Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005357.1 Hibiscus syriacus cultivar Beakdansim tig00012169_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: 73969
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Found at i:157 original size:21 final size:20
Alignment explanation
Indices: 133--187 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
123 TTTTAATTCA
133 TAAAATTTAGAATTATTATTT
1 TAAAATTTAGAATTA-TATTT
*
154 TAAAAATTATG-ATTATATTT
1 TAAAATTTA-GAATTATATTT
* *
174 GAAAATTTATAATT
1 TAAAATTTAGAATT
188 TTTGAAATCC
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
20 15 0.54
21 12 0.43
22 1 0.04
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.49
Consensus pattern (20 bp):
TAAAATTTAGAATTATATTT
Found at i:10893 original size:29 final size:28
Alignment explanation
Indices: 10856--10913 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 28
10846 ATTTTAATAA
10856 AAATATTTACTATGATATATTTAT-TTTTG
1 AAATATTTA--ATGATATATTTATATTTTG
* *
10885 AAATGTTTAATGATTTATTTATATTTTG
1 AAATATTTAATGATATATTTATATTTTG
10913 A
1 A
10914 TAAAATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 12 0.46
28 6 0.23
29 8 0.31
ACGTcount: A:0.34, C:0.02, G:0.09, T:0.55
Consensus pattern (28 bp):
AAATATTTAATGATATATTTATATTTTG
Found at i:11517 original size:2 final size:2
Alignment explanation
Indices: 11510--11540 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
11500 AATTTTGTAA
11510 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 A
11541 AATTTTATGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11745 original size:16 final size:18
Alignment explanation
Indices: 11724--11768 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 18
11714 AACATTCCCA
11724 GTAATCTTATT-CC-CTG
1 GTAATCTTATTCCCACTG
11740 GTAATCTTACATTCCCACTG
1 GTAATCTT--ATTCCCACTG
11760 GTAATCTTA
1 GTAATCTTA
11769 CATTCCGTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 8 0.32
18 4 0.16
19 2 0.08
20 11 0.44
ACGTcount: A:0.24, C:0.24, G:0.11, T:0.40
Consensus pattern (18 bp):
GTAATCTTATTCCCACTG
Found at i:11762 original size:20 final size:20
Alignment explanation
Indices: 11737--11774 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
11727 ATCTTATTCC
11737 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
11757 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
11775 GTGAACCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.11, T:0.37
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:12021 original size:28 final size:29
Alignment explanation
Indices: 11956--12014 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
11946 TTTGTCAAAG
* * *
11956 TACATATATTGTATTAGATATTTTTAAAA
1 TACAAATATTGCATTAGATATTTTAAAAA
11985 TACAAATATTGCATTAGATATTTTAAAAA
1 TACAAATATTGCATTAGATATTTTAAAAA
12014 T
1 T
12015 TAAATATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (29 bp):
TACAAATATTGCATTAGATATTTTAAAAA
Found at i:19392 original size:12 final size:12
Alignment explanation
Indices: 19375--19399 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19365 GTAAAATAAT
19375 TTAGGCACCAAA
1 TTAGGCACCAAA
19387 TTAGGCACCAAA
1 TTAGGCACCAAA
19399 T
1 T
19400 GGTACTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (12 bp):
TTAGGCACCAAA
