Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005940.1 Hibiscus syriacus cultivar Beakdansim tig00013950_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: 87207
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:7884 original size:21 final size:21
Alignment explanation
Indices: 7860--7913 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 21
7850 TATACATTTC
7860 TATAAAAATATA-TAAAATCAT
1 TATAAAAATATATTAAAAT-AT
* *
7881 TATAAAATAATATATTATAATGT
1 TAT-AAA-AATATATTAAAATAT
7904 TATAAAAATA
1 TATAAAAATA
7914 ATCTATACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
21 7 0.25
22 6 0.21
23 10 0.36
24 5 0.18
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
TATAAAAATATATTAAAATAT
Found at i:7920 original size:21 final size:21
Alignment explanation
Indices: 7842--7920 Score: 54
Period size: 21 Copynumber: 3.6 Consensus size: 21
7832 TAAAAAAATT
*
7842 AAATAATCTATACATTTCTATAA
1 AAATAATCTATA-ATAT-TATAA
* *
7865 AAAT-ATATAAAATCATTATAAA
1 AAATAATCTATAAT-ATTAT-AA
*
7887 ATAATATAT-TATAATGTTATAA
1 A-AATA-ATCTATAATATTATAA
7909 AAATAATCTATA
1 AAATAATCTATA
7921 CATTTAGTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 14
0.70 0.08 0.22
Matches are distributed among these distances:
20 2 0.04
21 13 0.29
22 12 0.27
23 11 0.24
24 5 0.11
25 2 0.04
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.38
Consensus pattern (21 bp):
AAATAATCTATAATATTATAA
Found at i:8625 original size:39 final size:39
Alignment explanation
Indices: 8582--8671 Score: 112
Period size: 39 Copynumber: 2.3 Consensus size: 39
8572 TTAAATCATC
8582 AAATTATTTCACTC-TAACATTATAAAATCCTAATTTCTT
1 AAATTATTTCAC-CATAACATTATAAAATCCTAATTTCTT
* * * *
8621 AAATT-TTGACACCATAACATTCTAAATTCTTAATTTCTT
1 AAATTATT-TCACCATAACATTATAAAATCCTAATTTCTT
8660 AAATTATTTCAC
1 AAATTATTTCAC
8672 ATTAACGTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
38 3 0.07
39 38 0.88
40 2 0.05
ACGTcount: A:0.38, C:0.18, G:0.01, T:0.43
Consensus pattern (39 bp):
AAATTATTTCACCATAACATTATAAAATCCTAATTTCTT
Found at i:8686 original size:39 final size:39
Alignment explanation
Indices: 8582--8687 Score: 110
Period size: 39 Copynumber: 2.7 Consensus size: 39
8572 TTAAATCATC
*
8582 AAATTATTTCAC-TCTAACATTATAAAATCCTAATTTCTT
1 AAATTATTTCACAT-TAACATTATAAATTCCTAATTTCTT
* * *
8621 AAATT-TTGACACCA-TAACATTCTAAATTCTTAATTTCTT
1 AAATTATT-TCA-CATTAACATTATAAATTCCTAATTTCTT
* *
8660 AAATTATTTCACATTAACGTTTTAAATT
1 AAATTATTTCACATTAACATTATAAATT
8688 ATTTTAACTT
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
38 4 0.07
39 48 0.87
40 3 0.05
ACGTcount: A:0.38, C:0.16, G:0.02, T:0.44
Consensus pattern (39 bp):
AAATTATTTCACATTAACATTATAAATTCCTAATTTCTT
Found at i:8949 original size:24 final size:26
Alignment explanation
Indices: 8912--8964 Score: 76
Period size: 24 Copynumber: 2.1 Consensus size: 26
8902 AACTTAAATG
8912 TTTTATATTAACTT-A-TT-AAATAT
1 TTTTATATTAACTTAATTTAAAATAT
8935 TTTTACTATTAACTTAATTTAAAATAT
1 TTTTA-TATTAACTTAATTTAAAATAT
8962 TTT
1 TTT
