Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001572.1 Hibiscus syriacus cultivar Beakdansim tig00003123_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: 87938
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:2970 original size:20 final size:20
Alignment explanation
Indices: 2945--2986 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
2935 AATTAAAATT
2945 ATTTTAA-TATTTTATTTGAA
1 ATTTTAACT-TTTTATTTGAA
2965 ATTTTAACTTTTTATTTGAA
1 ATTTTAACTTTTTATTTGAA
2985 AT
1 AT
2987 AATAAAAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 20 0.95
21 1 0.05
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (20 bp):
ATTTTAACTTTTTATTTGAA
Found at i:3557 original size:23 final size:21
Alignment explanation
Indices: 3531--3573 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
3521 AATCTTTAAC
*
3531 TTTAACTATTTTTCTTCAAAAAG
1 TTTAACT-TTTTTATT-AAAAAG
*
3554 TTTATCTTTTTTATTAAAAA
1 TTTAACTTTTTTATTAAAAA
3574 TAAGCATGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.28
22 7 0.39
23 6 0.33
ACGTcount: A:0.35, C:0.09, G:0.02, T:0.53
Consensus pattern (21 bp):
TTTAACTTTTTTATTAAAAAG
Found at i:11751 original size:16 final size:16
Alignment explanation
Indices: 11695--11751 Score: 50
Period size: 16 Copynumber: 3.8 Consensus size: 16
11685 GAGTAGCTCG
11695 AAAATA-TAATATATT-
1 AAAATATTAAT-TATTA
*
11710 AAGATATT-ATT-TTA
1 AAAATATTAATTATTA
* *
11724 AAAAAATAAATTATTA
1 AAAATATTAATTATTA
11740 AAAATATTAATT
1 AAAATATTAATT
11752 TTGATGTATT
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
13 2 0.06
14 6 0.19
15 10 0.31
16 14 0.44
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (16 bp):
AAAATATTAATTATTA
Found at i:11753 original size:31 final size:31
Alignment explanation
Indices: 11695--11753 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
11685 GAGTAGCTCG
*
11695 AAAATATAATATATTAAGATATTATTTTAAA
1 AAAATATAATATATTAAAATATTATTTTAAA
11726 AAAATA-AAT-TATTAAAAATATTAATTTT
1 AAAATATAATATATT-AAAATATT-ATTTT
11754 GATGTATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 4 0.16
30 10 0.40
31 11 0.44
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (31 bp):
AAAATATAATATATTAAAATATTATTTTAAA
Found at i:15149 original size:3 final size:3
Alignment explanation
Indices: 15141--15182 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
15131 TACTTCACCC
15141 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
15183 GTAGTAGTAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:25796 original size:13 final size:13
Alignment explanation
Indices: 25778--25804 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
25768 AGAAAATGAA
25778 AGATTTCAGAAAG
1 AGATTTCAGAAAG
25791 AGATTTCAGAAAG
1 AGATTTCAGAAAG
25804 A
1 A
25805 AAGAGAGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.22, T:0.22
Consensus pattern (13 bp):
AGATTTCAGAAAG
Found at i:43197 original size:2 final size:2
Alignment explanation
Indices: 43190--43224 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
43180 TCCTAAAGGC
43190 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 T
43225 TCATGTATAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:44791 original size:2 final size:2
Alignment explanation
Indices: 44779--44808 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
44769 ATTCAAAAAC
*
44779 TA TA TA CA 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
44809 ATTAACAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:45903 original size:2 final size:2
Alignment explanation