Found at i:31378 original size:3 final size:3
Alignment explanation
Indices: 31370--31427 Score: 73
Period size: 3 Copynumber: 19.0 Consensus size: 3
31360 CAGTTCATTT
**
31370 TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
31418 TTA TTTA TTA
1 TTA -TTA TTA
31428 AATATTACAA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
2 2 0.04
3 40 0.83
4 6 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:32735 original size:28 final size:31
Alignment explanation
Indices: 32676--32755 Score: 107
Period size: 29 Copynumber: 2.7 Consensus size: 31
32666 AAATAGCATG
32676 TTTAGTCACTGTAATTTTAA-ATAATTACTAA
1 TTTAGTCACT-TAATTTTAATATAATTACTAA
*
32707 -TTAGACACTTAATTTTAATAT-ATT-CTAA
1 TTTAGTCACTTAATTTTAATATAATTACTAA
32735 TTTAGTCA-TTAATTTTAATAT
1 TTTAGTCACTTAATTTTAATAT
32756 CTTTATTTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
28 17 0.38
29 18 0.40
30 10 0.22
ACGTcount: A:0.38, C:0.09, G:0.05, T:0.49
Consensus pattern (31 bp):
TTTAGTCACTTAATTTTAATATAATTACTAA
Found at i:32879 original size:3 final size:3
Alignment explanation
Indices: 32871--32897 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
32861 ATTATATTTA
32871 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
32898 TAGTTATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:32914 original size:2 final size:2
Alignment explanation
Indices: 32902--32933 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
32892 ATTATTTAGT
*
32902 TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
32934 ATAAACAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:33852 original size:60 final size:60
Alignment explanation
Indices: 33694--33853 Score: 205
Period size: 60 Copynumber: 2.7 Consensus size: 60
33684 TTTGGATGAA
* * * ** * *
33694 TTTAGGGATGAAATTGGAAAATTCAAAAACTTGAGGACCAATTTAGAATGAGAGTAATAG
1 TTTAGGGATGAAATTAGAATACTCAAAAGTTTAAGGACTAATTTAGAATGAGAGTAATAG
* * *
33754 TTTGGGGATGAAATTAGAATGCTCAAAAGTTTAAGGACTAATTTAGAATTAGAG-ATATAG
1 TTTAGGGATGAAATTAGAATACTCAAAAGTTTAAGGACTAATTTAGAATGAGAGTA-ATAG
*
33814 TTTAGGAATGAAATTAGAATACTCAAAAGTTTAAGGACTA
1 TTTAGGGATGAAATTAGAATACTCAAAAGTTTAAGGACTA
33854 GTTTGTAATT
Statistics
Matches: 86, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
59 1 0.01
60 85 0.99
ACGTcount: A:0.42, C:0.06, G:0.22, T:0.29
Consensus pattern (60 bp):
TTTAGGGATGAAATTAGAATACTCAAAAGTTTAAGGACTAATTTAGAATGAGAGTAATAG
Found at i:36575 original size:13 final size:13
Alignment explanation
Indices: 36557--36586 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
36547 GATTGCGAAG
36557 AATTAAAAATTTA
1 AATTAAAAATTTA
36570 AATT-AAAATTTA
1 AATTAAAAATTTA
36582 AATTA
1 AATTA
36587 CTCGATTCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AATTAAAAATTTA
Found at i:37163 original size:22 final size:22
Alignment explanation
Indices: 37133--37186 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
37123 CGGTGTAGCC
37133 CCGGCCGCCGCTCTCAGTCGCT
1 CCGGCCGCCGCTCTCAGTCGCT
*
37155 CTGGCCGCCGCTCTCAGTCGCT
1 CCGGCCGCCGCTCTCAGTCGCT
*
37177 CCGGCGGCCG
1 CCGGCCGCCG
37187 GGCCAACCCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.04, C:0.48, G:0.31, T:0.17
Consensus pattern (22 bp):
CCGGCCGCCGCTCTCAGTCGCT
Found at i:37431 original size:15 final size:16
