Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002426.1 Hibiscus syriacus cultivar Beakdansim tig00004964_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: 62685
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:2582 original size:17 final size:18
Alignment explanation
Indices: 2540--2582 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
2530 TTCCCTTTTA
2540 TCATTTTTCTATCTAGAT
1 TCATTTTTCTATCTAGAT
2558 TCATTTTTCTATCTAGAT
1 TCATTTTTCTATCTAGAT
2576 TCATTTT
1 TCATTTT
2583 AATCTAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.21, C:0.16, G:0.05, T:0.58
Consensus pattern (18 bp):
TCATTTTTCTATCTAGAT
Found at i:6989 original size:32 final size:32
Alignment explanation
Indices: 6939--7000 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
6929 TCTATGTGCT
* * *
6939 ATGATATATGTTATATGATATGAGATTAAGTG
1 ATGATATATGATATATGATATAAGAATAAGTG
6971 ATGATATAT-ATATGATGATATAAGAATAAG
1 ATGATATATGATAT-ATGATATAAGAATAAG
7001 ACATGAATCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 3 0.12
32 23 0.88
ACGTcount: A:0.44, C:0.00, G:0.19, T:0.37
Consensus pattern (32 bp):
ATGATATATGATATATGATATAAGAATAAGTG
Found at i:8146 original size:21 final size:21
Alignment explanation
Indices: 8120--8160 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
8110 GAAATTTATG
8120 TGCATCGATGCACTGTAGCAA
1 TGCATCGATGCACTGTAGCAA
8141 TGCATCGATGCACTGTAGCA
1 TGCATCGATGCACTGTAGCA
8161 CTATTCATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (21 bp):
TGCATCGATGCACTGTAGCAA
Found at i:8188 original size:22 final size:22
Alignment explanation
Indices: 8160--8212 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
8150 GCACTGTAGC
* *
8160 ACTATTCATTATTGTTTACGGT
1 ACTATTCATTACTGTTCACGGT
8182 ACTATTCATTACTGTTCACGGT
1 ACTATTCATTACTGTTCACGGT
*
8204 ACCATTCAT
1 ACTATTCAT
8213 ACCATATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.25, C:0.21, G:0.11, T:0.43
Consensus pattern (22 bp):
ACTATTCATTACTGTTCACGGT
Found at i:9916 original size:2 final size:2
Alignment explanation
Indices: 9909--9936 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
9899 ACTAGAAATA
9909 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
9937 GGATAGTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13527 original size:32 final size:32
Alignment explanation
Indices: 13478--13538 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
13468 ATGTGCTATG
* * *
13478 TGATATATGTTATATGATATGAGATTAAGTGA
1 TGATATATGATATATGATATAAGAATAAGTGA
13510 TGATATAT-ATATGATGATATAAGAATAAG
1 TGATATATGATAT-ATGATATAAGAATAAG
13539 ACATGAATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 3 0.12
32 22 0.88
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.38
Consensus pattern (32 bp):
TGATATATGATATATGATATAAGAATAAGTGA
Found at i:13995 original size:23 final size:23
Alignment explanation
Indices: 13969--14020 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
13959 GTGGTCCTCT
13969 GGGACATTTCTACGCGGTCATTC
1 GGGACATTTCTACGCGGTCATTC
*
13992 GGGACATTTCTACGCGGTCCTTC
1 GGGACATTTCTACGCGGTCATTC
14015 GGGACA
1 GGGACA
14021 AATATTCAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (23 bp):
GGGACATTTCTACGCGGTCATTC
Found at i:14671 original size:21 final size:21
