Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002496.1 Hibiscus syriacus cultivar Beakdansim tig00005089_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: 70123
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:2126 original size:14 final size:15
Alignment explanation
Indices: 2098--2131 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
2088 ATAAATTTAT
2098 AAAATTTTAAGATAA
1 AAAATTTTAAGATAA
*
2113 AAAATTTTCA-ATAA
1 AAAATTTTAAGATAA
2127 AAAAT
1 AAAAT
2132 ATTTTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (15 bp):
AAAATTTTAAGATAA
Found at i:6342 original size:9 final size:9
Alignment explanation
Indices: 6328--6356 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
6318 GAAATCGGTT
6328 AATTAACCG
1 AATTAACCG
6337 AATTAACCG
1 AATTAACCG
6346 AATTAACCG
1 AATTAACCG
6355 AA
1 AA
6357 ATAAAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.48, C:0.21, G:0.10, T:0.21
Consensus pattern (9 bp):
AATTAACCG
Found at i:8009 original size:2 final size:2
Alignment explanation
Indices: 8002--8046 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
7992 TGGTTTAGGG
*
8002 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8044 AT A
1 AT A
8047 GTAAAAGTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:17075 original size:13 final size:14
Alignment explanation
Indices: 17059--17093 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
17049 TTACATTAGG
17059 TTAATATTTATT-A
1 TTAATATTTATTAA
*
17072 TTAAGATTTATTAA
1 TTAATATTTATTAA
17086 TTAATATT
1 TTAATATT
17094 AGATATTTTT
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:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (14 bp):
TTAATATTTATTAA
Found at i:17084 original size:28 final size:27
Alignment explanation
Indices: 17039--17093 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
17029 ACATATACAC
*
17039 TATTATTAAATTACATTAGGTTAATATT
1 TATTATTAAATTACATTA-ATTAATATT
*
17067 TATTATTAAGATT-TATTAATTAATATT
1 TATTATTAA-ATTACATTAATTAATATT
17094 AGATATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 8 0.33
28 13 0.54
29 3 0.12
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (27 bp):
TATTATTAAATTACATTAATTAATATT
Found at i:19554 original size:25 final size:25
Alignment explanation
Indices: 19526--19574 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
19516 TCAGTCTTAA
19526 TTCATCACGTCATTTATGATCCCAT
1 TTCATCACGTCATTTATGATCCCAT
*
19551 TTCATCATGTCATTTATGATCCCA
1 TTCATCACGTCATTTATGATCCCA
19575 ATAAATTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.24, C:0.27, G:0.08, T:0.41
Consensus pattern (25 bp):
TTCATCACGTCATTTATGATCCCAT
Found at i:22883 original size:30 final size:30
Alignment explanation
Indices: 22782--22886 Score: 99
Period size: 30 Copynumber: 3.5 Consensus size: 30
22772 TGATGCATTT
22782 CTGATTCTGCATGGGA-TTCCATT-CTCTGTC
1 CTGATTCTGCATGGGACTT-CATTCCTC-GTC
* * * *
22812 CTGATTCTACATGAGACTTCATTCCCCTTC
1 CTGATTCTGCATGGGACTTCATTCCTCGTC
* **
22842 CTGACAT-TGCATGGGACTTTGTTCCTCGTC
1 CTGA-TTCTGCATGGGACTTCATTCCTCGTC
22872 CTGATTCTGCATGGG
1 CTGATTCTGCATGGG
22887 TACCTCTTAG
Statistics
