Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008455.1 Hibiscus syriacus cultivar Beakdansim tig00111263_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: 56297
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.32
Found at i:301 original size:99 final size:95
Alignment explanation
Indices: 198--494 Score: 242
Period size: 99 Copynumber: 3.0 Consensus size: 95
188 CATGGTAACA
**
198 TAATAGTCAACGTTTTTTTAATGTCAATATTTTAAGTTATAAGTATAAAACCTTTTATTTAATAG
1 TAATAGTCAACG-TTTTTTAATGTCAACCTTTTAAGTTATAAGTATAAAACCTTTTATTT-AT-G
263 -AAAAGTAAGACAAAACATATTTCTCATGATAATG
63 CAAAAGTAAGACAAAACA-ATTT-TCATGATAATG
* * * * * * * *
297 TAATAGGTAGAACATTTTTT-ATATCAACCGTTTAAGTTATAAGTATGAAATCATTTAAATTATG
1 TAATA-GT-CAACGTTTTTTAATGTCAACCTTTTAAGTTATAAGTAT-AAAACCTTTTATTTATG
* *
361 TAAAAGTAAGACAAAAC-ATGTTCATGATAATG
63 CAAAAGTAAGACAAAACAATTTTCATGATAATG
* * * * * * *
393 TATTAGTTAGCACAG-TTTTTAATGTTAACCTTTTAAGTTATAATTATGAAATCATTTATATTAT
1 TAATAGTCA--AC-GTTTTTTAATGTCAACCTTTTAAGTTATAAGTATAAAACCTTTTAT-TTAT
* * *
457 GCAAAAGTAAGATAAAATAGGTTTTTCATGATAATG
62 GCAAAAGTAAGACAAAACA--ATTTTCATGATAATG
493 TA
1 TA
495 GTTATAACAC
Statistics
Matches: 156, Mismatches: 30, Indels: 23
0.75 0.14 0.11
Matches are distributed among these distances:
94 1 0.01
95 2 0.01
96 27 0.17
97 44 0.28
98 1 0.01
99 45 0.29
100 33 0.21
101 3 0.02
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (95 bp):
TAATAGTCAACGTTTTTTAATGTCAACCTTTTAAGTTATAAGTATAAAACCTTTTATTTATGCAA
AAGTAAGACAAAACAATTTTCATGATAATG
Found at i:497 original size:97 final size:94
Alignment explanation
Indices: 212--509 Score: 296
Period size: 97 Copynumber: 3.1 Consensus size: 94
202 AGTCAACGTT
** * * *
212 TTTTTAATGTCAATATTTTAAGTTATAAGTATAAAACCTTTTAT-TTAATAGAAAAGTAAGACAA
1 TTTTTAATGTCAACCTTTTAAGTTATAAGTATGAAATCATTTATATT-AT-GAAAAGTAAGACAA
*
276 AACATATTTCTCATGATAATGTAATAGGTAGAACA
64 AACAT-TTT-TCATGATAATG--ATAGTTAGAACA
* * * *
311 TTTTTTATATCAACCGTTTAAGTTATAAGTATGAAATCATTTAAATTATGTAAAAGTAAGACAAA
1 TTTTTAATGTCAACCTTTTAAGTTATAAGTATGAAATCATTTATATTATG-AAAAGTAAGACAAA
* *
376 ACA-TGTTCATGATAATGTATTAGTTAGCACA
65 ACATTTTTCATGATAATG-A-TAGTTAGAACA
* * *
407 GTTTTTAATGTTAACCTTTTAAGTTATAATTATGAAATCATTTATATTATGCAAAAGTAAGATAA
1 -TTTTTAATGTCAACCTTTTAAGTTATAAGTATGAAATCATTTATATTATG-AAAAGTAAGACAA
* *
472 AATAGGTTTTTCATGATAATG-TAGTTATAACA
64 AACA--TTTTTCATGATAATGATAGTTAGAACA
504 CTTTTT
1 -TTTTT
510 TTATGCAAAG
Statistics
Matches: 166, Mismatches: 26, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
95 1 0.01
96 20 0.12
97 75 0.45
98 1 0.01
99 54 0.33
100 15 0.09
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (94 bp):
TTTTTAATGTCAACCTTTTAAGTTATAAGTATGAAATCATTTATATTATGAAAAGTAAGACAAAA
CATTTTTCATGATAATGATAGTTAGAACA
Found at i:1140 original size:81 final size:81
Alignment explanation
Indices: 1000--1231 Score: 254
Period size: 81 Copynumber: 3.0 Consensus size: 81
990 ATTTTTTTGT
* *
1000 GTAATCTATTTTATTAATAAGAATATTAACA-T--A--ACATATCACAACCTATTTCTTAGTGAA
1 GTAACCTATTTTATTAATAA-AATATTAACATTACATTACAAATCACAACCTATTTCTTAGTGAA
* *
1060 CCATGACATTCTT-GGAC
65 CAATGACATTATTAGG-C
* *
1077 GTAACCTATTTTATTAA-AAAATATTAACATTACATTACAAATGACAACTTATTTTCTTAGTGAA
1 GTAACCTATTTTATTAATAAAATATTAACATTACATTACAAATCACAACCTA-TTTCTTAGTGAA
* * *
1141 CAATAACAATATTAGGT
65 CAATGACATTATTAGGC
*
1158 GTAACCTATTTTATTAATAAAA-A-T---ATTACATTACAAATCATAACCTATTTCTTAGTGAAC
1 GTAACCTATTTTATTAATAAAATATTAACATTACATTACAAATCACAACCTATTTCTTAGTGAAC
*
1218 TATGACATTATTAG
66 AATGACATTATTAG
1232 ACACAACCGG
Statistics
Matches: 132, Mismatches: 15, Indels: 17
0.80 0.09 0.10
Matches are distributed among these distances:
75 10 0.08
76 27 0.20
77 36 0.27
78 1 0.01
80 13 0.10
81 39 0.30
82 6 0.05
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.38
Consensus pattern (81 bp):
GTAACCTATTTTATTAATAAAATATTAACATTACATTACAAATCACAACCTATTTCTTAGTGAAC
AATGACATTATTAGGC
Found at i:12024 original size:20 final size:20
