Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008807.1 Hibiscus syriacus cultivar Beakdansim tig00111960_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: 68633
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Found at i:5444 original size:31 final size:31
Alignment explanation
Indices: 5404--5500 Score: 153
Period size: 31 Copynumber: 3.1 Consensus size: 31
5394 TTCAATATCA
*
5404 TCCCCCAACATTTAGTT-TG-TTGTCAATATGG
1 TCCCTCAACATTTA-TTCTGTTTGT-AATATGG
5435 TCCCTCAACATTTATTCTGTTTGTAATATGG
1 TCCCTCAACATTTATTCTGTTTGTAATATGG
5466 TCCCTCAACATTTATTCTGTTTGTAATATGG
1 TCCCTCAACATTTATTCTGTTTGTAATATGG
5497 TCCC
1 TCCC
5501 AACGTAACTT
Statistics
Matches: 63, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
30 2 0.03
31 57 0.90
32 4 0.06
ACGTcount: A:0.22, C:0.23, G:0.13, T:0.42
Consensus pattern (31 bp):
TCCCTCAACATTTATTCTGTTTGTAATATGG
Found at i:8488 original size:31 final size:31
Alignment explanation
Indices: 8441--8514 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
8431 TAAAACATAC
* * *
8441 AATATAATCCCCCAACATTTAGTCTT-TTTGT
1 AATATGATCCCTCAACATTTAGT-TTGTCTGT
*
8472 AATATGGTCCCTCAACATTTAGTTTGTCTGT
1 AATATGATCCCTCAACATTTAGTTTGTCTGT
8503 AATATGATCCCT
1 AATATGATCCCT
8515 GATGTAACTG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 2 0.05
31 35 0.95
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.41
Consensus pattern (31 bp):
AATATGATCCCTCAACATTTAGTTTGTCTGT
Found at i:11729 original size:23 final size:23
Alignment explanation
Indices: 11702--11761 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
11692 CATTGAACCA
* **
11702 TTAATGCATACTATTCTCATTTT
1 TTAATGCATAATATTCTCATCGT
**
11725 TTAATTTATAATATTCTCATCGT
1 TTAATGCATAATATTCTCATCGT
*
11748 TTAATGAATAATAT
1 TTAATGCATAATAT
11762 ATTTATCTAT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.05, T:0.50
Consensus pattern (23 bp):
TTAATGCATAATATTCTCATCGT
Found at i:16324 original size:45 final size:45
Alignment explanation
Indices: 16252--16471 Score: 363
Period size: 45 Copynumber: 4.9 Consensus size: 45
16242 TATAAAATTT
* *
16252 CTTATCATTTA-TCCTATAAGCTCGTAAGCTTATTCTACCAATATA
1 CTTACCATTTATTCC-ATAAGCTCGTAAGCTTATTTTACCAATATA
*
16297 CTTACCATTTATTCCATAAGCTTGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
16342 CTTATCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
16387 CTTACCATTTATTCCATAAGCTCGTAAGCTTATCTTA-CATATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCA-ATATA
16432 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCA
16472 TTATTATATA
Statistics
Matches: 164, Mismatches: 8, Indels: 5
0.93 0.05 0.03
Matches are distributed among these distances:
44 2 0.01
45 157 0.96
46 5 0.03
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.41
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:21083 original size:8 final size:8
Alignment explanation
Indices: 21070--21116 Score: 60
Period size: 8 Copynumber: 6.0 Consensus size: 8
21060 AGGCGATAAC
21070 AGAAAAAA