Matches: 59, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
29 1 0.02
30 53 0.90
31 5 0.08
ACGTcount: A:0.15, C:0.28, G:0.20, T:0.37
Consensus pattern (30 bp):
CTGATTCTGCATGGGACTTCATTCCTCGTC
Found at i:27366 original size:29 final size:30
Alignment explanation
Indices: 27333--27389 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
27323 ATAATTTTCT
*
27333 TAATTAATAAAGTTTCCAAT-ATTATAAGA
1 TAATTAATAAAGTTTCAAATGATTATAAGA
**
27362 TAATTAATAATTTTTCAAATGATTATAA
1 TAATTAATAAAGTTTCAAATGATTATAA
27390 AATATCATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (30 bp):
TAATTAATAAAGTTTCAAATGATTATAAGA
Found at i:28065 original size:6 final size:6
Alignment explanation
Indices: 28054--28090 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
28044 TATATACACC
*
28054 GGAAGG GGAAGG GGAAGG GGAAGG GGAAGG GGGAGG G
1 GGAAGG GGAAGG GGAAGG GGAAGG GGAAGG GGAAGG G
28091 AGAGAGGATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.30, C:0.00, G:0.70, T:0.00
Consensus pattern (6 bp):
GGAAGG
Found at i:29231 original size:287 final size:287
Alignment explanation
Indices: 28715--29298 Score: 1096
Period size: 287 Copynumber: 2.0 Consensus size: 287
28705 TTCATTGTTT
28715 TGGTAGATTGAGAGCTAAATAGCAATGGCTTGAAGTTTCCTCAACTACCATGAAATTGTTAATCT
1 TGGTAGATTGAGAGCTAAATAGCAATGGCTTGAAGTTTCCTCAACTACCATGAAATTGTTAATCT
* *
28780 TTCATTTTGCCGACAAATTAAGGGTAGAATAAATCAAATTAGGTAGATGAGAAGCCGTTCACTTG
66 TTCATTTTGCCGACAAATCAAGGGTAAAATAAATCAAATTAGGTAGATGAGAAGCCGTTCACTTG
28845 GTATTTGGGTTGTACGATCTTTTTATGTTCTTGAAAATCGTAATCGCCTTGATCTAAAGCCCCCT
131 GTATTTGGGTTGTACGATCTTTTTATGTTCTTGAAAATCGTAATCGCCTTGATCTAAAGCCCCCT
* * *
28910 TTTTTCCAAATATTTGTTTACTTTAGCTATATCACGTATTTGTTTGACAATGATTTCGTCTGTTG
196 TTTTCCCAAAGATTTGTTTACTTTAGCTATATCACGTATTTGTTTGACAATGATTTCGCCTGTTG
*
28975 ATTGTCTGATGCAAACTTTTAAGAAAA
261 ATTGTCTGATGCAAACTATTAAGAAAA
29002 TGGTAGATTGAGAGCTAAATAGCAATGGCTTGAAGTTTCCTCAACTACCATGAAATTGTTAATCT
1 TGGTAGATTGAGAGCTAAATAGCAATGGCTTGAAGTTTCCTCAACTACCATGAAATTGTTAATCT
*
29067 TTCATTTTGCTGACAAATCAAGGGTAAAATAAATCAAATTAGGTAGATGAGAAGCCGTTCACTTG
66 TTCATTTTGCCGACAAATCAAGGGTAAAATAAATCAAATTAGGTAGATGAGAAGCCGTTCACTTG
*
29132 GTATTTGGGTTGTACGTTCTTTTTATGTTCTTGAAAATCGTAATCGCCTTGATCTAAAGCCCCCT
131 GTATTTGGGTTGTACGATCTTTTTATGTTCTTGAAAATCGTAATCGCCTTGATCTAAAGCCCCCT
29197 TTTTCCCAAAGATTTGTTTACTTTAGCTATATCACGTATTTGTTTGACAATGATTTCGCCTGTTG
196 TTTTCCCAAAGATTTGTTTACTTTAGCTATATCACGTATTTGTTTGACAATGATTTCGCCTGTTG
29262 ATTGTCTGATGCAAACTATTAAGAAAA
261 ATTGTCTGATGCAAACTATTAAGAAAA
29289 TGGTAGATTG
1 TGGTAGATTG
29299 GGTCTTCTGC
Statistics
Matches: 289, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
287 289 1.00
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.37
Consensus pattern (287 bp):
TGGTAGATTGAGAGCTAAATAGCAATGGCTTGAAGTTTCCTCAACTACCATGAAATTGTTAATCT
TTCATTTTGCCGACAAATCAAGGGTAAAATAAATCAAATTAGGTAGATGAGAAGCCGTTCACTTG
GTATTTGGGTTGTACGATCTTTTTATGTTCTTGAAAATCGTAATCGCCTTGATCTAAAGCCCCCT
TTTTCCCAAAGATTTGTTTACTTTAGCTATATCACGTATTTGTTTGACAATGATTTCGCCTGTTG
ATTGTCTGATGCAAACTATTAAGAAAA
Found at i:38669 original size:2 final size:2
