Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006892.1 Hibiscus syriacus cultivar Beakdansim tig00017586_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: 134713
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2226 original size:75 final size:75
Alignment explanation
Indices: 2103--2249 Score: 294
Period size: 75 Copynumber: 2.0 Consensus size: 75
2093 CAAACTCACC
2103 TCCAAATCCACCTCCTATCTAACAATTTCCTAATCCTAATCCCGATGATCCAAATATGACCATTC
1 TCCAAATCCACCTCCTATCTAACAATTTCCTAATCCTAATCCCGATGATCCAAATATGACCATTC
2168 TTAATTCGTG
66 TTAATTCGTG
2178 TCCAAATCCACCTCCTATCTAACAATTTCCTAATCCTAATCCCGATGATCCAAATATGACCATTC
1 TCCAAATCCACCTCCTATCTAACAATTTCCTAATCCTAATCCCGATGATCCAAATATGACCATTC
2243 TTAATTC
66 TTAATTC
2250 AGCTTCAATG
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 72 1.00
ACGTcount: A:0.31, C:0.31, G:0.05, T:0.32
Consensus pattern (75 bp):
TCCAAATCCACCTCCTATCTAACAATTTCCTAATCCTAATCCCGATGATCCAAATATGACCATTC
TTAATTCGTG
Found at i:5653 original size:75 final size:75
Alignment explanation
Indices: 5530--5681 Score: 268
Period size: 75 Copynumber: 2.0 Consensus size: 75
5520 TGAACCGAAT
* *
5530 TCTTTTTATTTGTATAATTGAAATGCAATCAAACAACAAAAGTTGTATGATATGAGTCAACAACG
1 TCTTTTTATTTGTACAATTGAAATGCAACCAAACAACAAAAGTTGTATGATATGAGTCAACAACG
*
5595 GAATTGCTAC
66 GAACTGCTAC
*
5605 TCTTTTTATTTGTACAATTGAAATGCAACCAAACTACAAAAGTTGTATGATATGAGTCAACAACG
1 TCTTTTTATTTGTACAATTGAAATGCAACCAAACAACAAAAGTTGTATGATATGAGTCAACAACG
5670 GAACTGCTAC
66 GAACTGCTAC
5680 TC
1 TC
5682 CTTACGTTAG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (75 bp):
TCTTTTTATTTGTACAATTGAAATGCAACCAAACAACAAAAGTTGTATGATATGAGTCAACAACG
GAACTGCTAC
Found at i:9605 original size:42 final size:42
Alignment explanation
Indices: 9494--9607 Score: 192
Period size: 42 Copynumber: 2.7 Consensus size: 42
9484 CGAATTCTTG
* *
9494 TGTTTGTTTCACGTAATTCGTTTTCCGAAAAATGTTTTCCCG
1 TGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCCCA
9536 TGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCCCA
1 TGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCCCA
* *
9578 TGTTTGTTTAACGTAATTGGTTTTCCGGAA
1 TGTTTGTTTCACGTAATTCGTTTTCCGGAA
9608 TGTAATTCAT
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 68 1.00
ACGTcount: A:0.19, C:0.17, G:0.18, T:0.46
Consensus pattern (42 bp):
TGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCCCA
Found at i:9856 original size:31 final size:29
Alignment explanation
Indices: 9794--9955 Score: 82
Period size: 28 Copynumber: 5.9 Consensus size: 29
9784 ATTATTTATT
9794 TATTTATTAATATTTATAATAATATAATA
1 TATTTATTAATATTTATAATAATATAATA
*
9823 TATTT-TTAATA-TTAT-ATAAAATAATCA
1 TATTTATTAATATTTATAATAATATAAT-A
* * * *
9850 -ATTATATT-ATAATAAT-ATAAGATATTA
1 TATT-TATTAATATTTATAATAATATAATA
* * *
9877 TATTT-TT-ATTTTAATAATATATAATAAAA
1 TATTTATTAATATTTATAATA-AT-ATAATA
* *
9906 AATTTA-T-ATATTTAATAATGA-ATAATA
1 TATTTATTAATATTT-ATAATAATATAATA
9933 TTATTTA-T-ATATTTA-AATAATAT
1 -TATTTATTAATATTTATAATAATAT
9956 TTTAATAAAA
Statistics
Matches: 105, Mismatches: 16, Indels: 26
0.71 0.11 0.18
Matches are distributed among these distances:
26 24 0.23
27 22 0.21
28 35 0.33
29 19 0.18
30 5 0.05
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (29 bp):
TATTTATTAATATTTATAATAATATAATA
Found at i:9922 original size:59 final size:62
Alignment explanation
Indices: 9852--9972 Score: 146
Period size: 59 Copynumber: 2.0 Consensus size: 62
9842 AATAATCAAT
* *
9852 TATATTATAATAAT--ATAAGATATTATATT-TTTATTTTAATAATA-TATAATAAAAA-ATTTA
1 TATATTATAATAATGAAT-A-ATATTAT-TTATATATTTAAATAATATTATAATAAAAATATTTA
*
9912 TATATT-TAATAATGAATAATATTATTTATATATTTAAATAATATTTTAATAAAAATATTTA
1 TATATTATAATAATGAATAATATTATTTATATATTTAAATAATATTATAATAAAAATATTTA
9973 AAATATACTA
Statistics
Matches: 53, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
58 2 0.04
59 27 0.51
60 17 0.32
61 7 0.13
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.49
Consensus pattern (62 bp):
TATATTATAATAATGAATAATATTATTTATATATTTAAATAATATTATAATAAAAATATTTA
Found at i:9984 original size:23 final size:23
Alignment explanation
Indices: 9958--10002 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
9948 AATAATATTT
9958 TAATAAAAATATTTAAAATATAC
1 TAATAAAAATATTTAAAATATAC
* * *
9981 TAATTAATATTTTTAAAATATA
1 TAATAAAAATATTTAAAATATA
10003 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
TAATAAAAATATTTAAAATATAC