1 AGAAAAAA
21078 AGAAAAAA
1 AGAAAAAA
21086 AG-AAAAA
1 AGAAAAAA
* *
21093 ATAAAGAA
1 AGAAAAAA
21101 AGAAAAAA
1 AGAAAAAA
*
21109 CGAAAAAA
1 AGAAAAAA
21117 TAAAGAGAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
7 6 0.18
8 27 0.82
ACGTcount: A:0.83, C:0.02, G:0.13, T:0.02
Consensus pattern (8 bp):
AGAAAAAA
Found at i:21093 original size:15 final size:15
Alignment explanation
Indices: 21073--21116 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
21063 CGATAACAGA
21073 AAAAAAGAAAAAAAG
1 AAAAAAGAAAAAAAG
* *
21088 AAAAAATAAAGAAAG
1 AAAAAAGAAAAAAAG
21103 AAAAAACGAAAAAA
1 AAAAAA-GAAAAAA
21117 TAAAGAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 19 0.79
16 5 0.21
ACGTcount: A:0.84, C:0.02, G:0.11, T:0.02
Consensus pattern (15 bp):
AAAAAAGAAAAAAAG
Found at i:21106 original size:13 final size:13
Alignment explanation
Indices: 21076--21154 Score: 68
Period size: 11 Copynumber: 6.7 Consensus size: 13
21066 TAACAGAAAA
21076 AAAGAAAA-AAAG
1 AAAGAAAATAAAG
21088 -AA-AAAATAAAG
1 AAAGAAAATAAAG
*
21099 AAAGAAAA-AACG
1 AAAGAAAATAAAG
21111 -AA-AAAATAAAG
1 AAAGAAAATAAAG
*
21122 AGA-AAAAT-AAG
1 AAAGAAAATAAAG
21133 AAAGAAAA-ATAAG
1 AAAGAAAATA-AAG
21146 AAAGAAAAT
1 AAAGAAAAT
21155 GGATCAACTA
Statistics
Matches: 54, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
10 8 0.15
11 16 0.30
12 15 0.28
13 15 0.28
ACGTcount: A:0.78, C:0.01, G:0.14, T:0.06
Consensus pattern (13 bp):
AAAGAAAATAAAG
Found at i:21106 original size:23 final size:23
Alignment explanation
Indices: 21076--21153 Score: 97
Period size: 23 Copynumber: 3.3 Consensus size: 23
21066 TAACAGAAAA
21076 AAAGAAAAAAAGAAAAAATAAAG
1 AAAGAAAAAAAGAAAAAATAAAG
*
21099 AAAGAAAAAACGAAAAAATAAAG
1 AAAGAAAAAAAGAAAAAATAAAG
*
21122 --AGAAAAATAAGAAAGAAAAATAAG
1 AAAGAAAAA-AAGAAA-AAATA-AAG
21146 AAAGAAAA
1 AAAGAAAA
21154 TGGATCAACT
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
21 7 0.15
22 5 0.11
23 26 0.55
24 3 0.06
26 6 0.13
ACGTcount: A:0.79, C:0.01, G:0.14, T:0.05
Consensus pattern (23 bp):
AAAGAAAAAAAGAAAAAATAAAG
Found at i:24314 original size:94 final size:97
Alignment explanation
Indices: 24211--24390 Score: 251
Period size: 94 Copynumber: 1.8 Consensus size: 97
24201 TTTGAGATTG
*
24211 TTTCTCTCAAAACAAATTTCGTCTCGCTTGAGACAATTTT-C-C-ACAAATTTTGAAATTTGTTT
1 TTTCTCTCAAAACAAATTTCGTCTCGCTTGAGACAATTTTCCTCAAAAAATTTTGAAA-TTGTTT
24273 CACTTGAAACAAAATTGTCACCTTTGAAATAGT
65 CACTTGAAACAAAATTGTCACCTTTGAAATAGT
* *
24306 TTTC-CTCAAAACAAATTTTGTCTCGCTTGAGATAATTTTCCCTCAAAAAAAAAATTTTGAAATT
1 TTTCTCTCAAAACAAATTTCGTCTCGCTTGAGACAATTTT-CCTC----AAAAAATTTTGAAATT
24370 GTTTCACTTGAAACAAAATTG
61 GTTTCACTTGAAACAAAATTG
24391 ATCTCACTTG
Statistics
Matches: 74, Mismatches: 3, Indels: 10
0.85 0.03 0.11
Matches are distributed among these distances:
94 33 0.45
95 4 0.05
96 1 0.01
97 1 0.01
101 23 0.31
102 12 0.16
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (97 bp):
TTTCTCTCAAAACAAATTTCGTCTCGCTTGAGACAATTTTCCTCAAAAAATTTTGAAATTGTTTC
