Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001808.1 Hibiscus syriacus cultivar Beakdansim tig00003653_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: 63506
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1959 original size:21 final size:21
Alignment explanation
Indices: 1917--1959 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1907 TTTCTGGGCT
* * *
1917 AGGGGAATCGGTACGCATTCA
1 AGGGGAATCGATACCCACTCA
*
1938 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
1959 A
1 A
1960 ATGAACCAGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.26, G:0.28, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:2032 original size:23 final size:22
Alignment explanation
Indices: 1988--2032 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1978 AATCTCATAG
*
1988 GGGAACCGATTCCCCCACAGGA
1 GGGAACCGATTCCCCCAAAGGA
2010 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATTCCCCC-AAAGGA
2033 AAATTGTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.29, C:0.33, G:0.27, T:0.11
Consensus pattern (22 bp):
GGGAACCGATTCCCCCAAAGGA
Found at i:3419 original size:103 final size:103
Alignment explanation
Indices: 3298--3611 Score: 533
Period size: 103 Copynumber: 3.1 Consensus size: 103
3288 GGGTCTACGC
*
3298 GGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
3363 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
66 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
* *
3401 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTTAGACATATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
3466 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
66 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
** *
3504 GGTCCTTCGAAACATATATGTATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
* * *
3569 CCCTAGTA-ATGTATA-GATTCTTAAGGAATGATATGT
66 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
3605 GGTCCTT
1 GGTCCTT
3612 ATGGACATTA
Statistics
Matches: 200, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
101 28 0.14
102 7 0.04
103 165 0.82
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (103 bp):
GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
Found at i:3662 original size:23 final size:23
Alignment explanation
Indices: 3628--3695 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
3618 ATTATTATAT
3628 GGCACTAC-GGTGCAATTCTACGC
1 GGCACT-CTGGTGCAATTCTACGC
*
3651 GGCACTCTGGTGCAATTCTACGT
1 GGCACTCTGGTGCAATTCTACGC
* *
3674 GGCACTTTGGTGCAATTATACG
1 GGCACTCTGGTGCAATTCTACG
3696 AGTTGTGGTG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
22 1 0.02
23 40 0.98
ACGTcount: A:0.21, C:0.25, G:0.26, T:0.28
Consensus pattern (23 bp):
GGCACTCTGGTGCAATTCTACGC
Found at i:9347 original size:42 final size:43
Alignment explanation
Indices: 9249--9370 Score: 156
Period size: 43 Copynumber: 2.9 Consensus size: 43
9239 TTGTATATAA
* * * *
9249 AAATGCTGCAATAGGTTCAGACATTTATTGAAGTTTTTTTTAC
1 AAATGCTGCAATAGGTTCATACATTTAGTGGAGTTTTTCTTAC
** *
9292 AAATGCCACAATAGGTTCATACATTTAGAGGAGTTTTTCTTAC
1 AAATGCTGCAATAGGTTCATACATTTAGTGGAGTTTTTCTTAC
* *
9335 AAATG-TGCAATAGGTTCATACATCTAGTGGCGTTTT
1 AAATGCTGCAATAGGTTCATACATTTAGTGGAGTTTT
9371 CCCTATAAAT
Statistics
Matches: 67, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
42 26 0.39
43 41 0.61
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (43 bp):
AAATGCTGCAATAGGTTCATACATTTAGTGGAGTTTTTCTTAC
Found at i:9381 original size:42 final size:43
Alignment explanation
Indices: 9289--9389 Score: 123
Period size: 42 Copynumber: 2.4 Consensus size: 43
9279 AAGTTTTTTT
* * * * *
9289 TACAAATGCCACAATAGGTTCATACATTTAGAGGAGTTTTTCT
1 TACAAATGTCGCAATAGGTTCATACATCTAGAGGAGTTTTCCC
* *
9332 TACAAATGT-GCAATAGGTTCATACATCTAGTGGCGTTTTCCC
1 TACAAATGTCGCAATAGGTTCATACATCTAGAGGAGTTTTCCC
*
9374 TATAAATGTCGCAATA
1 TACAAATGTCGCAATA
