Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold80
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: 1499392
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.28
Warning! 217494 characters in sequence are not A, C, G, or T
File 4 of 8
Found at i:478629 original size:15 final size:15
Alignment explanation
Indices: 478609--478639 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
478599 ATTTCGTTTG
*
478609 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
478624 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
478639 G
1 G
478640 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:480472 original size:21 final size:21
Alignment explanation
Indices: 480443--480487 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
480433 AAGTTTTCAT
*
480443 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
480463 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
480485 TTT
1 TTT
480488 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:482713 original size:13 final size:13
Alignment explanation
Indices: 482695--482720 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
482685 CAATTTTTTG
482695 TGTATCGATACAT
1 TGTATCGATACAT
482708 TGTATCGATACAT
1 TGTATCGATACAT
482721 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:483622 original size:113 final size:114
Alignment explanation
Indices: 483418--483624 Score: 281
Period size: 113 Copynumber: 1.8 Consensus size: 114
483408 TGTGACATCT
* * * * *
483418 CTTTTCAAAGCTCACATAAACTGGTGGCACCTTTTTAGTCCTCAGAGAGTAGAATGCCTTTTTCT
1 CTTTTCAAAGCCCACATAAACTGGTGGCACCATTTTAGTCCTCAAAGAGCAGAACGCCTTTTTCT
* *
483483 TTTCAAATCCCACACGAGTTGGTGGCACCTTCTTTAAAGAGCAGGACAC
66 TTTCAAAGCCCACACGAATTGGTGGCACCTTCTTTAAAGAGCAGGACAC
** * * **
483532 CTTTTCAAAGCCCACATAAGTTGGTGGCA-CATTTTAGTCCTTAAAGAGCAGGACGTTTTTTTCT
1 CTTTTCAAAGCCCACATAAACTGGTGGCACCATTTTAGTCCTCAAAGAGCAGAACGCCTTTTTCT
*
483596 TTTCAAAGCCCACACGAATTGTTGGCACC
66 TTTCAAAGCCCACACGAATTGGTGGCACC
483625 CTTTTATCCT
Statistics
Matches: 79, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
113 53 0.67
114 26 0.33
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.31
Consensus pattern (114 bp):
CTTTTCAAAGCCCACATAAACTGGTGGCACCATTTTAGTCCTCAAAGAGCAGAACGCCTTTTTCT
TTTCAAAGCCCACACGAATTGGTGGCACCTTCTTTAAAGAGCAGGACAC
Found at i:483635 original size:62 final size:62
Alignment explanation
Indices: 483532--483648 Score: 166
Period size: 62 Copynumber: 1.9 Consensus size: 62
483522 AGCAGGACAC
*
483532 CTTTTCAAAGCCCACATAAGTTGGTGGCACATTTTAGTCCTTAAAGAGCAGGACGTTTTTTT
1 CTTTTCAAAGCCCACAGAAGTTGGTGGCACATTTTAGTCCTTAAAGAGCAGGACGTTTTTTT
* * *
483594 CTTTTCAAAGCCCACACGAA-TTGTTGGCACCCTTTTA-TCCTTAAAGAGTAGGACG
1 CTTTTCAAAGCCCACA-GAAGTTGGTGGCA-CATTTTAGTCCTTAAAGAGCAGGACG
483649 CCACGAGTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
62 41 0.84
63 8 0.16
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.32
Consensus pattern (62 bp):
CTTTTCAAAGCCCACAGAAGTTGGTGGCACATTTTAGTCCTTAAAGAGCAGGACGTTTTTTT
Found at i:483730 original size:104 final size:104
Alignment explanation
Indices: 483550--483745 Score: 270
Period size: 104 Copynumber: 1.9 Consensus size: 104
483540 AGCCCACATA
* * ** *
483550 AGTTGGTGGCACATTTTAGTCCTTAAAGAGCAGGACGTTTTTTTCTTTTCAAAGCCCACACGAAT
1 AGTTGGTGGCACACTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAAC
* *
483615 TGTTGGCACCCTTTTA-TCCTTAAAGAGTAGGACGCCACG
66 TGGTGGCACCC-TTTAGTCCTCAAAGAGTAGGACGCCACG
* * *
483654 AGTTGGTGGCACCCTTTAGTCCTCAAAGAGCATGATGCCTTTTTCTTTTCAAAGCCCACAC-AAG
1 AGTTGGTGGCACACTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAA-
483718 CTGGTGGCACCCTTTAGTCCTCAAAGAG
65 CTGGTGGCACCCTTTAGTCCTCAAAGAG
483746 CAAGACACCT
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
103 6 0.08
104 74 0.93
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.30
Consensus pattern (104 bp):
AGTTGGTGGCACACTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAAC
TGGTGGCACCCTTTAGTCCTCAAAGAGTAGGACGCCACG
Found at i:483732 original size:62 final size:62
Alignment explanation
Indices: 483654--483867 Score: 302
Period size: 62 Copynumber: 3.4 Consensus size: 62
483644 GGACGCCACG
*
483654 AGTTGGTGGCACCCTTTAGTCCTCAAAGAGCATGATGCCTTTTTCTTTTCAAAGCCCACACA
1 AGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAAGATGCCTTTTTCTTTTCAAAGCCCACACA
* **
483716 AGCTGGTGGCACCCTTTAGTCCTCAAAGAGCAAGACACCTTTTTCTTTTCAAAGCCCACACA
1 AGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAAGATGCCTTTTTCTTTTCAAAGCCCACACA
* ** * * **
483778 AGTTGGTGGCACCCTTTAGTCCTCAAAAAATAGGATGCCATTTTTCTTTTCAAAGCCCATATG
1 AGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAAGATGCC-TTTTTCTTTTCAAAGCCCACACA
* *
483841 AGTTGGTGGCACCCTTTTGTCTTCAAA
1 AGTTGGTGGCACCCTTTAGTCCTCAAA
483868 AAAATACTTC
Statistics
Matches: 135, Mismatches: 16, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
62 90 0.67
63 45 0.33
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (62 bp):
AGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAAGATGCCTTTTTCTTTTCAAAGCCCACACA
Found at i:483993 original size:78 final size:78
Alignment explanation
Indices: 483884--484095 Score: 268
Period size: 78 Copynumber: 2.7 Consensus size: 78
483874 CTTCAACCTC
* * * * *
483884 GATTTTGTTCCTAAAACATCAATTTTTCACCATCGGGGATACTCCAACCCGATTATTTTTAAG-G
1 GATTTTATTTCTAAAACAACGATTTTTCACCATCGGGGATACTCCAACCCG-TTATTTTCAAGCG
483948 GAACACTCCAAC-TCT
65 G-ACACTCCAACAT-T
* * *
483963 GATTTT-TTTCTAAAATAACGATTTTCCACCATCGGGGATACTCCAATCCCGTTATTTTCGAGCG
1 GATTTTATTTCTAAAACAACGATTTTTCACCATCGGGGATACTCCAA-CCCGTTATTTTCAAGCG
*
484027 GATACTCCAACATT
65 GACACTCCAACATT
* *
484041 GATTTTATTTTTAAAACACCGATTTTTCACCATCGGGGATACTCCAACCCGTTAT
1 GATTTTATTTCTAAAACAACGATTTTTCACCATCGGGGATACTCCAACCCGTTAT
484096 CTCCGAGGGA
Statistics
Matches: 117, Mismatches: 12, Indels: 9
0.85 0.09 0.07
Matches are distributed among these distances:
78 68 0.58
79 49 0.42
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (78 bp):
GATTTTATTTCTAAAACAACGATTTTTCACCATCGGGGATACTCCAACCCGTTATTTTCAAGCGG
ACACTCCAACATT
Found at i:485146 original size:41 final size:40
Alignment explanation
Indices: 485016--485147 Score: 106
Period size: 41 Copynumber: 3.2 Consensus size: 40
485006 GATTGGTTAA
* * * *
485016 CTTTATCGATTTCACTATGGTCAATCCTTCTAACTTGTTGG
1 CTTTATCAATTTCACTCTGGTCAACCCTTCTAACTTATT-G
* * * * *
485057 CTTTATCGATTTCACCCTAG-CTAACCCCTC-AAATTGATTG
1 CTTTATCAATTTCACTCTGGTC-AACCCTTCTAACTT-ATTG
* *
485097 ACTGTATCAATTTCACTCTGGTCAACCCTTCTAACCTATTAG
1 -CTTTATCAATTTCACTCTGGTCAACCCTTCTAACTTATT-G
485139 CTTTATCAA
1 CTTTATCAA
485148 GTTTTCCTTG
Statistics
Matches: 70, Mismatches: 15, Indels: 12
0.72 0.15 0.12
Matches are distributed among these distances:
40 6 0.09
41 59 0.84
42 5 0.07
ACGTcount: A:0.24, C:0.27, G:0.11, T:0.39
Consensus pattern (40 bp):
CTTTATCAATTTCACTCTGGTCAACCCTTCTAACTTATTG
Found at i:485344 original size:82 final size:82
Alignment explanation
Indices: 485053--485836 Score: 459
Period size: 82 Copynumber: 9.6 Consensus size: 82
485043 TTCTAACTTG
* * * * * *
485053 TTGGCTTTATCGATTTCACCCTAGCTAACCCCTCAAATTGATTGACTGTATCA-ATTT-CACTCT
1 TTGGCTTTATCGATTTCACTCTAGCCAACCCCTCTAATTGGTTGACTTTATCAGTTTTGC-CT-T
* *
485116 GGTCAACCCTTCTAACCTA
64 GGTCAACCCCTCAAACCTA
* * * * * * *
485135 TTAGCTTTATCAAGTTTTC-CT-TGGCC-ATCCCT-TAAATTGATTAATTTTATCAGTTTTGCCT
1 TTGGCTTTATC--GATTTCACTCTAGCCAACCCCTCT-AATTGGTTGACTTTATCAGTTTTGCCT
* * * * * *
485196 TGGTTAGCCCGTTAAACTTG
63 TGGTCAACCCCTCAAACCTA
* * ** * *
485216 TTGGCTTTATTGGTTTTGC-C---CCAACCCCTCTAATTGGTTGAATTTATCAATTTTGCCTTGG
1 TTGGCTTTATCGATTTCACTCTAGCCAACCCCTCTAATTGGTTGACTTTATCAGTTTTGCCTTGG
* * *
485277 TCAACCCTTTAAATCTA
66 TCAACCCCTCAAACCTA
* * * *
485294 TTGGCTTAACTC-ATTTCACTCTGGCCAACCCCT-TAAATTGGTTGACTTTATTAGATTTGTCC-
1 TTGGCTTTA-TCGATTTCACTCTAGCCAACCCCTCT-AATTGGTTGACTTTATCAGTTTTG-CCT
* *
485356 TAGTCAACCCTTCAAACCTA
63 TGGTCAACCCCTCAAACCTA
* * * *
485376 ATGGCTTTATCGGTTTCGC-CTTAGCCAACCCCTCTAATTGGTTGACTTTATCAGTTTCG-CTTG
1 TTGGCTTTATCGATTTCACTC-TAGCCAACCCCTCTAATTGGTTGACTTTATCAGTTTTGCCTTG
*
485439 AGTCAACACCTCAAACCTA
65 -GTCAACCCCTCAAACCTA
* ** * * *
485458 TTGGCTTTATCAATTTTGCCCTAGCCAACCCCTCTAGTTGGTTGACTTTATC-GATTTTGCCCTG
1 TTGGCTTTATCGATTTCACTCTAGCCAACCCCTCTAATTGGTTGACTTTATCAG-TTTTGCCTTG
** * *
485522 ACCAACCCCTCAAACTTG
65 GTCAACCCCTCAAACCTA
* * * * * **
485540 TTGGTTTTATCGGTTTTGC-CT-TAGCCAA-CCTTTTAAATTAGTTGACTTTATTTGTTTTGTCC
1 TTGGCTTTATC-GATTT-CACTCTAGCCAACCCCTCT-AATTGGTTGACTTTATCAGTTTTG-CC
* * *
485602 -TAGTCAACCCGTCAAACCTG
62 TTGGTCAACCCCTCAAACCTA
* *
485622 TTGGCTTTAT-TAGTTTCAC-CTTAGCCAACCCCTCTAATTGGTTGACTTTATTAGTTTTGCCTT
1 TTGGCTTTATCGA-TTTCACTC-TAGCCAACCCCTCTAATTGGTTGACTTTATCAGTTTTGCCTT
* * * *
485685 AGTTAACCCCTTAAACCTG
64 GGTCAACCCCTCAAACCTA
* * * * * * *
485704 TTGGCTTAATTGGTTT-AGCTTTGGGCAACCCCT-TAAATTGGTTGACTTTATCAGTTTTACCTT
1 TTGGCTTTATCGATTTCA-CTCTAGCCAACCCCTCT-AATTGGTTGACTTTATCAGTTTTGCCTT
* ** *
485767 GGTTAACCCCTCAAAGTTG
64 GGTCAACCCCTCAAACCTA
* * * * *
485786 TTGGCTTTATCGGTCTT-ACCCTAGCCAA-CCTTCTAACTAGTTGACTTTATC
1 TTGGCTTTATCGAT-TTCACTCTAGCCAACCCCTCTAATTGGTTGACTTTATC
485837 GATTTCACCC
Statistics
Matches: 547, Mismatches: 114, Indels: 83
0.74 0.15 0.11
Matches are distributed among these distances:
77 2 0.00
78 54 0.10
79 7 0.01
80 3 0.01
81 78 0.14
82 375 0.69
83 23 0.04
84 5 0.01
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.39
Consensus pattern (82 bp):
TTGGCTTTATCGATTTCACTCTAGCCAACCCCTCTAATTGGTTGACTTTATCAGTTTTGCCTTGG
TCAACCCCTCAAACCTA
Found at i:485428 original size:164 final size:161
Alignment explanation
Indices: 485035--485835 Score: 536
Period size: 164 Copynumber: 4.9 Consensus size: 161
485025 TTTCACTATG
* * * * * * *
485035 GTCAATCCTTCTAACTTGTTGGCTTTATCGATTTCA-CCCTAGCTAACCCCTC-AAATTGATTGA
