Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004788.1 Hibiscus syriacus cultivar Beakdansim tig00010793_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: 94172
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:41 original size:15 final size:16
Alignment explanation
Indices: 21--54 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
11 AGGGCTCAAA
*
21 TTATTAA-TATTTGAT
1 TTATTAATTAGTTGAT
36 TTATTAATTAGTTGAT
1 TTATTAATTAGTTGAT
52 TTA
1 TTA
55 AATAAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.59
Consensus pattern (16 bp):
TTATTAATTAGTTGAT
Found at i:7527 original size:31 final size:32
Alignment explanation
Indices: 7471--7531 Score: 97
Period size: 31 Copynumber: 1.9 Consensus size: 32
7461 TCATAGTTTT
* *
7471 AATAAATTAAAATAAATTTACCTACAAATATA
1 AATAAATTAAAATAAAATTAACTACAAATATA
7503 AATAAATT-AAATAAAATTAACTACAAATA
1 AATAAATTAAAATAAAATTAACTACAAATA
7532 GTCCATGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 19 0.70
32 8 0.30
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.30
Consensus pattern (32 bp):
AATAAATTAAAATAAAATTAACTACAAATATA
Found at i:10744 original size:16 final size:16
Alignment explanation
Indices: 10723--10753 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
10713 TAATTTTAGC
10723 CTTACCTCACATCACA
1 CTTACCTCACATCACA
10739 CTTACCTCACATCAC
1 CTTACCTCACATCAC
10754 CCTGGTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.45, G:0.00, T:0.26
Consensus pattern (16 bp):
CTTACCTCACATCACA
Found at i:19519 original size:3 final size:3
Alignment explanation
Indices: 19511--19536 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
19501 CAACCTTAAA
19511 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
19537 GATGAGATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:24491 original size:2 final size:2
Alignment explanation
Indices: 24484--24520 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
24474 CGTATAAAAT
24484 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
24521 TTCCTTCTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:27758 original size:2 final size:2
Alignment explanation
Indices: 27751--27852 Score: 204
Period size: 2 Copynumber: 51.0 Consensus size: 2
27741 AAATCTTAGC
27751 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27793 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27835 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
27853 GGTTAAGATT
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 100 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:29053 original size:36 final size:37
Alignment explanation
Indices: 29006--29079 Score: 132
Period size: 36 Copynumber: 2.0 Consensus size: 37
28996 GATTACTGTA
29006 GTATTAGATTACTCTAATATG-GACTAACCTTTTTAT
1 GTATTAGATTACTCTAATATGAGACTAACCTTTTTAT
*
29042 GTATTAGATTACTCTAATATGAGACTAATCTTTTTAT
1 GTATTAGATTACTCTAATATGAGACTAACCTTTTTAT
29079 G
1 G
29080 ATAATAAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 21 0.58
37 15 0.42
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (37 bp):
GTATTAGATTACTCTAATATGAGACTAACCTTTTTAT
Found at i:29667 original size:114 final size:114
Alignment explanation
Indices: 29531--29761 Score: 428
Period size: 114 Copynumber: 2.0 Consensus size: 114
29521 AGCTGTAACA
29531 AATTTCTACATGGGATTCGGGTATTTCCAAGTCAAGATGTCTCTTGAAACAAGACCGACATTCAA
1 AATTTCTACATGGGATTCGGGTATTTCCAAGTCAAGATGTCTCTTGAAACAAGACCGACATTCAA
*
29596 TTAGCTTTT-CAACGCATTTTAAAATGTCTCAATCAGACATCAAGAACTT
66 TTAG-TTTTCCAACGCATTTTAAAACGTCTCAATCAGACATCAAGAACTT
*
29645 AATTTCTACATGGGATTTGGGTATTTCCAAGTCAAGATGTCTCTTGAAACAAGACCGACATTCAA
1 AATTTCTACATGGGATTCGGGTATTTCCAAGTCAAGATGTCTCTTGAAACAAGACCGACATTCAA
29710 TTAGTTTTCCAACGCATTTTAAAACGTCTCAATCAGACATCAAGAACTT
66 TTAGTTTTCCAACGCATTTTAAAACGTCTCAATCAGACATCAAGAACTT
29759 AAT
1 AAT
29762 ATATGCATAT
Statistics
Matches: 114, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
113 4 0.04
114 110 0.96
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.32
Consensus pattern (114 bp):
AATTTCTACATGGGATTCGGGTATTTCCAAGTCAAGATGTCTCTTGAAACAAGACCGACATTCAA
TTAGTTTTCCAACGCATTTTAAAACGTCTCAATCAGACATCAAGAACTT
Found at i:30212 original size:21 final size:21
Alignment explanation
Indices: 30186--30307 Score: 99
Period size: 21 Copynumber: 5.8 Consensus size: 21
