Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005136.1 Hibiscus syriacus cultivar Beakdansim tig00011560_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: 52697
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:2023 original size:13 final size:13
Alignment explanation
Indices: 2005--2033 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1995 GATTAATGTA
2005 AAAATAAGTGTTT
1 AAAATAAGTGTTT
2018 AAAATAAGTGTTT
1 AAAATAAGTGTTT
2031 AAA
1 AAA
2034 TTATATTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (13 bp):
AAAATAAGTGTTT
Found at i:10135 original size:2 final size:2
Alignment explanation
Indices: 10128--10171 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
10118 ATAAGATAGA
10128 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10170 AT
1 AT
10172 TATTAGAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14874 original size:20 final size:20
Alignment explanation
Indices: 14849--14901 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
14839 CACCGGTCAG
* *
14849 CCACCGCTTCCGGGCTCTGA
1 CCACCGCTGCCGGGCTCCGA
*
14869 CCACCGCTGCCAGGCTCCGA
1 CCACCGCTGCCGGGCTCCGA
14889 CCACCGCTGCCGG
1 CCACCGCTGCCGG
14902 CCACCGTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.11, C:0.49, G:0.26, T:0.13
Consensus pattern (20 bp):
CCACCGCTGCCGGGCTCCGA
Found at i:15656 original size:3 final size:3
Alignment explanation
Indices: 15650--15719 Score: 72
Period size: 3 Copynumber: 23.7 Consensus size: 3
15640 TAATATTTAT
* * * *
15650 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TTA TTA TTA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
15697 TTA TAA TAA TAA T-A TAAA TAA TA
1 TAA TAA TAA TAA TAA T-AA TAA TA
15720 TTTAAATGAA
Statistics
Matches: 62, Mismatches: 2, Indels: 6
0.89 0.03 0.09
Matches are distributed among these distances:
2 4 0.06
3 56 0.90
4 2 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:15689 original size:39 final size:39
Alignment explanation
Indices: 15637--15719 Score: 105
Period size: 39 Copynumber: 2.1 Consensus size: 39
15627 TTTGGGCCTG
*
15637 TAATAATATTTATTAATAATAAAATAATAATAATA-ATAA
1 TAATAATAATTATTAATAATAAAATAATAATAATATA-AA
* * **
15676 TAATAATAATTATTATTATTATTATAATAATAATATAAA
1 TAATAATAATTATTAATAATAAAATAATAATAATATAAA
15715 TAATA
1 TAATA
15720 TTTAAATGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
39 37 0.97
40 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (39 bp):
TAATAATAATTATTAATAATAAAATAATAATAATATAAA
Found at i:16072 original size:113 final size:113
Alignment explanation
Indices: 15940--16804 Score: 1457
Period size: 113 Copynumber: 7.6 Consensus size: 113
15930 GTAATCTAGC
* **
15940 AAAGGTTGAATAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
16005 ATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTTAAGCA
66 ATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTTAAGCA
16053 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
** * * * *
16118 ATGAACTCGAC-CTGGCAATGCTGATCCATTGAA-TGATGAATTTAAGCAA
66 ATGAACT-TTCTCTGGAAAAGTTGATCCA-TCAAGTGATGAATTTAAGC-A
16167 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
16232 ATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTTAAGCA
66 ATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTTAAGCA
*
16280 AAAGGTTGAACAAATTCTTCTCATTATGGACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
16345 ATAAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATGTAAGCA
66 ATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTTAAGCA
*
16393 AAAGGTTGAACAAATTTTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
16458 ATGAACTTGAC-CTGGTAATGTTGATCCATCAAGTGATGAATTTAAGCA
66 ATGAACTT-TCTCTGGAAAAGTTGATCCATCAAGTGATGAATTTAAGCA
*
16506 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCATATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * * *
16571 ATGAACTTTCTATAGAAAAATTGATCCATTAAGTGATGAATGTAAGCA
66 ATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTTAAGCA
*
16619 AAAGGTTTGAACAAATTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAGG-TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