8965 ATTTTCATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
23 5 0.19
24 9 0.35
25 1 0.04
26 2 0.08
27 9 0.35
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.57
Consensus pattern (26 bp):
TTTTATATTAACTTAATTTAAAATAT
Found at i:15582 original size:23 final size:23
Alignment explanation
Indices: 15556--15625 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
15546 TTGGAAGGTG
15556 GTACACCATTGAATAGAGAAGCA
1 GTACACCATTGAATAGAGAAGCA
* * *
15579 GT--ACCA--AAAGTTG-GAAGGA
1 GTACACCATTGAA-TAGAGAAGCA
15598 GGTACACCATTGAATAGAGAAGCA
1 -GTACACCATTGAATAGAGAAGCA
15622 GTAC
1 GTAC
15626 CAATAGTTGG
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
19 7 0.21
20 4 0.12
21 4 0.12
22 4 0.12
23 8 0.24
24 7 0.21
ACGTcount: A:0.41, C:0.16, G:0.26, T:0.17
Consensus pattern (23 bp):
GTACACCATTGAATAGAGAAGCA
Found at i:15584 original size:21 final size:21
Alignment explanation
Indices: 15560--15627 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
15550 AAGGTGGTAC
15560 ACCATTGAATAGAGAAGCAGT
1 ACCATTGAATAGAGAAGCAGT
* * *
15581 ACCA--AAAGTTG-GAAGGAGGT
1 ACCATTGAA-TAGAGAAGCA-GT
15601 ACACCATTGAATAGAGAAGCAGT
1 --ACCATTGAATAGAGAAGCAGT
15624 ACCA
1 ACCA
15628 ATAGTTGGGG
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
19 7 0.21
20 4 0.12
21 8 0.24
22 4 0.12
23 4 0.12
24 7 0.21
ACGTcount: A:0.43, C:0.16, G:0.25, T:0.16
Consensus pattern (21 bp):
ACCATTGAATAGAGAAGCAGT
Found at i:15602 original size:43 final size:43
Alignment explanation
Indices: 15541--15635 Score: 172
Period size: 43 Copynumber: 2.2 Consensus size: 43
15531 ATAGCGTGCA
*
15541 AAAAGTTGGAAGGTGGTACACCATTGAATAGAGAAGCAGTACC
1 AAAAGTTGGAAGGAGGTACACCATTGAATAGAGAAGCAGTACC
15584 AAAAGTTGGAAGGAGGTACACCATTGAATAGAGAAGCAGTACC
1 AAAAGTTGGAAGGAGGTACACCATTGAATAGAGAAGCAGTACC
*
15627 AATAGTTGG
1 AAAAGTTGG
15636 GGATGAGCAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.40, C:0.13, G:0.28, T:0.19
Consensus pattern (43 bp):
AAAAGTTGGAAGGAGGTACACCATTGAATAGAGAAGCAGTACC
Found at i:16958 original size:20 final size:21
Alignment explanation
Indices: 16916--16975 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 21
16906 TTTAAATCAA
16916 TTAG-TTAATTTAGATTATTT
1 TTAGATTAATTTAGATTATTT
16936 TTAGATTAATTT-G-TTATTAT
1 TTAGATTAATTTAGATTATT-T
*
16956 TTAAATTAATGTTTAGATTA
1 TTAGATTAA--TTTAGATTA
16976 ATTATTGTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
19 5 0.15
20 14 0.42
21 7 0.21
22 3 0.09
23 1 0.03
24 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (21 bp):
TTAGATTAATTTAGATTATTT
Found at i:18868 original size:26 final size:26
Alignment explanation
Indices: 18819--18870 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
18809 ATTGGGAGAA
* *
18819 TATTTTATTTAAAAGTATTTTATTTT
1 TATTTTATTTAAAAATATTATATTTT
18845 TATTTTCATTTAAAAATA-TATATTTT
1 TATTTT-ATTTAAAAATATTATATTTT
18871 ATGTTAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (26 bp):
TATTTTATTTAAAAATATTATATTTT
Found at i:19349 original size:30 final size:30
Alignment explanation