Found at i:10384 original size:15 final size:15
Alignment explanation
Indices: 10364--10438 Score: 132
Period size: 15 Copynumber: 5.0 Consensus size: 15
10354 TTCATTTTCT
10364 AGTTCCAGTAATTCA
1 AGTTCCAGTAATTCA
10379 AGTTCCAGTAATTCA
1 AGTTCCAGTAATTCA
*
10394 AATTCCAGTAATTCA
1 AGTTCCAGTAATTCA
10409 AGTTCCAGTAATTCA
1 AGTTCCAGTAATTCA
*
10424 AATTCCAGTAATTCA
1 AGTTCCAGTAATTCA
10439 TTTTCCGAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 57 1.00
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (15 bp):
AGTTCCAGTAATTCA
Found at i:10400 original size:30 final size:30
Alignment explanation
Indices: 10366--10438 Score: 146
Period size: 30 Copynumber: 2.4 Consensus size: 30
10356 CATTTTCTAG
10366 TTCCAGTAATTCAAGTTCCAGTAATTCAAA
1 TTCCAGTAATTCAAGTTCCAGTAATTCAAA
10396 TTCCAGTAATTCAAGTTCCAGTAATTCAAA
1 TTCCAGTAATTCAAGTTCCAGTAATTCAAA
10426 TTCCAGTAATTCA
1 TTCCAGTAATTCA
10439 TTTTCCGAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.34
Consensus pattern (30 bp):
TTCCAGTAATTCAAGTTCCAGTAATTCAAA
Found at i:14637 original size:25 final size:26
Alignment explanation
Indices: 14602--14651 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
14592 CTCAACATTA
* *
14602 TTGAAATAAT-CTATTGTTATTTTTT
1 TTGAAACAATCCTATTGTTAATTTTT
14627 TTGAAACAATCCTATTGTTAATTTT
1 TTGAAACAATCCTATTGTTAATTTT
14652 GAATATCCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.30, C:0.08, G:0.08, T:0.54
Consensus pattern (26 bp):
TTGAAACAATCCTATTGTTAATTTTT
Found at i:18393 original size:31 final size:30
Alignment explanation
Indices: 18355--18414 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
18345 CGAGGGTTAA
18355 CTATGTTCTACAGAACATATGGACAGTTTAC
1 CTATGTTCTACAGAACATATGGAC-GTTTAC
* * *
18386 CTATGTTCTTCGGAATATATGGACGTTTA
1 CTATGTTCTACAGAACATATGGACGTTTA
18415 GTAGGTCCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 5 0.19
31 21 0.81
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (30 bp):
CTATGTTCTACAGAACATATGGACGTTTAC
Found at i:19188 original size:20 final size:21
Alignment explanation
Indices: 19163--19204 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
19153 TGTAGCAGTA
19163 CTGTAGCA-GGGTATCAATAC
1 CTGTAGCAGGGGTATCAATAC
*
19183 CTGTAGCAGGGGTATCGATAC
1 CTGTAGCAGGGGTATCAATAC
19204 C
1 C
19205 CTGAAGCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (21 bp):
CTGTAGCAGGGGTATCAATAC
Found at i:19212 original size:22 final size:20
Alignment explanation
Indices: 19167--19212 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
19157 GCAGTACTGT
*
19167 AGCAGGGTATCAATACCTGT
1 AGCAGGGTATCAATACCTGA
*
19187 AGCAGGGGTATCGATACCCTGA
1 AGCA-GGGTATCAATA-CCTGA
19209 AGCA
1 AGCA
19213 ATCTGGAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 4 0.18
21 10 0.45
22 8 0.36
ACGTcount: A:0.30, C:0.22, G:0.28, T:0.20
Consensus pattern (20 bp):
AGCAGGGTATCAATACCTGA
Found at i:27337 original size:21 final size:21
Alignment explanation
Indices: 27311--27355 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
27301 GATTTCTGGG
* *
27311 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
27332 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
27353 CAA
1 CAA
27356 ACGAATAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:29066 original size:23 final size:23
Alignment explanation
Indices: 29036--29095 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
29026 ATTATTATAT
29036 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
*
29059 GGCACTACGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
*
29082 GGCACTTCGGTGCA
1 GGCACTACGGTGCA
29096 TTTATATGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.20, C:0.28, G:0.28, T:0.23
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:38269 original size:21 final size:21
Alignment explanation
Indices: 38199--38282 Score: 89
Period size: 21 Copynumber: 4.0 Consensus size: 21
38189 CCAGAACCCC
* **
38199 AGGGGGGTATCGATTCCCTTG
1 AGGGGGGAATCGATTCCCTCA
* *
38220 TGGGGGGAATCGGTTCCCCTTCA
1 AGGGGGGAATCGATT-CCC-TCA
*
38243 AAGGGGGAATCGATTCCCTCA
1 AGGGGGGAATCGATTCCCTCA
38264 AGGGGGGAA-CGATTCCCTC
1 AGGGGGGAATCGATTCCCTC
38283 TGCACCAAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 5
0.79 0.14 0.08
Matches are distributed among these distances:
20 10 0.19
21 23 0.44
22 6 0.12
23 13 0.25
ACGTcount: A:0.19, C:0.24, G:0.35, T:0.23
Consensus pattern (21 bp):
AGGGGGGAATCGATTCCCTCA