30176 CATATTCGCA
30186 TTGCGATAGTCCAAGTTTGCG
1 TTGCGATAGTCCAAGTTTGCG
* *
30207 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTTGCG
* *
30228 TTGCGATTTATTCCAA-ATT-CG
1 TTGCGA--TAGTCCAAGTTTGCG
* *
30249 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTTGCG
* *
30270 TTGCGATCTATTCCAA-ATT-CG
1 TTGCGA--TAGTCCAAGTTTGCG
*
30291 TTGCGATAGTCGAAGTT
1 TTGCGATAGTCCAAGTT
30308 CGCGATTTGT
Statistics
Matches: 77, Mismatches: 17, Indels: 15
0.71 0.16 0.14
Matches are distributed among these distances:
19 12 0.16
20 2 0.03
21 49 0.64
22 2 0.03
23 12 0.16
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.34
Consensus pattern (21 bp):
TTGCGATAGTCCAAGTTTGCG
Found at i:30232 original size:42 final size:41
Alignment explanation
Indices: 30205--30311 Score: 196
Period size: 42 Copynumber: 2.6 Consensus size: 41
30195 TCCAAGTTTG
30205 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TTATTCCAAATT
30247 CGTTGCGATAGTCGAAGTTCGCGTTGCGATCTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGAT-TATTCCAAATT
30289 CGTTGCGATAGTCGAAGTTCGCG
1 CGTTGCGATAGTCGAAGTTCGCG
30312 ATTTGTTTCT
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
41 1 0.02
42 63 0.98
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.33
Consensus pattern (41 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTATTCCAAATT
Found at i:30914 original size:6 final size:6
Alignment explanation
Indices: 30893--30929 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
30883 GTCCGTCTCG
30893 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
30930 AATACATGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.32
6 21 0.68
ACGTcount: A:0.00, C:0.16, G:0.54, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:31033 original size:21 final size:21
Alignment explanation
Indices: 31007--31057 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
30997 AATACCGTCG
31007 TTGCGATTTTGAACTATCGCA
1 TTGCGATTTTGAACTATCGCA
*
31028 TTGCGATTTTGGACTATCGCA
1 TTGCGATTTTGAACTATCGCA
31049 TTGCGATTT
1 TTGCGATTT
31058 ACATATTTGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.41
Consensus pattern (21 bp):
TTGCGATTTTGAACTATCGCA
Found at i:32970 original size:14 final size:14
Alignment explanation
Indices: 32951--32987 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
32941 TTAATAAATA
32951 TATATTTAAAAGAT
1 TATATTTAAAAGAT
32965 TATA-TTAAAAGAT
1 TATATTTAAAAGAT
*
32978 TATATCTAAA
1 TATATTTAAA
32988 TTCTCGAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 13 0.62
14 8 0.38
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (14 bp):
TATATTTAAAAGAT
Found at i:40520 original size:13 final size:13
Alignment explanation
Indices: 40502--40526 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40492 ACAGACATGT
40502 ATATGAAGACTGC
1 ATATGAAGACTGC
40515 ATATGAAGACTG
1 ATATGAAGACTG
40527 TTCAACTATA
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:0.40, C:0.12, G:0.24, T:0.24
Consensus pattern (13 bp):
ATATGAAGACTGC
Found at i:42075 original size:13 final size:13
Alignment explanation
Indices: 42057--42081 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42047 TACATACGCG
42057 CATATGAAGACTA
1 CATATGAAGACTA
42070 CATATGAAGACT
1 CATATGAAGACT
42082 GTTCAACTAT
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:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (13 bp):
CATATGAAGACTA
Found at i:43591 original size:30 final size:29
Alignment explanation
Indices: 43537--43626 Score: 74
Period size: 30 Copynumber: 3.0 Consensus size: 29
43527 AAATATTTAA
* * * *
43537 AAGTTTGAGGACTAATTTAGAATATAATC
1 AAGTTTAAGGAATAAATTAAAATATAATC
* **
43566 AGAGTTT-AGGGATGAAATTAAAATATTTTC
1 A-AGTTTAAGGAAT-AAATTAAAATATAATC
*
43596 AAGTTTAAGGAATAATTTAAAATGATAATC
1 AAGTTTAAGGAATAAATTAAAAT-ATAATC
43626 A
1 A
43627 TACTTTGAAG
Statistics
Matches: 47, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
29 19 0.40
30 28 0.60
ACGTcount: A:0.44, C:0.04, G:0.17, T:0.34
Consensus pattern (29 bp):
AAGTTTAAGGAATAAATTAAAATATAATC
Found at i:43612 original size:59 final size:61
Alignment explanation
Indices: 43485--43626 Score: 182
Period size: 59 Copynumber: 2.4 Consensus size: 61
43475 AAAGTATGGC
* * * *
43485 GAATAATTTAGAATGCAT-GTCATAGTTTGGGGATGAAATTAAAAATATTTAAAAGTTTGAG