16684 TATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTTAAGCA
65 TATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTTAAGCA
16733 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
16798 ATGAACT
66 ATGAACT
16805 CGACCTGGTA
Statistics
Matches: 701, Mismatches: 43, Indels: 16
0.92 0.06 0.02
Matches are distributed among these distances:
112 1 0.00
113 488 0.70
114 212 0.30
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.38
Consensus pattern (113 bp):
AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTTAAGCA
Found at i:16485 original size:340 final size:339
Alignment explanation
Indices: 15940--16842 Score: 1610
Period size: 340 Copynumber: 2.7 Consensus size: 339
15930 GTAATCTAGC
* **
15940 AAAGGTTGAATAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
16005 ATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTTAAGCAAAAGGTTGAACAAATTC
66 ATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTTAAGCAAAAGGTTGAACAAATTC
*
16070 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGCA
131 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGTA
*
16135 ATGCTGATCCATTGAATGATGAATTTAAGCAAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
196 ATGTTGATCCATTGAATGATGAATTTAAGC-AAAAGGTTGAACAAATTCTTCTCATTATGAACTT
* * *
16200 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATCAAG
260 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTATAGAAAAATTGATCCATCAAG
*
16265 TGATGAATTTAAGCA
325 TGATGAATGTAAGCA
*
16280 AAAGGTTGAACAAATTCTTCTCATTATGGACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
16345 ATAAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATGTAAGCAAAAGGTTGAACAAATTT
66 ATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTTAAGCAAAAGGTTGAACAAATTC
*
16410 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTGACCTGGTA
131 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGTA
*
16475 ATGTTGATCCA-TCAAGTGATGAATTTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
196 ATGTTGATCCATTGAA-TGATGAATTTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
* *
16539 CTTCTTCCTTCTTCATATGAGTTCTTCTCATTATGAACTTTCTATAGAAAAATTGATCCATTAAG
260 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTATAGAAAAATTGATCCATCAAG
16604 TGATGAATGTAAGCA
325 TGATGAATGTAAGCA
*
16619 AAAGGTTTGAACAAATTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAGG-TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
16684 TATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTTAAGCAAAAGGTTGAACAAATT
65 TATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTTAAGCAAAAGGTTGAACAAATT
16749 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGT
130 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGT
16814 AATGTTGATCCATTGAATGATGAATTTAA
195 AATGTTGATCCATTGAATGATGAATTTAA
16843 ACTTTGCTAA
Statistics
Matches: 536, Mismatches: 24, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
339 116 0.22
340 417 0.78
341 3 0.01
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.38
Consensus pattern (339 bp):
AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTTAAGCAAAAGGTTGAACAAATTC
TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGTA
ATGTTGATCCATTGAATGATGAATTTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTATAGAAAAATTGATCCATCAAGT
GATGAATGTAAGCA
Found at i:16557 original size:24 final size:23
Alignment explanation
Indices: 16522--16566 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
16512 TGAACAAATT
16522 CTTCTCATTATGAACTTCTTCTTC
1 CTTCTCATTATG-ACTTCTTCTTC
*
16546 CTTCTTCA-TATGAGTTCTTCT
1 CTTC-TCATTATGACTTCTTCT
16567 CATTATGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 8 0.42
24 8 0.42
25 3 0.16
ACGTcount: A:0.16, C:0.27, G:0.07, T:0.51
Consensus pattern (23 bp):
CTTCTCATTATGACTTCTTCTTC
Found at i:16704 original size:453 final size:452
Alignment explanation
Indices: 15957--16804 Score: 1488
Period size: 453 Copynumber: 1.9 Consensus size: 452
15947 GAATAAGCTC
*
