Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005879.1 Hibiscus syriacus cultivar Beakdansim tig00013811_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: 71084
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Found at i:1775 original size:42 final size:42
Alignment explanation
Indices: 1729--1837 Score: 173
Period size: 42 Copynumber: 2.6 Consensus size: 42
1719 TTATAAAGCC
* *
1729 TTAATTGTTAAAGTCCATGGCTTTGTCTTATTCCATAGTCCT
1 TTAATTATTAAATTCCATGGCTTTGTCTTATTCCATAGTCCT
* * *
1771 TTAATTATTAAATTTCATGGCTTTTTCTTATTCCATAGTGCT
1 TTAATTATTAAATTCCATGGCTTTGTCTTATTCCATAGTCCT
1813 TTAATTATTAAATTCCATGGCTTTG
1 TTAATTATTAAATTCCATGGCTTTG
1838 CCTTCTCCCT
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 60 1.00
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.49
Consensus pattern (42 bp):
TTAATTATTAAATTCCATGGCTTTGTCTTATTCCATAGTCCT
Found at i:2481 original size:3 final size:3
Alignment explanation
Indices: 2473--2529 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
2463 CACTATTAGC
2473 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2521 TTA TTA TTA
1 TTA TTA TTA
2530 CTTTAAACAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:6840 original size:22 final size:20
Alignment explanation
Indices: 6789--6841 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
6779 AAAAACCTTC
*
6789 AGTATCGATACTCTTATGGG
1 AGTATCGATACTCCTATGGG
*
6809 AGTATTGATACTCCTATAGGTG
1 AGTATCGATACTCCTAT-GG-G
*
6831 AGTACCGATAC
1 AGTATCGATAC
6842 AAAAAGTGGC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 15 0.56
21 2 0.07
22 10 0.37
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
AGTATCGATACTCCTATGGG
Found at i:16845 original size:25 final size:25
Alignment explanation
Indices: 16814--16946 Score: 151
Period size: 25 Copynumber: 5.3 Consensus size: 25
16804 ATGCACTTTA
* *
16814 AAAGTGCCTCGTAGTATTGCACTCG
1 AAAGTGCCTCGTAGGATTACACTCG
* *
16839 AAAGTGCCTCGTAGGCTTACAGTCG
1 AAAGTGCCTCGTAGGATTACACTCG
* * * *
16864 TAAGTACCTCGTAGTATTGCACTCG
1 AAAGTGCCTCGTAGGATTACACTCG
* *
16889 AAAGGGCCTCGTAGGGTTACACTC-
1 AAAGTGCCTCGTAGGATTACACTCG
*
16913 ATAAGTGCCTCGTAGAATTACACTCG
1 A-AAGTGCCTCGTAGGATTACACTCG
16939 AAAGTGCC
1 AAAGTGCC
16947 ATATAAACAG
Statistics
Matches: 87, Mismatches: 19, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
24 1 0.01
25 85 0.98
26 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (25 bp):
AAAGTGCCTCGTAGGATTACACTCG
Found at i:16898 original size:50 final size:50
Alignment explanation
Indices: 16815--16942 Score: 193
Period size: 50 Copynumber: 2.6 Consensus size: 50
16805 TGCACTTTAA
* * *
16815 AAGTGCCTCGTAGTATTGCACTCGAAAGTGCCTCGTAGGCTTACAGTCGT
1 AAGTGCCTCGTAGTATTGCACTCGAAAGGGCCTCGTAGGCTTACACTCAT
* *
