Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001485.1 Hibiscus syriacus cultivar Beakdansim tig00002881_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: 68541
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2335 original size:28 final size:30
Alignment explanation
Indices: 2304--2371 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 30
2294 TTTAAATAGT
*
2304 TATTTTTATATT-AAT-ATATTTATGTAAA
1 TATTTTTATATTAAATAATATTTATATAAA
* *
2332 TATTTTTTTATTAAAATAATATTTATATAAT
1 TATTTTTATATT-AAATAATATTTATATAAA
2363 TATTTTTAT
1 TATTTTTAT
2372 TTAGAATTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 11 0.33
30 3 0.09
31 19 0.58
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (30 bp):
TATTTTTATATTAAATAATATTTATATAAA
Found at i:4139 original size:21 final size:21
Alignment explanation
Indices: 4113--4206 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
4103 ATTGCCATCT
*
4113 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCTAGC
4134 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
*
4155 CCGCCA-GGTTACATACCTAGC
1 CCG-CAGGGTTACATTCCTAGC
*
4176 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCTAGC
4197 CCGCAGGGTT
1 CCGCAGGGTT
4207 TTATACCATA
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
20 2 0.03
21 64 0.94
22 2 0.03
ACGTcount: A:0.19, C:0.35, G:0.26, T:0.20
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCTAGC
Found at i:4778 original size:33 final size:34
Alignment explanation
Indices: 4719--4815 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 34
4709 AAATGTTTTT
*
4719 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
4753 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
4786 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
4816 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:4822 original size:34 final size:33
Alignment explanation
Indices: 4717--4822 Score: 133
Period size: 34 Copynumber: 3.2 Consensus size: 33
4707 ATAAATGTTT
*
4717 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTT-AAA
* *
4751 TAAAAATAAAAATAATATTATTC-AAATTTAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAA
* *
4783 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTCGAAATTTAA-A
4818 TTAAA
1 TTAAA
4823 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAA
Found at i:5726 original size:127 final size:128
Alignment explanation
Indices: 5199--6190 Score: 1863
Period size: 127 Copynumber: 7.8 Consensus size: 128
5189 TTTAAGTTAT
*
5199 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA--AAATAATGGAAG
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
*
5262 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATATGTACTGATATATCTAGTG
66 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
5325 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
*
5390 GCGCGCCCCCGGGAACGCACCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
* *
5453 TCCCCGAGGGACATGAATAACATAATAGGGCAATGATAACATATTCTTTGACGAAATAATGGAAG
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
5518 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
5581 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
5646 GCGCG-CCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
5708 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
5773 GCGC-CCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
*
5835 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGATGAAATAATGGAAG
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
5900 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATAT-TCTAGTG
66 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
5962 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
6027 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTG--ATATCTAGTG
66 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
6088 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
* *
6153 GCGCGCCCCCAGGAACGCGTCTTCATGTGAATAGTGAA