Alignment explanation
Indices: 12001--12078 Score: 97
Period size: 20 Copynumber: 4.0 Consensus size: 20
11991 GAGGGATTAT
12001 CAGTGGTCCTTCGGGACAAA
1 CAGTGGTCCTTCGGGACAAA
*** *
12021 CAGTGGTCCTTCAAAACAAT
1 CAGTGGTCCTTCGGGACAAA
12041 CAGTGGTCCTTCGGGAC--A
1 CAGTGGTCCTTCGGGACAAA
*
12059 TAGTGGTCCTTCGGGACAAA
1 CAGTGGTCCTTCGGGACAAA
12079 TATTCAGTGC
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
18 16 0.34
20 31 0.66
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (20 bp):
CAGTGGTCCTTCGGGACAAA
Found at i:12445 original size:2 final size:2
Alignment explanation
Indices: 12438--12493 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
12428 AATGATAATG
12438 AT AT AT AT AT 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 AT AT AT AT AT
12480 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
12494 GTATGTATGT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18835 original size:21 final size:21
Alignment explanation
Indices: 18771--18856 Score: 88
Period size: 21 Copynumber: 4.2 Consensus size: 21
18761 CAGGTTCCAA
*
18771 AAATT-GCAACGCG-ATTTTT
1 AAATTCGCAACGCGAATTTGT
* * *
18790 CAAATTCGCAATGCGATTTTCT
1 -AAATTCGCAACGCGAATTTGT
*
18812 AAATTCGCAACGCGAATATGT
1 AAATTCGCAACGCGAATTTGT
*
18833 AAA-TCGTAACGCGAATTTGT
1 AAATTCGCAACGCGAATTTGT
18853 AAAT
1 AAAT
18857 CGTAACACAG
Statistics
Matches: 54, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
20 23 0.43
21 27 0.50
22 4 0.07
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.31
Consensus pattern (21 bp):
AAATTCGCAACGCGAATTTGT
Found at i:18845 original size:20 final size:20
Alignment explanation
Indices: 18820--18862 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
18810 CTAAATTCGC
18820 AACGCGAATATGTAAATCGT
1 AACGCGAATATGTAAATCGT
*
18840 AACGCGAATTTGTAAATCGT
1 AACGCGAATATGTAAATCGT
18860 AAC
1 AAC
18863 ACAGAAGTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.26
Consensus pattern (20 bp):
AACGCGAATATGTAAATCGT
Found at i:18965 original size:40 final size:40
Alignment explanation
Indices: 18921--19025 Score: 113
Period size: 40 Copynumber: 2.6 Consensus size: 40
18911 TATTTTTCAT
* *
18921 AACAC-AAGTTTCCTTTTCGCAACAAGATTTTCTAAATCGC
1 AACACGAA-TTTCCATTTCGCAACAAGATTTTCGAAATCGC
** ** *
18961 AACACGAATTTTGATTTCGCAACTCGATTTTCGAATTCGC
1 AACACGAATTTCCATTTCGCAACAAGATTTTCGAAATCGC
**
19001 AACACGAATTTTAATTTCGCAACAA
1 AACACGAATTTCCATTTCGCAACAA
19026 CTTTTATTTT
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
40 52 0.96
41 2 0.04
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.32
Consensus pattern (40 bp):
AACACGAATTTCCATTTCGCAACAAGATTTTCGAAATCGC
Found at i:18980 original size:20 final size:20
Alignment explanation
Indices: 18957--19050 Score: 97
Period size: 20 Copynumber: 4.8 Consensus size: 20
18947 ATTTTCTAAA
18957 TCGCAACACGAATTTTGATT
1 TCGCAACACGAATTTTGATT
* *
18977 TCGCAACTCG-ATTTTCGAAT
1 TCGCAACACGAATTTT-GATT
*
18997 TCGCAACACGAATTTTAATT
1 TCGCAACACGAATTTTGATT
*
19017 TCGCAACA--ACTTTT-ATTT
1 TCGCAACACGAATTTTGA-TT
*
19035 TCGCAACACAAATTTT
1 TCGCAACACGAATTTT
19051 TTGGGTATAT
Statistics
Matches: 62, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
17 1 0.02
18 15 0.24
19 5 0.08
20 36 0.58
21 5 0.08
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (20 bp):
TCGCAACACGAATTTTGATT
Found at i:19216 original size:16 final size:15
Alignment explanation
Indices: 19181--19219 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
19171 TCCCCATCTC
*
19181 TAATTTTTTTTTACA
1 TAATTTTTTTCTACA
*
19196 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
19212 TAATTTTT
1 TAATTTTT
19220 CAATGATTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:19836 original size:24 final size:24
Alignment explanation
Indices: 19809--19858 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
19799 TCAAAATTTT
19809 ATCTTGGTCAATACTCGGACTTTG
1 ATCTTGGTCAATACTCGGACTTTG