16865 AAGTACCTCGTAGTATTGCACTCGAAAGGGCCTCGTAGGGTTACACTCAT
1 AAGTGCCTCGTAGTATTGCACTCGAAAGGGCCTCGTAGGCTTACACTCAT
* *
16915 AAGTGCCTCGTAGAATTACACTCGAAAG
1 AAGTGCCTCGTAGTATTGCACTCGAAAG
16943 TGCCATATAA
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 70 1.00
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26
Consensus pattern (50 bp):
AAGTGCCTCGTAGTATTGCACTCGAAAGGGCCTCGTAGGCTTACACTCAT
Found at i:22101 original size:44 final size:44
Alignment explanation
Indices: 22053--22405 Score: 517
Period size: 44 Copynumber: 8.0 Consensus size: 44
22043 ATACCATGAG
* * *
22053 TGGCACCTTTATGCCAATAATTCACCATTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* **
22097 TGGCACCTTTATGCCAATAATGCATAGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
** * *
22141 TGAAACCTTTCTACCAATAATGCACCGTTATGCATTTTTATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* *
22185 TGGTACCTTTCTGCCAGTAATGCACCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * * *
22229 TGGCACATTTCTTCCAGTAATGCACTGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* *
22273 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTGTCATTTT
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* *
22317 TGGCACTTTTCTGCCAATAATGCATCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
*
22361 TGGCACCTTTATGCCAATAATGCACCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
22405 T
1 T
22406 TTCAGTAATA
Statistics
Matches: 276, Mismatches: 33, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 276 1.00
ACGTcount: A:0.24, C:0.22, G:0.13, T:0.41
Consensus pattern (44 bp):
TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
Found at i:22234 original size:25 final size:25
Alignment explanation
Indices: 22206--22279 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 25
22196 TGCCAGTAAT
22206 GCACCGTTATGCATTTTCATTTATG
1 GCACCGTTATGCATTTTCATTTATG
* * * *
22231 GCA-CATT-T-C--TTCCAGTAAT-
1 GCACCGTTATGCATTTTCATTTATG
*
22250 GCACTGTTATGCATTTTCATTTATG
1 GCACCGTTATGCATTTTCATTTATG
22275 GCACC
1 GCACC
22280 TTTCTGCCAA
Statistics
Matches: 33, Mismatches: 10, Indels: 12
0.60 0.18 0.22
Matches are distributed among these distances:
19 3 0.09
20 9 0.27
21 1 0.03
22 2 0.06
23 1 0.03
24 10 0.30
25 7 0.21
ACGTcount: A:0.22, C:0.23, G:0.15, T:0.41
Consensus pattern (25 bp):
GCACCGTTATGCATTTTCATTTATG
Found at i:26348 original size:15 final size:15
Alignment explanation
Indices: 26328--26366 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
26318 TAAACTCCGT
26328 TGGAGCCATTCGATA
1 TGGAGCCATTCGATA
26343 TGGAGCCATTCGATA
1 TGGAGCCATTCGATA
26358 TGGAGCCAT
1 TGGAGCCAT
26367 ATAAATAGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (15 bp):
TGGAGCCATTCGATA
Found at i:29027 original size:25 final size:25
