Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005692.1 Hibiscus syriacus cultivar Beakdansim tig00013313_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 77519
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.33
Found at i:11510 original size:54 final size:54
Alignment explanation
Indices: 11435--12142 Score: 467
Period size: 54 Copynumber: 13.1 Consensus size: 54
11425 AATGCACCCG
* * * * * * *
11435 TAGTGCCCATACGGTCATTCATAAACAAATTATGAATTTCATGGTTTACACACA
1 TAGTGCCAAAACGGTTATTCATCAACATATGATGAATTTCATGATTTACACACA
* * * * * *
11489 TAGTGTCGAAATGGTTATTCATCAACATATGATGAATTTCGTGATTTGCACACT
1 TAGTGCCAAAACGGTTATTCATCAACATATGATGAATTTCATGATTTACACACA
* * * * **
11543 TAGTGCCAAAACGGTTATTCATCAACATATGATGAATTCCGTGATTTGCGCATT
1 TAGTGCCAAAACGGTTATTCATCAACATATGATGAATTTCATGATTTACACACA
* * * * * *** *
11597 TAGTTCCGAAATGGTTATTCATCACCATATGATGAA-TTCTGTGATTTATGTACT
1 TAGTGCCAAAACGGTTATTCATCAACATATGATGAATTTC-ATGATTTACACACA
** * * * *
11651 TAGTGCTGAAATGGTTATTCATCACCATATGATGAA-TTCTGTGATTTGCACA-A
1 TAGTGCCAAAACGGTTATTCATCAACATATGATGAATTTC-ATGATTTACACACA
* * * * ** * *
11704 TTAGTGTCGAAACAGTTATTCATCACCATATGATGAATTTTGTGATTTGCACACT
1 -TAGTGCCAAAACGGTTATTCATCAACATATGATGAATTTCATGATTTACACACA
* * * * * * **
11759 TAGTACCGAAACTGTTATTCATCATCATATGATGAATTACATGATTTGCACATT
1 TAGTGCCAAAACGGTTATTCATCAACATATGATGAATTTCATGATTTACACACA
* * * * * **
11813 TAGTGTCGAAACGGTTATTCATCACCATATAATGAA-TTCTGTGATTTGTACAC-
1 TAGTGCCAAAACGGTTATTCATCAACATATGATGAATTTC-ATGATTTACACACA
* * * * * * * * *
11866 TTGTGTCGAAACAGTTATTCATCACCATATGATTAATTCCGTGATTTGCACACA
1 TAGTGCCAAAACGGTTATTCATCAACATATGATGAATTTCATGATTTACACACA
** ** * * * *
11920 TAGTGCTGAAATAGTTATTCATCACCATATGATGAATTCCGTGATTTACACACT
1 TAGTGCCAAAACGGTTATTCATCAACATATGATGAATTTCATGATTTACACACA
* * * * * * * *
11974 TATTACCGAAACGGTTATTCATCAACACATGATGAATTAT-GTGATTTGCAAACT
1 TAGTGCCAAAACGGTTATTCATCAACATATGATGAATT-TCATGATTTACACACA
* * * ** *
12028 TAGTGTCGAAACGGTTATTCATCAACATATGATGAATTAT-GTGATTTGTACACT
1 TAGTGCCAAAACGGTTATTCATCAACATATGATGAATT-TCATGATTTACACACA
* * * * * *
12082 TAGTACCGAAACAGTTATTCATCAACATATGATGAATTTTATGATTTGCACACT
1 TAGTGCCAAAACGGTTATTCATCAACATATGATGAATTTCATGATTTACACACA
12136 TAGTGCC
1 TAGTGCC
12143 TATTTGGTAA
Statistics
Matches: 553, Mismatches: 92, Indels: 18
0.83 0.14 0.03
Matches are distributed among these distances:
53 49 0.09
54 502 0.91
55 2 0.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (54 bp):
TAGTGCCAAAACGGTTATTCATCAACATATGATGAATTTCATGATTTACACACA
Found at i:11616 original size:108 final size:108
Alignment explanation
Indices: 11445--12140 Score: 801
Period size: 108 Copynumber: 6.5 Consensus size: 108
11435 TAGTGCCCAT
* * * * * * * * * *
11445 ACGGTCATTCATAAACAAATTATGAATTTCATGGTTTACACACATAGTGTCGAAATGGTTATTCA
1 ACGGTTATTCATCAACATATGATGAATTCCGTGATTTGCACACTTAGTGTCGAAACGGTTATTCA
* * *
11510 TCAACATATGATGAATTTCGTGATTTGCACACTTAGTGCCAAA
66 TCACCATATGATGAATTTCGTGATTTGCACACTTAGTACCGAA
* * *
11553 ACGGTTATTCATCAACATATGATGAATTCCGTGATTTGCGCATTTAGT-TCCGAAATGGTTATTC
1 ACGGTTATTCATCAACATATGATGAATTCCGTGATTTGCACACTTAGTGT-CGAAACGGTTATTC
**** * *
11617 ATCACCATATGATGAA-TTCTGTGATTTATGTACTTAGTGCTGAA
65 ATCACCATATGATGAATTTC-GTGATTTGCACACTTAGTACCGAA
* * * * *
11661 ATGGTTATTCATCACCATATGATGAATTCTGTGATTTGCACAATTAGTGTCGAAACAGTTATTCA
1 ACGGTTATTCATCAACATATGATGAATTCCGTGATTTGCACACTTAGTGTCGAAACGGTTATTCA
*
11726 TCACCATATGATGAATTTTGTGATTTGCACACTTAGTACCGAA
66 TCACCATATGATGAATTTCGTGATTTGCACACTTAGTACCGAA
* * * * *
11769 ACTGTTATTCATCATCATATGATGAATTACATGATTTGCACATTTAGTGTCGAAACGGTTATTCA
1 ACGGTTATTCATCAACATATGATGAATTCCGTGATTTGCACACTTAGTGTCGAAACGGTTATTCA
* * **
11834 TCACCATATAATGAA-TTCTGTGATTTGTACACTT-GTGTCGAA
66 TCACCATATGATGAATTTC-GTGATTTGCACACTTAGTACCGAA
* * * * **
11876 ACAGTTATTCATCACCATATGATTAATTCCGTGATTTGCACACATAGTG-CTGAAATAGTTATTC
1 ACGGTTATTCATCAACATATGATGAATTCCGTGATTTGCACACTTAGTGTC-GAAACGGTTATTC
* * *
11940 ATCACCATATGATGAATTCCGTGATTTACACACTTATTACCGAA
65 ATCACCATATGATGAATTTCGTGATTTGCACACTTAGTACCGAA
* ** *
11984 ACGGTTATTCATCAACACATGATGAATTATGTGATTTGCAAACTTAGTGTCGAAACGGTTATTCA
1 ACGGTTATTCATCAACATATGATGAATTCCGTGATTTGCACACTTAGTGTCGAAACGGTTATTCA
* *
12049 TCAACATATGATGAATTAT-GTGATTTGTACACTTAGTACCGAA
66 TCACCATATGATGAATT-TCGTGATTTGCACACTTAGTACCGAA
* ***
12092 ACAGTTATTCATCAACATATGATGAATTTTATGATTTGCACACTTAGTG
1 ACGGTTATTCATCAACATATGATGAATTCCGTGATTTGCACACTTAGTG
12141 CCTATTTGGT
Statistics
Matches: 497, Mismatches: 81, Indels: 20
0.83 0.14 0.03
Matches are distributed among these distances:
106 1 0.00
107 93 0.19
108 399 0.80
109 4 0.01
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (108 bp):
ACGGTTATTCATCAACATATGATGAATTCCGTGATTTGCACACTTAGTGTCGAAACGGTTATTCA
TCACCATATGATGAATTTCGTGATTTGCACACTTAGTACCGAA
Found at i:12136 original size:162 final size:162
Alignment explanation
Indices: 11466--12142 Score: 829
Period size: 162 Copynumber: 4.2 Consensus size: 162