1 GAATAATTTAGAATG-ATAATCAGAGTTTAGGGATGAAATTAAAAATATTTAAAAGTTTAAG
* **
43546 GACTAATTTAGAAT-ATAATCAGAGTTTAGGGATGAAATT-AAAATATTTTCAAGTTTAAG
1 GAATAATTTAGAATGATAATCAGAGTTTAGGGATGAAATTAAAAATATTTAAAAGTTTAAG
*
43605 GAATAATTTAAAATGATAATCA
1 GAATAATTTAGAATGATAATCA
43627 TACTTTGAAG
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
59 31 0.44
60 26 0.37
61 13 0.19
ACGTcount: A:0.44, C:0.04, G:0.18, T:0.35
Consensus pattern (61 bp):
GAATAATTTAGAATGATAATCAGAGTTTAGGGATGAAATTAAAAATATTTAAAAGTTTAAG
Found at i:43615 original size:29 final size:28
Alignment explanation
Indices: 43521--43618 Score: 79
Period size: 29 Copynumber: 3.4 Consensus size: 28
43511 TTGGGGATGA
* ** *
43521 AATTAAAAATATTTAAAAGTTTGAGGACT
1 AATTTAAAATATTTTCAAGTTT-AGGAAT
* ** *
43550 AATTTAGAATATAATCAGAGTTTAGGGAT
1 AATTTAAAATATTTTCA-AGTTTAGGAAT
*
43579 GAAATTAAAATATTTTCAAGTTTAAGGAAT
1 -AATTTAAAATATTTTCAAGTTT-AGGAAT
43609 AATTTAAAAT
1 AATTTAAAAT
43619 GATAATCATA
Statistics
Matches: 52, Mismatches: 14, Indels: 6
0.72 0.19 0.08
Matches are distributed among these distances:
29 29 0.56
30 23 0.44
ACGTcount: A:0.47, C:0.03, G:0.14, T:0.36
Consensus pattern (28 bp):
AATTTAAAATATTTTCAAGTTTAGGAAT
Found at i:44985 original size:16 final size:17
Alignment explanation
Indices: 44966--45002 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
44956 TTAGTTGAAA
*
44966 CGAAAAT-AACCCGAAT
1 CGAAAATCAACCCGAAC
44982 CG-AAATCAACCCGAAC
1 CGAAAATCAACCCGAAC
44998 CGAAA
1 CGAAA
45003 GCAACTCGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 4 0.22
16 12 0.67
17 2 0.11
ACGTcount: A:0.49, C:0.30, G:0.14, T:0.08
Consensus pattern (17 bp):
CGAAAATCAACCCGAAC
Found at i:45007 original size:16 final size:16
Alignment explanation
Indices: 44973--45012 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
44963 AAACGAAAAT
* *
44973 AACCCGAATCGAAATC
1 AACCCGAACCGAAAGC
44989 AACCCGAACCGAAAGC
1 AACCCGAACCGAAAGC
*
45005 AACTCGAA
1 AACCCGAA
45013 TTTAATTTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.45, C:0.33, G:0.15, T:0.07
Consensus pattern (16 bp):
AACCCGAACCGAAAGC
Found at i:45825 original size:31 final size:32
Alignment explanation
Indices: 45790--45865 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
45780 AACCGATACA
*
45790 ATATTGA-CTCGACCTGAAAA-CAACTGATCCG
1 ATATTGACCT-GACCCGAAAATCAACTGATCCG
**
45821 ATATTGACCTGACCCGAAAATCAACTGATTTG
1 ATATTGACCTGACCCGAAAATCAACTGATCCG
*
45853 ATATTAACCTGAC
1 ATATTGACCTGAC
45866 ATGACTTATC
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
31 16 0.41
32 23 0.59
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (32 bp):
ATATTGACCTGACCCGAAAATCAACTGATCCG
Found at i:56291 original size:3 final size:3
Alignment explanation
Indices: 56283--56389 Score: 214
Period size: 3 Copynumber: 35.7 Consensus size: 3
56273 TGTTTGATAC
56283 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
56331 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
56379 AAG AAG AAG AA
1 AAG AAG AAG AA
56390 ACTAAACCGT
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 104 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:59987 original size:29 final size:29
Alignment explanation
Indices: 59945--60050 Score: 185
Period size: 29 Copynumber: 3.6 Consensus size: 29
59935 CTACAGTGGT
59945 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
59974 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
60003 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
60032 CTGTGTGTAGGTCGCCATG
1 CT-TG-G-AGGTCGCCATG
60051 CAATCAACAT
Statistics
Matches: 74, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
29 60 0.81
30 2 0.03
31 1 0.01
32 11 0.15
ACGTcount: A:0.13, C:0.29, G:0.38, T:0.20
Consensus pattern (29 bp):
CTTGGAGGTCGCCATGGCATCCGGGCGAC
Found at i:60080 original size:17 final size:16
Alignment explanation
Indices: 60058--60128 Score: 90
Period size: 17 Copynumber: 4.4 Consensus size: 16
60048 ATGCAATCAA
60058 CATGGGACGTGGGAATG
1 CATGGG-CGTGGGAATG
* * *
60075 CATGGGGGAGGGGATG
1 CATGGGCGTGGGAATG
60091 CATGGGACGTGGGAATG
1 CATGGG-CGTGGGAATG
60108 CATGGG-GTGGGAATG
1 CATGGGCGTGGGAATG
60123 CATGGG
1 CATGGG
60129 GGAGGGGATG
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
15 15 0.32
16 13 0.28
17 19 0.40
ACGTcount: A:0.21, C:0.10, G:0.52, T:0.17
Consensus pattern (16 bp):