* *
19833 ATCTTGGTCAATACTCTGATTTTG
1 ATCTTGGTCAATACTCGGACTTTG
19857 AT
1 AT
19859 GATGTTTCAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.42
Consensus pattern (24 bp):
ATCTTGGTCAATACTCGGACTTTG
Found at i:21432 original size:64 final size:65
Alignment explanation
Indices: 21364--21504 Score: 158
Period size: 64 Copynumber: 2.2 Consensus size: 65
21354 GAACACTTGA
* * *
21364 TGCATCGGTGCACCAAGTGTGCATCGATACGTGAAATGCATTCGATG-TTTGAAAATAGCCTGCG
1 TGCATCGATGCACCAAGTGTGCATCGATACATCAAATGCATTCGATGTTTTGAAAATAGCCTGCG
***** * ** * *
21428 TGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAG
1 TGCATCGATGCACCAAGTGTGCATCGATACATCAAATGCATTCGATGTTTTGAAAATAGCCTGCG
21493 TGCATCGATGCA
1 TGCATCGATGCA
21505 TGGAGAATGC
Statistics
Matches: 63, Mismatches: 13, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
64 38 0.60
65 25 0.40
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (65 bp):
TGCATCGATGCACCAAGTGTGCATCGATACATCAAATGCATTCGATGTTTTGAAAATAGCCTGCG
Found at i:21516 original size:65 final size:65
Alignment explanation
Indices: 21383--21542 Score: 196
Period size: 65 Copynumber: 2.5 Consensus size: 65
21373 GCACCAAGTG
* * * * ****
21383 TGCATCGATACGTGAAATGCATTCGATG-TTTGAAAATAGCCTGCGTGCATCGATGCATGGCTTG
1 TGCATCGATGCATGAAATGCATTCGATGTTTTGAAAATAGCCAGAGTGCATCGATGCATGGAGAA
* **
21447 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGGAGAA
1 TGCATCGATGCATGAAATGCATTCGATGTTTTGAAAATAGCCAGAGTGCATCGATGCATGGAGAA
* *
21512 TGCATCGGTGCATGGAATGCATTCGATGTTT
1 TGCATCGATGCATGAAATGCATTCGATGTTT
21543 CAATTAATTC
Statistics
Matches: 81, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
64 25 0.31
65 56 0.69
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.31
Consensus pattern (65 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTTGAAAATAGCCAGAGTGCATCGATGCATGGAGAA
Found at i:21531 original size:17 final size:19
Alignment explanation
Indices: 21493--21539 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
21483 ATATTCAGAG
21493 TGCATCGATGCATGGAGAA
1 TGCATCGATGCATGGAGAA
*
21512 TGCATCGGTGCAT-G-GAA
1 TGCATCGATGCATGGAGAA
21529 TGCATTCGATG
1 TGCA-TCGATG
21540 TTTCAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.28
18 6 0.24
19 12 0.48
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCATGGAGAA
Found at i:23320 original size:18 final size:18
Alignment explanation
Indices: 23297--23332 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
23287 ATACAAAAGG
*
23297 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
23315 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
23333 CAACCGACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:23702 original size:20 final size:20
Alignment explanation
Indices: 23637--23711 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
23627 AGGTATACTT
* * *
23637 TCGCAACGCAAAAATCAAAT
1 TCGCAACGCGAAAGTCAAAA
* **
23657 TCACAACAAGAAAGTCAAAA
1 TCGCAACGCGAAAGTCAAAA
23677 TCGCAACGCGAAAGTCAAAA
1 TCGCAACGCGAAAGTCAAAA
*
23697 TTGCAACGCGAAAGT
1 TCGCAACGCGAAAGT
23712 GTACCTTCTG
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.48, C:0.23, G:0.16, T:0.13
Consensus pattern (20 bp):
TCGCAACGCGAAAGTCAAAA
Found at i:23959 original size:20 final size:20
Alignment explanation
Indices: 23899--23959 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
23889 TGCGATTGTT
*
23899 GCGAAAGACAAATTCGCAAC
1 GCGAAAGTCAAATTCGCAAC
* **
23919 ACGAAAGTCAAATTTACAAC
1 GCGAAAGTCAAATTCGCAAC
*
23939 GCGAAAGTCAAAATCGCAAC
1 GCGAAAGTCAAATTCGCAAC
23959 G
1 G
23960 AGAATTTGAT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.46, C:0.23, G:0.18, T:0.13
Consensus pattern (20 bp):
GCGAAAGTCAAATTCGCAAC
Found at i:25671 original size:21 final size:21
Alignment explanation
Indices: 25645--25759 Score: 117
Period size: 21 Copynumber: 5.5 Consensus size: 21
25635 GTGAATCGGG
25645 CTCTTGAACGGTGGGAG-GGAC
1 CTCTTGAACGGTGGGAGAGG-C
* ** *