Alignment explanation
Indices: 37401--37434 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
37391 TCTGACTTGG
*
37401 GTTTGGTTGGTTTTGT
1 GTTTGGTTGATTTTGT
37417 GTTTGGTT-ATTTTGT
1 GTTTGGTTGATTTTGT
37432 GTT
1 GTT
37435 GTTTTTAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.03, C:0.00, G:0.32, T:0.65
Consensus pattern (16 bp):
GTTTGGTTGATTTTGT
Found at i:38064 original size:26 final size:27
Alignment explanation
Indices: 38018--38068 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
38008 AATAAATAAT
38018 ATATATATATATAAACGTTTTCAAAAAC
1 ATATATATATATAAACGTTTT-AAAAAC
*
38046 ATATA-ATATATAAA-TTTTTAAAA
1 ATATATATATATAAACGTTTTAAAA
38069 TGTTTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 4 0.18
26 4 0.18
27 9 0.41
28 5 0.23
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (27 bp):
ATATATATATATAAACGTTTTAAAAAC
Found at i:38093 original size:38 final size:36
Alignment explanation
Indices: 38030--38215 Score: 157
Period size: 36 Copynumber: 5.1 Consensus size: 36
38020 ATATATATAT
*
38030 AAACGTTTTCAAAAAC-ATATAATATATAAATTTTTA
1 AAACGTTTTTAAAAACTATAT-ATATATAAATTTTTA
* * *
38066 AAATGTTTTTTTAAAAACTATATATATATATATTTTCA
1 AAACG--TTTTTAAAAACTATATATATATAAATTTTTA
* *
38104 AAATGGTTTTTAAAAATTATAT-TATATAAATGTTTTCA
1 AAA-CGTTTTTAAAAACTATATATATATAAAT-TTTT-A
* * * *
38142 TAACG-TTTTCAAAAGTATATAT-TATATATATTTTA
1 AAACGTTTTTAAAAACTATATATATATAAAT-TTTTA
* *
38177 AAACGTTTTCAAAAACTATATAT-TATATAATTTTCA
1 AAACGTTTTTAAAAACTATATATATATA-AATTTTTA
38213 AAA
1 AAA
38216 AAAATATATT
Statistics
Matches: 121, Mismatches: 20, Indels: 18
0.76 0.13 0.11
Matches are distributed among these distances:
35 5 0.04
36 60 0.50
37 22 0.18
38 29 0.24
39 5 0.04
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (36 bp):
AAACGTTTTTAAAAACTATATATATATAAATTTTTA
Found at i:38200 original size:27 final size:26
Alignment explanation
Indices: 38165--38268 Score: 84
Period size: 25 Copynumber: 3.8 Consensus size: 26
38155 AGTATATATT
38165 ATATATATTTTAAAACGTTTTCAAAAA
1 ATATATATTTTAAAA-GTTTTCAAAAA
* * *
38192 CTATATATTATATAA-TTTTCAAAAA
1 ATATATATTTTAAAAGTTTTCAAAAA
* *
38217 AAATATATTTTCAAAATGGTTTTTAAAAA
1 ATATATATTTT-AAAA--GTTTTCAAAAA
* * *
38246 TTATATATATATAAATGTTTTCA
1 ATATATAT-TTTAAAAGTTTTCA
38269 TAACGTTTTC
Statistics
Matches: 59, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
25 18 0.31
26 3 0.05
27 18 0.31
29 18 0.31
30 2 0.03
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (26 bp):
ATATATATTTTAAAAGTTTTCAAAAA
Found at i:38285 original size:127 final size:127
Alignment explanation
Indices: 38093--38344 Score: 488
Period size: 127 Copynumber: 2.0 Consensus size: 127
38083 CTATATATAT
38093 ATATATTTTCAAAATGGTTTTTAAAAATTATATTATATAAATGTTTTCATAACGTTTTCAAAAGT
1 ATATATTTTCAAAATGGTTTTTAAAAATTATATTATATAAATGTTTTCATAACGTTTTCAAAAGT
38158 ATATATTATATATATTTT-AAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAAAA
66 ATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAAAA
38219 ATATATTTTCAAAATGGTTTTTAAAAATTATATATATATAAATGTTTTCATAACGTTTTCAAAAG
1 ATATATTTTCAAAATGGTTTTTAAAAATTATAT-TATATAAATGTTTTCATAACGTTTTCAAAAG
38284 TATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
65 TATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