CATGGGCGTGGGAATG
Found at i:60093 original size:16 final size:16
Alignment explanation
Indices: 60068--60134 Score: 82
Period size: 16 Copynumber: 4.2 Consensus size: 16
60058 CATGGGACGT
60068 GGGAATGCATGGGGGA
1 GGGAATGCATGGGGGA
* * *
60084 GGGGATGCATGGGACGT
1 GGGAATGCATGGG-GGA
*
60101 GGGAATGCAT-GGGGT
1 GGGAATGCATGGGGGA
60116 GGGAATGCATGGGGGA
1 GGGAATGCATGGGGGA
60132 GGG
1 GGG
60135 GATGGTGCAT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
15 12 0.28
16 21 0.49
17 10 0.23
ACGTcount: A:0.21, C:0.07, G:0.57, T:0.15
Consensus pattern (16 bp):
GGGAATGCATGGGGGA
Found at i:60100 original size:33 final size:32
Alignment explanation
Indices: 60058--60128 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 32
60048 ATGCAATCAA
*
60058 CATGGGACGTGGGAATGCATGGGGGAGGGGATG
1 CATGGGACGTGGGAATGCAT-GGGGAGGGAATG
*
60091 CATGGGACGTGGGAATGCATGGGGTGGGAATG
1 CATGGGACGTGGGAATGCATGGGGAGGGAATG
60123 CATGGG
1 CATGGG
60129 GGAGGGGATG
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 16 0.44
33 20 0.56
ACGTcount: A:0.21, C:0.10, G:0.52, T:0.17
Consensus pattern (32 bp):
CATGGGACGTGGGAATGCATGGGGAGGGAATG
Found at i:60119 original size:15 final size:15
Alignment explanation
Indices: 60066--60129 Score: 83
Period size: 15 Copynumber: 4.1 Consensus size: 15
60056 AACATGGGAC
60066 GTGGGAATGCATGGGG
1 GTGGGAATGCAT-GGG
* *
60082 GAGGGGATGCATGGG
1 GTGGGAATGCATGGG
60097 ACGTGGGAATGCATGGG
1 --GTGGGAATGCATGGG
60114 GTGGGAATGCATGGG
1 GTGGGAATGCATGGG
60129 G
1 G
60130 GAGGGGATGG
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
15 19 0.45
16 10 0.24
17 13 0.31
ACGTcount: A:0.20, C:0.08, G:0.55, T:0.17
Consensus pattern (15 bp):
GTGGGAATGCATGGG
Found at i:60164 original size:60 final size:60
Alignment explanation
Indices: 60099--60221 Score: 246
Period size: 60 Copynumber: 2.0 Consensus size: 60
60089 TGCATGGGAC
60099 GTGGGAATGCATGGGGTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAACT
1 GTGGGAATGCATGGGGTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAACT
60159 GTGGGAATGCATGGGGTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAACT
1 GTGGGAATGCATGGGGTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAACT
60219 GTG
1 GTG
60222 CATGGCCATG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 63 1.00
ACGTcount: A:0.20, C:0.08, G:0.52, T:0.20
Consensus pattern (60 bp):
GTGGGAATGCATGGGGTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAACT
Found at i:60179 original size:15 final size:15
Alignment explanation
Indices: 60159--60189 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
60149 CGTGGGAACT
60159 GTGGGAATGCATGGG
1 GTGGGAATGCATGGG
60174 GTGGGAATGCATGGG
1 GTGGGAATGCATGGG
60189 G
1 G
60190 GAGGGGATGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.55, T:0.19
Consensus pattern (15 bp):
GTGGGAATGCATGGG
Found at i:60673 original size:21 final size:21
Alignment explanation
Indices: 60648--60691 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
60638 AATCTAGTTA
60648 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
60669 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
60690 AT
1 AT
60692 ATTATATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:60701 original size:28 final size:30
Alignment explanation
Indices: 60668--60730 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
60658 TAGTATAAAT
*
60668 TATTAGTTTGTTAGTTTAAG-T-TATATTA
1 TATTAGTTTATTAGTTTAAGTTATATATTA
60696 TATTAGTTTATTAGTTTAAGTTATATATTA
1 TATTAGTTTATTAGTTTAAGTTATATATTA
60726 TATTA
1 TATTA
60731 TATAAAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 19 0.59
29 1 0.03
30 12 0.38
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (30 bp):
TATTAGTTTATTAGTTTAAGTTATATATTA
Found at i:61278 original size:20 final size:21
Alignment explanation
Indices: 61234--61278 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
61224 AAATATTGTG
**
61234 TTTAAAAATATTTAGTGTTGT
1 TTTAAAAATATTTAGTGTTAA
*
61255 TTTAAAAATATTTTGT-TTAA
1 TTTAAAAATATTTAGTGTTAA
61275 TTTA
1 TTTA
61279 CATTGTATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (21 bp):
TTTAAAAATATTTAGTGTTAA
Found at i:61568 original size:26 final size:25
Alignment explanation
Indices: 61539--61597 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
61529 AAATCATATT
*
