT-TCAAAATTTTGATT
1 TTGACCCT-AAACTTTCT-AAAAATTTCATT
52612 TT-ACCCTA
1 TTGACCCTA
52620 TTTTCCTTAT
Statistics
Matches: 132, Mismatches: 20, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
28 1 0.01
29 52 0.39
30 54 0.41
32 25 0.19
ACGTcount: A:0.34, C:0.22, G:0.04, T:0.39
Consensus pattern (29 bp):
TTGACCCTAAACTTTCTAAAAATTTCATT
Found at i:52470 original size:29 final size:30
Alignment explanation
Indices: 52432--52556 Score: 166
Period size: 29 Copynumber: 4.2 Consensus size: 30
52422 AAAATCAAAC
52432 TTGACCCCTAAACTTTCT-AAAATTTCATTT
1 TTGACCCCTAAACTTTCTAAAAATTTCA-TT
* * *
52462 TTGA-CCCTAATCTTTCCAAAATTTTCATT
1 TTGACCCCTAAACTTTCTAAAAATTTCATT
*
52491 TTGACCCCTAAACTTTCTAAAAAATTCATT
1 TTGACCCCTAAACTTTCTAAAAATTTCATT
*
52521 TTGA-CCCTAAACTTTCTAAAAATTACATT
1 TTGACCCCTAAACTTTCTAAAAATTTCATT
*
52550 TTCACCC
1 TTGACCC
52557 TCGAACTTTA
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
29 43 0.52
30 39 0.48
ACGTcount: A:0.32, C:0.25, G:0.03, T:0.40
Consensus pattern (30 bp):
TTGACCCCTAAACTTTCTAAAAATTTCATT
Found at i:52550 original size:59 final size:59
Alignment explanation
Indices: 52389--52556 Score: 180
Period size: 59 Copynumber: 2.8 Consensus size: 59
52379 CTATTTTGTT
* * * **
52389 TAAAAATT-ATATTTTAAGCCTAAACTTTCCCAAAAAAT-CAAACTTGACCCCTAAACTTTC
1 TAAAAATTCAT-TTTTGACCCTAAACTTT-CCAAAAATTAC-ATTTTGACCCCTAAACTTTC
* * * *
52449 TAAAATTTCATTTTTGACCCTAATCTTTCCAAAATTTTCATTTTGACCCCTAAACTTTC
1 TAAAAATTCATTTTTGACCCTAAACTTTCCAAAAATTACATTTTGACCCCTAAACTTTC
* *
52508 TAAAAAATTCA-TTTTGACCCTAAACTTTCTAAAAATTACATTTTCACCC
1 T-AAAAATTCATTTTTGACCCTAAACTTTCCAAAAATTACATTTTGACCC
52557 TCGAACTTTA
Statistics
Matches: 91, Mismatches: 14, Indels: 7
0.81 0.12 0.06
Matches are distributed among these distances:
59 59 0.65
60 30 0.33
61 2 0.02
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.38
Consensus pattern (59 bp):
TAAAAATTCATTTTTGACCCTAAACTTTCCAAAAATTACATTTTGACCCCTAAACTTTC
Found at i:52557 original size:29 final size:29
Alignment explanation
Indices: 52432--52605 Score: 156
Period size: 29 Copynumber: 5.8 Consensus size: 29
52422 AAAATCAAAC
*
52432 TTGACCCCTAAACTTTCT-AAAATTTCATTT
1 TTGA-CCCTAAACTTTCTAAAAATTACA-TT
* * * *
52462 TTGACCCTAATCTTTCCAAAATTTTCATT
1 TTGACCCTAAACTTTCTAAAAATTACATT
52491 TTGACCCCTAAACTTTCTAAAAAATT-CATT
1 TTGA-CCCTAAACTTTCT-AAAAATTACATT
52521 TTGACCCTAAACTTTCTAAAAATTACATT
1 TTGACCCTAAACTTTCTAAAAATTACATT
* * **
52550 TTCACCCTCGAACTTTAAGGAAAAATTACATT
1 TTGACCCT-AAACTTT--CTAAAAATTACATT
* *
52582 TTAACCCTAAAACTTT-TCAAAATT
1 TTGACCCT-AAACTTTCTAAAAATT
52606 TTGATTTTAC
Statistics
Matches: 122, Mismatches: 15, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
28 7 0.06
29 47 0.39
30 37 0.30
31 6 0.05
32 25 0.20
ACGTcount: A:0.35, C:0.22, G:0.04, T:0.39
Consensus pattern (29 bp):
TTGACCCTAAACTTTCTAAAAATTACATT
Found at i:52596 original size:32 final size:29
Alignment explanation
Indices: 52390--52597 Score: 123
Period size: 29 Copynumber: 6.9 Consensus size: 29
52380 TATTTTGTTT
* * *
52390 AAAAATTATATTTTAAGCCTAAACTTTCCCA
1 AAAAATTACATTTTAACCCTAAACTTT--CG
* * * * *
52421 AAAAATCAAACTTGACCCCTAAACTTTC-
1 AAAAATTACATTTTAACCCTAAACTTTCG
* * * * *
52449 TAAAATTTCATTTTTGACCCTAATCTTTCC
1 AAAAATTACA-TTTTAACCCTAAACTTTCG
* * * *
52479 AAAATTTTCATTTTGACCCCTAAACTTTCTA
1 AAAAATTACATTTT-AACCCTAAACTTTC-G
* *
52510 AAAAATT-CATTTTGACCCTAAACTTTCT
1 AAAAATTACATTTTAACCCTAAACTTTCG
* * *
52538 AAAAATTACATTTTCACCCTCGAACTTTAAGG
1 AAAAATTACATTTTAACCCT-AAACTTT--CG
52570 AAAAATTACATTTTAACCCTAAAACTTT
1 AAAAATTACATTTTAACCCT-AAACTTT
52598 TCAAAATTTT
Statistics
Matches: 137, Mismatches: 32, Indels: 15
0.74 0.17 0.08
Matches are distributed among these distances:
28 13 0.09
29 41 0.30
30 31 0.23
31 27 0.20
32 25 0.18
ACGTcount: A:0.38, C:0.22, G:0.04, T:0.37
Consensus pattern (29 bp):
AAAAATTACATTTTAACCCTAAACTTTCG
Found at i:56420 original size:30 final size:30
Alignment explanation
Indices: 56345--56689 Score: 186
Period size: 29 Copynumber: 12.1 Consensus size: 30
56335 TAATTTTGAG
*
56345 AGTTTCGAGGTCGAAAATGGAGA-TTTTGG-
1 AGTTTCGAGGTCAAAAATGGA-ATTTTTGGA
* * * *
56374 AGGTT-AAGGGCAAAAATGAAATTTTTGGA
1 AGTTTCGAGGTCAAAAATGGAATTTTTGGA
*
56403 AGTTTCGAGGTCAAAAATAG-ATTTTTGGA
1 AGTTTCGAGGTCAAAAATGGAATTTTTGGA
* *
56432 AG-TTC-ATGGGT-AAAAATGAAATTTTTAGA
1 AGTTTCGA--GGTCAAAAATGGAATTTTTGGA
* * *
56461 AGTTTCG-GGATTAAAAATGGGATTCTTGGA
1 AGTTTCGAGG-TCAAAAATGGAATTTTTGGA
* *
56491 AATTT--AGGGCTAAAAATGGAATTTTT---
1 AGTTTCGAGGTC-AAAAATGGAATTTTTGGA
* *
56517 -G----G-GGTTAAAAATGGGATTTTTGGA
1 AGTTTCGAGGTCAAAAATGGAATTTTTGGA
* * ** *
56541 A-ATTCGGGGGT-AAAAACAGAATTTTTTGA
1 AGTTTC-GAGGTCAAAAATGGAATTTTTGGA
* ** *
56570 AGTGTCGAGGAAAAAAATGGGATTGTTT-GA
1 AGTTTCGAGGTCAAAAATGGAATT-TTTGGA
56600 AG-TTCGAGGGT-AAAAATGGAATTTTTGGA
1 AGTTTCGA-GGTCAAAAATGGAATTTTTGGA
*
56629 AGTTTCGAGGTCAAAAATGGGATTGTTT-GA
1 AGTTTCGAGGTCAAAAATGGAATT-TTTGGA
56659 AG-TTCGAGGGT-AAAAATGGAATTTTTGGA
1 AGTTTCGA-GGTCAAAAATGGAATTTTTGGA
56688 AG
1 AG
56690 GTTTAGGGAC
Statistics
Matches: 241, Mismatches: 42, Indels: 66
0.69 0.12 0.19
Matches are distributed among these distances:
21 14 0.06
22 2 0.01
27 2 0.01
28 34 0.14
29 109 0.45
30 74 0.31
31 6 0.02
ACGTcount: A:0.35, C:0.05, G:0.29, T:0.32
Consensus pattern (30 bp):
AGTTTCGAGGTCAAAAATGGAATTTTTGGA
Found at i:56515 original size:59 final size:58
Alignment explanation
Indices: 56299--56689 Score: 319
Period size: 59 Copynumber: 6.8 Consensus size: 58
56289 TTCGGGGTTT
* * *
56299 AAAAATGGAATTTTTGGACA-TTCAGGAGT-AAAAGGGTAA-TTTT-GAGAGTTTCGAGGTC
1 AAAAATGGGATTGTTGGA-AGTTCAGG-GTAAAAATGG-AATTTTTGGA-AGTTTCGAGGTC
* * * * *
56357 GAAAATGGAGATT-TTGGAGGTTAAGGGCAAAAATGAAATTTTTGGAAGTTTCGAGGTC
1 AAAAATGG-GATTGTTGGAAGTTCAGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTC
* * * * *
56415 AAAAAT-AGATTTTTGGAAGTTCATGGGTAAAAATGAAATTTTTAGAAGTTTCG-GGATT
1 AAAAATGGGATTGTTGGAAGTTCA-GGGTAAAAATGGAATTTTTGGAAGTTTCGAGG-TC
* * * *
56473 AAAAATGGGATTCTTGGAAATTTAGGGCTAAAAATGGAATTTTT----G----G-GGTT
1 AAAAATGGGATTGTTGGAAGTTCAGGG-TAAAAATGGAATTTTTGGAAGTTTCGAGGTC
* * * ** * * **
56523 AAAAATGGGATTTTTGGAAATTCGGGGGTAAAAACAGAATTTTTTGAAGTGTCGAGGAA
1 AAAAATGGGATTGTTGGAAGTTC-AGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTC
*
56582 AAAAATGGGATTGTTTGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTC
1 AAAAATGGGATTGTTGGAAGTTC-AGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTC
*
56641 AAAAATGGGATTGTTTGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAG
1 AAAAATGGGATTGTTGGAAGTTC-AGGGTAAAAATGGAATTTTTGGAAG
56690 GTTTAGGGAC
Statistics
Matches: 277, Mismatches: 36, Indels: 39
0.79 0.10 0.11
Matches are distributed among these distances:
50 37 0.13
51 6 0.02
54 1 0.00
55 1 0.00
56 4 0.01
57 14 0.05
58 81 0.29
59 133 0.48
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.32
Consensus pattern (58 bp):
AAAAATGGGATTGTTGGAAGTTCAGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTC
Found at i:56555 original size:50 final size:50
Alignment explanation
Indices: 56471--56566 Score: 138
Period size: 50 Copynumber: 1.9 Consensus size: 50
56461 AGTTTCGGGA
* **
56471 TTAAAAATGGGATTCTTGGAAATTTAGGGCTAAAAATGGAATTTTTGGGG
1 TTAAAAATGGGATTCTTGGAAATTCAGGGCTAAAAACAGAATTTTTGGGG
* * *
56521 TTAAAAATGGGATTTTTGGAAATTCGGGGGTAAAAACAGAATTTTT
1 TTAAAAATGGGATTCTTGGAAATTCAGGGCTAAAAACAGAATTTTT
56567 TGAAGTGTCG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 40 1.00
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.34
Consensus pattern (50 bp):
TTAAAAATGGGATTCTTGGAAATTCAGGGCTAAAAACAGAATTTTTGGGG