1 GTCAACCCTTCAAACCTGTTGGCTTTATCGGTTT-AGCCTTAGCCAACCCCTCTAAATTGGTTGA
* * * * * *
485098 CTGTATCA-ATTT-CACTCTGGTCAACCCTTCTAACCTATTAGCTTTATCAAGTTTTC-CTTGGC
65 CTTTATCAGTTTTGC-CT-TGGTCAACCC-TCAAACCTATTGGCTTTATC-A--TTTCACCTAGC
* * * * * * *
485160 C-ATCCCT-TAAATTGATTAATTTTATCAGTTTTGCCTTG
124 CAACCCCTCT-AATTGGTTGACTTTATTAGATTTGCC-TA
* * * * *
485198 GTTAGCCCGTT-AAACTTGTTGGCTTTATTGGTTTTGCC----CCAACCCCTCT-AATTGGTTGA
1 GTCAACCC-TTCAAACCTGTTGGCTTTATCGGTTTAGCCTTAGCCAACCCCTCTAAATTGGTTGA
* * * * * *
485257 ATTTATCAATTTTGCCTTGGTCAACCCTTTAAATCTATTGGCTTAACTCATTTCACTCTGGCCAA
65 CTTTATCAGTTTTGCCTTGGTCAACCC-TCAAACCTATTGGCTTTA-TCATTTCAC-CTAGCCAA
485322 CCCCT-TAAATTGGTTGACTTTATTAGATTTGTCCTA
127 CCCCTCT-AATTGGTTGACTTTATTAGATTTG-CCTA
** *
485358 GTCAACCCTTCAAACCTAATGGCTTTATCGGTTTCGCCTTAGCCAACCCCTCT-AATTGGTTGAC
1 GTCAACCCTTCAAACCTGTTGGCTTTATCGGTTTAGCCTTAGCCAACCCCTCTAAATTGGTTGAC
*
485422 TTTATCAGTTTCG-CTTGAGTCAACACCTCAAACCTATTGGCTTTATCAATTTTGC-CCTAGCCA
66 TTTATCAGTTTTGCCTTG-GTCAAC-CCTCAAACCTATTGGCTTTATC-A-TTT-CACCTAGCCA
* *
485485 ACCCCTCTAGTTGGTTGACTTTA-TCGATTTTGCCCT-
126 ACCCCTCTAATTGGTTGACTTTATTAGA-TTTG-CCTA
* * * * * * * *
485521 GACCAACCCCTCAAACTTGTTGGTTTTATCGGTTTTGCCTTAGCCAA-CCTTTTAAATTAGTTGA
1 G-TCAACCCTTCAAACCTGTTGGCTTTATCGGTTTAGCCTTAGCCAACCCCTCTAAATTGGTTGA
** * * *
485585 CTTTATTTGTTTTGTCC-TAGTCAACCCGTCAAACCTGTTGGCTTTATTAGTTTCACCTTAGCCA
65 CTTTATCAGTTTTG-CCTTGGTCAACCC-TCAAACCTATTGGCTTTATCA-TTTCACC-TAGCCA
*
485649 ACCCCTCTAATTGGTTGACTTTATTAGTTTTGCCTTA
126 ACCCCTCTAATTGGTTGACTTTATTAGATTTGCC-TA
* * * * * *
485686 GTTAACCCCTT-AAACCTGTTGGCTTAATTGGTTTAGCTTTGGGCAACCCCT-TAAATTGGTTGA
1 GTCAA-CCCTTCAAACCTGTTGGCTTTATCGGTTTAGCCTTAGCCAACCCCTCTAAATTGGTTGA
* * ** * *
485749 CTTTATCAGTTTTACCTTGGTTAACCCCTCAAAGTTGTTGGCTTTATCGGTCTT-ACCCTAGCCA
65 CTTTATCAGTTTTGCCTTGGTCAA-CCCTCAAACCTATTGGCTTTATC-AT-TTCA-CCTAGCCA
* * *
485813 A-CCTTCTAACTAGTTGACTTTAT
126 ACCCCTCTAATTGGTTGACTTTAT
485836 CGATTTCACC
Statistics
Matches: 512, Mismatches: 87, Indels: 78
0.76 0.13 0.12
Matches are distributed among these distances:
157 4 0.01
158 1 0.00
159 56 0.11
160 62 0.12
161 3 0.01
162 1 0.00
163 72 0.14
164 286 0.56
165 25 0.05
166 2 0.00
ACGTcount: A:0.21, C:0.25, G:0.14, T:0.39
Consensus pattern (161 bp):
GTCAACCCTTCAAACCTGTTGGCTTTATCGGTTTAGCCTTAGCCAACCCCTCTAAATTGGTTGAC
TTTATCAGTTTTGCCTTGGTCAACCCTCAAACCTATTGGCTTTATCATTTCACCTAGCCAACCCC
TCTAATTGGTTGACTTTATTAGATTTGCCTA
Found at i:485775 original size:41 final size:41
Alignment explanation
Indices: 485319--485815 Score: 166
Period size: 41 Copynumber: 12.1 Consensus size: 41
485309 TCACTCTGGC
* *
485319 CAACCCCTTAAA-TTGGTTGACTTTATTAGATTTGT-CC-TAGT
1 CAACCCCTTAAACTT-GTTGGCTTTATCAG-TTT-TACCTTAGT
* ** * ** *
485360 CAA-CCCTTCAAACCTAATGGCTTTATCGGTTTCGCCTTAGC
1 CAACCCCTT-AAACTTGTTGGCTTTATCAGTTTTACCTTAGT
*
485401 CAACCCCTCT-AA-TTGGTTGACTTTATCAG-TTT-CGCTTGAGT
1 CAACCCCT-TAAACTT-GTTGGCTTTATCAGTTTTAC-CTT-AGT
* * * * * * * *
485442 CAACACCTCAAACCTATTGGCTTTATCAATTTTGCCCTAGC
1 CAACCCCTTAAACTTGTTGGCTTTATCAGTTTTACCTTAGT
* * * * *
485483 CAACCCCTCT--AGTTGGTTGACTTTATC-GATTTTGCCCT-GAC
1 CAACCCCT-TAAACTT-GTTGGCTTTATCAG-TTTTACCTTAG-T
* * * * *
485524 CAACCCCTCAAACTTGTTGGTTTTATCGGTTTTGCCTTAGC
1 CAACCCCTTAAACTTGTTGGCTTTATCAGTTTTACCTTAGT
** * ** *
485565 CAACCTTTTAAA-TTAGTTGACTTTATTTGTTTTGTCC-TAGT
1 CAACCCCTTAAACTT-GTTGGCTTTATCAGTTTT-ACCTTAGT
* * * * * *
485606 CAACCCGTCAAACCTGTTGGCTTTATTAGTTTCACCTTAGC
1 CAACCCCTTAAACTTGTTGGCTTTATCAGTTTTACCTTAGT
* * *
485647 CAACCCCTCT-AA-TTGGTTGACTTTATTAGTTTTGCCTTAGT
1 CAACCCCT-TAAACTT-GTTGGCTTTATCAGTTTTACCTTAGT
* * * * * * * *
485688 TAACCCCTTAAACCTGTTGGCTTAAT-TGGTTTAGCTTTGGG
1 CAACCCCTTAAACTTGTTGGCTTTATCAGTTTTA-CCTTAGT
* *
485729 CAACCCCTTAAA-TTGGTTGACTTTATCAGTTTTACCTTGGT
1 CAACCCCTTAAACTT-GTTGGCTTTATCAGTTTTACCTTAGT
* * * * * * *
485770 TAACCCCTCAAAGTTGTTGGCTTTATCGGTCTTACCCTAGC
1 CAACCCCTTAAACTTGTTGGCTTTATCAGTTTTACCTTAGT
485811 CAACC
1 CAACC
485816 TTCTAACTAG
Statistics
Matches: 336, Mismatches: 87, Indels: 66
0.69 0.18 0.13
Matches are distributed among these distances:
39 1 0.00
40 30 0.09
41 276 0.82
42 27 0.08
43 2 0.01
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.38
Consensus pattern (41 bp):
CAACCCCTTAAACTTGTTGGCTTTATCAGTTTTACCTTAGT
Found at i:491066 original size:60 final size:61
Alignment explanation
Indices: 490968--491122 Score: 231
Period size: 60 Copynumber: 2.5 Consensus size: 61
490958 GCCATCAGGA
* * * * *
490968 TTAATAGAAAAGGCGTCTTGCTCTTTGAGGACTGGAAAATGCCACCAACTTTTGTGGGC-T
1 TTAAAAGAAAAGGCATCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGGGGGCTT
**
491028 TTAAAAGAAAAGGCATCCTGCTCTTTGAGGACTGGAAAATGCCATTAACTTGTGGGGGCTT
1 TTAAAAGAAAAGGCATCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGGGGGCTT
491089 TTAAAAGGAAAAGGCATCCTGCTCTTTGAGGACT
1 TTAAAA-GAAAAGGCATCCTGCTCTTTGAGGACT
491123 AAAAAGCGGA
Statistics
Matches: 86, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
60 52 0.60
61 7 0.08
62 27 0.31
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.28
Consensus pattern (61 bp):
TTAAAAGAAAAGGCATCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGGGGGCTT
Found at i:492108 original size:1 final size:1
Alignment explanation
Indices: 492104--492192 Score: 52
Period size: 1 Copynumber: 89.0 Consensus size: 1
492094 CTTTTCTCTC
* * * * * ** * * * *
492104 TTTTTCTTTGTTTTGTTTTGTTTTTTTTTTTGTTTTTGGTTTTGTTTTTGTTTTTGTTTTTGTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
492169 TTGTTTTTTTTTGTTTTTGTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTT
492193 AAGAGAAGGT
Statistics
Matches: 62, Mismatches: 26, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 62 1.00
ACGTcount: A:0.00, C:0.01, G:0.15, T:0.84
Consensus pattern (1 bp):
T
Found at i:492111 original size:6 final size:6
Alignment explanation
Indices: 492110--492192 Score: 120
Period size: 6 Copynumber: 14.5 Consensus size: 6
492100 TCTCTTTTTC
* *
492110 TTTG-T TTTG-T TTTGTT TTTTTT TTTGTT TTTGGT TTTGTT TTTGTT
1 TTTGTT TTTGTT TTTGTT TTTGTT TTTGTT TTTGTT TTTGTT TTTGTT
492156 TTTGTT TTTGTT TTTG-T TTT-TT TTTGTT TTTGTT TTT
1 TTTGTT TTTGTT TTTGTT TTTGTT TTTGTT TTTGTT TTT
492193 AAGAGAAGGT
Statistics
Matches: 71, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
5 17 0.24
6 54 0.76
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (6 bp):
TTTGTT
Found at i:493691 original size:20 final size:19
Alignment explanation
Indices: 493665--493739 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 19
493655 AATTAACTAG
493665 ATGTATCGATACATTTTCCA
1 ATGTATCGATACATTTT-CA
* * *
493685 TTGTATCGATACATGTATGA
1 ATGTATCGATACAT-TTTCA
*
493705 ATGTATCGATACATTTTATA
1 ATGTATCGATACATTTT-CA
*
493725 ATGTATCTATACATT
1 ATGTATCGATACATT
493740 ATGTTTTTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.04
20 42 0.91
21 2 0.04
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (19 bp):
ATGTATCGATACATTTTCA
Found at i:493730 original size:40 final size:39
Alignment explanation
Indices: 493665--493742 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
493655 AATTAACTAG
* *
493665 ATGTATCGATACATTTTCCATTGTATCGATACATGTATGA
1 ATGTATCGATACATTTTACAATGTATCGATACAT-TATGA
* *
493705 ATGTATCGATACATTTTATAATGTATCTATACATTATG
1 ATGTATCGATACATTTTACAATGTATCGATACATTATG
493743 TTTTTTTTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (39 bp):
ATGTATCGATACATTTTACAATGTATCGATACATTATGA
Found at i:493789 original size:20 final size:20
Alignment explanation
Indices: 493755--493810 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
493745 TTTTTTACCC
*
493755 AAATGTAT-GATACATTGAA
1 AAATGTATCGATACATCGAA
*
493774 AAATGTATCAATACATCGAA
1 AAATGTATCGATACATCGAA
493794 AAATGTATCGATACATC
1 AAATGTATCGATACATC
493811 TGGGTAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 8 0.24
20 25 0.76
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.29
Consensus pattern (20 bp):
AAATGTATCGATACATCGAA
Found at i:496432 original size:22 final size:22
Alignment explanation
Indices: 496400--496445 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
496390 TTTCATTTAA
*
496400 AAAAAAATTTCTCCCCCTTGAT
1 AAAAAAATTTCTCCCCATTGAT
* *
496422 AAAAAATTTTCTCCCTATTGAT
1 AAAAAAATTTCTCCCCATTGAT
496444 AA
1 AA
496446 TCGTTTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.35
Consensus pattern (22 bp):
AAAAAAATTTCTCCCCATTGAT
Found at i:498813 original size:20 final size:19
Alignment explanation
Indices: 498771--498824 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
498761 CACACCCAGA
498771 TGTATCGATACATGATCAT
1 TGTATCGATACATGATCAT
498790 TGTATCGATACATAGA-CAAT
1 TGTATCGATACAT-GATC-AT
498810 TGTATCGATACATGA
1 TGTATCGATACATGA
498825 AACTGGCAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (19 bp):
TGTATCGATACATGATCAT
Found at i:498898 original size:33 final size:33
Alignment explanation
Indices: 498856--498919 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 33
498846 CACTGTTTGT
*
498856 ATCGATACATGGT-ACATTGTATCGATACATTAC
1 ATCGATACATGATGA-ATTGTATCGATACATTAC
498889 ATCGATACATGATGAATTGTATCGATACATT
1 ATCGATACATGATGAATTGTATCGATACATT
498920 GCTTGTAACA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (33 bp):
ATCGATACATGATGAATTGTATCGATACATTAC
Found at i:500514 original size:9 final size:9
Alignment explanation
Indices: 500497--500530 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
500487 GTCAACCATC
500497 AATGATGAT
1 AATGATGAT
500506 GAA-GATGAT
1 -AATGATGAT
500515 AATGATGAT
1 AATGATGAT
500524 AATGATG
1 AATGATG
500531 GTGACTCGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 2 0.09
9 19 0.83
10 2 0.09
ACGTcount: A:0.44, C:0.00, G:0.26, T:0.29
Consensus pattern (9 bp):
AATGATGAT
Found at i:500934 original size:21 final size:20
Alignment explanation