ACTTGAAACAAAATTGTCACCTTTGAAATAGT
Found at i:24327 original size:36 final size:36
Alignment explanation
Indices: 24279--24358 Score: 83
Period size: 36 Copynumber: 2.2 Consensus size: 36
24269 GTTTCACTTG
*
24279 AAACAAAATTGTCAC-CTTTGAAATAGTTTT-CCTCA
1 AAACAAAATTGTCACGC-TTGAAATAATTTTCCCTCA
* * *
24314 AAACAAATTTTGTCTCGCTTGAGATAATTTTCCCTCA
1 AAACAAA-ATTGTCACGCTTGAAATAATTTTCCCTCA
*
24351 AAAAAAAA
1 AAACAAAA
24359 ATTTTGAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
35 7 0.19
36 17 0.47
37 12 0.33
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.33
Consensus pattern (36 bp):
AAACAAAATTGTCACGCTTGAAATAATTTTCCCTCA
Found at i:25438 original size:19 final size:18
Alignment explanation
Indices: 25398--25442 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
25388 TTAACACTAA
*
25398 CATTTTATTTTTTTATTG
1 CATTTTATTTTCTTATTG
*
25416 CATTTTATTTTCCTTATTT
1 CATTTTATTTT-CTTATTG
25435 CATTTTAT
1 CATTTTAT
25443 GCACTTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.18, C:0.11, G:0.02, T:0.69
Consensus pattern (18 bp):
CATTTTATTTTCTTATTG
Found at i:25715 original size:16 final size:16
Alignment explanation
Indices: 25696--25741 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
25686 TTATTTATTT
25696 ATGTATATATTATATC
1 ATGTATATATTATATC
*
25712 ATGT-TATA-GATATAC
1 ATGTATATATTATAT-C
25727 ATGTATATATT-TATC
1 ATGTATATATTATATC
25742 TAATATTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
14 4 0.16
15 10 0.40
16 11 0.44
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (16 bp):
ATGTATATATTATATC
Found at i:27165 original size:20 final size:20
Alignment explanation
Indices: 27140--27186 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
27130 CTTACAGTAT
27140 CGATACTGCATGAACAATAC
1 CGATACTGCATGAACAATAC
27160 CGATACTGCATGAACAATAC
1 CGATACTGCATGAACAATAC
*
27180 TGATACT
1 CGATACT
27187 ATTCACGTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (20 bp):
CGATACTGCATGAACAATAC
Found at i:27317 original size:18 final size:18
Alignment explanation
Indices: 27294--27340 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
27284 ATGCAAAATA
27294 GGTACTGATACCCAAAGG
1 GGTACTGATACCCAAAGG
27312 GGTACTGATACCCAAAGG
1 GGTACTGATACCCAAAGG
*
27330 GGTACCGATAC
1 GGTACTGATAC
27341 TACTTTACAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.32, C:0.23, G:0.28, T:0.17
Consensus pattern (18 bp):
GGTACTGATACCCAAAGG
Found at i:28557 original size:553 final size:551
Alignment explanation
Indices: 27507--28594 Score: 1779
Period size: 553 Copynumber: 2.0 Consensus size: 551
27497 CAGAAAATTA
* * * * *
27507 ATCCCCAGCGGCTAGAAGCGATCACAAACTCTTTCCAACATATAAAAACAAGTTGAGGGCACTTG
1 ATCCCCAACGGCTAGAAACGACCACAAACTCATTCCAACATATAAAAACAAGTTGAGGACACTTG
* *
27572 AAGAATGATTTGAACACCTATCAAAGCAATCAAACACAAGAGAAGAGCTTTTCATTTATTTCCCT
66 AAGAAGGATTAGAACACCTATCAAAGCAATCAAACACAAGAGAAGAGCTTTTCATTTATTTCCCT
27637 TTCTCTTGTAAATATTTGTGTTTTGAGCTTAATTGTATATCAATATGTTTTGCTTTTGTGAGCTA