66 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAA
6191 CCGATTATAG
Statistics
Matches: 849, Mismatches: 12, Indels: 10
0.97 0.01 0.01
Matches are distributed among these distances:
125 2 0.00
126 158 0.19
127 373 0.44
128 316 0.37
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (128 bp):
TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
Found at i:5905 original size:382 final size:383
Alignment explanation
Indices: 5199--6190 Score: 1861
Period size: 382 Copynumber: 2.6 Consensus size: 383
5189 TTTAAGTTAT
*
5199 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA--AAATAATGGAAG
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
*
5262 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATATGTACTGATATATCTAGTGTC
66 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTC
5327 CCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGC
131 CCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGC
*
5392 GCGCCCCCGGGAACGCACCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCC
196 GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCC
*
5457 CGAGGGACATGAATAACATAATAGGGCAATGATAACATATTCTTTGACGAAATAATGGAAGGCGC
261 CGAGGGACATGAATAACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGCGC
5522 GCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
326 GCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATAT-TCTAGTG
5581 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
5646 GCGCG-CCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTC
66 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTC
5710 CCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGC
131 CCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGC
5775 GC-CCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCC
196 GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCC
* *
5839 CGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGATGAAATAATGGAAGGCGC
261 CGAGGGACATGAATAACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGCGC
5904 GCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATTCTAGTG
326 GCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATTCTAGTG
5962 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
6027 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTG--ATATCTAGTGTC
66 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTC
6090 CCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGC
131 CCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGC
* *
6155 GCGCCCCCAGGAACGCGTCTTCATGTGAATAGTGAA
196 GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAA
6191 CCGATTATAG
Statistics
Matches: 598, Mismatches: 8, Indels: 9
0.97 0.01 0.01
Matches are distributed among these distances:
380 79 0.13
381 108 0.18
382 269 0.45
383 125 0.21
384 17 0.03
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (383 bp):
TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTC
CCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGC
GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCC
CGAGGGACATGAATAACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGCGC
GCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATTCTAGTG
Found at i:6270 original size:8 final size:8
Alignment explanation
Indices: 6257--6297 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
6247 TCACAATCTT
6257 TCAAATTC
1 TCAAATTC
6265 TCAAATTC
1 TCAAATTC
* *
6273 CCAAACTC
1 TCAAATTC
6281 T-AAATTC
1 TCAAATTC
6288 TCAAATTC
1 TCAAATTC
6296 TC
1 TC
6298 TGAAAATGAG
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:12685 original size:13 final size:13
Alignment explanation
Indices: 12657--12690 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
12647 ATATGATAAT
12657 TTATAAAATTATA
1 TTATAAAATTATA
12670 TTATAGAAATTA-A
1 TTATA-AAATTATA
12683 TTATAAAA
1 TTATAAAA
12691 AAAAATCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 3 0.15
13 11 0.55
14 6 0.30