Indices: 500908--500946 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
500898 AGGTCAAAAC
500908 CCTAGAAAGTATCGATACACA
1 CCTAG-AAGTATCGATACACA
*
500929 CCTAGATGTATCGATACA
1 CCTAGAAGTATCGATACA
500947 TATTGCTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (20 bp):
CCTAGAAGTATCGATACACA
Found at i:500990 original size:13 final size:13
Alignment explanation
Indices: 500956--500980 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
500946 ATATTGCTTA
500956 GTATTGATACATT
1 GTATTGATACATT
500969 GTATTGATACAT
1 GTATTGATACAT
500981 GTTCTTGATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (13 bp):
GTATTGATACATT
Found at i:502680 original size:20 final size:20
Alignment explanation
Indices: 502655--502692 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
502645 CATAAATTTA
*
502655 GTTTTATCAATTTAGCTTTG
1 GTTTTATCAACTTAGCTTTG
502675 GTTTTATCAACTTAGCTT
1 GTTTTATCAACTTAGCTT
502693 ATAACAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.13, G:0.13, T:0.53
Consensus pattern (20 bp):
GTTTTATCAACTTAGCTTTG
Found at i:502776 original size:30 final size:29
Alignment explanation
Indices: 502742--502826 Score: 100
Period size: 30 Copynumber: 2.9 Consensus size: 29
502732 GGGTGATAAC
*
502742 GTATTAAGGTGGAGAGTTTGCATAAAATTT
1 GTATTAAGG-GGAGAGCTTGCATAAAATTT
*
502772 GTATTACGGAGGAGAGCTTG-ATAAAATTT
1 GTATTAAGG-GGAGAGCTTGCATAAAATTT
* *
502801 TTACTAAAGGGGAGAGCTTGCATAAA
1 GTA-TTAAGGGGAGAGCTTGCATAAA
502827 CTTTTGGTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
29 21 0.45
30 26 0.55
ACGTcount: A:0.35, C:0.07, G:0.27, T:0.31
Consensus pattern (29 bp):
GTATTAAGGGGAGAGCTTGCATAAAATTT
Found at i:503703 original size:20 final size:19
Alignment explanation
Indices: 503679--503751 Score: 78
Period size: 20 Copynumber: 3.7 Consensus size: 19
503669 CACACCTAGA
503679 TGTATCGATACATATTGCT
1 TGTATCGATACATATTGCT
*
503698 TAGTATCGATACATGTT-CT
1 T-GTATCGATACATATTGCT
*
503717 TGATATCGATACATCA-TGAAT
1 TG-TATCGATACAT-ATTG-CT
503738 TGTATCGATACATA
1 TGTATCGATACATA
503752 AAATTGGCAG
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
18 1 0.02
19 17 0.37
20 25 0.54
21 3 0.07
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATATTGCT
Found at i:511618 original size:13 final size:13
Alignment explanation
Indices: 511600--511626 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
511590 ACATTATGCT
511600 TTGTATCGATACA
1 TTGTATCGATACA
511613 TTGTATCGATACA
1 TTGTATCGATACA
511626 T
1 T
511627 GATCATTATA
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:511621 original size:33 final size:32
Alignment explanation
Indices: 511579--511645 Score: 98
Period size: 33 Copynumber: 2.1 Consensus size: 32
511569 ACACACCTAG
* * *
511579 ATTGTATCGATACATTATGCTTTGTATCGATAC
1 ATTGTATCGATACATGAT-CATTATATCGATAC
511612 ATTGTATCGATACATGATCATTATATCGATAC
1 ATTGTATCGATACATGATCATTATATCGATAC
511644 AT
1 AT
511646 GGACAATTGT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
32 14 0.45
33 17 0.55
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.40
Consensus pattern (32 bp):
ATTGTATCGATACATGATCATTATATCGATAC
Found at i:511638 original size:19 final size:18
Alignment explanation
Indices: 511610--511667 Score: 80
Period size: 19 Copynumber: 3.1 Consensus size: 18
511600 TTGTATCGAT
511610 ACATTGTATCGATACATG
1 ACATTGTATCGATACATG
*
511628 ATCATTATATCGATACATGG
1 A-CATTGTATCGATACAT-G
511648 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
511667 A
1 A
511668 AACTGATAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 1 0.03
19 18 0.51
20 16 0.46
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (18 bp):
ACATTGTATCGATACATG
Found at i:511660 original size:20 final size:20
Alignment explanation
Indices: 511611--511666 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
511601 TGTATCGATA
511611 CATTGTATCGATACAT-GAT
1 CATTGTATCGATACATGGAT
*
511630 CATTATATCGATACATGGA-
1 CATTGTATCGATACATGGAT
511649 CAATTGTATCGATACATG
1 C-ATTGTATCGATACATG
511667 AAACTGATAG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (20 bp):
CATTGTATCGATACATGGAT
Found at i:511720 original size:20 final size:20
Alignment explanation
Indices: 511695--511748 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
511685 CTACCACTGT
*
511695 TTGTATCGATACATGGT-ACA
1 TTGTATCGATACATGATGA-A
511715 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGATGAA
511735 TTGTATCGATACAT
1 TTGTATCGATACAT
511749 TGCTTGTAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGATGAA
Found at i:516384 original size:3 final size:3
Alignment explanation
Indices: 516376--516406 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
516366 TCTGAGTCAA
*
516376 CAT CAT CAT CAT CAT CAT CAT CAT CTT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
516407 GCCTTTGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
CAT
Found at i:518595 original size:31 final size:32
Alignment explanation
Indices: 518500--518791 Score: 173
Period size: 31 Copynumber: 9.4 Consensus size: 32
518490 AAAGGACATA
* *
518500 CCACCAACTTTTGTGGGCTTTAGAGAAGAGGTTG
1 CCACCAACTTGTGTAGGCTTTAGA-AA-AGGTTG
* *
518534 CCA-CAAGCTTGTGTGGGATTTAGAGAAAGG-TG
1 CCACCAA-CTTGTGTAGGCTTTAGA-AAAGGTTG
* *
518566 CCACCAACTTATGTAGGCTTTTGAAAAGGTTG
1 CCACCAACTTGTGTAGGCTTTAGAAAAGGTTG
* * *** *
518598 CCACCAGCTTGTAT-GAGCTTTAG-TGGGGGTG
1 CCACCAACTTGTGTAG-GCTTTAGAAAAGGTTG
*
518629 CCACCAACTTGTG-AGGGCTTTAGAAGAGG-TG
1 CCACCAACTTGTGTA-GGCTTTAGAAAAGGTTG
* * **
518660 CCACCGACTTGTGTGGGCTTTAG-AGGGGTTG
1 CCACCAACTTGTGTAGGCTTTAGAAAAGGTTG
* * *
518691 CCACCGACTTGTGTGGGCTTTAGAAAAGGGTG
1 CCACCAACTTGTGTAGGCTTTAGAAAAGGTTG
** * *
518723 CCACTGAC-T-TGTAGG-TTT-TAAAAGGATG
1 CCACCAACTTGTGTAGGCTTTAGAAAAGGTTG
** *
518751 CCACTGACTTGTG--GGCTTTAG--AAGGATG
1 CCACCAACTTGTGTAGGCTTTAGAAAAGGTTG
*
518779 CCACTAACTTGTG
1 CCACCAACTTGTG
518792 GACTTTGCAA
Statistics
Matches: 214, Mismatches: 30, Indels: 34
0.77 0.11 0.12
Matches are distributed among these distances:
28 37 0.17
29 7 0.03
30 11 0.05
31 76 0.36
32 53 0.25
33 9 0.04
34 21 0.10
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.28
Consensus pattern (32 bp):
CCACCAACTTGTGTAGGCTTTAGAAAAGGTTG
Found at i:518693 original size:62 final size:63
Alignment explanation
Indices: 518500--518734 Score: 230
Period size: 62 Copynumber: 3.7 Consensus size: 63
518490 AAAGGACATA
* * * * *
518500 CCACCAACTTTTGTGGGCTTTAGAGAAGAGGTTGCCA-CAAGCTTGTGTGGGATTTAGAGAAAGG
1 CCACCAACTTGTGAGGGCTTTAGA-AA-AGGTTGCCACCGAGCTTGTGTGGGCTTTAGAG--GGG
518564 TG
62 TG
* * * * *
518566 CCACCAACTTATGTA-GGCTTTTGAAAAGGTTGCCACC-AGCTTGTATGAGCTTTAGTGGGGGTG
1 CCACCAACTTGTG-AGGGCTTTAGAAAAGGTTGCCACCGAGCTTGTGTGGGCTTTAG-AGGGGTG
*
518629 CCACCAACTTGTGAGGGCTTTAGAAGAGG-TGCCACCGA-CTTGTGTGGGCTTTAGAGGGGTTG
1 CCACCAACTTGTGAGGGCTTTAGAAAAGGTTGCCACCGAGCTTGTGTGGGCTTTAGAGGGG-TG
* * * *
518691 CCACCGACTTGTGTGGGCTTTAGAAAAGGGTGCCACTGA-CTTGT
1 CCACCAACTTGTGAGGGCTTTAGAAAAGGTTGCCACCGAGCTTGT
518735 AGGTTTTAAA
Statistics
Matches: 144, Mismatches: 18, Indels: 17
0.80 0.10 0.09
Matches are distributed among these distances:
61 4 0.03
62 50 0.35
63 42 0.29
64 24 0.17
65 4 0.03
66 20 0.14
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.28
Consensus pattern (63 bp):
CCACCAACTTGTGAGGGCTTTAGAAAAGGTTGCCACCGAGCTTGTGTGGGCTTTAGAGGGGTG
Found at i:518849 original size:29 final size:29
Alignment explanation
Indices: 518643--519083 Score: 314
Period size: 28 Copynumber: 15.3 Consensus size: 29
518633 CAACTTGTGA
* *
518643 GGGCTTTAGAAGAGG-TGCCACCGACTTGTGT
1 GGGCTTTGGAAG-GGATGCCACTGAC-T-TGT
* * * *
518674 GGGCTTTAGAGGGGTTGCCACCGACTTGTGT
1 GGGCTTTGGAAGGGATGCCACTGAC-T-TGT
*
518705 GGGCTTTAGAAAAGGG-TGCCACTGACTTGT
1 GGGCTTT-G-GAAGGGATGCCACTGACTTGT
* ** *
518735 AGG-TTTTAAAAGGATGCCACTGACTTGT
1 GGGCTTTGGAAGGGATGCCACTGACTTGT
* *
518763 GGGCTTTAGAA-GGATGCCACTAACTTGT
1 GGGCTTTGGAAGGGATGCCACTGACTTGT
* * *
518791 GGACTTTGCAAGGG-TGCCACTAACTTGT
1 GGGCTTTGGAAGGGATGCCACTGACTTGT
* *
518819 GGGCTTTGGAAGGGATGCCACTAACTCGT
1 GGGCTTTGGAAGGGATGCCACTGACTTGT
* *** *
518848 GGG-TTTTGAAAAAAGTGCCATTGACTTGT
1 GGGCTTTGGAAGGGA-TGCCACTGACTTGT
*
518877 GGGCTTTAGAAGGGATGCCACTGACTTGT
1 GGGCTTTGGAAGGGATGCCACTGACTTGT
** * * *
518906 GGGCTTT-GAAATGAAGCCATTAACTTGT
1 GGGCTTTGGAAGGGATGCCACTGACTTGT
* *
518934 GGGTTTTGAAAAGGG-TGCCACTGACTTGT
1 GGGCTTTG-GAAGGGATGCCACTGACTTGT
* *
518963 GGACTTTGAAAGGGATGCCACTGACTTGT
1 GGGCTTTGGAAGGGATGCCACTGACTTGT
* ** *
518992 GGGCTTT-CAAATGAAGCCACT-AGCTTGT
1 GGGCTTTGGAAGGGATGCCACTGA-CTTGT
* *
519020 GGGCTTTGGAAAAGG-TGCTACTGACTTGT
1 GGGCTTTGG-AAGGGATGCCACTGACTTGT
* * *
519049 GGGTTTTGAAAGGG-TGCC-CTGACTCGT
1 GGGCTTTGGAAGGGATGCCACTGACTTGT
519076 GGGCTTTG
1 GGGCTTTG
519084 AAAAAAAAAA
Statistics
Matches: 335, Mismatches: 59, Indels: 36
0.78 0.14 0.08
Matches are distributed among these distances:
27 21 0.06
28 130 0.39
29 114 0.34
30 22 0.07
31 35 0.10
32 9 0.03
33 4 0.01
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (29 bp):
GGGCTTTGGAAGGGATGCCACTGACTTGT
Found at i:518890 original size:86 final size:85
Alignment explanation
Indices: 518702--519086 Score: 427
Period size: 86 Copynumber: 4.5 Consensus size: 85
518692 CACCGACTTG
* * * * *
518702 TGTGGGCTTTAGAAAAGGGTGCCACTGACTTGTAGGTTTTAAAAGGATGCCACTGACTTGTGGGC
1 TGTGGGCTTT-G-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGAAGCCACTAACTTGTGGGC
* *
518767 TTT--AGAAGGATGCCACTAACT
64 TTTGAAAAAGG-TGCCACTGACT
* * * * * * *
518788 TGTGGACTTTGCAAGGGTGCCACTAACTTGTGGGCTTTGGAAGGGATGCCACTAACTCGTGGGTT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTT-GAAAGGAAGCCACTAACTTGTGGGCT
* *
518853 TTGAAAAAAGTGCCATTGACT
65 TTGAAAAAGGTGCCACTGACT
* * *
518874 TGTGGGCTTT-AGAAGGGATGCCACTGACTTGTGGGCTTTGAAATGAAGCCATTAACTTGTGGGT
1 TGTGGGCTTTGA-AAGGG-TGCCACTGACTTGTGGGCTTTGAAAGGAAGCCACTAACTTGTGGGC
*