Alignment explanation
Indices: 14647--14694 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
14637 TTACGAAACT
*
14647 CACTGTAGCAGTGCATCGATG
1 CACTGTAGCAATGCATCGATG
*
14668 CACTATAGCAATGCATCGATG
1 CACTGTAGCAATGCATCGATG
14689 CACTGT
1 CACTGT
14695 TCATTATTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (21 bp):
CACTGTAGCAATGCATCGATG
Found at i:17820 original size:18 final size:20
Alignment explanation
Indices: 17794--17844 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 20
17784 GGCCAAATTG
*
17794 GTATTGATACTCA-TGG-GA
1 GTATCGATACTCATTGGAGA
17812 GTATCGATACT-ATTGGAAGA
1 GTATCGATACTCATTGG-AGA
*
17832 TTATCGATACTCA
1 GTATCGATACTCA
17845 ACATTAGGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 1 0.04
18 13 0.48
20 12 0.44
21 1 0.04
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (20 bp):
GTATCGATACTCATTGGAGA
Found at i:18032 original size:10 final size:10
Alignment explanation
Indices: 18017--18046 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
18007 AGTTTATTGA
18017 AGGGTTTATG
1 AGGGTTTATG
*
18027 AGGGTTTATA
1 AGGGTTTATG
18037 AGGGTTTATG
1 AGGGTTTATG
18047 CTCAGGTTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.37, T:0.40
Consensus pattern (10 bp):
AGGGTTTATG
Found at i:25622 original size:23 final size:23
Alignment explanation
Indices: 25591--25659 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
25581 CACCACAGCT
* * *
25591 CGTATAATTACACTGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
25614 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
25637 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
25660 TATAATAATG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:27958 original size:46 final size:47
Alignment explanation
Indices: 27864--27960 Score: 142
Period size: 47 Copynumber: 2.1 Consensus size: 47
27854 ACTGATTAAT
* * *
27864 TAAACAAGAATACGATATAAGAAAAGAGATTAAAAAGCACTAAATAA
1 TAAACAAGAAAACGATACAAGAAAAGAGATTAAAAAGAACTAAATAA
* *
27911 TAAACAAGAAAACGATACAAGAAAA-TGATTAAAAATAACTAAATAA
1 TAAACAAGAAAACGATACAAGAAAAGAGATTAAAAAGAACTAAATAA
27957 TAAA
1 TAAA
27961 ATCATTCAGT
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
46 22 0.49
47 23 0.51
ACGTcount: A:0.64, C:0.08, G:0.10, T:0.18
Consensus pattern (47 bp):
TAAACAAGAAAACGATACAAGAAAAGAGATTAAAAAGAACTAAATAA
Found at i:28061 original size:15 final size:16
Alignment explanation
Indices: 28041--28076 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
28031 CAATTGTTGG
28041 TAAATA-AAAAAAAAT
1 TAAATACAAAAAAAAT
*
28056 TAAATACAAAAATAAT
1 TAAATACAAAAAAAAT
28072 TAAAT
1 TAAAT
28077 GTATGAATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (16 bp):
TAAATACAAAAAAAAT
Found at i:30149 original size:23 final size:24
Alignment explanation
Indices: 30105--30154 Score: 61
Period size: 23 Copynumber: 2.1 Consensus size: 24
30095 AATTTTAAAT
30105 AAATTAAATATTAACAATAA-TTA
1 AAATTAAATATTAACAATAATTTA
30128 AAATTAAA-ATTAA-AATAGAATTTA
1 AAATTAAATATTAACAAT--AATTTA
30152 AAA
1 AAA
30155 ATGTTACTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 3 0.12
22 5 0.21
23 10 0.42
24 6 0.25
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (24 bp):
AAATTAAATATTAACAATAATTTA