61539 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AGTAAATATCAAATC
*
61565 ATTAGATT-AATAGTAATTATCAAATC
1 ATT--ATTAAATAGTAAATATCAAATC
61591 ATTATTA
1 ATTATTA
61598 GGTTATTAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
24 3 0.11
26 19 0.68
27 3 0.11
28 3 0.11
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (25 bp):
ATTATTAAATAGTAAATATCAAATC
Found at i:63483 original size:12 final size:12
Alignment explanation
Indices: 63466--63497 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
63456 CAATCCAGGC
63466 GACATACGGGGT
1 GACATACGGGGT
63478 GACATACGGGGT
1 GACATACGGGGT
63490 GACATACG
1 GACATACG
63498 AGCCATACGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.28, C:0.19, G:0.38, T:0.16
Consensus pattern (12 bp):
GACATACGGGGT
Found at i:63532 original size:35 final size:35
Alignment explanation
Indices: 63492--63714 Score: 277
Period size: 35 Copynumber: 6.0 Consensus size: 35
63482 TACGGGGTGA
*
63492 CATACGAGCCATACGAGCCAATGTTTCTCCCCATG
1 CATACGAGCCATACGAGCCAATGGTTCTCCCCATG
63527 CATACGAGCCATACGAGCCAATGGTTCTCCCCATG
1 CATACGAGCCATACGAGCCAATGGTTCTCCCCATG
**
63562 CATACGAGCCATACGAGCCAATGGTTCT-CCGGTG
1 CATACGAGCCATACGAGCCAATGGTTCTCCCCATG
*
63596 ACATACGGGGTGACATACGAGCCATACGAGCCAATAGTTCTCCCCATG
1 -CATAC-----G-------AGCCATACGAGCCAATGGTTCTCCCCATG
63644 CATACGAGCCATACGAGCCAATGGTTCTCCCCATG
1 CATACGAGCCATACGAGCCAATGGTTCTCCCCATG
*
63679 CATACGAGCCATATGAGCCAATGGTTCTCCCCATG
1 CATACGAGCCATACGAGCCAATGGTTCTCCCCATG
63714 C
1 C
63715 GAGGTCGCCA
Statistics
Matches: 166, Mismatches: 8, Indels: 28
0.82 0.04 0.14
Matches are distributed among these distances:
34 4 0.02
35 130 0.78
40 1 0.01
42 1 0.01
47 26 0.16
48 4 0.02
ACGTcount: A:0.26, C:0.32, G:0.21, T:0.21
Consensus pattern (35 bp):
CATACGAGCCATACGAGCCAATGGTTCTCCCCATG
Found at i:63681 original size:117 final size:117
Alignment explanation
Indices: 63475--63708 Score: 443
Period size: 117 Copynumber: 2.0 Consensus size: 117
63465 CGACATACGG
63475 GGTGACATACGGGGTGACATACGAGCCATACGAGCCAATGTTTCTCCCCATGCATACGAGCCATA
1 GGTGACATACGGGGTGACATACGAGCCATACGAGCCAATGTTTCTCCCCATGCATACGAGCCATA
63540 CGAGCCAATGGTTCTCCCCATGCATACGAGCCATACGAGCCAATGGTTCTCC
66 CGAGCCAATGGTTCTCCCCATGCATACGAGCCATACGAGCCAATGGTTCTCC
63592 GGTGACATACGGGGTGACATACGAGCCATACGAGCCAATAG-TTCTCCCCATGCATACGAGCCAT
1 GGTGACATACGGGGTGACATACGAGCCATACGAGCCAAT-GTTTCTCCCCATGCATACGAGCCAT
*
63656 ACGAGCCAATGGTTCTCCCCATGCATACGAGCCATATGAGCCAATGGTTCTCC
65 ACGAGCCAATGGTTCTCCCCATGCATACGAGCCATACGAGCCAATGGTTCTCC
63709 CCATGCGAGG
Statistics
Matches: 115, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
117 114 0.99
118 1 0.01
ACGTcount: A:0.26, C:0.30, G:0.23, T:0.21
Consensus pattern (117 bp):
GGTGACATACGGGGTGACATACGAGCCATACGAGCCAATGTTTCTCCCCATGCATACGAGCCATA
CGAGCCAATGGTTCTCCCCATGCATACGAGCCATACGAGCCAATGGTTCTCC
Found at i:63683 original size:82 final size:82
Alignment explanation
Indices: 63527--63684 Score: 273
Period size: 82 Copynumber: 1.9 Consensus size: 82
63517 TCTCCCCATG
*
63527 CATACGAGCCATACGAGCCAATGGTTCTCCCCATGCATACGAGCCATACGAGCCAATGGTTCTCC
1 CATACGAGCCATACGAGCCAATAGTTCTCCCCATGCATACGAGCCATACGAGCCAATGGTTCTCC
**
63592 GGTGACATACGGGGTGA
66 CATGACATACGGGGTGA
63609 CATACGAGCCATACGAGCCAATAGTTCTCCCCATGCATACGAGCCATACGAGCCAATGGTTCTCC
1 CATACGAGCCATACGAGCCAATAGTTCTCCCCATGCATACGAGCCATACGAGCCAATGGTTCT-C
63674 CCATG-CATACG
65 CCATGACATACG
63685 AGCCATATGA
Statistics
Matches: 72, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
82 68 0.94
83 4 0.06
ACGTcount: A:0.27, C:0.32, G:0.22, T:0.20
Consensus pattern (82 bp):
CATACGAGCCATACGAGCCAATAGTTCTCCCCATGCATACGAGCCATACGAGCCAATGGTTCTCC
CATGACATACGGGGTGA
Found at i:63799 original size:29 final size:29
Alignment explanation
Indices: 63749--63828 Score: 126
Period size: 29 Copynumber: 2.8 Consensus size: 29
63739 AGGAATAGAG
* *
63749 AGGTCGCCATGCAG-CCTAGGCGACCTTGT
1 AGGTCGCCATGTAGTCC-CGGCGACCTTGT
63778 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
63807 AGGTCGCCATGTAGTCCCGGCG
1 AGGTCGCCATGTAGTCCCGGCG
63829 CCATTCCCAT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
29 46 0.96
30 2 0.04
ACGTcount: A:0.15, C:0.31, G:0.33, T:0.21
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:64044 original size:25 final size:25
Alignment explanation