Indices: 45898--45925 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
45888 AATTATGTAG
45898 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
45926 CAATCCTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50468 original size:13 final size:14
Alignment explanation
Indices: 50440--50471 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
50430 GTGCAAGATT
50440 ACCCGACCCGGTTG
1 ACCCGACCCGGTTG
50454 ACCCGACCC-GTTG
1 ACCCGACCCGGTTG
50467 ACCCG
1 ACCCG
50472 TCGTGTAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.16, C:0.47, G:0.25, T:0.12
Consensus pattern (14 bp):
ACCCGACCCGGTTG
Found at i:51288 original size:23 final size:22
Alignment explanation
Indices: 51244--51288 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
51234 AATGTCATGG
*
51244 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
51266 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
51289 AAATTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:52717 original size:31 final size:31
Alignment explanation
Indices: 52591--52718 Score: 134
Period size: 31 Copynumber: 4.1 Consensus size: 31
52581 AGAGTCGAGG
*
52591 GTTTACCTATGTTCTACGGAATATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
*
52622 GTTTTACCTATG-TCTTTC-GAGACATATGGACA
1 G-TTTACCTATGTTC-TACGGA-ACATATGGACA
* *
52654 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
* * * * *
52685 GTTTACCTAGGTTCTTCGGGACCTATGAACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
52716 GTT
1 GTT
52719 ACCGAGGATC
Statistics
Matches: 80, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
31 53 0.66
32 27 0.34
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTACGGAACATATGGACA
Found at i:52738 original size:30 final size:30
Alignment explanation
Indices: 52704--52768 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
52694 GGTTCTTCGG
52704 GACCTATGAACAGTTACCGAGGATCTTTAT
1 GACCTATGAACAGTTACCGAGGATCTTTAT
* * *
52734 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTATGAACAGTTACCGAGGATCTTTAT
52764 GACCT
1 GACCT
52769 CTGGATAGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.31
Consensus pattern (30 bp):
GACCTATGAACAGTTACCGAGGATCTTTAT
Found at i:52769 original size:30 final size:30
Alignment explanation
Indices: 52715--52776 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
52705 ACCTATGAAC
52715 AGTTACCGAGGATCTTTATGACCTCTGGAT
1 AGTTACCGAGGATCTTTATGACCTCTGGAT
52745 AGTTACCGAGGATCTTTATGACCTCTGGAT
1 AGTTACCGAGGATCTTTATGACCTCTGGAT
52775 AG
1 AG
52777 GTCATTCGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.32
Consensus pattern (30 bp):
AGTTACCGAGGATCTTTATGACCTCTGGAT
Found at i:56261 original size:9 final size:9
Alignment explanation
Indices: 56247--56359 Score: 82
Period size: 10 Copynumber: 11.8 Consensus size: 9
56237 GGCTGCTGGA
56247 AACCGGTTT
1 AACCGGTTT
56256 AACCGGTTTT
1 AACCGG-TTT
56266 CAACCGGTTCT
1 -AACCGGTT-T
*
56277 GACCGGTTT
1 AACCGGTTT
*
56286 GACCGGTTT
1 AACCGGTTT
*
56295 CAACCGGTTCG
1 -AACCGGTT-T
56306 AACCGGTTT
1 AACCGGTTT
*
56315 GACCGGTCTT
1 AACCGGT-TT
*
56325 AATCGGTTT
1 AACCGGTTT
* * *
56334 GACCAGTCT
1 AACCGGTTT
56343 AAGCCGGTTT
1 AA-CCGGTTT
*
56353 GACCGGT
1 AACCGGT
56360 CTGAATCGAC
Statistics
Matches: 82, Mismatches: 15, Indels: 14
0.74 0.14 0.13
Matches are distributed among these distances:
9 35 0.43
10 40 0.49
11 7 0.09
ACGTcount: A:0.18, C:0.26, G:0.27, T:0.30
Consensus pattern (9 bp):
AACCGGTTT
Found at i:56292 original size:19 final size:18
Alignment explanation
Indices: 56247--56361 Score: 95
