Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007240.1 Hibiscus syriacus cultivar Beakdansim tig00019179_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: 87917
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:3336 original size:107 final size:110
Alignment explanation
Indices: 3148--3362 Score: 348
Period size: 107 Copynumber: 2.0 Consensus size: 110
3138 TGCATGCCAT
*
3148 AATGTACTTGATTGTTACTTTTAATACATTAATCTTTGCTTCTGGAATAACTTAAATGTTTATAA
1 AATGTACTTGATTGTTACTTTTAATACATTAATCTTTGCTTCCGGAATAACTTAAATGTTTATAA
*
3213 CAAAATGCATGATTTCCTCTAGCAATATAAAACAA-TTCATCAGG
66 CAAAATCCATGATTTCCTCTAGCAATATAAAACAATTTCATCAGG
* *
3257 AATGTACTTGATTGTTA-TTTTATTACATTACTCTTTGCTTCCGGAA-AACTTAAATGTCTT-TA
1 AATGTACTTGATTGTTACTTTTAATACATTAATCTTTGCTTCCGGAATAACTTAAATGT-TTATA
*
3319 ACAAAATCCATGATTTCCTCTGGCAATATAAAACAATTTCATCA
65 ACAAAATCCATGATTTCCTCTAGCAATATAAAACAATTTCATCA
3363 ACAGTAGTGT
Statistics
Matches: 99, Mismatches: 5, Indels: 5
0.91 0.05 0.05
Matches are distributed among these distances:
107 47 0.47
108 35 0.35
109 17 0.17
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.39
Consensus pattern (110 bp):
AATGTACTTGATTGTTACTTTTAATACATTAATCTTTGCTTCCGGAATAACTTAAATGTTTATAA
CAAAATCCATGATTTCCTCTAGCAATATAAAACAATTTCATCAGG
Found at i:4688 original size:18 final size:18
Alignment explanation
Indices: 4667--4701 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
4657 TCAACGGGAA
4667 GGGTCAACAGGTCGGGTC
1 GGGTCAACAGGTCGGGTC
*
4685 GGGTCAACGGGTCGGGT
1 GGGTCAACAGGTCGGGT
4702 TATGACCGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.20, G:0.49, T:0.17
Consensus pattern (18 bp):
GGGTCAACAGGTCGGGTC
Found at i:9719 original size:22 final size:22
Alignment explanation
Indices: 9676--9717 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
9666 TTTTTAATAA
* *
9676 CTCTGCCTTTATGGTACATTTC
1 CTCTGCATTTATGGCACATTTC
9698 CTCTGCATTTAT-GCACATTT
1 CTCTGCATTTATGGCACATTT
9718 TCGATCGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.17, C:0.26, G:0.12, T:0.45
Consensus pattern (22 bp):
CTCTGCATTTATGGCACATTTC
Found at i:16572 original size:60 final size:60
Alignment explanation
Indices: 16454--16572 Score: 166
Period size: 60 Copynumber: 2.0 Consensus size: 60
16444 AACATATAAC
* * * * * *
16454 TCAAAAGATCATTTTGTAACTTTTAATAGTTAAGGGATTTAACAAAACATTATTCTATAG
1 TCAAAAGATCATTTTGTAACTTTTAATAGTCAAAGGACTCAACAAAACAATATCCTATAG
* *
16514 TCAAAAGATCATTTTGTAACTTTTAATAGTCAAATGACTCAACAAAATAATATCCTATA
1 TCAAAAGATCATTTTGTAACTTTTAATAGTCAAAGGACTCAACAAAACAATATCCTATA
16573 ATGGAGGGAA
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.42, C:0.13, G:0.09, T:0.36
Consensus pattern (60 bp):
TCAAAAGATCATTTTGTAACTTTTAATAGTCAAAGGACTCAACAAAACAATATCCTATAG
Found at i:22758 original size:41 final size:41
Alignment explanation
Indices: 22701--22783 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
22691 AAAGCAATAC
*
22701 TAGATGGAACAACAATTATGATTGATTAAAAGTCGCTCTAT
1 TAGATGGAACAACAATTATGATTGATTAAAAGTCACTCTAT
22742 TAGATGGAACAACAATTATGATTGATTAAAAGTCACTCTAT