Found at i:56564 original size:109 final size:109
Alignment explanation
Indices: 56422--56627 Score: 265
Period size: 109 Copynumber: 1.9 Consensus size: 109
56412 GTCAAAAATA
* * * * *
56422 GATTTTTGGAAGTTCATGGGTAAAAATGAAATTTTTAGAAGTTTCG-GGATTAAAAATGGGATTC
1 GATTTTTGGAAATTCAGGGGTAAAAAAGAAATTTTTAGAAGTGTCGAGGA-AAAAAATGGGATTC
*
56486 TTGGAAATT-TAGGGCTAAAAATGGAATTTTTGGGGTTAAAAATGG
65 TTGGAAATTCGAGGG-TAAAAATGGAATTTTTGGGGTTAAAAATGG
* * *
56531 GATTTTTGGAAATTCGGGGGTAAAAACAG-AATTTTTTGAAGTGTCGAGGAAAAAAATGGGATTG
1 GATTTTTGGAAATTCAGGGGTAAAAA-AGAAATTTTTAGAAGTGTCGAGGAAAAAAATGGGATTC
* *
56595 TTTGAAGTTCGAGGGTAAAAATGGAATTTTTGG
65 TTGGAAATTCGAGGGTAAAAATGGAATTTTTGG
56628 AAGTTTCGAG
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
109 75 0.90
110 8 0.10
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.33
Consensus pattern (109 bp):
GATTTTTGGAAATTCAGGGGTAAAAAAGAAATTTTTAGAAGTGTCGAGGAAAAAAATGGGATTCT
TGGAAATTCGAGGGTAAAAATGGAATTTTTGGGGTTAAAAATGG
Found at i:57694 original size:21 final size:20
Alignment explanation
Indices: 57666--57725 Score: 70
Period size: 18 Copynumber: 3.0 Consensus size: 20
57656 TTCTTTTTTT
57666 ATTTATTATTATTAATAATA
1 ATTTATTATTATTAATAATA
* *
57686 ATATTATTATTATCAA-AA-C
1 AT-TTATTATTATTAATAATA
57705 ATTTATTATTATTAATGAATA
1 ATTTATTATTATTAAT-AATA
57726 TTAAGAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
18 12 0.38
19 2 0.06
20 6 0.19
21 12 0.38
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (20 bp):
ATTTATTATTATTAATAATA
Found at i:57773 original size:12 final size:12
Alignment explanation
Indices: 57741--57782 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
57731 AAAAACTTAT
57741 TTATTATTAATGA
1 TTATTATTAAT-A
*
57754 -TATCATTAATA
1 TTATTATTAATA
*
57765 TTATTATTATTA
1 TTATTATTAATA
57777 TTATTA
1 TTATTA
57783 AAACAGTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
11 1 0.04
12 24 0.96
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (12 bp):
TTATTATTAATA
Found at i:57782 original size:21 final size:20
Alignment explanation
Indices: 57758--57804 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
57748 TAATGATATC
57758 ATTAATATTATTATTATTATT
1 ATTAA-ATTATTATTATTATT
**
57779 ATTAAAACAGTTATTATTATT
1 ATTAAATTA-TTATTATTATT
57800 ATTAA
1 ATTAA
57805 GAATTATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
ATTAAATTATTATTATTATT
Found at i:58499 original size:17 final size:17
Alignment explanation
Indices: 58461--58529 Score: 84
Period size: 17 Copynumber: 4.0 Consensus size: 17
58451 TTTTAACTTC
*
58461 TTTAAATTTAAATTTAAA
1 TTTAAATTTAAAATT-AA
*
58479 TTTAAATTTAAGATTAA
1 TTTAAATTTAAAATTAA
**
58496 TTTAAATTTAAAAAAAA
1 TTTAAATTTAAAATTAA
*
58513 TCTAAATTTAAAATTAA
1 TTTAAATTTAAAATTAA
58530 AAAGGGGCCC
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
17 30 0.70
18 13 0.30
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (17 bp):
TTTAAATTTAAAATTAA
Found at i:58520 original size:23 final size:22
Alignment explanation
Indices: 58468--58532 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 22
58458 TTCTTTAAAT
* *
58468 TTAAATTTAAATTTAAATTTAAGA
1 TTAAATTTAAATTTAAA--AAAAA
58492 TT-AATTTAAATTTAAAAAAAA
1 TTAAATTTAAATTTAAAAAAAA
*
58513 TCTAAATTTAAAATTAAAAA
1 T-TAAATTTAAATTTAAAAA
58533 GGGGCCCGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
21 4 0.11
22 1 0.03
23 29 0.81
24 2 0.06
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (22 bp):
TTAAATTTAAATTTAAAAAAAA
Found at i:58531 original size:6 final size:6
Alignment explanation
Indices: 58461--58530 Score: 74
Period size: 6 Copynumber: 12.0 Consensus size: 6
58451 TTTTAACTTC
58461 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAGA -TT-AA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA
** * *
58508 -AAAAA TCTAAA TTTAAA ATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA
58531 AAGGGGCCCG
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
4 1 0.02
5 6 0.11
6 46 0.85
7 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:59229 original size:205 final size:205
Alignment explanation
Indices: 58980--59707 Score: 1053
Period size: 205 Copynumber: 3.5 Consensus size: 205
58970 TACTTCGACT
* * *
58980 TGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCAAGCGTGAGTTTGA
1 TGCTTCTCCGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGAGTTTGA
*
59045 TTTGGTCTTCTTCTCAGTATCTCATCAGAAAGATGACTGCGTCGTTTGTTTCAATTCGCTTCTCT
66 TTTGGTCTTCTTCTCAGTATCTCATCAGAAAGATGACTGCATCGTTTGTTTCAATTCGCTTCTCT
*
59110 GTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAATCTAACCCTTTAT
131 GTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCCTTTAT
*
59175 TGTTTCACCC
196 TGCTTCACCC
* * * * *
59185 TGCTTCTTCGTATCTCATCAGGAAGCTAGGGTTCGAGGATTTGCTCACATCGGGAGTGAGTTTGA
1 TGCTTCTCCGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGAGTTTGA
*
59250 TTTGGTCTTCTTCTCAGTATCTCATTA-AGAAGATGACTGCATCGTTTGTTTCAATTCGCTTCTC
66 TTTGGTCTTCTTCTCAGTATCTCATCAGA-AAGATGACTGCATCGTTTGTTTCAATTCGCTTCTC
*
59314 TGTATCTCATCAGGAATACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCCTTTA
130 TGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCCTTTA
59379 TTGCTTCACCC
195 TTGCTTCACCC
* * * * * *
59390 TGCTTCTCCGTATCTCATCAGGGAGTTGGGGTTCGAGGATTTGCTTACATCGGGCGTAAGTTTGA
1 TGCTTCTCCGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGAGTTTGA
*
59455 TTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACTGCATCGTTTGTTTCAATTCGCTTCTCT
66 TTTGGTCTTCTTCTCAGTATCTCATCAGAAAGATGACTGCATCGTTTGTTTCAATTCGCTTCTCT
* * * * * *
59520 GTATCTCATCAGGAAGGCAAATTTAGTTCACTTCTCAGCTATCTCATCAAGAAGCTAACCTTTTA
131 GTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAG-TATCTCATCAGGAAGCTAACCCTTTA
**
59585 TTGCTTCACAT
195 TTGCTTCACCC
* * * ** * * **
59596 TGCTTCTCCGTATCTCAACAGGAAGCTGGGGTTCGAAGACTTACTCATTTTGAGCCTCGTTTCAT
1 TGCTTCTCCGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGT-GAGT--T
* *
59661 TGATTTGGTTTTCTTCTCAGTATCTCATCAGGAAGATGACTGCATCG
63 TGATTTGGTCTTCTTCTCAGTATCTCATCAGAAAGATGACTGCATCG
59708 CTGTTTTGTG
Statistics
Matches: 470, Mismatches: 47, Indels: 8
0.90 0.09 0.02
Matches are distributed among these distances:
204 1 0.00
205 343 0.73
206 78 0.17
207 1 0.00
209 47 0.10
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.36
Consensus pattern (205 bp):
TGCTTCTCCGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGAGTTTGA
TTTGGTCTTCTTCTCAGTATCTCATCAGAAAGATGACTGCATCGTTTGTTTCAATTCGCTTCTCT
GTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCCTTTAT
TGCTTCACCC
Found at i:71592 original size:29 final size:28
Alignment explanation
Indices: 71557--71861 Score: 203
Period size: 29 Copynumber: 10.4 Consensus size: 28
71547 ACAAAAAAGG
*
71557 GATTTTTGGAAGTTTCGGGTCGAAAATGA
1 GATTTTTGGAAGTTTCGGGT-AAAAATGA
71586 GATTTTTGGAAG-TTCGGGGGTAAAAATGTA
1 GATTTTTGGAAGTTTC--GGGTAAAAATG-A
*
71616 -ATTTTTGGAAGTTTCGGGGTTAAAAATGG
1 GATTTTTGGAAGTTTC-GGG-TAAAAATGA
* * *
71645 GATTCTTGGAAATTTAGGGGTAAAAAT-A
1 GATTTTTGGAAGTTT-CGGGTAAAAATGA
* *
71673 TAATTTTTGGAAGTTTTGAGGTCAAAAATGA
1 -GATTTTTGGAAGTTTCG-GGT-AAAAATGA
** *
71704 GATTTTT-GAAAATTCAAGAGTAAAAATG-
1 GATTTTTGGAAGTTTC--GGGTAAAAATGA
* *
71732 GAATTTTTAGAAGTTTCGAGGTAAAAAATGG
1 G-ATTTTTGGAAGTTTCG-GGT-AAAAATGA
**
71763 GATTTTTGGAAG-TTCGGGGGTAAAAACAA
1 GATTTTTGGAAGTTTC--GGGTAAAAATGA
* * *
71792 AATTTTTGGAAGTTTTGGGGTTAAAATG-
1 GATTTTTGGAAG-TTTCGGGTAAAAATGA
*
71820 GAATTTTTGGAAGTTTGGGGGTAAAAATG-
1 G-ATTTTTGGAAGTTT-CGGGTAAAAATGA
71849 GAATTTTTGGAAG
1 G-ATTTTTGGAAG
71862 GTTTAAGGAT
Statistics
Matches: 223, Mismatches: 29, Indels: 48