518938 TTTGAAAAGGGTGCCACTGACT
64 TTTGAAAAAGGTGCCACTGACT
* * * *
518960 TGTGGACTTTGAAAGGGATGCCACTGACTTGTGGGCTTTCAAATGAAGCCACTAGCTTGTGGGCT
1 TGTGGGCTTTGAAAGGG-TGCCACTGACTTGTGGGCTTTGAAAGGAAGCCACTAACTTGTGGGCT
* *
519025 TTGGAAAAGGTGCTACTGACT
65 TTGAAAAAGGTGCCACTGACT
* *
519046 TGTGGGTTTTGAAAGGGTGCC-CTGACTCGTGGGCTTTGAAA
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAA
519087 AAAAAAAGAT
Statistics
Matches: 256, Mismatches: 37, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
84 41 0.16
85 28 0.11
86 162 0.63
87 25 0.10
ACGTcount: A:0.23, C:0.16, G:0.31, T:0.30
Consensus pattern (85 bp):
TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGAAGCCACTAACTTGTGGGCTT
TGAAAAAGGTGCCACTGACT
Found at i:519903 original size:13 final size:13
Alignment explanation
Indices: 519885--519935 Score: 84
Period size: 13 Copynumber: 3.9 Consensus size: 13
519875 TACTATCACA
519885 TGTATCGATACAG
1 TGTATCGATACAG
519898 TGTATCGATACAG
1 TGTATCGATACAG
* *
519911 TGTATCGATATAA
1 TGTATCGATACAG
519924 TGTATCGATACA
1 TGTATCGATACA
519936 TAAATAGTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 35 1.00
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:519980 original size:14 final size:14
Alignment explanation
Indices: 519961--519994 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
519951 AGTAATAAAT
519961 AGTGATACATGAAC
1 AGTGATACATGAAC
*
519975 AGTGATACGTGAAC
1 AGTGATACATGAAC
*
519989 AATGAT
1 AGTGAT
519995 GAACAGTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.24
Consensus pattern (14 bp):
AGTGATACATGAAC
Found at i:520100 original size:13 final size:13
Alignment explanation
Indices: 520082--520106 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
520072 TACCATGAAC
520082 ATGTATCGATACA
1 ATGTATCGATACA
520095 ATGTATCGATAC
1 ATGTATCGATAC
520107 TAAGCAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:531465 original size:20 final size:19
Alignment explanation
Indices: 531440--531495 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
531430 GTTGGGCATA
*
531440 ATGTATTGATACTATTTACC
1 ATGTATCGATAC-ATTTACC
* *
531460 ATGTATCGATACAATGTCCC
1 ATGTATCGATAC-ATTTACC
531480 ATGTATCGATACATTT
1 ATGTATCGATACATTT
531496 CACATAGGGT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 3 0.10
20 28 0.90
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (19 bp):
ATGTATCGATACATTTACC
Found at i:531547 original size:20 final size:19
Alignment explanation
Indices: 531522--531612 Score: 78
Period size: 20 Copynumber: 4.6 Consensus size: 19
531512 TGCCAGTTTC
531522 ATGTATCGATACAATTCAGT
1 ATGTATCGATACAA-TCAGT
* **
531542 ATGTATCGATACAATGAAC
1 ATGTATCGATACAATCAGT
* *
531561 ATGTATCGATAAAAAGCA-T
1 ATGTATCGAT-ACAATCAGT
531580 AATGTATCGATAC-ATCTAGAT
1 -ATGTATCGATACAATC-AG-T
531601 ATGTATCGATAC
1 ATGTATCGATAC
531613 TTTCGAGGGT
Statistics
Matches: 57, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
18 2 0.04
19 14 0.25
20 40 0.70
21 1 0.02
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (19 bp):
ATGTATCGATACAATCAGT
Found at i:536714 original size:20 final size:20
Alignment explanation
Indices: 536689--536726 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
536679 TATTGCCAGT
536689 TTCATGTA-TCGATACAATTC
1 TTCATGTACT-GATACAATTC
536709 TTCATGTACTGATACAAT
1 TTCATGTACTGATACAAT
536727 GAACATGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (20 bp):
TTCATGTACTGATACAATTC
Found at i:536759 original size:44 final size:45
Alignment explanation
Indices: 536693--536781 Score: 110
Period size: 44 Copynumber: 2.0 Consensus size: 45
536683 GCCAGTTTCA
** ** *
536693 TGTATCGATACAATTCTTCATGTA-CTGATACAATG-AACATGTAT
1 TGTATCGATACAAAGCAACATGTATC-GATACAAAGCAACATGTAT
536737 TGTATCGATACAAAGCAACATGTATCGATACAAAGCAACATGTAT
1 TGTATCGATACAAAGCAACATGTATCGATACAAAGCAACATGTAT
536782 CGATACTTTC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
44 28 0.74
45 10 0.26
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (45 bp):
TGTATCGATACAAAGCAACATGTATCGATACAAAGCAACATGTAT
Found at i:536762 original size:20 final size:20
Alignment explanation
Indices: 536737--536787 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
536727 GAACATGTAT
536737 TGTATCGATACAAAGCAACA
1 TGTATCGATACAAAGCAACA
536757 TGTATCGATACAAAGCAACA
1 TGTATCGATACAAAGCAACA
536777 TGTATCGATAC
1 TGTATCGATAC
536788 TTTCTAGGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.24
Consensus pattern (20 bp):
TGTATCGATACAAAGCAACA
Found at i:537421 original size:19 final size:21
Alignment explanation
Indices: 537378--537427 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
537368 CAATTTATAA
537378 CTCCCCTTTAATAAAACACTT
1 CTCCCCTTTAATAAAACACTT
537399 CTCCCCTTTAATAAAA-A-TT
1 CTCCCCTTTAATAAAACACTT
537418 CT-CCCTTTAA
1 CTCCCCTTTAA
537428 AGAAAATATC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
18 8 0.28
19 4 0.14
20 1 0.03
21 16 0.55
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (21 bp):
CTCCCCTTTAATAAAACACTT
Found at i:537433 original size:19 final size:19
Alignment explanation
Indices: 537378--537433 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 19
537368 CAATTTATAA
*
537378 CTCCCCTTTAATAAAACACTT
1 CTCCCCTTTAAGAAAA-A-TT
*
537399 CTCCCCTTTAATAAAAATT
1 CTCCCCTTTAAGAAAAATT
537418 CT-CCCTTTAAAGAAAA
1 CTCCCCTTT-AAGAAAA
537434 TATCTCTCCT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
18 6 0.18
19 10 0.30
20 1 0.03
21 16 0.48
ACGTcount: A:0.38, C:0.29, G:0.02, T:0.32
Consensus pattern (19 bp):
CTCCCCTTTAAGAAAAATT
Found at i:542671 original size:13 final size:13
Alignment explanation
Indices: 542653--542678 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
542643 CATTTTTTGG
542653 TGTATCGATACAT
1 TGTATCGATACAT
542666 TGTATCGATACAT
1 TGTATCGATACAT
542679 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:542693 original size:32 final size:33
Alignment explanation
Indices: 542633--542696 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
542623 TGCAAGCCAA
**
542633 TGTATCAATACATTTTTTGGTGTATCGATACAT
1 TGTATCAATACATACTTTGGTGTATCGATACAT
*
542666 TGTATCGATACATACTTT-GTGTATCGATACA
1 TGTATCAATACATACTTTGGTGTATCGATACA
542697 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCAATACATACTTTGGTGTATCGATACAT
Found at i:544765 original size:21 final size:20
Alignment explanation
Indices: 544736--544778 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
544726 GGCTAGTGTG
*
544736 GGGACTGCCCGGTTGCGACCT
1 GGGACTG-CCGGTCGCGACCT
*
544757 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCGCGACCT
544777 GG
1 GG
544779 TGGGTGCTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.09, C:0.30, G:0.44, T:0.16
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:545487 original size:8 final size:8
Alignment explanation
Indices: 545455--545486 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
545445 CATCATTCAA
545455 CACAAAAT
1 CACAAAAT
545463 CACAAAAT
1 CACAAAAT
545471 CACAAAAT
1 CACAAAAT
*
545479 TACAAAAT
1 CACAAAAT
545487 TTAATCAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.62, C:0.22, G:0.00, T:0.16
Consensus pattern (8 bp):
CACAAAAT
Found at i:547981 original size:32 final size:30
Alignment explanation
Indices: 547945--548003 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
547935 GAAAACAAAT
547945 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
547977 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
548004 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:548302 original size:13 final size:13
Alignment explanation
Indices: 548284--548309 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
548274 CAATTTTTTG
548284 TGTATCGATACAT
1 TGTATCGATACAT
548297 TGTATCGATACAT
1 TGTATCGATACAT
548310 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:548324 original size:32 final size:33
Alignment explanation
Indices: 548264--548327 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
548254 TACAAGCCAA
** *
548264 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
548297 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
548328 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:549017 original size:39 final size:40
Alignment explanation
Indices: 548942--549022 Score: 110
Period size: 39 Copynumber: 2.0 Consensus size: 40
548932 TTTTATTTCT
**
548942 CCCTTAATCAAAATAATTTTAACAAATTCGTACATTCTCC
1 CCCTTAATCAAAATAATTTTAACAAATTCACACATTCTCC
* * *
548982 CCCTTAAT-AAGATAATTTTAGCAAATTCACGCATTCTCC
1 CCCTTAATCAAAATAATTTTAACAAATTCACACATTCTCC
549021 CC
1 CC
549023 TTTTATTAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
39 28 0.78
40 8 0.22
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.33
Consensus pattern (40 bp):
CCCTTAATCAAAATAATTTTAACAAATTCACACATTCTCC
Found at i:550883 original size:13 final size:13
Alignment explanation
Indices: 550865--550902 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
550855 ATAATCACCC
550865 TGTATCGATACAG
1 TGTATCGATACAG
*
550878 TGTATCGATACAT
1 TGTATCGATACAG
550891 TGTATCGATACA
1 TGTATCGATACA
550903 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:553001 original size:15 final size:15
Alignment explanation
Indices: 552981--553011 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
552971 ATTTCGTTTG
*
552981 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
552996 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
553011 G
1 G
553012 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:554522 original size:21 final size:21
Alignment explanation
Indices: 554493--554537 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
554483 AAGTTTTTAT
*
554493 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCGAACTTCATTA
*
554513 TTTTCATTAGCGAACTTCTTTA
1 TTTTC-TTAGCGAACTTCATTA
554535 TTT
1 TTT