25666 CTCTTGAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGAGGC
25687 CTCTTGAACGGTGGGAGAGGC
1 CTCTTGAACGGTGGGAGAGGC
** *
25708 CTCTTGAA-GGATGATAGTGGC
1 CTCTTGAACGG-TGGGAGAGGC
* *
25729 CTCTTGAACGATAGGAGAGGC
1 CTCTTGAACGGTGGGAGAGGC
25750 CTCTTGAACG
1 CTCTTGAACG
25760 ATGACAGGTG
Statistics
Matches: 76, Mismatches: 15, Indels: 6
0.78 0.15 0.06
Matches are distributed among these distances:
20 2 0.03
21 71 0.93
22 3 0.04
ACGTcount: A:0.23, C:0.20, G:0.36, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGAGGC
Found at i:25711 original size:42 final size:42
Alignment explanation
Indices: 25645--25767 Score: 185
Period size: 42 Copynumber: 2.9 Consensus size: 42
25635 GTGAATCGGG
25645 CTCTTGAACGGTGGGAG-GGACCTCTTGAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGAGG-CCTCTTGAACGATGACAGGGGC
* * *
25687 CTCTTGAACGGTGGGAGAGGCCTCTTGAAGGATGATAGTGGC
1 CTCTTGAACGGTGGGAGAGGCCTCTTGAACGATGACAGGGGC
* *
25729 CTCTTGAACGATAGGAGAGGCCTCTTGAACGATGACAGG
1 CTCTTGAACGGTGGGAGAGGCCTCTTGAACGATGACAGG
25768 TGAATCGGGC
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
42 70 0.97
43 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.36, T:0.21
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGAGGCCTCTTGAACGATGACAGGGGC
Found at i:26164 original size:63 final size:63
Alignment explanation
Indices: 26059--26180 Score: 156
Period size: 63 Copynumber: 1.9 Consensus size: 63
26049 CGTAGAGCGG
* *
26059 CTACCTCACCACGTAAAGTAGATATCTCACCACGTAAAGCACCATTGTCATCACGTAAAACCT
1 CTACCTCACCACGTAAAGTAGATACCTCACCACGCAAAGCACCATTGTCATCACGTAAAACCT
* * * * * *
26122 CTACCTCACCACGTAAAGATCG-TACCTCATCACGCCATGCACCATTGTCGTCATGTAAA
1 CTACCTCACCACGTAAAG-TAGATACCTCACCACGCAAAGCACCATTGTCATCACGTAAA
26181 GTACCGACCT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
63 48 0.96
64 2 0.04
ACGTcount: A:0.32, C:0.33, G:0.12, T:0.23
Consensus pattern (63 bp):
CTACCTCACCACGTAAAGTAGATACCTCACCACGCAAAGCACCATTGTCATCACGTAAAACCT
Found at i:27922 original size:19 final size:19
Alignment explanation
Indices: 27885--27940 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
27875 TCTGAAACTT
27885 AAAATCGCAACGCGAAAATA
1 AAAATCGCAACGCG-AAATA
* *
27905 AAAATCGTAACGCGAAATG
1 AAAATCGCAACGCGAAATA
27924 AAAATCGCAACGC-AAAT
1 AAAATCGCAACGCGAAAT
27941 TTCATTTTCG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
18 4 0.12
19 16 0.48
20 13 0.39
ACGTcount: A:0.52, C:0.20, G:0.16, T:0.12
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:28519 original size:19 final size:19
Alignment explanation
Indices: 28481--28522 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
28471 GTTTCGAATT
*
28481 CGAAAATAAAATCGCGTTG
1 CGAAAATAAAAGCGCGTTG
* *
28500 CGAAAATAAACGCGCTTTG
1 CGAAAATAAAAGCGCGTTG
28519 CGAA
1 CGAA
28523 TTTGACTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.19
Consensus pattern (19 bp):
CGAAAATAAAAGCGCGTTG
Found at i:28541 original size:20 final size:20
Alignment explanation
Indices: 28516--28558 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
28506 TAAACGCGCT
28516 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTCTGTG
28536 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTCTGTG
28556 TTG
1 TTG
28559 TGATTTACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.14, C:0.14, G:0.26, T:0.47
Consensus pattern (20 bp):
TTGCGAATTTGACTTCTGTG
Found at i:28583 original size:20 final size:20
Alignment explanation
Indices: 28555--28644 Score: 135
Period size: 20 Copynumber: 4.5 Consensus size: 20
28545 TGACTTCTGT
* *
28555 GTTGTGATTTACAAATTCGC
1 GTTGCGATTTACATATTCGC
28575 GTTGCGATTTACATATTCGC
1 GTTGCGATTTACATATTCGC
**
28595 GTTGCGATTTACATATTATC
1 GTTGCGATTTACATATTCGC
*
28615 GTTGCGATTTACCTATTCGC
1 GTTGCGATTTACATATTCGC
28635 GTTGCGATTT
1 GTTGCGATTT
28645 TGGAACCTAT
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 63 1.00
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.42
