Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005400.1 Hibiscus syriacus cultivar Beakdansim tig00012375_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: 54661
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1220 original size:27 final size:27
Alignment explanation
Indices: 1182--1238 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
1172 ATCAACCTAC
1182 ATATATAATGATATTTGTATAACTCAA
1 ATATATAATGATATTTGTATAACTCAA
1209 ATATATAATGATATTTGTATAACTCAA
1 ATATATAATGATATTTGTATAACTCAA
1236 ATA
1 ATA
1239 GTGAAACTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.40
Consensus pattern (27 bp):
ATATATAATGATATTTGTATAACTCAA
Found at i:3042 original size:21 final size:22
Alignment explanation
Indices: 3000--3051 Score: 72
Period size: 21 Copynumber: 2.4 Consensus size: 22
2990 AAATGTAAAA
3000 TATAATAAA-TAATATTATTTAT
1 TATAA-AAATTAATATTATTTAT
3022 TATAAAAATTAATATTA-TTAT
1 TATAAAAATTAATATTATTTAT
*
3043 TTTAAAAAT
1 TATAAAAAT
3052 ATTAGAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 15 0.54
22 13 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TATAAAAATTAATATTATTTAT
Found at i:3455 original size:25 final size:25
Alignment explanation
Indices: 3403--3490 Score: 81
Period size: 25 Copynumber: 3.6 Consensus size: 25
3393 TAACAGTATC
* *
3403 ATATATTATTATAAT-ATAAT-TGA
1 ATATATTATTTTAATAATAATATTA
*
3426 GTATATTATTTTAATAATAATATTA
1 ATATATTATTTTAATAATAATATTA
* * * *
3451 TTATATTATATTATTAAAAATATTA
1 ATATATTATTTTAATAATAATATTA
*
3476 ATAAATATATTTTAA
1 ATATAT-TATTTTAA
3491 ATATGTTAAT
Statistics
Matches: 51, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
23 13 0.25
24 5 0.10
25 27 0.53
26 6 0.12
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (25 bp):
ATATATTATTTTAATAATAATATTA
Found at i:3499 original size:23 final size:23
Alignment explanation
Indices: 3457--3512 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
3447 ATTATTATAT
3457 TATATTATTAAAAATATTAATAAA
1 TATATT-TTAAAAATATTAATAAA
* * *
3481 TATATTTTAAATATGTTAATAAT
1 TATATTTTAAAAATATTAATAAA
3504 TAATATTTT
1 T-ATATTTT
3513 TATTAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 15 0.54
24 13 0.46
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATAAA
Found at i:7082 original size:19 final size:19
Alignment explanation
Indices: 7055--7091 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
7045 ATGTTGCCAA
7055 GGGACTAATTGTATACTTG
1 GGGACTAATTGTATACTTG
*
7074 GGGATTAATTGTATACTT
1 GGGACTAATTGTATACTT
7092 AGATATTGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.27, C:0.08, G:0.24, T:0.41
Consensus pattern (19 bp):
GGGACTAATTGTATACTTG
Found at i:8789 original size:22 final size:22
Alignment explanation
Indices: 8764--8809 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
8754 GTTTACAAAT
*
8764 AGGGAATCGATTCCCCTGCTAC
1 AGGGAACCGATTCCCCTGCTAC
8786 AGGGAACCGATTCCCCTGCTAC
1 AGGGAACCGATTCCCCTGCTAC
8808 AG
1 AG
8810 TACTGCCGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.24, C:0.33, G:0.24, T:0.20
Consensus pattern (22 bp):
AGGGAACCGATTCCCCTGCTAC
Found at i:9338 original size:22 final size:21
Alignment explanation
Indices: 9312--9375 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