Indices: 64015--64066 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
64005 TGTACAATTA
64015 TTGGTGAAATAATTGAGGCAGCCGG
1 TTGGTGAAATAATTGAGGCAGCCGG
64040 TTGGTGAAATAATTGAGGCAGCCGG
1 TTGGTGAAATAATTGAGGCAGCCGG
64065 TT
1 TT
64067 ATAAAAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.27, C:0.12, G:0.35, T:0.27
Consensus pattern (25 bp):
TTGGTGAAATAATTGAGGCAGCCGG
Found at i:64107 original size:23 final size:23
Alignment explanation
Indices: 64079--64124 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
64069 AAAAGAAAGA
64079 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
64102 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
64125 CCGAGAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.04, G:0.39, T:0.09
Consensus pattern (23 bp):
AAGAAAGGGAGAAGAGATTGCAG
Found at i:64139 original size:25 final size:23
Alignment explanation
Indices: 64079--64139 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
64069 AAAAGAAAGA
**
64079 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
**
64102 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
*
64125 CCGAGAAAGAAAGAA
1 --AAGAAAGAAAGAA
64140 AGGGAGAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 23 0.70
25 10 0.30
ACGTcount: A:0.51, C:0.07, G:0.36, T:0.07
Consensus pattern (23 bp):
AAGAAAGAAAGAAGAGATTGCAG
Found at i:64153 original size:21 final size:21
Alignment explanation
Indices: 64129--64181 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
64119 TTGCAGCCGA
64129 GAAAGAAAGAAAGGGAGAAAG
1 GAAAGAAAGAAAGGGAGAAAG
64150 GAAAGAAAGAAAGGGAGAAAG
1 GAAAGAAAGAAAGGGAGAAAG
*
64171 GAAAGTAAGAA
1 GAAAGAAAGAA
64182 GAAGAAAGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.62, C:0.00, G:0.36, T:0.02
Consensus pattern (21 bp):
GAAAGAAAGAAAGGGAGAAAG
Found at i:64175 original size:17 final size:16
Alignment explanation
Indices: 64127--64158 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
64117 GATTGCAGCC
64127 GAGAAAGAAAGAAAGG
1 GAGAAAGAAAGAAAGG
64143 GAGAAAGGAAAGAAAG
1 GAGAAA-GAAAGAAAG
64159 AAAGGGAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (16 bp):
GAGAAAGAAAGAAAGG
Found at i:64302 original size:45 final size:45
Alignment explanation
Indices: 64245--64351 Score: 205
Period size: 45 Copynumber: 2.4 Consensus size: 45
64235 AAATGTTTAA
64245 TTTGTTAGTTTAGGGTTTAGGGTAAAACAAAAAGCAGCTAATTAG
1 TTTGTTAGTTTAGGGTTTAGGGTAAAACAAAAAGCAGCTAATTAG
*
64290 TTTGTTAGTTTAGGGTTTAGGGTAAAACAAAAAGTAGCTAATTAG
1 TTTGTTAGTTTAGGGTTTAGGGTAAAACAAAAAGCAGCTAATTAG
64335 TTTGTTAGTTTAGGGTT
1 TTTGTTAGTTTAGGGTT
64352 ATATGATTGT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 61 1.00
ACGTcount: A:0.32, C:0.05, G:0.25, T:0.38
Consensus pattern (45 bp):
TTTGTTAGTTTAGGGTTTAGGGTAAAACAAAAAGCAGCTAATTAG
Found at i:64492 original size:45 final size:45
Alignment explanation
Indices: 64389--64520 Score: 134
Period size: 45 Copynumber: 3.0 Consensus size: 45
64379 TACATAAATT
*
64389 AAAAATTATTTAATTAGTATATG-TTTG---ATAGTTA--TATAGTTA
1 AAAAATTATTTAATTAGT-T-TGTTTTGTTAATAGTTAGTTATA-TAA
*
64431 AAAAA-TAATTAATTAGTTTGTTTTGTTAATAGTTAGTTATATAA
1 AAAAATTATTTAATTAGTTTGTTTTGTTAATAGTTAGTTATATAA
*
64475 AAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAATTATTTAATTAGTTTGT-TTTGTT-AATAGTT-AGTTATAT
64521 TTGTTTGTTG
Statistics
Matches: 76, Mismatches: 4, Indels: 14
0.81 0.04 0.15
Matches are distributed among these distances:
39 2 0.03
40 5 0.07
41 11 0.14
42 5 0.07
43 7 0.09
44 7 0.09
45 19 0.25
46 5 0.07
47 7 0.09
48 8 0.11
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (45 bp):
AAAAATTATTTAATTAGTTTGTTTTGTTAATAGTTAGTTATATAA
Found at i:65420 original size:17 final size:17
Alignment explanation
Indices: 65398--65430 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
65388 CAATGATTTT
*
65398 TAGTATCAAATCATTAC
1 TAGTATCAAATAATTAC
65415 TAGTATCAAATAATTA
1 TAGTATCAAATAATTA
65431 AATATTTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (17 bp):
TAGTATCAAATAATTAC
Found at i:65447 original size:24 final size:22
Alignment explanation
Indices: 65415--65483 Score: 77
Period size: 22 Copynumber: 3.0 Consensus size: 22
65405 AAATCATTAC
65415 TAGTATCAAATAATTAAATATT
1 TAGTATCAAATAATTAAATATT
* *
65437 TAGTAAATCAACTATTTTAAATCA-T
1 TAGT--ATCAAATA-ATTAAAT-ATT
65462 TAGTATCAAATAATTAAATATT
1 TAGTATCAAATAATTAAATATT