Consensus pattern (20 bp):
GTTGCGATTTACATATTCGC
Found at i:34714 original size:28 final size:28
Alignment explanation
Indices: 34682--34747 Score: 123
Period size: 28 Copynumber: 2.4 Consensus size: 28
34672 TTAGAACGAT
34682 ATATTTAAAAGCAGTAAAATAAATGAAA
1 ATATTTAAAAGCAGTAAAATAAATGAAA
34710 ATATTTAAAAGCAGTAAAATAAATGAAA
1 ATATTTAAAAGCAGTAAAATAAATGAAA
*
34738 ACATTTAAAA
1 ATATTTAAAA
34748 TTAATGACTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.61, C:0.05, G:0.09, T:0.26
Consensus pattern (28 bp):
ATATTTAAAAGCAGTAAAATAAATGAAA
Found at i:36049 original size:3 final size:3
Alignment explanation
Indices: 36043--36108 Score: 80
Period size: 3 Copynumber: 22.0 Consensus size: 3
36033 TATTATTTTT
* * *
36043 TAA TAA TAA TAA T-A TATA TAA TAA TTA TAA TAA TAA TAA TTA TGA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
36088 TAA TAA TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
36109 AATGGGTAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
2 2 0.04
3 49 0.91
4 3 0.06
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:36081 original size:27 final size:27
Alignment explanation
Indices: 36043--36108 Score: 116
Period size: 27 Copynumber: 2.4 Consensus size: 27
36033 TATTATTTTT
36043 TAATAATAATAATATAT-ATAATAATTA
1 TAATAATAATAAT-TATGATAATAATTA
36070 TAATAATAATAATTATGATAATAATTA
1 TAATAATAATAATTATGATAATAATTA
36097 TAATAATAATAA
1 TAATAATAATAA
36109 AATGGGTAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
26 3 0.08
27 35 0.92
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (27 bp):
TAATAATAATAATTATGATAATAATTA
Found at i:36571 original size:113 final size:114
Alignment explanation
Indices: 36348--36598 Score: 414
Period size: 113 Copynumber: 2.2 Consensus size: 114
36338 TTAAATAAGC
* * ****
36348 TCTTCTCATTATGAACTTCTTCTTTCTCCTTCAGATGAGTTCTTCTCATTATGAACTTTTTTCTG
1 TCTTCTCATTATGAACTTCTTCTTCCTCCTTCAGATAAGTTCTTCTCATTATGAACTTCGAACTG
36413 GAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
66 GAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
* *
36462 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGTTAAGTTCTTCTCATTATGAA-TTCGAACTG
1 TCTTCTCATTATGAACTTCTTCTTCCTCCTTCAGATAAGTTCTTCTCATTATGAACTTCGAACTG
*
36526 GAAAAGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
66 GAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
36575 TCTTCTCATTATGAACTTCTTCTT
1 TCTTCTCATTATGAACTTCTTCTT
36599 TGATGCAGGG
Statistics
Matches: 128, Mismatches: 9, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
113 77 0.60
114 51 0.40
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (114 bp):
TCTTCTCATTATGAACTTCTTCTTCCTCCTTCAGATAAGTTCTTCTCATTATGAACTTCGAACTG
GAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
Found at i:37079 original size:36 final size:35
Alignment explanation
Indices: 37032--37108 Score: 136
Period size: 36 Copynumber: 2.2 Consensus size: 35
37022 TGATTTTCGG
*
37032 GATTTTGCTATTTTTGGCAAAATTCGAATAAATAC
1 GATTTTGCTATTTTTGGCAAAATTCGAATAAAGAC
37067 GATTTTAGCTATTTTTGGCAAAATTCGAATAAAGAC
1 GATTTT-GCTATTTTTGGCAAAATTCGAATAAAGAC
37103 GATTTT
1 GATTTT
37109 TTTGCTATAA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
35 6 0.15
36 34 0.85
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (35 bp):
GATTTTGCTATTTTTGGCAAAATTCGAATAAAGAC
Found at i:40293 original size:3 final size:3
Alignment explanation
Indices: 40287--40354 Score: 82
Period size: 3 Copynumber: 22.0 Consensus size: 3
40277 TATTATTTTT
* * *
40287 TAA TAA TAA TAA TATA TATA TAA TAA TTA TAA TAA TAA TAA TTA TGA
1 TAA TAA TAA TAA TA-A TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
40334 TAA TAA TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
40355 AATGGGTAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
3 50 0.88
4 7 0.12
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:40818 original size:113 final size:114
Alignment explanation