Found at i:46823 original size:21 final size:21
Alignment explanation
Indices: 46798--46878 Score: 83
Period size: 21 Copynumber: 3.8 Consensus size: 21
46788 CAGAACCCCA
* **
46798 GGGGGTATCGATTCCCTTGTG
1 GGGGGAATCGATTCCCTTAAG
* *
46819 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGATT-CCCTT-AAG
*
46842 GGGGGAATCGATTCCCTCAAG
1 GGGGGAATCGATTCCCTTAAG
46863 GGGGG-ATCGATTCCCT
1 GGGGGAATCGATTCCCT
46879 CTGCACCAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
20 11 0.22
21 18 0.36
22 9 0.18
23 12 0.24
ACGTcount: A:0.17, C:0.23, G:0.35, T:0.25
Consensus pattern (21 bp):
GGGGGAATCGATTCCCTTAAG
Found at i:46865 original size:20 final size:21
Alignment explanation
Indices: 46819--46879 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
46809 TTCCCTTGTG
*
46819 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGATT-CCC-TCAAA
46842 GGGGGAATCGATTCCCTC-AA
1 GGGGGAATCGATTCCCTCAAA
*
46862 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
46880 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 19 0.53
21 2 0.06
22 3 0.08
23 12 0.33
ACGTcount: A:0.20, C:0.26, G:0.33, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGATTCCCTCAAA
Found at i:54287 original size:14 final size:15
Alignment explanation
Indices: 54263--54292 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
54253 ATATGAAATG
54263 TTATATAGTTTTATA
1 TTATATAGTTTTATA
54278 TTATAT-GTTTTATA
1 TTATATAGTTTTATA
54292 T
1 T
54293 GCCTCACTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (15 bp):
TTATATAGTTTTATA
Found at i:56504 original size:30 final size:30
Alignment explanation
Indices: 56463--56543 Score: 135
Period size: 30 Copynumber: 2.7 Consensus size: 30
56453 AATTGAAAGA
56463 TAAGTGGTCAAAATAGAATCTCCCAATAAT
1 TAAGTGGTCAAAATAGAATCTCCCAATAAT
* *
56493 TAAGTGATCAAAATAAAATCTCCCAATAAT
1 TAAGTGGTCAAAATAGAATCTCCCAATAAT
*
56523 TAAGTGGTAAAAATAGAATCT
1 TAAGTGGTCAAAATAGAATCT
56544 ATTAATAGTT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.27
Consensus pattern (30 bp):
TAAGTGGTCAAAATAGAATCTCCCAATAAT
Found at i:56727 original size:42 final size:42
Alignment explanation
Indices: 56665--56758 Score: 161
Period size: 42 Copynumber: 2.2 Consensus size: 42
56655 CCTTCCTCTA
*
56665 TCTAAAACCCCATTTCTCATTTTATAGTTCTAATCTAGGCAC
1 TCTAAAACCCCATTTCTCATTTTATAGTTCCAATCTAGGCAC
* *
56707 TCTAAAACCCCATTTTTCATTTTATATTTCCAATCTAGGCAC
1 TCTAAAACCCCATTTCTCATTTTATAGTTCCAATCTAGGCAC
56749 TCTAAAACCC
1 TCTAAAACCC
56759 TAAACCTCCT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.30, C:0.28, G:0.05, T:0.37
Consensus pattern (42 bp):
TCTAAAACCCCATTTCTCATTTTATAGTTCCAATCTAGGCAC
Found at i:60518 original size:12 final size:12
Alignment explanation
Indices: 60501--60534 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
60491 AGTTCCAGAC
60501 TTCTCTTCTTCA
1 TTCTCTTCTTCA
60513 TTCTCTTCTTCA
1 TTCTCTTCTTCA
60525 TTCTCTTCTT
1 TTCTCTTCTT
60535 TTCCACCGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.06, C:0.32, G:0.00, T:0.62
Consensus pattern (12 bp):
TTCTCTTCTTCA
Found at i:61110 original size:23 final size:22
Alignment explanation
Indices: 61066--61110 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
61056 AATCTCATAG
* *
61066 GGGAATCGATTCCCCCACAGGA
1 GGGAACCGATTCCCCCAAAGGA
*
61088 GGGAACCGATTACCCCTAAAGGA
1 GGGAACCGATT-CCCCCAAAGGA
61111 AAAATGTGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.31, C:0.29, G:0.27, T:0.13
Consensus pattern (22 bp):
GGGAACCGATTCCCCCAAAGGA
Found at i:62621 original size:103 final size:103
Alignment explanation
Indices: 62396--62613 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
62386 GTCGAGGGTC
* *
62396 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTTTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
62461 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
62499 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
62564 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
62602 TATGTGGTCCTT
1 TATGTGGTCCTT
62614 ATGGACATTA
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:62663 original size:23 final size:23
Alignment explanation
Indices: 62629--62697 Score: 111
Period size: 23 Copynumber: 3.0 Consensus size: 23
62619 CATTATTATA
62629 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
*
62652 TGGCACTCCGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
62675 TGGCACTTCGGTGCAATTATACG
1 TGGCACTACGGTGCAATTCTACG