Alignment explanation
Indices: 38664--38700 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
38654 TTCTCTCCAA
38664 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
38701 AAAAATAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:38979 original size:2 final size:2
Alignment explanation
Indices: 38972--39002 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
38962 AATCATCTTT
38972 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39003 GAAAATATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39978 original size:122 final size:123
Alignment explanation
Indices: 39764--39985 Score: 311
Period size: 122 Copynumber: 1.8 Consensus size: 123
39754 AACAGTGTAA
* * *
39764 TACTAATACGAAAGAAAAACTAAACATTAGGTATGATTTTGAAAAAAAATGAAATTTTAGGTACT
1 TACTAAAACGAAACAAAAACTAAACATTAGGTATGATTTTGAAAAAAAATAAAATTTTAGGTACT
* * *
39829 AAAATGGACTAAAACTGATAGTGTAGGTAGTAAACACGTGATTTTTTTAATGGCGGAG
66 AAAATGGACCAAAACTAATAGTGTAGGTACTAAACACGTGATTTTTTTAATGGCGGAG
* * * * * * *
39887 TACTAAAATGAAACAAAAGCTAAACGTTAGGTATGGTTTTG-AAAAAATTAAAATTTTTGTTACT
1 TACTAAAACGAAACAAAAACTAAACATTAGGTATGATTTTGAAAAAAAATAAAATTTTAGGTACT
*
39951 AAAATGGACCAAAACTAATAGTTTAGGTACTAAAC
66 AAAATGGACCAAAACTAATAGTGTAGGTACTAAAC
39986 GCATAGTTTA
Statistics
Matches: 85, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
122 50 0.59
123 35 0.41
ACGTcount: A:0.44, C:0.09, G:0.17, T:0.30
Consensus pattern (123 bp):
TACTAAAACGAAACAAAAACTAAACATTAGGTATGATTTTGAAAAAAAATAAAATTTTAGGTACT
AAAATGGACCAAAACTAATAGTGTAGGTACTAAACACGTGATTTTTTTAATGGCGGAG
Found at i:40316 original size:14 final size:15
Alignment explanation
Indices: 40288--40316 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40278 TTAACTATCA
40288 AATCACTCATAATTT
1 AATCACTCATAATTT
40303 AATCACTC-TAATTT
1 AATCACTCATAATTT
40317 TCTTTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (15 bp):
AATCACTCATAATTT
Found at i:40341 original size:13 final size:13
Alignment explanation
Indices: 40325--40359 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
40315 TTTCTTTTTT
40325 TATTTTTAATATA
1 TATTTTTAATATA
*
40338 TATTTTTAACATA
1 TATTTTTAATATA
40351 T-TTTTTAAT
1 TATTTTTAAT
40360 TAAATAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 7 0.35
13 13 0.65
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (13 bp):
TATTTTTAATATA
Found at i:42171 original size:26 final size:28
Alignment explanation
Indices: 42114--42165 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
42104 ATTAATATTC
*
42114 TATTTAAATG-AATGTTTTTGTTTCTAA
1 TATTTAAATGTAATGTATTTGTTTCTAA
42141 TATTTAAATGTAAT-TATTT-TTTCTA
1 TATTTAAATGTAATGTATTTGTTTCTA
42166 TAATTTCTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 6 0.26
27 14 0.61
28 3 0.13
ACGTcount: A:0.31, C:0.04, G:0.08, T:0.58
Consensus pattern (28 bp):
TATTTAAATGTAATGTATTTGTTTCTAA
Found at i:42226 original size:25 final size:25
Alignment explanation
Indices: 42189--42247 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
42179 TAGGTACACC
* *
42189 TAAATAATTTTTTTTAATTTTTATT
1 TAAATAATTTTTTATAATATTTATT
*
42214 TAAA-AATTATTTTATGATATTTATT