Alignment explanation
Indices: 28999--29071 Score: 61
Period size: 25 Copynumber: 3.2 Consensus size: 25
28989 TGCCAATAAT
28999 GCACTGTTATGCATTTTCATTTATG
1 GCACTGTTATGCATTTTCATTTATG
* * *
29024 GCACAT-TTCTGC-----CAATAAT-
1 GCAC-TGTTATGCATTTTCATTTATG
29043 GCACTGTTATGCATTTTCATTTATG
1 GCACTGTTATGCATTTTCATTTATG
29068 GCAC
1 GCAC
29072 ATTTCTGCGA
Statistics
Matches: 34, Mismatches: 6, Indels: 16
0.61 0.11 0.29
Matches are distributed among these distances:
18 1 0.03
19 9 0.26
20 5 0.15
24 5 0.15
25 13 0.38
26 1 0.03
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.41
Consensus pattern (25 bp):
GCACTGTTATGCATTTTCATTTATG
Found at i:29033 original size:44 final size:44
Alignment explanation
Indices: 28978--29418 Score: 602
Period size: 44 Copynumber: 10.0 Consensus size: 44
28968 ATACCATGAG
*
28978 TGGCACCTTTCTGCCAATAATGCACTGTTATGCATTTTCATTTA
1 TGGCACATTTCTGCCAATAATGCACTGTTATGCATTTTCATTTA
29022 TGGCACATTTCTGCCAATAATGCACTGTTATGCATTTTCATTTA
1 TGGCACATTTCTGCCAATAATGCACTGTTATGCATTTTCATTTA
* *
29066 TGGCACATTTCTGCGAATAATGCACCGTTATGCATTTTCATTTA
1 TGGCACATTTCTGCCAATAATGCACTGTTATGCATTTTCATTTA
* * *
29110 TTGTATC-TTTCTGCCAATAATGCA-TCATTATGCATTTTCATTTA
1 TGGCA-CATTTCTGCCAATAATGCACT-GTTATGCATTTTCATTTA
* **
29154 TTGCACCCTTCTGCCAATAATGCACTGTTATGCATTTTCATTTA
1 TGGCACATTTCTGCCAATAATGCACTGTTATGCATTTTCATTTA
* * **
29198 TGGCACATTTCTTCCAGTAATGCACAATTACT-CATTTTCATTTA
1 TGGCACATTTCTGCCAATAATGCACTGTTA-TGCATTTTCATTTA
* * ** *
29242 TGGCACCTATCTTTCAATAATGCA-TCGTTATGCATTTTTATTTA
1 TGGCACATTTCTGCCAATAATGCACT-GTTATGCATTTTCATTTA
*
29286 TGGCACATTTCTGTCAATAATGCACTGTTATGCATTTTCATTTA
1 TGGCACATTTCTGCCAATAATGCACTGTTATGCATTTTCATTTA
* *
29330 TGGCACATTTTTTCCAATAATGCACTGTTATGCATTTTCATTTA
1 TGGCACATTTCTGCCAATAATGCACTGTTATGCATTTTCATTTA
* **
29374 TGGCACCTTTCTGCCAATAATGCACCATTATGCATTTTCATTTA
1 TGGCACATTTCTGCCAATAATGCACTGTTATGCATTTTCATTTA
29418 T
1 T
29419 TTCGGTAACA
Statistics
Matches: 352, Mismatches: 37, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
43 2 0.01
44 346 0.98
45 4 0.01
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.42
Consensus pattern (44 bp):
TGGCACATTTCTGCCAATAATGCACTGTTATGCATTTTCATTTA
Found at i:29379 original size:25 final size:25
Alignment explanation
Indices: 29307--29379 Score: 68
Period size: 20 Copynumber: 3.2 Consensus size: 25
29297 TGTCAATAAT
29307 GCACTGTTATGCATTTTCATTTATG
1 GCACTGTTATGCATTTTCATTTATG
* * * *
29332 GCAC-ATT-T---TTTCCAATAAT-
1 GCACTGTTATGCATTTTCATTTATG
29351 GCACTGTTATGCATTTTCATTTATG
1 GCACTGTTATGCATTTTCATTTATG
29376 GCAC
1 GCAC
29380 CTTTCTGCCA
Statistics
Matches: 34, Mismatches: 8, Indels: 12
0.63 0.15 0.22
Matches are distributed among these distances:
19 4 0.12
20 10 0.29