Indices: 40595--40845 Score: 414
Period size: 113 Copynumber: 2.2 Consensus size: 114
40585 TTAAATAAGC
* * ****
40595 TCTTCTCATTATGAACTTCTTCTTTCTCCTTCAGATGAGTTCTTCTCATTATGAACTTTTTTCTG
1 TCTTCTCATTATGAACTTCTTCTTCCTCCTTCAGATAAGTTCTTCTCATTATGAACTTCGAACTG
40660 GAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
66 GAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
* *
40709 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGTTAAGTTCTTCTCATTATGAA-TTCGAACTG
1 TCTTCTCATTATGAACTTCTTCTTCCTCCTTCAGATAAGTTCTTCTCATTATGAACTTCGAACTG
*
40773 GAAAAGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
66 GAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
40822 TCTTCTCATTATGAACTTCTTCTT
1 TCTTCTCATTATGAACTTCTTCTT
40846 TGATGCAGGG
Statistics
Matches: 128, Mismatches: 9, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
113 77 0.60
114 51 0.40
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (114 bp):
TCTTCTCATTATGAACTTCTTCTTCCTCCTTCAGATAAGTTCTTCTCATTATGAACTTCGAACTG
GAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
Found at i:41322 original size:35 final size:35
Alignment explanation
Indices: 41276--41351 Score: 127
Period size: 35 Copynumber: 2.2 Consensus size: 35
41266 TGATTTTCGG
*
41276 GATTTTGCTATTTTTGGCAAAATTCGAA-AAATAC
1 GATTTTGCTATTTTTGGCAAAATTCGAATAAAGAC
41310 GATTTTAGCTATTTTTGGCAAAATTCGAATAAAGAC
1 GATTTT-GCTATTTTTGGCAAAATTCGAATAAAGAC
41346 GATTTT
1 GATTTT
41352 TTTGCTATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
34 6 0.15
35 22 0.56
36 11 0.28
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (35 bp):
GATTTTGCTATTTTTGGCAAAATTCGAATAAAGAC
Found at i:44593 original size:3 final size:3
Alignment explanation
Indices: 44578--44626 Score: 62
Period size: 3 Copynumber: 16.3 Consensus size: 3
44568 TAAAATATAT
* * * *
44578 ATA ATA ATT ATA ATA ATA ATA ATT ATG ATA ATA ATT ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
44626 A
1 A
44627 AATGGGTAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (3 bp):
ATA
Found at i:44595 original size:12 final size:12
Alignment explanation
Indices: 44577--44624 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
44567 ATAAAATATA
*
44577 TATAATAATTAT
1 TATAATAATAAT
*
44589 AATAATAATAAT
1 TATAATAATAAT
*
44601 TATGATAATAAT
1 TATAATAATAAT
44613 TATAATAATAAT
1 TATAATAATAAT
44625 AAAATGGGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (12 bp):
TATAATAATAAT
Found at i:45090 original size:113 final size:114
Alignment explanation
Indices: 44867--45117 Score: 414
Period size: 113 Copynumber: 2.2 Consensus size: 114
44857 TTAAATAAGC
* * ****
44867 TCTTCTCATTATGAACTTCTTCTTTCTCCTTCAGATGAGTTCTTCTCATTATGAACTTTTTTCTG
1 TCTTCTCATTATGAACTTCTTCTTCCTCCTTCAGATAAGTTCTTCTCATTATGAACTTCGAACTG
44932 GAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
66 GAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
* *
44981 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGTTAAGTTCTTCTCATTATGAA-TTCGAACTG
1 TCTTCTCATTATGAACTTCTTCTTCCTCCTTCAGATAAGTTCTTCTCATTATGAACTTCGAACTG
*
45045 GAAAAGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
66 GAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
45094 TCTTCTCATTATGAACTTCTTCTT
1 TCTTCTCATTATGAACTTCTTCTT
45118 TGATGCAGGG
Statistics
Matches: 128, Mismatches: 9, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
113 77 0.60
114 51 0.40
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (114 bp):
TCTTCTCATTATGAACTTCTTCTTCCTCCTTCAGATAAGTTCTTCTCATTATGAACTTCGAACTG
GAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
Found at i:45589 original size:35 final size:35
Alignment explanation
Indices: 45550--45625 Score: 143
Period size: 35 Copynumber: 2.2 Consensus size: 35
45540 TGATTTTCGG
*
45550 GATTTTGCTATTTTTGGCAAAATTCGAATAAATAC
1 GATTTTGCTATTTTTGGCAAAATTCGAATAAAGAC
45585 GATTTTGCTATTTTTGGCAAAATTCGAATAAAGAC
1 GATTTTGCTATTTTTGGCAAAATTCGAATAAAGAC
