Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007419.1 Hibiscus syriacus cultivar Beakdansim tig00020068_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: 130909
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:3380 original size:9 final size:9
Alignment explanation
Indices: 3366--3458 Score: 62
Period size: 9 Copynumber: 9.8 Consensus size: 9
3356 GGCTGCTGGA
3366 AACCGGTTT
1 AACCGGTTT
3375 AACCGGTTTT
1 AACCGG-TTT
3385 CAACCGGTTCT
1 -AACCGGTT-T
*
3396 GACCGGTTT
1 AACCGGTTT
*
3405 GACCGGTTT
1 AACCGGTTT
*
3414 CAACC-GTTCG
1 -AACCGGTT-T
3424 AACCGGTTT
1 AACCGGTTT
* *
3433 GACCGGTCTG
1 AACCGGT-TT
*
3443 AATCGGTTT
1 AACCGGTTT
*
3452 GACCGGT
1 AACCGGT
3459 CTGACCCGAC
Statistics
Matches: 66, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
9 35 0.53
10 24 0.36
11 7 0.11
ACGTcount: A:0.17, C:0.26, G:0.27, T:0.30
Consensus pattern (9 bp):
AACCGGTTT
Found at i:3391 original size:20 final size:21
Alignment explanation
Indices: 3366--3404 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3356 GGCTGCTGGA
3366 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGGTTTTC
*
3386 AACCGGTTCTGACCGGTTT
1 AACCGGTTCTAACCGGTTT
3405 GACCGGTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (21 bp):
AACCGGTTCTAACCGGTTTTC
Found at i:3411 original size:19 final size:19
Alignment explanation
Indices: 3368--3464 Score: 69
Period size: 19 Copynumber: 5.1 Consensus size: 19
3358 CTGCTGGAAA
* * *
3368 CCGGTTTAACCGGTTTTCAA
1 CCGGTTTGACCGGTTCT-GA
3388 CCGGTTCTGACCGGTT-TGA
1 CCGGTT-TGACCGGTTCTGA
*
3407 CCGGTTTCAACC-GTTC-GAA
1 CCGGTTT-GACCGGTTCTG-A
3426 CCGGTTTGACCGG-TCTGAA
1 CCGGTTTGACCGGTTCTG-A
*
3445 TCGGTTTGACCGG-TCTGA
1 CCGGTTTGACCGGTTCTGA
3463 CC
1 CC
3465 CGACCCGACC
Statistics
Matches: 65, Mismatches: 6, Indels: 14
0.76 0.07 0.16
Matches are distributed among these distances:
18 12 0.18
19 38 0.58
20 7 0.11
21 8 0.12
ACGTcount: A:0.15, C:0.28, G:0.27, T:0.30
Consensus pattern (19 bp):
CCGGTTTGACCGGTTCTGA
Found at i:3431 original size:28 final size:30
Alignment explanation
Indices: 3366--3464 Score: 109
Period size: 28 Copynumber: 3.4 Consensus size: 30
3356 GGCTGCTGGA
*
3366 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
3397 -ACCGGTTTGACCGGTTTCAACC-GTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
* * *
3424 AACCGGTTTGACCGGTCTGAATCGGTT-TG
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
*
3453 -ACCGGTCTGACC
1 AACCGGTTTGACC
3465 CGACCCGACC
Statistics
Matches: 60, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
27 1 0.02
28 34 0.57
29 12 0.20
30 13 0.22
ACGTcount: A:0.17, C:0.27, G:0.26, T:0.29
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:3471 original size:5 final size:5
Alignment explanation
Indices: 3461--3517 Score: 51
Period size: 5 Copynumber: 10.8 Consensus size: 5
3451 TGACCGGTCT
* * * *
3461 GACCC GACCC GACCGT GACCT TACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC-C GACCC GACCC GACCC GACC--C GACCC GACCC
3509 GACCC GACC
1 GACCC GACC
3518 GTTGACCGTT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
5 35 0.81
6 4 0.09
7 4 0.09
ACGTcount: A:0.19, C:0.51, G:0.21, T:0.09