554538 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.18, G:0.07, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCGAACTTCATTA
Found at i:556344 original size:13 final size:13
Alignment explanation
Indices: 556326--556351 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
556316 CAATTTTTTG
556326 TGTATCGATACAT
1 TGTATCGATACAT
556339 TGTATCGATACAT
1 TGTATCGATACAT
556352 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:560639 original size:13 final size:13
Alignment explanation
Indices: 560621--560646 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
560611 CATTTTTTGG
560621 TGTATCGATACAT
1 TGTATCGATACAT
560634 TGTATCGATACAT
1 TGTATCGATACAT
560647 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:560661 original size:32 final size:33
Alignment explanation
Indices: 560601--560664 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
560591 TGCAAGCCAA
**
560601 TGTATCGATACATTTTTTGGTGTATCGATACAT
1 TGTATCGATACATACTTTGGTGTATCGATACAT
560634 TGTATCGATACATACTTT-GTGTATCGATACA
1 TGTATCGATACATACTTTGGTGTATCGATACA
560665 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 13 0.45
33 16 0.55
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATACTTTGGTGTATCGATACAT
Found at i:560923 original size:21 final size:21
Alignment explanation
Indices: 560890--560930 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
560880 CTAAGTAAAA
560890 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
560911 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
560931 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:561016 original size:20 final size:20
Alignment explanation
Indices: 560968--561021 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
560958 AAACCCTGAA
*
560968 AAGTATCGATACACATTTTC
1 AAGTATCGATACACATTTGC
*
560988 AATGTATCGATACAGA-TTGC
1 AA-GTATCGATACACATTTGC
561008 ATAGTATCGATACA
1 A-AGTATCGATACA
561022 TTGGAAGTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (20 bp):
AAGTATCGATACACATTTGC
Found at i:561126 original size:13 final size:13
Alignment explanation
Indices: 561108--561172 Score: 103
Period size: 13 Copynumber: 5.0 Consensus size: 13
561098 TCACTATTCA
561108 TGTATCGATACAT
1 TGTATCGATACAT
*
561121 TGTATCGATACAG
1 TGTATCGATACAT
*
561134 TGTATTGATACAT
1 TGTATCGATACAT
*
561147 TGTATCGATACAA
1 TGTATCGATACAT
561160 TGTATCGATACAT
1 TGTATCGATACAT
561173 CATAAATAGT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 46 1.00
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:561137 original size:26 final size:26
Alignment explanation
Indices: 561107--561172 Score: 114
Period size: 26 Copynumber: 2.5 Consensus size: 26
561097 ATCACTATTC
561107 ATGTATCGATACATTGTATCGATACA
1 ATGTATCGATACATTGTATCGATACA
* *
561133 GTGTATTGATACATTGTATCGATACA
1 ATGTATCGATACATTGTATCGATACA
561159 ATGTATCGATACAT
1 ATGTATCGATACAT
561173 CATAAATAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (26 bp):
ATGTATCGATACATTGTATCGATACA
Found at i:567549 original size:3 final size:3
Alignment explanation
Indices: 567534--567577 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
567524 AACCGCCAAA
* *
567534 GAT GAT GAA GAT GAT GAT GAT GAT GAT GAT GAT GAT AAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
567578 GGTTAACTTG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.39, C:0.00, G:0.32, T:0.30
Consensus pattern (3 bp):
GAT
Found at i:571301 original size:20 final size:21
Alignment explanation
Indices: 571251--571303 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
571241 GCCAGTCACC
*
571251 TGTATCGATACATTCTTTGCA
1 TGTATCGATACATTCTGTGCA
* *
571272 AGTATTGATACATT-TG-GTCA
1 TGTATCGATACATTCTGTG-CA
571292 TGTATCGATACA
1 TGTATCGATACA
571304 ATGTATCGAT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 1 0.04
20 13 0.50
21 12 0.46
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATTCTGTGCA
Found at i:571309 original size:13 final size:13
Alignment explanation
Indices: 571291--571315 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
571281 ACATTTGGTC
571291 ATGTATCGATACA
1 ATGTATCGATACA
571304 ATGTATCGATAC
1 ATGTATCGATAC
571316 TGTGCATTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:579549 original size:19 final size:20
Alignment explanation
Indices: 579510--579562 Score: 99
Period size: 19 Copynumber: 2.7 Consensus size: 20
579500 TTTCAATGAT
579510 TTGTATCGATACATAAAGTG
1 TTGTATCGATACATAAAGTG
579530 TTGTATCGATACAT-AAGTG
1 TTGTATCGATACATAAAGTG
579549 TTGTATCGATACAT
1 TTGTATCGATACAT
579563 TGTATCGATA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 19 0.58
20 14 0.42
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (20 bp):
TTGTATCGATACATAAAGTG
Found at i:579567 original size:13 final size:13
Alignment explanation
Indices: 579549--579575 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
579539 TACATAAGTG
579549 TTGTATCGATACA
1 TTGTATCGATACA
579562 TTGTATCGATACA
1 TTGTATCGATACA
579575 T
1 T
579576 AAGTTTTGTA
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:579571 original size:32 final size:32
Alignment explanation
Indices: 579530--579592 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
579520 ACATAAAGTG
*
579530 TTGTATCGATACATAAGTGTTGTATCGATACA
1 TTGTATCGATACATAAGTGTTGTATCAATACA
*
579562 TTGTATCGATACATAAGTTTTGTATCAATAC
1 TTGTATCGATACATAAGTGTTGTATCAATAC
579593 CATTTAAGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.40
Consensus pattern (32 bp):
TTGTATCGATACATAAGTGTTGTATCAATACA
Found at i:579654 original size:13 final size:13
Alignment explanation
Indices: 579636--579660 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
579626 ATTACTCAAA
579636 TGTATCGATACAT
1 TGTATCGATACAT
579649 TGTATCGATACA
1 TGTATCGATACA
579661 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:579715 original size:52 final size:52
Alignment explanation
Indices: 579669--579849 Score: 276
Period size: 52 Copynumber: 3.5 Consensus size: 52
579659 CACTGATCTT
***
579669 TGTATCGATACATGCAGGCAAATTTGCCCAGATTTATCGATACACTGAT-CTT
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATTTATCGATACACT-ATAAAA
579721 TGTATCGATACATGCAGGCAAATTTGCCCAG-TTGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATT-TATCGATACACTATAAAA
* *
579773 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATTGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATTTATCGATACACTATAAAA
*
579825 TGTATCGATACATGCTGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
579850 TCATATTTCG
Statistics
Matches: 120, Mismatches: 6, Indels: 6
0.91 0.05 0.05
Matches are distributed among these distances:
51 4 0.03
52 115 0.96
53 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATTTATCGATACACTATAAAA
Found at i:582998 original size:19 final size:19
Alignment explanation
Indices: 582974--583011 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
582964 ACCAATCATT
*
582974 GGTTTCGCCGATATCGGTC
1 GGTTTCACCGATATCGGTC
*
582993 GGTTTCACCGATTTCGGTC
1 GGTTTCACCGATATCGGTC
583012 CTTATTGGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.11, C:0.26, G:0.29, T:0.34
Consensus pattern (19 bp):
GGTTTCACCGATATCGGTC
Found at i:586753 original size:14 final size:14
Alignment explanation
Indices: 586734--586779 Score: 74
Period size: 15 Copynumber: 3.1 Consensus size: 14
586724 TGGAACAGTC
586734 AAAAGTCAAAAAAA
1 AAAAGTCAAAAAAA
586748 AAAAGTCAAAAAAAA
1 AAAAGTC-AAAAAAA
586763 AGAAAGTCAAAAAAA
1 A-AAAGTCAAAAAAA
586778 AA
1 AA
586780 GTGCAAAGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.27
15 16 0.53
16 6 0.20
ACGTcount: A:0.78, C:0.07, G:0.09, T:0.07
Consensus pattern (14 bp):
AAAAGTCAAAAAAA
Found at i:586780 original size:16 final size:16
Alignment explanation
Indices: 586735--586780 Score: 78
Period size: 16 Copynumber: 3.0 Consensus size: 16
586725 GGAACAGTCA
586735 AAAGTC-AAAAAAAA-
1 AAAGTCAAAAAAAAAG
586749 AAAGTCAAAAAAAAAG
1 AAAGTCAAAAAAAAAG
586765 AAAGTCAAAAAAAAAG
1 AAAGTCAAAAAAAAAG
586781 TGCAAAGGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.20
15 8 0.27
16 16 0.53
ACGTcount: A:0.76, C:0.07, G:0.11, T:0.07
Consensus pattern (16 bp):
AAAGTCAAAAAAAAAG
Found at i:587123 original size:18 final size:17
Alignment explanation
Indices: 587100--587143 Score: 70
Period size: 17 Copynumber: 2.5 Consensus size: 17
587090 ATCTTCACAA
587100 AAAAAAAAACAAAAAAAC
1 AAAAAAAAAC-AAAAAAC
*
587118 AAAAAAAAACAACAAAC
1 AAAAAAAAACAAAAAAC
587135 AAAAAAAAA
1 AAAAAAAAA
587144 GGAAAAAGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 15 0.60
18 10 0.40
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAAAAAAACAAAAAAC
Found at i:588183 original size:30 final size:30
Alignment explanation
Indices: 588139--588236 Score: 108
Period size: 30 Copynumber: 3.1 Consensus size: 30
588129 TTCTCAAAAC
588139 CCACGAATCAGTGGCATTTTGTCCTAAAGT
1 CCACGAATCAGTGGCATTTTGTCCTAAAGT
* * *
588169 CCACGACTCCGTGGCACCTTTT-TCTTCTCAAAGC
1 CCACGAATCAGTGGCA--TTTTGTC--CT-AAAGT
*
588203 CCACGATTCAGTGGCATTTTGTCCTAAAGT
1 CCACGAATCAGTGGCATTTTGTCCTAAAGT
588233 CCAC
1 CCAC
588237 AATTTACTGG
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
30 22 0.39
31 4 0.07
32 8 0.14
33 4 0.07
34 18 0.32
ACGTcount: A:0.22, C:0.31, G:0.17, T:0.30
Consensus pattern (30 bp):
CCACGAATCAGTGGCATTTTGTCCTAAAGT
Found at i:588208 original size:34 final size:33
Alignment explanation
Indices: 588162--588752 Score: 434
Period size: 34 Copynumber: 17.8 Consensus size: 33
588152 GCATTTTGTC
* *
588162 CTAAAGTCCACGACTCCGTGGCACCTTTTTCTT
1 CTAAAGCCCACAACTCCGTGGCACCTTTTTCTT
* * *
588195 CTCAAAGCCCACGATTCAGTGGCA--TTTTGTC--
1 CT-AAAGCCCACAACTCCGTGGCACCTTTT-TCTT
* * * * *
588226 CTAAAGTCCACAATTTAC-TGGCATCTCTTTC--
1 CTAAAGCCCACAA-CTCCGTGGCACCTTTTTCTT
588257 C-AAAGCCCACAACTCCGTGGCACCTTTTTCATT
1 CTAAAGCCCACAACTCCGTGGCACCTTTTTC-TT