15957 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
1 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTACTCTGGAA
16022 AAGTTGATCCATCAAGTGATGAATTTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
66 AAGTTGATCCATCAAGTGATGAATTTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
* * **
16087 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGCAATGCTGATCCATTGAAT
131 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGA-CTAGAAAAACTGATCCATTGAAT
* *
16152 GATGAATTTAAGCAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
195 GATGAATGTAAGCAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGA
16217 TGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTTAAGCAAA
260 TGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTTAAGCAAA
*
16282 AGGTTGAACAAATTCTTCTCATTATGGACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTAT
325 AGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTAT
16347 AAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATGTAAGCAAAAGGTTGAACAAATTT
390 AAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATGTAAGCAAAAGGTTGAACAAATTT
*
16410 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTGAC-CTGGT
1 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTT-ACTCTGGA
*
16474 AATGTTGATCCATCAAGTGATGAATTTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
65 AAAGTTGATCCATCAAGTGATGAATTTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
* * *
16539 CTTCTTCCTTCTTCATATGAGTTCTTCTCATTATGAACTTTCTA-TAGAAAAATTGATCCATT-A
130 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC--TCGACTAGAAAAACTGATCCATTGA
16602 AGTGATGAATGTAAGC-AAAAGGTTTGAACAAATTCTTCTCATTATGAACTTCTTATTCCTTCTT
193 A-TGATGAATGTAAGCAAAAAGG-TTGAACAAATTCTTCTCATTATGAACTTCTTATTCCTTCTT
16666 CAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTTAAG
256 CAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTTAAG
16731 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
321 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
16796 TTATGAACT
386 TTATAAACT
16805 CGACCTGGTA
Statistics
Matches: 376, Mismatches: 14, Indels: 10
0.94 0.04 0.03
Matches are distributed among these distances:
452 8 0.02
453 364 0.97
454 1 0.00
455 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.39
Consensus pattern (452 bp):
TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTACTCTGGAA
AAGTTGATCCATCAAGTGATGAATTTAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTC
TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACTAGAAAAACTGATCCATTGAATG
ATGAATGTAAGCAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGAT
GAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTTAAGCAAAA
GGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATA
AACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATGTAAGCAAAAGGTTGAACAAATTT
Found at i:17267 original size:22 final size:22
Alignment explanation
Indices: 17242--17296 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
17232 GATAAAGCTT
* *
17242 TCATCTTTGAAAAGAGAATTTG
1 TCATCTTTGAAAAGAGAATCTA
* *
17264 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
17286 TCATCTTTGAA
1 TCATCTTTGAA
17297 GAGTGTAGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:17737 original size:50 final size:48
Alignment explanation
Indices: 17683--17791 Score: 108
Period size: 40 Copynumber: 2.4 Consensus size: 48
17673 TCTTCATCTC
17683 ATGTGGTTTCAGCTCAGATGTAAAACACTTGACAACACATTCATCCTTTT
1 ATGTGG-TTC-GCTCAGATGTAAAACACTTGACAACACATTCATCCTTTT
*
17733 ATGT-G---G----GATGTAAAACACTTGACAACATATTCATCCTTTT
1 ATGTGGTTCGCTCAGATGTAAAACACTTGACAACACATTCATCCTTTT
*
17773 CTGTGGCTTCTGCTCAGAT
1 ATGTGG-TTC-GCTCAGAT
17792 TTCTCAATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 20
0.68 0.03 0.29
Matches are distributed among these distances:
40 36 0.77
41 1 0.02
44 1 0.02
46 1 0.02
49 1 0.02
50 7 0.15
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.35
Consensus pattern (48 bp):
ATGTGGTTCGCTCAGATGTAAAACACTTGACAACACATTCATCCTTTT
Found at i:17754 original size:40 final size:40