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (13 bp):
TTATAAAATTATA
Found at i:16337 original size:21 final size:22
Alignment explanation
Indices: 16311--16352 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
16301 AAATTAATTT
16311 TATAATT-A-TTTTTTAGAAAAA
1 TATAATTAACTTTTTTA-AAAAA
16332 TATAATTAACTTTTTTAAAAA
1 TATAATTAACTTTTTTAAAAA
16353 GTGTTTTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 5 0.26
23 7 0.37
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
TATAATTAACTTTTTTAAAAAA
Found at i:23363 original size:18 final size:17
Alignment explanation
Indices: 23340--23378 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
23330 TTGCTTAAGT
*
23340 AAGTTTGAGATTTAAATA
1 AAGTTTGAGA-ATAAATA
*
23358 AAGTTTTAGAATAAATA
1 AAGTTTGAGAATAAATA
23375 AAGT
1 AAGT
23379 AAGGGGATGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.49, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
AAGTTTGAGAATAAATA
Found at i:29229 original size:16 final size:16
Alignment explanation
Indices: 29208--29238 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29198 AGCTTAACTT
*
29208 ATAAAATTATGCTAAC
1 ATAAAATTATACTAAC
29224 ATAAAATTATACTAA
1 ATAAAATTATACTAA
29239 TATTATAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.10, G:0.03, T:0.32
Consensus pattern (16 bp):
ATAAAATTATACTAAC
Found at i:30465 original size:14 final size:14
Alignment explanation
Indices: 30430--30475 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
30420 TTCATTTGTA
30430 ATAATAAAATAATA-
1 ATAAT-AAATAATAT
30444 ATAA-AAATAATAT
1 ATAATAAATAATAT
*
30457 ATAATAAATATTAT
1 ATAATAAATAATAT
30471 ATAAT
1 ATAAT
30476 TATTATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 8 0.28
13 4 0.14
14 17 0.59
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
ATAATAAATAATAT
Found at i:31245 original size:20 final size:20
Alignment explanation
Indices: 31194--31371 Score: 171
Period size: 20 Copynumber: 8.9 Consensus size: 20
31184 AGACTAACAG
* *
31194 ATGACCCAAAGGATTTACAA
1 ATGACCCGAAGGCTTTACAA
* * *
31214 ATTACTC-AGAGGTTTTACAA
1 ATGACCCGA-AGGCTTTACAA
* *
31234 ATGACCCGGAGGCTTTAAAA
1 ATGACCCGAAGGCTTTACAA
* *
31254 ATGAGCC-AGAGGCTTTATAA
1 ATGACCCGA-AGGCTTTACAA
*
31274 ATGACCCGGAGGCTTTACAA
1 ATGACCCGAAGGCTTTACAA
* *
31294 ATGAACCGAAGGCTTTGCAA
1 ATGACCCGAAGGCTTTACAA
* *
31314 ATGACTCGAAGGCTTTGCAA
1 ATGACCCGAAGGCTTTACAA
* *
31334 ATGACTCAAAGGCTTTACAA
1 ATGACCCGAAGGCTTTACAA
*
31354 ATAACCCGAAGGCTTTAC
1 ATGACCCGAAGGCTTTAC
31372 TTAAATGAGA
Statistics
Matches: 130, Mismatches: 24, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
19 1 0.01
20 129 0.99
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (20 bp):
ATGACCCGAAGGCTTTACAA
Found at i:38336 original size:16 final size:16
Alignment explanation
Indices: 38315--38345 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
38305 AGCTTAACTT
*
38315 ATAAAATTATCCTAAC
1 ATAAAATTATACTAAC
38331 ATAAAATTATACTAA
1 ATAAAATTATACTAA
38346 TATTATAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (16 bp):
ATAAAATTATACTAAC
Found at i:38501 original size:15 final size:16
Alignment explanation
Indices: 38465--38501 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
38455 TATAATTCAG
38465 GACTAAAATATAAATA
1 GACTAAAATATAAATA
*
38481 -ATTAAAATATAAA-A
1 GACTAAAATATAAATA
38495 GACTAAA
1 GACTAAA
38502 TAGGTTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 3
0.78 0.09 0.13
Matches are distributed among these distances:
14 1 0.06
15 17 0.94
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.24
Consensus pattern (16 bp):
GACTAAAATATAAATA
Found at i:39611 original size:34 final size:30
Alignment explanation
Indices: 39573--39641 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
39563 TCGATATAAC
39573 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
39607 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
39636 AATTTA
1 AATTTA