45620 GATTTT
1 GATTTT
45626 TTTGCTATAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.41
Consensus pattern (35 bp):
GATTTTGCTATTTTTGGCAAAATTCGAATAAAGAC
Found at i:46067 original size:15 final size:15
Alignment explanation
Indices: 46047--46076 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
46037 TATCACAATC
46047 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
46062 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
46077 AGCACCGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.47, T:0.13
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Found at i:48865 original size:3 final size:3
Alignment explanation
Indices: 48859--48917 Score: 68
Period size: 3 Copynumber: 20.0 Consensus size: 3
48849 ATTATTTTTT
* *
48859 TAA TAA TAA TAA T-A TATA TAA TAA TTA TAA TAA TAA T-A TGA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
48903 TAA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA
48918 AAATGGGTAA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
2 4 0.08
3 41 0.85
4 3 0.06
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:48881 original size:12 final size:12
Alignment explanation
Indices: 48861--48917 Score: 82
Period size: 12 Copynumber: 4.8 Consensus size: 12
48851 TATTTTTTTA
48861 ATAATAATAA-T
1 ATAATAATAATT
48872 ATATATAATAATT
1 ATA-ATAATAATT
48885 ATAATAATAA-T
1 ATAATAATAATT
*
48896 ATGATAATAATT
1 ATAATAATAATT
48908 ATAATAATAA
1 ATAATAATAA
48918 AAATGGGTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
11 13 0.32
12 24 0.59
13 4 0.10
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (12 bp):
ATAATAATAATT
Found at i:49380 original size:113 final size:114
Alignment explanation
Indices: 49157--49407 Score: 414
Period size: 113 Copynumber: 2.2 Consensus size: 114
49147 TTAAATAAGC
* * ****
49157 TCTTCTCATTATGAACTTCTTCTTTCTCCTTCAGATGAGTTCTTCTCATTATGAACTTTTTTCTG
1 TCTTCTCATTATGAACTTCTTCTTCCTCCTTCAGATAAGTTCTTCTCATTATGAACTTCGAACTG
49222 GAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
66 GAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
* *
49271 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGTTAAGTTCTTCTCATTATGAA-TTCGAACTG
1 TCTTCTCATTATGAACTTCTTCTTCCTCCTTCAGATAAGTTCTTCTCATTATGAACTTCGAACTG
*
49335 GAAAAGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
66 GAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
49384 TCTTCTCATTATGAACTTCTTCTT
1 TCTTCTCATTATGAACTTCTTCTT
49408 TGATGCAGGG
Statistics
Matches: 128, Mismatches: 9, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
113 77 0.60
114 51 0.40
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (114 bp):
TCTTCTCATTATGAACTTCTTCTTCCTCCTTCAGATAAGTTCTTCTCATTATGAACTTCGAACTG
GAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
Found at i:49888 original size:36 final size:35
Alignment explanation
Indices: 49841--49917 Score: 136
Period size: 36 Copynumber: 2.2 Consensus size: 35
49831 TGATTTTCGG
*
49841 GATTTTGCTATTTTTGGCAAAATTCGAATAAATAC
1 GATTTTGCTATTTTTGGCAAAATTCGAATAAAGAC
49876 GATTTTAGCTATTTTTGGCAAAATTCGAATAAAGAC
1 GATTTT-GCTATTTTTGGCAAAATTCGAATAAAGAC
49912 GATTTT
1 GATTTT
49918 TTTGCTATAA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
35 6 0.15
36 34 0.85
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (35 bp):
GATTTTGCTATTTTTGGCAAAATTCGAATAAAGAC
Found at i:50358 original size:15 final size:15
Alignment explanation
Indices: 50338--50367 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
50328 TATCACAATC
50338 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
50353 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
50368 AGCACCGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.47, T:0.13
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Found at i:53139 original size:3 final size:3
Alignment explanation
Indices: 53133--53191 Score: 66
Period size: 3 Copynumber: 19.0 Consensus size: 3