1 TAAATAATT-TTTTATAATATTTATT
42239 TAATATAAT
1 TAA-ATAAT
42248 AATTAATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 4 0.14
25 20 0.71
26 1 0.04
27 3 0.11
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (25 bp):
TAAATAATTTTTTATAATATTTATT
Found at i:46275 original size:30 final size:29
Alignment explanation
Indices: 46241--46306 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
46231 ATTGGTTCTT
* *
46241 TGAAAAATAAATTATTAGAATTTAAATTAC
1 TGAAAAATAAATCACTAGAATTTAAATT-C
* * *
46271 TGAAAAATGAATCACTGGAATTTAAATTT
1 TGAAAAATAAATCACTAGAATTTAAATTC
46300 TGAAAAA
1 TGAAAAA
46307 ATGAATTACA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
29 7 0.23
30 24 0.77
ACGTcount: A:0.52, C:0.05, G:0.11, T:0.33
Consensus pattern (29 bp):
TGAAAAATAAATCACTAGAATTTAAATTC
Found at i:46312 original size:21 final size:20
Alignment explanation
Indices: 46292--46347 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
46282 TCACTGGAAT
46292 TTAAATTTTGAAAAAATGAA
1 TTAAATTTTGAAAAAATGAA
* *
46312 TTACATTTCT-AGAAAATGAA
1 TTAAATTT-TGAAAAAATGAA
*
46332 TTACAATTCTGAAAAA
1 TTA-AATTTTGAAAAA
46348 CATCTAGAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
20 20 0.71
21 8 0.29
ACGTcount: A:0.50, C:0.07, G:0.09, T:0.34
Consensus pattern (20 bp):
TTAAATTTTGAAAAAATGAA
Found at i:46327 original size:20 final size:19
Alignment explanation
Indices: 46304--46346 Score: 68
Period size: 20 Copynumber: 2.2 Consensus size: 19
46294 AAATTTTGAA
*
46304 AAAATGAATTACATTTCTAG
1 AAAATGAATTACAATTCT-G
46324 AAAATGAATTACAATTCTG
1 AAAATGAATTACAATTCTG
46343 AAAA
1 AAAA
46347 ACATCTAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.30
Consensus pattern (19 bp):
AAAATGAATTACAATTCTG
Found at i:46686 original size:23 final size:23
Alignment explanation
Indices: 46637--46709 Score: 67
Period size: 23 Copynumber: 3.1 Consensus size: 23
46627 AGTGTTATAT
* *
46637 TATATTTTAAAAATATTAATTAA
1 TATATTTTAAATATATTAACTAA
* *
46660 TATATTTTAAATATCTTTACTAGTA
1 TATATTTTAAATATATTAACTA--A
* *
46685 TATGTTTTAAATATA-TAAATAA
1 TATATTTTAAATATATTAACTAA
46707 TAT
1 TAT
46710 TATTCATTAT
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
22 4 0.10
23 18 0.45
24 4 0.10
25 14 0.35
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (23 bp):
TATATTTTAAATATATTAACTAA
Found at i:46739 original size:19 final size:21
Alignment explanation
Indices: 46717--46759 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
46707 TATTATTCAT
46717 TATTAAATA-TA-TAAAAAAA
1 TATTAAATATTATTAAAAAAA
*
46736 TATTATATATTATTAAAAAAA
1 TATTAAATATTATTAAAAAAA
46757 TAT
1 TAT
46760 ATAATATCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.38
20 2 0.10
21 11 0.52
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TATTAAATATTATTAAAAAAA
Found at i:46747 original size:29 final size:28
Alignment explanation
Indices: 46683--46752 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 28
46673 TCTTTACTAG
* *
46683 TATATGTT-TTAAATATATAAATAATAT
1 TATATATTATTAAATATATAAAAAATAT
46710 TAT-TCATTATTAAATATATAAAAAAATAT
1 TATAT-ATTATTAAATATAT-AAAAAATAT
46739 TATATATTATTAAA
1 TATATATTATTAAA