39642 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:39653 original size:29 final size:30
Alignment explanation
Indices: 39582--39641 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
39572 CAATTTAAGG
39582 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
39613 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
39642 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:39764 original size:22 final size:23
Alignment explanation
Indices: 39731--39774 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
39721 TTCAAGATTG
* *
39731 CCCAGGGGGGTATAGATTCCCCC
1 CCCAGGGGGGTACAGATACCCCC
39754 CCCA-GGGGGTACAGATACCCC
1 CCCAGGGGGGTACAGATACCCC
39775 GGGTACAGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.20, C:0.36, G:0.30, T:0.14
Consensus pattern (23 bp):
CCCAGGGGGGTACAGATACCCCC
Found at i:39799 original size:19 final size:18
Alignment explanation
Indices: 39753--39808 Score: 82
Period size: 15 Copynumber: 3.2 Consensus size: 18
39743 TAGATTCCCC
39753 CCCCAGGGGGTACAGATA
1 CCCCAGGGGGTACAGATA
39771 CCCC---GGGTACAGATA
1 CCCCAGGGGGTACAGATA
39786 CACCCAGGGGGTACAGATA
1 C-CCCAGGGGGTACAGATA
39805 CCCC
1 CCCC
39809 CTGCAGGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
15 12 0.35
16 3 0.09
18 7 0.21
19 12 0.35
ACGTcount: A:0.27, C:0.34, G:0.29, T:0.11
Consensus pattern (18 bp):
CCCCAGGGGGTACAGATA
Found at i:39807 original size:17 final size:17
Alignment explanation
Indices: 39754--39807 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
39744 AGATTCCCCC
39754 CCCAGGGGGTACAGATA
1 CCCAGGGGGTACAGATA
*
39771 CCC--CGGGTACAGATACA
1 CCCAGGGGGTACAGAT--A
39788 CCCAGGGGGTACAGATA
1 CCCAGGGGGTACAGATA
39805 CCC
1 CCC
39808 CCTGCAGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
15 10 0.32
17 11 0.35
19 10 0.32
ACGTcount: A:0.28, C:0.31, G:0.30, T:0.11
Consensus pattern (17 bp):
CCCAGGGGGTACAGATA
Found at i:39867 original size:20 final size:20
Alignment explanation
Indices: 39842--39881 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
39832 AAACAGAATG
39842 TCCAGGGGGTACCGATTCCC
1 TCCAGGGGGTACCGATTCCC
39862 TCCAGGGGGTACCGATTCCC
1 TCCAGGGGGTACCGATTCCC
39882 CCCCCTGTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.35, G:0.30, T:0.20
Consensus pattern (20 bp):
TCCAGGGGGTACCGATTCCC
Found at i:39948 original size:21 final size:21
Alignment explanation
Indices: 39922--39964 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
39912 ATTTGAATAT
*
39922 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
39943 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
39964 T
1 T
39965 CTATTCTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:40029 original size:20 final size:22
Alignment explanation
Indices: 39991--40030 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
39981 TTTTAGTATA
39991 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
40013 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
40031 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:40284 original size:34 final size:32
Alignment explanation
Indices: 40245--40314 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
40235 TTTTGTAAAG
*
40245 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
40279 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
40311 GGGA
1 GGGA
40315 GTTTGTAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:41324 original size:15 final size:15
Alignment explanation
Indices: 41306--41342 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
41296 GAAAGGGAAG
41306 AGAAGAAAAACAAGA
1 AGAAGAAAAACAAGA
* *
41321 AGAAGAAGAATAAGA
1 AGAAGAAAAACAAGA
41336 AGAAGAA
1 AGAAGAA
41343 TGAGGACGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.70, C:0.03, G:0.24, T:0.03
Consensus pattern (15 bp):
AGAAGAAAAACAAGA
Found at i:43165 original size:29 final size:30
Alignment explanation
Indices: 43094--43153 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