9302 CATATGAAAT
*
9312 TTGTCCCGAAGGACCTGTGAA
1 TTGTCCCGAAGGACCTATGAA
*
9333 TATGTCCCGAAGGACCTATGAG
1 T-TGTCCCGAAGGACCTATGAA
*
9355 TTATCCCGAAGGACCTATGAA
1 TTGTCCCGAAGGACCTATGAA
9376 ACCCTCGACT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
21 19 0.50
22 19 0.50
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.23
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATGAA
Found at i:15655 original size:22 final size:22
Alignment explanation
Indices: 15630--15674 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
15620 GTTTACAAAT
*
15630 AGGGAATCGATTCCCCTACTAC
1 AGGGAACCGATTCCCCTACTAC
*
15652 AGGGAACCGATTCCCCTGCTAC
1 AGGGAACCGATTCCCCTACTAC
15674 A
1 A
15675 ATACTGGTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.27, C:0.33, G:0.20, T:0.20
Consensus pattern (22 bp):
AGGGAACCGATTCCCCTACTAC
Found at i:16237 original size:21 final size:21
Alignment explanation
Indices: 16188--16251 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
16178 CATATGAAAT
*
16188 TTGTCCCGAAGGACCTGTGAA
1 TTGTCCCGAAGGACCTATGAA
* *
16209 TATGTCCCGAATGACCTATGAG
1 T-TGTCCCGAAGGACCTATGAA
16231 TTGTCCCGAAGGACCTATGAA
1 TTGTCCCGAAGGACCTATGAA
16252 ACCCTCGACT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 19 0.51
22 18 0.49
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATGAA
Found at i:17688 original size:22 final size:22
Alignment explanation
Indices: 17663--17705 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
17653 TGAATCGACT
17663 TGTTGA-TCATTAATATGTTGAC
1 TGTTGACTCATTAA-ATGTTGAC
17685 TGTTGACTCATTAAATGTTGA
1 TGTTGACTCATTAAATGTTGA
17706 TTATTGATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.44
Consensus pattern (22 bp):
TGTTGACTCATTAAATGTTGAC
Found at i:17712 original size:22 final size:22
Alignment explanation
Indices: 17665--17713 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
17655 AATCGACTTG
*
17665 TTGATCATTAATATGTTGACTG
1 TTGATCATTAATATGTTGACTA
*
17687 TTGACTCATTAA-ATGTTGATTA
1 TTGA-TCATTAATATGTTGACTA
17709 TTGAT
1 TTGAT
17714 TGTTGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 16 0.67
23 7 0.29
ACGTcount: A:0.29, C:0.08, G:0.16, T:0.47
Consensus pattern (22 bp):
TTGATCATTAATATGTTGACTA
Found at i:17932 original size:3 final size:3
Alignment explanation
Indices: 17920--18009 Score: 108
Period size: 3 Copynumber: 28.7 Consensus size: 3
17910 TTTTTCATTC
* * *
17920 TAT TATT TAT TAT TAT TAT TAT TAT TAT TAT TAAA TAA AAT ATAT TAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT -TAT TAT
*
17968 TAT TAT TAT TAT TAT TAT TCT ATAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TA
18010 AATAAAAAAT
Statistics
Matches: 77, Mismatches: 6, Indels: 8
0.85 0.07 0.09
Matches are distributed among these distances:
3 68 0.88
4 9 0.12
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:20390 original size:28 final size:26
Alignment explanation
Indices: 20359--20429 Score: 72
Period size: 30 Copynumber: 2.6 Consensus size: 26
20349 TAATTCTTTC
20359 TTTTCAAAATTTTTATATATACTTATT
1 TTTTCAAAATTTTTATATATA-TTATT
* *
20386 ATTTTCATAATATTTATATGTATATTATT
1 -TTTTCA-AA-ATTTTTATATATATTATT
*
20415 TTTT-AATATTTTTAT
1 TTTTCAAAATTTTTAT