Consensus pattern (5 bp):
GACCC
Found at i:3508 original size:22 final size:22
Alignment explanation
Indices: 3461--3524 Score: 103
Period size: 22 Copynumber: 3.0 Consensus size: 22
3451 TGACCGGTCT
*
3461 GACCCGACCCGACCG-TGACCT
1 GACCCGACCCGACCGTTGACCC
*
3482 TACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
3504 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
3525 GTTGACCGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
21 14 0.36
22 25 0.64
ACGTcount: A:0.19, C:0.48, G:0.22, T:0.11
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:3524 original size:17 final size:16
Alignment explanation
Indices: 3466--3512 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
3456 GGTCTGACCC
*
3466 GACCCGACCGTGACCTT
1 GACCCGACC-CGACCTT
3483 -ACCCGACCCGACCGTT
1 GACCCGACCCGACC-TT
3499 GACCCGACCCGACC
1 GACCCGACCCGACC
3513 CGACCGTTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 4 0.15
16 10 0.37
17 13 0.48
ACGTcount: A:0.19, C:0.49, G:0.21, T:0.11
Consensus pattern (16 bp):
GACCCGACCCGACCTT
Found at i:10483 original size:2 final size:2
Alignment explanation
Indices: 10478--10503 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10468 AAAGAGGTTT
10478 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
10504 GAGAGAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14463 original size:14 final size:15
Alignment explanation
Indices: 14432--14465 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
14422 CAGTGTTGTT
*
14432 ATATAAATTTGAATA
1 ATATAAATTTGAAAA
14447 ATATAAA-TTGAAAA
1 ATATAAATTTGAAAA
14461 ATATA
1 ATATA
14466 CATAGTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (15 bp):
ATATAAATTTGAAAA
Found at i:17259 original size:37 final size:37
Alignment explanation
Indices: 17183--17259 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
17173 TTTTTTTATT
*
17183 TTTAATTTTGTAAACAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAACAAAATTATATAAATATTATCAA
* * *
17220 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAACAAAATTATATAAATATTAT-CAA
17257 TTT
1 TTT
17260 GTAATATTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAACAAAATTATATAAATATTATCAA
Found at i:21678 original size:14 final size:14
Alignment explanation
Indices: 21661--21695 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
21651 AAAATAAATT
21661 ATATTTTTTGAAAA
1 ATATTTTTTGAAAA
*
21675 ATATTTTTTTAAAA
1 ATATTTTTTGAAAA
21689 ATATTTT
1 ATATTTT
21696 AGGATATCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (14 bp):
ATATTTTTTGAAAA
Found at i:21952 original size:16 final size:16
Alignment explanation
Indices: 21931--21970 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
21921 ATAATAAAAT
*
21931 ATTATTAATTATATTA
1 ATTATTAATTATAATA
*
21947 ATTATTTATTATAATA
1 ATTATTAATTATAATA
21963 ATATATTA
1 AT-TATTA
21971 TTAAAGTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTATTAATTATAATA
Found at i:21967 original size:44 final size:42
Alignment explanation
Indices: 21881--21962 Score: 114
Period size: 41 Copynumber: 2.0 Consensus size: 42
21871 CAATTTTATA
*
21881 AATAAAATTATTATAAATTTTATATATTATTTATTAAAATAT