Period size: 19 Copynumber: 6.0 Consensus size: 18
56237 GGCTGCTGGA
* *
56247 AACCGGTTTAACCGGTTTT
1 AACCGGTTTGACCGG-TCT
*
56266 CAACCGGTTCTGACCGGTTT
1 -AACCGGTT-TGACCGGTCT
* * *
56286 GACCGGTTTCAACCGGTTCG
1 AACCGGTTT-GACCGG-TCT
56306 AACCGGTTTGACCGGTCTT
1 AACCGGTTTGACCGGTC-T
* *
56325 AATCGGTTTGACCAGTCT
1 AACCGGTTTGACCGGTCT
56343 AAGCCGGTTTGACCGGTCT
1 AA-CCGGTTTGACCGGTCT
56362 GAATCGACCC
Statistics
Matches: 78, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
18 6 0.08
19 46 0.59
20 20 0.26
21 6 0.08
ACGTcount: A:0.17, C:0.26, G:0.26, T:0.30
Consensus pattern (18 bp):
AACCGGTTTGACCGGTCT
Found at i:56332 original size:29 final size:30
Alignment explanation
Indices: 56247--56321 Score: 118
Period size: 29 Copynumber: 2.5 Consensus size: 30
56237 GGCTGCTGGA
*
56247 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
56278 -ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
56306 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
56322 CTTAATCGGT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 1 0.02
29 28 0.67
30 13 0.31
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:56387 original size:5 final size:5
Alignment explanation
Indices: 56379--56419 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
56369 CCCGACCGTT
*
56379 GACCC GACCC GACCC GACCGTT GACCC GACCC GACCC GACC
1 GACCC GACCC GACCC GACC--C GACCC GACCC GACCC GACC
56420 GTTGACCGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 28 0.88
7 4 0.12
ACGTcount: A:0.20, C:0.54, G:0.22, T:0.05
Consensus pattern (5 bp):
GACCC
Found at i:56392 original size:22 final size:22
Alignment explanation
Indices: 56366--56426 Score: 122
Period size: 22 Copynumber: 2.8 Consensus size: 22
56356 CGGTCTGAAT
56366 CGACCCGACCGTTGACCCGACC
1 CGACCCGACCGTTGACCCGACC
56388 CGACCCGACCGTTGACCCGACC
1 CGACCCGACCGTTGACCCGACC
56410 CGACCCGACCGTTGACC
1 CGACCCGACCGTTGACC
56427 GTTGACCGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.18, C:0.49, G:0.23, T:0.10
Consensus pattern (22 bp):
CGACCCGACCGTTGACCCGACC
Found at i:57411 original size:63 final size:63
Alignment explanation
Indices: 57309--57432 Score: 162
Period size: 63 Copynumber: 2.0 Consensus size: 63
57299 CTAATGTGAC
** * *
57309 TCTTAGGTAGGCTCTGCGGCCCTGAGATTATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTGT
1 TCTTAGGTAGGCTCCACGGCCCCGAAATTATTCTCGGGTAGGCCCT-CAGGCCCTAAGATGTGT
* *
57372 TCTTAGGTAGGCTCCACGGCCCCGAAATCTA-TCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCTCCACGGCCCCGAAAT-TATTCTCGGGTAGGCCCTCAGGCCCTAAGATGT
57433 TCCCTTAGGG
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
62 1 0.02
63 50 0.94
64 2 0.04
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (63 bp):
TCTTAGGTAGGCTCCACGGCCCCGAAATTATTCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:66064 original size:77 final size:78
Alignment explanation
Indices: 65972--66150 Score: 270
Period size: 77 Copynumber: 2.3 Consensus size: 78
65962 TGACCTGCTG
* * *
65972 ATGGTATACAGATCGATAATAGTATAAAACTTGAAAGATTATCGACGAAGCAGTCGACTCTTTAG
1 ATGGTATACAGATCGATAATAGTATAAAAATTGAAAGATTATCAACCAAGCAGTCGACTCTTTAG
*
66037 CCCACAT-ACAAA
66 CCCACATAAAAAA
* * *
66049 ATGGTATACAGATCGATAATAGTATAAAAATTGTAAGATTATCAACCAAGCAGTTGGCTCTTTAG
1 ATGGTATACAGATCGATAATAGTATAAAAATTGAAAGATTATCAACCAAGCAGTCGACTCTTTAG
66114 CCCACATAAAAAAA
66 CCCACAT-AAAAAA
*
66128 ATGGTATACAGATCTATAATAGT
1 ATGGTATACAGATCGATAATAGT
66151 TTTTTAAAAA
Statistics
Matches: 92, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