9390 AATAGGTAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 35 0.71
43 14 0.29
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Consensus pattern (43 bp):
TACAAATGTCGCAATAGGTTCATACATCTAGAGGAGTTTTCCC
Found at i:15501 original size:20 final size:20
Alignment explanation
Indices: 15476--15524 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
15466 CCCAATAATA
15476 AAAAAATCAGTAGAAAAAAT
1 AAAAAATCAGTAGAAAAAAT
15496 AAAAAATCAGTAGAAAAAAT
1 AAAAAATCAGTAGAAAAAAT
15516 AAAAAATCA
1 AAAAAATCA
15525 ATAGTGCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.71, C:0.06, G:0.08, T:0.14
Consensus pattern (20 bp):
AAAAAATCAGTAGAAAAAAT
Found at i:16312 original size:16 final size:15
Alignment explanation
Indices: 16275--16325 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
16265 TATAAGGTAA
*
16275 TTTTGTTATAAATT-T
1 TTTTATTAT-AATTAT
16290 TTTTATTATAATTAT
1 TTTTATTATAATTAT
*
16305 TGTTTATTATGATTAT
1 T-TTTATTATAATTAT
16321 TTTTA
1 TTTTA
16326 AAAATATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 4 0.12
15 14 0.44
16 14 0.44
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (15 bp):
TTTTATTATAATTAT
Found at i:17798 original size:15 final size:15
Alignment explanation
Indices: 17778--17857 Score: 160
Period size: 15 Copynumber: 5.3 Consensus size: 15
17768 CCGTAGGACC
17778 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
17793 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
17808 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
17823 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
17838 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
17853 ACTAC
1 ACTAC
17858 AGAACCCTCG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 65 1.00
ACGTcount: A:0.28, C:0.34, G:0.25, T:0.14
Consensus pattern (15 bp):
ACTACGTCCCGAAGG
Found at i:23382 original size:16 final size:16
Alignment explanation
Indices: 23361--23396 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
23351 ACCACGCCCA
23361 AGACTGCAGCAGTAGG
1 AGACTGCAGCAGTAGG
23377 AGACTGCAGCAGTAGG
1 AGACTGCAGCAGTAGG
23393 AGAC
1 AGAC
23397 ATCCGCCGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.33, C:0.19, G:0.36, T:0.11
Consensus pattern (16 bp):
AGACTGCAGCAGTAGG
Found at i:24274 original size:17 final size:18
Alignment explanation
Indices: 24241--24278 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
24231 AAATACTTAA
*
24241 ATAAATTATATATAAAAT
1 ATAAAATATATATAAAAT
24259 ATAAAATATA-ATAAAAT
1 ATAAAATATATATAAAAT
24276 ATA
1 ATA
24279 CCTTAAAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
ATAAAATATATATAAAAT
Found at i:25176 original size:34 final size:33
Alignment explanation
Indices: 25100--25206 Score: 85
Period size: 34 Copynumber: 3.1 Consensus size: 33
25090 GTGGTAAGAA
* *
25100 ATTTATTTTTATGTTAGTAT-TTT-TTTAAATAGTT
1 ATTT-TTTTTAT-TTAATATATTTATATAAATA-TT
*
25134 ATTATTTTTTATATTAATATATTTATGTAAATATT
1 ATT-TTTTTTAT-TTAATATATTTATATAAATATT
* *
25169 A-TTTTTTTATTAAAATAATATTTATATAATTATT
1 ATTTTTTTTATT-TAAT-ATATTTATATAAATATT
25203 ATTT
1 ATTT
25207 ATTTAGAATT
Statistics
Matches: 61, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
32 1 0.02
33 11 0.18
34 33 0.54
35 9 0.15
36 7 0.11
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (33 bp):
ATTTTTTTTATTTAATATATTTATATAAATATT
Found at i:25188 original size:36 final size:34
Alignment explanation
Indices: 25133--25211 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 34
25123 TTTAAATAGT
*
25133 TATTATTTTTTATATT--AAT-ATATTTATGTAAA
1 TATTATTTTTT-TATTAAAATAATATTTATATAAA
*
25165 TATTATTTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTTATTAAAATAATATTTATATAAA
*
25199 TATTATTTATTTA
1 TATTATTTTTTTA
25212 GAATTATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
31 4 0.10
32 11 0.27
33 3 0.07
34 23 0.56
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (34 bp):