Alignment explanation
Indices: 17699--17778 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
17689 TTTCAGCTCA
17699 GATGTAAAACACTTGACAACACATTCATCCTTTTATGTGG
1 GATGTAAAACACTTGACAACACATTCATCCTTTTATGTGG
* *
17739 GATGTAAAACACTTGACAACATATTCATCCTTTTCTGTGG
1 GATGTAAAACACTTGACAACACATTCATCCTTTTATGTGG
17779 CTTCTGCTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (40 bp):
GATGTAAAACACTTGACAACACATTCATCCTTTTATGTGG
Found at i:20073 original size:115 final size:114
Alignment explanation
Indices: 19904--20130 Score: 357
Period size: 115 Copynumber: 2.0 Consensus size: 114
19894 GATCATGCAG
* * * *
19904 TTCATCTTTTAATTCCAATGATTGGTTCTGTGGTTCCTACCGAACCAGATCAGATAACTCAAAAA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAAA
*
19969 ACATTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
*
20018 TTCATCTTTCAAATCCAATGATTGGTT-TTTAGGGTTCATACCAAACCAGATCAGATAACTCAAA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGT--GGTTCATACCAAACCAGATCAGATAACTCAAA
* *
20082 GAACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCA
64 AAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCA
20131 CATGGCACTT
Statistics
Matches: 103, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
113 2 0.02
114 25 0.24
115 76 0.74
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAAA
ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
Found at i:22301 original size:16 final size:16
Alignment explanation
Indices: 22280--22333 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 16
22270 CCCTTCTTCT
22280 TTTTTCCTTTTTTTTC
1 TTTTTCCTTTTTTTTC
* *
22296 TTTTTCCTCATTTTTCC
1 TTTTTCCT-TTTTTTTC
22313 TTTTTCATCTTTTTTTTC
1 TTTTTC--CTTTTTTTTC
22331 TTT
1 TTT
22334 CTTTGCTGGA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
16 8 0.26
17 12 0.39
18 9 0.29
19 2 0.06
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTCCTTTTTTTTC
Found at i:23305 original size:18 final size:18
Alignment explanation
Indices: 23268--23305 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
23258 TGATTGGAAG
23268 TTTGGTTTATTTGAGGTTT
1 TTTGGTTTA-TTGAGGTTT
23287 TTTGGTTTA-TGATGGTTT
1 TTTGGTTTATTGA-GGTTT
23305 T
1 T
23306 GTGTTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 3 0.17
18 6 0.33
19 9 0.50
ACGTcount: A:0.11, C:0.00, G:0.26, T:0.63
Consensus pattern (18 bp):
TTTGGTTTATTGAGGTTT
Found at i:25956 original size:14 final size:14
Alignment explanation
Indices: 25914--25956 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
25904 CAAAGATGCC
*
25914 AAATGCAAATGTAA
1 AAATGTAAATGTAA
* * *
25928 ATATGTGAATATAA
1 AAATGTAAATGTAA
25942 AAATGTAAATGTAA
1 AAATGTAAATGTAA
25956 A
1 A
25957 TTATTTAAAA
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.56, C:0.02, G:0.14, T:0.28
Consensus pattern (14 bp):
AAATGTAAATGTAA
Found at i:27529 original size:13 final size:13
Alignment explanation
Indices: 27513--27565 Score: 61
Period size: 14 Copynumber: 3.9 Consensus size: 13
27503 TTAATACTTG
*
27513 AATAAAATAAATA
1 AATAAAAAAAATA
27526 AATAAAAAAAATA
1 AATAAAAAAAATA
*
27539 ATATAAAAATAATA
1 A-ATAAAAAAAATA
*
27553 AGTAATAAAAAAT
1 AATAA-AAAAAAT
27566 TTGAAAGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
13 16 0.47
14 18 0.53
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (13 bp):
AATAAAAAAAATA
Found at i:27544 original size:14 final size:14
Alignment explanation
Indices: 27514--27564 Score: 59
Period size: 13 Copynumber: 3.6 Consensus size: 14
27504 TAATACTTGA
*
27514 ATAAAATAAATAA-
1 ATAAAAAAAATAAT
27527 ATAAAAAAAATAAT
1 ATAAAAAAAATAAT
*
27541 ATAAAAATAATAAGT
1 ATAAAAAAAATAA-T
27556 AATAAAAAA
1 -ATAAAAAA
27565 TTTGAAAGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
13 12 0.38
14 12 0.38
15 1 0.03
16 7 0.22
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (14 bp):
ATAAAAAAAATAAT
Found at i:33353 original size:36 final size:35
Alignment explanation
Indices: 33255--33367 Score: 145
Period size: 35 Copynumber: 3.2 Consensus size: 35
33245 TCTAAACCTT
* *