0.74 0.10 0.16
Matches are distributed among these distances:
28 9 0.04
29 137 0.61
30 71 0.32
31 6 0.03
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.35
Consensus pattern (28 bp):
GATTTTTGGAAGTTTCGGGTAAAAATGA
Found at i:71669 original size:59 final size:59
Alignment explanation
Indices: 71549--71861 Score: 342
Period size: 59 Copynumber: 5.3 Consensus size: 59
71539 GGTTAAGCAC
* * * *
71549 AAAAAAGGGATTTTTGGAAGTTTC-GGGTCGAAAATGAGATTTTTGGAAGTTCGGGGGT
1 AAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* * * * **
71607 AAAAATGTAATTTTTGGAAGTTTCGGGGTTAAAAATGGGATTCTTGGAAATTTAGGGGT
1 AAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
** * * * * * ** *
71666 AAAAATATAATTTTTGGAAGTTTTGAGGTCAAAAATGAGATTTTTGAAAATTCAAGAGT
1 AAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* * *
71725 AAAAATGGAATTTTTAGAAGTTTCGAGGTAAAAAATGGGATTTTTGGAAGTTCGGGGGT
1 AAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
*** * * * *
71784 AAAAACAAAATTTTTGGAAGTTTTGGGGT-TAAAATGGAATTTTTGGAAGTTTGGGGGT
1 AAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
71842 AAAAATGGAATTTTTGGAAG
1 AAAAATGGAATTTTTGGAAG
71862 GTTTAAGGAT
Statistics
Matches: 211, Mismatches: 43, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
58 64 0.30
59 147 0.70
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (59 bp):
AAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
Found at i:71737 original size:118 final size:117
Alignment explanation
Indices: 71558--71861 Score: 396
Period size: 118 Copynumber: 2.6 Consensus size: 117
71548 CAAAAAAGGG
* * *
71558 ATTTTTGGAAGTTTCGGGTCGAAAATGAGATTTTTGGAAGTTCGGGGGTAAAAATGTAATTTTTG
1 ATTTTTGGAAGTTTTGGGTCAAAAATGAGATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTG
* * * * *
71623 GAAGTTTCGGGGTTAAAAATGGGATTCTTGGAAATTTAGGGGTAAAAATATA
66 GAAGTTTCGAGGTAAAAAATGGGATTCTTGGAAATTCAGGGGTAAAAACAAA
* * ** *
71675 ATTTTTGGAAGTTTTGAGGTCAAAAATGAGATTTTTGAAAATTCAAGAGTAAAAATGGAATTTTT
1 ATTTTTGGAAGTTTTG-GGTCAAAAATGAGATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTT
* * * *
71740 AGAAGTTTCGAGGTAAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAACAAA
65 GGAAGTTTCGAGGTAAAAAATGGGATTCTTGGAAATTCAGGGGTAAAAACAAA
* *
71793 ATTTTTGGAAGTTTTGGGGT-TAAAATG-GAATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTT
1 ATTTTTGGAAGTTTT-GGGTCAAAAATGAG-ATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTT
71856 TGGAAG
64 TGGAAG
71862 GTTTAAGGAT
Statistics
Matches: 159, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
116 1 0.01
117 54 0.34
118 103 0.65
119 1 0.01
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.35
Consensus pattern (117 bp):
ATTTTTGGAAGTTTTGGGTCAAAAATGAGATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTG
GAAGTTTCGAGGTAAAAAATGGGATTCTTGGAAATTCAGGGGTAAAAACAAA
Found at i:72836 original size:21 final size:22
Alignment explanation
Indices: 72812--72874 Score: 53
Period size: 21 Copynumber: 3.0 Consensus size: 22
72802 TCCTTTTTTT
72812 TATTTATTATATTAAT-AATAA
1 TATTTATTATATTAATCAATAA
*
72833 TA-TTATTGTTATT-ATCAA-AA
1 TATTTATT-ATATTAATCAATAA
* *
72853 CATTTATTATTATTAATGAATA
1 TATTTATTA-TATTAATCAATA
72875 TTAAGAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
20 10 0.31
21 17 0.53
22 4 0.12
23 1 0.03
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (22 bp):
TATTTATTATATTAATCAATAA
Found at i:73652 original size:17 final size:17
Alignment explanation
Indices: 73623--73697 Score: 89
Period size: 17 Copynumber: 4.3 Consensus size: 17
73613 TTGAATTTTT
* *
73623 TTAATTTTAAAATTAAA
1 TTAAATTTAAATTTAAA
73640 TTTAAATTTAAATTTAAGA
1 -TTAAATTTAAATTTAA-A
73659 TT-AATTTAAATTTAAA
1 TTAAATTTAAATTTAAA
*
73675 ATAAATTTAAATTTAAAA
1 TTAAATTTAAATTT-AAA
73693 TTAAA
1 TTAAA
73698 AAGGGGTCCG
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
16 2 0.04
17 24 0.48
18 23 0.46
19 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (17 bp):
TTAAATTTAAATTTAAA
Found at i:73687 original size:23 final size:22
Alignment explanation
Indices: 73632--73698 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 22
73622 TTTAATTTTA
*
73632 AAATTAAATTTAAATTTAAATTT
1 AAATTAAATTTAAATTTAAA-AT
73655 AAGATT-AATTTAAATTTAAAAT
1 AA-ATTAAATTTAAATTTAAAAT
*
73677 AAATTTAAATTTAAAATTAAAA
1 AAA-TTAAATTTAAATTTAAAA
73699 AGGGGTCCGG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
21 1 0.03
22 5 0.13
23 30 0.77
24 3 0.08
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (22 bp):
AAATTAAATTTAAATTTAAAAT
Found at i:73698 original size:6 final size:6
Alignment explanation
Indices: 73622--73697 Score: 86
Period size: 6 Copynumber: 13.0 Consensus size: 6
73612 TTTGAATTTT
* *
73622 TTTAAT TTTAAA ATTAAA TTTAAA TTTAAA TTTAAGA -TT-AA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA
* *
73669 TTTAAA -ATAAA TTTAAA TTTAAA ATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
73698 AAGGGGTCCG
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
4 1 0.02
5 7 0.12
6 51 0.85
7 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:94845 original size:2 final size:2
Alignment explanation
Indices: 94838--94871 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
94828 TGCCTTTCAA
94838 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
94872 ATGCAGTGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:95989 original size:21 final size:21
Alignment explanation
Indices: 95965--96019 Score: 85
Period size: 21 Copynumber: 2.6 Consensus size: 21
95955 ATAGTTCGAG
95965 GTTTAAGGTTTAGAGTTATAA
1 GTTTAAGGTTTAGAGTTATAA
*
95986 GTTTAGGGTTTAGAGTTATAA
1 GTTTAAGGTTTAGAGTTATAA
96007 GTTT-AGAGTTTAG
1 GTTTAAG-GTTTAG
96020 GATTCATGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.97
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (21 bp):
GTTTAAGGTTTAGAGTTATAA
Found at i:95998 original size:7 final size:7
Alignment explanation
Indices: 95972--96019 Score: 55
Period size: 7 Copynumber: 6.9 Consensus size: 7
95962 GAGGTTTAAG
95972 GTTTAGA
1 GTTTAGA
95979 GTTATA-A
1 GTT-TAGA
*
95986 GTTTAGG
1 GTTTAGA
95993 GTTTAGA
1 GTTTAGA
96000 GTTATA-A
1 GTT-TAGA
96007 GTTTAGA
1 GTTTAGA
96014 GTTTAG
1 GTTTAG
96020 GATTCATGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
6 4 0.11
7 27 0.77
8 4 0.11
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (7 bp):
GTTTAGA
Found at i:97455 original size:20 final size:20
Alignment explanation
Indices: 97393--97455 Score: 99
Period size: 20 Copynumber: 3.1 Consensus size: 20
97383 AGTTTTTTAG
97393 TATTTACATGTATTTTATTT
1 TATTTACATGTATTTTATTT
* **
97413 TAATTACAAATATTTTATTT
1 TATTTACATGTATTTTATTT
97433 TATTTACATGTATTTTATTT
1 TATTTACATGTATTTTATTT
97453 TAT
1 TAT
97456 AATTTAAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (20 bp):
TATTTACATGTATTTTATTT
Found at i:98766 original size:5 final size:5
Alignment explanation
Indices: 98751--98784 Score: 50
Period size: 5 Copynumber: 6.4 Consensus size: 5
98741 AAATATTACC
98751 CTTTT CTTTTT CTTTTT CTTTT CTTTT CTTTT CT
1 CTTTT C-TTTT C-TTTT CTTTT CTTTT CTTTT CT
98785 CCAAGATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 17 0.61
6 11 0.39
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (5 bp):
CTTTT
Found at i:104153 original size:19 final size:19
Alignment explanation
Indices: 104129--104166 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
104119 GCATTATGAA
104129 ACTCATATGTAAGAACGTC
1 ACTCATATGTAAGAACGTC
*
104148 ACTCATATGTAGGAACGTC
1 ACTCATATGTAAGAACGTC
104167 CATGGGCTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.26