11456 TAAACAAATT
* * * * *
11466 ATGAATTTCATGGTTTACACACATAGTGTCGAAATGGTTATTCATCAACATATGATGAATT-TCG
1 ATGAATTCCATGATTTACACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCT-G
* * * * *
11530 TGATTTGCACACTTAGTGCCAAAACGGTTATTCATCAACATATGATGAATTCCGTGATTTGCGCA
65 TGATTTGCAAACTTAGTGTCGAAACAGTTATTCATCAACATATGATGAATTCCGTGATTTGCACA
* * **
11595 TTTAGTTCCGAAATGGTTATTCATCACCATATG
130 CTTAGTACCGAAACAGTTATTCATCACCATATG
** *** * * *
11628 ATGAATTCTGTGATTTATGTACTTAGTGCTGAAATGGTTATTCATCACCATATGATGAATTCTGT
1 ATGAATTCCATGATTTACACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCTGT
* **
11693 GATTTGCACAA-TTAGTGTCGAAACAGTTATTCATCACCATATGATGAATTTTGTGATTTGCACA
66 GATTTGCA-AACTTAGTGTCGAAACAGTTATTCATCAACATATGATGAATTCCGTGATTTGCACA
* *
11757 CTTAGTACCGAAACTGTTATTCATCATCATATG
130 CTTAGTACCGAAACAGTTATTCATCACCATATG
* * * * * *
11790 ATGAATTACATGATTTGCACATTTAGTGTCGAAACGGTTATTCATCACCATATAATGAATTCTGT
1 ATGAATTCCATGATTTACACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCTGT
* * * *
11855 GATTTGTACACTT-GTGTCGAAACAGTTATTCATCACCATATGATTAATTCCGTGATTTGCACAC
66 GATTTGCAAACTTAGTGTCGAAACAGTTATTCATCAACATATGATGAATTCCGTGATTTGCACAC
* * * *
11919 ATAGTGCTGAAATAGTTATTCATCACCATATG
131 TTAGTACCGAAACAGTTATTCATCACCATATG
* * * * *
11951 ATGAATTCCGTGATTTACACACTTATTACCGAAACGGTTATTCATCAACACATGATGAATTATGT
1 ATGAATTCCATGATTTACACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCTGT
* ** *
12016 GATTTGCAAACTTAGTGTCGAAACGGTTATTCATCAACATATGATGAATTATGTGATTTGTACAC
66 GATTTGCAAACTTAGTGTCGAAACAGTTATTCATCAACATATGATGAATTCCGTGATTTGCACAC
*
12081 TTAGTACCGAAACAGTTATTCATCAACATATG
131 TTAGTACCGAAACAGTTATTCATCACCATATG
** *
12113 ATGAATTTTATGATTTGCACACTTAGTGCC
1 ATGAATTCCATGATTTACACACTTAGTGCC
12143 TATTTGGTAA
Statistics
Matches: 434, Mismatches: 77, Indels: 8
0.84 0.15 0.02
Matches are distributed among these distances:
161 140 0.32
162 292 0.67
163 2 0.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (162 bp):
ATGAATTCCATGATTTACACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCTGT
GATTTGCAAACTTAGTGTCGAAACAGTTATTCATCAACATATGATGAATTCCGTGATTTGCACAC
TTAGTACCGAAACAGTTATTCATCACCATATG
Found at i:12447 original size:20 final size:21
Alignment explanation
Indices: 12408--12460 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
12398 TCTGTGATCA
*
12408 ATAGTATTGATA-TCATCCTC
1 ATAGTATTGATACTCACCCTC
12428 ATAGTATTGATACTC-CCCTC
1 ATAGTATTGATACTCACCCTC
* *
12448 TTGGTATTGATAC
1 ATAGTATTGATAC
12461 CACTTGAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 27 0.93
21 2 0.07
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (21 bp):
ATAGTATTGATACTCACCCTC
Found at i:15575 original size:10 final size:10
Alignment explanation
Indices: 15550--15583 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
15540 ATATGATATG
15550 TTTATTATTA
1 TTTATTATTA
15560 -TTATTATTA
1 TTTATTATTA
15569 TTTATTATTA
1 TTTATTATTA
*
15579 ATTAT
1 TTTAT
15584 GCATAACTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.41
10 13 0.59
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTATTATTA
Found at i:17882 original size:18 final size:17
Alignment explanation
Indices: 17859--17892 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
17849 GGGAAATCAA
17859 TTTAAATTTTAGTAATAC
1 TTTAAATTTTAG-AATAC
17877 TTTAAATTTTAGAATA
1 TTTAAATTTTAGAATA
17893 TGTGCTTGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (17 bp):
TTTAAATTTTAGAATAC
Found at i:18903 original size:20 final size:20
Alignment explanation
Indices: 18875--18923 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
18865 ATTGAGATAA
18875 GGATCGATCCATTAGAGGAG
1 GGATCGATCCATTAGAGGAG
* * *
18895 GGATTGATCCTTTAGGGGAG
1 GGATCGATCCATTAGAGGAG
18915 GGATCGATC
1 GGATCGATC
18924 ATTTGCATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.24, C:0.14, G:0.37, T:0.24
Consensus pattern (20 bp):
GGATCGATCCATTAGAGGAG
Found at i:21293 original size:24 final size:23
Alignment explanation
Indices: 21244--21292 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
21234 TGGTGGTTGG
*
21244 TTTAATGGATGTTTAGACTTTAT
1 TTTAATGGATATTTAGACTTTAT
*
21267 TTTAATGGTATATTTA-AGTTTAT
1 TTTAATGG-ATATTTAGACTTTAT
21290 TTT
1 TTT
21293 TGGTTCTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.27, C:0.02, G:0.14, T:0.57
Consensus pattern (23 bp):
TTTAATGGATATTTAGACTTTAT
Found at i:39845 original size:3 final size:3
Alignment explanation
Indices: 39837--39954 Score: 204
Period size: 3 Copynumber: 39.7 Consensus size: 3
39827 TATGATTTGT
39837 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
39885 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
39933 TTA -TA TT- TTA TTT TGTA TTA TT
1 TTA TTA TTA TTA TTA T-TA TTA TT
39955 GATTTGCCTC
Statistics
Matches: 110, Mismatches: 2, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
2 4 0.04
3 104 0.95
4 2 0.02