* * * * *
588290 -TCAAAGTCCACAACTCCATTGTA-C-TCTT-TT
1 CT-AAAGCCCACAACTCCGTGGCACCTTTTTCTT
588320 -TAAAGCCCACAACTCCGTGGCACTCTTTTTCCTT
1 CTAAAGCCCACAACTCCGTGGCAC-CTTTTT-CTT
*
588354 -TTAAGCCCACAACTCCGTGGCACTCTTTTTCCTT
1 CTAAAGCCCACAACTCCGTGGCAC-CTTTTT-CTT
*
588388 CT-AAGCCCACAACTCTGTGGCACTCTTTTTCCTT
1 CTAAAGCCCACAACTCCGTGGCAC-CTTTTT-CTT
*
588422 CT-AAGCCCACAACTCTGTGGCACTCTTTTTCCTT
1 CTAAAGCCCACAACTCCGTGGCAC-CTTTTT-CTT
* *
588456 CT-AAGTCCACAACTTCGTGGCACCTTTTTCTTT
1 CTAAAGCCCACAACTCCGTGGCACCTTTTTC-TT
*
588489 TTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTT
1 CTAAAGCCCACAACTCCGTGGCAC-CTTTTT-CTT
* *
588524 CT-AAGCCCATAACTACGTGGCACTCTTTTTCCTT
1 CTAAAGCCCACAACTCCGTGGCAC-CTTTTT-CTT
* * *
588558 CT-GAGTCCACAACTCCATGGCACCTTTTTCTTT
1 CTAAAGCCCACAACTCCGTGGCACCTTTTTC-TT
* *
588591 TTAAAGCCCACAACTCCGTGGCACTCTTTCTCCTT
1 CTAAAGCCCACAACTCCGTGGCAC-CTTT-TTCTT
* * * * *
588626 -TTAAGTCCACGACTCTGTGGCACCTTCTT-TT
1 CTAAAGCCCACAACTCCGTGGCACCTTTTTCTT
588657 C-AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTT
1 CTAAAGCCCACAACTCCGTGGCAC-CTTTTT--CTT
* * * *
588692 TTAAAGGCCACAACTCTGTGGCACCTTGTTCTT
1 CTAAAGCCCACAACTCCGTGGCACCTTTTTCTT
* * * * *
588725 TTTAAGTCCACAACTTCGTGGCATCTTT
1 CTAAAGCCCACAACTCCGTGGCACCTTT
588753 CACCCTTTCT
Statistics
Matches: 462, Mismatches: 65, Indels: 62
0.78 0.11 0.11
Matches are distributed among these distances:
29 19 0.04
30 38 0.08
31 28 0.06
32 21 0.05
33 51 0.11
34 259 0.56
35 23 0.05
36 23 0.05
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.34
Consensus pattern (33 bp):
CTAAAGCCCACAACTCCGTGGCACCTTTTTCTT
Found at i:588214 original size:64 final size:61
Alignment explanation
Indices: 588102--588236 Score: 198
Period size: 64 Copynumber: 2.2 Consensus size: 61
588092 AATACCTTCT
588102 TAAAGTCCACGACTCAGTGGCCATCTCTTCTCAAAACCCACGAATCAGTGGCATTTTGTCC
1 TAAAGTCCACGACTCAGTGGCCATCTCTTCTCAAAACCCACGAATCAGTGGCATTTTGTCC
* * * * *
588163 TAAAGTCCACGACTCCGTGGCACCTTTTTCTTCTCAAAGCCCACGATTCAGTGGCATTTTGTCC
1 TAAAGTCCACGACTCAGTGG--CC-ATCTCTTCTCAAAACCCACGAATCAGTGGCATTTTGTCC
588227 TAAAGTCCAC
1 TAAAGTCCAC
588237 AATTTACTGG
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
61 19 0.29
63 2 0.03
64 45 0.68
ACGTcount: A:0.24, C:0.31, G:0.16, T:0.28
Consensus pattern (61 bp):
TAAAGTCCACGACTCAGTGGCCATCTCTTCTCAAAACCCACGAATCAGTGGCATTTTGTCC
Found at i:588267 original size:30 final size:29
Alignment explanation
Indices: 588197--588268 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 29
588187 TTTTTCTTCT
* *
588197 CAAAGCCCACGATTCAGTGGCATTTTGTC
1 CAAAGCCCACAATTCACTGGCATTTTGTC
* *
588226 CTAAAGTCCACAATTTACTGGCATCTCTT-TC
1 C-AAAGCCCACAATTCACTGGCAT-T-TTGTC
588257 CAAAGCCCACAA
1 CAAAGCCCACAA
588269 CTCCGTGGCA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
29 1 0.03
30 28 0.80
31 4 0.11
32 2 0.06
ACGTcount: A:0.29, C:0.31, G:0.14, T:0.26
Consensus pattern (29 bp):
CAAAGCCCACAATTCACTGGCATTTTGTC
Found at i:588409 original size:68 final size:68
Alignment explanation
Indices: 588259--588752 Score: 546
Period size: 68 Copynumber: 7.4 Consensus size: 68
588249 TCTCTTTCCA
* * * * * *
588259 AAGCCCACAACTCCGTGGCAC-CTTTTTCATTTCAAAGTCCACAACTCCATTGTACTC--TTT--
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTT-TAAGCCCACAACTCCGTGGCACTCTTTTTCC
*
588319 TT-A
65 TTCT
588322 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCT
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCT
588387 TCT
66 TCT
* * *
588390 AAGCCCACAACTCTGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCTGTGGCACTCTTTTTCCT
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCT
588455 TCT
66 TCT
* * *
588458 AAGTCCACAACTTCGTGGCAC-CTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTTT-AAGCCCACAACTCCGTGGCACTCTTTTTCC
588522 TTCT
65 TTCT
* * * * * * *
588526 AAGCCCATAACTACGTGGCACTCTTTTTCCTTCTGAGTCCACAACTCCATGGCAC-CTTTTTCTT
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCT
*
588590 TTT
66 TCT
* * * * *
588593 AAAGCCCACAACTCCGTGGCACTCTTTCTCCTTTTAAGTCCACGACTCTGTGGCAC-CTTCTT--
1 -AAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCC
*
588655 TTCA
65 TTCT
* * *
588659 AAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAAGGCCACAACTCTGTGGCAC-CTTGTTC
1 AAGCCCACAACTCCGTGGCACTCTTTTT-CCTTTT-AAGCCCACAACTCCGTGGCACTCTTTTTC
* *
588723 TTTTT
64 CTTCT
* *
588728 AAGTCCACAACTTCGTGGCA-TCTTT
1 AAGCCCACAACTCCGTGGCACTCTTT
588753 CACCCTTTCT
Statistics
Matches: 373, Mismatches: 45, Indels: 21
0.85 0.10 0.05
Matches are distributed among these distances:
63 40 0.11
64 10 0.03
65 30 0.08
66 8 0.02
67 46 0.12
68 209 0.56
69 30 0.08
ACGTcount: A:0.20, C:0.33, G:0.12, T:0.35
Consensus pattern (68 bp):
AAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCT
TCT
Found at i:588469 original size:102 final size:102
Alignment explanation
Indices: 588259--588752 Score: 573
Period size: 102 Copynumber: 4.9 Consensus size: 102
588249 TCTCTTTCCA
* * * * * *
588259 AAGCCCACAACTCCGTGGCACCTTTTTCATTTCAAAGTCCACAACTCCATTGTACTC--TTT--T
1 AAGCCCACAACTCCGTGGCACCTTTTTCCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCT
* * *
588320 T-AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTT
66 TCTAAGCCCACAACTCTGTGGCACTCTTTTTCCTTCT
* *
588356 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT-AAGCCCACAACTCTGTGGCACTCTTTTTCC
1 AAGCCCACAACTCCGTGGCAC-CTTTTTCCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
588420 TTCTAAGCCCACAACTCTGTGGCACTCTTTTTCCTTCT
65 TTCTAAGCCCACAACTCTGTGGCACTCTTTTTCCTTCT
* * *
588458 AAGTCCACAACTTCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCT
1 AAGCCCACAACTCCGTGGCACCTTTTTCCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCT
*
588523 TCTAAGCCCATAACTAC-GTGGCACTCTTTTTCCTTCT
66 TCTAAGCCCACAACT-CTGTGGCACTCTTTTTCCTTCT
* * * * *
588560 GAGTCCACAACTCCATGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTCTCCT
1 AAGCCCACAACTCCGTGGCACCTTTTTCCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCT
* * * * *
588625 TTTAAGTCCACGACTCTGTGGCAC-CTTCTT--TTCA
66 TCTAAGCCCACAACTCTGTGGCACTCTTTTTCCTTCT
* * *
588659 AAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAAGGCCACAACTCTGTGGCAC-CTTGTTC
1 AAGCCCACAACTCCGTGGCAC-CTTTTT-CCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTC
* * *
588723 TTTTTAAGTCCACAACT-TCGTGGCA-TCTTT
64 CTTCTAAGCCCACAACTCT-GTGGCACTCTTT
588753 CACCCTTTCT
Statistics
Matches: 346, Mismatches: 38, Indels: 23
0.85 0.09 0.06
Matches are distributed among these distances:
97 39 0.11
98 9 0.03
99 25 0.07
100 35 0.10
101 43 0.12
102 194 0.56
103 1 0.00
ACGTcount: A:0.20, C:0.33, G:0.12, T:0.35
Consensus pattern (102 bp):
AAGCCCACAACTCCGTGGCACCTTTTTCCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCT
TCTAAGCCCACAACTCTGTGGCACTCTTTTTCCTTCT
Found at i:588832 original size:32 final size:32
Alignment explanation
Indices: 588754--588898 Score: 168
Period size: 33 Copynumber: 4.5 Consensus size: 32
588744 GGCATCTTTC
* * * *
588754 ACCCTTTCTAAAGCCCACAAAAGTCAGTGGAAA
1 ACCCTCTCTAAAGCCCACACAAGTCGGTGG-CA
* *
588787 ACCTTCTCTAAAGCCCACACAAGTCGGTGCCA
1 ACCCTCTCTAAAGCCCACACAAGTCGGTGGCA
*
588819 ACCCTCTCTAAAGCCCACACAAGTTGGTGGCA
1 ACCCTCTCTAAAGCCCACACAAGTCGGTGGCA
* * *
588851 ACCATTCTCTAAAGCCCACGCAAGTTGGTGGCA
1 ACC-CTCTCTAAAGCCCACACAAGTCGGTGGCA
588884 ACCCT-TCT-AAGCCCA
1 ACCCTCTCTAAAGCCCA
588899 ATATAGCTGG
Statistics
Matches: 99, Mismatches: 12, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
30 7 0.07
31 3 0.03
32 34 0.34
33 55 0.56
ACGTcount: A:0.30, C:0.34, G:0.17, T:0.19
Consensus pattern (32 bp):
ACCCTCTCTAAAGCCCACACAAGTCGGTGGCA
Found at i:588835 original size:65 final size:64
Alignment explanation
Indices: 588754--588898 Score: 186
Period size: 65 Copynumber: 2.2 Consensus size: 64
588744 GGCATCTTTC
588754 ACCCTTTCTAAAGCCCACAAAAGTCAGTGGAAAACC-TTCTCTAAAGCCCACACAAGTCGGTGCC
1 ACCC-TTCTAAAGCCCACAAAAGTCAGTGG-AAACCATTCTCTAAAGCCCACACAAGTCGGTGCC
588818 A
64 A
* ** * * * *
588819 ACCCTCTCTAAAGCCCACACAAGTTGGTGGCAACCATTCTCTAAAGCCCACGCAAGTTGGTGGCA
1 ACCCT-TCTAAAGCCCACAAAAGTCAGTGGAAACCATTCTCTAAAGCCCACACAAGTCGGTGCCA
588884 ACCCTTCT-AAGCCCA
1 ACCCTTCTAAAGCCCA
588899 ATATAGCTGG
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
63 7 0.10
64 8 0.11
65 56 0.79
ACGTcount: A:0.30, C:0.34, G:0.17, T:0.19
Consensus pattern (64 bp):
ACCCTTCTAAAGCCCACAAAAGTCAGTGGAAACCATTCTCTAAAGCCCACACAAGTCGGTGCCA
Found at i:589195 original size:92 final size:92
Alignment explanation
Indices: 588886--590264 Score: 2332
Period size: 92 Copynumber: 15.0 Consensus size: 92
588876 TGGTGGCAAC
* * *
588886 CCTTCTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATG
1 CCTT-TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
588951 TAGCTGGCCTTGAATCAGCACATTGGCA
65 TAGCTGGCCTTGAATCAGCACATTGGCA
* *
588979 CCTTTAAGTCCAATATCGCTAGCCTTGAACCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
589044 AGCTGG-CTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
*
589070 CCTTTAAGTCCAATATCGCTCGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
* * *
589135 AGCTGGCCCTGAACCAGTACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
*
589162 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
*
589227 AGTTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
* *
589254 CCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
*
589319 AGATGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
* * **
589346 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGGATATTGGCATTTTCATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
589411 AGCTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
589438 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
589503 AGCTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
* *