62698 AGCTGTGGTG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:64323 original size:12 final size:12
Alignment explanation
Indices: 64284--64326 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
64274 GTTCGAATGA
64284 AGTTCAAATTCG
1 AGTTCAAATTCG
* *
64296 AGCTC-AATTCA
1 AGTTCAAATTCG
64307 AGTTCAAATTCG
1 AGTTCAAATTCG
*
64319 TGTTCAAA
1 AGTTCAAA
64327 CCTGAAACTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
11 9 0.36
12 16 0.64
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (12 bp):
AGTTCAAATTCG
Found at i:64717 original size:31 final size:31
Alignment explanation
Indices: 64689--64802 Score: 103
Period size: 31 Copynumber: 3.7 Consensus size: 31
64679 CCATTATAGG
64689 ATAAT-TATTAAATTTATCGAAATGTTATAA
1 ATAATATATTAAATTTATCGAAATGTTATAA
** *
64719 ATTTTATATTAAATTTATCGAACTGTTATAA
1 ATAATATATTAAATTTATCGAAATGTTATAA
** *
64750 ATTTTATATTAAATTTTATC-AAATTATTAT-A
1 ATAATATATTAAA-TTTATCGAAA-TGTTATAA
*
64781 A-AATATCA-TAAATTTATAGAAA
1 ATAATAT-ATTAAATTTATCGAAA
64803 CATCGCAGTT
Statistics
Matches: 71, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
29 5 0.07
30 13 0.18
31 42 0.59
32 11 0.15
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (31 bp):
ATAATATATTAAATTTATCGAAATGTTATAA
Found at i:64784 original size:21 final size:20
Alignment explanation
Indices: 64744--64795 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
64734 TATCGAACTG
64744 TTATAAATTTTATATTAAATT
1 TTATAAATTTTATA-TAAATT
*
64765 TTATCAAATTATTATA-AAATA
1 TTAT-AAATT-TTATATAAATT
*
64786 TCATAAATTT
1 TTATAAATTT
64796 ATAGAAACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
19 1 0.04
20 5 0.19
21 11 0.41
22 5 0.19
23 5 0.19
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (20 bp):
TTATAAATTTTATATAAATT
Found at i:64835 original size:14 final size:14
Alignment explanation
Indices: 64816--64845 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
64806 CGCAGTTATT
64816 ATAATTTTATAATA
1 ATAATTTTATAATA
64830 ATAATTTTATAATA
1 ATAATTTTATAATA
64844 AT
1 AT
64846 TTAGTAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATAATTTTATAATA
Found at i:67398 original size:22 final size:23
Alignment explanation
Indices: 67371--67423 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
67361 CATTCCACTC
67371 CCCTAAATTCTCAAAC-TT-AAAT
1 CCCTAAATT-TCAAACATTCAAAT
67393 CCCTAAAATTTCAAACATTCAAAT
1 CCCT-AAATTTCAAACATTCAAAT
*
67417 CTCTAAA
1 CCCTAAA
67424 AATCTCCTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 10 0.37
23 10 0.37
24 7 0.26
ACGTcount: A:0.43, C:0.26, G:0.00, T:0.30
Consensus pattern (23 bp):
CCCTAAATTTCAAACATTCAAAT
Found at i:67422 original size:24 final size:23
Alignment explanation
Indices: 67371--67429 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 23
67361 CATTCCACTC
67371 CCCT-AAATTCTCAAACTTAAAT
1 CCCTAAAATTCTCAAACTTAAAT
67393 CCCTAAAATT-TCAAACATTCAAAT
1 CCCTAAAATTCTCAAAC-TT-AAAT
* *
67417 CTCTAAAAATCTC
1 CCCTAAAATTCTC
67430 CTTAATCTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 10 0.32
23 7 0.23
24 12 0.39
25 2 0.06
ACGTcount: A:0.42, C:0.27, G:0.00, T:0.31
Consensus pattern (23 bp):
CCCTAAAATTCTCAAACTTAAAT
Found at i:68433 original size:42 final size:42
Alignment explanation
Indices: 68369--68648 Score: 400
Period size: 42 Copynumber: 6.7 Consensus size: 42
68359 GGCATCGTCC
* * *
68369 GGGATTTCAGCACTCGGTGAGGAACTTCCAATGTTTAAGCTT
1 GGGATTTCAGCACCCGGCGAGGAACTTTCAATGTTTAAGCTT
* * *
68411 GGGGTTTCAGCACCCGACGAGGAGCTTTCAATGTTTAAGCTT
1 GGGATTTCAGCACCCGGCGAGGAACTTTCAATGTTTAAGCTT
* *
68453 GGGATTTCAGCA-CCGGCGAGGAGCTTTCAATGTTTAGGCTT
1 GGGATTTCAGCACCCGGCGAGGAACTTTCAATGTTTAAGCTT
*
68494 GGGATTTCAGCATCCGGCGAGGAACTTTCAATGTTTAAGCTT
1 GGGATTTCAGCACCCGGCGAGGAACTTTCAATGTTTAAGCTT
* * *
68536 GGGATTTCAGCACCTGGCGAGGAATTTTCAATGTTTACGCTT
1 GGGATTTCAGCACCCGGCGAGGAACTTTCAATGTTTAAGCTT
* * *
68578 GGGATTTCAGCGCACAGCGAGGAACTTTCAATGTTTAAGCTT
1 GGGATTTCAGCACCCGGCGAGGAACTTTCAATGTTTAAGCTT
* *
68620 GGGATTTCAGCACACAGCGAGGAACTTTC
1 GGGATTTCAGCACCCGGCGAGGAACTTTC
68649 GTCTTCACCG
Statistics
Matches: 215, Mismatches: 22, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
41 39 0.18
42 176 0.82
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (42 bp):
GGGATTTCAGCACCCGGCGAGGAACTTTCAATGTTTAAGCTT
Found at i:72953 original size:18 final size:18
Alignment explanation
Indices: 72932--72984 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 18