20430 TTTATTTTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
25 7 0.19
26 1 0.03
27 1 0.03
28 10 0.27
29 7 0.19
30 11 0.30
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.62
Consensus pattern (26 bp):
TTTTCAAAATTTTTATATATATTATT
Found at i:20411 original size:26 final size:27
Alignment explanation
Indices: 20359--20425 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 27
20349 TAATTCTTTC
* *
20359 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCATAATATTTATATATAC-TATTA
*
20387 TTTTCATAATATTTATATGTA-TATTA
1 TTTTCATAATATTTATATATACTATTA
*
20413 TTTT-TTAATATTT
1 TTTTCATAATATTT
20426 TTATTTTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
25 8 0.23
26 9 0.26
28 18 0.51
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.61
Consensus pattern (27 bp):
TTTTCATAATATTTATATATACTATTA
Found at i:20926 original size:9 final size:9
Alignment explanation
Indices: 20896--20920 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
20886 AACTTTTTGT
20896 TTTTTTAAA
1 TTTTTTAAA
20905 TTTTTTAAA
1 TTTTTTAAA
20914 TTTTTTA
1 TTTTTTA
20921 TTTTTTCTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (9 bp):
TTTTTTAAA
Found at i:25647 original size:11 final size:11
Alignment explanation
Indices: 25631--25678 Score: 68
Period size: 11 Copynumber: 4.7 Consensus size: 11
25621 TATTATACTT
25631 GAAAAAAAAAG
1 GAAAAAAAAAG
25642 G-AAAAAAAAG
1 GAAAAAAAAAG
25652 G---AAAAAAG
1 GAAAAAAAAAG
25660 GAAAAAAAAAG
1 GAAAAAAAAAG
25671 GAAAAAAA
1 GAAAAAAA
25679 GGAAAAATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
8 8 0.24
10 10 0.29
11 16 0.47
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (11 bp):
GAAAAAAAAAG
Found at i:25648 original size:8 final size:8
Alignment explanation
Indices: 25635--25700 Score: 51
Period size: 8 Copynumber: 7.4 Consensus size: 8
25625 ATACTTGAAA
25635 AAAAAAGG
1 AAAAAAGG
25643 AAAAAAAAGG
1 --AAAAAAGG
25653 AAAAAAGG
1 AAAAAAGG
25661 AAAAAAAAAGG
1 ---AAAAAAGG
25672 AAAAAAAGG
1 -AAAAAAGG
* *
25681 AAAAATGA
1 AAAAAAGG
25689 AAAAAAGAG
1 AAAAAAG-G
25698 AAA
1 AAA
25701 GAATTAAACC
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
8 20 0.42
9 12 0.25
10 8 0.17
11 8 0.17
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.02
Consensus pattern (8 bp):
AAAAAAGG
Found at i:25658 original size:19 final size:19
Alignment explanation
Indices: 25634--25685 Score: 88
Period size: 19 Copynumber: 2.7 Consensus size: 19
25624 TATACTTGAA
25634 AAAAAAAGGAAAAAAAAGG
1 AAAAAAAGGAAAAAAAAGG
25653 -AAAAAAGGAAAAAAAAAGG
1 AAAAAAAGG-AAAAAAAAGG
25672 AAAAAAAGGAAAAA
1 AAAAAAAGGAAAAA
25686 TGAAAAAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.26
19 15 0.48
20 8 0.26
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (19 bp):
AAAAAAAGGAAAAAAAAGG
Found at i:25675 original size:28 final size:28
Alignment explanation
Indices: 25631--25694 Score: 103
Period size: 27 Copynumber: 2.3 Consensus size: 28
25621 TATTATACTT
25631 GAAAAAAAAAGGAAAAAAAAGGAAAAAAG
1 GAAAAAAAAAGGAAAAAAAAGG-AAAAAG
*
25660 GAAAAAAAAAGG-AAAAAAAGGAAAAAT
1 GAAAAAAAAAGGAAAAAAAAGGAAAAAG
25687 GAAAAAAA
1 GAAAAAAA
25695 GAGAAAGAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
27 13 0.38
28 9 0.26
29 12 0.35