Consensus pattern (19 bp):
ACTCATATGTAAGAACGTC
Found at i:115163 original size:47 final size:47
Alignment explanation
Indices: 115094--115201 Score: 171
Period size: 47 Copynumber: 2.3 Consensus size: 47
115084 ATTAAGTTCG
* * *
115094 ATGAATTCATCAAGTCCATCTCAATAGGATCACCCAAAGTTAGGAAT
1 ATGAATTCATTAAGTCCATCTCAATAGGATCACCCAAACTCAGGAAT
* *
115141 ATGAATTCATTAAGTTCGTCTCAATAGGATCACCCAAACTCAGGAAT
1 ATGAATTCATTAAGTCCATCTCAATAGGATCACCCAAACTCAGGAAT
115188 ATGAATTCATTAAG
1 ATGAATTCATTAAG
115202 AGTAATAAAC
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 56 1.00
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (47 bp):
ATGAATTCATTAAGTCCATCTCAATAGGATCACCCAAACTCAGGAAT
Found at i:117768 original size:15 final size:15
Alignment explanation
Indices: 117743--117788 Score: 58
Period size: 17 Copynumber: 3.0 Consensus size: 15
117733 TTTATAATTT
*
117743 ACTTA-TAAACTAGA
1 ACTTATTAAACTAAA
117757 ACTTATTAAACTAAA
1 ACTTATTAAACTAAA
117772 ACCCTTATTAAACTAAA
1 A--CTTATTAAACTAAA
117789 GTTTACATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 5 0.18
15 9 0.32
17 14 0.50
ACGTcount: A:0.50, C:0.17, G:0.02, T:0.30
Consensus pattern (15 bp):
ACTTATTAAACTAAA
Found at i:121738 original size:22 final size:22
Alignment explanation
Indices: 121713--121771 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
121703 TTTTATAAAA
*
121713 TATTTATTTTTAATTTTAATAT
1 TATTTATATTTAATTTTAATAT
* *
121735 TA-TTA-ATATAATATTTTATAT
1 TATTTATATTTAAT-TTTAATAT
121756 TATTT-TATTTAATTTT
1 TATTTATATTTAATTTT
121772 TGGTAAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
20 5 0.17
21 15 0.50
22 10 0.33
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
TATTTATATTTAATTTTAATAT
Found at i:122193 original size:23 final size:23
Alignment explanation
Indices: 122167--122210 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
122157 TGTAGTGAAG
*
122167 CTTCACTGTTCATTGCAAAGACT
1 CTTCACTATTCATTGCAAAGACT
* *
122190 CTTCATTATTCATTGGAAAGA
1 CTTCACTATTCATTGCAAAGA
122211 ATTTTACAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (23 bp):
CTTCACTATTCATTGCAAAGACT
Found at i:132565 original size:18 final size:18
Alignment explanation
Indices: 132532--132566 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
132522 TTGCAATTTG
*
132532 TCAAAATGTTCACAATAT
1 TCAAAATGGTCACAATAT
*
132550 TCAAAATGGTCCCAATA
1 TCAAAATGGTCACAATA
132567 CTAACACTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.29
Consensus pattern (18 bp):
TCAAAATGGTCACAATAT
Found at i:134990 original size:26 final size:26
Alignment explanation
Indices: 134941--134990 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
134931 TGGTTTCCTT
*
134941 AATTTTAGTTTCTTATTCTTCAAGTA
1 AATTTTAGTTTCTTATTCTACAAGTA
*
134967 AATTTTGGTTTCTTAGTT-TACAAG
1 AATTTTAGTTTCTTA-TTCTACAAG
134991 AATAGACCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 19 0.90
27 2 0.10
ACGTcount: A:0.26, C:0.10, G:0.12, T:0.52
Consensus pattern (26 bp):
AATTTTAGTTTCTTATTCTACAAGTA
Found at i:135151 original size:29 final size:29
Alignment explanation
Indices: 135088--135152 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
135078 CTCTCAATCT
* *
135088 AAGAG-TCTAAGGTTAGGAGCTCCATTTG
1 AAGAGTTCTAAGGTTAGGAGCTCCACTTC
*
135116 AATAGTTCTAAGGTTAGGAGCTCC-CTTC
1 AAGAGTTCTAAGGTTAGGAGCTCCACTTC
135144 AACGAGTTC
1 AA-GAGTTC
135153 CATACGTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
28 8 0.26
29 23 0.74
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (29 bp):
AAGAGTTCTAAGGTTAGGAGCTCCACTTC
Found at i:148735 original size:18 final size:18
Alignment explanation
Indices: 148698--148734 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
148688 ATAATATAAC
148698 TTCTATTCTTCTTTTCTT
1 TTCTATTCTTCTTTTCTT
*
148716 TTCTTTTCTT-TTTTCTT
1 TTCTATTCTTCTTTTCTT
148733 TT
1 TT
148735 TATAAAACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (18 bp):
TTCTATTCTTCTTTTCTT
Found at i:159056 original size:46 final size:46
Alignment explanation
Indices: 158989--159078 Score: 144
Period size: 46 Copynumber: 2.0 Consensus size: 46
158979 TTGCAAGTAT
* *
158989 AGTTTTAGTTTTATTTATTTTCTTTATTATATCAGGTATTTATTAG
1 AGTTTTAGTTTTACTTATTTTCTCTATTATATCAGGTATTTATTAG
* *
159035 AGTTTTAGTTTTACTTATTTTCTCTATTATATTAGGTTTTTATT
1 AGTTTTAGTTTTACTTATTTTCTCTATTATATCAGGTATTTATT
159079 TCCTCATAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.22, C:0.06, G:0.10, T:0.62
Consensus pattern (46 bp):
AGTTTTAGTTTTACTTATTTTCTCTATTATATCAGGTATTTATTAG
Found at i:164466 original size:15 final size:14
Alignment explanation
Indices: 164437--164470 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
164427 TTGTGTTGGG
*
164437 ATTATGTGTTTATT
1 ATTATGTGATTATT
164451 ATTATGATGATTATT
1 ATTATG-TGATTATT
164466 ATTAT
1 ATTAT
164471 TATTATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.59
Consensus pattern (14 bp):
ATTATGTGATTATT
Found at i:167382 original size:7 final size:7
Alignment explanation
Indices: 167370--167394 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
167360 TTAAAGAAAC
167370 TTGTATT
1 TTGTATT
167377 TTGTATT
1 TTGTATT
167384 TTGTATT
1 TTGTATT
167391 TTGT
1 TTGT
167395 TACTTAGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.16, T:0.72
Consensus pattern (7 bp):
TTGTATT
Found at i:171717 original size:62 final size:60
Alignment explanation
Indices: 171610--171759 Score: 185
Period size: 62 Copynumber: 2.5 Consensus size: 60
171600 GCATTTGGTA
* * * **
171610 ACTCATGATGACACATAGTCATCAGACCTTTAAACTGTAATAGGATTCACTTCTCATTTAAT
1 ACTCACGATGACACATAGTCATCGGACCTATAAACCATAATAGGATTCA-TT-TCATTTAAT
*
171672 ACTCACGATGACACATAGTCATCGGACCTCATAATCCATAA-AGGATTCATTTCATTTAAT
1 ACTCACGATGACACATAGTCATCGGACCT-ATAAACCATAATAGGATTCATTTCATTTAAT
* * *
171732 ACTTACAATGACATATAGTCATCGGACC
1 ACTCACGATGACACATAGTCATCGGACC
171760 ATTTTCATTT
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
60 34 0.44
61 2 0.03
62 35 0.45
63 7 0.09
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.31
Consensus pattern (60 bp):
ACTCACGATGACACATAGTCATCGGACCTATAAACCATAATAGGATTCATTTCATTTAAT
Found at i:171879 original size:23 final size:23
Alignment explanation
Indices: 171842--171929 Score: 137
Period size: 23 Copynumber: 3.9 Consensus size: 23
171832 ATTTAGTGAT
171842 GGGC-AAT-AGAGAGCACACACAA
1 GGGCTAATCAGAGAGCACACA-AA
*
171864 -TGCTAATCAGAGAGCACACAAA
1 GGGCTAATCAGAGAGCACACAAA
171886 GGGCTAATCAGAGAGCACACAAA
1 GGGCTAATCAGAGAGCACACAAA
171909 GGGCTAATCAGAGAGCACACA
1 GGGCTAATCAGAGAGCACACA
171930 CGTGCTAACA
Statistics
Matches: 61, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
21 2 0.03
22 5 0.08
23 54 0.89
ACGTcount: A:0.43, C:0.23, G:0.25, T:0.09
Consensus pattern (23 bp):
GGGCTAATCAGAGAGCACACAAA
Found at i:171949 original size:24 final size:23
Alignment explanation
Indices: 171849--171971 Score: 92
Period size: 23 Copynumber: 5.3 Consensus size: 23
171839 GATGGGCAAT
* *
171849 AGAGAGCAC-ACACAATGCTAATC
1 AGAGAGCACGACAC-GTGCTAAAC
* * *
171872 AGAGAGCAC-ACAAAGGGCTAATC
1 AGAGAGCACGAC-ACGTGCTAAAC
* * *
171895 AGAGAGCAC-ACAAAGGGCTAATC
1 AGAGAGCACGAC-ACGTGCTAAAC
171918 AGAGAGCAC-ACACGTGCTAACAAC
1 AGAGAGCACGACACGTGCT-A-AAC
*
171942 AGAGAGCACGAGACGTGCTAAAC
1 AGAGAGCACGACACGTGCTAAAC
171965 AGAGAGC
1 AGAGAGC
171972 GCGCTAGTGT
Statistics
Matches: 89, Mismatches: 7, Indels: 8
0.86 0.07 0.08
Matches are distributed among these distances:
22 5 0.06
23 63 0.71
24 13 0.15
25 8 0.09
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (23 bp):
AGAGAGCACGACACGTGCTAAAC
Found at i:171970 original size:25 final size:24