77 66 0.72
79 26 0.28
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (78 bp):
ATGGTATACAGATCGATAATAGTATAAAAATTGAAAGATTATCAACCAAGCAGTCGACTCTTTAG
CCCACATAAAAAA
Found at i:67000 original size:2 final size:2
Alignment explanation
Indices: 66993--67046 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
66983 ATTGTATCTT
66993 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
67035 CA CA CA CA CA CA
1 CA CA CA CA CA CA
67047 TGGATTTAGA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:76457 original size:39 final size:39
Alignment explanation
Indices: 76403--76484 Score: 164
Period size: 39 Copynumber: 2.1 Consensus size: 39
76393 GATAATTAAG
76403 TTAGATTTTTTTGTTGTAATTTTAAGGGTTAAAGATGAC
1 TTAGATTTTTTTGTTGTAATTTTAAGGGTTAAAGATGAC
76442 TTAGATTTTTTTGTTGTAATTTTAAGGGTTAAAGATGAC
1 TTAGATTTTTTTGTTGTAATTTTAAGGGTTAAAGATGAC
76481 TTAG
1 TTAG
76485 TAATTAGGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.28, C:0.02, G:0.21, T:0.49
Consensus pattern (39 bp):
TTAGATTTTTTTGTTGTAATTTTAAGGGTTAAAGATGAC
Found at i:78481 original size:65 final size:63
Alignment explanation
Indices: 78386--78527 Score: 171
Period size: 65 Copynumber: 2.2 Consensus size: 63
78376 CACATTGAAT
* *
78386 GTGCATCGATGCACTCTTTAAAGAAGAAACATCAAATGCAATTAGTGCATCGATGCATAAGG-A
1 GTGCATCGATGCACCCTTTAAAGAAGAAACATCAAAGGCAATTAGTGCATCGATGCAT-AGGTA
* * * * *
78449 GTGCATCGATGCATCCCTTTAAA-AATGAAAACATCGAAGGTAATTTGTGTATCGATGCATGGGT
1 GTGCATCGATGCA-CCCTTTAAAGAA-G-AAACATCAAAGGCAATTAGTGCATCGATGCATAGGT
78513 A
63 A
78514 GTGCATCGATGCAC
1 GTGCATCGATGCAC
78528 ATGATAAAGA
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
63 15 0.22
64 12 0.18
65 41 0.60
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.26
Consensus pattern (63 bp):
GTGCATCGATGCACCCTTTAAAGAAGAAACATCAAAGGCAATTAGTGCATCGATGCATAGGTA
Found at i:78560 original size:20 final size:22
Alignment explanation
Indices: 78515--78572 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
78505 GCATGGGTAG
78515 TGCATCGATGCACATGATAAAGAA
1 TGCATCGATGCAC-TGAT-AAGAA
78539 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGATAAGAA
78559 TGCATCGATGCACT
1 TGCATCGATGCACT
78573 TCATGGGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 18 0.53
22 1 0.03
23 2 0.06
24 13 0.38
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (22 bp):
TGCATCGATGCACTGATAAGAA
Found at i:79366 original size:18 final size:18
Alignment explanation
Indices: 79343--79414 Score: 99
Period size: 18 Copynumber: 4.0 Consensus size: 18
79333 GAGGGTCTAC
*
79343 GTGGTCCTTCGGGACATA
1 GTGGTCATTCGGGACATA
* *
79361 GTGGTCATTTGGGACCTA
1 GTGGTCATTCGGGACATA
* *
79379 GTGGTCCTTTGGGACATA
1 GTGGTCATTCGGGACATA
79397 GTGGTCATTCGGGACATA
1 GTGGTCATTCGGGACATA
79415 TATGTTATAT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.18, C:0.18, G:0.33, T:0.31
Consensus pattern (18 bp):
GTGGTCATTCGGGACATA
Found at i:79393 original size:36 final size:36
Alignment explanation
Indices: 79343--79411 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
79333 GAGGGTCTAC
*
79343 GTGGTCCTTCGGGACATAGTGGTCATTTGGGACCTA
1 GTGGTCCTTCGGGACATAGTGGTCATTCGGGACCTA
*
79379 GTGGTCCTTTGGGACATAGTGGTCATTCGGGAC
1 GTGGTCCTTCGGGACATAGTGGTCATTCGGGAC
79412 ATATATGTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.16, C:0.19, G:0.35, T:0.30
Consensus pattern (36 bp):
GTGGTCCTTCGGGACATAGTGGTCATTCGGGACCTA
Found at i:82436 original size:65 final size:65
Alignment explanation
Indices: 82366--82523 Score: 153
Period size: 65 Copynumber: 2.4 Consensus size: 65