21 1 0.03
23 1 0.03
24 10 0.29
25 8 0.24
ACGTcount: A:0.23, C:0.19, G:0.14, T:0.44
Consensus pattern (25 bp):
GCACTGTTATGCATTTTCATTTATG
Found at i:31484 original size:27 final size:28
Alignment explanation
Indices: 31443--31499 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 28
31433 TTGTTTAAAC
* * *
31443 TTGCTTTTGATTTTG-TCTATTGCTTGA
1 TTGCTCTTGAATTTGATCAATTGCTTGA
31470 TTGCTCTTGAATTTGATCAATTGCTTGA
1 TTGCTCTTGAATTTGATCAATTGCTTGA
31498 TT
1 TT
31500 TTGATTCACT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 13 0.50
28 13 0.50
ACGTcount: A:0.16, C:0.12, G:0.18, T:0.54
Consensus pattern (28 bp):
TTGCTCTTGAATTTGATCAATTGCTTGA
Found at i:39189 original size:23 final size:22
Alignment explanation
Indices: 39118--39198 Score: 92
Period size: 23 Copynumber: 3.6 Consensus size: 22
39108 TACACTACCT
**
39118 TGTGCATATATGCATCCCTTGAA
1 TGTGCATCGATGCAT-CCTTGAA
* *
39141 TGTGCATCGATTCA-CCATGAA
1 TGTGCATCGATGCATCCTTGAA
*
39162 GGTGCATCGATGCATGCCTTGAA
1 TGTGCATCGATGCAT-CCTTGAA
39185 TGTGCATCGATGCA
1 TGTGCATCGATGCA
39199 CTCTGTTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
21 18 0.38
23 30 0.62
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (22 bp):
TGTGCATCGATGCATCCTTGAA
Found at i:42978 original size:24 final size:25
Alignment explanation
Indices: 42950--43003 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
42940 ATTATGGGAG
42950 TTATCTTTTGC-AATTTAGTAGGAA
1 TTATCTTTTGCTAATTTAGTAGGAA
* **
42974 TTATC-TTTGCTATTTTTTTAGGAA
1 TTATCTTTTGCTAATTTAGTAGGAA
42998 TTATCT
1 TTATCT
43004 CTTAGGATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 5 0.20
24 20 0.80
ACGTcount: A:0.24, C:0.09, G:0.13, T:0.54
Consensus pattern (25 bp):
TTATCTTTTGCTAATTTAGTAGGAA
Found at i:44529 original size:15 final size:15
Alignment explanation
Indices: 44509--44538 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
44499 ATTTTCCCAT
*
44509 TTTCATATTCTTTTC
1 TTTCATATACTTTTC
44524 TTTCATATACTTTTC
1 TTTCATATACTTTTC
44539 ATAACTTTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.20, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTCATATACTTTTC
Found at i:45072 original size:174 final size:174
Alignment explanation
Indices: 44782--45130 Score: 646
Period size: 174 Copynumber: 2.0 Consensus size: 174
44772 GGGTTTTCAG
44782 ATCATATTATTTTCAATTAAAGATCACTATTTTCTAAATCAGATTATTTTCCATTCATCATCATA
1 ATCATATTATTTTCAATTAAAGATCACTATTTTCTAAATCAGATTATTTTCCATTCATCATCATA
*
44847 TAAATCTTAACTTGGGCAGTTTATACCCAAAAATAATTTAGATAATATTTCTAAAATCATTAAAG
66 TAAATCTTAACTTGGGCAGTTTATACCCAAAAATAATTCAGATAATATTTCTAAAATCATTAAAG
44912 AAATATTTCATCATTAAAATTTCATATCATTCCTTAATTATTTT
131 AAATATTTCATCATTAAAATTTCATATCATTCCTTAATTATTTT
*