Alignment explanation
Indices: 171917--171971 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
171907 AAGGGCTAAT
171917 CAGAGAGCACACACGTGCTAACAA
1 CAGAGAGCACACACGTGCTAACAA
*
171941 CAGAGAGCACGAGACGTGCT-A-AA
1 CAGAGAGCAC-ACACGTGCTAACAA
171964 CAGAGAGC
1 CAGAGAGC
171972 GCGCTAGTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 10 0.34
24 11 0.38
25 8 0.28
ACGTcount: A:0.40, C:0.25, G:0.27, T:0.07
Consensus pattern (24 bp):
CAGAGAGCACACACGTGCTAACAA
Found at i:179084 original size:23 final size:25
Alignment explanation
Indices: 179032--179090 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
179022 AAGTGCTGGG
179032 CAACAGAGAGCACACACAGTGCTAA
1 CAACAGAGAGCACACACAGTGCTAA
*
179057 CAACAGAGAGCACGAGAC-GTGCT-A
1 CAACAGAGAGCAC-ACACAGTGCTAA
179081 -AACAGAGAGC
1 CAACAGAGAGC
179091 GCGCTAGTGT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 10 0.31
24 1 0.03
25 18 0.56
26 3 0.09
ACGTcount: A:0.42, C:0.25, G:0.25, T:0.07
Consensus pattern (25 bp):
CAACAGAGAGCACACACAGTGCTAA
Found at i:183779 original size:116 final size:116
Alignment explanation
Indices: 183575--183803 Score: 458
Period size: 116 Copynumber: 2.0 Consensus size: 116
183565 TAGAAATACA
183575 TTGTACATAGATTTAACATTTCATACATCTCACATAGTATGGGTATATCATAATGAACTAACATA
1 TTGTACATAGATTTAACATTTCATACATCTCACATAGTATGGGTATATCATAATGAACTAACATA
183640 CAAACTTATGCAACATTTAACTAAAAAATCAAAGCAAAAGATTTATTCTAC
66 CAAACTTATGCAACATTTAACTAAAAAATCAAAGCAAAAGATTTATTCTAC
183691 TTGTACATAGATTTAACATTTCATACATCTCACATAGTATGGGTATATCATAATGAACTAACATA
1 TTGTACATAGATTTAACATTTCATACATCTCACATAGTATGGGTATATCATAATGAACTAACATA
183756 CAAACTTATGCAACATTTAACTAAAAAATCAAAGCAAAAGATTTATTC
66 CAAACTTATGCAACATTTAACTAAAAAATCAAAGCAAAAGATTTATTC
183804 ATCCATACAA
Statistics
Matches: 113, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
116 113 1.00
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (116 bp):
TTGTACATAGATTTAACATTTCATACATCTCACATAGTATGGGTATATCATAATGAACTAACATA
CAAACTTATGCAACATTTAACTAAAAAATCAAAGCAAAAGATTTATTCTAC
Found at i:184143 original size:35 final size:35
Alignment explanation
Indices: 184077--184180 Score: 145
Period size: 36 Copynumber: 2.9 Consensus size: 35
184067 TGATCGTTAT
*
184077 TCGTTTTACTCCTTGTTGACCCCAAAGGTCATGATGC
1 TCGTTTTACTCC-TATTGA-CCCAAAGGTCATGATGC
*
184114 TCGTTTTACTCCTATTGACCCAAAGGTCATTATGC
1 TCGTTTTACTCCTATTGACCCAAAGGTCATGATGC
* *
184149 TCATTTTTCTCCCTATTGACCCAAAGGTCATG
1 TCGTTTTACT-CCTATTGACCCAAAGGTCATG
184181 CCTATTACCA
Statistics
Matches: 61, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
35 24 0.39
36 25 0.41
37 12 0.20
ACGTcount: A:0.21, C:0.27, G:0.15, T:0.37
Consensus pattern (35 bp):
TCGTTTTACTCCTATTGACCCAAAGGTCATGATGC
Found at i:193442 original size:17 final size:15
Alignment explanation
Indices: 193400--193455 Score: 55
Period size: 16 Copynumber: 3.8 Consensus size: 15
193390 TTTTATAGCT
193400 TTAAATTTATTT-T-
1 TTAAATTTATTTATC
*
193413 TT-AATTAATTTATAC
1 TTAAATTTATTTAT-C
*
193428 TTAAATTCTATTTATT
1 TTAAATT-TATTTATC
193444 TTAAATTTATTT
1 TTAAATTTATTT
193456 CAGAGTTGGT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
12 8 0.23
13 3 0.09
15 7 0.20
16 11 0.31
17 6 0.17
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (15 bp):
TTAAATTTATTTATC
Found at i:196312 original size:9 final size:9
Alignment explanation
Indices: 196284--196313 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
196274 GTTGAATTAG
196284 TTTTTATTT
1 TTTTTATTT
*
196293 TGTTTATTT
1 TTTTTATTT
196302 TTTTTATTT
1 TTTTTATTT
196311 TTT
1 TTT
196314 AAATAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.10, C:0.00, G:0.03, T:0.87
Consensus pattern (9 bp):
TTTTTATTT
Found at i:199016 original size:21 final size:21
Alignment explanation
Indices: 198990--199029 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
198980 TTACTACTAT
198990 TTACTACTTTCCATAATATAA
1 TTACTACTTTCCATAATATAA
* *
199011 TTACTATTTTTCATAATAT
1 TTACTACTTTCCATAATAT
199030 TTTTTTTGGT
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:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (21 bp):
TTACTACTTTCCATAATATAA
Found at i:199676 original size:22 final size:23
Alignment explanation
Indices: 199650--199701 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
199640 AAAAATACTC
*
199650 TTATAATTTT-ATTTTTTTAATA
1 TTATAATTTTAATTTTTTAAATA
*
199672 TTATAATTTTAATTTTTTAAATT
1 TTATAATTTTAATTTTTTAAATA
199695 TTATAAT
1 TTATAAT
199702 AAGTACTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 10 0.37
23 17 0.63
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
TTATAATTTTAATTTTTTAAATA
Found at i:199914 original size:15 final size:15
Alignment explanation
Indices: 199891--199925 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
199881 GCATAAATTA
*
199891 GTTTTTATGCATTGT
1 GTTTCTATGCATTGT
199906 GTTTCTATGCATTGT
1 GTTTCTATGCATTGT
*
199921 ATTTC
1 GTTTC
199926 AATGATGAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.14, C:0.11, G:0.17, T:0.57
Consensus pattern (15 bp):
GTTTCTATGCATTGT
Found at i:200864 original size:44 final size:44
Alignment explanation
Indices: 200814--200898 Score: 125
Period size: 44 Copynumber: 1.9 Consensus size: 44
200804 CAAGGTACAG
* * * *
200814 GGGACACATGGGCTTGTGTTAGACCGTGTGTGTACACTATTGGC
1 GGGACACATGGACGTGTGTCAGACCGTGTGAGTACACTATTGGC
*
200858 GGGACACATGGACGTGTGTCAGACCGTGTGAGTATACTATT
1 GGGACACATGGACGTGTGTCAGACCGTGTGAGTACACTATT
200899 TTATAATTAC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.21, C:0.18, G:0.33, T:0.28
Consensus pattern (44 bp):
GGGACACATGGACGTGTGTCAGACCGTGTGAGTACACTATTGGC
Found at i:203550 original size:36 final size:36
Alignment explanation
Indices: 203510--203585 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
203500 CCACATCACC
*
203510 TCTCTACTACCATAATCCTTTACATTTTATAACATA
1 TCTCTACTACCATAATCCTTTACATTTTAAAACATA
203546 TCTCTACTACCATAATCCTTTACATTTTAAAACATA
1 TCTCTACTACCATAATCCTTTACATTTTAAAACATA
203582 TCTC
1 TCTC
203586 ATTAACTAGA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.41
Consensus pattern (36 bp):
TCTCTACTACCATAATCCTTTACATTTTAAAACATA
Found at i:208860 original size:51 final size:51
Alignment explanation
Indices: 208784--208990 Score: 346
Period size: 51 Copynumber: 4.1 Consensus size: 51
208774 CTATAAACGA
*
208784 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTA-AGGATT
1 AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACA-GATT
* *
208835 AAAGGT-TCGATGACTAAGTGTCATCGTGAGTAAATAAATCCTTTACGGATT
1 AAAGGTCT-GATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACAGATT
*
208886 AAAGGTCTGATGTCTAAGTGTCATCGTGAGTAAATGAATCCTTTACAGATT
1 AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACAGATT
208937 AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACAGATT
1 AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACAGATT
208988 AAA
1 AAA
208991 TGCATAATTA
Statistics
Matches: 146, Mismatches: 7, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
51 145 0.99
52 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.31
Consensus pattern (51 bp):
AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACAGATT
Found at i:215873 original size:21 final size:21
Alignment explanation
Indices: 215828--215874 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
215818 TCCATGACTT
**
215828 GTATCGGTAGAAATTACACTT
1 GTATCGGTAGAAATTACACAA
* *
215849 GTATCGGTAGAACTTGCACAA
1 GTATCGGTAGAAATTACACAA
215870 GTATC
1 GTATC
215875 AATAAAAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (21 bp):
GTATCGGTAGAAATTACACAA