131 TTCTCTTGTAAATATTTGTGTTTTGAGCTTAATTGTATATCAATATGTTTTGCTTTTGTGAGCTA
* * *
27702 AATTTTTGTAAACACCGTCCTTTAAGAGGTTTTCTTTTTTACATCTTTCAACATTTGTAAAATAG
196 AATTTTTGTAAACACCGTCCTTTAAGAGGTTTCCTTGTTTACATCTTTCAACATTTGTAAAAGAG
*
27767 GATTGGTTCTAGCTTAGCCTGTGAAAAGCTAAGGAGTTGTAAAGGTTATCTCTTGATCTTGTAAA
261 GATTGGTTCTAGCTTAGCCTGTGAAAAGCTAAGGAGTTGTAAAGGTTATCTATTGATCTTGTAAA
* *
27832 AAGAAAGAACAAATTAGTAAATTTGTTAGAAAATCTTAGTGGGGAGCTAAGGTAGTGGATGTAGA
326 AAGAAAGAAAAAATTAGTAAATTTGTTAGAAAATCTTAGTGAGGAGCTAAGGTAGTGGATGTAGA
27897 CTTTGTTGAGAAGTCGAACCACTATAAAACCTTGTGCAAACTATCTATCTTTTTATACTCCTCAC
391 CTTTGTTGAGAAGTCGAACCACTATAAAACCTTGTGCAAACTATCTATCTTTTTATACTCCTCAC
* *
27962 TCCCTAAACTCAAAAAGCCAATTCACCCCCTCTTGGCAAATTATTC-AGTTTTTCAATT-GAGCT
456 TCCCTAAACTCAAAAAGCCAATTCACCCCCTCTTGACAAATTATTCGA-TTGTTCAATTAG-GCT
28025 TCATCGATAATCCCAACCCAATGGCTCCAAAAC
519 TCATCGATAATCCCAACCCAATGGCTCCAAAAC
*
28058 ATCCCCAACGGCTAGAAACGACCACAAACTCATTCCAACATATAAAAACAAGTTGATGACACTTG
1 ATCCCCAACGGCTAGAAACGACCACAAACTCATTCCAACATATAAAAACAAGTTGAGGACACTTG
* * * * *
28123 AATAAGGATTAGAGCACCTATCAAAGCAATCAAACACATGATAAGAGCTTTTCATTCTAATTTTC
66 AAGAAGGATTAGAACACCTATCAAAGCAATCAAACACAAGAGAAGAGCTTTTCATT-T-ATTTCC
* **
28188 CTTTGTCTTGTAAATATTTGTGTTTTGAGCTTAATTGTATATCCTTATGTTTTGCTTTTGTGAGC
129 CTTTCTCTTGTAAATATTTGTGTTTTGAGCTTAATTGTATATCAATATGTTTTGCTTTTGTGAGC
* * *
28253 TAAATTTTTGTAAACACCTTCCTTTAAGAGGTTTCCTTGTTTACATCTTTCAACCTTTGTAACAG
194 TAAATTTTTGTAAACACCGTCCTTTAAGAGGTTTCCTTGTTTACATCTTTCAACATTTGTAAAAG
* *
28318 GGGATTGGTTCTAGCTTAGCCTGTGAAAAGCTAGGGAGTTGTAAAGGTTATCTATTGATCTTGTA
259 AGGATTGGTTCTAGCTTAGCCTGTGAAAAGCTAAGGAGTTGTAAAGGTTATCTATTGATCTTGTA
*
28383 AAAA-AAAGAAAAAATTAGTGAATTTGTTAGAAAATCCTTAGTGAGGAGCTAAGGTAGTGGATGT
324 AAAAGAAAGAAAAAATTAGTAAATTTGTTAGAAAAT-CTTAGTGAGGAGCTAAGGTAGTGGATGT
* *
28447 AGAC-TTGATTGAGAAGTCGAACCACTATAAATCCTTGTGCAAATTATCTATCTTTTTATACTCC
388 AGACTTTG-TTGAGAAGTCGAACCACTATAAAACCTTGTGCAAACTATCTATCTTTTTATACTCC
* * *
28511 TTACTCCCTAAACTTAAAAAGTCAATTCACCCCCTCTTGACAAATTATTCGATTGTTCAATTAGG
452 TCACTCCCTAAACTCAAAAAGCCAATTCACCCCCTCTTGACAAATTATTCGATTGTTCAATTAGG
28576 CTTCATCGATAATCCCAAC
517 CTTCATCGATAATCCCAAC
28595 ATAATGTTAT
Statistics
Matches: 496, Mismatches: 35, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
551 109 0.22
552 33 0.07
553 352 0.71
554 2 0.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (551 bp):
ATCCCCAACGGCTAGAAACGACCACAAACTCATTCCAACATATAAAAACAAGTTGAGGACACTTG
AAGAAGGATTAGAACACCTATCAAAGCAATCAAACACAAGAGAAGAGCTTTTCATTTATTTCCCT
TTCTCTTGTAAATATTTGTGTTTTGAGCTTAATTGTATATCAATATGTTTTGCTTTTGTGAGCTA
AATTTTTGTAAACACCGTCCTTTAAGAGGTTTCCTTGTTTACATCTTTCAACATTTGTAAAAGAG
GATTGGTTCTAGCTTAGCCTGTGAAAAGCTAAGGAGTTGTAAAGGTTATCTATTGATCTTGTAAA
AAGAAAGAAAAAATTAGTAAATTTGTTAGAAAATCTTAGTGAGGAGCTAAGGTAGTGGATGTAGA
CTTTGTTGAGAAGTCGAACCACTATAAAACCTTGTGCAAACTATCTATCTTTTTATACTCCTCAC
TCCCTAAACTCAAAAAGCCAATTCACCCCCTCTTGACAAATTATTCGATTGTTCAATTAGGCTTC
ATCGATAATCCCAACCCAATGGCTCCAAAAC