44956 ATCATATTATTTTCAATTAAATATCAAC-ATTTTCTAAATCAGATTATTTTCCATTCATCATCAT
1 ATCATATTATTTTCAATTAAAGATC-ACTATTTTCTAAATCAGATTATTTTCCATTCATCATCAT
*
45020 ATAAATCTTAACTTGGGCAGTTTATACCCTAAAATAATTCAGATAATATTTCTAAAATCATTAAA
65 ATAAATCTTAACTTGGGCAGTTTATACCCAAAAATAATTCAGATAATATTTCTAAAATCATTAAA
*
45085 GAAATATTTCATCATTAAAATTTCATATTATTCCTTAATTATTTT
130 GAAATATTTCATCATTAAAATTTCATATCATTCCTTAATTATTTT
45130 A
1 A
45131 GAAAATTCAT
Statistics
Matches: 170, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
174 168 0.99
175 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.04, T:0.43
Consensus pattern (174 bp):
ATCATATTATTTTCAATTAAAGATCACTATTTTCTAAATCAGATTATTTTCCATTCATCATCATA
TAAATCTTAACTTGGGCAGTTTATACCCAAAAATAATTCAGATAATATTTCTAAAATCATTAAAG
AAATATTTCATCATTAAAATTTCATATCATTCCTTAATTATTTT
Found at i:47261 original size:30 final size:30
Alignment explanation
Indices: 47227--47292 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 30
47217 AAAATACATT
* *
47227 TTTGGTCCCTT-AACTTTTTAAAACTTATAC
1 TTTGGTCCCTTAAAC-TTTCAAAACTTACAC
* *
47257 TTTGG-CCTTTAAACTTTCAAAACTTACAT
1 TTTGGTCCCTTAAACTTTCAAAACTTACAC
47286 TTTGGTC
1 TTTGGTC
47293 ATTACCCAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
29 21 0.70
30 9 0.30
ACGTcount: A:0.26, C:0.20, G:0.09, T:0.45
Consensus pattern (30 bp):
TTTGGTCCCTTAAACTTTCAAAACTTACAC
Found at i:51587 original size:22 final size:20
Alignment explanation
Indices: 51542--51593 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
51532 AAACCTTCAA
* *
51542 TATCGATAATCTTATGGGAG
1 TATCGATACTCCTATGGGAG
51562 TATCGATACTCCTATAGGAGAG
1 TATCGATACTCCTAT-GG-GAG
51584 TATCGATACT
1 TATCGATACT
51594 ACCTCGAGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 13 0.46
21 2 0.07
22 13 0.46
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (20 bp):
TATCGATACTCCTATGGGAG
Found at i:67063 original size:21 final size:21
Alignment explanation
Indices: 67039--67078 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
67029 AAAATTTTTC
67039 GAGAAAAACTATCTCGAGTGA
1 GAGAAAAACTATCTCGAGTGA
* *
67060 GAGAAAAATTGTCTCGAGT
1 GAGAAAAACTATCTCGAGT
67079 AATAAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.12, G:0.25, T:0.23
Consensus pattern (21 bp):
GAGAAAAACTATCTCGAGTGA
Found at i:67863 original size:34 final size:34
Alignment explanation
Indices: 67768--68024 Score: 144
Period size: 34 Copynumber: 7.4 Consensus size: 34
67758 CAGAGAACTG
* *
67768 TCTCAAGCGAGA-CAAAAATTTCCAAGA-AAAATA
1 TCTCAAGTGAGATGAAAAATTT-CAAGAGAAAATA
*** ** *
67801 TCTCAAGTGAGATGAATTTTTTTGAGAGAAAATG
1 TCTCAAGTGAGATGAAAAATTTCAAGAGAAAATA
**
67835 TCTTGAGTGAGATGAAAAATTTCAAGAGAAAATA
1 TCTCAAGTGAGATGAAAAATTTCAAGAGAAAATA
** * * *
67869 TCTCAAGTGAGATGAAATTTGGTTTCAAGGGAAACTG
1 TCTCAAGTGAGATGAAA---AATTTCAAGAGAAAATA