Indices: 19313--19373 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
19303 ATATATCAGG
* **
19313 GGCGGATGCATTAAGTCTCATAGGGGTCAA
1 GGCGGATGCACTAAACCTCATAGGGGTCAA
19343 GGCGGATGCACTAAACCTCATAGGGGTCAA
1 GGCGGATGCACTAAACCTCATAGGGGTCAA
19373 G
1 G
19374 TGCATCCCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.28, C:0.20, G:0.33, T:0.20
Consensus pattern (30 bp):
GGCGGATGCACTAAACCTCATAGGGGTCAA
Found at i:25860 original size:19 final size:18
Alignment explanation
Indices: 25836--25872 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
25826 CCTCACACAT
25836 TTCTTTGTCTTCTTTCTTC
1 TTCTTTGTCTTC-TTCTTC
25855 TTCTTTGTCTTCTTCTTC
1 TTCTTTGTCTTCTTCTTC
25873 CTCTCCAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.00, C:0.27, G:0.05, T:0.68
Consensus pattern (18 bp):
TTCTTTGTCTTCTTCTTC
Found at i:26634 original size:18 final size:20
Alignment explanation
Indices: 26608--26657 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 20
26598 GTCAATTTTG
*
26608 GTATAGATACTC-ACGG-GA
1 GTATCGATACTCAACGGAGA
*
26626 GTATCGATAC-CAAGGGTAGA
1 GTATCGATACTCAACGG-AGA
26646 GTATCGATACTC
1 GTATCGATACTC
26658 CCCATGGGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 1 0.04
18 12 0.46
20 12 0.46
21 1 0.04
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (20 bp):
GTATCGATACTCAACGGAGA
Found at i:27837 original size:17 final size:17
Alignment explanation
Indices: 27815--27849 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
27805 TGGAAAATAT
*
27815 AAACTTTTATTAACATA
1 AAACTTGTATTAACATA
*
27832 AAACTTGTATTTACATA
1 AAACTTGTATTAACATA
27849 A
1 A
27850 CTAGGTTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.11, G:0.03, T:0.40
Consensus pattern (17 bp):
AAACTTGTATTAACATA
Found at i:28368 original size:30 final size:30
Alignment explanation
Indices: 28333--28390 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
28323 GAAGGACCTA
* *
28333 TCCATATGTTCCAAAGAATATACGTAACTG
1 TCCATATGTCCCAAAGAACATACGTAACTG
*
28363 TCCATATGTCCCAAAGAACATAGGTAAC
1 TCCATATGTCCCAAAGAACATACGTAAC
28391 CCTCGACTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (30 bp):
TCCATATGTCCCAAAGAACATACGTAACTG
Found at i:28990 original size:19 final size:19
Alignment explanation
Indices: 28966--29021 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
28956 ACATTCCTTA
28966 ACATGTGTATCGATACACT
1 ACATGTGTATCGATACACT
28985 ACATGTGTATCGATACACT
1 ACATGTGTATCGATACACT
* * *
29004 ACCTATGTATCGGTACAC
1 ACATGTGTATCGATACAC
29022 AAATTACATT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.30
Consensus pattern (19 bp):
ACATGTGTATCGATACACT
Found at i:31661 original size:2 final size:2
Alignment explanation
Indices: 31654--31689 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
31644 CAAACTTTTC
31654 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
31690 TCTTTACAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33619 original size:17 final size:17
Alignment explanation