72922 GAGAGAAGAA
72932 AAAATTAATATATAATAT
1 AAAATTAATATATAATAT
*
72950 AAAATT-ATGA-AT-ACAT
1 AAAATTAAT-ATATAATAT
72966 AAAA-TAATATATATATAT
1 AAAATTAATATATA-ATAT
72984 A
1 A
72985 TAATGGACGT
Statistics
Matches: 28, Mismatches: 2, Indels: 10
0.70 0.05 0.25
Matches are distributed among these distances:
15 2 0.07
16 11 0.39
17 4 0.14
18 11 0.39
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (18 bp):
AAAATTAATATATAATAT
Found at i:73468 original size:2 final size:2
Alignment explanation
Indices: 73453--73508 Score: 94
Period size: 2 Copynumber: 27.5 Consensus size: 2
73443 CTATTTTACC
*
73453 TA TA TA AA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
73496 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
73509 TCACCTTAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
2 49 0.96
3 2 0.04
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:99795 original size:12 final size:12
Alignment explanation
Indices: 99778--99803 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
99768 GACCACCACC
99778 GTCAAAAGCAGT
1 GTCAAAAGCAGT
99790 GTCAAAAGCAGT
1 GTCAAAAGCAGT
99802 GT
1 GT
99804 ACTGATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.15, G:0.27, T:0.19
Consensus pattern (12 bp):
GTCAAAAGCAGT
Found at i:103972 original size:20 final size:19
Alignment explanation
Indices: 103947--104000 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
103937 TTAATAAAAC
*
103947 ATTTATTAAAAATATATAT
1 ATTTATTAAAAATATAAAT
103966 AATTTA-TAAAAAGTA-AAAT
1 -ATTTATTAAAAA-TATAAAT
103985 ATTTATTTAAAAATAT
1 ATTTA-TTAAAAATAT
104001 CAGAAAATGA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
18 5 0.17
19 11 0.38
20 13 0.45
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
ATTTATTAAAAATATAAAT
Found at i:104384 original size:29 final size:30
Alignment explanation
Indices: 104330--104388 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
104320 ATTGCAATTA
104330 AATAGTGACTAAAACATATAAAATTAAAAT
1 AATAGTGACTAAAACATATAAAATTAAAAT
* *
104360 AATAG-GATTAAAATATA-AAATATTAAAAT
1 AATAGTGACTAAAACATATAAA-ATTAAAAT
104389 TTATAACCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 3 0.12
29 18 0.69
30 5 0.19
ACGTcount: A:0.61, C:0.03, G:0.07, T:0.29
Consensus pattern (30 bp):
AATAGTGACTAAAACATATAAAATTAAAAT
Found at i:105598 original size:3 final size:3
Alignment explanation
Indices: 105590--105636 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
105580 ATTAATTATT
*
105590 TAA TAA TAA TAA T-A TAA T-A TAA TAA TAA -AA CAA -AA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
105634 TAA
1 TAA
105637 ATAAAACAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
2 8 0.20
3 32 0.80
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:105613 original size:13 final size:13
Alignment explanation
Indices: 105577--105640 Score: 51
Period size: 13 Copynumber: 4.9 Consensus size: 13
105567 TGTATTAAAA
*
105577 ATAAT-TAATTAT
1 ATAATATAATAAT
*
105589 TTAATAATAATAAT
1 ATAAT-ATAATAAT
105603 ATAATATAATAAT
1 ATAATATAATAAT
* * *
105616 AAAACAAAATAAT
1 ATAATATAATAAT
105629 AATAATA-AATAA
1 -ATAATATAATAA
105641 AACAAATAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
12 4 0.10
13 23 0.56
14 14 0.34
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (13 bp):
ATAATATAATAAT
Found at i:105613 original size:16 final size:15
Alignment explanation
Indices: 105592--105639 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
105582 TAATTATTTA
105592 ATAATAATAATATAAT
1 ATAATAATAATA-AAT
* *
105608 ATAATAATAAAACAAA
1 ATAATAATAATA-AAT
105624 ATAATAATAATAAAT
1 ATAATAATAATAAAT
105639 A
1 A
105640 AAACAAATAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
15 3 0.11
16 24 0.89
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (15 bp):
ATAATAATAATAAAT
Found at i:105648 original size:19 final size:18
Alignment explanation
Indices: 105591--105655 Score: 57
Period size: 19 Copynumber: 3.7 Consensus size: 18
105581 TTAATTATTT
*
105591 AATAATAAT-AAT-ATAA
1 AATAATAATAAATAAAAA
*
105607 TATAATAATAAA-ACAAAA
1 AATAATAATAAATA-AAAA
105625 TAATAATAATAAATAAAACA
1 -AATAATAATAAATAAAA-A
105645 AATAA-AATAAA
1 AATAATAATAAA
105656 AACTAGTGTC
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
16 8 0.20
17 2 0.05
18 9 0.22
19 19 0.47
20 2 0.05
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (18 bp):
AATAATAATAAATAAAAA