1 TAGATGGAACAACAATTATGATTGATTAAAAGTCACTCTAT
22783 T
1 T
22784 GTAATTCGAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.33
Consensus pattern (41 bp):
TAGATGGAACAACAATTATGATTGATTAAAAGTCACTCTAT
Found at i:24382 original size:17 final size:17
Alignment explanation
Indices: 24362--24394 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
24352 TTACAGACCC
24362 TTTCTCCTTAAATCATT
1 TTTCTCCTTAAATCATT
*
24379 TTTCTCTTTAAATCAT
1 TTTCTCCTTAAATCAT
24395 GTCTCATTTT
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:0.24, C:0.21, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTCTCCTTAAATCATT
Found at i:24816 original size:21 final size:21
Alignment explanation
Indices: 24792--24834 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
24782 TCTTACAACA
24792 CTGCACATAATAATACATCTC
1 CTGCACATAATAATACATCTC
24813 CTGCACATAATAATACATCTC
1 CTGCACATAATAATACATCTC
24834 C
1 C
24835 CACGACATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.30, G:0.05, T:0.28
Consensus pattern (21 bp):
CTGCACATAATAATACATCTC
Found at i:57941 original size:21 final size:19
Alignment explanation
Indices: 57903--57942 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
57893 TAAGTCTTTA
57903 TTATGTTCATGTAGCTTAT
1 TTATGTTCATGTAGCTTAT
*
57922 TTATGATTTATGTATGCTTAT
1 TTATG-TTCATGTA-GCTTAT
57943 GTTGTATTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 7 0.39
21 6 0.33
ACGTcount: A:0.23, C:0.07, G:0.15, T:0.55
Consensus pattern (19 bp):
TTATGTTCATGTAGCTTAT
Found at i:58095 original size:23 final size:23
Alignment explanation
Indices: 58069--58136 Score: 84
Period size: 23 Copynumber: 2.9 Consensus size: 23
58059 GTGTTTGTGT
58069 TGTTCGTTTATGTTCATTTATTA
1 TGTTCGTTTATGTTCATTTATTA
*
58092 TGTTCGTTTATGTTCATTCGT-TTG
1 TGTTCGTTTATGTTCATT--TATTA
* *
58116 TATTCGTTTATGTTCGTTTAT
1 TGTTCGTTTATGTTCATTTAT
58137 CACTTAAATG
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
22 1 0.03
23 19 0.49
24 18 0.46
25 1 0.03
ACGTcount: A:0.13, C:0.10, G:0.16, T:0.60
Consensus pattern (23 bp):
TGTTCGTTTATGTTCATTTATTA
Found at i:61560 original size:21 final size:21
Alignment explanation
Indices: 61498--61560 Score: 56
Period size: 21 Copynumber: 2.8 Consensus size: 21
61488 ACAAACTTTT
*
61498 AAAAAAATTATATTATAAATTAAA
1 AAAAAAATTA-A-TA-AAAATAAA
*
61522 ATAACAAAATT-TTAAAAATAAA
1 A-AA-AAAATTAATAAAAATAAA
61544 AAAAAAATTAATAAAAA
1 AAAAAAATTAATAAAAA
61561 ATATTTAAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
20 6 0.18
21 8 0.24
22 8 0.24
23 2 0.06
24 1 0.03
25 2 0.06
26 6 0.18
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (21 bp):
AAAAAAATTAATAAAAATAAA
Found at i:62381 original size:2 final size:2
Alignment explanation
Indices: 62374--62405 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
62364 GATAAATTAA
62374 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
62406 TCTAATTCAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:63020 original size:19 final size:20
Alignment explanation