Indices: 33597--33631 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
33587 TAGAAAATTT
*
33597 AAACTTTTATTAACATA
1 AAACTTGTATTAACATA
*
33614 AAACTTGTATTTACATA
1 AAACTTGTATTAACATA
33631 A
1 A
33632 CTAGGTTCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.11, G:0.03, T:0.40
Consensus pattern (17 bp):
AAACTTGTATTAACATA
Found at i:34841 original size:30 final size:30
Alignment explanation
Indices: 34806--34864 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
34796 GATTTATTTA
* *
34806 GTGACCAAATTATAAA-TTTGGTAAAGTTTG
1 GTGACCAAAGTATAAACTTT-GAAAAGTTTG
34836 GTGACCAAAGTATAAACTTTGAAAAGTTT
1 GTGACCAAAGTATAAACTTTGAAAAGTTT
34865 AGGAACCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 23 0.88
31 3 0.12
ACGTcount: A:0.39, C:0.08, G:0.19, T:0.34
Consensus pattern (30 bp):
GTGACCAAAGTATAAACTTTGAAAAGTTTG
Found at i:34873 original size:30 final size:30
Alignment explanation
Indices: 34809--34874 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
34799 TTATTTAGTG
* * *
34809 ACCAAATTATAAATTTGGTAAAGTTTGGTG
1 ACCAAAGTATAAATTTGGAAAAGTTTGGTA
34839 ACCAAAGTATAAACTTT-GAAAAGTTTAGG-A
1 ACCAAAGTATAAA-TTTGGAAAAGTTT-GGTA
34869 ACCAAA
1 ACCAAA
34875 ATGTAATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
30 26 0.84
31 5 0.16
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.29
Consensus pattern (30 bp):
ACCAAAGTATAAATTTGGAAAAGTTTGGTA
Found at i:36989 original size:22 final size:22
Alignment explanation
Indices: 36962--37013 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
36952 TACACTGTTA
36962 ACTGTTCACGGTACTGTTTATC
1 ACTGTTCACGGTACTGTTTATC
*
36984 ACTGTTCACGGTATTGTTTATC
1 ACTGTTCACGGTACTGTTTATC
*
37006 ACTATTCA
1 ACTGTTCA
37014 TAAAAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.42
Consensus pattern (22 bp):
ACTGTTCACGGTACTGTTTATC
Found at i:44525 original size:3 final size:3
Alignment explanation
Indices: 44506--44562 Score: 71
Period size: 3 Copynumber: 18.7 Consensus size: 3
44496 TCGAAAAGCA
* *
44506 TAT TAAT TAT ATAT TAT TAT TAA T-T TAT TAT TAT TAT AAT TAT TAT
1 TAT T-AT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
44552 TAT TAT TAT TA
1 TAT TAT TAT TA
44563 AACATATTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 1 0.02
3 40 0.85
4 6 0.13
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:46288 original size:30 final size:30
Alignment explanation
Indices: 46245--46405 Score: 143
Period size: 30 Copynumber: 5.4 Consensus size: 30
46235 AAATTGTTGT
* * *
46245 TTTTTTCTTTTTTAATCCCTTAAATTTCTA
1 TTTTTGCTATTTTAATCCCTTAAGTTTCTA
* *
46275 TTTTTGCTATTTTAGTCCTTTAAGTTTCTA
1 TTTTTGCTATTTTAATCCCTTAAGTTTCTA
* * * * *
46305 TATTTGTTATTTT-GTCCTTTAAGTTTCTG
1 TTTTTGCTATTTTAATCCCTTAAGTTTCTA
46334 TTTTTGCTA-TTTAGA-CCCTTAAGTTT-TGA
1 TTTTTGCTATTTTA-ATCCCTTAAGTTTCT-A
* *
46363 TTTTTACTATTTT-ATCCCTTCAAGTTTTTA
1 TTTTTGCTATTTTAATCCCTT-AAGTTTCTA
*
46393 TTTTTGCCATTTT
1 TTTTTGCTATTTT
46406 GGTCCTTTAA
Statistics
Matches: 108, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
28 5 0.05