82356 GGCAAGGTGT
* *
82366 ATCGATGCACATTGAATGTGCATCGATGCA-CTCTTTAAAGAA-G-AAACATC-AAATGCAATTA
1 ATCGATGCACA-AGAA-GTGCATCGATGCATCCCTTTAAA-AATGAAAACATCGAAA-GCAATTA
82427 GTGC
62 GTGC
* * * * *
82431 ATCGATGCATAAGGAGTGCATCGATGCATCCCTTTAAAAATGAAAACATCGAAAGTAATTTGTGT
1 ATCGATGCACAAGAAGTGCATCGATGCATCCCTTTAAAAATGAAAACATCGAAAGCAATTAGTGC
*** *
82496 ATCGATGCATGGGTAGTGCATCGATGCA
1 ATCGATGCACAAGAAGTGCATCGATGCA
82524 CATGATAAAG
Statistics
Matches: 79, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
63 15 0.19
64 11 0.14
65 50 0.63
66 3 0.04
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.27
Consensus pattern (65 bp):
ATCGATGCACAAGAAGTGCATCGATGCATCCCTTTAAAAATGAAAACATCGAAAGCAATTAGTGC
Found at i:82557 original size:20 final size:22
Alignment explanation
Indices: 82512--82569 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
82502 GCATGGGTAG
82512 TGCATCGATGCACATGATAAAGAA
1 TGCATCGATGCAC-TGAT-AAGAA
82536 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGATAAGAA
82556 TGCATCGATGCACT
1 TGCATCGATGCACT
82570 TCATGGGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 18 0.53
22 1 0.03
23 2 0.06
24 13 0.38
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (22 bp):
TGCATCGATGCACTGATAAGAA
Found at i:83390 original size:18 final size:17
Alignment explanation
Indices: 83339--83392 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 17
83329 GAGGGTCTAC
83339 GTGGTCCTTCGGAACATA
1 GTGGTCCTTCGG-ACATA
*
83357 GTGGTCCTTTGAGACATA
1 GTGGTCCTTCG-GACATA
83375 GTGGTCCTTCAGGACATA
1 GTGGTCCTTC-GGACATA
83393 TGTGTTATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 30 0.94
19 2 0.06
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (17 bp):
GTGGTCCTTCGGACATA
Found at i:84018 original size:16 final size:16
Alignment explanation
Indices: 83997--84052 Score: 112
Period size: 16 Copynumber: 3.5 Consensus size: 16
83987 TTAAAAGATT
83997 TGAATTGTATAAGCTC
1 TGAATTGTATAAGCTC
84013 TGAATTGTATAAGCTC
1 TGAATTGTATAAGCTC
84029 TGAATTGTATAAGCTC
1 TGAATTGTATAAGCTC
84045 TGAATTGT
1 TGAATTGT
84053 TCTGTAAACG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (16 bp):
TGAATTGTATAAGCTC
Found at i:84748 original size:168 final size:168
Alignment explanation
Indices: 84470--84806 Score: 611
Period size: 168 Copynumber: 2.0 Consensus size: 168
84460 GTTGAGCTGC
*
84470 ATGAATTTGCTTATATTTTCAATCGAATTGCAATTTACAATCCTAAAACTGCCGCAAAATGCAAT
1 ATGAATTTGCTTATATTTTCAATCGAATTACAATTTACAATCCTAAAACTGCCGCAAAATGCAAT
* * * *
84535 TTGCAACCCAAAAAAATGTTGATGGCCATTAGGTGGGTGGGTGGTGGTGGAGCCAGTCGATAGTA
66 TTGCAACCCAAAAAAATATTGATGGCCATTAGGTGGGTGGGTGGTGGTAGAGCCAGTCGACAATA
*
84600 ATGGTGGTCGGAGGCTCATTGATGCATAGAACTACGTG
131 ATGGTGGTCGGAGGCTCATTGATCCATAGAACTACGTG
84638 ATGAATTTGCTTATATTTTCAATCGAATTACAATTTACAATCCTAAAACTGCCGCAAAATGCAAT
1 ATGAATTTGCTTATATTTTCAATCGAATTACAATTTACAATCCTAAAACTGCCGCAAAATGCAAT
*
84703 TTGTAACCCAAAAAAATATTGATGGCCATTAGGTGGGTGGGTGGTGGTAGAGCCAGTCGACAATA
66 TTGCAACCCAAAAAAATATTGATGGCCATTAGGTGGGTGGGTGGTGGTAGAGCCAGTCGACAATA
84768 ATGGTGGTCGGAGGCTCATTGATCCATAGAACTACGTG
131 ATGGTGGTCGGAGGCTCATTGATCCATAGAACTACGTG
84806 A
1 A
84807 GGTTTTGATG
Statistics
Matches: 162, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
168 162 1.00
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.28
Consensus pattern (168 bp):
ATGAATTTGCTTATATTTTCAATCGAATTACAATTTACAATCCTAAAACTGCCGCAAAATGCAAT
TTGCAACCCAAAAAAATATTGATGGCCATTAGGTGGGTGGGTGGTGGTAGAGCCAGTCGACAATA
ATGGTGGTCGGAGGCTCATTGATCCATAGAACTACGTG
Done.