65484 AACAATAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
21 1 0.03
22 11 0.29
23 7 0.18
24 7 0.18
25 11 0.29
26 1 0.03
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (22 bp):
TAGTATCAAATAATTAAATATT
Found at i:65659 original size:14 final size:14
Alignment explanation
Indices: 65640--65679 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
65630 TAGTAATAAT
65640 TATTAAATCATTAG
1 TATTAAATCATTAG
*
65654 TATTAAATCATTAT
1 TATTAAATCATTAG
*
65668 TA-TAAATAATTA
1 TATTAAATCATTA
65680 CTAAATAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 9 0.38
14 15 0.62
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (14 bp):
TATTAAATCATTAG
Found at i:65684 original size:11 final size:11
Alignment explanation
Indices: 65666--65701 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
65656 TTAAATCATT
65666 ATTA-TAAATA
1 ATTACTAAATA
65676 ATTACTAAATA
1 ATTACTAAATA
*
65687 ATAACTAAATA
1 ATTACTAAATA
65698 ATTA
1 ATTA
65702 TTATAAAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 4 0.17
11 19 0.83
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (11 bp):
ATTACTAAATA
Found at i:65703 original size:35 final size:37
Alignment explanation
Indices: 65622--65708 Score: 99
Period size: 38 Copynumber: 2.4 Consensus size: 37
65612 TTAGTATTCT
* * *
65622 ATAATTATTAGT-AATAATTATTAAATCATTAGTATTAA
1 ATAATTATTA-TAAATAATTACTAAATCAATAG-ACTAA
*
65660 ATCATTATTATAAATAATTACTAAAT-AATA-ACTAA
1 ATAATTATTATAAATAATTACTAAATCAATAGACTAA
65695 ATAATTATTATAAA
1 ATAATTATTATAAA
65709 ATCATTATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
35 17 0.40
37 4 0.09
38 22 0.51
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (37 bp):
ATAATTATTATAAATAATTACTAAATCAATAGACTAA
Found at i:65726 original size:17 final size:17
Alignment explanation
Indices: 65713--65746 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
65703 TATAAAATCA
65713 TTATTTAAACAAAATAT
1 TTATTTAAACAAAATAT
65730 TTATTTAAACAACAATA
1 TTATTTAAACAA-AATA
65747 GCTCCCACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (17 bp):
TTATTTAAACAAAATAT
Found at i:66040 original size:28 final size:30
Alignment explanation
Indices: 65992--66054 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
65982 TTTTTTTATA
*
65992 TAATATAATATATAACTTAAACTAATAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
66022 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
66050 TAATA
1 TAATA
66055 ATTTATACTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 25 0.78
29 1 0.03
30 6 0.19
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:66061 original size:28 final size:28
Alignment explanation
Indices: 65996--66061 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
65986 TTTATATAAT
*
65996 ATAATATATAACTTAAACTAATAAACTA
1 ATAATATATAACTTAAACTAACAAACTA
66024 AT-ATAATATAACTTAAACTAACAAACTA
1 ATAAT-ATATAACTTAAACTAACAAACTA
*
66052 ATAATTTATA
1 ATAATATATA
66062 CTAACAAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 30 0.88
29 2 0.06
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAACTA
Found at i:66064 original size:21 final size:21
Alignment explanation
Indices: 66031--66079 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
66021 CTAATATAAT
66031 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
66052 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
66073 ATTAACT
1 A-TAACT
66080 AGATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:66567 original size:15 final size:14
Alignment explanation
Indices: 66538--66564 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
66528 CCATCCCCTC
66538 CCCCATGCATTCCA
1 CCCCATGCATTCCA
66552 CCCCATGCATTCC
1 CCCCATGCATTCC
66565 CACAGTTCCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.52, G:0.07, T:0.22
Consensus pattern (14 bp):
CCCCATGCATTCCA
Found at i:66598 original size:59 final size:60
Alignment explanation
Indices: 66506--66627 Score: 237
Period size: 59 Copynumber: 2.0 Consensus size: 60
66496 CATGGCCATG
66506 CACAGTTCCCACGTCCAATGCACCATCCCCTCCCCCATGCATT-CCACCCCATGCATTCC
1 CACAGTTCCCACGTCCAATGCACCATCCCCTCCCCCATGCATTCCCACCCCATGCATTCC
66565 CACAGTTCCCACGTCCAATGCACCATCCCCTCCCCCATGCATTCCCACCCCATGCATTCC
1 CACAGTTCCCACGTCCAATGCACCATCCCCTCCCCCATGCATTCCCACCCCATGCATTCC
66625 CAC
1 CAC
66628 GTCCCATGCA