Found at i:105649 original size:32 final size:32
Alignment explanation
Indices: 105591--105656 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
105581 TTAATTATTT
* *
105591 AATAATAATAATATAATATAATAATAAAACAA
1 AATAATAATAATATAATAAAAAAATAAAACAA
*
105623 AATAATAATAATA-AATAAAACAAATAAAATAA
1 AATAATAATAATATAATAAAA-AAATAAAACAA
105655 AA
1 AA
105657 ACTAGTGTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 6 0.20
32 24 0.80
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (32 bp):
AATAATAATAATATAATAAAAAAATAAAACAA
Found at i:106267 original size:54 final size:54
Alignment explanation
Indices: 106185--106448 Score: 366
Period size: 54 Copynumber: 4.9 Consensus size: 54
106175 AGAATAGCAG
* * *
106185 GTTCGTAAAACATTTGATAGCACATTCATCCTTTCCTATGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
* * *
106239 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTTCAGAA
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
* * *
106293 GTTCGTAAAGCGTTTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
* * * * *
106347 GTTCGTAAAACATTTGACAACACATTCATCATTTCCTGTGGGTTCTGTTTAGAC
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
* * **
106401 GTTCGTAAAGCGTTTGACAACACATTCATCCTTTTTTGTGGCTTCTGC
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGC
106449 CAAGATTTCT
Statistics
Matches: 183, Mismatches: 27, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 183 1.00
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.38
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
Found at i:106374 original size:108 final size:108
Alignment explanation
Indices: 106185--106448 Score: 429
Period size: 108 Copynumber: 2.4 Consensus size: 108
106175 AGAATAGCAG
* * * * * *
106185 GTTCGTAAAACATTTGATAGCACATTCATCCTTTCCTATGGCTTCTGCTCAGATGTTCGTAAAAC
1 GTTCGTAAAGCGTTTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGATGTTCGTAAAAC
* *
106250 ATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTTCAGAA
66 ATTTGACAACACATTCATCATTTCCTGTGGGTTCTGTTCAGAA
106293 GTTCGTAAAGCGTTTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGATGTTCGTAAAAC
1 GTTCGTAAAGCGTTTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGATGTTCGTAAAAC
* *
106358 ATTTGACAACACATTCATCATTTCCTGTGGGTTCTGTTTAGAC
66 ATTTGACAACACATTCATCATTTCCTGTGGGTTCTGTTCAGAA
*
106401 GTTCGTAAAGCGTTTGACAACACATTCATCCTTTTTTGTGGCTTCTGC
1 GTTCGTAAAGCGTTTGACAACACATTCATCCTTTTCTGTGGCTTCTGC
106449 CAAGATTTCT
Statistics
Matches: 145, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
108 145 1.00
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.38
Consensus pattern (108 bp):
GTTCGTAAAGCGTTTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGATGTTCGTAAAAC
ATTTGACAACACATTCATCATTTCCTGTGGGTTCTGTTCAGAA
Found at i:108840 original size:114 final size:114
Alignment explanation
Indices: 108640--108854 Score: 378
Period size: 114 Copynumber: 1.9 Consensus size: 114
108630 TGCAGTTCAT
* * *
108640 CTTTCAATTCCAATGATTGGTTCTGGGGTTCCTACCGAAACAGATCAGATAACTCAAAGAACACT
1 CTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCGAAACAAATCAGATAACTCAAAGAACACT
108705 TCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAACAAATTAAG
66 TCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAACAAATTAAG
*
108754 CTTTCAAATCCAATGATTGGTTTTGGGGTTCATACC-AAATCAAATCAGATAACTCAAAGAACAC
1 CTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCGAAA-CAAATCAGATAACTCAAAGAACAC
108818 TTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTA
65 TTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTA
108855 CGAGAATGTG
Statistics
Matches: 96, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
113 3 0.03
114 93 0.97
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.32
Consensus pattern (114 bp):
CTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCGAAACAAATCAGATAACTCAAAGAACACT
TCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAACAAATTAAG
Found at i:110487 original size:24 final size:24
Alignment explanation
Indices: 110460--110531 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
110450 GTAAACGGAG
* *
110460 ATATCAAAAATCAAAACATAATTC
1 ATATCAAAAATCAGAACAGAATTC
* * *
110484 ATATCAGATATCAGAACAGAATCC
1 ATATCAAAAATCAGAACAGAATTC
*
110508 ATATC-AGAATCAGAACAGAATTC
1 ATATCAAAAATCAGAACAGAATTC
110531 A
1 A
110532 GGTAACGTAT
Statistics
Matches: 39, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
23 15 0.38