53123 TATTATTTTT
* *
53133 TAA TAA TAA TAA TATA TATA TAA TAA T-A TAA TAA TTA TGA TAA TAA
1 TAA TAA TAA TAA TA-A TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
53179 TATA TAA TAA TAA
1 TA-A TAA TAA TAA
53192 AATGGGTAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.04
3 38 0.76
4 10 0.20
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:53158 original size:20 final size:21
Alignment explanation
Indices: 53133--53189 Score: 75
Period size: 20 Copynumber: 2.8 Consensus size: 21
53123 TATTATTTTT
53133 TAATAATAATAAT-ATATAT-A
1 TAATAATAATAATAAT-TATGA
53153 TAATAAT-ATAATAATTATGA
1 TAATAATAATAATAATTATGA
53173 TAATAATATATAATAAT
1 TAATAATA-ATAATAAT
53190 AAAATGGGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
19 8 0.24
20 17 0.52
22 8 0.24
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
TAATAATAATAATAATTATGA
Found at i:53164 original size:25 final size:24
Alignment explanation
Indices: 53135--53191 Score: 75
Period size: 23 Copynumber: 2.4 Consensus size: 24
53125 TTATTTTTTA
53135 ATAATAATAATAT-ATATATAATA-
1 ATAATAATAATATGATA-ATAATAT
53158 AT-ATAATAATTATGATAATAATAT
1 ATAATAATAA-TATGATAATAATAT
53182 ATAATAATAA
1 ATAATAATAA
53192 AATGGGTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
22 7 0.23
23 11 0.37
24 5 0.17
25 7 0.23
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (24 bp):
ATAATAATAATATGATAATAATAT
Found at i:53166 original size:22 final size:24
Alignment explanation
Indices: 53133--53190 Score: 79
Period size: 22 Copynumber: 2.5 Consensus size: 24
53123 TATTATTTTT
53133 TAATAATAATAATATAT-AT-ATAA
1 TAAT-ATAATAATATATGATAATAA
53156 TAATATAATAAT-TATGATAATAA
1 TAATATAATAATATATGATAATAA
53179 T-ATATAATAATA
1 TAATATAATAATA
53191 AAATGGGTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
21 3 0.09
22 20 0.62
23 9 0.28
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (24 bp):
TAATATAATAATATATGATAATAA
Found at i:53653 original size:113 final size:114
Alignment explanation
Indices: 53430--53677 Score: 387
Period size: 113 Copynumber: 2.2 Consensus size: 114
53420 TTAAATAAGC
* * ****
53430 TCTTCTCATTATGAACTTCTTCTTTCTCCTTCAGATGAGTTCTTCTCATTATGAACTTTTTTCTG
1 TCTTCTCATTATGAACTTCTTCTTCCTCCTTCAGATAAGTTCTTCTCATTATGAACTTCGAACTG
53495 GAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
66 GAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
* *
53544 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGTTAAGTTCTTCTCATTATGAA-TTCGAACTG
1 TCTTCTCATTATGAACTTCTTCTTCCTCCTTCAGATAAGTTCTTCTCATTATGAACTTCGAACTG
*
53608 GAAAAGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
66 GAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
53657 TC-T-TCATTATGAAC-TCTTCTT
1 TCTTCTCATTATGAACTTCTTCTT
53678 TGATGCAGGG
Statistics
Matches: 125, Mismatches: 9, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
110 7 0.06
111 11 0.09
112 1 0.01
113 55 0.44
114 51 0.41
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (114 bp):
TCTTCTCATTATGAACTTCTTCTTCCTCCTTCAGATAAGTTCTTCTCATTATGAACTTCGAACTG
GAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
Found at i:54152 original size:36 final size:36
Alignment explanation
Indices: 54111--54186 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
54101 ATTTTCGGGA
*
54111 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
54147 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
54183 TTTT
1 TTTT
54187 TTGCTATAAC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:54628 original size:15 final size:15
Alignment explanation
Indices: 54608--54637 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
54598 TATCACAATC
54608 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
54623 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
54638 AGCACCGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.47, T:0.13
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Done.