Found at i:32312 original size:18 final size:18
Alignment explanation
Indices: 32269--32306 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
32259 GTGAAGTATG
*
32269 AATGGCGTTGTCGTGGCA
1 AATGGTGTTGTCGTGGCA
*
32287 AATGGTGTTGTTGTGGCA
1 AATGGTGTTGTCGTGGCA
32305 AA
1 AA
32307 GTGTGTAACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.11, G:0.37, T:0.32
Consensus pattern (18 bp):
AATGGTGTTGTCGTGGCA
Found at i:41327 original size:20 final size:22
Alignment explanation
Indices: 41304--41352 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
41294 AATTTAGTAC
41304 TTAAATTATAAGT-TTT-ATTT
1 TTAAATTATAAGTATTTAATTT
*
41324 TT-AATT-TAATTATTTAATTT
1 TTAAATTATAAGTATTTAATTT
41344 TTAAATTAT
1 TTAAATTAT
41353 TTAAAATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 4 0.17
19 7 0.29
20 8 0.33
21 4 0.17
22 1 0.04
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
TTAAATTATAAGTATTTAATTT
Found at i:41362 original size:16 final size:16
Alignment explanation
Indices: 41326--41363 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
41316 TTTTATTTTT
41326 AATTT-AATTATTTAA
1 AATTTAAATTATTTAA
**
41341 TTTTTAAATTATTTAA
1 AATTTAAATTATTTAA
41357 AATTTAA
1 AATTTAA
41364 TCACTTTAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 1
0.78 0.17 0.04
Matches are distributed among these distances:
15 3 0.17
16 15 0.83
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
AATTTAAATTATTTAA
Found at i:47948 original size:24 final size:23
Alignment explanation
Indices: 47903--47950 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
47893 TCCTAATTAA
*
47903 ATAAATAATATAAAAATTTAAAT
1 ATAAATAATATAAAAATATAAAT
47926 ATAAATTAATACTAAAAA-ATAAAT
1 ATAAA-TAATA-TAAAAATATAAAT
47950 A
1 A
47951 AATAATTCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 5 0.23
24 11 0.50
25 6 0.27
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (23 bp):
ATAAATAATATAAAAATATAAAT
Found at i:49003 original size:26 final size:29
Alignment explanation
Indices: 48974--49028 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
48964 ATATTTTATT
*
48974 AATTTAAT-TT-TAATCTTAAT-ATAATA
1 AATTTAATCTTATAATCTAAATAATAATA
49000 AATTTAATCTTATAATCTAAATAATAATA
1 AATTTAATCTTATAATCTAAATAATAATA
49029 TACCATTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 8 0.32
27 2 0.08
28 9 0.36
29 6 0.24
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.45
Consensus pattern (29 bp):
AATTTAATCTTATAATCTAAATAATAATA
Found at i:49271 original size:14 final size:13
Alignment explanation
Indices: 49254--49292 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
49244 ACTTATAGTG
49254 TTTAAAAAGATATT
1 TTTAAAAA-ATATT
*
49268 TTTAAATAATATT
1 TTTAAAAAATATT
49281 TTT-AAAAATATT
1 TTTAAAAAATATT
49293 AAAAATATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 8 0.35
13 8 0.35
14 7 0.30
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (13 bp):
TTTAAAAAATATT
Found at i:49290 original size:12 final size:12
Alignment explanation