1 AATAAAATTATTATAAATTATATATATTATTTATTAAAATAT
* *
21923 AATAAAA-TATTATTAATTATAT-TAATTATTTATTATAATA
1 AATAAAATTATTATAAATTATATAT-ATTATTTATTAAAATA
21963 ATATATTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
40 1 0.03
41 28 0.78
42 7 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (42 bp):
AATAAAATTATTATAAATTATATATATTATTTATTAAAATAT
Found at i:21971 original size:16 final size:16
Alignment explanation
Indices: 21924--21973 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
21914 TTAAAATATA
21924 ATAA-AATATTATTAATT
1 ATAATAATA-TATT-ATT
*
21941 ATATTAAT-TATTTATT
1 ATAATAATATA-TTATT
21957 ATAATAATATATTATT
1 ATAATAATATATTATT
21973 A
1 A
21974 AAGTATTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
16 18 0.64
17 7 0.25
18 3 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATAATAATATATTATT
Found at i:33718 original size:22 final size:22
Alignment explanation
Indices: 33676--33719 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
33666 GTATAATTTT
* *
33676 AAAATTTTATTTATCTTATACA
1 AAAATTTCATTTATCTGATACA
33698 AAAATTTCATATTAT-TGATACA
1 AAAATTTCAT-TTATCTGATACA
33720 TATGTGTACT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.45
Consensus pattern (22 bp):
AAAATTTCATTTATCTGATACA
Found at i:40345 original size:11 final size:11
Alignment explanation
Indices: 40329--40353 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
40319 CCTTTGACTT
40329 TTTTAATTAAA
1 TTTTAATTAAA
40340 TTTTAATTAAA
1 TTTTAATTAAA
40351 TTT
1 TTT
40354 CGTAACTCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTTAATTAAA
Found at i:41645 original size:22 final size:22
Alignment explanation
Indices: 41603--41646 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
41593 GTATCATTTT
* *
41603 AAAATTTTATTTATCTTATACA
1 AAAATTTCATTTATCTGATACA
41625 AAAATTTCATATTAT-TGATACA
1 AAAATTTCAT-TTATCTGATACA
41647 TATGTGTACT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.45
Consensus pattern (22 bp):
AAAATTTCATTTATCTGATACA
Found at i:60797 original size:11 final size:13
Alignment explanation
Indices: 60765--60791 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
60755 ACCTAATATG
60765 TTCGTTTAACATT
1 TTCGTTTAACATT
60778 TTCGTTTAACATT
1 TTCGTTTAACATT
60791 T
1 T
60792 GTTTAATATT
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:0.22, C:0.15, G:0.07, T:0.56
Consensus pattern (13 bp):
TTCGTTTAACATT
Found at i:63147 original size:225 final size:225
Alignment explanation
Indices: 62836--63484 Score: 1156
Period size: 225 Copynumber: 2.9 Consensus size: 225
62826 TTAGAAATCA
*
62836 AGAATTGCAGTGGATTGAGGTCACTCTTTCCTG-GATTCCAACATCTCACTTCTCTTGAAAGTCT
1 AGAATTGCAATGGATTGAGGTCACTCTTTCCTGTG-TTCCAACATCTCACTTCTCTTGAAAGTCT
* *
62900 TTCTATCAGACACTGTAAGGAGCTCGAGCTATCTGCAGAGGGCATCCAAATATTCGAAGATTATA
65 TTCTATTAGACACTGCAAGGAGCTCGAGCTATCTGCAGAGGGCATCCAAATATTCGAAGATTATA
*
62965 CAAGCCTAAAGAATCTCCATCTGGTAAACATTCCAAAGTGTCGGCATCTTCCGGAGTGGCTTCAA
130 CGAGCCTAAAGAATCTCCATCTGGTAAACATTCCAAAGTGTCGGCATCTTCCGGAGTGGCTTCAA
63030 CATCTTGTTCACTTGAAATCGTTGCATATAC
195 CATCTTGTTCACTTGAAATCGTTGCATATAC
*
63061 AGATTTGCAATGGATTGAGGTCACTCTTTCCTGTGTTCCAACATCTCACTTCTCTTGAAAGTCTT