* * * * *
67906 TATCAAGTGAGACGAAAACTTTTAA-AGGGAAATA
1 TCTCAAGTGAGATGAAAAATTTCAAGA-GAAAATA
** * *
67940 TCTCAAGTGAGATGAAATTTTGTTTCGAGTG-AAATAA
1 TCTCAAGTGAGATGAAA---AATTTCAAGAGAAAAT-A
* * *
67977 TCTCGAGTGAGATGAAAATTTTCAAGGGAAAACTA
1 TCTCAAGTGAGATGAAAAATTTCAAGAGAAAA-TA
*
68012 TCTCAAGCGAGAT
1 TCTCAAGTGAGAT
68025 AAATTTTTGT
Statistics
Matches: 165, Mismatches: 46, Indels: 24
0.70 0.20 0.10
Matches are distributed among these distances:
33 14 0.08
34 82 0.50
35 15 0.09
36 5 0.03
37 49 0.30
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.28
Consensus pattern (34 bp):
TCTCAAGTGAGATGAAAAATTTCAAGAGAAAATA
Found at i:67912 original size:37 final size:35
Alignment explanation
Indices: 67854--68030 Score: 128
Period size: 37 Copynumber: 5.0 Consensus size: 35
67844 AGATGAAAAA
* *
67854 TTTCAAGAGAAAATATCTCAAGTGAGATGAAATTTGG
1 TTTCAAG-GGAAATATATCAAGTGAGATGAAATTT-G
* * **
67891 TTTCAAGGGAAACTGTATCAAGTGAGACGAAAACT-
1 TTTCAAGGGAAA-TATATCAAGTGAGATGAAATTTG
* *
67926 TTTAAAGGGAAATATCTCAAGTGAGATGAAATTTTG
1 TTTCAAGGGAAATATATCAAGTGAGATGAAA-TTTG
* * * * *
67962 TTTCGAGTGAAATAATCTCGAGTGAGATGAAA-AT-
1 TTTCAAGGGAAAT-ATATCAAGTGAGATGAAATTTG
* *
67996 TTTCAAGGGAAAACTATCTCAAGCGAGAT-AAATTT
1 TTTCAAGGG-AAA-TATATCAAGTGAGATGAAATTT
68031 TTGTTTGAGA
Statistics
Matches: 111, Mismatches: 22, Indels: 16
0.74 0.15 0.11
Matches are distributed among these distances:
34 26 0.23
35 29 0.26
36 15 0.14
37 41 0.37
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (35 bp):
TTTCAAGGGAAATATATCAAGTGAGATGAAATTTG
Found at i:67944 original size:71 final size:68
Alignment explanation
Indices: 67493--68129 Score: 325
Period size: 71 Copynumber: 9.1 Consensus size: 68
67483 TGGAAAGTTT
* * * * *
67493 TCTCGAGTGAGA--AAGAGTTTTCAA-GAAAATATCTCAAGTGAGATAAAATTT-ATTCAAGAGA
1 TCTCGAGTGAGATGAA-AATTTTCAAGGGAAATATCTCAAGTGAGATGAAATTTGTTTCGAGAGA
**
67554 AACA
65 AATG
* * * *
67558 TTTTGAGTGAGA-CAAAATTTTTCAAGGGAAATATCTCAAGAT-AGATGCAACTTTGTTTCGAGA
1 TCTCGAGTGAGATGAAAA-TTTTCAAGGGAAATATCTCAAG-TGAGATG-AAATTTGTTTCGAGA
*
67621 GAAGCTG
63 GAA-ATG
* * * * * * ***** *
67628 TCTCGAGTGAAATGAAATTTTTCACGAGAAGATATCTCGAGTGTGAT-AAAAAAAATTCTAGA-A
1 TCTCGAGTGAGATGAAAATTTTCAAGGGAA-ATATCTCAAGTGAGATGAAATTTGTTTCGAGAGA
*
67691 AACTA
65 AA-TG
* * * * * * *
67696 TCTCAAGTGAGA-CAAAATTGGTTTTAAGGAAAACTATCTCGAGCGAGATAAAACTCTAT-TTTC
1 TCTCGAGTGAGATGAAAA-T--TTTCAAGGGAAA-TATCTCAAGTGAGATGAAA-T-T-TGTTTC
*
67759 -AGAGAACTG
59 GAGAGAAATG
* * ** * ** *
67768 TCTCAAGCGAGACAAAAATTTCCAAGAAAAATATCTCAAGTGAGATG-AATTT-TTTTGAGAGAA
1 TCTCGAGTGAGATGAAAATTTTCAAGGGAAATATCTCAAGTGAGATGAAATTTGTTTCGAGAG-A
67831 AATG
65 AATG
* * * * *
67835 TCTTGAGTGAGATGAAAAATTTCAAGAGAAAATATCTCAAGTGAGATGAAATTTGGTTTCAAGGG