24 24 0.62
ACGTcount: A:0.51, C:0.18, G:0.08, T:0.22
Consensus pattern (24 bp):
ATATCAAAAATCAGAACAGAATTC
Found at i:111489 original size:18 final size:18
Alignment explanation
Indices: 111468--111503 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
111458 CTTCCATCCG
*
111468 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
111486 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
111504 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:112839 original size:18 final size:18
Alignment explanation
Indices: 112818--112863 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
112808 CGACGGTCAA
112818 CGGGTCGGGTCAACAGGT
1 CGGGTCGGGTCAACAGGT
*
112836 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACAGGT
112854 CGGGTCGGGT
1 CGGGTCGGGT
112864 TGTGACCAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.11, C:0.22, G:0.50, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACAGGT
Found at i:112859 original size:13 final size:13
Alignment explanation
Indices: 112812--112841 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
112802 GGTCAGCGAC
*
112812 GGTCAACGGGTCG
1 GGTCAACAGGTCG
112825 GGTCAACAGGTCG
1 GGTCAACAGGTCG
112838 GGTC
1 GGTC
112842 GGGTCAACGG
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:0.17, C:0.23, G:0.43, T:0.17
Consensus pattern (13 bp):
GGTCAACAGGTCG
Found at i:115055 original size:17 final size:16
Alignment explanation
Indices: 115033--115084 Score: 79
Period size: 17 Copynumber: 3.2 Consensus size: 16
115023 CTTGATTCAA
115033 TTTTTTT-TTTCTTTCC
1 TTTTTTTCTTT-TTTCC
115049 TTTTTTTCTTTTTTCC
1 TTTTTTTCTTTTTTCC
115065 TCTTTTTTCTTTTTTCC
1 T-TTTTTTCTTTTTTCC
115082 TTT
1 TTT
115085 CTTTACTGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.44
17 19 0.56
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTTTCTTTTTTCC
Found at i:115139 original size:25 final size:25
Alignment explanation
Indices: 115068--115140 Score: 119
Period size: 25 Copynumber: 2.8 Consensus size: 25
115058 TTTTTCCTCT
*
115068 TTTTTCTTTTTTCCTTTCTTTACTGGA
1 TTTTTC-TTTTT-CTTTCTTTGCTGGA
115095 TTTTTCTTTTTCTTTCTTTGCTGGA
1 TTTTTCTTTTTCTTTCTTTGCTGGA
115120 TTTTTCTTTTTCTTTCTTTGC
1 TTTTTCTTTTTCTTTCTTTGC
115141 ATGATGAGTA
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
25 34 0.76
26 5 0.11
27 6 0.13
ACGTcount: A:0.04, C:0.18, G:0.08, T:0.70
Consensus pattern (25 bp):
TTTTTCTTTTTCTTTCTTTGCTGGA
Found at i:117849 original size:32 final size:31
Alignment explanation
Indices: 117798--117915 Score: 132
Period size: 32 Copynumber: 3.7 Consensus size: 31
117788 GTTCCTTAGA
* *
117798 ACATAGGTATACTGTCCATATATCTCAAAAG
1 ACATAGGTATTCTGTCCATATGTCTCAAAAG
***
117829 ACATAGGTAATTCTGTCCATATGT-TCCGTAG
1 ACATAGGT-ATTCTGTCCATATGTCTCAAAAG
117860 AACATAGGTATAT-TGTCCATATGTCTCAAAAG
1 -ACATAGGTAT-TCTGTCCATATGTCTCAAAAG
*
117892 ACATAGGTAATTATGTCCATATGT
1 ACATAGGT-ATTCTGTCCATATGT
117916 TCCGTAGAAC
Statistics
Matches: 73, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
31 34 0.47
32 39 0.53
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (31 bp):
ACATAGGTATTCTGTCCATATGTCTCAAAAG
Found at i:117861 original size:63 final size:63
Alignment explanation
Indices: 117781--117935 Score: 274
Period size: 63 Copynumber: 2.5 Consensus size: 63
117771 AGGTAAACTA
* *
117781 TCCATATGTTCCTTAGAACATAGGTATACTGTCCATATATCTCAAAAGACATAGGTAATTCTG
1 TCCATATGTTCCGTAGAACATAGGTATACTGTCCATATATCTCAAAAGACATAGGTAATTATG
* *
117844 TCCATATGTTCCGTAGAACATAGGTATATTGTCCATATGTCTCAAAAGACATAGGTAATTATG
1 TCCATATGTTCCGTAGAACATAGGTATACTGTCCATATATCTCAAAAGACATAGGTAATTATG
117907 TCCATATGTTCCGTAGAACATAGGTATAC
1 TCCATATGTTCCGTAGAACATAGGTATAC
117936 CCTCGACTCT
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 87 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (63 bp):
TCCATATGTTCCGTAGAACATAGGTATACTGTCCATATATCTCAAAAGACATAGGTAATTATG
Found at i:117928 original size:32 final size:32
Alignment explanation
Indices: 117746--117932 Score: 163
Period size: 31 Copynumber: 5.9 Consensus size: 32
117736 ATCATCGGTA
* * *
117746 ACTGTCTATAGGTTCCGAT-GAACCTAGGTAA-
1 ACTGTCCATATGTTCC-ATAGAACATAGGTAAT
* *
117777 ACTATCCATATGTTCCTTAGAACATAGGT-AT
1 ACTGTCCATATGTTCCATAGAACATAGGTAAT
* * *
117808 ACTGTCCATATATCTCAAAAG-ACATAGGTAAT
1 ACTGTCCATATGT-TCCATAGAACATAGGTAAT
* *
117840 TCTGTCCATATGTTCCGTAGAACATAGGT-AT
1 ACTGTCCATATGTTCCATAGAACATAGGTAAT
* * *
117871 ATTGTCCATATGTCTCAAAAG-ACATAGGTAATT