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.02
Consensus pattern (28 bp):
GAAAAAAAAAGGAAAAAAAAGGAAAAAG
Found at i:25694 original size:10 final size:10
Alignment explanation
Indices: 25633--25685 Score: 76
Period size: 10 Copynumber: 5.5 Consensus size: 10
25623 TTATACTTGA
25633 AAAAAAAAGG
1 AAAAAAAAGG
25643 AAAAAAAAGG
1 AAAAAAAAGG
25653 --AAAAAAGG
1 AAAAAAAAGG
25661 AAAAAAAAAGG
1 -AAAAAAAAGG
25672 -AAAAAAAGG
1 AAAAAAAAGG
25681 AAAAA
1 AAAAA
25686 TGAAAAAAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
8 8 0.21
9 9 0.23
10 14 0.36
11 8 0.21
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGG
Found at i:25700 original size:10 final size:9
Alignment explanation
Indices: 25634--25685 Score: 70
Period size: 9 Copynumber: 5.6 Consensus size: 9
25624 TATACTTGAA
25634 AAAAAAAGG
1 AAAAAAAGG
25643 AAAAAAAAGG
1 -AAAAAAAGG
25653 -AAAAAAGG
1 AAAAAAAGG
25661 AAAAAAAAAGG
1 --AAAAAAAGG
25672 AAAAAAAGG
1 AAAAAAAGG
25681 AAAAA
1 AAAAA
25686 TGAAAAAAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
8 8 0.21
9 14 0.36
10 9 0.23
11 8 0.21
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (9 bp):
AAAAAAAGG
Found at i:29084 original size:74 final size:75
Alignment explanation
Indices: 28927--29098 Score: 184
Period size: 74 Copynumber: 2.3 Consensus size: 75
28917 ATTAACAAGA
* * * * * * * *
28927 AGCAAATGCTAGGGCATACTAAAAGCCCCTCTCAATCAGAATCATGAATGTTGATGTATTTTGAA
1 AGCAAATGTTGGGGCATGCTGAAAGCCCCTCTCAATCAGAATAAAGAATGTTGACGCATTTTGAA
*
28992 CATTTATATC
66 CACTTATATC
* *
29002 AGTAAATGTTGGGGCATGCTGAAAG-CCCTTTCAATCAGAATAAAGAATGTTGACGCATTTTGAA
1 AGCAAATGTTGGGGCATGCTGAAAGCCCCTCTCAATCAGAATAAAGAATGTTGACGCATTTTGAA
** * *
29066 TGCTTGTATT
66 CACTTATATC
* *
29076 AGCCAATGTTGGGGCATGTTGAA
1 AGCAAATGTTGGGGCATGCTGAA
29099 GGCCTATATC
Statistics
Matches: 79, Mismatches: 18, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
74 59 0.75
75 20 0.25
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.31
Consensus pattern (75 bp):
AGCAAATGTTGGGGCATGCTGAAAGCCCCTCTCAATCAGAATAAAGAATGTTGACGCATTTTGAA
CACTTATATC
Found at i:30407 original size:22 final size:22
Alignment explanation
Indices: 30378--30432 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
30368 ATCTACACTC
* *
30378 TTCAAAGATGATATATTCTCTT
1 TTCAAAGATGATAGATTCTATT
*
30400 TTTAAAGATGATAGATTCTATT
1 TTCAAAGATGATAGATTCTATT
30422 TTCAAAGATGA
1 TTCAAAGATGA
30433 AAGCTTTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTATT
Found at i:31197 original size:45 final size:46
Alignment explanation
Indices: 31097--31233 Score: 195
Period size: 45 Copynumber: 3.0 Consensus size: 46
31087 CTATTTCCCA
* * *
31097 CATCTGTAAGTCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTTGGGT
*
31143 CATCTGTAAGCCCTTCAGTGCATGATGCTTTC-AAAACCTTTGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTTGGGT
* * *
31188 CATCCGTAAGCCCTGCAGTGCAGGATGTTTTCAAAAAGCCTTTGGG
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAA-CCTTTGGG
31234 AGCTTTTTGA
Statistics
Matches: 81, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
45 40 0.49
46 33 0.41
47 8 0.10
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.32
Consensus pattern (46 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTTGGGT
Found at i:31364 original size:45 final size:46
Alignment explanation
Indices: 31241--31400 Score: 198
Period size: 45 Copynumber: 3.5 Consensus size: 46
31231 GGGAGCTTTT
* * * * * *
31241 TGATATTTTC-AAAGCCTTCGGGTTATCTGTAAGTCCTTCAGTGCT
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTCCAGTGCA
*
31286 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTCCAATGCA
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTCCAGTGCA
* * *
31332 TGATGCTTTC-AAAACCTTCGGGTCATCCGTAAGCCCTGCAGTGCA
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTCCAGTGCA
*
31377 GGATGTTTTCAAAAAGCCTTCGGG
1 TGATGTTTTCAAAAA-CCTTCGGG
31401 AGCTTTTTGA
Statistics
Matches: 99, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
45 49 0.49
46 42 0.42
47 8 0.08
ACGTcount: A:0.23, C:0.24, G:0.21, T:0.32
Consensus pattern (46 bp):
TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTCCAGTGCA
Found at i:31374 original size:167 final size:167
Alignment explanation
Indices: 31097--31631 Score: 971
Period size: 167 Copynumber: 3.2 Consensus size: 167
31087 CTATTTCCCA
31097 CATCTGTAAGTCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
1 CATCTGTAAGTCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
*
31162 GCATGATGCTTTCAAAACCTTTGGGTCATCCGTAAGCCCTGCAGTGCAGGATGTTTTCAAAAAGC
66 GCATGATGCTTTCAAAACCTTCGGGTCATCCGTAAGCCCTGCAGTGCAGGATGTTTTCAAAAAGC
*
31227 CTTTGGGAGCTTTTTGATATTTTCAAAGCCTTCGGGT
131 CTTCGGGAGCTTTTTGATATTTTCAAAGCCTTCGGGT
* * *
31264 TATCTGTAAGTCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTCCAAT
1 CATCTGTAAGTCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
31329 GCATGATGCTTTCAAAACCTTCGGGTCATCCGTAAGCCCTGCAGTGCAGGATGTTTTCAAAAAGC
66 GCATGATGCTTTCAAAACCTTCGGGTCATCCGTAAGCCCTGCAGTGCAGGATGTTTTCAAAAAGC
* *
31394 CTTCGGGAGCTTTTTGATATTTTCAAAACTTTCGGGT
131 CTTCGGGAGCTTTTTGATATTTTCAAAGCCTTCGGGT
*
31431 CATCTGTAAGTCCTTCAGTGCTTGATATTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
1 CATCTGTAAGTCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
31496 GCATGATGCTTTCAAAACCTTCGGGTCATCCGTAAGCCCTGCAGTGCAGGATGTTTTCAAAAAGC
66 GCATGATGCTTTCAAAACCTTCGGGTCATCCGTAAGCCCTGCAGTGCAGGATGTTTTCAAAAAGC
*
31561 CTTCAGGAGCTTTTTGATATTTTCAAAGCCTTCGGGT
131 CTTCGGGAGCTTTTTGATATTTTCAAAGCCTTCGGGT
* *
31598 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCTTGATGTTTTCAA
31632 CATTTCAAGA
Statistics
Matches: 351, Mismatches: 17, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
167 351 1.00
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.34
Consensus pattern (167 bp):
CATCTGTAAGTCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
GCATGATGCTTTCAAAACCTTCGGGTCATCCGTAAGCCCTGCAGTGCAGGATGTTTTCAAAAAGC
CTTCGGGAGCTTTTTGATATTTTCAAAGCCTTCGGGT
Found at i:31479 original size:46 final size:45
Alignment explanation
Indices: 31408--31557 Score: 210
Period size: 45 Copynumber: 3.3 Consensus size: 45
31398 GGGAGCTTTT
* * *
31408 TGATATTTTCAAAACTTTCGGGTCATCTGTAAGTCCTTCAGTGCT
1 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
31453 TGATATTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATATTTTC-AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
** * *
31499 TGATGCTTTCAAAACCTTCGGGTCATCCGTAAGCCCTGCAGTGCA