TATTATTTTTTTATTAAAATAATATTTATATAAA
Found at i:25375 original size:17 final size:17
Alignment explanation
Indices: 25353--25406 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
25343 AATGTTAATA
25353 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
25370 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
25387 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
25404 TTT
1 TTT
25407 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:26967 original size:21 final size:21
Alignment explanation
Indices: 26937--26984 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
26927 GTAGGGGTAC
* *
26937 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
26958 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
26979 ATGCCA
1 ATGCCA
26985 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:27014 original size:21 final size:21
Alignment explanation
Indices: 26988--27081 Score: 136
Period size: 21 Copynumber: 4.5 Consensus size: 21
26978 TATGCCATCT
26988 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
*
27009 CCGCAGGGTTACATTCCGATC
1 CCGCAGGGTTACATTCCGAGC
*
27030 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCGAGC
* *
27051 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCGAGC
27072 CCGCAGGGTT
1 CCGCAGGGTT
27082 TTATACCATA
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
20 2 0.03
21 63 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.34, G:0.27, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCGAGC
Found at i:27632 original size:28 final size:28
Alignment explanation
Indices: 27600--27694 Score: 100
Period size: 28 Copynumber: 3.2 Consensus size: 28
27590 GATAAATGTT
* * *
27600 TTTAAAATACAAATTATATTATTCGAAA
1 TTTAAAATAAAAATAATATTATTCAAAA
27628 TTTAAAATAAAAATAATATTATTCAAAA
1 TTTAAAATAAAAATAATATTATTCAAAA
*
27656 TTTAAATTTAAAATATAAATTATAGTATTCAAAA
1 TTTAAA-ATAAAA-AT-AA-TAT--TATTCAAAA
27690 TTTAA
1 TTTAA
27695 CATTAAATTT
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
28 31 0.54
29 5 0.09
30 2 0.04
31 2 0.04
32 3 0.05
34 14 0.25
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (28 bp):
TTTAAAATAAAAATAATATTATTCAAAA
Found at i:27663 original size:34 final size:34
Alignment explanation
Indices: 27625--27694 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 34
27615 ATATTATTCG
*
27625 AAATTTAAAATAAAAATAATATTATTCAAAATTT
1 AAATTTAAAATAAAAATAATAGTATTCAAAATTT
* *
27659 AAATTTAAAATATAAATTATAGTATTCAAAATTT
1 AAATTTAAAATAAAAATAATAGTATTCAAAATTT
27693 AA
1 AA
27695 CATTAAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (34 bp):
AAATTTAAAATAAAAATAATAGTATTCAAAATTT
Found at i:27701 original size:34 final size:32
Alignment explanation
Indices: 27601--27701 Score: 111
Period size: 34 Copynumber: 3.2 Consensus size: 32
27591 ATAAATGTTT
* *
27601 TTAAAATACAAATTATATTATTCGAAATTTAAA
1 TTAAAATATAAATTATA-TATTCAAAATTTAAA
*
27634 ATAAAA-AT-AA-TAT-TATTCAAAATTTAAA
1 TTAAAATATAAATTATATATTCAAAATTTAAA
27662 TTTAAAATATAAATTATAGTATTCAAAATTTAACA
1 -TTAAAATATAAATTATA-TATTCAAAATTTAA-A
27697 TTAAA
1 TTAAA
27702 TTTCAACTTA
Statistics
Matches: 57, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
28 14 0.25
29 5 0.09
30 5 0.09
31 4 0.07
32 4 0.07
33 5 0.09
34 19 0.33
35 1 0.02
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (32 bp):
TTAAAATATAAATTATATATTCAAAATTTAAA
Found at i:28720 original size:128 final size:128
Alignment explanation
Indices: 28093--28720 Score: 1021
Period size: 128 Copynumber: 4.9 Consensus size: 128
28083 TTACCTGATT
*
28093 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATA-GGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *** *
28157 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCT-GAGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
* *
28220 TACTGATATGA-ATAATGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT
1 TACTGATAT-ATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT
* * * *** *
28284 ATGACAAAATAATGGAAGGCGCACCCCCGGGAACGCGCCTTCATGTCCCCT-GAGAAATAATAGG
65 CTGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
28348 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
28413 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
28476 TACTGATATATTTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
28541 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCTCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
28604 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* * *
28669 TGATGAAATAATGGAAGGCGCCCCCCCGGGAACGTGCCTTCATGTGAATAGT
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
28721 ACTCCGATTA
Statistics
Matches: 478, Mismatches: 19, Indels: 7
0.95 0.04 0.01
Matches are distributed among these distances:
127 42 0.09
128 436 0.91
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:28804 original size:8 final size:8
Alignment explanation
Indices: 28791--28831 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
28781 TCACAATCTT
28791 TCAAATTC
1 TCAAATTC
28799 TCAAATTC
1 TCAAATTC
* *
28807 CCAAACTC
1 TCAAATTC
28815 T-AAATTC
1 TCAAATTC
28822 TCAAATTC
1 TCAAATTC
28830 TC
1 TC
28832 TGCAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:33234 original size:2 final size:2
Alignment explanation
Indices: 33229--33263 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
33219 TCTCTCTCTC
* *
33229 TA TA TA TA TA TA TA TC TA TC 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
33264 CCAGACTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:33252 original size:20 final size:20
Alignment explanation
Indices: 33227--33264 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
33217 TCTCTCTCTC
33227 TCTATATATATATATATCTA
1 TCTATATATATATATATCTA
33247 TCTATATATATATATATC
1 TCTATATATATATATATC
33265 CAGACTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (20 bp):
TCTATATATATATATATCTA
Found at i:33280 original size:15 final size:15
Alignment explanation
Indices: 33262--33298 Score: 56
Period size: 17 Copynumber: 2.3 Consensus size: 15
33252 ATATATATAT
33262 ATCCAGACTATATTC
1 ATCCAGACTATATTC
33277 ATCCAGAGACTATATTC
1 ATCC--AGACTATATTC
33294 ATCCA
1 ATCCA
33299 TGGACAGAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 5 0.25
17 15 0.75
ACGTcount: A:0.35, C:0.27, G:0.08, T:0.30
Consensus pattern (15 bp):
ATCCAGACTATATTC
Found at i:33286 original size:17 final size:17
Alignment explanation
Indices: 33266--33298 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
33256 ATATATATCC
33266 AGACTATATTCATCCAG
1 AGACTATATTCATCCAG
33283 AGACTATATTCATCCA
1 AGACTATATTCATCCA
33299 TGGACAGAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.24, G:0.09, T:0.30
Consensus pattern (17 bp):
AGACTATATTCATCCAG
Found at i:33931 original size:23 final size:23
Alignment explanation
Indices: 33905--33955 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
33895 AGCATTCATG
33905 TTTGATATTTATATCGGCACATA
1 TTTGATATTTATATCGGCACATA
33928 TTTGATATTTATATCGGCACATA
1 TTTGATATTTATATCGGCACATA
33951 TTTGA
1 TTTGA
33956 ACATGGTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (23 bp):
TTTGATATTTATATCGGCACATA
Found at i:38118 original size:13 final size:14
Alignment explanation
Indices: 38102--38136 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
38092 CTCGTGTCAG
38102 TTTTATAATTTT-T
1 TTTTATAATTTTAT
*
38115 TTTTAAAATTTTAT
1 TTTTATAATTTTAT
38129 TTTTATAA
1 TTTTATAA
38137 AACATTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTATAATTTTAT
Found at i:42857 original size:41 final size:41
Alignment explanation
Indices: 42812--42892 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 41
42802 TTAGGTTCGT
* ** *
42812 TTGTTTCATAGAAAGCAGATTTTGGAAATGAAATATTTAGC