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:42753 original size:126 final size:126
Alignment explanation
Indices: 42596--42836 Score: 304
Period size: 126 Copynumber: 1.9 Consensus size: 126
42586 TTCATAAAAG
* * * * * * *
42596 AAAATATATGAATTAGCATATACTTACATTGGTTTGAGTATGTGCGTCTCTCAATATCTTGGTAC
1 AAAATATATCAATTAACATATACTTACATTGGTGTAAGTATGTGCATCTCCCAATATCTTAGTAC
* * * * *
42661 CTAAAAATATATACATAATTATATTGGTGTGAGTATGTT-TCTATATTTTCTAAAAATTAAT
66 CTAAAAATAAACACATAATTATATTGGTATAACTATGTTCT-TATATTTTCTAAAAATTAAT
* * * *
42722 AAAATGTATCAATTAACATGTACTTATATTGGTGTAAGTATGTGCATCTCCCAATATCTTAGTGC
1 AAAATATATCAATTAACATATACTTACATTGGTGTAAGTATGTGCATCTCCCAATATCTTAGTAC
* *
42787 TTAAAAATAAACATATAATTATATTGGTATAACTATGTTCTTATATTTTC
66 CTAAAAATAAACACATAATTATATTGGTATAACTATGTTCTTATATTTTC
42837 ATATAAATAA
Statistics
Matches: 96, Mismatches: 18, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
126 95 0.99
127 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.41
Consensus pattern (126 bp):
AAAATATATCAATTAACATATACTTACATTGGTGTAAGTATGTGCATCTCCCAATATCTTAGTAC
CTAAAAATAAACACATAATTATATTGGTATAACTATGTTCTTATATTTTCTAAAAATTAAT
Found at i:42862 original size:126 final size:126
Alignment explanation
Indices: 42596--42875 Score: 298
Period size: 126 Copynumber: 2.2 Consensus size: 126
42586 TTCATAAAAG
* * * * * * * *
42596 AAAATATATGAATTAGCATATACTTACATTGGTTTGAGTATGTGCGTCTCTCAATATCTTGGTAC
1 AAAATGTATAAATTAACATATACTTACATTGGTGTAAGTATGTGCATCTCCCAATATCTTAGTAC
* * * * *
42661 CTAAAAATATATACATAATTATATTGGTGTGAGTATGTTTCTATATTTTCTAAAAATTAAT
66 CTAAAAATAAACACATAATTATATTGGTATAACTATGTTTCTATATTTTCTAAAAATTAAT
* * * *
42722 AAAATGTATCAATTAACATGTACTTATATTGGTGTAAGTATGTGCATCTCCCAATATCTTAGTGC
1 AAAATGTATAAATTAACATATACTTACATTGGTGTAAGTATGTGCATCTCCCAATATCTTAGTAC
* * *
42787 TTAAAAATAAACATATAATTATATTGGTATAACTATG-TTCTTATATTTTCATATAAA-TAA-
66 CTAAAAATAAACACATAATTATATTGGTATAACTATGTTTC-TATATTTTC-TAAAAATTAAT
* *
42847 AAAAGTGT-TGAAATTAATACATACTTACA
1 AAAA-TGTAT-AAATTAACATATACTTACA
42876 CGGGTAACTA
Statistics
Matches: 126, Mismatches: 24, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
125 8 0.06
126 113 0.90
127 5 0.04
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.40
Consensus pattern (126 bp):
AAAATGTATAAATTAACATATACTTACATTGGTGTAAGTATGTGCATCTCCCAATATCTTAGTAC
CTAAAAATAAACACATAATTATATTGGTATAACTATGTTTCTATATTTTCTAAAAATTAAT
Found at i:43256 original size:3 final size:3
Alignment explanation
Indices: 43248--43341 Score: 188
Period size: 3 Copynumber: 31.3 Consensus size: 3
43238 AGGACACACA
43248 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
43296 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
43342 GAAAAATAAC
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 91 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:43534 original size:2 final size:2
Alignment explanation
Indices: 43527--43580 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
43517 GCCGGGAAGC
43527 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
43569 AT AT AT AT AT AT
1 AT AT AT AT AT AT
43581 CCATTTTAAC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52772 original size:2 final size:2
Alignment explanation
Indices: 52765--52806 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
52755 TTATGAAATA
52765 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52807 GTGAATCAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54106 original size:37 final size:35
Alignment explanation
Indices: 53962--54103 Score: 119
Period size: 36 Copynumber: 3.9 Consensus size: 35
53952 AGGAAAAAGT
* *
53962 GTTTCAAGAGAAACACAT-TCAAATGAGATAAAATTC-
1 GTTTTAAGA-AAACA-ATCTCAAGTGAGATAAAA-TCA
* *
53998 GTTTTAAGGAAAACAATGTCAAGTGAGATAGAA-CA
1 GTTTTAA-GAAAACAATCTCAAGTGAGATAAAATCA
* * * *
54033 TGTTATAAGAAAAAATTATCTAAACTGAGATAAAATCA
1 -GTTTTAAGAAAACA--ATCTCAAGTGAGATAAAATCA
54071 GTTTTAAGAAATACAATCTCAAGTGAGATAAAA
1 GTTTTAAGAAA-ACAATCTCAAGTGAGATAAAA
54104 ATCTAAGTGA
Statistics
Matches: 85, Mismatches: 13, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
34 1 0.01
35 8 0.09
36 46 0.54
37 26 0.31
38 4 0.05
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.26
Consensus pattern (35 bp):
GTTTTAAGAAAACAATCTCAAGTGAGATAAAATCA
Found at i:56083 original size:36 final size:37
Alignment explanation
Indices: 56043--56190 Score: 151
Period size: 36 Copynumber: 4.1 Consensus size: 37
56033 TGAGAGAAGG
* * *
56043 AAAATTTGTTTCAAGAG-AAACACTTTCAAATGAGAT
1 AAAATTTGTTTTAAGAGAAAACAATCTCAAATGAGAT
*
56079 AAAATTTGTTTTAAG-GAAAACAATCTCAAGTGAGAT
1 AAAATTTGTTTTAAGAGAAAACAATCTCAAATGAGAT
* * ** *
56115 AGAATATGTTTTAAGA-AAAATGATCTAAAATGAGAT
1 AAAATTTGTTTTAAGAGAAAACAATCTCAAATGAGAT
* * * *
56151 GAAATTAGTTTTAATA-AAAACAATCTCAAGTGAGAT
1 AAAATTTGTTTTAAGAGAAAACAATCTCAAATGAGAT
56187 AAAA
1 AAAA
56191 ATCTGAGTGA
Statistics
Matches: 90, Mismatches: 20, Indels: 4
0.79 0.18 0.04
Matches are distributed among these distances:
35 1 0.01
36 89 0.99
ACGTcount: A:0.48, C:0.07, G:0.15, T:0.30
Consensus pattern (37 bp):
AAAATTTGTTTTAAGAGAAAACAATCTCAAATGAGAT
Found at i:56460 original size:97 final size:97
Alignment explanation
Indices: 56351--56585 Score: 323
Period size: 97 Copynumber: 2.4 Consensus size: 97
56341 GTTGATCCAA
*
56351 CTCAAGTTAGATAAAAATCTGAGTGAAATGATAATGAAGTTTAGATTTCAAGGGAAACTGTCTCA
1 CTCAAGTGAGATAAAAATCTGAGTGAAATGATAATGAAGTTTAGATTTCAAGGGAAACTGTCTCA
56416 AGTGAGACAAAATCAGTTTTAAGAAAGAA-AAT
66 AGTGAGACAAAATCAGTTTTAAGAAA-AACAAT
* * * * * * *
56448 CTCAAGTGAGATAAATATCCGAGTGAAATGATATTGAATTTTGGATTTCAATGGAAACTTTCTCA
1 CTCAAGTGAGATAAAAATCTGAGTGAAATGATAATGAAGTTTAGATTTCAAGGGAAACTGTCTCA
**
56513 AGTGAGACAAAATTTGTTTTAAGAAAAACAAT
66 AGTGAGACAAAATCAGTTTTAAGAAAAACAAT
* *
56545 CTCAAGTGAGAT-AAAATCTTGAGTAAAATGATTATG-AGTTT
1 CTCAAGTGAGATAAAAATC-TGAGTGAAATGATAATGAAGTTT
56586 TAGGGAAACT
Statistics
Matches: 120, Mismatches: 16, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
96 11 0.09
97 109 0.91
ACGTcount: A:0.42, C:0.09, G:0.19, T:0.30
Consensus pattern (97 bp):
CTCAAGTGAGATAAAAATCTGAGTGAAATGATAATGAAGTTTAGATTTCAAGGGAAACTGTCTCA
AGTGAGACAAAATCAGTTTTAAGAAAAACAAT
Found at i:57048 original size:18 final size:18
Alignment explanation
Indices: 57023--57067 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
57013 CTTCTCTAAA
57023 GCTTGACTTCTCATTTAT
1 GCTTGACTTCTCATTTAT
*
57041 GTTTGACTTCTCATTTAT
1 GCTTGACTTCTCATTTAT
57059 GCTTGACTT
1 GCTTGACTT
57068 TTCGAATATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.16, C:0.20, G:0.13, T:0.51
Consensus pattern (18 bp):
GCTTGACTTCTCATTTAT
Found at i:62166 original size:18 final size:19
Alignment explanation
Indices: 62133--62172 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
62123 ACACGTAACA
*
62133 AGATAAAAGGAAATCAGGTT
1 AGATAAAA-GAAATCAAGTT
62153 AGATAAAA-AAATCAAGTT
1 AGATAAAAGAAATCAAGTT
62171 AG
1 AG
62173 TAAGAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
20 8 0.42
ACGTcount: A:0.55, C:0.05, G:0.20, T:0.20
Consensus pattern (19 bp):
AGATAAAAGAAATCAAGTT
Found at i:63242 original size:96 final size:94
Alignment explanation
Indices: 63125--63325 Score: 231
Period size: 94 Copynumber: 2.1 Consensus size: 94
63115 CCGTTGATGC
* * * * * * * * *
63125 AGTATCGATACCATTGTAAGGGTATTGATACCCTGCAAACATCGAATCTAATTTTGGTATCGATA
1 AGTATCGATACCATGGAAAGGGTATCGAT-CCAT-AAAACAACAAAGCTAATTTCGGTATCGATA
** * *
63190 CCTTAAGGGGGTATCGGTACCATAGTATAGT
64 CCAGAAGGGGGTATCAGTACCATAGTATAGA
* * *
63221 AGTATCGATACCGTGGAAAGGGTATCGATCCATAAAACAACAAAGCTAATTTCGGTATCGTTATC
1 AGTATCGATACCATGGAAAGGGTATCGATCCATAAAACAACAAAGCTAATTTCGGTATCGATACC
*
63286 AGAAGGGGGTATCAGTGCCATAGTATAGA
66 AGAAGGGGGTATCAGTACCATAGTATAGA
63315 AGTATCGATAC
1 AGTATCGATAC
63326 TAGGATAGAA
Statistics
Matches: 88, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
94 60 0.68
95 3 0.03
96 25 0.28
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (94 bp):
AGTATCGATACCATGGAAAGGGTATCGATCCATAAAACAACAAAGCTAATTTCGGTATCGATACC
AGAAGGGGGTATCAGTACCATAGTATAGA
Found at i:63335 original size:20 final size:20
Alignment explanation
Indices: 63310--63347 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
63300 GTGCCATAGT
*
63310 ATAGAAGTATCGATACTAGG
1 ATAGAAGTACCGATACTAGG
63330 ATAGAAGTACCGATACTA
1 ATAGAAGTACCGATACTA
63348 TGGAGCCTGG
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:0.42, C:0.13, G:0.21, T:0.24
Consensus pattern (20 bp):
ATAGAAGTACCGATACTAGG
Found at i:63783 original size:47 final size:47
Alignment explanation
Indices: 63729--64014 Score: 421
Period size: 47 Copynumber: 6.1 Consensus size: 47
63719 AAATCAAATT
* * *
63729 CATAATTGAAAATACATGAAAGGATGCACTAAGGCATGAATGGATGC
1 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* *
63776 CATAATTGAAAATGCATGAAATGATGCATTAAGGCATGAATGGATGC
1 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* * *
63823 CATAATTAAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGT
1 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* * *
63870 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAACGAATTC
1 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
* *
63917 CATAATTGAAAATGCATGAAAGGAAGCATTAAGACATGAACA-GATGC
1 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAA-AGGATGC
*
63964 CATAATTGAAAATGCATGAAAAGGATTCATTAAGGCATGAAAGGATGC
1 CATAATTGAAAATGCATG-AAAGGATGCATTAAGGCATGAAAGGATGC
64012 CAT
1 CAT
64015 GTTTATTAAA
Statistics
Matches: 216, Mismatches: 20, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
47 189 0.88
48 27 0.12
ACGTcount: A:0.43, C:0.12, G:0.22, T:0.23
Consensus pattern (47 bp):
CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
Found at i:63801 original size:27 final size:26
Alignment explanation
Indices: 63762--63896 Score: 82
Period size: 27 Copynumber: 5.5 Consensus size: 26
63752 ATGCACTAAG