Found at i:31276 original size:17 final size:18
Alignment explanation
Indices: 31254--31297 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
31244 GATTTTTACC
31254 GGGTTTGAG-CTTTAAGA
1 GGGTTTGAGACTTTAAGA
*
31271 GGGTTTG-GACTTTGAGA
1 GGGTTTGAGACTTTAAGA
31288 GGGTTTGAGA
1 GGGTTTGAGA
31298 GGATTTGAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 1 0.04
17 21 0.88
18 2 0.08
ACGTcount: A:0.20, C:0.05, G:0.41, T:0.34
Consensus pattern (18 bp):
GGGTTTGAGACTTTAAGA
Found at i:31804 original size:51 final size:51
Alignment explanation
Indices: 31728--31829 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
31718 ATGCACGTCG
31728 AAAGACTGTCGTTTCCATTCAAGTTTCAGCTTTCAGATCAATGTATTTATT
1 AAAGACTGTCGTTTCCATTCAAGTTTCAGCTTTCAGATCAATGTATTTATT
31779 AAAGACTGTCGTTTCCATTCAAGTTTCAGCTTTCAGATCAATGTATTTATT
1 AAAGACTGTCGTTTCCATTCAAGTTTCAGCTTTCAGATCAATGTATTTATT
31830 TATACATGCT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (51 bp):
AAAGACTGTCGTTTCCATTCAAGTTTCAGCTTTCAGATCAATGTATTTATT
Found at i:32568 original size:14 final size:16
Alignment explanation
Indices: 32534--32571 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
32524 CATCAACTTC
32534 TTAAATATCACATTAT
1 TTAAATATCACATTAT
*
32550 TTAAATAT-A-ATTTT
1 TTAAATATCACATTAT
32564 TTAAATAT
1 TTAAATAT
32572 TTAAATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 12 0.57
15 1 0.05
16 8 0.38
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAAATATCACATTAT
Found at i:33278 original size:9 final size:9
Alignment explanation
Indices: 33272--33384 Score: 51
Period size: 9 Copynumber: 12.4 Consensus size: 9
33262 AAAAAAAAGT
33272 AATAAAATA
1 AATAAAATA
*
33281 AATAAAACCA
1 AATAAAA-TA
33291 AATAAAA-A
1 AATAAAATA
33299 AACCTAAAA-A
1 AA--TAAAATA
*
33309 ATAGAAAATA
1 A-ATAAAATA
*
33319 AA-ATAA-A
1 AATAAAATA
*
33326 AATAATAATGG
1 AATAA-AAT-A
*
33337 AATTAAATA
1 AATAAAATA
33346 AGAT-AAA-A
1 A-ATAAAATA
33354 AATAAAATA
1 AATAAAATA
33363 AATAAAA-A
1 AATAAAATA
*
33371 ATAAAAAATA
1 A-ATAAAATA
33381 AATA
1 AATA
33385 TATATATATA
Statistics
Matches: 81, Mismatches: 9, Indels: 28
0.69 0.08 0.24
Matches are distributed among these distances:
7 5 0.06
8 14 0.17
9 33 0.41
10 24 0.30
11 5 0.06
ACGTcount: A:0.74, C:0.04, G:0.04, T:0.19
Consensus pattern (9 bp):
AATAAAATA
Found at i:33359 original size:16 final size:15
Alignment explanation
Indices: 33275--33382 Score: 64
Period size: 14 Copynumber: 7.1 Consensus size: 15
33265 AAAAAGTAAT
*
33275 AAAATAAATAAA-AC
1 AAAATAAATAAATAA
* *
33289 CAAATAAAAAAACCTAA
1 AAAATAAATAAA--TAA
*
33306 AAAATAGA-AAATAA
1 AAAATAAATAAATAA
33320 AATAA-AAAT-AATAA
1 AA-AATAAATAAATAA
* *
33334 TGGAATTAAATAAGATAA
1 --AAAATAAATAA-ATAA
33352 AAAATAAAATAAATAA
1 AAAAT-AAATAAATAA
33368 AAAATAAA-AAATAA
1 AAAATAAATAAATAA
33382 A
1 A
33383 TATATATATA
Statistics
Matches: 73, Mismatches: 10, Indels: 22
0.70 0.10 0.21
Matches are distributed among these distances:
14 29 0.40
15 6 0.08
16 20 0.27
17 14 0.19
18 4 0.05
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.18
Consensus pattern (15 bp):
AAAATAAATAAATAA
Found at i:33360 original size:7 final size:7
Alignment explanation
Indices: 33348--33382 Score: 52
Period size: 7 Copynumber: 4.7 Consensus size: 7