1 TTGTTTCATAGAAAACAGATTCCGGAAACGAAATATTTAGC
* *
42853 TTGTTTCATTGAAAACATATTCCGGAAACGAAATATTTAG
1 TTGTTTCATAGAAAACAGATTCCGGAAACGAAATATTTAG
42893 GGTGTGTTGT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (41 bp):
TTGTTTCATAGAAAACAGATTCCGGAAACGAAATATTTAGC
Found at i:43824 original size:20 final size:21
Alignment explanation
Indices: 43779--43824 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
43769 TTGGATAATT
*
43779 AGATTTAATTTAAATCTTATA
1 AGATTTAATTTAAATCTTAAA
43800 A-ATTTAATTT-AAT-TTAAAA
1 AGATTTAATTTAAATCTT-AAA
43819 AGATTT
1 AGATTT
43825 GAAAGAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
18 2 0.09
19 6 0.27
20 13 0.59
21 1 0.05
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (21 bp):
AGATTTAATTTAAATCTTAAA
Found at i:44461 original size:15 final size:16
Alignment explanation
Indices: 44432--44462 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
44422 ATTACTTAAT
44432 TTATATTTTTATTCAA
1 TTATATTTTTATTCAA
44448 TTATATTTTT-TTCAA
1 TTATATTTTTATTCAA
44463 AATCATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATATTTTTATTCAA
Found at i:55562 original size:21 final size:19
Alignment explanation
Indices: 55538--55594 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 19
55528 CATATTTGCA
*
55538 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAATT--CG
*
55559 TTGCGATTTATTCCAAATTCG
1 TTGCGA--TAGTCCAAATTCG
55580 TTGCGATAGTCCAAA
1 TTGCGATAGTCCAAA
55595 ATTGCAACGA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 8 0.26
21 14 0.45
23 9 0.29
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (19 bp):
TTGCGATAGTCCAAATTCG
Found at i:56527 original size:21 final size:21
Alignment explanation
Indices: 56501--56675 Score: 209
Period size: 21 Copynumber: 8.4 Consensus size: 21
56491 TTGGAATAAA
56501 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* *
56522 ATCGCAA--CGAACTTGGAAT
1 ATCGCAACGCGAACTTCGACT
56541 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTCGACT
56564 ATCGCAA--CGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
56583 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
*
56604 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
* * *
56625 ATCGCAACGC--ATTTGGAAT
1 ATCGCAACGCGAACTTCGACT
*
56644 AAATCGCAACGCGAACTTGGACT
1 --ATCGCAACGCGAACTTCGACT
56667 ATCGCAACG
1 ATCGCAACG
56676 AATTTGGAAA
Statistics
Matches: 135, Mismatches: 9, Indels: 20
0.82 0.05 0.12
Matches are distributed among these distances:
19 36 0.27
21 82 0.61
23 17 0.13
ACGTcount: A:0.32, C:0.29, G:0.20, T:0.19
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:56558 original size:42 final size:40
Alignment explanation
Indices: 56475--56634 Score: 221
Period size: 42 Copynumber: 3.8 Consensus size: 40
56465 TGCAATTTTG
*
56475 GACTATCGCAACGAATTTGGAATAAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAAT---ATCGCAACGCGAACTTC
56518 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAAT--ATCGCAACGCGAACTTC
* *
56560 GACTATCGCAACGAACTTCGACTATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATATCGCAACGCGAACTTC
*
56600 GACTATCGCAACGCGAACTTGGACTATCGCAACGC
1 GACTATCGCAA--CGAACTTGGAATATCGCAACGC
56635 ATTTGGAATA
Statistics
Matches: 111, Mismatches: 4, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
40 28 0.25
42 61 0.55
43 22 0.20
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.19
Consensus pattern (40 bp):
GACTATCGCAACGAACTTGGAATATCGCAACGCGAACTTC
Found at i:56579 original size:61 final size:60
Alignment explanation
Indices: 56501--56675 Score: 190
Period size: 61 Copynumber: 2.8 Consensus size: 60
56491 TTGGAATAAA
*
56501 ATCGCAACGCGAACTTCGACTATCGCAA-CGAACTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAA--CGAACTTCGACTATCGCAACCGAACTTCGAAT--ATCGCAACGCGAACTTCGACT
* *
56564 ATCGCAACGAACTTCGACTATCGCAACGCGAACTTCGACTATCGCAACGCGAACTTGGACT