63762 GCATGAATGGATGCCATAATTGAAAAT
1 GCATGAATGGATGCCATAATT-AAAAT
*
63789 GCATGAAAT-GATG-C---ATT--AAG
1 GCATG-AATGGATGCCATAATTAAAAT
63809 GCATGAATGGATGCCATAATTAAAAAT
1 GCATGAATGGATGCCATAATT-AAAAT
*
63836 GCATGAAAT-GATG-C---ATT--AAG
1 GCATG-AATGGATGCCATAATTAAAAT
* *
63856 GCATGAAAGGATGTCATAATTGAAAAT
1 GCATGAATGGATGCCATAATT-AAAAT
*
63883 GCATGAAAGGATGC
1 GCATGAATGGATGC
63897 ATTAAGGCAT
Statistics
Matches: 84, Mismatches: 6, Indels: 36
0.67 0.05 0.29
Matches are distributed among these distances:
19 5 0.06
20 22 0.26
21 2 0.02
23 6 0.07
24 6 0.07
26 2 0.02
27 35 0.42
28 6 0.07
ACGTcount: A:0.41, C:0.10, G:0.24, T:0.24
Consensus pattern (26 bp):
GCATGAATGGATGCCATAATTAAAAT
Found at i:63814 original size:20 final size:20
Alignment explanation
Indices: 63789--63909 Score: 64
Period size: 20 Copynumber: 5.3 Consensus size: 20
63779 AATTGAAAAT
63789 GCATGAAATGATGCATTAAG
1 GCATGAAATGATGCATTAAG
*
63809 GCATG-AATGGATGCCATAATTAAAAAT
1 GCATGAAAT-GATG-C---ATT---AAG
63836 GCATGAAATGATGCATTAAG
1 GCATGAAATGATGCATTAAG
* *
63856 GCATGAAAGGATGTCATAATTGAAAAT
1 GCATGAAATGATG-C---ATT---AAG
*
63883 GCATGAAAGGATGCATTAAG
1 GCATGAAATGATGCATTAAG
63903 GCATGAA
1 GCATGAA
63910 CGAATTCCAT
Statistics
Matches: 80, Mismatches: 5, Indels: 32
0.68 0.04 0.27
Matches are distributed among these distances:
19 3 0.04
20 32 0.40
21 2 0.03
23 6 0.08
24 6 0.08
26 2 0.03
27 26 0.32
28 3 0.04
ACGTcount: A:0.42, C:0.10, G:0.24, T:0.24
Consensus pattern (20 bp):
GCATGAAATGATGCATTAAG
Found at i:70185 original size:22 final size:22
Alignment explanation
Indices: 70160--70236 Score: 104
Period size: 22 Copynumber: 3.6 Consensus size: 22
70150 CCTTAAGGGG
*
70160 GTATCGGTACCATAGTATAGTA
1 GTATCGATACCATAGTATAGTA
70182 GTATCGATACCATAGTATAGTA
1 GTATCGATACCATAGTATAGTA
* * *
70204 GTATCGATACCGTGGTA-AG-G
1 GTATCGATACCATAGTATAGTA
70224 GTATCGATACCAT
1 GTATCGATACCAT
70237 GAAACATTGA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
20 12 0.24
21 2 0.04
22 36 0.72
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (22 bp):
GTATCGATACCATAGTATAGTA
Found at i:70288 original size:116 final size:116
Alignment explanation
Indices: 70065--70300 Score: 307
Period size: 116 Copynumber: 2.0 Consensus size: 116
70055 TGATTTAATC
* * *
70065 AGTATCGATACCATTGATGCAATATCGATACCATTGTAAGGGTATTGATACCATGCAAACATCAA
1 AGTATCGATACCATAGATGCAATATCGATACCATGGTAAGGGTATCGATACCATGCAAACATCAA
* * * *
70130 ATCTAATTTTGGTATTGATACCTTAAGGGGGTATCGGTACCATAGTATAGT
66 AGCTAATTTTGGTATCGATACCTTAAAGGGGTATCGGTACCATAGTATAGA
* * * *
70181 AGTATCGATACCATAGTATAGTAGTATCGATACCGTGGTAAGGGTATCGATACCATG-AAACATT
1 AGTATCGATACCATAG-AT-GCAATATCGATACCATGGTAAGGGTATCGATACCATGCAAACATC
* *
70245 GAAGCTAATTTTGGTATCGATA-C-TAGAAGGGGTATCGGTACCATATTATAGA
64 AAAGCTAATTTTGGTATCGATACCTTA-AAGGGGTATCGGTACCATAGTATAGA
70297 AGTA
1 AGTA
70301 ATGGTACTAG
Statistics
Matches: 104, Mismatches: 13, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
115 2 0.02
116 43 0.41
117 27 0.26
118 32 0.31
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (116 bp):
AGTATCGATACCATAGATGCAATATCGATACCATGGTAAGGGTATCGATACCATGCAAACATCAA
AGCTAATTTTGGTATCGATACCTTAAAGGGGTATCGGTACCATAGTATAGA
Found at i:70328 original size:20 final size:20
Alignment explanation
Indices: 70292--70329 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
70282 GTACCATATT
*
70292 ATAGAAGTAATGGTACTAGG
1 ATAGAAGTAATGATACTAGG
70312 ATAGAAGT-ATCGATACTA
1 ATAGAAGTAAT-GATACTA
70330 TAGAGCCTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.42, C:0.08, G:0.24, T:0.26
Consensus pattern (20 bp):
ATAGAAGTAATGATACTAGG
Found at i:70800 original size:20 final size:20
Alignment explanation
Indices: 70775--70848 Score: 121
Period size: 20 Copynumber: 3.7 Consensus size: 20
70765 AATTGAAAAT
*
70775 GCATGAAAGTATGCATTAAG
1 GCATGAAAGGATGCATTAAG
70795 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
70815 GCATGAAAGGATACATTAAG
1 GCATGAAAGGATGCATTAAG
*
70835 GCATGAACGGATGC
1 GCATGAAAGGATGC
70849 CATAATTGAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.39, C:0.12, G:0.28, T:0.20
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:70865 original size:27 final size:27
Alignment explanation
Indices: 70835--70920 Score: 80
Period size: 27 Copynumber: 3.4 Consensus size: 27
70825 ATACATTAAG
70835 GCATGAACGGATGCCATAATTGAAAAT
1 GCATGAACGGATGCCATAATTGAAAAT
*
70862 GCATGAA-GTGATG-C---ATT---AAG
1 GCATGAACG-GATGCCATAATTGAAAAT
*
70882 GCATGAACGAATGCCATAATTGAAAAT
1 GCATGAACGGATGCCATAATTGAAAAT
*
70909 GCATGAAAGGAT
1 GCATGAACGGAT
70921 TCATTAAGTC
Statistics
Matches: 45, Mismatches: 5, Indels: 18
0.66 0.07 0.26
Matches are distributed among these distances:
20 12 0.27
21 2 0.04
23 3 0.07
24 3 0.07
26 2 0.04
27 23 0.51
ACGTcount: A:0.41, C:0.13, G:0.24, T:0.22
Consensus pattern (27 bp):
GCATGAACGGATGCCATAATTGAAAAT
Found at i:70884 original size:47 final size:47