589530 CCTTTAAGTCCAATATCGCTGACCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
589595 AGCTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
*
589622 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
589687 AGCTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
* * * * *
589714 CCTTTAAGTCCAATATAGTTGGCCTTGAATTAGCATATTGGCATCTTAATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
589779 AGCTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
*
589806 CCTTTAAGTCCAATATCGCTGGTCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
589871 AGCTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
*
589898 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCCTCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
589963 AGCTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
* *
589990 CCTTTAAGTCCATTATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTACA-TCCAATG
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTA-AGTCCAATG
*
590054 TAGCTGGCATTGAATCAGCACATTGGCA
65 TAGCTGGCCTTGAATCAGCACATTGGCA
* * * *
590082 CCTTTAAGTCCAATATAGTTGGCCCTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
590147 AGCTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
* * * *
590174 CCTTTAAGTCTAATATAGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAAGT-TA
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC--CTT-CATCTTT-AAGTCCA
590238 ATGTAGCTGGCCTTGAATCAGCACATT
62 ATGTAGCTGGCCTTGAATCAGCACATT
590265 AACATCCTTT
Statistics
Matches: 1218, Mismatches: 61, Indels: 12
0.94 0.05 0.01
Matches are distributed among these distances:
91 90 0.07
92 1083 0.89
93 5 0.00
94 2 0.00
95 34 0.03
96 4 0.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (92 bp):
CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
AGCTGGCCTTGAATCAGCACATTGGCA
Found at i:589533 original size:21 final size:20
Alignment explanation
Indices: 589509--589576 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 20
589499 ATGTAGCTGG
589509 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCA-ATTGGCA
* *
589530 CCTTTAAGTC--CAATATCGCTGA
1 CCTTGAA-TCAGCAAT-TGGC--A
589552 CCTTGAATCAGCATATTGGCA
1 CCTTGAATCAGCA-ATTGGCA
589573 CCTT
1 CCTT
589577 CTTCTTTAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 14
0.67 0.07 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.14
21 13 0.36
22 9 0.25
23 5 0.14
24 2 0.06
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.29
Consensus pattern (20 bp):
CCTTGAATCAGCAATTGGCA
Found at i:590036 original size:21 final size:21
Alignment explanation
Indices: 589969--590036 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 21
589959 ATGTAGCTGG
*
589969 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCATATTGGCA
* ** *
589990 CCTTTAAGTCCATTATAGCTGG--
1 CCTTGAA-T-CAGCATA-TTGGCA
590012 CCTTGAATCAGCATATTGGCA
1 CCTTGAATCAGCATATTGGCA
590033 CCTT
1 CCTT
590037 CATCTTTACA
Statistics
Matches: 33, Mismatches: 9, Indels: 10
0.63 0.17 0.19
Matches are distributed among these distances:
19 3 0.09
20 5 0.15
21 11 0.33
22 7 0.21
23 4 0.12
24 3 0.09
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (21 bp):
CCTTGAATCAGCATATTGGCA
Found at i:591006 original size:19 final size:19
Alignment explanation
Indices: 590967--591050 Score: 108
Period size: 19 Copynumber: 4.7 Consensus size: 19
590957 TTCAACTGAT
590967 TTGTATCGATACATAAAGTG
1 TTGTATCGATACAT-AAGTG
590987 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
591006 TTGTATCGATAC---A---
1 TTGTATCGATACATAAGTG
*
591019 TTGTATCGATACATAAGTT
1 TTGTATCGATACATAAGTG
591038 TTGTATCGATACA
1 TTGTATCGATACA
591051 ATTTAAGCTA
Statistics
Matches: 58, Mismatches: 0, Indels: 13
0.82 0.00 0.18
Matches are distributed among these distances:
13 12 0.21
16 2 0.03
19 30 0.52
20 14 0.24
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:591024 original size:13 final size:13
Alignment explanation
Indices: 591006--591032 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
590996 TACATAAGTG
591006 TTGTATCGATACA
1 TTGTATCGATACA
591019 TTGTATCGATACA
1 TTGTATCGATACA
591032 T
1 T
591033 AAGTTTTGTA
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:591028 original size:32 final size:32
Alignment explanation
Indices: 590987--591050 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
590977 ACATAAAGTG
590987 TTGTATCGATACATAAGTGTTGTATCGATACA
1 TTGTATCGATACATAAGTGTTGTATCGATACA
*
591019 TTGTATCGATACATAAGTTTTGTATCGATACA
1 TTGTATCGATACATAAGTGTTGTATCGATACA
591051 ATTTAAGCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.39
Consensus pattern (32 bp):
TTGTATCGATACATAAGTGTTGTATCGATACA
Found at i:591111 original size:13 final size:13
Alignment explanation
Indices: 591093--591117 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
591083 ATTACTCAAA
591093 TGTATCGATACAT
1 TGTATCGATACAT
591106 TGTATCGATACA
1 TGTATCGATACA
591118 CTGATCTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:591309 original size:52 final size:52
Alignment explanation
Indices: 591129--591307 Score: 288
Period size: 52 Copynumber: 3.4 Consensus size: 52
591119 TGATCTTTTT
* ***
591129 TATCGATACATGCAGGCAAATTTGCCCAGATTTATCGATACACTGAT-CTTTG
1 TATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACT-ATAAAATG
591181 TATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAATG
1 TATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAATG
*
591233 TATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATAAAATG
1 TATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAATG
*
591285 TATCGATACATGCTGGCAAATTT
1 TATCGATACATGCAGGCAAATTT
591308 TCATATTTCG
Statistics
Matches: 120, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
51 2 0.02
52 118 0.98
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.30
Consensus pattern (52 bp):
TATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAATG
Found at i:591720 original size:21 final size:21
Alignment explanation
Indices: 591673--591730 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
591663 AAAAATTATC
*
591673 CAAATGTATCGATACATTTGT
1 CAAATGTATCGATACATTTGA
**
591694 GGAATGTATCGATACATTCT-A
1 CAAATGTATCGATACATT-TGA
591715 CAAATGTATCGATACA
1 CAAATGTATCGATACA
591731 GGGTCCCAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 30 0.97
22 1 0.03
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (21 bp):
CAAATGTATCGATACATTTGA
Found at i:591859 original size:13 final size:13
Alignment explanation
Indices: 591841--591866 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
591831 CATTTTTCTG
591841 TGTATCGATACAT
1 TGTATCGATACAT
591854 TGTATCGATACAT
1 TGTATCGATACAT
591867 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:591863 original size:33 final size:33
Alignment explanation
Indices: 591821--591887 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
591811 GCCAAGGAAA
***
591821 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
591854 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
591887 T
1 T
591888 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:594364 original size:28 final size:28
Alignment explanation
Indices: 594331--594400 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 28
594321 TCACAATCGA
* **
594331 GGATACTCCAACCTCGTTATTTCATCGG
1 GGATACTCCAACCCCGTTATTTCAGAGG
* *
594359 GTATACTCCAACCCCGTTATTTCCGAGG
1 GGATACTCCAACCCCGTTATTTCAGAGG
594387 GGATACTCCAACCC
1 GGATACTCCAACCC
594401 AGACTTTATT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.23, C:0.33, G:0.17, T:0.27
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTATTTCAGAGG
Found at i:594448 original size:51 final size:50
Alignment explanation
Indices: 594385--594554 Score: 205
Period size: 52 Copynumber: 3.3 Consensus size: 50
594375 TTATTTCCGA
* ***
594385 GGGGATACTCCAACCCAGACTTTATTTTCAAAATATTGATTTTTCATAATC
1 GGGGATACTCCAACCC-GATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * *
594436 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATC
1 GGGGATACTCCAA-CCCGATTTTATTTTCAAAATACCAATTTTTC-ATAATC
*
594488 GGGGATACTCCAACACCGATTTTATTTTCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAAC-CCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
594540 GAGGATACTCCAACC
1 GGGGATACTCCAACC
594555 TCGTTATTTC
Statistics
Matches: 101, Mismatches: 14, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
51 36 0.36
52 51 0.50
53 14 0.14
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (50 bp):
GGGGATACTCCAACCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:594511 original size:52 final size:50
Alignment explanation
Indices: 594220--594554 Score: 203
Period size: 51 Copynumber: 6.4 Consensus size: 50
594210 AATTCTCCAC
* *
594220 AATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTAT
1 AATCGGGGATACTCCAAC-CCGATTTTATTTTCAAAACACCAATTTTCTAT
* *
594271 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAA-TTTCTTCAC
1 AATCGGGGATACTCCAAC-CCGATTTTATTTTC--AAAACACCAATTTTC-T-AT
* * ***** * * ***
594325 AATCGAGGATACTCCAACCTCGTTATTTCATCGGGTATACTCCAA-CCCCGT-T
1 AATCGGGGATACTCCAACC-CG--ATTTTATTTTCAAAACACCAATTTTC-TAT
* * * ***
594377 ATTTCCGAGGGGATACTCCAACCCAGACTTTATTTTCAAAATATTGATTTT-TCAT
1 A-AT-C--GGGGATACTCCAACCC-GATTTTATTTTCAAAACACCAATTTTCT-AT
* *
594432 AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTT
1 AATCGGGGATACTCCAA-CCCGATTTTATTTTCAAAACACCAATTTT-CTAT
* *
594484 AATCGGGGATACTCCAACACCGATTTTATTTTCAAAAATACCAATTTT-TCAC
1 AATCGGGGATACTCCAAC-CCGATTTTATTTTC-AAAACACCAATTTTCT-AT
*
594536 AATCGAGGATACTCCAACC
1 AATCGGGGATACTCCAACC
594555 TCGTTATTTC
Statistics
Matches: 214, Mismatches: 49, Indels: 42
0.70 0.16 0.14
Matches are distributed among these distances:
51 67 0.31
52 56 0.26
53 28 0.13
54 39 0.18
55 3 0.01
56 21 0.10
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (50 bp):