1 ACTGTCCATATGT-TCCATAGAACATAGGTAA-T
*
117904 A-TGTCCATATGTTCCGTAGAACATAGGTA
1 ACTGTCCATATGTTCCATAGAACATAGGTA
117933 TACCCTCGAC
Statistics
Matches: 124, Mismatches: 23, Indels: 17
0.76 0.14 0.10
Matches are distributed among these distances:
30 2 0.02
31 70 0.56
32 50 0.40
33 2 0.02
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (32 bp):
ACTGTCCATATGTTCCATAGAACATAGGTAAT
Found at i:120411 original size:7 final size:7
Alignment explanation
Indices: 120377--120418 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
120367 ATAAAAGTAT
120377 AAATGCA
1 AAATGCA
* *
120384 CAATGAA
1 AAATGCA
120391 AAATGCA
1 AAATGCA
120398 AAGATGCA
1 AA-ATGCA
120406 AAATGC-
1 AAATGCA
120412 AAATGCA
1 AAATGCA
120419 TGTATGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
6 6 0.21
7 16 0.55
8 7 0.24
ACGTcount: A:0.55, C:0.14, G:0.17, T:0.14
Consensus pattern (7 bp):
AAATGCA
Found at i:121955 original size:28 final size:26
Alignment explanation
Indices: 121900--121957 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 26
121890 AAACATTAAT
*
121900 AAAATAATATACATATAAATATTATG
1 AAAATAATATACATATAAAAATTATG
* *
121926 AAAATAATAAGTATATATAAAAATTTTG
1 AAAATAAT-A-TACATATAAAAATTATG
121954 AAAA
1 AAAA
121958 GAAAAAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 8 0.30
27 1 0.04
28 18 0.67
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (26 bp):
AAAATAATATACATATAAAAATTATG
Found at i:122589 original size:20 final size:20
Alignment explanation
Indices: 122561--122620 Score: 65
Period size: 19 Copynumber: 3.1 Consensus size: 20
122551 AATAAATATA
122561 ATAAA-AATTTATTAAAAAT
1 ATAAATAATTTATTAAAAAT
*
122580 ATATATAATTTA-TAAAAAGT
1 ATAAATAATTTATTAAAAA-T
122600 A-AAAT-ATTTATTTAAAAAT
1 ATAAATAATTTA-TTAAAAAT
122619 AT
1 AT
122621 CAGAAAATGG
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
18 5 0.15
19 15 0.44
20 14 0.41
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
ATAAATAATTTATTAAAAAT
Found at i:122971 original size:14 final size:14
Alignment explanation
Indices: 122952--122999 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
122942 AAATAGTGAC
122952 TAAAATATAAAAAT
1 TAAAATATAAAAAT
**
122966 TAAAATA-ATAGGAT
1 TAAAATATA-AAAAT
*
122980 TAAAATATAAATAT
1 TAAAATATAAAAAT
122994 TAAAAT
1 TAAAAT
123000 TTAAGCCCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 1 0.04
14 26 0.93
15 1 0.04
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (14 bp):
TAAAATATAAAAAT
Found at i:122984 original size:28 final size:29
Alignment explanation
Indices: 122943--122999 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 29
122933 ATTGCAATTA
122943 AATAGTGACTAAAATATAAAAATTAAAAT
1 AATAGTGACTAAAATATAAAAATTAAAAT
* *
122972 AATAG-GATTAAAATATAAATATTAAAAT
1 AATAGTGACTAAAATATAAAAATTAAAAT
123000 TTAAGCCCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 21 0.81
29 5 0.19
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.30
Consensus pattern (29 bp):
AATAGTGACTAAAATATAAAAATTAAAAT
Found at i:123670 original size:3 final size:3
Alignment explanation
Indices: 123662--123708 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
123652 ATTAATTATT
*
123662 TAA TAA TAA TAA T-A TAA T-A TAA TAA TAA -AA CAA -AA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
123706 TAA
1 TAA
123709 ATAAAACAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
2 8 0.20
3 32 0.80
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:123685 original size:16 final size:15
Alignment explanation
Indices: 123664--123711 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
123654 TAATTATTTA
123664 ATAATAATAATATAAT
1 ATAATAATAATA-AAT
* *
123680 ATAATAATAAAACAAA
1 ATAATAATAATA-AAT
123696 ATAATAATAATAAAT
1 ATAATAATAATAAAT
123711 A
1 A
123712 AAACAAATGA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
15 3 0.11
16 24 0.89
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (15 bp):
ATAATAATAATAAAT
Found at i:133985 original size:22 final size:21
Alignment explanation
Indices: 133960--134004 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
133950 TTAGGTACGA
* *
133960 ACTTTTAAAATTTTAAGGACAG
1 ACTTATAAAATTTGAAGGA-AG
133982 ACTTATAAAATTTGAAGGAAG
1 ACTTATAAAATTTGAAGGAAG
134003 AC
1 AC
134005 GAAAACAGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.44, C:0.09, G:0.16, T:0.31
Consensus pattern (21 bp):
ACTTATAAAATTTGAAGGAAG
Done.