Alignment explanation
Indices: 70815--71225 Score: 653
Period size: 47 Copynumber: 8.7 Consensus size: 47
70805 ATGCATTAAG
*
70815 GCATGAAAGGATACATTAAGGCATGAACGGATGCCATAATTGAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAAT
*
70862 GCATG-AAGTGATGCATTAAGGCATGAACGAATGCCATAATTGAAAAT
1 GCATGAAAG-GATGCATTAAGGCATGAACGGATGCCATAATTGAAAAT
* *
70909 GCATGAAAGGATTCATTAAGTCATGAACGGATGCCATAATTGAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAAT
* *
70956 GCATGAAAGGATGCATTAAGGCATCAACGGATACCATAATTGAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAAT
71003 GCATGAAAGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAAT
* *
71050 GCATGAAAGGATGCATTAAGGCATGAACGAATTCCATAATTGAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAAT
* * *
71097 ACATGAAAAGGAGGCATTAAGGCATGAAAGGATGCCATAATTGAAAAT
1 GCATG-AAAGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAAT
71145 GCATGAAAGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAAT
* * * *
71192 GCATGAAAATGATGCATTAATGCATAAATGGATG
1 GCATG-AAAGGATGCATTAAGGCATGAACGGATG
71226 TGTTAATACG
Statistics
Matches: 335, Mismatches: 25, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
46 3 0.01
47 263 0.79
48 69 0.21
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.22
Consensus pattern (47 bp):
GCATGAAAGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAAT
Found at i:70953 original size:94 final size:94
Alignment explanation
Indices: 70716--71225 Score: 750
Period size: 94 Copynumber: 5.5 Consensus size: 94
70706 AAATTAAATT
* *
70716 CATAATTGAAAATGCATGAAATGATGCATT-AGGCATGAAAGGATGCCATAATTGAAAATGCATG
1 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAATGCATG
* *
70780 AAAGTATGCATTAAGGCATGAAAGGATG-
66 AAAGGATGCATTAAGGCATGAACGGATGC
* *
70808 C---ATT---AAGGCATGAAAGGATACATTAAGGCATGAACGGATGCCATAATTGAAAATGCATG
1 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAATGCATG
*
70867 -AAGTGATGCATTAAGGCATGAACGAATGC
66 AAAG-GATGCATTAAGGCATGAACGGATGC
* *
70896 CATAATTGAAAATGCATGAAAGGATTCATTAAGTCATGAACGGATGCCATAATTGAAAATGCATG
1 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAATGCATG
* *
70961 AAAGGATGCATTAAGGCATCAACGGATAC
66 AAAGGATGCATTAAGGCATGAACGGATGC
70990 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAATGCATG
1 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAATGCATG
* *
71055 AAAGGATGCATTAAGGCATGAACGAATTC
66 AAAGGATGCATTAAGGCATGAACGGATGC
* * *
71084 CATAATTGAAAATACATGAAAAGGAGGCATTAAGGCATGAAAGGATGCCATAATTGAAAATGCAT
1 CATAATTGAAAATGCATG-AAAGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAATGCAT
71149 GAAAGGATGCATTAAGGCATGAACGGATGC
65 GAAAGGATGCATTAAGGCATGAACGGATGC
* * * *
71179 CATAATTGAAAATGCATGAAAATGATGCATTAATGCATAAATGGATG
1 CATAATTGAAAATGCATG-AAAGGATGCATTAAGGCATGAACGGATG
71226 TGTTAATACG
Statistics
Matches: 378, Mismatches: 29, Indels: 19
0.89 0.07 0.04
Matches are distributed among these distances:
86 20 0.05
87 54 0.14
88 1 0.00
89 3 0.01
91 3 0.01
92 1 0.00
94 180 0.48
95 116 0.31
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.23
Consensus pattern (94 bp):
CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAATGCATG
AAAGGATGCATTAAGGCATGAACGGATGC
Found at i:70968 original size:27 final size:27
Alignment explanation
Indices: 70930--71063 Score: 107
Period size: 27 Copynumber: 5.5 Consensus size: 27
70920 TTCATTAAGT
*
70930 CATGAACGGATGCCATAATTGAAAATG
1 CATGAAAGGATGCCATAATTGAAAATG
*
70957 CATGAAAGGATG-C---ATT---AAGG
1 CATGAAAGGATGCCATAATTGAAAATG
* * *
70977 CATCAACGGATACCATAATTGAAAATG
1 CATGAAAGGATGCCATAATTGAAAATG
*
71004 CATGAAAGGATG-C---ATT---AAGG
1 CATGAAAGGATGCCATAATTGAAAATG
*
71024 CATGAACGGATGCCATAATTGAAAATG
1 CATGAAAGGATGCCATAATTGAAAATG
71051 CATGAAAGGATGC
1 CATGAAAGGATGC
71064 ATTAAGGCAT
Statistics
Matches: 80, Mismatches: 13, Indels: 28
0.66 0.11 0.23
Matches are distributed among these distances:
20 26 0.32
21 2 0.03
23 6 0.08
24 6 0.08
26 2 0.03
27 38 0.47
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.21
Consensus pattern (27 bp):
CATGAAAGGATGCCATAATTGAAAATG
Found at i:71016 original size:141 final size:141
Alignment explanation
Indices: 70716--71225 Score: 750
Period size: 141 Copynumber: 3.7 Consensus size: 141
70706 AAATTAAATT
* *
70716 CATAATTGAAAATGCATGAAATGATGCATT-AGGCATGAAAGGATGCCATAATTGAAAATGCATG
1 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAATGCATG
* * * *
70780 AAAGTATGCATTAAGGCATGAAAGGATG-C---ATT---AAGGCATGAAAGGATACATTAAGGCA
66 AAAGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAATGCATGAAAGGATGCATTAAGGCA
70838 TGAACGGATGC
131 TGAACGGATGC
*
70849 CATAATTGAAAATGCATG-AAGTGATGCATTAAGGCATGAACGAATGCCATAATTGAAAATGCAT
1 CATAATTGAAAATGCATGAAAG-GATGCATTAAGGCATGAACGGATGCCATAATTGAAAATGCAT
* *
70913 GAAAGGATTCATTAAGTCATGAACGGATGCCATAATTGAAAATGCATGAAAGGATGCATTAAGGC
65 GAAAGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAATGCATGAAAGGATGCATTAAGGC