38345 TATTTTAAAA
Statistics
Matches: 124, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
126 33 0.27
127 50 0.40
128 41 0.33
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.44
Consensus pattern (127 bp):
ATATATTTTCAAAATGGTTTTTAAAAATTATATTATATAAATGTTTTCATAACGTTTTCAAAAGT
ATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAAAA
Found at i:38325 original size:37 final size:37
Alignment explanation
Indices: 38219--38419 Score: 205
Period size: 37 Copynumber: 5.4 Consensus size: 37
38209 TTCAAAAAAA
** *
38219 ATATATTTTCAAAATGGTTTTTAAAAATTATATATATAT
1 ATATATTTTCAAAAACG-TTTTAAAAACTATATAT-TAT
* * * * *
38258 AAATGTTTTC-ATAACGTTTTCAAAAGTATATATTAT
1 ATATATTTTCAAAAACGTTTTAAAAACTATATATTAT
38294 ATATATTTT-AAAAACGTTTTCAAAAACTATATATTAT
1 ATATATTTTCAAAAACGTTTT-AAAAACTATATATTAT
** *
38331 ATA-ATTTTCAAAAATATTTTAAAAACTATATAATAT
1 ATATATTTTCAAAAACGTTTTAAAAACTATATATTAT
* *
38367 ACATATTTTCAAAAATGTTTT--AAACTATATATTAT
1 ATATATTTTCAAAAACGTTTTAAAAACTATATATTAT
38402 ATATGTATTTTCAAAAAC
1 ATA--TATTTTCAAAAAC
38420 AATTTGCAAA
Statistics
Matches: 136, Mismatches: 20, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
35 15 0.11
36 41 0.30
37 69 0.51
38 3 0.02
39 8 0.06
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (37 bp):
ATATATTTTCAAAAACGTTTTAAAAACTATATATTAT
Found at i:38441 original size:37 final size:34
Alignment explanation
Indices: 38316--38442 Score: 101
Period size: 37 Copynumber: 3.5 Consensus size: 34
38306 AACGTTTTCA
* * *
38316 AAAACTATATATTATATAATTTTCAAAAATATTTT
1 AAAACTATATAATATATTATTTTCAAAAA-AATTT
* **
38351 AAAAACTATATAATATACATATTTTCAAAAATGTTT
1 -AAAACTATATAATATA-TTATTTTCAAAAAAATTT
*
38387 TAAACTATATATTATATATGTATTTTCAAAAACAATTT
1 AAAACTATATA--ATATAT-TATTTTCAAAAA-AATTT
* *
38425 GCAAACTGTATAATATAT
1 -AAAACTATATAATATAT
38443 ATGTGTATAT
Statistics
Matches: 74, Mismatches: 11, Indels: 11
0.77 0.11 0.11
Matches are distributed among these distances:
35 10 0.14
36 18 0.24
37 34 0.46
38 3 0.04
39 9 0.12
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (34 bp):
AAAACTATATAATATATTATTTTCAAAAAAATTT
Found at i:39174 original size:84 final size:80
Alignment explanation
Indices: 39037--39813 Score: 854
Period size: 84 Copynumber: 9.4 Consensus size: 80
39027 TTGAATATAA
* * *
39037 TCGAACTCGAAGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCT
1 TCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCT
*
39102 TGGAGCTGAGCGGAG
66 TGGAGCTGAGCGTAG
* * ** *
39117 TCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGACTTAAGTTGTATTGCAAATGATAT
1 TCGAACTCGAAGGTC-TTTGG---CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
39182 GCCTTGGAGCTGAGCGTAG
62 GCCTTGGAGCTGAGCGTAG
* *
39201 TCGAACTCGAAGGTTTTTTGTTGGCAGATAACCCTTCTCAACTTAAGTTATGCTGCAAATGATGT
1 TCGAACTCGAAGG---TCT-TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
*
39266 GCCTTGGAGCTGAGCGGAG
62 GCCTTGGAGCTGAGCGTAG
39285 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTC---T-TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
** * * *
39350 GCCCCCGAAGCTGAGTGTAA
62 G-CCTTGGAGCTGAGCGTAG
* ** * * *
39370 TCGAACTTGGGGGACTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCT
1 TCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCT
39435 TGGAGCTGAGCGTAG
66 TGGAGCTGAGCGTAG
* * * * * * *
39450 TCGAACTCGAAGGTCTTTGGTGACAGATAACCCTCCTAGCCTTGAGTTATGCTGTAAATGTTATG
1 TCGAACTCGAAGGTCTTT-G-G-CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG
* * *
39515 CCCTTGAAGCTGAGTGTAA
63 -CCTTGGAGCTGAGCGTAG
* * * *
39534 TCGAACT-TAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCC
1 TCGAACTCGAA-GGTCTTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC
*
39598 TAGGAGCTGAGCGTAG
65 TTGGAGCTGAGCGTAG
* * * * * *
39614 TCGAACTCGAAGGTCTTTGGCGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATG
1 TCGAACTCGAAGGTCTTT-G-G-CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG
* * *
39679 CCCTTGAAGCTGAGTGTAA
63 -CCTTGGAGCTGAGCGTAG
** * * *
39698 TCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCT
1 TCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCT
39763 TGGAGCTGAGCGTAG
66 TGGAGCTGAGCGTAG
*
39778 TCGAACTCGAAGGTCTTGGTGGCAGATAGCCCTTCT
1 TCGAACTCGAAGGTCTT--TGGCAGATAACCCTTCT
39814 GGCCTTGAGC
Statistics
Matches: 576, Mismatches: 97, Indels: 46
0.80 0.13 0.06
Matches are distributed among these distances:
80 100 0.17
81 118 0.20
82 22 0.04
83 70 0.12
84 237 0.41
85 23 0.04
86 1 0.00
87 5 0.01
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (80 bp):
TCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCT
TGGAGCTGAGCGTAG
Found at i:39208 original size:164 final size:165
Alignment explanation
Indices: 39034--39794 Score: 1073
Period size: 164 Copynumber: 4.6 Consensus size: 165
39024 AAGTTGAATA
*
39034 TAATCGAACTCGAAGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
*
39099 CCTTGGAGCTGAGCGGAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGACTTAAG
66 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGACTTAAG
* ** * *
39164 TTGTATTGCAAATGATATG-CCTTGGAGCTGAGCG
131 TTATGCTGCAAATGATATGCCCTTGAAGCTGAGTG
* * * * *
39198 TAGTCGAACTCGAAGGTTTTTTGTTGGCAGATAACCCTTCTCAACTTAAGTTATGCTGCAAATGA
1 TAATCGAACTCGAAGG---TCT-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGA
* * ** *
39263 TGTGCCTTGGAGCTGAGCGGAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACT
62 TGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGACT
* **
39328 TAAGTTATGCTGCAAATGATGTGCCCCCGAAGCTGAGTG
127 TAAGTTATGCTGCAAATGATATGCCCTTGAAGCTGAGTG
* ** *
39367 TAATCGAACTTGGGGGACTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
* * * *
39432 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGACAGATAACCCTCCTAGCCTTGAG
66 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGACTTAAG
* *
39496 TTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTG
131 TTATGCTGCAAATGATATGCCCTTGAAGCTGAGTG
* *
39531 TAATCGAACT-TAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGT
1 TAATCGAACTCGAA-GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
* * *
39595 GCCTAGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGG-CGACAGATAACCCTTCTAGCCTTG
65 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC-ACAGATAACCCTTCTAGACTTA
* *
39658 AGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTG
129 AGTTATGCTGCAAATGATATGCCCTTGAAGCTGAGTG
** *
39695 TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTG
1 TAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