1 TCTCGAGTGAGATGAAAATTTTCAAG-GGAAATATCTCAAGTGAGATGAAATTT-GTTTCGAGAG
67900 AAACTG
64 AAA-TG
* * * * *
67906 TATCAAGTGAGACGAAAACTTTTAAAGGGAAATATCTCAAGTGAGATGAAATTTTGTTTCGAGTG
1 TCTCGAGTGAGATGAAAA-TTTTCAAGGGAAATATCTCAAGTGAGATGAAA-TTTGTTTCGAGAG
*
67971 AAATAA
64 AAAT-G
*
67977 TCTCGAGTGAGATGAAAATTTTCAAGGGAAAACTATCTCAAGCGAGAT-AAATTTTTGTTT-GAG
1 TCTCGAGTGAGATGAAAATTTTCAAGGG-AAA-TATCTCAAGTGAGATGAAA--TTTGTTTCGAG
68040 AGAAACTG
62 AGAAA-TG
* * * ** * *
68048 ACTCGAGTGAGA-CACAAATTACTTCTAGAAAAAATATCTCAAGTGAGATAAAAATTGTTTCGAG
1 TCTCGAGTGAGATGA-AAATT--TTCAAG-GGAAATATCTCAAGTGAGATGAAATTTGTTTCGAG
*
68112 AGAATTTG
62 AGAA-ATG
*
68120 TCTCAAGTGA
1 TCTCGAGTGA
68130 AACAAAATTA
Statistics
Matches: 437, Mismatches: 93, Indels: 77
0.72 0.15 0.13
Matches are distributed among these distances:
65 15 0.03
66 14 0.03
67 44 0.10
68 42 0.10
69 36 0.08
70 63 0.14
71 124 0.28
72 79 0.18
73 20 0.05
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.28
Consensus pattern (68 bp):
TCTCGAGTGAGATGAAAATTTTCAAGGGAAATATCTCAAGTGAGATGAAATTTGTTTCGAGAGAA
ATG
Found at i:68057 original size:142 final size:143
Alignment explanation
Indices: 67794--68115 Score: 369
Period size: 142 Copynumber: 2.3 Consensus size: 143
67784 AATTTCCAAG
* *
67794 AAAAATATCTCAAGTGAGATG-AATTTT-TTT-GAGAGAAAATGTCTTGAGTGAGATGAAAAATT
1 AAAAATATCTCAAGTGAGATGAAATTTTGTTTCGAGAGAAAATATCTCGAGTGAGATGAAAAATT
* * *
67856 TCAAGAGAAAATATCTCAAGTGAGATGAAATTTGGTTTCAAGGGAAACTGTATCAAGTGAGAC-G
66 TCAAGAGAAAATATCTCAAGCGAGATGAAATTTGGTTTCAAGAGAAACTGTATCAAGTGAGACAC
*
67920 AAA-ACTTTTA-A
131 AAATACTTCTAGA
* *
67931 AGGGAAATATCTCAAGTGAGATGAAATTTTGTTTCGAGTG-AAATAATCTCGAGTGAGATGAAAA
1 A--AAAATATCTCAAGTGAGATGAAATTTTGTTTCGAGAGAAAAT-ATCTCGAGTGAGATGAAAA
* * * * *
67995 TTTTCAAGGGAAAACTATCTCAAGCGAGAT-AAATTTTTGTTT-GAGAGAAACTG-ACTCGAGTG
63 ATTTCAAGAGAAAA-TATCTCAAGCGAGATGAAA-TTTGGTTTCAAGAGAAACTGTA-TCAAGTG
68057 AGACACAAATTACTTCTAGA
125 AGACACAAA-TACTTCTAGA
**
68077 AAAAATATCTCAAGTGAGAT-AAAAATTGTTTCGAGAGAA
1 AAAAATATCTCAAGTGAGATGAAATTTTGTTTCGAGAGAA
68116 TTTGTCTCAA
Statistics
Matches: 154, Mismatches: 17, Indels: 21
0.80 0.09 0.11
Matches are distributed among these distances:
137 1 0.01
139 19 0.12
140 6 0.04
141 8 0.05
142 55 0.36
143 38 0.25
144 19 0.12
145 6 0.04
146 2 0.01
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.29
Consensus pattern (143 bp):
AAAAATATCTCAAGTGAGATGAAATTTTGTTTCGAGAGAAAATATCTCGAGTGAGATGAAAAATT
TCAAGAGAAAATATCTCAAGCGAGATGAAATTTGGTTTCAAGAGAAACTGTATCAAGTGAGACAC
AAATACTTCTAGA
Found at i:68093 original size:36 final size:35
Alignment explanation
Indices: 68053--68214 Score: 110
Period size: 36 Copynumber: 4.4 Consensus size: 35
68043 AACTGACTCG
* *
68053 AGTGAGACACAAATTACTTCTAGAAAAAATATCTCA