Indices: 62998--63038 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
62988 TTATAAATTT
62998 AAAATAATAAAATTA-ATAA
1 AAAATAATAAAATTATATAA
* *
63017 AAAATATTTAAATTATATAA
1 AAAATAATAAAATTATATAA
63037 AA
1 AA
63039 TTTTTGAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAATAATAAAATTATATAA
Found at i:77293 original size:24 final size:24
Alignment explanation
Indices: 77235--77281 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
77225 AGTCAGTATT
*
77235 CGAAATTTGATCTTGGTCAATACC
1 CGAACTTTGATCTTGGTCAATACC
77259 CGAACTTTGATCTTGGTCAATAC
1 CGAACTTTGATCTTGGTCAATAC
77282 TCGGATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (24 bp):
CGAACTTTGATCTTGGTCAATACC
Found at i:79910 original size:33 final size:33
Alignment explanation
Indices: 79831--79922 Score: 134
Period size: 33 Copynumber: 2.8 Consensus size: 33
79821 GGAAATAACT
79831 ATCGCAATGCGAAATGAAAATCGCAA--AGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
79862 ATCGCAATGCGAAATGAAAATCACAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
79895 ATCGCAAAGCAAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
79923 CGAATTTAGT
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
31 25 0.46
33 29 0.54
ACGTcount: A:0.48, C:0.18, G:0.22, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:79944 original size:19 final size:19
Alignment explanation
Indices: 79922--79996 Score: 63
Period size: 19 Copynumber: 4.2 Consensus size: 19
79912 AAATCGCAAC
79922 GCGAATTT-AGTTTCGCGTT
1 GCGAATTTCA-TTTCGCGTT
*
79941 GCGATTTTCATTTCGCGTT
1 GCGAATTTCATTTCGCGTT
*
79960 GCG-A-TTC---TCTCGTT
1 GCGAATTTCATTTCGCGTT
* *
79974 GCGATTTTCATTTCGCATT
1 GCGAATTTCATTTCGCGTT
79993 GCGA
1 GCGA
79997 TAGTCATTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
14 9 0.20
16 3 0.07
17 3 0.07
19 28 0.64
20 1 0.02
ACGTcount: A:0.13, C:0.21, G:0.23, T:0.43
Consensus pattern (19 bp):
GCGAATTTCATTTCGCGTT
Found at i:79997 original size:19 final size:19
Alignment explanation
Indices: 79932--79997 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
79922 GCGAATTTAG
79932 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
79951 TTTCGCGTTGCGA--TTC-
1 TTTCGCGTTGCGATTTTCA
*
79967 --TCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
79984 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
79998 AGTCATTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
14 10 0.26
16 3 0.08
17 3 0.08
19 23 0.59
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.45
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:80123 original size:14 final size:14
Alignment explanation
Indices: 80104--80140 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
80094 CATCAATTAA
80104 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
80118 ACAAATCATCTTTT
1 ACAAATCAACTTTT
80132 ACAAATCAA
1 ACAAATCAA
80141 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:81553 original size:21 final size:21
Alignment explanation
Indices: 81484--81553 Score: 52
Period size: 21 Copynumber: 3.3 Consensus size: 21
81474 CAAGTGAATC