46753 AAAATATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
26 1 0.03
27 5 0.14
28 10 0.27
29 20 0.54
30 1 0.03
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (28 bp):
TATATATTATTAAATATATAAAAAATAT
Found at i:46845 original size:27 final size:27
Alignment explanation
Indices: 46703--46834 Score: 89
Period size: 28 Copynumber: 4.8 Consensus size: 27
46693 AAATATATAA
46703 ATAATATTATTCATTATTAAATATATAAAA-
1 ATAATATTA-T-ATTATTAAA-ATA-AAAAT
*
46733 A-AATATTATATATTATTAAAA-AAATAT
1 ATAATA-T-TATATTATTAAAATAAAAAT
* *
46760 ATAATATCTCATATTATTATAAT-ATAAT
1 ATAATAT-T-ATATTATTAAAATAAAAAT
* *
46788 -T--GATTATATTATTAAACTAAAAAT
1 ATAATATTATATTATTAAAATAAAAAT
46812 ATAATATTATATTATTATAAATA
1 ATAATATTATATTATTA-AAATA
46835 TTAATAAATA
Statistics
Matches: 80, Mismatches: 11, Indels: 24
0.70 0.10 0.21
Matches are distributed among these distances:
23 11 0.14
24 5 0.06
25 3 0.04
26 3 0.04
27 17 0.21
28 23 0.29
29 13 0.16
30 3 0.04
31 2 0.03
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (27 bp):
ATAATATTATATTATTAAAATAAAAAT
Found at i:49400 original size:11 final size:10
Alignment explanation
Indices: 49357--49415 Score: 55
Period size: 10 Copynumber: 5.7 Consensus size: 10
49347 AAAAAAAATA
*
49357 ATTTATATTC
1 ATTTTTATTC
* *
49367 TTTTTGTATTG
1 ATTTT-TATTC
*
49378 AATTTTATTC
1 ATTTTTATTC
49388 ATTTTTAATTC
1 ATTTTT-ATTC
*
49399 ATTTTTATTG
1 ATTTTTATTC
49409 ATTTTTA
1 ATTTTTA
49416 AAAAAAAATG
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
10 22 0.56
11 17 0.44
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (10 bp):
ATTTTTATTC
Found at i:49765 original size:23 final size:23
Alignment explanation
Indices: 49699--49765 Score: 62
Period size: 23 Copynumber: 2.7 Consensus size: 23
49689 TAAAATAAAC
*
49699 TTTTAAAATTAATAAAGTTTATTATT
1 TTTTAAAATT-A-AAA-TTTAATATT
**
49725 TTTAATAAAATTTGAATTTAATATT
1 TTT--TAAAATTAAAATTTAATATT
49750 TTTTAAAATTAAAATT
1 TTTTAAAATTAAAATT
49766 AGAAAGAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
23 11 0.32
25 11 0.32
26 5 0.15
28 7 0.21
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (23 bp):
TTTTAAAATTAAAATTTAATATT
Found at i:49870 original size:21 final size:21
Alignment explanation
Indices: 49815--49872 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
49805 TTTATATTAT
*
49815 TTTTTATTGAATTTTATTCAC
1 TTTTTATTGATTTTTATTCAC
* **
49836 TTTTAATTCTTTTTTATT-AC
1 TTTTTATTGATTTTTATTCAC
49856 ATTTTTATTGATTTTTA
1 -TTTTTATTGATTTTTA
49873 AAAAAAGAGA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
20 2 0.07
21 27 0.93
ACGTcount: A:0.22, C:0.07, G:0.03, T:0.67
Consensus pattern (21 bp):
TTTTTATTGATTTTTATTCAC
Found at i:49872 original size:10 final size:10
Alignment explanation
Indices: 49815--49872 Score: 53
Period size: 10 Copynumber: 5.6 Consensus size: 10
49805 TTTATATTAT
*
49815 TTTTTATTGA
1 TTTTTATTCA
*
49825 ATTTTATTCA
1 TTTTTATTCA
* *
49835 CTTTTAATTCT
1 -TTTTTATTCA
49846 TTTTTATTACA
1 TTTTTATT-CA
*
49857 TTTTTATTGA
1 TTTTTATTCA
49867 TTTTTA
1 TTTTTA
49873 AAAAAAGAGA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
10 22 0.58