1 AGAATTGCAATGGATTGAGGTCACTCTTTCCTGTGTTCCAACATCTCACTTCTCTTGAAAGTCTT
*
63126 TCTATTAGGCACTGCAAGGAGCTCGAGCTATCTGCAGAGGGCATCCAAATATTCGAAGATTATAC
66 TCTATTAGACACTGCAAGGAGCTCGAGCTATCTGCAGAGGGCATCCAAATATTCGAAGATTATAC
*
63191 GAGCCGAAAGAATCTCCATCTGGTAAACATTCCAAAGTGTCGGCATCTTCCGGAGTGGCTTCAAC
131 GAGCCTAAAGAATCTCCATCTGGTAAACATTCCAAAGTGTCGGCATCTTCCGGAGTGGCTTCAAC
* *
63256 ACCATGTTCACTTGAAATCGTTGCATATAC
196 ATCTTGTTCACTTGAAATCGTTGCATATAC
*
63286 AGAATTGCAATGGATTGAGGTCACTCTTTCCTGTGTTCCGACATCTCACTTCTCTTGAAAGTCTT
1 AGAATTGCAATGGATTGAGGTCACTCTTTCCTGTGTTCCAACATCTCACTTCTCTTGAAAGTCTT
*
63351 TCTATTAGACACTGCAAGGATCTCGAGCTATCTGCAGAGGGCATCCAAATATTCGAAGATTATAC
66 TCTATTAGACACTGCAAGGAGCTCGAGCTATCTGCAGAGGGCATCCAAATATTCGAAGATTATAC
* * *
63416 GAGCCTAAAGATTCTACATTTGGTAAACATTCCAAAGTGTCGGCATCTTCCGGAGTGGCTTCAAC
131 GAGCCTAAAGAATCTCCATCTGGTAAACATTCCAAAGTGTCGGCATCTTCCGGAGTGGCTTCAAC
63481 ATCT
196 ATCT
63485 AACAAATCTG
Statistics
Matches: 404, Mismatches: 19, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
225 403 1.00
226 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (225 bp):
AGAATTGCAATGGATTGAGGTCACTCTTTCCTGTGTTCCAACATCTCACTTCTCTTGAAAGTCTT
TCTATTAGACACTGCAAGGAGCTCGAGCTATCTGCAGAGGGCATCCAAATATTCGAAGATTATAC
GAGCCTAAAGAATCTCCATCTGGTAAACATTCCAAAGTGTCGGCATCTTCCGGAGTGGCTTCAAC
ATCTTGTTCACTTGAAATCGTTGCATATAC
Found at i:70754 original size:180 final size:180
Alignment explanation
Indices: 70434--70779 Score: 439
Period size: 180 Copynumber: 1.9 Consensus size: 180
70424 ACTCTTCCAG
* * * *
70434 GAAATAACTGATATTTTAGGATCTGTTAATGTTACTCCAGATGAAACCAAATCTGGGTTTTCAAT
1 GAAATAACTGAAATTTTAGGAGCTGTTAAAGTAACTCCAGATGAAACCAAATCTGGGTTTTCAAT
* * * * * *
70499 AACTCCACGAAACACAGCCAGTGAGCTTGAGTTTATAGAACAATCGTTGTCTAGAAGGCCGGGTG
66 AACCCCACGAAACACAGCCAGGGAGCTTGAGTTTATAAAACAATCGTCGTCTAGAAGGCCAGATG
*
70564 TTTGTCAAAATGCCCAGCAGAAGAGTGAATTGGTGGAAAAGGAGCGAAAT
131 TTTATCAAAATGCCCAGCAGAAGAGTGAATTGGTGGAAAAGGAGCGAAAT
* * * *
70614 GAAATAACTGAAATTTTTGGAGCTGTTAAAGTAAC-CTCAGGTGAAATCC-CATCTTGGTTTTCA
1 GAAATAACTGAAATTTTAGGAGCTGTTAAAGTAACTC-CAGATGAAA-CCAAATCTGGGTTTTCA
* * * * *
70677 GTTACCCCACGAACCA-ATGCCAGGGAG-TCTGAGTTTATAAAACAATCGTCGTCTGGCAGGCCA
64 ATAACCCCACGAAACACA-GCCAGGGAGCT-TGAGTTTATAAAACAATCGTCGTCTAGAAGGCCA
*
70740 GATGTTTATCAAAATGCCCAGGAGAAGAGTGAATTGGTGG
127 GATGTTTATCAAAATGCCCAGCAGAAGAGTGAATTGGTGG
70780 GAACAGAGGA
Statistics
Matches: 141, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
179 3 0.02
180 136 0.96
181 2 0.01
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.26
Consensus pattern (180 bp):
GAAATAACTGAAATTTTAGGAGCTGTTAAAGTAACTCCAGATGAAACCAAATCTGGGTTTTCAAT
AACCCCACGAAACACAGCCAGGGAGCTTGAGTTTATAAAACAATCGTCGTCTAGAAGGCCAGATG
TTTATCAAAATGCCCAGCAGAAGAGTGAATTGGTGGAAAAGGAGCGAAAT
Found at i:79272 original size:13 final size:13
Alignment explanation
Indices: 79254--79278 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
79244 AATTTAAAAT
79254 AAACATAGATTTC
1 AAACATAGATTTC
79267 AAACATAGATTT
1 AAACATAGATTT
79279 AGTGCATTTT
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:0.48, C:0.12, G:0.08, T:0.32
Consensus pattern (13 bp):