**
81484 GGACTCTTGAATAGTGGGA-G
1 GGACTCTTGAACGGTGGGAGG
* * ** *
81504 GGACCTCTTCAACGATGACAGT
1 GGA-CTCTTGAACGGTGGGAGG
*
81526 GGCCTCTTGAACGGTGGGAGG
1 GGACTCTTGAACGGTGGGAGG
81547 GGACTCT
1 GGACTCT
81554 CGAGGAATGA
Statistics
Matches: 34, Mismatches: 14, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 3 0.09
21 29 0.85
22 2 0.06
ACGTcount: A:0.21, C:0.20, G:0.36, T:0.23
Consensus pattern (21 bp):
GGACTCTTGAACGGTGGGAGG
Found at i:82048 original size:19 final size:19
Alignment explanation
Indices: 82026--82109 Score: 88
Period size: 19 Copynumber: 4.6 Consensus size: 19
82016 AAAAATAACT
*
82026 ATCGCAACGCTAAATGAAA
1 ATCGCAACGCGAAATGAAA
82045 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
82064 ATCGCAA--CG--A-CAAA
1 ATCGCAACGCGAAATGAAA
**
82078 ATCGCAACGCGAAACCAAAA
1 ATCGCAACGCGAAA-TGAAA
82098 ATCGCAACGCGA
1 ATCGCAACGCGA
82110 TTATAGTTTC
Statistics
Matches: 56, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 25 0.45
20 15 0.27
ACGTcount: A:0.46, C:0.26, G:0.18, T:0.10
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:82084 original size:33 final size:34
Alignment explanation
Indices: 82042--82106 Score: 105
Period size: 33 Copynumber: 1.9 Consensus size: 34
82032 ACGCTAAATG
**
82042 AAAATCGCAACGCGAAA-TGAAAATCGCAACGAC
1 AAAATCGCAACGCGAAACCAAAAATCGCAACGAC
82075 AAAATCGCAACGCGAAACCAAAAATCGCAACG
1 AAAATCGCAACGCGAAACCAAAAATCGCAACG
82107 CGATTATAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 17 0.59
34 12 0.41
ACGTcount: A:0.49, C:0.26, G:0.17, T:0.08
Consensus pattern (34 bp):
AAAATCGCAACGCGAAACCAAAAATCGCAACGAC
Found at i:82128 original size:19 final size:19
Alignment explanation
Indices: 82115--82248 Score: 179
Period size: 19 Copynumber: 7.3 Consensus size: 19
82105 CGCGATTATA
82115 GTTTCGCGTTGCGATTTT-
1 GTTTCGCGTTGCGATTTTC
82133 G--T--CGTTGCGATTTTC
1 GTTTCGCGTTGCGATTTTC
*
82148 ATTTCGCGTTGCGATTTTC
1 GTTTCGCGTTGCGATTTTC
82167 GTTTCGCGTTGCGATTTTC
1 GTTTCGCGTTGCGATTTTC
82186 GTTTCGCGTTGCGATTTTC
1 GTTTCGCGTTGCGATTTTC
*
82205 GTTTCGCGTTACGATTTTC
1 GTTTCGCGTTGCGATTTTC
* *
82224 ATTCTCTCGTTGCGATTTTC
1 GTT-TCGCGTTGCGATTTTC
*
82244 ATTTC
1 GTTTC
82249 AACCAAAAGA
Statistics
Matches: 104, Mismatches: 6, Indels: 11
0.86 0.05 0.09
Matches are distributed among these distances:
14 12 0.12
16 1 0.01
17 1 0.01
18 1 0.01
19 72 0.69
20 17 0.16
ACGTcount: A:0.08, C:0.21, G:0.22, T:0.49
Consensus pattern (19 bp):
GTTTCGCGTTGCGATTTTC
Found at i:82447 original size:94 final size:93
Alignment explanation
Indices: 82337--82712 Score: 580
Period size: 94 Copynumber: 4.1 Consensus size: 93
82327 ATGGATTGCA
* * *
82337 TTACTTCAACCAAAAGATAAAACAAAGACAAATACTAACTTCATAGTATTAAAGAATACACAGTT
1 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
** * *
82402 TAGCAGAATTGATAGCAAACGAACAATT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
82430 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
82495 TTAGCATAATTGGCAGCAACCGAACAAAT
65 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
82524 TTACTTTCAACCAAAAGATAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
82589 TTAGCAGAATTGGCAGCAACCGAATAAAT
65 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
82618 TTACTTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTT----AATAAACAGT
1 TTACTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
82679 TTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTAGCAGAATTGGCAGCAACCGAACAAAT
82708 TTACT
1 TTACT
82713 AAGCAATCTA
Statistics
Matches: 267, Mismatches: 14, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
90 42 0.16
93 22 0.08
94 203 0.76
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.23
Consensus pattern (93 bp):
TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:84421 original size:20 final size:19
Alignment explanation
Indices: 84395--84501 Score: 116
Period size: 20 Copynumber: 5.8 Consensus size: 19
84385 CTTTTGGTTA
84395 AAATGAAAATCGCAACGAG
1 AAATGAAAATCGCAACGAG
*
84414 AGAATGAAAATCGCAACGCAA
1 A-AATGAAAATCGCAACG-AG
**
84435 AAATGACTATCGCAACGAG
1 AAATGAAAATCGCAACGAG
*
84454 --A-G--AATCGCAACGCG
1 AAATGAAAATCGCAACGAG
*
84468 AAATGAAAATCGCAACGCG
1 AAATGAAAATCGCAACGAG
84487 AAATGAAAATCGCAA
1 AAATGAAAATCGCAA
84502 TGCGATTTTG
Statistics
Matches: 75, Mismatches: 6, Indels: 14
0.79 0.06 0.15
Matches are distributed among these distances:
14 10 0.13
16 2 0.03
17 2 0.03
19 29 0.39
20 30 0.40
21 2 0.03
ACGTcount: A:0.49, C:0.20, G:0.21, T:0.11
Consensus pattern (19 bp):
AAATGAAAATCGCAACGAG
Found at i:84480 original size:19 final size:19
Alignment explanation
Indices: 84395--84506 Score: 117
Period size: 19 Copynumber: 6.1 Consensus size: 19
84385 CTTTTGGTTA
*
84395 AAATGAAAATCGCAACGAG
1 AAATGAAAATCGCAACGCG
*
84414 AGAATGAAAATCGCAACGCAA
1 A-AATGAAAATCGCAACGC-G
**
84435 AAATGACTATCGCAA--CG
1 AAATGAAAATCGCAACGCG
*
84452 --A-GAGAATCGCAACGCG
1 AAATGAAAATCGCAACGCG
84468 AAATGAAAATCGCAACGCG
1 AAATGAAAATCGCAACGCG
*
84487 AAATGAAAATCGCAATGCG
1 AAATGAAAATCGCAACGCG
84506 A
1 A
84507 TTTTGGTTTC
Statistics
Matches: 77, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
14 9 0.12
15 1 0.01
16 2 0.03
18 2 0.03
19 34 0.44
20 28 0.36
21 1 0.01
ACGTcount: A:0.47, C:0.20, G:0.21, T:0.12
Consensus pattern (19 bp):
AAATGAAAATCGCAACGCG
Found at i:84550 original size:33 final size:33
Alignment explanation
Indices: 84502--84594 Score: 123
Period size: 33 Copynumber: 2.8 Consensus size: 33
84492 AAAATCGCAA
**
84502 TGCGATTTTGGTTTCGCGTTGCGATTATCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
*
84535 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
* **
84568 TGCAATAGTCATTTCCGCGTTGCGATT
1 TGCGATTTTCATTT-CGCGTTGCGATT
84595 TTCATTCTCG
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 41 0.77
34 12 0.23
ACGTcount: A:0.12, C:0.22, G:0.24, T:0.43
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
Found at i:85189 original size:21 final size:20
Alignment explanation
Indices: 85125--85199 Score: 96
Period size: 20 Copynumber: 3.7 Consensus size: 20
85115 GCTATGTAAA
** *
85125 TCGCATTGCGATAGTCAGAT