Found at i:220982 original size:71 final size:70
Alignment explanation
Indices: 220880--221015 Score: 236
Period size: 71 Copynumber: 1.9 Consensus size: 70
220870 TAATTTTTTG
* *
220880 AAATTTAATCCTCTACATTATTAAAACTAATTCAATTGTTGATAAAAACATATAAATTAAAACCA
1 AAATTTAATCCCCTACAATATTAAAACTAATTCAATTGTTGATAAAAACATATAAATTAAAACCA
220945 AAATT
66 AAATT
*
220950 AAATTTAATCCCCATACAATATTAAAACTAATTCAATTGTTGATAAAAACATATAAATTTAAACC
1 AAATTTAATCCCC-TACAATATTAAAACTAATTCAATTGTTGATAAAAACATATAAATTAAAACC
221015 A
65 A
221016 TTGATTCTTT
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
70 12 0.19
71 50 0.81
ACGTcount: A:0.50, C:0.14, G:0.03, T:0.33
Consensus pattern (70 bp):
AAATTTAATCCCCTACAATATTAAAACTAATTCAATTGTTGATAAAAACATATAAATTAAAACCA
AAATT
Found at i:222439 original size:107 final size:107
Alignment explanation
Indices: 222321--222521 Score: 375
Period size: 107 Copynumber: 1.9 Consensus size: 107
222311 CATCTGAAAG
* *
222321 AGTCATATATGTTTATGTTTATAATATAATTTTTATAATTTAAATTTATAAAAAAGTATTTTATT
1 AGTCATATATGTTTATGTTTATAATATAATTTTTATAACTTAAATTTATAAAAAAATATTTTATT
*
222386 AAAATTAAATCATGTACGAGTGTTTGGAAGACATGGGTAAAA
66 AAAATTAAATCATATACGAGTGTTTGGAAGACATGGGTAAAA
222428 AGTCATATATGTTTATGTTTATAATATAATTTTTATAACTTAAATTTATAAAAAAATATTTTATT
1 AGTCATATATGTTTATGTTTATAATATAATTTTTATAACTTAAATTTATAAAAAAATATTTTATT
222493 AAAATTAAATCATATACGAGTGTTTGGAA
66 AAAATTAAATCATATACGAGTGTTTGGAA
222522 ACCATGAGGT
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
107 91 1.00
ACGTcount: A:0.42, C:0.04, G:0.11, T:0.43
Consensus pattern (107 bp):
AGTCATATATGTTTATGTTTATAATATAATTTTTATAACTTAAATTTATAAAAAAATATTTTATT
AAAATTAAATCATATACGAGTGTTTGGAAGACATGGGTAAAA
Found at i:228946 original size:19 final size:19
Alignment explanation
Indices: 228905--228945 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
228895 GTGAGCGATA
*
228905 TTTTAAAATTTAATTAATC
1 TTTTAAAATTTAATAAATC
*
228924 TTTTAAAATTTAA-AAATA
1 TTTTAAAATTTAATAAATC
228942 TTTT
1 TTTT
228946 TTATACTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTTAAAATTTAATAAATC
Found at i:228977 original size:22 final size:22
Alignment explanation
Indices: 228932--228978 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
228922 TCTTTTAAAA
*
228932 TTTAAAAATATTTTTTATACTT
1 TTTAAAAATATTTTTTATAATT
*
228954 TTTAAATATATTTTTT-TGAATT
1 TTTAAAAATATTTTTTAT-AATT
228976 TTT
1 TTT
228979 TAATTTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (22 bp):
TTTAAAAATATTTTTTATAATT
Found at i:229099 original size:16 final size:16
Alignment explanation
Indices: 229080--229110 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
229070 TACAAATTTT
229080 AAAATTAAAAAAATGA
1 AAAATTAAAAAAATGA
*
229096 AAAATTAAATAAATG
1 AAAATTAAAAAAATG
229111 GATAAAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (16 bp):
AAAATTAAAAAAATGA
Found at i:232360 original size:15 final size:16
Alignment explanation
Indices: 232328--232370 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
232318 TTAAGTACCA
**
232328 AAAAAATAAGTGTTTG
1 AAAAAATAAGTGACTG
232344 AAAAAATAAGT-ACTG
1 AAAAAATAAGTGACTG
*
232359 AAAAATTAAGTG
1 AAAAAATAAGTG
232371 TAGAATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.56, C:0.02, G:0.16, T:0.26
Consensus pattern (16 bp):
AAAAAATAAGTGACTG
Found at i:232873 original size:30 final size:31
Alignment explanation
Indices: 232827--232897 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
232817 AATAGTTTAT
* * *
232827 ATTTTTAT-AATTTTAAAGAATTAAATTA-A
1 ATTTTTATCATTTTTAAAGAATCAAAATATA
*
232856 ATTTTTATCATTTTTAAAGTATCAAAATATA
1 ATTTTTATCATTTTTAAAGAATCAAAATATA
232887 A-TTTTATCATT
1 ATTTTTATCATT
232898 ATTATTTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 8 0.22
30 26 0.72
31 2 0.06
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.51
Consensus pattern (31 bp):
ATTTTTATCATTTTTAAAGAATCAAAATATA
Found at i:234492 original size:22 final size:23
Alignment explanation
Indices: 234447--234500 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
234437 AATATCTATT
* *
234447 ATTATTTAATAAATTATACCTAAA
1 ATTATTT-ATAAATTACACATAAA
234471 ATTATTTAT-AATTACACATAAA
1 ATTATTTATAAATTACACATAAA
*
234493 ATAATTTA
1 ATTATTTA
234501 CTTTTGCTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 18 0.67
23 2 0.07
24 7 0.26
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (23 bp):
ATTATTTATAAATTACACATAAA
Found at i:238908 original size:49 final size:49
Alignment explanation
Indices: 238836--238934 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
238826 GTAGAAAACC
238836 TAATTTCACAATTGAATGTGCATTTCTATAAAGAAAATTACATAGCATA
1 TAATTTCACAATTGAATGTGCATTTCTATAAAGAAAATTACATAGCATA
238885 TAATTTCACAATTGAATGTGCATTTCTATAAAGAAAATTACATAGCATA
1 TAATTTCACAATTGAATGTGCATTTCTATAAAGAAAATTACATAGCATA
238934 T
1 T
238935 TGTTATTTTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.35
Consensus pattern (49 bp):
TAATTTCACAATTGAATGTGCATTTCTATAAAGAAAATTACATAGCATA
Found at i:239747 original size:6 final size:6
Alignment explanation
Indices: 239738--239799 Score: 124
Period size: 6 Copynumber: 10.3 Consensus size: 6
239728 GTGATGCTGA
239738 TGGTGT TGGTGT TGGTGT TGGTGT TGGTGT TGGTGT TGGTGT TGGTGT
1 TGGTGT TGGTGT TGGTGT TGGTGT TGGTGT TGGTGT TGGTGT TGGTGT
239786 TGGTGT TGGTGT TG
1 TGGTGT TGGTGT TG
239800 AGGGGGAGGG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 56 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (6 bp):
TGGTGT
Found at i:247349 original size:25 final size:24
Alignment explanation
Indices: 247315--247394 Score: 62
Period size: 25 Copynumber: 3.4 Consensus size: 24
247305 TTTCCCTCAT
247315 AAAATATATAAACATAAATTAAAATA
1 AAAAT-TATAAACATAAATT-AAATA
* *
247341 AAAATTATAATC--GAA-TAAA-A
1 AAAATTATAAACATAAATTAAATA
* *
247361 AATA-TATAAACATAAATTGTAATA
1 AAAATTATAAACATAAATT-AAATA
247385 AAAATTATAA
1 AAAATTATAA
247395 CACTCAAATG
Statistics
Matches: 41, Mismatches: 7, Indels: 13
0.67 0.11 0.21
Matches are distributed among these distances:
19 6 0.15
20 4 0.10
21 5 0.12
22 2 0.05
23 4 0.10
24 4 0.10
25 11 0.27
26 5 0.12
ACGTcount: A:0.65, C:0.04, G:0.03, T:0.29
Consensus pattern (24 bp):
AAAATTATAAACATAAATTAAATA
Found at i:247403 original size:26 final size:25
Alignment explanation
Indices: 247358--247407 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
247348 TAATCGAATA
247358 AAAAATATATAAACATAAATTGTAAT
1 AAAAATATATAAACATAAA-TGTAAT
247384 AAAAAT-TAT-AACACTCAAATGTAA
1 AAAAATATATAAACA-T-AAATGTAA
247408 AGTATCTGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
24 4 0.18
25 9 0.41
26 9 0.41
ACGTcount: A:0.60, C:0.08, G:0.04, T:0.28
Consensus pattern (25 bp):
AAAAATATATAAACATAAATGTAAT
Found at i:253758 original size:87 final size:87
Alignment explanation
Indices: 253574--253736 Score: 240
Period size: 87 Copynumber: 1.9 Consensus size: 87
253564 TTAAGTTCGG
* * *
253574 TGAATTCATCAAGTCTGTCTCAATATGACCACCCAAACTCTAGGATATGAATTCATTAAGAGTAA
1 TGAATTCATCAAGTCTGTCTCAATAGGACCACCAAAACTCTAGGATATGAACTCATTAAGAGTAA
253639 TAAACTCAACCTCCCATGTCGA
66 TAAACTCAACCTCCCATGTCGA
* * *
253661 TGAATTCATCAAGTCTGTCTTAATAGGACCACCAAAA-TCTTGGGATATGAACTCATTAAGAGTG
1 TGAATTCATCAAGTCTGTCTCAATAGGACCACCAAAACTC-TAGGATATGAACTCATTAAGAGTA
*
253725 A-GAACTCAACCT
65 ATAAACTCAACCT
253737 TATGCATGTA
Statistics
Matches: 68, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
86 12 0.18
87 56 0.82
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.28
Consensus pattern (87 bp):
TGAATTCATCAAGTCTGTCTCAATAGGACCACCAAAACTCTAGGATATGAACTCATTAAGAGTAA
TAAACTCAACCTCCCATGTCGA