Indices: 49258--49292 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
49248 ATAGTGTTTA
49258 AAAAGATATTTTT
1 AAAA-ATATTTTT
49271 AAATAATATTTTT
1 AAA-AATATTTTT
49284 AAAAATATT
1 AAAAATATT
49293 AAAAATATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 6 0.29
13 14 0.67
14 1 0.05
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (12 bp):
AAAAATATTTTT
Found at i:49574 original size:17 final size:18
Alignment explanation
Indices: 49546--49581 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
49536 CACCCACGGG
49546 TCCCTATCCTTTTAAATT
1 TCCCTATCCTTTTAAATT
*
49564 TCCCT-TCCTTTTTAATT
1 TCCCTATCCTTTTAAATT
49581 T
1 T
49582 TATTTGGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.17, C:0.28, G:0.00, T:0.56
Consensus pattern (18 bp):
TCCCTATCCTTTTAAATT
Found at i:49863 original size:32 final size:32
Alignment explanation
Indices: 49780--49869 Score: 103
Period size: 32 Copynumber: 2.8 Consensus size: 32
49770 CTTATGTGGT
* * * *
49780 ACATTTCATGTCATCATTTTTGATTACATGAC
1 ACATGTCATGTCATCATTTTTGGTGACATAAC
49812 ACATGCTACA--TCATCATTTTTGGTGACATAAC
1 ACATG-T-CATGTCATCATTTTTGGTGACATAAC
*
49844 ACATGTCATGTCATTATTTTTGGTGA
1 ACATGTCATGTCATCATTTTTGGTGA
49870 TGTGGCATAT
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
30 2 0.04
31 1 0.02
32 43 0.88
33 1 0.02
34 2 0.04
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (32 bp):
ACATGTCATGTCATCATTTTTGGTGACATAAC
Found at i:49920 original size:32 final size:32
Alignment explanation
Indices: 49790--49923 Score: 117
Period size: 32 Copynumber: 4.2 Consensus size: 32
49780 ACATTTCATG
* *
49790 TCATCATTTTTGATTACATGACACATG-CTACA
1 TCATCATTTTTGGTGACATGACACATGTC-ACA
* **
49822 TCATCATTTTTGGTGACATAACACATGTCATG
1 TCATCATTTTTGGTGACATGACACATGTCACA
* ** * * **
49854 TCATTATTTTTGGTGATGTGGCATATGTTGCA
1 TCATCATTTTTGGTGACATGACACATGTCACA
* * *
49886 TCATCATTTTTGGTGACGTGACATATGACACA
1 TCATCATTTTTGGTGACATGACACATGTCACA
49918 TCATCA
1 TCATCA
49924 ATTGAACAAA
Statistics
Matches: 80, Mismatches: 21, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
32 79 0.99
33 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (32 bp):
TCATCATTTTTGGTGACATGACACATGTCACA
Found at i:50430 original size:32 final size:32
Alignment explanation
Indices: 50392--50462 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
50382 GTTGTCGTCT
* *
50392 ATCATTTTTGGTGATGTGACATATATTACATC
1 ATCATTTTTGGTGACGTGACATATATCACATC
* *
50424 ATCATTTTTGGTGACGTGACATATGTCACGTC
1 ATCATTTTTGGTGACGTGACATATATCACATC
50456 ATCATTT
1 ATCATTT
50463 GAACATATGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.42
Consensus pattern (32 bp):
ATCATTTTTGGTGACGTGACATATATCACATC
Found at i:52855 original size:15 final size:13
Alignment explanation
Indices: 52833--52863 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
52823 TTTGAAAAAT
*
52833 AATTTTTGTGAAC
1 AATTTTTTTGAAC
52846 AATTTTTTTGAAC
1 AATTTTTTTGAAC
52859 AATTT
1 AATTT