33338 ATTAAATAAG
33348 ATAAAAA
1 ATAAAAA
33355 ATAAAATAA
1 AT-AAA-AA
33364 ATAAAAA
1 ATAAAAA
33371 ATAAAAA
1 ATAAAAA
33378 ATAAA
1 ATAAA
33383 TATATATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 16 0.62
8 6 0.23
9 4 0.15
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (7 bp):
ATAAAAA
Found at i:33383 original size:39 final size:38
Alignment explanation
Indices: 33272--33384 Score: 88
Period size: 39 Copynumber: 2.8 Consensus size: 38
33262 AAAAAAAAGT
*
33272 AATAAAATAAATAAAACCAAATAAAAAAACCTAAA-AAATAGAA
1 AATAAAATAAAT-AAA--AAAT-AAAAAA--TAAATAAATAAAA
** *
33315 AATAAAATAAA-AATAATAAT-GGAATTAAATAAGATAAAA
1 AATAAAATAAATAA-AA-AATAAAAAATAAATAA-ATAAAA
33354 AATAAAATAAATAAAAAATAAAAAATAAATA
1 AATAAAATAAATAAAAAATAAAAAATAAATA
33385 TATATATATA
Statistics
Matches: 57, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
37 4 0.07
38 5 0.09
39 28 0.49
40 3 0.05
41 5 0.09
42 1 0.02
43 11 0.19
ACGTcount: A:0.74, C:0.04, G:0.04, T:0.19
Consensus pattern (38 bp):
AATAAAATAAATAAAAAATAAAAAATAAATAAATAAAA
Found at i:34933 original size:23 final size:20
Alignment explanation
Indices: 34882--34921 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
34872 TAAATGTATA
34882 TTAAATAATAATTAAGTTAT
1 TTAAATAATAATTAAGTTAT
34902 TTAAATAATAATTAAGTTAT
1 TTAAATAATAATTAAGTTAT
34922 GTTTTAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (20 bp):
TTAAATAATAATTAAGTTAT
Found at i:36632 original size:6 final size:7
Alignment explanation
Indices: 36615--36647 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
36605 CTTAATTACG
36615 AAAAATT
1 AAAAATT
36622 AAAAATT
1 AAAAATT
36629 -AAAATT
1 AAAAATT
36635 AAAAATT
1 AAAAATT
36642 AAAAAT
1 AAAAAT
36648 CCAATTCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
AAAAATT
Found at i:36634 original size:13 final size:13
Alignment explanation
Indices: 36616--36645 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
36606 TTAATTACGA
36616 AAAATTAAAAATT
1 AAAATTAAAAATT
36629 AAAATTAAAAATT
1 AAAATTAAAAATT
36642 AAAA
1 AAAA
36646 ATCCAATTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (13 bp):
AAAATTAAAAATT
Found at i:39379 original size:171 final size:172
Alignment explanation
Indices: 39119--40267 Score: 1517
Period size: 171 Copynumber: 6.7 Consensus size: 172
39109 GACAATTTCT
* ** * * * * * ** * *
39119 TGTTGACAGATATCTTTTCTCGACTTAAGTTATGCTATGAATTTGACATGCCATTGAGCTGAATG
1 TGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTGGATGTGCCTTTGAGCTGAGTG
* * * * *
39184 GAATCGAACTCGAAGGT-ATTTGTTGACAGATTA-CCCTTCTTGCCTTGAGCTATGTTGTAAATT
66 TAATCGAACTCGAAGGTCTTTTGTTGACAGA-TAGCCCTTCTCGCCTTGAGCTATGCTGCAAATT
39247 TGATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTG
130 TGATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTG
* * *
39290 T-TTGACAGATAACCCTTCTCGTCTTGAGTTTTGCTGTAAATTGGATGTGCCTTTGAGGTGAGTG
1 TGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTGGATGTGCCTTTGAGCTGAGTG
*
39354 TAATCAAACTCGAAGGTCTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGCAAATTT
66 TAATCGAACTCGAAGGTCTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGCAAATTT
*
39419 GATGTGCCTTTGAGCTAAGTGTAATCAAACTCGAAGGTCTTG
131 GATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTG
* * * * * *
39461 -GTTAACAGATAACCCTTCTCACCTTAAGTTATGCTATAAATTTGATATGCCTTTGAGCTGAGTG
1 TGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTGGATGTGCCTTTGAGCTGAGTG
* * *
39525 TAATCGAACTCGAAGGTC-TTGGTTGGCAGATAGCTCTTCTCGCCTTGAGCTATGCTGCAAATTT
66 TAATCGAACTCGAAGGTCTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGCAAATTT
*
39589 GATATGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTG
131 GATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTG
* * * *
39631 -GATGAAAGATAACCCTTCTCCCCTTGAGTTATGCTGTAAATTTGATGTGCCTTTGAGCTGAGTG
1 TGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTGGATGTGCCTTTGAGCTGAGTG
* * * * *
39695 TAATCGAACTCGAATGTCTTTTGTTGACATATAGTCATTCTCGCCTTGAGCTATGCTGTAAATTT
66 TAATCGAACTCGAAGGTCTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGCAAATTT
* *
39760 AATGTGCCTTTGAGCTGAGTGTAATCGAAA-TCGAAGGTCTTT
131 GATGTGCCTTTGAGCTGAGTGTAATC-AAACTCGAAGGTCTTG
* * * * *
39802 TGTTGACAAATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATGTGCCTTTGAGTTGAGTG
1 TGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTGGATGTGCCTTTGAGCTGAGTG
* * * *
39867 TAATCAAACTCGAAGGTATTTTATTGAAAGATAGCCCTTCTCGCCTTGAGCTATGCTGCAAATTT
66 TAATCGAACTCGAAGGTCTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGCAAATTT
* * * *
39932 GATGTGCCATTAAGCTGAGTGTATTCCAAA-TCGAAGGTCTTT
131 GATGTGCCTTTGAGCTGAGTGTAAT-CAAACTCGAAGGTCTTG
* * *
39974 TGTTGACAGATAGCCTTTCTCGCCTTGAGCTATGCTGTAAATTGGATGTGCCTTTGAGCTGAGTG
1 TGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTGGATGTGCCTTTGAGCTGAGTG
* * * * * *
40039 TAATCGAACTCGAAGGTCTTTTATTGACAGATA-ACCTTCTCTCCATGAGCTATGTTGAAAATTT
66 TAATCGAACTCGAAGGTCTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGCAAATTT
* *
40103 GATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTT
131 GATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTG
* * * *
40145 TGTTGACAGATAGCCCTTCTTGCCTTGAGTTATGCTGTAAATTGGATATGCCTTTGAGCTGAATG
1 TGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTGGATGTGCCTTTGAGCTGAGTG
* * * * *
40210 CAATCAAACTCGAAGGTC-TTGGTTGACATATAGCCCTTCTCGCCTTGAGTTATGCTGC
66 TAATCGAACTCGAAGGTCTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGC
40268 CAATATTTCC
Statistics
Matches: 863, Mismatches: 106, Indels: 18
0.87 0.11 0.02
Matches are distributed among these distances:
170 237 0.27
171 382 0.44
172 243 0.28
173 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (172 bp):
TGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTGGATGTGCCTTTGAGCTGAGTG
TAATCGAACTCGAAGGTCTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGCAAATTT
GATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTG
Found at i:39423 original size:86 final size:86
Alignment explanation
Indices: 39088--40266 Score: 1482
Period size: 85 Copynumber: 13.8 Consensus size: 86
39078 CTGTGTCATC
* * * * ** * * *
39088 GAGCTGAATGGAATCAAACTCGACA-AT-TTCTTGTTGACAGATATCTTTTCTCGACTTAAGTTA
1 GAGCTGAGTGTAATCAAACTCGA-AGGTCTT-TTGTTGACAGATAGCCCTTCTCGCCTTGAGCTA
* * ** *
39151 TGCTATGAATTTGACATGCCATT
64 TGCTGTAAATTTGATGTGCCTTT
* * * * *
39174 GAGCTGAATGGAATCGAACTCGAAGGT-ATTTGTTGACAGATTA-CCCTTCTTGCCTTGAGCTAT
1 GAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGACAGA-TAGCCCTTCTCGCCTTGAGCTAT