43084 CAATTTAAGG
43094 CAAAATGATTTTTGGACTTGAATTGAATTTA
1 CAAAATG-TTTTTGGACTTGAATTGAATTTA
43125 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
43154 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:43287 original size:20 final size:20
Alignment explanation
Indices: 43243--43305 Score: 90
Period size: 20 Copynumber: 3.0 Consensus size: 20
43233 TTCAAGATTG
*
43243 CCCAGGGGGTATAGATTCCCCC
1 CCCAGGGGGTATAGA-T-ACCC
*
43265 CCCAGGGGGTACAGATACCC
1 CCCAGGGGGTATAGATACCC
43285 CCCAGGGGGTATAGATACCC
1 CCCAGGGGGTATAGATACCC
43305 C
1 C
43306 TGTAGGTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
20 23 0.61
21 1 0.03
22 14 0.37
ACGTcount: A:0.22, C:0.35, G:0.29, T:0.14
Consensus pattern (20 bp):
CCCAGGGGGTATAGATACCC
Found at i:43422 original size:21 final size:21
Alignment explanation
Indices: 43396--43438 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
43386 ATTTGAATAT
*
43396 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
43417 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
43438 T
1 T
43439 CTATTCTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:43503 original size:20 final size:22
Alignment explanation
Indices: 43465--43504 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
43455 TTTTAGTATA
43465 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
43487 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
43505 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:43758 original size:34 final size:32
Alignment explanation
Indices: 43719--43788 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
43709 TTTTGTAAAG
*
43719 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
43753 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
43785 GGGA
1 GGGA
43789 GTTTGTAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:46272 original size:9 final size:9
Alignment explanation
Indices: 46258--46287 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
46248 ATTTTCAATC
46258 AAATCATTT
1 AAATCATTT
46267 AAATCATTT
1 AAATCATTT
46276 -AATCATTT
1 AAATCATTT
46284 AAAT
1 AAAT
46288 AATATTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (9 bp):
AAATCATTT
Found at i:46576 original size:39 final size:39
Alignment explanation
Indices: 46521--46608 Score: 131
Period size: 39 Copynumber: 2.3 Consensus size: 39
46511 CGTGCACTTA
*
46521 TGGAGTATTCTCCATTTGTCTGAAGATGTCATGCAGTCG
1 TGGAGTCTTCTCCATTTGTCTGAAGATGTCATGCAGTCG
* * *
46560 TGGAGTCTTCTTCATTTTTTTGAAGATGTCATGCAGTCG
1 TGGAGTCTTCTCCATTTGTCTGAAGATGTCATGCAGTCG
*
46599 TTGAGTCTTC
1 TGGAGTCTTC
46609 ATATTTAACT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.18, C:0.17, G:0.24, T:0.41
Consensus pattern (39 bp):
TGGAGTCTTCTCCATTTGTCTGAAGATGTCATGCAGTCG
Found at i:46622 original size:39 final size:39
Alignment explanation
Indices: 46541--46624 Score: 116
Period size: 39 Copynumber: 2.2 Consensus size: 39
46531 TCCATTTGTC
* **
46541 TGAAGATGTCATGCAGTCGTGGAGTCTTCTTCATTTTTT
1 TGAAGATGTCATGCAGTCGTGGAGTCTTCATCATTTACT
*
46580 TGAAGATGTCATGCAGTCGTTGAGTCTTCAT-ATTTAACT
1 TGAAGATGTCATGCAGTCGTGGAGTCTTCATCATTT-ACT
46619 TGAAGA
1 TGAAGA
46625 CGCGTGGAGC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
38 4 0.10
39 36 0.90
ACGTcount: A:0.24, C:0.14, G:0.23, T:0.39
Consensus pattern (39 bp):
TGAAGATGTCATGCAGTCGTGGAGTCTTCATCATTTACT
Found at i:52009 original size:3 final size:3
Alignment explanation
Indices: 51997--52027 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
51987 CCAGGGCAAA
51997 GAG GAGG GAG GAG GAG GAG GAG GAG GAG GAG
1 GAG GA-G GAG GAG GAG GAG GAG GAG GAG GAG
52028 AATGGAAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:52916 original size:23 final size:23
Alignment explanation
Indices: 52889--52964 Score: 97
Period size: 23 Copynumber: 3.4 Consensus size: 23
52879 TATCAATTAT
*
52889 AAATTTTAAATAATAATTAATCA
1 AAATTTAAAATAATAATTAATCA
52912 AAATTTAAAAT-ATCAATT-AT--