11 16 0.42
ACGTcount: A:0.22, C:0.07, G:0.03, T:0.67
Consensus pattern (10 bp):
TTTTTATTCA
Found at i:50021 original size:25 final size:23
Alignment explanation
Indices: 49993--50038 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
49983 AAGTCAAAAA
49993 AATTTCAAAAATATATAAAATTTAT
1 AATTT-AAAAAT-TATAAAATTTAT
**
50018 AATTTTTAAATTATAAAATTT
1 AATTTAAAAATTATAAAATTT
50039 TTATTATCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 10 0.53
24 4 0.21
25 5 0.26
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
AATTTAAAAATTATAAAATTTAT
Found at i:53872 original size:21 final size:21
Alignment explanation
Indices: 53847--53886 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
53837 AGGATGTCCA
53847 GGGGGTATCGATTCCCCCTGG
1 GGGGGTATCGATTCCCCCTGG
53868 GGGGGTATCGATTCCCCCT
1 GGGGGTATCGATTCCCCCT
53887 AAATGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.10, C:0.30, G:0.35, T:0.25
Consensus pattern (21 bp):
GGGGGTATCGATTCCCCCTGG
Found at i:54267 original size:14 final size:15
Alignment explanation
Indices: 54239--54267 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
54229 TGATATGCAT
54239 AAACATAAGAGTATA
1 AAACATAAGAGTATA
54254 AAACATAAGA-TATA
1 AAACATAAGAGTATA
54268 TGATATGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.62, C:0.07, G:0.10, T:0.21
Consensus pattern (15 bp):
AAACATAAGAGTATA
Found at i:59979 original size:21 final size:21
Alignment explanation
Indices: 59954--59993 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
59944 AGAATGTCCA
59954 GGGGGTATCGATTCCCCCTGG
1 GGGGGTATCGATTCCCCCTGG
59975 GGGGGTATCGATTCCCCCT
1 GGGGGTATCGATTCCCCCT
59994 AAATGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.10, C:0.30, G:0.35, T:0.25
Consensus pattern (21 bp):
GGGGGTATCGATTCCCCCTGG
Found at i:60653 original size:15 final size:15
Alignment explanation
Indices: 60633--60667 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
60623 TGAGGGTATT
60633 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
60648 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
60663 GTAGT
1 GTAGT
60668 GGTCCTACGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.14, C:0.23, G:0.34, T:0.29
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:64763 original size:24 final size:26
Alignment explanation
Indices: 64710--64763 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
64700 CATATAACAT
* * *
64710 ATTTGAAATATATAATAGTTTTAAAT
1 ATTTAAAATACATAATAGTTTTAAAC
64736 ATTTAAAATACATAA-A-TTTTAAAC
1 ATTTAAAATACATAATAGTTTTAAAC
64760 ATTT
1 ATTT
64764 TAATAACATC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 11 0.44
25 1 0.04
26 13 0.52
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (26 bp):
ATTTAAAATACATAATAGTTTTAAAC
Found at i:65339 original size:13 final size:13
Alignment explanation
Indices: 65317--65350 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
65307 ACCCATTTTT
65317 TTTATAATTTTCA
1 TTTATAATTTTCA
*
65330 TTTATTATTTTCA
1 TTTATAATTTTCA
*
65343 ATTATAAT
1 TTTATAAT
65351 AGCGTGGTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTATAATTTTCA
Done.