39760 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTT
66 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTT
39795 GGTGGCAGAT
Statistics
Matches: 537, Mismatches: 51, Indels: 17
0.89 0.08 0.03
Matches are distributed among these distances:
164 317 0.59
165 76 0.14
166 1 0.00
167 2 0.00
168 118 0.22
169 23 0.04
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (165 bp):
TAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGACTTAAG
TTATGCTGCAAATGATATGCCCTTGAAGCTGAGTG
Found at i:44856 original size:13 final size:13
Alignment explanation
Indices: 44838--44867 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
44828 GATTGCGAAG
44838 AATTAAAAATTTA
1 AATTAAAAATTTA
44851 AATT-AAAATTTA
1 AATTAAAAATTTA
44863 AATTA
1 AATTA
44868 CTCGATTCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AATTAAAAATTTA
Found at i:44976 original size:23 final size:24
Alignment explanation
Indices: 44965--45024 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
44955 TTAAATAAAT
*
44965 AAATAACAAAACAATAGAATAATA
1 AAATAAAAAAACAATAGAATAATA
*
44989 AAATAAAAAAA-AATCGAAATTGAAT-
1 AAATAAAAAAACAATAG-AA-T-AATA
45014 AAATAAAAAAA
1 AAATAAAAAAA
45025 AAGGGTCAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 4 0.13
24 12 0.39
25 12 0.39
26 3 0.10
ACGTcount: A:0.73, C:0.05, G:0.05, T:0.17
Consensus pattern (24 bp):
AAATAAAAAAACAATAGAATAATA
Found at i:45448 original size:22 final size:22
Alignment explanation
Indices: 45418--45471 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
45408 CGGTGTAGCC
45418 CCGGCCGCCGCTCTCAGTCGCT
1 CCGGCCGCCGCTCTCAGTCGCT
*
45440 CTGGCCGCCGCTCTCAGTCGCT
1 CCGGCCGCCGCTCTCAGTCGCT
*
45462 CCGGCGGCCG
1 CCGGCCGCCG
45472 GGCCAACCCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.04, C:0.48, G:0.31, T:0.17
Consensus pattern (22 bp):
CCGGCCGCCGCTCTCAGTCGCT
Found at i:46350 original size:26 final size:25
Alignment explanation
Indices: 46306--46354 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
46296 AATAATAATA
46306 ATATATATATAAACGTTTTCAAAAAC
1 ATATATATATAAACGTTTT-AAAAAC
*
46332 ATATAATATATAAA-TTTTTAAAA
1 ATAT-ATATATAAACGTTTTAAAA
46355 TGTTTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 4 0.19
26 8 0.38
27 9 0.43
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (25 bp):
ATATATATATAAACGTTTTAAAAAC
Found at i:46488 original size:27 final size:25
Alignment explanation
Indices: 46453--46555 Score: 84
Period size: 27 Copynumber: 3.9 Consensus size: 25
46443 AGTATATATT
*
46453 ATATATATTTTAAAACGTTTTCAAAA
1 ATATATATTATAAAA-GTTTTCAAAA
*
46479 ACTATATATTATATAA-TTTTCAAAA
1 A-TATATATTATAAAAGTTTTCAAAA
* *
46504 A-ATATATTTTCAAAATGGTTTTTAAAA
1 ATATATATTAT-AAAA--GTTTTCAAAA
46531 ATTATATATTATATAAATGTTTTCA
1 A-TATATATTATA-AAA-GTTTTCA
46556 TAACGTTTTC
Statistics
Matches: 61, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
23 8 0.13
24 3 0.05
25 10 0.16
26 1 0.02
27 21 0.34
28 7 0.11
29 11 0.18
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.46
Consensus pattern (25 bp):
ATATATATTATAAAAGTTTTCAAAA
Found at i:46492 original size:36 final size:37
Alignment explanation
Indices: 46316--46706 Score: 221
Period size: 36 Copynumber: 10.1 Consensus size: 37
46306 ATATATATAT
* * *
46316 AAACGTTTTCAAAAAC-ATATAATATATAAATTTTTA