*
39237 GTTGTAAATTTGATGTGCCTTT
65 GCTGTAAATTTGATGTGCCTTT
* * * * *
39259 GAGCTGAGTGTAATCAAACTCGAAGGTCTTGT-TTGACAGATAACCCTTCTCGTCTTGAGTTTTG
1 GAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATG
*
39323 CTGTAAATTGGATGTGCCTTT
66 CTGTAAATTTGATGTGCCTTT
*
39344 GAGGTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATG
1 GAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATG
*
39409 CTGCAAATTTGATGTGCCTTT
66 CTGTAAATTTGATGTGCCTTT
* * * * * * *
39430 GAGCTAAGTGTAATCAAACTCGAAGGTC-TTGGTTAACAGATAACCCTTCTCACCTTAAGTTATG
1 GAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATG
* *
39494 CTATAAATTTGATATGCCTTT
66 CTGTAAATTTGATGTGCCTTT
* * * *
39515 GAGCTGAGTGTAATCGAACTCGAAGGTC-TTGGTTGGCAGATAGCTCTTCTCGCCTTGAGCTATG
1 GAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATG
* *
39579 CTGCAAATTTGATATGCCTTT
66 CTGTAAATTTGATGTGCCTTT
* * * * * *
39600 GAGCTGAGTGTAATCAAACTCGAAGGTC-TTGGATGAAAGATAACCCTTCTCCCCTTGAGTTATG
1 GAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATG
39664 CTGTAAATTTGATGTGCCTTT
66 CTGTAAATTTGATGTGCCTTT
* * * * *
39685 GAGCTGAGTGTAATCGAACTCGAATGTCTTTTGTTGACATATAGTCATTCTCGCCTTGAGCTATG
1 GAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATG
*
39750 CTGTAAATTTAATGTGCCTTT
66 CTGTAAATTTGATGTGCCTTT
*
39771 GAGCTGAGTGTAATCGAAA-TCGAAGGTCTTTTGTTGACAAATAGCCCTTCTCGCCTTGAGCTAT
1 GAGCTGAGTGTAATC-AAACTCGAAGGTCTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTAT
39835 GCTGTAAATTTGATGTGCCTTT
65 GCTGTAAATTTGATGTGCCTTT
* * * *
39857 GAGTTGAGTGTAATCAAACTCGAAGGTATTTTATTGAAAGATAGCCCTTCTCGCCTTGAGCTATG
1 GAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATG
* *
39922 CTGCAAATTTGATGTGCCATT
66 CTGTAAATTTGATGTGCCTTT
* * *
39943 AAGCTGAGTGTATTCCAAA-TCGAAGGTCTTTTGTTGACAGATAGCCTTTCTCGCCTTGAGCTAT
1 GAGCTGAGTGTAAT-CAAACTCGAAGGTCTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTAT
*
40007 GCTGTAAATTGGATGTGCCTTT
65 GCTGTAAATTTGATGTGCCTTT
* * * * *
40029 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTTATTGACAGATA-ACCTTCTCTCCATGAGCTATG
1 GAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATG
* *
40093 TTGAAAATTTGATGTGCCTTT
66 CTGTAAATTTGATGTGCCTTT
* * *
40114 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAGCCCTTCTTGCCTTGAGTTATG
1 GAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATG
* *
40179 CTGTAAATTGGATATGCCTTT
66 CTGTAAATTTGATGTGCCTTT
* * * * *
40200 GAGCTGAATGCAATCAAACTCGAAGGTC-TTGGTTGACATATAGCCCTTCTCGCCTTGAGTTATG
1 GAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATG
40264 CTG
66 CTG
40267 CCAATATTTC
Statistics
Matches: 954, Mismatches: 128, Indels: 23
0.86 0.12 0.02
Matches are distributed among these distances:
84 2 0.00
85 482 0.51
86 464 0.49
87 6 0.01
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (86 bp):
GAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATG
CTGTAAATTTGATGTGCCTTT
Found at i:40882 original size:15 final size:15
Alignment explanation
Indices: 40862--40890 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
40852 AAGGACCCTT
40862 CCTATTTGAGACTGA
1 CCTATTTGAGACTGA
40877 CCTATTTGAGACTG
1 CCTATTTGAGACTG
40891 TTTTTCTCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (15 bp):