1 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
31544 GGATGTTTTCAAAA
1 TGATATTTTCAAAA
31558 AGCCTTCAGG
Statistics
Matches: 95, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
45 55 0.58
46 40 0.42
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (45 bp):
TGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:31748 original size:3 final size:3
Alignment explanation
Indices: 31740--31816 Score: 86
Period size: 3 Copynumber: 26.0 Consensus size: 3
31730 ATTTTTCATT
* ** *
31740 TTA TTA TTA TTA TTA TTA TTA TTA TT- TAA AAA ATA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
31786 TTA TTA TTC TATA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA
31817 AATAAAAAAT
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
2 3 0.05
3 61 0.92
4 2 0.03
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:31798 original size:22 final size:22
Alignment explanation
Indices: 31773--31815 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
31763 ATTTAAAAAA
31773 TATATTATTATTATTATTATTC
1 TATATTATTATTATTATTATTC
31795 TATATTATTATTATTATTATT
1 TATATTATTATTATTATTATT
31816 AAATAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (22 bp):
TATATTATTATTATTATTATTC
Found at i:35371 original size:30 final size:32
Alignment explanation
Indices: 35304--35372 Score: 97
Period size: 31 Copynumber: 2.2 Consensus size: 32
35294 CATATTCAAT
35304 ATTTGAGCTCAAAACAAATATTTCAACATAAC
1 ATTTGAGCTCAAAACAAATATTTCAACATAAC
* * *
35336 ATTTGAGCTTAAAA-AAATATTTGAACAT-CC
1 ATTTGAGCTCAAAACAAATATTTCAACATAAC
35366 ATTTGAG
1 ATTTGAG
35373 TGACGCACAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 8 0.24
31 13 0.38
32 13 0.38
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.32
Consensus pattern (32 bp):
ATTTGAGCTCAAAACAAATATTTCAACATAAC
Found at i:36544 original size:17 final size:17
Alignment explanation
Indices: 36504--36544 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
36494 TATTACTACC
36504 TATT-TTTTAATTAATG
1 TATTATTTTAATTAATG
36520 TAATTATTTTAATTATAT-
1 T-ATTATTTTAATTA-ATG
36538 TATTATT
1 TATTATT
36545 AATTTTCGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 1 0.05
17 9 0.41
18 10 0.45
19 2 0.09
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
TATTATTTTAATTAATG
Found at i:43608 original size:5 final size:5
Alignment explanation
Indices: 43598--43636 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
43588 ACCACGACCA
* *
43598 CGAGC CGAGC CGAGC CGTGC CGTGC CGAGC CGAGC CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
43637 ATGAACGGCG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.15, C:0.38, G:0.41, T:0.05
Consensus pattern (5 bp):
CGAGC
Found at i:46944 original size:25 final size:27
Alignment explanation
Indices: 46910--46963 Score: 69
Period size: 25 Copynumber: 2.1 Consensus size: 27
46900 TTATTTCAAA
46910 TACATATGAT-ATTAT-TGATATTT-TG
1 TACATATGATGATTATATGAT-TTTATG
*
46935 TACATGTGATGATTATATGATTTTATG
1 TACATATGATGATTATATGATTTTATG
46962 TA
1 TA
46964 TTATATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 9 0.36
26 8 0.32
27 8 0.32
ACGTcount: A:0.31, C:0.04, G:0.15, T:0.50
Consensus pattern (27 bp):
TACATATGATGATTATATGATTTTATG
Done.