AAACATAGATTTC
Found at i:86481 original size:180 final size:180
Alignment explanation
Indices: 86175--86520 Score: 439
Period size: 180 Copynumber: 1.9 Consensus size: 180
86165 ACTCTTCCAG
* * *
86175 GAAATAACTGATATTTTAGGATCTGTTAATGTAACTCCAGATGAAACCGAATCTGGGTTTTCAAT
1 GAAATAACTGAAATTTTAGGAGCTGTTAAAGTAACTCCAGATGAAACCGAATCTGGGTTTTCAAT
* * * * *
86240 AACTCCACGAAACACAGCCAGTGAGCTTGAGTTTATAGAACAATCGTTGTCTAGAAGGCCAGGTG
66 AACCCCACGAAACACAGCCAGGGAGCTTGAGTTTATAAAACAATCGTCGTCTAGAAGGCCAGATG
* *
86305 TTTGTCAAAATGCCCAGCAGAGGAGTGAATTGGTGGAAAAGGAGCGAAAT
131 TTTATCAAAATGCCCAGCAGAAGAGTGAATTGGTGGAAAAGGAGCGAAAT
* * *
86355 GAAATAACTGAAATTTTTGGAGCTGTTAAAGTAAC-CTCAGGTGAAATCC-CATCTGGGTTTTCA
1 GAAATAACTGAAATTTTAGGAGCTGTTAAAGTAACTC-CAGATGAAA-CCGAATCTGGGTTTTCA
* * * * * * *
86418 GTTACCCCACGAACCA-ATGCCAGGGA-ATCTGGGTTTATAAAACAATCGTCGTCTGGCAGGCCA
64 ATAACCCCACGAAACACA-GCCAGGGAGCT-TGAGTTTATAAAACAATCGTCGTCTAGAAGGCCA
*
86481 GATGTTTATCAAAATGCCCAGGAGAAGAGTGAATTGGTGG
127 GATGTTTATCAAAATGCCCAGCAGAAGAGTGAATTGGTGG
86521 GAACAGAGGA
Statistics
Matches: 141, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
179 3 0.02
180 136 0.96
181 2 0.01
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (180 bp):
GAAATAACTGAAATTTTAGGAGCTGTTAAAGTAACTCCAGATGAAACCGAATCTGGGTTTTCAAT
AACCCCACGAAACACAGCCAGGGAGCTTGAGTTTATAAAACAATCGTCGTCTAGAAGGCCAGATG
TTTATCAAAATGCCCAGCAGAAGAGTGAATTGGTGGAAAAGGAGCGAAAT
Found at i:91097 original size:23 final size:22
Alignment explanation
Indices: 91069--91118 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
91059 ATAAAACTAA
91069 AAATGAATATATAAACGAACACT
1 AAATGAA-ATATAAACGAACACT
* *
91092 AAATG-AATATAAACGAATATT
1 AAATGAAATATAAACGAACACT
91113 AAATGA
1 AAATGA
91119 GCACTAAACG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 18 0.75
22 1 0.04
23 5 0.21
ACGTcount: A:0.58, C:0.08, G:0.10, T:0.24
Consensus pattern (22 bp):
AAATGAAATATAAACGAACACT
Found at i:95728 original size:2 final size:2
Alignment explanation
Indices: 95721--95751 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
95711 CATTTTTAAC
95721 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
95752 CCCCCTTCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:101937 original size:2 final size:2
Alignment explanation
Indices: 101932--101971 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
101922 CTCGTGTGTG
101932 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
101972 GGATATAATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:113295 original size:2 final size:2
Alignment explanation
Indices: 113288--113312 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
113278 AAATTTCATT
113288 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
113313 GAGGTAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:113584 original size:16 final size:16
Alignment explanation
Indices: 113563--113624 Score: 106
Period size: 16 Copynumber: 3.9 Consensus size: 16
113553 TAAATAAACC
113563 AACATAAACGAACACG
1 AACATAAACGAACACG
113579 AACATAAACGAACACG
1 AACATAAACGAACACG
*
113595 AACATAAATGAACACG
1 AACATAAACGAACACG
*
113611 ACCATAAACGAACA
1 AACATAAACGAACA