Found at i:262915 original size:53 final size:53
Alignment explanation
Indices: 262847--262957 Score: 213
Period size: 53 Copynumber: 2.1 Consensus size: 53
262837 TAGACTTACT
262847 AATTTCATGAATTCTTTTCTTGCAGTAAAAACAAGATCAACCCGACTATGCGA
1 AATTTCATGAATTCTTTTCTTGCAGTAAAAACAAGATCAACCCGACTATGCGA
*
262900 AATTTCATGAGTTCTTTTCTTGCAGTAAAAACAAGATCAACCCGACTATGCGA
1 AATTTCATGAATTCTTTTCTTGCAGTAAAAACAAGATCAACCCGACTATGCGA
262953 AATTT
1 AATTT
262958 GTGCAGAATT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 57 1.00
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.32
Consensus pattern (53 bp):
AATTTCATGAATTCTTTTCTTGCAGTAAAAACAAGATCAACCCGACTATGCGA
Found at i:264434 original size:3 final size:3
Alignment explanation
Indices: 264426--264502 Score: 127
Period size: 3 Copynumber: 25.7 Consensus size: 3
264416 GGCAACCTAA
* * *
264426 TAT TAT TAT TAT TAT TAT TAT TAT CAT AAT CAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
264474 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
264503 GTTTTAGTTT
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:265486 original size:104 final size:104
Alignment explanation
Indices: 265302--265502 Score: 253
Period size: 104 Copynumber: 1.9 Consensus size: 104
265292 GAAAATAAAA
* * * * **
265302 AATAAATTAGGAGTGTGTTGGGCTGAGTAATCGGGATGGAGTGTTTGGGTTGTCATTCCATTTCG
1 AATAAATTAGGAGTCTATTGGGCTGAGTAACCGGGATGGAGTGCTTAAGTTGTCATTCCATTTCG
*
265367 CATCAAAAGAGCCAATACATTCTTAAGTAAAAAAATGAT
66 CATCAAAAGAGCCAATACATTCTTAAGCAAAAAAATGAT
* * *
265406 AATAAATTGGGAGTCTATTGGGCTTAGTAACCGGGATAGG-GTGCTTAAGTTGTCATTCTATTTC
1 AATAAATTAGGAGTCTATTGGGCTGAGTAACCGGGAT-GGAGTGCTTAAGTTGTCATTCCATTTC
** *
265470 GTGTCAGAAAGA-CCAATATATTCTTAAGCAAAA
65 GCATCA-AAAGAGCCAATACATTCTTAAGCAAAA
265503 GAAAAAAAAA
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
104 75 0.91
105 7 0.09
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.31
Consensus pattern (104 bp):
AATAAATTAGGAGTCTATTGGGCTGAGTAACCGGGATGGAGTGCTTAAGTTGTCATTCCATTTCG
CATCAAAAGAGCCAATACATTCTTAAGCAAAAAAATGAT
Found at i:273609 original size:14 final size:14
Alignment explanation
Indices: 273590--273630 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
273580 AAGTTTTAAT
273590 ATTAAAATTAAAAA
1 ATTAAAATTAAAAA
*
273604 ATTAAAATT-ATAA
1 ATTAAAATTAAAAA
*
273617 ATTAAATTTAAAAA
1 ATTAAAATTAAAAA
273631 GTAATAGTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
ATTAAAATTAAAAA
Found at i:278424 original size:20 final size:17
Alignment explanation
Indices: 278399--278442 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 17
278389 GCTAAGAATA
278399 TGAAATAACATGATGAAAAG
1 TGAAATAAC-TGA--AAAAG
278419 TGAAATAACTGAAAAAG
1 TGAAATAACTGAAAAAG
278436 T-AAATAA
1 TGAAATAA
278443 AATAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.25
17 6 0.25
19 3 0.12
20 9 0.38
ACGTcount: A:0.59, C:0.05, G:0.16, T:0.20
Consensus pattern (17 bp):
TGAAATAACTGAAAAAG
Found at i:287878 original size:22 final size:23
Alignment explanation
Indices: 287853--287895 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
287843 CAACGTTAAG
287853 TTCAAT-A-CTCACTACAAGAAAA
1 TTCAATAATCTCA-TACAAGAAAA
*
287875 TTCATTAATCTCATACAAGAA
1 TTCAATAATCTCATACAAGAA
287896 GAACAAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 5 0.28
23 9 0.50
24 4 0.22
ACGTcount: A:0.47, C:0.21, G:0.05, T:0.28
Consensus pattern (23 bp):
TTCAATAATCTCATACAAGAAAA
Found at i:297275 original size:17 final size:17
Alignment explanation
Indices: 297253--297325 Score: 85
Period size: 17 Copynumber: 4.3 Consensus size: 17
297243 CCAACAGGAT
297253 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
**
297270 TTAAATTTATTTTAAGT
1 TTAAATTTATTTTAAAA
*
297287 TTAAATTTA-CTTAAAA
1 TTAAATTTATTTTAAAA
* *
297303 TTTAAATTTATTATAAAT
1 -TTAAATTTATTTTAAAA
297321 TTAAA
1 TTAAA
297326 GTTAAAATCT
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
16 4 0.09
17 38 0.83
18 4 0.09
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:297289 original size:6 final size:6
Alignment explanation
Indices: 297251--297331 Score: 55
Period size: 6 Copynumber: 14.2 Consensus size: 6
297241 GCCCAACAGG
* * * *
297251 ATTTAA ATTT-A TTTTAA AATTAA ATTT-A TTTTAA GTTTAA ATTT-A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* * *
297296 CTTAAA ATTTAA ATTT-- ATTATAA ATTTAA AGTTAA A
1 ATTTAA ATTTAA ATTTAA ATT-TAA ATTTAA ATTTAA A
297332 ATCTATTTAA
Statistics
Matches: 57, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
4 3 0.05
5 12 0.21
6 39 0.68
7 3 0.05
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (6 bp):
ATTTAA
Found at i:297295 original size:34 final size:34
Alignment explanation
Indices: 297251--297325 Score: 107
Period size: 34 Copynumber: 2.2 Consensus size: 34
297241 GCCCAACAGG
* *
297251 ATTTAAATTTATTTTAAAA-TTAAATTTATTTTAA
1 ATTTAAATTTA-CTTAAAATTTAAATTTATTATAA
*
297285 GTTTAAATTTACTTAAAATTTAAATTTATTATAA
1 ATTTAAATTTACTTAAAATTTAAATTTATTATAA
297319 ATTTAAA
1 ATTTAAA
297326 GTTAAAATCT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
33 6 0.17
34 30 0.83
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (34 bp):
ATTTAAATTTACTTAAAATTTAAATTTATTATAA
Found at i:297324 original size:24 final size:23
Alignment explanation
Indices: 297297--297343 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
297287 TTAAATTTAC
* *
297297 TTAAAATTTAAATTTATTATAAAT
1 TTAAAATTAAAATCTATT-TAAAT
*
297321 TTAAAGTTAAAATCTATTTAAAT
1 TTAAAATTAAAATCTATTTAAAT
297344 AAAGTCCAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
TTAAAATTAAAATCTATTTAAAT
Found at i:298064 original size:3 final size:3
Alignment explanation
Indices: 298015--298047 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
298005 TAAGTATCAT
298015 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
298048 ATGTAGCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:299184 original size:29 final size:29
Alignment explanation
Indices: 299137--299427 Score: 365
Period size: 30 Copynumber: 9.9 Consensus size: 29
299127 GAGGTCCTTA
299137 AACTATCCAAAAATTCCATTTTTACCCTCG
1 AACT-TCCAAAAATTCCATTTTTACCCTCG
* **
299167 AACTTCCAAAAATTCCATTTTTGACCTTAA
1 AACTTCCAAAAATTCCATTTTT-ACCCTCG
* *
299197 AACTTCTAAAAATTCCATCTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
* *
299226 AACTTCCAAAAATTCCATTTTTAACCTTG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
299255 AAACTTCCAAAAATTCCATTTTTACCC-CG
1 -AACTTCCAAAAATTCCATTTTTACCCTCG
* *
299284 AAATACCAAAAATTCCATTTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
*
299313 AACTTCCAAAAATTCCATTTTTGACCC-CAA
1 AACTTCCAAAAATTCCATTTTT-ACCCTC-G
*
299343 AACTTCAAAAAATTCCATTTTTACCCCTCG
1 AACTTCCAAAAATTCCATTTTTA-CCCTCG
* *
299373 AACTTCCAAAAATTCCATTTTGA-CCTTG
1 AACTTCCAAAAATTCCATTTTTACCCTCG
299401 AAACTTCCAAAAATTACCA-TTTTACCC
1 -AACTTCCAAAAATT-CCATTTTTACCC
299428 CCGGATGTCC
Statistics
Matches: 226, Mismatches: 25, Indels: 20
0.83 0.09 0.07
Matches are distributed among these distances:
28 28 0.12
29 90 0.40
30 107 0.47
31 1 0.00
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.33
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTTACCCTCG
Found at i:299224 original size:59 final size:58
Alignment explanation
Indices: 299132--299423 Score: 358
Period size: 59 Copynumber: 5.0 Consensus size: 58
299122 CCTTAGAGGT
299132 CCTT-AAACTATCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGA
1 CCTTCAAACT-TCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTT-A
* * *
299191 CCTTAAAACTTCTAAAAATTCCATCTTTACCCTCGAACTTCCAAAAATTCCATTTTTAA