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
59 43 0.69
60 19 0.31
ACGTcount: A:0.20, C:0.52, G:0.08, T:0.20
Consensus pattern (60 bp):
CACAGTTCCCACGTCCAATGCACCATCCCCTCCCCCATGCATTCCCACCCCATGCATTCC
Found at i:66617 original size:15 final size:15
Alignment explanation
Indices: 66597--66660 Score: 83
Period size: 15 Copynumber: 4.1 Consensus size: 15
66587 CCATCCCCTC
66597 CCCCATGCATTCCCA
1 CCCCATGCATTCCCA
66612 CCCCATGCATTCCCA
1 CCCCATGCATTCCCA
* *
66627 CGTCCCATGCATCCCCTC
1 C--CCCATGCATTCCC-A
66645 CCCCATGCATTCCCA
1 CCCCATGCATTCCCA
66660 C
1 C
66661 GTCCCATGTT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
15 17 0.40
16 12 0.29
17 12 0.29
18 1 0.02
ACGTcount: A:0.17, C:0.55, G:0.08, T:0.20
Consensus pattern (15 bp):
CCCCATGCATTCCCA
Found at i:66635 original size:17 final size:16
Alignment explanation
Indices: 66598--66668 Score: 90
Period size: 17 Copynumber: 4.4 Consensus size: 16
66588 CATCCCCTCC
66598 CCCATGCATTCCCAC-
1 CCCATGCATTCCCACT
66613 CCCATGCATTCCCACGT
1 CCCATGCATTCCCAC-T
* * *
66630 CCCATGCATCCCCTCC
1 CCCATGCATTCCCACT
66646 CCCATGCATTCCCACGT
1 CCCATGCATTCCCAC-T
66663 CCCATG
1 CCCATG
66669 TTGATTGCAT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
15 15 0.32
16 13 0.28
17 19 0.40
ACGTcount: A:0.17, C:0.52, G:0.10, T:0.21
Consensus pattern (16 bp):
CCCATGCATTCCCACT
Found at i:66649 original size:16 final size:16
Alignment explanation
Indices: 66588--66654 Score: 73
Period size: 16 Copynumber: 4.2 Consensus size: 16
66578 TCCAATGCAC
66588 CATCCCCTCCCCCATG
1 CATCCCCTCCCCCATG
* *
66604 CATTCCC-ACCCCATG
1 CATCCCCTCCCCCATG
* * *
66619 CATTCCCACGTCCCATG
1 CATCCCCTC-CCCCATG
66636 CATCCCCTCCCCCATG
1 CATCCCCTCCCCCATG
66652 CAT
1 CAT
66655 TCCCACGTCC
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
15 14 0.33
16 15 0.36
17 13 0.31
ACGTcount: A:0.16, C:0.55, G:0.07, T:0.21
Consensus pattern (16 bp):
CATCCCCTCCCCCATG
Found at i:66653 original size:33 final size:32
Alignment explanation
Indices: 66598--66668 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 32
66588 CATCCCCTCC
*
66598 CCCATGCATTCCCACCCCATGCATTCCCACGT
1 CCCATGCATCCCCACCCCATGCATTCCCACGT
*
66630 CCCATGCATCCCCTCCCCCATGCATTCCCACGT
1 CCCATGCATCCCC-ACCCCATGCATTCCCACGT
66663 CCCATG
1 CCCATG
66669 TTGATTGCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 12 0.33
33 24 0.67
ACGTcount: A:0.17, C:0.52, G:0.10, T:0.21
Consensus pattern (32 bp):
CCCATGCATCCCCACCCCATGCATTCCCACGT
Found at i:66732 original size:29 final size:29
Alignment explanation
Indices: 66676--66781 Score: 185
Period size: 29 Copynumber: 3.6 Consensus size: 29
66666 ATGTTGATTG
66676 CATGGCGACCTACACACAGGTCGCCCGGATGC
1 CATGGCGACCT-C-CA-AGGTCGCCCGGATGC
66708 CATGGCGACCTCCAAGGTCGCCCGGATGC
1 CATGGCGACCTCCAAGGTCGCCCGGATGC
66737 CATGGCGACCTCCAAGGTCGCCCGGATGC
1 CATGGCGACCTCCAAGGTCGCCCGGATGC
66766 CATGGCGACCTCCAAG
1 CATGGCGACCTCCAAG
66782 ACCACTGTAG
Statistics
Matches: 74, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
29 60 0.81
30 2 0.03
31 1 0.01
32 11 0.15
ACGTcount: A:0.20, C:0.38, G:0.29, T:0.13
Consensus pattern (29 bp):
CATGGCGACCTCCAAGGTCGCCCGGATGC
Found at i:68983 original size:3 final size:3
Alignment explanation
Indices: 68975--69073 Score: 198
Period size: 3 Copynumber: 33.0 Consensus size: 3
68965 ATACCATTAA
68975 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
69023 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
69071 ATT
1 ATT
69074 GAAACGGTGG
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 96 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:88985 original size:11 final size:11
Alignment explanation
Indices: 88971--88997 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
88961 TTAATGCTGC
88971 TTTTTTTTTCT
1 TTTTTTTTTCT
88982 TTTTTTTTTCT
1 TTTTTTTTTCT
88993 TTTTT
1 TTTTT
88998 CACTTCGGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (11 bp):
TTTTTTTTTCT
Found at i:89959 original size:15 final size:15
Alignment explanation
Indices: 89939--89968 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
89929 GATAAAGGAT
89939 TAGTATAAAGATATA
1 TAGTATAAAGATATA
89954 TAGTATAAAGATATA
1 TAGTATAAAGATATA
89969 AGGTGATTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.13, T:0.33
Consensus pattern (15 bp):
TAGTATAAAGATATA
Done.