113625 TAAACGTTGG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.56, C:0.24, G:0.11, T:0.08
Consensus pattern (16 bp):
AACATAAACGAACACG
Found at i:114741 original size:14 final size:14
Alignment explanation
Indices: 114724--114779 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
114714 AATGAACATA
114724 AACGAACATAACCG
1 AACGAACATAACCG
114738 AACGAACAT-A---
1 AACGAACATAACCG
*
114748 AACAAACATAACCG
1 AACGAACATAACCG
*
114762 AACGAACATAGCCG
1 AACGAACATAACCG
114776 AACG
1 AACG
114780 TTCACGAACG
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 8 0.23
11 1 0.03
13 1 0.03
14 25 0.71
ACGTcount: A:0.52, C:0.27, G:0.14, T:0.07
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:114744 original size:24 final size:24
Alignment explanation
Indices: 114703--114771 Score: 102
Period size: 24 Copynumber: 2.9 Consensus size: 24
114693 AGATTGGGTT
** *
114703 AAACATAAATGAATGAACATAAAC
1 AAACATAACCGAACGAACATAAAC
*
114727 GAACATAACCGAACGAACATAAAC
1 AAACATAACCGAACGAACATAAAC
114751 AAACATAACCGAACGAACATA
1 AAACATAACCGAACGAACATA
114772 GCCGAACGTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.58, C:0.20, G:0.10, T:0.12
Consensus pattern (24 bp):
AAACATAACCGAACGAACATAAAC
Found at i:114841 original size:39 final size:37
Alignment explanation
Indices: 114796--114881 Score: 91
Period size: 40 Copynumber: 2.2 Consensus size: 37
114786 AACGTAAATG
* *
114796 AACGAACGAGACCTATGTTTATGTTCGTTCATTTAATTA
1 AACGAACGAAACCT-TGTTCATGTTCGTTCATTTAA-TA
* *
114835 AACGAACACAAAATCTTGTTCATGTTCGTTCATTTAATA
1 AACG-A-ACGAAACCTTGTTCATGTTCGTTCATTTAATA
*
114874 AACAAACG
1 AACGAACG
114882 CACATAAACG
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
37 2 0.05
38 1 0.03
39 9 0.23
40 21 0.54
41 6 0.15
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (37 bp):
AACGAACGAAACCTTGTTCATGTTCGTTCATTTAATA
Found at i:118551 original size:16 final size:16
Alignment explanation
Indices: 118530--118562 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
118520 ACCCATGCCC
118530 ATCCCTAATGCTAGCT
1 ATCCCTAATGCTAGCT
118546 ATCCCTAATGCTAGCT
1 ATCCCTAATGCTAGCT
118562 A
1 A
118563 AGAAAATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.27, C:0.30, G:0.12, T:0.30
Consensus pattern (16 bp):
ATCCCTAATGCTAGCT
Found at i:118767 original size:2 final size:2
Alignment explanation
Indices: 118760--118788 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
118750 GTTGAAAGTT
118760 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 T
118789 GAATGAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:120043 original size:2 final size:2
Alignment explanation
Indices: 120036--120087 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
120026 CTATTTTTAT
120036 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
120078 TA TA TA TA TA
1 TA TA TA TA TA
120088 AGTGAAAATA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:121781 original size:60 final size:60
Alignment explanation
Indices: 121688--121808 Score: 242
Period size: 60 Copynumber: 2.0 Consensus size: 60
121678 TATATGATGC
121688 GTCGTCACCATTTTTCGCCCGGGTGGGGAAAAACTAGTACGACTTAGAATTTTAGAATTT