1 CCTTCAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTT-A
* * *
299250 CCTTGAAACTTCCAAAAATTCCATTTTTACCC-CGAAATACCAAAAATTCCATTTTTA
1 CCTTCAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTA
* * * *
299307 CCCTCGAACTTCCAAAAATTCCATTTTTGACCC-CAAAACTTCAAAAAATTCCATTTTTA
1 CCTTCAAACTTCCAAAAATTCCATTTTT-ACCCTC-GAACTTCCAAAAATTCCATTTTTA
* * * *
299366 CCCCTCGAACTTCCAAAAATTCCATTTTGA-CCTTGAAACTTCCAAAAATTACCATTTT
1 -CCTTCAAACTTCCAAAAATTCCATTTTTACCCTCG-AACTTCCAAAAATT-CCATTTT
299424 ACCCCCGGAT
Statistics
Matches: 207, Mismatches: 19, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
57 26 0.13
58 29 0.14
59 113 0.55
60 39 0.19
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (58 bp):
CCTTCAAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTA
Found at i:299424 original size:59 final size:58
Alignment explanation
Indices: 299137--299464 Score: 353
Period size: 59 Copynumber: 5.6 Consensus size: 58
299127 GAGGTCCTTA
* * **
299137 AACTATCCAAAAATTCCATTTTTACCCTCG-AACTTCCAAAAATTCCATTTTTGACCTTAA
1 AACT-TCCAAAAATTCCATTTTGA-CCTCGAAACTTCCAAAAATTCCATTTTT-ACCCTCG
* * *
299197 AACTTCTAAAAATTCCATCTTT-ACCCTCG-AACTTCCAAAAATTCCATTTTTAACCTTG
1 AACTTCCAAAAATTCCAT-TTTGA-CCTCGAAACTTCCAAAAATTCCATTTTTACCCTCG
* * *
299255 AAACTTCCAAAAATTCCATTTTTACCCCGAAA-TACCAAAAATTCCATTTTTACCCTCG
1 -AACTTCCAAAAATTCCATTTTGACCTCGAAACTTCCAAAAATTCCATTTTTACCCTCG
* * *
299313 AACTTCCAAAAATTCCATTTTTGACCCCAAAACTTCAAAAAATTCCATTTTTACCCCTCG
1 AACTTCCAAAAATTCCA-TTTTGACCTCGAAACTTCCAAAAATTCCATTTTTA-CCCTCG
* *
299373 AACTTCCAAAAATTCCATTTTGACCTTGAAACTTCCAAAAATTACCA-TTTTACCCCCG
1 AACTTCCAAAAATTCCATTTTGACCTCGAAACTTCCAAAAATT-CCATTTTTACCCTCG
* * *
299431 GA-TGTCCAAAAACTCTATTTTCGACCTCGAAACT
1 AACT-TCCAAAAATTCCATTTT-GACCTCGAAACT
299465 CTCAAAATTA
Statistics
Matches: 235, Mismatches: 23, Indels: 21
0.84 0.08 0.08
Matches are distributed among these distances:
57 18 0.08
58 66 0.28
59 118 0.50
60 33 0.14
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.33
Consensus pattern (58 bp):
AACTTCCAAAAATTCCATTTTGACCTCGAAACTTCCAAAAATTCCATTTTTACCCTCG
Found at i:299548 original size:59 final size:58
Alignment explanation
Indices: 299137--299548 Score: 315
Period size: 59 Copynumber: 7.0 Consensus size: 58
299127 GAGGTCCTTA
* ****
299137 AACTATCCAAAAATTCCATTTTT-ACCCTCGAACTTCCAAAAATT-CCATTTTTGACCTTAA
1 AACT-TCCAAAAATTCCATTTTTGACCC-CGAAATTCCAAAAATTACCA-TTTT-ACCCCCG
* * * * **
299197 AACTTCTAAAAATTCCATCTTT-ACCCTCGAACTTCCAAAAATT-CCATTTTTAACCTTG
1 AACTTCCAAAAATTCCATTTTTGACCC-CGAAATTCCAAAAATTACCA-TTTTACCCCCG
* *
299255 AAACTTCCAAAAATTCCATTTTT-ACCCCGAAATACCAAAAATT-CCATTTTTACCCTCG
1 -AACTTCCAAAAATTCCATTTTTGACCCCGAAATTCCAAAAATTACCA-TTTTACCCCCG
* *
299313 AACTTCCAAAAATTCCATTTTTGACCCCAAAACTTCAAAAAATT-CCATTTTTACCCCTCG
1 AACTTCCAAAAATTCCATTTTTGACCCCGAAA-TTCCAAAAATTACCA-TTTTACCCC-CG
**
299373 AACTTCCAAAAATTCCA-TTTTGACCTTGAAACTTCCAAAAATTACCATTTTACCCCCG
1 AACTTCCAAAAATTCCATTTTTGACCCCGAAA-TTCCAAAAATTACCATTTTACCCCCG
* * * * * * ** *
299431 GA-TGTCCAAAAACTCTATTTTCGACCTCGAAACTCTC-AAAATTACCCGTTTACTCCCG
1 AACT-TCCAAAAATTCCATTTTTGACCCCGAAATTC-CAAAAATTACCATTTTACCCCCG
* * * * * *
299489 AA-TGTCTAAAAATTCCGTTTTTAACCCCAAAATTTCCCAAAATTACCATTTCACCCCCG
1 AACT-TCCAAAAATTCCATTTTTGACCCCGAAA-TTCCAAAAATTACCATTTTACCCCCG
299548 A
1 A
299549 GAATCCAAAA
Statistics
Matches: 299, Mismatches: 43, Indels: 21
0.82 0.12 0.06
Matches are distributed among these distances:
57 23 0.08
58 96 0.32
59 154 0.52
60 26 0.09
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.32
Consensus pattern (58 bp):
AACTTCCAAAAATTCCATTTTTGACCCCGAAATTCCAAAAATTACCATTTTACCCCCG
Found at i:300800 original size:23 final size:21
Alignment explanation
Indices: 300740--300806 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 21
300730 ATTATTAATT
300740 AATAAAATT-ATAAATTTATA
1 AATAAAATTAATAAATTTATA
*
300760 AA-ATAATTAAATATAATTTGATA
1 AATAAAATT-AATA-AATTT-ATA
*
300783 AATTAAAATTAATAAATTAATA
1 AA-TAAAATTAATAAATTTATA
300805 AA
1 AA
300807 AATCCAAGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
19 5 0.13
20 2 0.05
21 3 0.08
22 10 0.26
23 9 0.24
24 4 0.11
25 5 0.13
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (21 bp):
AATAAAATTAATAAATTTATA
Found at i:302830 original size:34 final size:34
Alignment explanation
Indices: 302791--302859 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 34
302781 ATTTAATATC
302791 ATTTTTAA-GAAAAAAAATAGCATGTTATTCTCAA
1 ATTTTTAAGGAAAAAAAATAGCATGTTATT-TCAA
* * * *
302825 ATTTTTAAGGAGAAATAATATCTTGTTATTTCAA
1 ATTTTTAAGGAAAAAAAATAGCATGTTATTTCAA
302859 A
1 A
302860 ACTTTTTCCT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 13 0.43
35 17 0.57
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.39
Consensus pattern (34 bp):
ATTTTTAAGGAAAAAAAATAGCATGTTATTTCAA
Found at i:303073 original size:15 final size:16
Alignment explanation
Indices: 303053--303090 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
303043 GCATTTCTAG
303053 AATAATTG-TGTTTAA
1 AATAATTGTTGTTTAA
* *
303068 AATAATCGTTGTTTGA
1 AATAATTGTTGTTTAA
303084 AATAATT
1 AATAATT
303091 TTTATTTAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.39, C:0.03, G:0.13, T:0.45
Consensus pattern (16 bp):
AATAATTGTTGTTTAA
Found at i:303559 original size:11 final size:11
Alignment explanation
Indices: 303527--303560 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
303517 CTTATGTTAC
303527 AATATTATTAT
1 AATATTATTAT
*
303538 AATATCATTAT
1 AATATTATTAT
*
303549 AATATTTTTAT
1 AATATTATTAT
303560 A
1 A
303561 TTAACCGCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (11 bp):
AATATTATTAT
Found at i:308252 original size:2 final size:2
Alignment explanation
Indices: 308245--308307 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
308235 ATAAAGTCTC
308245 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
308287 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
308308 GCTAACTAAG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:309482 original size:17 final size:17
Alignment explanation
Indices: 309441--309499 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
309431 TAACAAAATA
* *
309441 ATGAAAATAATAGTAAC
1 ATGATAATAATAGCAAC
*
309458 A-AATAATAATA-CAAC
1 ATGATAATAATAGCAAC
*
309473 TATGATAATAATAGTAAC
1 -ATGATAATAATAGCAAC
309491 ATGATAATA
1 ATGATAATA
309500 GCAATAACAC
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
15 3 0.09
16 9 0.26
17 19 0.56
18 3 0.09
ACGTcount: A:0.58, C:0.07, G:0.08, T:0.27
Consensus pattern (17 bp):
ATGATAATAATAGCAAC
Found at i:309680 original size:21 final size:20
Alignment explanation
Indices: 309656--309712 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
309646 TAAAAGATAA
*
309656 AAAAAAAAAAGGACTAAATTG
1 AAAAAAAAAAGGA-AAAATTG
* *
309677 AAAAATAAAAGTAAAAATTG
1 AAAAAAAAAAGGAAAAATTG
*
309697 AAAAAAAAAAAGAAAA
1 AAAAAAAAAAGGAAAA
309713 TAAAGGGCTA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 19 0.63
21 11 0.37
ACGTcount: A:0.75, C:0.02, G:0.11, T:0.12
Consensus pattern (20 bp):
AAAAAAAAAAGGAAAAATTG
Found at i:309712 original size:20 final size:20
Alignment explanation
Indices: 309655--309712 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 20
309645 ATAAAAGATA
*
309655 AAAAAAAAAAAGGACTAAATTG
1 AAAAAAAAAAA-GA-AAAATTG
*
309677 -AAAAATAAAAGTAAAAATTG
1 AAAAAAAAAAAG-AAAAATTG
309697 AAAAAAAAAAAGAAAA
1 AAAAAAAAAAAGAAAA
309713 TAAAGGGCTA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 11 0.35
21 20 0.65
ACGTcount: A:0.76, C:0.02, G:0.10, T:0.12
Consensus pattern (20 bp):
AAAAAAAAAAAGAAAAATTG
Done.