1 AAACGTTTTCAAAAACTATATATTATATATATTTTAA
* *
46352 AAATGTTTTTTTTAAAAACTATATATTATATATATTTTCAA
1 AAACG---TTTTCAAAAACTATATATTATATATATTTT-AA
** * * *
46393 AATGGTTTTTAAAAA-T-TATATTATATAAATGTTTTCA
1 AAACGTTTTCAAAAACTATATATTATAT--ATATTTTAA
* *
46430 TAACGTTTTC-AAAAGTATATATTATATATATTTT-A
1 AAACGTTTTCAAAAACTATATATTATATATATTTTAA
46465 AAACGTTTTCAAAAACTATATATTATATA-ATTTTCAAAAA
1 AAACGTTTTCAAAAACTATATATTATATATATTTT----AA
* * * * *
46505 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCA
1 A-A-A----C------GTTTTCAAAAACTATATATTATATATATTTTA--A
* *
46556 TAACGTTTTC-AAAAGTATATATTATATATATTTTAA
1 AAACGTTTTCAAAAACTATATATTATATATATTTTAA
46592 AAACGTTTTCAAAAACTATATATTATATA-ATTTTCAA
1 AAACGTTTTCAAAAACTATATATTATATATATTTT-AA
** * *
46629 AAATATTTT-AAAAACTATATAATATACATATTTTCAA
1 AAACGTTTTCAAAAACTATATATTATATATATTTT-AA
*
46666 AAATGTTTT---AAACTATATATTATATATGTATTTTCAA
1 AAACGTTTTCAAAAACTATATATTATATA--TATTTT-AA
46703 AAAC
1 AAAC
46707 AATTTGCAAA
Statistics
Matches: 284, Mismatches: 36, Indels: 69
0.73 0.09 0.18
Matches are distributed among these distances:
35 30 0.11
36 73 0.26
37 63 0.22
38 47 0.17
39 15 0.05
40 18 0.06
41 5 0.02
42 1 0.00
45 1 0.00
46 1 0.00
49 1 0.00
50 1 0.00
51 1 0.00
52 23 0.08
53 4 0.01
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.45
Consensus pattern (37 bp):
AAACGTTTTCAAAAACTATATATTATATATATTTTAA
Found at i:46514 original size:15 final size:16
Alignment explanation
Indices: 46489--46518 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
46479 ACTATATATT
46489 ATATAATTTTCAAAAA
1 ATATAATTTTCAAAAA
46505 ATAT-ATTTTCAAAA
1 ATATAATTTTCAAAA
46519 TGGTTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATAATTTTCAAAAA
Found at i:46617 original size:37 final size:37
Alignment explanation
Indices: 46505--46706 Score: 207
Period size: 37 Copynumber: 5.4 Consensus size: 37
46495 TTTTCAAAAA
** *
46505 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTAT
1 ATATATTTTCAAAAACG-TTTTAAAAACTATATATTAT
* * * *
46543 ATAAATGTTTTC-ATAACGTTTTCAAAAGTATATATTAT
1 AT--ATATTTTCAAAAACGTTTTAAAAACTATATATTAT
46581 ATATATTTT-AAAAACGTTTTCAAAAACTATATATTAT
1 ATATATTTTCAAAAACGTTTT-AAAAACTATATATTAT
** *
46618 ATA-ATTTTCAAAAATATTTTAAAAACTATATAATAT
1 ATATATTTTCAAAAACGTTTTAAAAACTATATATTAT
* *
46654 ACATATTTTCAAAAATGTTTT--AAACTATATATTAT
1 ATATATTTTCAAAAACGTTTTAAAAACTATATATTAT
46689 ATATGTATTTTCAAAAAC
1 ATA--TATTTTCAAAAAC
46707 AATTTGCAAA
Statistics
Matches: 138, Mismatches: 18, Indels: 17
0.80 0.10 0.10
Matches are distributed among these distances:
35 15 0.11
36 37 0.27
37 54 0.39
38 22 0.16
39 3 0.02
40 7 0.05
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.45
Consensus pattern (37 bp):
ATATATTTTCAAAAACGTTTTAAAAACTATATATTAT
Found at i:46634 original size:126 final size:124
Alignment explanation
Indices: 46381--46631 Score: 475
Period size: 126 Copynumber: 2.0 Consensus size: 124
46371 TATATATTAT
46381 ATATATTTTCAAAATGGTTTTTAAAAATTATATTATATAAATGTTTTCATAACGTTTTCAAAAGT
1 ATATATTTTCAAAATGGTTTTTAAAAATTATATTATATAAATGTTTTCATAACGTTTTCAAAAGT
46446 ATATATTATATATATTTTAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
66 ATATATTATATATATTTTAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
46505 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAA
1 ATATATTTTCAAAATGGTTTTTAAAAA-T-TATATTATATAAATGTTTTCATAACGTTTTCAAAA
46570 GTATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
64 GTATATATTATATATATTTT-AAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
46632 TATTTTAAAA
Statistics
Matches: 124, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
124 27 0.22
125 1 0.01
126 55 0.44
127 41 0.33
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (124 bp):
ATATATTTTCAAAATGGTTTTTAAAAATTATATTATATAAATGTTTTCATAACGTTTTCAAAAGT
ATATATTATATATATTTTAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
Found at i:46718 original size:74 final size:71
Alignment explanation
Indices: 46566--46728 Score: 184
Period size: 74 Copynumber: 2.2 Consensus size: 71
46556 TAACGTTTTC
* * *
46566 AAAAGTATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAA
1 AAAACTATATAATATACATATTTTAAAAACGTTTT--AAAACTATATATTATATAATTTTCAAAA
* *
46631 ATATTTTA
64 ACAATTTA
*
46639 AAAACTATATAATATACATATTTTCAAAAATGTTTT-AAACTATATATTATATATGTATTTTCAA
1 AAAACTATATAATATACATATTTT-AAAAACGTTTTAAAACTATATATTATATA---ATTTTCAA
*
46703 AAACAATTTG
62 AAACAATTTA
* *
46713 CAAACTGTATAATATA
1 AAAACTATATAATATA
46729 TATGTGTATA
Statistics
Matches: 77, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
71 17 0.22
73 21 0.27
74 39 0.51
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (71 bp):
AAAACTATATAATATACATATTTTAAAAACGTTTTAAAACTATATATTATATAATTTTCAAAAAC
AATTTA
Found at i:46728 original size:37 final size:34
Alignment explanation
Indices: 46603--46729 Score: 101
Period size: 37 Copynumber: 3.5 Consensus size: 34
46593 AACGTTTTCA
* * *
46603 AAAACTATATATTATATAATTTTCAAAAATATTTT
1 AAAACTATATAATATATTATTTTCAAAAA-AATTT
* **
46638 AAAAACTATATAATATACATATTTTCAAAAATGTTT
1 -AAAACTATATAATATA-TTATTTTCAAAAAAATTT
*
46674 TAAACTATATATTATATATGTATTTTCAAAAACAATTT
1 AAAACTATATA--ATATAT-TATTTTCAAAAA-AATTT
* *
46712 GCAAACTGTATAATATAT
1 -AAAACTATATAATATAT
46730 ATGTGTATAT
Statistics
Matches: 74, Mismatches: 11, Indels: 11
0.77 0.11 0.11
Matches are distributed among these distances:
35 10 0.14
36 18 0.24
37 34 0.46
38 3 0.04
39 9 0.12
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (34 bp):
AAAACTATATAATATATTATTTTCAAAAAAATTT
Found at i:50066 original size:21 final size:22
Alignment explanation
Indices: 50030--50081 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
50020 TTAGAAATTC
*
50030 AAATTACAAAATTTAAAGA-TAA
1 AAATTACAAAAGTTAAA-ATTAA
50052 AAATTA-AAAAGTTAAAATTAA
1 AAATTACAAAAGTTAAAATTAA
*
50073 AAAATACAA
1 AAATTACAA
50082 TTAAATTTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 1 0.04
21 17 0.65
22 8 0.31
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.25
Consensus pattern (22 bp):
AAATTACAAAAGTTAAAATTAA
Found at i:50083 original size:13 final size:14
Alignment explanation
Indices: 50044--50086 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
50034 TACAAAATTT
50044 AAAGATAAAAATTAA
1 AAAGAT-AAAATTAA
*
50059 AAAGTTAAAATTAA
1 AAAGATAAAATTAA
*
50073 AAA-ATACAATTAA
1 AAAGATAAAATTAA
50086 A
1 A
50087 TTTAGAGTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 9 0.36
14 11 0.44
15 5 0.20
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (14 bp):
AAAGATAAAATTAA
Done.