* *
70978 ATCAACGGATAC
130 ATGAACGGATGC
70990 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAATGCATG
1 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAATGCATG
* * * *
71055 AAAGGATGCATTAAGGCATGAACGAATTCCATAATTGAAAATACATGAAAAGGAGGCATTAAGGC
66 AAAGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAATGCATG-AAAGGATGCATTAAGGC
*
71120 ATGAAAGGATGC
130 ATGAACGGATGC
71132 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAATGCATG
1 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAATGCATG
* * * *
71197 AAAATGATGCATTAATGCATAAATGGATG
66 -AAAGGATGCATTAAGGCATGAACGGATG
71226 TGTTAATACG
Statistics
Matches: 338, Mismatches: 27, Indels: 14
0.89 0.07 0.04
Matches are distributed among these distances:
132 2 0.01
133 26 0.08
134 56 0.17
135 1 0.00
138 3 0.01
141 135 0.40
142 93 0.28
143 22 0.07
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.23
Consensus pattern (141 bp):
CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAATGCATG
AAAGGATGCATTAAGGCATGAACGGATGCCATAATTGAAAATGCATGAAAGGATGCATTAAGGCA
TGAACGGATGC
Found at i:71028 original size:20 final size:20
Alignment explanation
Indices: 71003--71076 Score: 67
Period size: 20 Copynumber: 3.4 Consensus size: 20
70993 AATTGAAAAT
71003 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
71023 GCATGAACGGATGCCATAATTGAAAAT
1 GCATGAAAGGATG-C---ATT---AAG
71050 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
71070 GCATGAA
1 GCATGAA
71077 CGAATTCCAT
Statistics
Matches: 43, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
20 21 0.49
21 1 0.02
23 3 0.07
24 3 0.07
26 1 0.02
27 14 0.33
ACGTcount: A:0.41, C:0.12, G:0.27, T:0.20
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:71156 original size:27 final size:27
Alignment explanation
Indices: 71118--71199 Score: 97
Period size: 27 Copynumber: 3.3 Consensus size: 27
71108 AGGCATTAAG
71118 GCATGAAAGGATGCCATAATTGAAAAT
1 GCATGAAAGGATGCCATAATTGAAAAT
*
71145 GCATGAAAGGATG-C---ATT---AAG
1 GCATGAAAGGATGCCATAATTGAAAAT
*
71165 GCATGAACGGATGCCATAATTGAAAAT
1 GCATGAAAGGATGCCATAATTGAAAAT
71192 GCATGAAA
1 GCATGAAA
71200 ATGATGCATT
Statistics
Matches: 44, Mismatches: 4, Indels: 14
0.71 0.06 0.23
Matches are distributed among these distances:
20 14 0.32
21 1 0.02
23 3 0.07
24 3 0.07
26 1 0.02
27 22 0.50
ACGTcount: A:0.43, C:0.12, G:0.24, T:0.21
Consensus pattern (27 bp):
GCATGAAAGGATGCCATAATTGAAAAT
Found at i:71170 original size:20 final size:20
Alignment explanation
Indices: 71098--71178 Score: 63
Period size: 20 Copynumber: 3.6 Consensus size: 20
71088 ATTGAAAATA
*
71098 CATGAAAAGGAGGCATTAAGG
1 CATG-AAAGGATGCATTAAGG
*
71119 CATGAAAGGATGCCATAATTGAAAATG
1 CATGAAAGGATG-C---ATT---AAGG
71146 CATGAAAGGATGCATTAAGG
1 CATGAAAGGATGCATTAAGG
*
71166 CATGAACGGATGC
1 CATGAAAGGATGC
71179 CATAATTGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
20 22 0.45
21 5 0.10
23 3 0.06
24 3 0.06
26 1 0.02
27 15 0.31
ACGTcount: A:0.41, C:0.12, G:0.28, T:0.19
Consensus pattern (20 bp):
CATGAAAGGATGCATTAAGG
Found at i:72971 original size:13 final size:13
Alignment explanation
Indices: 72937--72975 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
72927 GTGTGAGAAA
72937 TCTAAATTT-AAG
1 TCTAAATTTAAAG
*
72949 GCTAAATTTAAAG
1 TCTAAATTTAAAG
*
72962 TCTAAGTTTAAAG
1 TCTAAATTTAAAG
72975 T
1 T
72976 GTAAGGTTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 8 0.35
13 15 0.65
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.38
Consensus pattern (13 bp):
TCTAAATTTAAAG
Found at i:74305 original size:55 final size:55
Alignment explanation
Indices: 74212--74405 Score: 216
Period size: 55 Copynumber: 3.5 Consensus size: 55
74202 TGCAAGGCCC
* * *
74212 AAAAATAGGGGCCTCAAAATCGAATATATCTATTAGTTGTTGCTATTAATAAGCAT
1 AAAAATAGGGGCC-CAAAATCGAGTATATCTATCAGTTGTTGCTATTAAAAAGCAT
* *
74268 AAAATTAGGGGCCCAAAATCGAGTATATATATCAGTTGTTGCTATTAAAAAGCAT
1 AAAAATAGGGGCCCAAAATCGAGTATATCTATCAGTTGTTGCTATTAAAAAGCAT
* * * *
74323 AAAAATAGGAGTCTCGAAATCGAGTATATCTATCA-TTGTTGCCATTAAGAAA-CAT
1 AAAAATAGG-GGCCCAAAATCGAGTATATCTATCAGTTGTTGCTATTAA-AAAGCAT
* * * *
74378 --AAATAGGGTCCCATAATCAAATATATCT
1 AAAAATAGGGGCCCAAAATCGAGTATATCT
74406 CTATTTATCA
Statistics
Matches: 120, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
52 16 0.13
53 7 0.06
55 61 0.51
56 36 0.30
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (55 bp):
AAAAATAGGGGCCCAAAATCGAGTATATCTATCAGTTGTTGCTATTAAAAAGCAT
Found at i:74625 original size:31 final size:31
Alignment explanation
Indices: 74587--74649 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
74577 TCTCATAAAA
74587 TAGGGGTCTCGAAATTGAATATATATATCAG
1 TAGGGGTCTCGAAATTGAATATATATATCAG
* *
74618 TAGGGGTCTCGAAATTGAGTATATCTATCAG
1 TAGGGGTCTCGAAATTGAATATATATATCAG
74649 T
1 T
74650 TGTTGCATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (31 bp):
TAGGGGTCTCGAAATTGAATATATATATCAG