AATCGGGGATACTCCAACCCGATTTTATTTTCAAAACACCAATTTTCTAT
Found at i:594573 original size:28 final size:28
Alignment explanation
Indices: 594537--594618 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
594527 ATTTTTCACA
* *
594537 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
*
594565 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTATTTC
*
594593 --CGAGGGAACACTCCAACCCCGTTATT
1 ATCG-GGG-ATACTCCAACCCCGTTATT
594619 ATCTCCAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
26 2 0.04
27 3 0.06
28 42 0.89
ACGTcount: A:0.24, C:0.33, G:0.17, T:0.26
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATTTC
Found at i:594585 original size:211 final size:212
Alignment explanation
Indices: 594220--594611 Score: 653
Period size: 211 Copynumber: 1.9 Consensus size: 212
594210 AATTCTCCAC
* * *
594220 AATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATACTC
1 AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTC
*
594285 CAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCTCGTTA
66 CAACACCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCTCGTTA
* * * *
594350 TTTCATCGGGTATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCAGACTTTATTTTCA
131 TTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACCCAGACTTTATTTTCA
594415 AAATATTGATTTTTCAT
196 AAATATTGATTTTTCAT
* *
594432 AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATACT
1 AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTT-CTATAATCGGGGATACT
* *
594497 CCAACACCGATTTTATTTTC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCAACCTCGTT
65 CCAACACCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCTCGTT
594560 ATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACCC
130 ATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACCC
594612 CGTTATTATC
Statistics
Matches: 167, Mismatches: 12, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
211 77 0.46
212 56 0.34
213 34 0.20
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.32
Consensus pattern (212 bp):
AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTC
CAACACCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCTCGTTA
TTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACCCAGACTTTATTTTCA
AAATATTGATTTTTCAT
Found at i:601095 original size:13 final size:13
Alignment explanation
Indices: 601077--601113 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
601067 ACAATGTTCT
601077 TTGTATCGATACA
1 TTGTATCGATACA
601090 TTGTATCGATACA
1 TTGTATCGATACA
*
601103 ATGTATCGATA
1 TTGTATCGATA
601114 TATGGGTTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:603747 original size:21 final size:21
Alignment explanation
Indices: 603707--603747 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
603697 TTAAGTATAA
*
603707 ATATTTTTCAAGCAATAAATC
1 ATATTTTTCAAGCAAAAAATC
603728 ATATGTTTTCAAG-AAAAAAT
1 ATAT-TTTTCAAGCAAAAAAT
603748 AATCCAGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.37
Consensus pattern (21 bp):
ATATTTTTCAAGCAAAAAATC
Found at i:606924 original size:13 final size:13
Alignment explanation
Indices: 606906--606989 Score: 51
Period size: 13 Copynumber: 5.5 Consensus size: 13
606896 AGCTTCGTAG
606906 CGATACATTGTAT
1 CGATACATTGTAT
606919 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
606938 CGATACATTGTAT
1 CGATACATTGTAT
*
606951 CGATACAACACTGATGCAT
1 CGAT---ACA-T--TGTAT
606970 CGATACATTGTAT
1 CGATACATTGTAT
606983 CGATACA
1 CGATACA
606990 AATTGTTGAA
Statistics
Matches: 57, Mismatches: 2, Indels: 24
0.69 0.02 0.29
Matches are distributed among these distances:
13 25 0.44
15 3 0.05
16 8 0.14
17 3 0.05
19 18 0.32
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:606947 original size:32 final size:32
Alignment explanation
Indices: 606906--606991 Score: 145
Period size: 32 Copynumber: 2.7 Consensus size: 32
606896 AGCTTCGTAG
* *
606906 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTGATGCAT
*
606938 CGATACATTGTATCGATACAACACTGATGCAT
1 CGATACATTGTATCGATACAAAACTGATGCAT
606970 CGATACATTGTATCGATACAAA
1 CGATACATTGTATCGATACAAA
606992 TTGTTGAAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTGATGCAT
Found at i:608859 original size:13 final size:13
Alignment explanation
Indices: 608838--608867 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
608828 ACTTTTCACT
608838 ATGTATCGATACA
1 ATGTATCGATACA
*
608851 ATGTTTCGATACA
1 ATGTATCGATACA
608864 ATGT
1 ATGT
608868 CCCATGTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:608936 original size:20 final size:20
Alignment explanation
Indices: 608911--608948 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
608901 TATTGCTAGA
608911 TTCATGTATCGATACAATTC
1 TTCATGTATCGATACAATTC
*
608931 TTCATGTATTGATACAAT
1 TTCATGTATCGATACAAT
608949 GAATATGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.42
Consensus pattern (20 bp):
TTCATGTATCGATACAATTC
Found at i:615699 original size:20 final size:20
Alignment explanation
Indices: 615674--615713 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
615664 ATTTATCAAA
*
615674 ACCAAGATCTCAAATTCTCT
1 ACCAAGATCTCAAATCCTCT
615694 ACCAAGATCTCAAATCCTCT
1 ACCAAGATCTCAAATCCTCT
615714 CAACTTTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.33, G:0.05, T:0.28
Consensus pattern (20 bp):
ACCAAGATCTCAAATCCTCT
Found at i:619495 original size:8 final size:8
Alignment explanation
Indices: 619482--619508 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
619472 ATTGGATTCA
619482 AATGTAAT
1 AATGTAAT
619490 AATGTAAT
1 AATGTAAT
619498 AATGTAAT
1 AATGTAAT
619506 AAT
1 AAT
619509 TTGAATTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (8 bp):
AATGTAAT
Found at i:619811 original size:20 final size:20
Alignment explanation
Indices: 619783--619822 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
619773 AAACTAAAAA
*
619783 AATCAAATCAAGTGACGTTT
1 AATCAAATCAAGTGAAGTTT
*
619803 AATCGAATCAAGTGAAGTTT
1 AATCAAATCAAGTGAAGTTT
619823 GTCCCCATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.30
Consensus pattern (20 bp):
AATCAAATCAAGTGAAGTTT
Found at i:621051 original size:13 final size:13
Alignment explanation
Indices: 621033--621058 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
621023 CAATTTTTTG
621033 TGTATCGATACAT
1 TGTATCGATACAT
621046 TGTATCGATACAT
1 TGTATCGATACAT
621059 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:623456 original size:21 final size:21
Alignment explanation
Indices: 623432--623478 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
623422 TTTAATGCTG
623432 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
623452 -TATTTGAAGTGAAAAACAAGT
1 AT-TTTGAAGTGAAAAACAAGT
623473 ATTTTG
1 ATTTTG
623479 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 9 0.39
22 9 0.39
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:623617 original size:13 final size:13
Alignment explanation
Indices: 623599--623637 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
623589 ATAATCACCC
*
623599 TGTATCGATACAG
1 TGTATCGATACAA
623612 TGTATCGATACAA
1 TGTATCGATACAA
623625 TGTATCGATACAA
1 TGTATCGATACAA
623638 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:623648 original size:20 final size:20
Alignment explanation
Indices: 623623--623701 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
623613 GTATCGATAC
623623 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
623643 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
623668 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
623688 CATGTATCGATACA
1 AATGTATCGATACA
623702 TTTTGGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:625736 original size:15 final size:15
Alignment explanation
Indices: 625716--625746 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
625706 ATTTCGTTTG
*
625716 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
625731 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
625746 G
1 G
625747 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:627579 original size:21 final size:21
Alignment explanation
Indices: 627550--627594 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
627540 AAGTTTTCAT
*
627550 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
627570 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
627592 TTT
1 TTT
627595 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:629830 original size:13 final size:13
Alignment explanation
Indices: 629812--629837 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
629802 CAATTTTTTG
629812 TGTATCGATACAT
1 TGTATCGATACAT
629825 TGTATCGATACAT
1 TGTATCGATACAT
629838 ACTTGCTGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:630301 original size:16 final size:16
Alignment explanation
Indices: 630280--630310 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
630270 AATGCTTTAG
630280 CTCAATCTGCCATGTA
1 CTCAATCTGCCATGTA
*
630296 CTCAATTTGCCATGT
1 CTCAATCTGCCATGT
630311 GCTTCTCTAT
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:0.23, C:0.29, G:0.13, T:0.35
Consensus pattern (16 bp):
CTCAATCTGCCATGTA
Found at i:633941 original size:13 final size:13
Alignment explanation
Indices: 633923--633948 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
633913 ATATAATGCT
633923 TTGTATCGATACA
1 TTGTATCGATACA
633936 TTGTATCGATACA
1 TTGTATCGATACA
633949 CGTTCATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:633958 original size:19 final size:20
Alignment explanation
Indices: 633934--633987 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 20
633924 TGTATCGATA
*
633934 CATTGTATCGATACACG-TT
1 CATTGTATCGATACACGCAT
* *
633953 CATTGTATAGATACATGCAT
1 CATTGTATCGATACACGCAT
*
633973 AATTGTATCGATACA
1 CATTGTATCGATACA
633988 TGAAACTGGC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (20 bp):
CATTGTATCGATACACGCAT
Done.