1 TCGCATTGCGATTTTCATAT
* *
85145 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTTCATAT
85165 TCGCATTGCGATTTTCATAAT
1 TCGCATTGCGATTTTCAT-AT
85186 TCGCATTGCGATTT
1 TCGCATTGCGATTT
85200 ACTTAATCGC
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
20 31 0.66
21 16 0.34
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTTCATAT
Found at i:85195 original size:41 final size:40
Alignment explanation
Indices: 85123--85215 Score: 123
Period size: 41 Copynumber: 2.3 Consensus size: 40
85113 GCGCTATGTA
*
85123 AATCGCATTGCGATAGTCAGATTCGCATTGCGATTTACGT
1 AATCGCATTGCGATAGTCAAATTCGCATTGCGATTTACGT
* ** *
85163 ATTCGCATTGCGATTTTCATAATTCGCATTGCGATTTACTT
1 AATCGCATTGCGATAGTCA-AATTCGCATTGCGATTTACGT
*
85204 AATCGCGTTGCG
1 AATCGCATTGCG
85216 GTTTACGTAT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
40 16 0.36
41 29 0.64
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (40 bp):
AATCGCATTGCGATAGTCAAATTCGCATTGCGATTTACGT
Found at i:85214 original size:20 final size:20
Alignment explanation
Indices: 85123--85221 Score: 92
Period size: 20 Copynumber: 4.9 Consensus size: 20
85113 GCGCTATGTA
* *
85123 AATCGCATTGCGATAGT-CAG
1 AATCGCATTGCGAT-TTACAT
* *
85143 ATTCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTACAT
* *
85163 ATTCGCATTGCGATTTTCAT
1 AATCGCATTGCGATTTACAT
*
85183 AATTCGCATTGCGATTTACTT
1 AA-TCGCATTGCGATTTACAT
* *
85204 AATCGCGTTGCGGTTTAC
1 AATCGCATTGCGATTTAC
85222 GTATTCGCAA
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
19 1 0.02
20 47 0.71
21 18 0.27
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.37
Consensus pattern (20 bp):
AATCGCATTGCGATTTACAT
Found at i:85229 original size:20 final size:20
Alignment explanation
Indices: 85143--85230 Score: 113
Period size: 20 Copynumber: 4.3 Consensus size: 20
85133 CGATAGTCAG
85143 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
85163 ATTCGCATTGCGATTTTCAT
1 ATTCGCATTGCGATTTACGT
*
85183 AATTCGCATTGCGATTTACTT
1 -ATTCGCATTGCGATTTACGT
* * *
85204 AATCGCGTTGCGGTTTACGT
1 ATTCGCATTGCGATTTACGT
85224 ATTCGCA
1 ATTCGCA
85231 ACGCGAATTT
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
20 39 0.68
21 18 0.32
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:85269 original size:61 final size:61
Alignment explanation
Indices: 85122--85273 Score: 162
Period size: 61 Copynumber: 2.5 Consensus size: 61
85112 GGCGCTATGT
* * ** * *
85122 AAATCGCATTGCGATAGTCAGATTCGCATTGCGATTTACGTATTCGCATTGCGATTTTCAT
1 AAATCGCATTGCGATAGTCAGAATCGCGTTGCGATTTACGTATTCGCAACGCGAATTTCAG
* * ** * **
85183 AATTCGCATTGCGAT-TTACTTAATCGCGTTGCGGTTTACGTATTCGCAACGCGAATTTGGG
1 AAATCGCATTGCGATAGT-CAGAATCGCGTTGCGATTTACGTATTCGCAACGCGAATTTCAG
*
85244 AAATCGCAATGCGATAGTCAGAATCGCGTT
1 AAATCGCATTGCGATAGTCAGAATCGCGTT
85274 ACGAATCTGG
Statistics
Matches: 71, Mismatches: 18, Indels: 4
0.76 0.19 0.04
Matches are distributed among these distances:
60 1 0.01
61 69 0.97
62 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (61 bp):
AAATCGCATTGCGATAGTCAGAATCGCGTTGCGATTTACGTATTCGCAACGCGAATTTCAG
Done.