1 ATCGCAACGAACTTCGACTATCGCAAC-CGAACTTCGAATATCGCAACGCGAACTTCGACT
* * * * * *
56625 ATCGCAACGCATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACG
1 ATCGCAACGAACTTCGACT--ATCGCAAC-CGAACTTCGAATATCGCAACG
56676 AATTTGGAAA
Statistics
Matches: 100, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
61 54 0.54
63 46 0.46
ACGTcount: A:0.32, C:0.29, G:0.20, T:0.19
Consensus pattern (60 bp):
ATCGCAACGAACTTCGACTATCGCAACCGAACTTCGAATATCGCAACGCGAACTTCGACT
Found at i:56650 original size:42 final size:40
Alignment explanation
Indices: 56564--56691 Score: 152
Period size: 42 Copynumber: 3.1 Consensus size: 40
56554 AACTTCGACT
* * * **
56564 ATCGCAA--CGAACTTCGACTATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTGGACTATCGCAA--CGAATTTGGAAA
*
56604 ATCGCAACGCGAACTTGGACTATCGCAACGCATTTGGAATAA
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGG-A-AA
56646 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAAA
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAAA
56686 ATCGCA
1 ATCGCA
56692 TTGCGATAGT
Statistics
Matches: 77, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
40 21 0.27
41 2 0.03
42 54 0.70
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (40 bp):
ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAAA
Found at i:56689 original size:19 final size:19
Alignment explanation
Indices: 56625--56691 Score: 62
Period size: 19 Copynumber: 3.3 Consensus size: 19
56615 AACTTGGACT
*
56625 ATCGCAACGCATTTGGAATAA
1 ATCGCAACGAATTTGG-A-AA
* **
56646 ATCGCAACGCGAACTTGGACT
1 ATCGCAA--CGAATTTGGAAA
56667 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
56686 ATCGCA
1 ATCGCA
56692 TTGCGATAGT
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
19 15 0.41
21 14 0.38
22 1 0.03
23 7 0.19
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (19 bp):
ATCGCAACGAATTTGGAAA
Found at i:56690 original size:103 final size:103
Alignment explanation
Indices: 56501--56691 Score: 310
Period size: 103 Copynumber: 1.9 Consensus size: 103
56491 TTGGAATAAA
56501 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTAT
1 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTAT
**
56566 CGCAACGAACTTCGACTATCGCAACGCGAACTTCGACT
66 CGCAACGAACTTCGAAAATCGCAACGCGAACTTCGACT
* * * *
56604 ATCGCAACGCGAACTTGGACTATCGCAACGCATTTGGAATAAATCGCAACGCGAACTTGGACTAT
1 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTAT
* *
56669 CGCAACGAATTTGGAAAATCGCA
66 CGCAACGAACTTCGAAAATCGCA
56692 TTGCGATAGT
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
103 80 1.00
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (103 bp):
ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTAT
CGCAACGAACTTCGAAAATCGCAACGCGAACTTCGACT
Found at i:56716 original size:21 final size:21
Alignment explanation
Indices: 56687--56739 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
56677 ATTTGGAAAA
*
56687 TCGCATTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCGAAGT
*
56708 TCGCGTTGCGATAGTCGATGT
1 TCGCGTTGCGATAGTCGAAGT
56729 TCGCGTTGCGA
1 TCGCGTTGCGA
56740 ATCTGGAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.17, C:0.21, G:0.32, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCGAAGT
Found at i:59571 original size:15 final size:15
Alignment explanation
Indices: 59551--59660 Score: 51
Period size: 15 Copynumber: 7.4 Consensus size: 15
59541 TATATCTATA
59551 ATTATATAAATAAGG
1 ATTATATAAATAAGG
*** **
59566 ATTATACCTATAAAT
1 ATTATATAAATAAGG
*
59581 ATAATATAAATAAGG
1 ATTATATAAATAAGG
*** **
59596 ATTATACCTATAAAT
1 ATTATATAAATAAGG
*
59611 ATAATAT-AATAAGG
1 ATTATATAAATAAGG
*** **
59625 ATTATACCTATAAAT
1 ATTATATAAATAAGG
*
59640 ATAATATAAATAAGG
1 ATTATATAAATAAGG
59655 ATTATA
1 ATTATA
59661 CCTATAAATA
Statistics
Matches: 60, Mismatches: 34, Indels: 2
0.62 0.35 0.02
Matches are distributed among these distances:
14 9 0.15
15 51 0.85