52864 ACTCCCCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.06, G:0.10, T:0.52
Consensus pattern (13 bp):
AATTTTTTTGAAC
Found at i:54647 original size:13 final size:13
Alignment explanation
Indices: 54629--54662 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
54619 ATTGGGCAAT
54629 TTTGAAAACTAA-G
1 TTTGAAAAC-AAGG
54642 TTTGAAAACAAGG
1 TTTGAAAACAAGG
54655 TTTGAAAA
1 TTTGAAAA
54663 TCAATATACG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 2 0.10
13 18 0.90
ACGTcount: A:0.47, C:0.06, G:0.18, T:0.29
Consensus pattern (13 bp):
TTTGAAAACAAGG
Found at i:55152 original size:20 final size:22
Alignment explanation
Indices: 55127--55178 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
55117 GTGGAGGGTG
*
55127 TCGATTCCC-T-AAAGGGGGAA
1 TCGATTCCCATCAAAGGGGAAA
55147 TCGATTCCCATTCAAAGGGGAAA
1 TCGATTCCCA-TCAAAGGGGAAA
*
55170 TCGGTTCCC
1 TCGATTCCC
55179 CTTCAAGGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 9 0.33
22 1 0.04
23 17 0.63
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.23
Consensus pattern (22 bp):
TCGATTCCCATCAAAGGGGAAA
Found at i:55171 original size:23 final size:23
Alignment explanation
Indices: 55137--55200 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
55127 TCGATTCCCT
55137 AAAGGGGGAATCGATTCCCATTC
1 AAAGGGGGAATCGATTCCCATTC
* * *
55160 AAAGGGGAAATCGGTTCCCCTTC
1 AAAGGGGGAATCGATTCCCATTC
* *
55183 AAGGGGGGCATCGATTCC
1 AAAGGGGGAATCGATTCC
55201 TCATGCACTA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.27, C:0.23, G:0.30, T:0.20
Consensus pattern (23 bp):
AAAGGGGGAATCGATTCCCATTC
Found at i:59374 original size:22 final size:21
Alignment explanation
Indices: 59332--59371 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
59322 GAGATTATTT
*
59332 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTAAAATA
59353 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
59372 ATAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAATA
Found at i:64894 original size:34 final size:35
Alignment explanation
Indices: 64828--64896 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
64818 GAAGTCTCTT
*
64828 TAGGTTCAGATCGATCAAACTGGTAATTCCTTATA
1 TAGGTTCAGATCGATCAAACTGCTAATTCCTTATA
* **
64863 TAGGTTTAGATCGATTGAA-TGCTAATTCCTTATA
1 TAGGTTCAGATCGATCAAACTGCTAATTCCTTATA
64897 GACCTAAGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 14 0.47
35 16 0.53
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.38
Consensus pattern (35 bp):
TAGGTTCAGATCGATCAAACTGCTAATTCCTTATA
Found at i:68529 original size:13 final size:14
Alignment explanation
Indices: 68511--68553 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
68501 GAAAGTGTAT
68511 ATTAATTTAAG-CA
1 ATTAATTTAAGTCA
68524 ATTAA-TTAAGTCA
1 ATTAATTTAAGTCA
*
68537 TTTAATTTAAGGTCA
1 ATTAATTTAA-GTCA
68552 AT
1 AT
68554 AACTGAAGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 5 0.20
13 11 0.44
14 4 0.16
15 5 0.20
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (14 bp):
ATTAATTTAAGTCA
Done.