1 GTCGTCACCATTTTTCGCCCGGGTGGGGAAAAACTAGTACGACTTAGAATTTTAGAATTT
121748 GTCGTCACCATTTTTCGCCCGGGTGGGGAAAAACTAGTACGACTTAGAATTTTAGAATTT
1 GTCGTCACCATTTTTCGCCCGGGTGGGGAAAAACTAGTACGACTTAGAATTTTAGAATTT
121808 G
1 G
121809 GGGATAAAAG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.31
Consensus pattern (60 bp):
GTCGTCACCATTTTTCGCCCGGGTGGGGAAAAACTAGTACGACTTAGAATTTTAGAATTT
Found at i:123448 original size:18 final size:18
Alignment explanation
Indices: 123399--123450 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
123389 GGGTCTACGC
*
123399 GGTCCTTCGGGACATAGT
1 GGTCCTTCGGGACATAAT
* *
123417 GGTCTTTTGGGACATAAT
1 GGTCCTTCGGGACATAAT
*
123435 GGTCCTTCGAGACATA
1 GGTCCTTCGGGACATA
123451 TGTGTTATAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.31
Consensus pattern (18 bp):
GGTCCTTCGGGACATAAT
Found at i:125818 original size:18 final size:18
Alignment explanation
Indices: 125769--125820 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
125759 GGGTCTACGC
*
125769 GGTCCTTCGGGACATAGT
1 GGTCCTTCGGGACATAAT
* *
125787 GGTCTTTTGGGACATAAT
1 GGTCCTTCGGGACATAAT
*
125805 GGTCCTTCGAGACATA
1 GGTCCTTCGGGACATA
125821 TGTGTTATAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.31
Consensus pattern (18 bp):
GGTCCTTCGGGACATAAT
Found at i:127345 original size:29 final size:28
Alignment explanation
Indices: 127296--127374 Score: 79
Period size: 30 Copynumber: 2.7 Consensus size: 28
127286 TCCTTTAATT
127296 TAAGGA-CTAAGGTGGTAAAAATATAAATAC
1 TAAGGACCTAA-GT-GTAAAAATATAAAT-C
* *
127326 TAAGGACCTAAGTGTAAAAAATCTAAGTC
1 TAAGGACCTAAGTGT-AAAAATATAAATC
* *
127355 TAGGGACCTAAGGGTAAAAA
1 TAAGGACCTAAGTGTAAAAA
127375 ACTAAAGTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
28 5 0.12
29 16 0.37
30 18 0.42
31 4 0.09
ACGTcount: A:0.47, C:0.10, G:0.22, T:0.22
Consensus pattern (28 bp):
TAAGGACCTAAGTGTAAAAATATAAATC
Found at i:127346 original size:30 final size:29
Alignment explanation
Indices: 127296--127375 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 29
127286 TCCTTTAATT
127296 TAAGGA-CTAAGGTGGT-AAAAATATAAATAC
1 TAAGGACCTAA-GT-GTAAAAAATATAAAT-C
* *
127326 TAAGGACCTAAGTGTAAAAAATCTAAGTC
1 TAAGGACCTAAGTGTAAAAAATATAAATC
* *
127355 TAGGGACCTAAGGGTAAAAAA
1 TAAGGACCTAAGTGTAAAAAA
127376 CTAAAGTTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
29 22 0.50
30 18 0.41
31 4 0.09
ACGTcount: A:0.47, C:0.10, G:0.21, T:0.21
Consensus pattern (29 bp):
TAAGGACCTAAGTGTAAAAAATATAAATC
Found at i:127375 original size:29 final size:29
Alignment explanation
Indices: 127329--127439 Score: 93
Period size: 29 Copynumber: 3.8 Consensus size: 29
127319 TAAATACTAA
*
127329 GGACCTAAGTGTAAAAAATCT-AAGTCTAG
1 GGACCTAAGGGTAAAAAA-CTAAAGTCTAG
*
127358 GGACCTAAGGGTAAAAAACTAAAGTTTAG
1 GGACCTAAGGGTAAAAAACTAAAGTCTAG
** * **
127387 GGA-CTAACATGTAAAAACCTAAAGGATAG
1 GGACCTAA-GGGTAAAAAACTAAAGTCTAG
*
127416 AGA-CTAAGGAGTAAAAAATCTAAA
1 GGACCTAAGG-GTAAAAAA-CTAAA
127440 TTCAAAGATA
Statistics
Matches: 67, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
28 6 0.09
29 56 0.84
30 5 0.07
ACGTcount: A:0.48, C:0.12, G:0.21, T:0.20
Consensus pattern (29 bp):
GGACCTAAGGGTAAAAAACTAAAGTCTAG
Done.