CCTATTTGAGACTGA
Found at i:41658 original size:99 final size:98
Alignment explanation
Indices: 41469--41669 Score: 251
Period size: 99 Copynumber: 2.0 Consensus size: 98
41459 GGACAGCTCA
* * * * *
41469 ATATTATATCACCTTTATCAGGCTAGCTGAATCCTATCCATAAAGTCGTGGCGTTTAACCAATTG
1 ATATTATATAACCTTTATCAGGCTAGCTAAATCCTATCCATAAAGCCGTAGAGTTTAACCAATTG
* *
41534 CCTTAGAGGGACAATTCAAAATTTATTGTATAG
66 CCTTAGAGGGACAACTCAAAATTTATTATATAG
* * *
41567 ATATTATAATAACCTTTATCATGTTAGCTAAATCGTATCCATAAAGCCAG-AGAGTTTAACCAAT
1 ATATTAT-ATAACCTTTATCAGGCTAGCTAAATCCTATCCATAAAGCC-GTAGAGTTTAACCAAT
* ** *
41631 TGCTTTAGAGGGACAACTCAAGCTTTATTATATAT
64 TGCCTTAGAGGGACAACTCAAAATTTATTATATAG
41666 ATAT
1 ATAT
41670 AATCTGGGTA
Statistics
Matches: 87, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
98 7 0.08
99 79 0.91
100 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (98 bp):
ATATTATATAACCTTTATCAGGCTAGCTAAATCCTATCCATAAAGCCGTAGAGTTTAACCAATTG
CCTTAGAGGGACAACTCAAAATTTATTATATAG
Found at i:54996 original size:25 final size:24
Alignment explanation
Indices: 54921--54998 Score: 77
Period size: 25 Copynumber: 3.2 Consensus size: 24
54911 AACCATAGTG
*
54921 CAAAAGAATCAAAAGCTTAAAACC
1 CAAAAAAATCAAAAGCTTAAAACC
* ***
54945 AAAAAAAATCTTTTCA-CTTAAAACC
1 CAAAAAAATC--AAAAGCTTAAAACC
54970 CAAAAAAATCAAAAGCTTAAAAGCC
1 CAAAAAAATCAAAAGCTTAAAA-CC
54995 CAAA
1 CAAA
54999 CCGACCCCCT
Statistics
Matches: 41, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
23 1 0.02
24 15 0.37
25 24 0.59
26 1 0.02
ACGTcount: A:0.58, C:0.21, G:0.05, T:0.17
Consensus pattern (24 bp):
CAAAAAAATCAAAAGCTTAAAACC
Found at i:56416 original size:30 final size:31
Alignment explanation
Indices: 56354--56430 Score: 111
Period size: 30 Copynumber: 2.5 Consensus size: 31
56344 TCAAAAAACA
*
56354 TAAGTTTTGGTCACTTACATTATTATTTTAT
1 TAAGTTTTGGTCACTTACATTATTAGTTTAT
* *
56385 TAAGTTTTGGTCACTTACGTTA-TCGTTTAT
1 TAAGTTTTGGTCACTTACATTATTAGTTTAT
*
56415 TAAGTTTAGGTCACTT
1 TAAGTTTTGGTCACTT
56431 GAACATTGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 21 0.50
31 21 0.50
ACGTcount: A:0.23, C:0.12, G:0.14, T:0.51
Consensus pattern (31 bp):
TAAGTTTTGGTCACTTACATTATTAGTTTAT
Found at i:57740 original size:31 final size:31
Alignment explanation
Indices: 57682--57754 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
57672 CTCAATGTCC
*
57682 AAGTGACCAAAACTTAACAAAACAATAACGT
1 AAGTGACCAAAACTTAACAAAACAATAACAT
* * *
57713 AAGTGACCAAAA-TTAAATAAAATAATAATAT
1 AAGTGACCAAAACTT-AACAAAACAATAACAT
*
57744 AAGTGATCAAA
1 AAGTGACCAAA
57755 GCTTTTTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
30 2 0.06
31 34 0.94
ACGTcount: A:0.58, C:0.12, G:0.10, T:0.21
Consensus pattern (31 bp):
AAGTGACCAAAACTTAACAAAACAATAACAT
Found at i:61519 original size:28 final size:28
Alignment explanation
Indices: 61479--61541 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 28
61469 CGAGGTGGAT
61479 GACAAGGAAATAAAGAAAGCTTTGTTTA
1 GACAAGGAAATAAAGAAAGCTTTGTTTA
*
61507 GACAAGGAAATAAAGGAAGCTTTGTTTA
1 GACAAGGAAATAAAGAAAGCTTTGTTTA
61535 GACAAGG
1 GACAAGG
61542 TAATGGAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.44, C:0.08, G:0.25, T:0.22
Consensus pattern (28 bp):
GACAAGGAAATAAAGAAAGCTTTGTTTA
Done.