1 AGTGAGACA-AAATTATTTCTAGAAAAATTATCTCA
* * * * * *
68089 AGTGAGATAAAAATTGTTTCGAGAGAATTTGTCTCA
1 AGTGAGA-CAAAATTATTTCTAGAAAAATTATCTCA
* * *
68125 AGTGAAACAAAATTATTTTTGAGGAAAATTATCTCA
1 AGTGAGACAAAATTATTTCT-AGAAAAATTATCTCA
* * *
68161 AGTGAGATAGAAAATTTTTGTTCCAAGAAAAATTATCTCAA
1 AGTGAG--ACAAAA-TTAT-TT-CTAGAAAAATTATCTC-A
68202 AG-GAGACAAAATT
1 AGTGAGACAAAATT
68215 TTGTTTTAAA
Statistics
Matches: 94, Mismatches: 24, Indels: 15
0.71 0.18 0.11
Matches are distributed among these distances:
35 9 0.10
36 48 0.51
37 3 0.03
38 10 0.11
39 3 0.03
40 18 0.19
41 3 0.03
ACGTcount: A:0.44, C:0.10, G:0.16, T:0.30
Consensus pattern (35 bp):
AGTGAGACAAAATTATTTCTAGAAAAATTATCTCA
Found at i:68211 original size:76 final size:72
Alignment explanation
Indices: 68077--68214 Score: 161
Period size: 76 Copynumber: 1.9 Consensus size: 72
68067 TACTTCTAGA
* * * * *
68077 AAAAATATCTCAAGTGAGATAAAAATTGTTTCGAGAGAATTTGTCTCAAGTGAAACAAAATTATT
1 AAAAATATCTCAAGTGAGATAAAAATTGTTCCAAGAAAAATTATCTCAAGTGAAACAAAATTATT
68142 TTTGAGG
66 TTTGAGG
* *
68149 AAAATTATCTCAAGTGAGATAGAAAATTTTTGTTCCAAGAAAAATTATCTCAAAG-GAGACAAAA
1 AAAAATATCTCAAGTGAGATA-AAAA---TTGTTCCAAGAAAAATTATCTC-AAGTGAAACAAAA
68213 TT
61 TT
68215 TTGTTTTAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
72 20 0.37
73 4 0.07
76 27 0.50
77 3 0.06
ACGTcount: A:0.44, C:0.09, G:0.16, T:0.30
Consensus pattern (72 bp):
AAAAATATCTCAAGTGAGATAAAAATTGTTCCAAGAAAAATTATCTCAAGTGAAACAAAATTATT
TTTGAGG
Found at i:69540 original size:11 final size:11
Alignment explanation
Indices: 69516--69549 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
69506 ATGTAGAATC
*
69516 ATTCTAATATCA
1 ATTCTAAT-CCA
69528 ATTCTAATCCA
1 ATTCTAATCCA
69539 ATTCTAATCCA
1 ATTCTAATCCA
69550 TGGGAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 13 0.62
12 8 0.38
ACGTcount: A:0.38, C:0.24, G:0.00, T:0.38
Consensus pattern (11 bp):
ATTCTAATCCA
Found at i:70587 original size:18 final size:18
Alignment explanation
Indices: 70560--70594 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
70550 CGGAATGTAA
70560 GATTACCAGTGGGAATAG
1 GATTACCAGTGGGAATAG
*
70578 GATTATCAGTGGGAATA
1 GATTACCAGTGGGAATA
70595 AAATTACTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.09, G:0.31, T:0.26
Consensus pattern (18 bp):
GATTACCAGTGGGAATAG
Found at i:70600 original size:18 final size:18
Alignment explanation
Indices: 70561--70601 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
70551 GGAATGTAAG
**
70561 ATTACCAGTGGGAATAGG
1 ATTACCAGTGGGAATAAA
*
70579 ATTATCAGTGGGAATAAA
1 ATTACCAGTGGGAATAAA
70597 ATTAC
1 ATTAC
70602 TGGGAATGTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.39, C:0.10, G:0.24, T:0.27
Consensus pattern (18 bp):
ATTACCAGTGGGAATAAA
Done.