33255 AAATTGAAGTATTTTAGAATTTGGGGTTTAAAATT
1 AAATTGAATTATTTTAGAATTTGGGGTTTAAAATG
* * *
33290 TAATTGAATTATTTTAGAATTTAGGGTTTAGAATG
1 AAATTGAATTATTTTAGAATTTGGGGTTTAAAATG
* * *
33325 AAAATTGAATTACTTTGGAAATTGGGGTTTAAAATG
1 -AAATTGAATTATTTTAGAATTTGGGGTTTAAAATG
33361 AAATTGA
1 AAATTGA
33368 GGACTATTTT
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
35 37 0.56
36 29 0.44
ACGTcount: A:0.38, C:0.01, G:0.20, T:0.41
Consensus pattern (35 bp):
AAATTGAATTATTTTAGAATTTGGGGTTTAAAATG
Found at i:34834 original size:21 final size:21
Alignment explanation
Indices: 34808--34946 Score: 137
Period size: 21 Copynumber: 6.8 Consensus size: 21
34798 GGTAGAGCAC
*
34808 TACCTAAAATGTTAATTTTGT
1 TACCTAAAATGTTAATTTCGT
34829 TACCTAAAATGTTAATTTCGT
1 TACCTAAAATGTTAATTTCGT
*
34850 TACCTATAATGTTAATCTT--T
1 TACCTAAAATGTTAAT-TTCGT
** ** * *
34870 T---TAACGT-TTCCGGTTGCGC
1 TACCTAAAATGTT--AATTTCGT
34889 TACCTAAAATGTTAATTTCGT
1 TACCTAAAATGTTAATTTCGT
34910 TACCTAAAATGTTAATTTCGT
1 TACCTAAAATGTTAATTTCGT
34931 TACCTAAAATGTTAAT
1 TACCTAAAATGTTAAT
34947 CTTTTTAACG
Statistics
Matches: 94, Mismatches: 15, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
16 2 0.02
17 4 0.04
18 1 0.01
19 1 0.01
20 2 0.02
21 76 0.81
22 6 0.06
23 2 0.02
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (21 bp):
TACCTAAAATGTTAATTTCGT
Found at i:34903 original size:81 final size:81
Alignment explanation
Indices: 34807--34967 Score: 304
Period size: 81 Copynumber: 2.0 Consensus size: 81
34797 TGGTAGAGCA
* *
34807 CTACCTAAAATGTTAATTTTGTTACCTAAAATGTTAATTTCGTTACCTATAATGTTAATCTTTTT
1 CTACCTAAAATGTTAATTTCGTTACCTAAAATGTTAATTTCGTTACCTAAAATGTTAATCTTTTT
34872 AACGTTTCCGGTTGCG
66 AACGTTTCCGGTTGCG
34888 CTACCTAAAATGTTAATTTCGTTACCTAAAATGTTAATTTCGTTACCTAAAATGTTAATCTTTTT
1 CTACCTAAAATGTTAATTTCGTTACCTAAAATGTTAATTTCGTTACCTAAAATGTTAATCTTTTT
34953 AACGTTTCCGGTTGC
66 AACGTTTCCGGTTGC
34968 AACCGGAAAT
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
81 78 1.00
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.43
Consensus pattern (81 bp):
CTACCTAAAATGTTAATTTCGTTACCTAAAATGTTAATTTCGTTACCTAAAATGTTAATCTTTTT
AACGTTTCCGGTTGCG
Found at i:35167 original size:27 final size:27
Alignment explanation
Indices: 35137--35193 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
35127 ATGGCTATGG
35137 AAATAAAT-GAAAGCTATGGAAAGAAAT
1 AAATAAATCGAAA-CTATGGAAAGAAAT
* * **
35164 AAATGAGTCTTAACTATGGAAAGAAAT
1 AAATAAATCGAAACTATGGAAAGAAAT
35191 AAA
1 AAA
35194 AGCTATGGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
27 23 0.92
28 2 0.08
ACGTcount: A:0.56, C:0.05, G:0.18, T:0.21
Consensus pattern (27 bp):
AAATAAATCGAAACTATGGAAAGAAAT
Found at i:45038 original size:13 final size:13
Alignment explanation
Indices: 45020--45044 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45010 ATAGTTAATA
45020 TAAAAATAATAAC
1 TAAAAATAATAAC
45033 TAAAAATAATAA
1 TAAAAATAATAA
45045 TAATAATTAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAAAATAATAAC
Found at i:45784 original size:2 final size:2
Alignment explanation
Indices: 45779--45816 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
45769 AAGCGCGCAC
45779 AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45817 TTTTAAATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:47889 original size:12 final size:12
Alignment explanation
Indices: 47872--47899 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
47862 TACGAAAATT
47872 AAAAAATTTAAA
1 AAAAAATTTAAA
47884 AAAAAATTTAAA
1 AAAAAATTTAAA
47896 AAAA
1 AAAA
47900 TTTAATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (12 bp):
AAAAAATTTAAA
Found at i:49932 original size:12 final size:11
Alignment explanation
Indices: 49914--49946 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
49904 TACGAAAATT
49914 AAAAAATTTAA
1 AAAAAATTTAA
49925 ATAAAAATTT-A
1 A-AAAAATTTAA
49936 AAAAAATTTAA
1 AAAAAATTTAA
49947 TTTTAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 8 0.40
11 4 0.20
12 8 0.40
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
AAAAAATTTAA
Done.