1 AAATTTAAAATAAT-AATTAATCA
*
52932 AAATTTCAAATAATAATTAATCA
1 AAATTTAAAATAATAATTAATCA
52955 AAATTTAAAA
1 AAATTTAAAA
52965 GAATTGATAA
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
20 14 0.31
21 4 0.09
22 4 0.09
23 23 0.51
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (23 bp):
AAATTTAAAATAATAATTAATCA
Found at i:52923 original size:20 final size:20
Alignment explanation
Indices: 52900--52969 Score: 70
Period size: 20 Copynumber: 3.4 Consensus size: 20
52890 AATTTTAAAT
52900 AATAATTAATCAAAATTTAA
1 AATAATTAATCAAAATTTAA
* *
52920 AAT-ATCAATTATAAATTTCAAA
1 AATAATTAATCA-AAATTT--AA
52942 TAATAATTAATCAAAATTTAA
1 -AATAATTAATCAAAATTTAA
*
52963 AAGAATT
1 AATAATT
52970 GATAAAAAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
19 6 0.15
20 15 0.38
21 2 0.05
22 2 0.05
23 9 0.22
24 6 0.15
ACGTcount: A:0.57, C:0.06, G:0.01, T:0.36
Consensus pattern (20 bp):
AATAATTAATCAAAATTTAA
Found at i:52928 original size:43 final size:43
Alignment explanation
Indices: 52879--52964 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
52869 TATATATTTT
*
52879 TATCAATTATAAATTTTAAATAATAATTAATCAAAATTTAAAA
1 TATCAATTATAAATTTCAAATAATAATTAATCAAAATTTAAAA
52922 TATCAATTATAAATTTCAAATAATAATTAATCAAAATTTAAAA
1 TATCAATTATAAATTTCAAATAATAATTAATCAAAATTTAAAA
52965 GAATTGATAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (43 bp):
TATCAATTATAAATTTCAAATAATAATTAATCAAAATTTAAAA
Found at i:58435 original size:194 final size:193
Alignment explanation
Indices: 58092--58482 Score: 525
Period size: 194 Copynumber: 2.0 Consensus size: 193
58082 TATGATGATA
* * *
58092 TTATGCATAATCATCATTCATAATATTATTAGGTAATAATATATTATGTTACTAAAAATGTGGCA
1 TTATGCATAAACATCATTCATAATATTATTAGGTAATAATATATTATGTCACTAAAAATGTGACA
** * * *
58157 ATATCTTTTTCGTCACATATAAGTTGATTTTAATGCATTATTTGTGACAATATAAACGATTAATA
66 ATATCTCATTCGTCACATATAAGTTGATTTTAATGCATAATTCGTGACAATATAAACGATCAATA
* ** *
58222 ACGAGATTTTATTTAATTTAGTGATGTAATCAACTGTCATAGAATATAAATTATAAAGTGACG
131 ACGAAATTTTACATAATTTAGTGATATAATCAACTGTCATAGAATATAAATTATAAAGTGACG
* * *
58285 TTATGCATAAACGTCATTCATAATATTATTAGGTAACGT-TTATATTATGTCACTAAAAATTTGA
1 TTATGCATAAACATCATTCATAATATTATTAGGTAA--TAATATATTATGTCACTAAAAATGTGA
* * *
58349 CAATATCTCATTCGTCACATATAGGTTGATTTTAATGTATAATTCGTGACGATATAAATC-ATCA
64 CAATATCTCATTCGTCACATATAAGTTGATTTTAATGCATAATTCGTGACAATATAAA-CGATCA
* ** * * *
58413 ATAACGAAATTTTACATAATTTAGTGATATAATTAGTTGTCATTGAATATTAATTATATAGTGAC
128 ATAACGAAATTTTACATAATTTAGTGATATAATCAACTGTCATAGAATATAAATTATAAAGTGAC
58478 G
193 G
58479 TTAT
1 TTAT
58483 ATATAAATGC
Statistics
Matches: 171, Mismatches: 24, Indels: 5
0.86 0.12 0.03
Matches are distributed among these distances:
193 34 0.20
194 135 0.79
195 2 0.01
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (193 bp):
TTATGCATAAACATCATTCATAATATTATTAGGTAATAATATATTATGTCACTAAAAATGTGACA
ATATCTCATTCGTCACATATAAGTTGATTTTAATGCATAATTCGTGACAATATAAACGATCAATA
ACGAAATTTTACATAATTTAGTGATATAATCAACTGTCATAGAATATAAATTATAAAGTGACG
Found at i:66284 original size:3 final size:3
Alignment explanation
Indices: 66278--66336 Score: 68
Period size: 3 Copynumber: 20.0 Consensus size: 3
66268 ACTAGTTTTT
*
66278 TTA TTA TTA TTA TTA CTA TTA -TA TTA TTA TTTA TT- TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
* *
66322 ATA TTT TTA TTA TTA
1 TTA TTA TTA TTA TTA
66337 CAAACATGCC
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
2 4 0.09
3 40 0.85
4 3 0.06
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:67681 original size:35 final size:35
Alignment explanation
Indices: 67638--67707 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
67628 ACTATTATTA
67638 TTATTTAGTCATGTAAATATATATATAAATAATAT
1 TTATTTAGTCATGTAAATATATATATAAATAATAT
67673 TTATTTAGTCATGTAAATATATATATAAATAATAT
1 TTATTTAGTCATGTAAATATATATATAAATAATAT
67708 ATAACTACTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.46
Consensus pattern (35 bp):
TTATTTAGTCATGTAAATATATATATAAATAATAT
Done.