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (15 bp):
ATTATATAAATAAGG
Found at i:59579 original size:19 final size:19
Alignment explanation
Indices: 59555--59611 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
59545 TCTATAATTA
59555 TATAAATAAGGATTATACC
1 TATAAATAAGGATTATACC
59574 TATAAAT----A-TA-A--
1 TATAAATAAGGATTATACC
59585 TATAAATAAGGATTATACC
1 TATAAATAAGGATTATACC
59604 TATAAATA
1 TATAAATA
59612 TAATATAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 16
0.65 0.00 0.35
Matches are distributed among these distances:
11 7 0.23
13 1 0.03
14 2 0.07
15 2 0.07
16 2 0.07
17 1 0.03
19 15 0.50
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (19 bp):
TATAAATAAGGATTATACC
Found at i:59590 original size:30 final size:30
Alignment explanation
Indices: 59554--59672 Score: 231
Period size: 30 Copynumber: 4.0 Consensus size: 30
59544 ATCTATAATT
59554 ATATAAATAAGGATTATACCTATAAATATA
1 ATATAAATAAGGATTATACCTATAAATATA
59584 ATATAAATAAGGATTATACCTATAAATATA
1 ATATAAATAAGGATTATACCTATAAATATA
59614 ATAT-AATAAGGATTATACCTATAAATATA
1 ATATAAATAAGGATTATACCTATAAATATA
59643 ATATAAATAAGGATTATACCTATAAATATA
1 ATATAAATAAGGATTATACCTATAAATATA
59673 TAATAATATT
Statistics
Matches: 88, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
29 29 0.33
30 59 0.67
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.34
Consensus pattern (30 bp):
ATATAAATAAGGATTATACCTATAAATATA
Found at i:59623 original size:59 final size:58
Alignment explanation
Indices: 59541--59680 Score: 237
Period size: 59 Copynumber: 2.4 Consensus size: 58
59531 AACTTAGAAA
* *
59541 TATATCTATAATTATATA-AATAAGGATTATACCTATAAATATAATATAAATAAGGAT
1 TATACCTATAAATATATATAATAAGGATTATACCTATAAATATAATATAAATAAGGAT
59598 TATACCTATAAATATAATATAATAAGGATTATACCTATAAATATAATATAAATAAGGAT
1 TATACCTATAAATAT-ATATAATAAGGATTATACCTATAAATATAATATAAATAAGGAT
59657 TATACCTATAAATATATAATAATA
1 TATACCTATAAATATAT-ATAATA
59681 TTAATAGTAC
Statistics
Matches: 78, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
57 13 0.17
58 5 0.06
59 60 0.77
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (58 bp):
TATACCTATAAATATATATAATAAGGATTATACCTATAAATATAATATAAATAAGGAT
Found at i:62979 original size:9 final size:10
Alignment explanation
Indices: 62951--62989 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
62941 TTCATCACAC
62951 CAAATTCTCT
1 CAAATTCTCT
62961 CAAATTCTCT
1 CAAATTCTCT
*
62971 -AACTTCTCT
1 CAAATTCTCT
*
62980 CAAATACTCT
1 CAAATTCTCT
62990 TATATCTCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
9 8 0.32
10 17 0.68
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:63036 original size:24 final size:24
Alignment explanation
Indices: 63009--63055 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
62999 ATTTAAGGTA
*
63009 TATTTTATATATTTTAA-TATTTTG
1 TATTTAATATA-TTTAAGTATTTTG
*
63033 TATTTAATTTATTTAAGTATTTT
1 TATTTAATATATTTAAGTATTTT
63056 AATTTATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (24 bp):
TATTTAATATATTTAAGTATTTTG
Found at i:63060 original size:23 final size:22
Alignment explanation
Indices: 63012--63065 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
63002 TAAGGTATAT
* *
63012 TTTATATATTTTAATATTTTGTA
1 TTTATTTA-TTTAATATTTTGAA
63035 TTTAATTTATTTAAGTATTTT-AA
1 TTT-ATTTATTTAA-TATTTTGAA
63058 TTTATTTA
1 TTTATTTA
63066 ATATTTTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 5 0.19
23 12 0.44
24 10 0.37
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (22 bp):
TTTATTTATTTAATATTTTGAA
Found at i:63072 original size:17 final size:18
Alignment explanation
Indices: 63035--63072 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
63025 ATATTTTGTA
63035 TTTAATTTATTTAAGTAT
1 TTTAATTTATTTAAGTAT
63053 TTTAATTTATTTAA-TAT
1 TTTAATTTATTTAAGTAT
63070 TTT
1 TTT
63073 CTTATATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (18 bp):
TTTAATTTATTTAAGTAT
Done.