Found at i:74702 original size:55 final size:56
Alignment explanation
Indices: 74618--74755 Score: 199
Period size: 56 Copynumber: 2.5 Consensus size: 56
74608 TATATATCAG
* * *
74618 TAGGGGTCTCGAAATTGAGTATATCTATCAGTTGTTG-CATTAAGAAGCATAAAAA
1 TAGGGGTCCCGAAATCGAGTATATCTATCAATTGTTGCCATTAAGAAGCATAAAAA
74673 TAGGGGTCCCGAAATCGAGTATATCTATCAATTGTTGCCATTAAGAAGCATAAAAA
1 TAGGGGTCCCGAAATCGAGTATATCTATCAATTGTTGCCATTAAGAAGCATAAAAA
** *
74729 TAAAGGTCCC-AGAATCGAATATATCTA
1 TAGGGGTCCCGA-AATCGAGTATATCTA
74756 GAAAATAGGG
Statistics
Matches: 75, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
55 35 0.47
56 40 0.53
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (56 bp):
TAGGGGTCCCGAAATCGAGTATATCTATCAATTGTTGCCATTAAGAAGCATAAAAA
Found at i:75413 original size:18 final size:18
Alignment explanation
Indices: 75386--75439 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
75376 CTAGAATGTT
*
75386 TATGAGGGAATTGAAATC
1 TATGAAGGAATTGAAATC
*
75404 TATGAAGGAATTGGAATC
1 TATGAAGGAATTGAAATC
* *
75422 TGT-CAGGAATTGAAATC
1 TATGAAGGAATTGAAATC
75439 T
1 T
75440 GAATCTAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
17 13 0.42
18 18 0.58
ACGTcount: A:0.37, C:0.07, G:0.26, T:0.30
Consensus pattern (18 bp):
TATGAAGGAATTGAAATC
Found at i:76054 original size:31 final size:30
Alignment explanation
Indices: 75986--76122 Score: 107
Period size: 31 Copynumber: 4.5 Consensus size: 30
75976 AGGCAGTGAG
* * * *
75986 ATAAAT-AAACTAAAGAAAAATAAAATAAA
1 ATAAATAAAAATAAAAAAAAAAAAAAAAAA
** *
76015 GGAAATAAAAATGAAAAAAAAAAAAAAGAAA
1 ATAAATAAAAAT-AAAAAAAAAAAAAAAAAA
* **
76046 ATACATAAAAATAAAAAAAATAAAAAACTAA
1 ATAAATAAAAATAAAAAAAA-AAAAAAAAAA
* *
76077 ATAAATAAAGAACATAAAAACAAAAAAAAAAA
1 ATAAATAAA-AATA-AAAAAAAAAAAAAAAAA
*
76109 A-AAATAAAGATAAA
1 ATAAATAAAAATAAA
76123 TAATAAAATA
Statistics
Matches: 85, Mismatches: 18, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
29 6 0.07
30 14 0.16
31 47 0.55
32 12 0.14
33 6 0.07
ACGTcount: A:0.79, C:0.04, G:0.05, T:0.12
Consensus pattern (30 bp):
ATAAATAAAAATAAAAAAAAAAAAAAAAAA
Found at i:76065 original size:40 final size:39
Alignment explanation
Indices: 76021--76112 Score: 107
Period size: 40 Copynumber: 2.3 Consensus size: 39
76011 TAAAGGAAAT
*
76021 AAAAATGAAAAAAAAAAAAAAGAAA-ATACATAAAAATAAA
1 AAAAAT-AAAAAAAAAAAAAAGAAAGA-ACATAAAAACAAA
* * *
76061 AAAAATAAAAAACTAAATAAATAAAGAACATAAAAACAAA
1 AAAAATAAAAAA-AAAAAAAAGAAAGAACATAAAAACAAA
76101 AAAAA-AAAAAAA
1 AAAAATAAAAAAA
76113 TAAAGATAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
39 12 0.27
40 32 0.71
41 1 0.02
ACGTcount: A:0.83, C:0.04, G:0.03, T:0.10
Consensus pattern (39 bp):
AAAAATAAAAAAAAAAAAAAGAAAGAACATAAAAACAAA
Found at i:76116 original size:62 final size:60
Alignment explanation
Indices: 76028--76175 Score: 149
Period size: 62 Copynumber: 2.4 Consensus size: 60
76018 AATAAAAATG
*
76028 AAAAAAAAAAAAAAGAAAATACATAAAAATAAAAAAAATAAAA-AA-CTAAATAA-ATAAAGAAC
1 AAAAAAAAAAAAAA-AAAA-AAATAAAAAT--AAAAAATAAAATAATC-AAATAAGATAAAGAAC
* * *
76090 ATAAAAACAAAAAAAAAAAAAAATAAAGATAAATAATAAAATAATCAAATAAGATAAAGAGC
1 A-AAAAA-AAAAAAAAAAAAAAATAAAAATAAAAAATAAAATAATCAAATAAGATAAAGAAC
76152 AAAAAATAAAAATAAAAAAGAAAA
1 AAAAAA-AAAAA-AAAAAA-AAAA
76176 GAAATACTAA
Statistics
Matches: 74, Mismatches: 5, Indels: 13
0.80 0.05 0.14
Matches are distributed among these distances:
60 10 0.14
61 18 0.24
62 25 0.34
63 13 0.18
64 8 0.11
ACGTcount: A:0.79, C:0.04, G:0.05, T:0.12
Consensus pattern (60 bp):
AAAAAAAAAAAAAAAAAAAAATAAAAATAAAAAATAAAATAATCAAATAAGATAAAGAAC
Found at i:76168 original size:5 final size:6
Alignment explanation
Indices: 76017--76169 Score: 56
Period size: 6 Copynumber: 24.5 Consensus size: 6
76007 AAAATAAAGG
76017 AAATAA AAATGAA AAA-AA AAA-AA AAGA-AA ATACATAA AAATAA AAA-AA
1 AAATAA AAAT-AA AAATAA AAATAA AA-ATAA A-A-ATAA AAATAA AAATAA
* *
76065 ATAA-AA AACTAAA TAAATAAA GAACATAA AAACAA AAA-AA AAA-AA
1 A-AATAA AAAT-AA -AAAT-AA -AA-ATAA AAATAA AAATAA AAATAA
* *
76110 AAATAA AGATAA ATAAT-A AAATAA TCAAAT-A AGATAA AGAGCA-AA
1 AAATAA AAATAA A-AATAA AAATAA --AAATAA AAATAA A-A--ATAA
76155 AAATAA AAATAA AAA
1 AAATAA AAATAA AAA
76170 AGAAAAGAAA
Statistics
Matches: 119, Mismatches: 9, Indels: 38
0.72 0.05 0.23
Matches are distributed among these distances:
5 30 0.25
6 50 0.42
7 16 0.13
8 20 0.17
9 3 0.03
ACGTcount: A:0.78, C:0.04, G:0.05, T:0.13
Consensus pattern (6 bp):
AAATAA
Found at i:76232 original size:17 final size:15
Alignment explanation
Indices: 76200--76245 Score: 56
Period size: 17 Copynumber: 2.9 Consensus size: 15
76190 TGTACTACAT
76200 AATAATAAATAAATA
1 AATAATAAATAAATA
76215 AATAATACAATGAAATA
1 AATAATA-AAT-AAATA
*
76232 AATATATAATTAAA
1 AATA-ATAAATAAA
76246 ATTATATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 7 0.26
16 6 0.22
17 11 0.41
18 3 0.11
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (15 bp):
AATAATAAATAAATA
Done.