29 45 0.42
30 57 0.53
31 1 0.01
ACGTcount: A:0.17, C:0.14, G:0.08, T:0.60
Consensus pattern (30 bp):
TTTTTGCTATTTTAATCCCTTAAGTTTCTA
Found at i:46339 original size:59 final size:60
Alignment explanation
Indices: 46254--46433 Score: 181
Period size: 59 Copynumber: 3.0 Consensus size: 60
46244 TTTTTTTCTT
* **
46254 TTTTAATCCC-TTAAATTTCTATTTTTGCTATTTTAGTCCTTTAAGTTTCT-ATATTTGTTA
1 TTTT-ATCCCTTTAAGTTTCTATTTTTGCTATTTTAGTCCTTTAAGTTT-TGATATTTACTA
* * * * *
46314 TTTTGT-CCTTTAAGTTTCTGTTTTTGCTA-TTTAGACCCTTAAGTTTTGATTTTTACTA
1 TTTTATCCCTTTAAGTTTCTATTTTTGCTATTTTAGTCCTTTAAGTTTTGATATTTACTA
* * * * *
46372 TTTTATCCCTTCAAGTTTTTATTTTTGCCATTTTGGTCCTTTAACTTTATG-TATTTACTA
1 TTTTATCCCTTTAAGTTTCTATTTTTGCTATTTTAGTCCTTTAAGTTT-TGATATTTACTA
46432 TT
1 TT
46434 CAACCCTTTA
Statistics
Matches: 97, Mismatches: 18, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
57 1 0.01
58 29 0.30
59 38 0.39
60 27 0.28
61 2 0.02
ACGTcount: A:0.19, C:0.14, G:0.09, T:0.58
Consensus pattern (60 bp):
TTTTATCCCTTTAAGTTTCTATTTTTGCTATTTTAGTCCTTTAAGTTTTGATATTTACTA
Found at i:47771 original size:14 final size:13
Alignment explanation
Indices: 47752--47804 Score: 54
Period size: 14 Copynumber: 4.0 Consensus size: 13
47742 TTAGTTTACT
47752 ATAACTTTTGAAAA
1 ATAACTTTT-AAAA
47766 ATAACTTTT-AAA
1 ATAACTTTTAAAA
* *
47778 ATTATTTTTAGAAA
1 ATAACTTTTA-AAA
*
47792 AGAACTTTTAAAA
1 ATAACTTTTAAAA
47805 GTGTTAAACA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
12 10 0.31
13 3 0.09
14 19 0.59
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.40
Consensus pattern (13 bp):
ATAACTTTTAAAA
Found at i:49785 original size:75 final size:75
Alignment explanation
Indices: 49635--49820 Score: 246
Period size: 75 Copynumber: 2.5 Consensus size: 75
49625 CAAAGCCAAA
* * * * **
49635 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGATT--CCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
49700 TTTGGCTCCGAG
64 TTTGGCTCCGAG
* *
49712 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACATTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
* *
49777 TTGTTCCGAG
66 TGGCTCCGAG
* *
49787 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCC
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCC
49821 CTGTTCAACG
Statistics
Matches: 96, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
75 71 0.74
77 25 0.26
ACGTcount: A:0.25, C:0.31, G:0.23, T:0.22
Consensus pattern (75 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
TGGCTCCGAG
Found at i:57135 original size:15 final size:15
Alignment explanation
Indices: 57095--57135 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
57085 TTGTTTCAAC
* *
57095 ATTTTGAATTGTTTG
1 ATTTTGGATTGTTGG
57110 ATTTGTGGATTGTTGG
1 ATTT-TGGATTGTTGG
57126 ATTTTGGATT
1 ATTTTGGATT
57136 TATGAATGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.17, C:0.00, G:0.27, T:0.56
Consensus pattern (15 bp):
ATTTTGGATTGTTGG
Found at i:57886 original size:75 final size:75
Alignment explanation
Indices: 57736--57921 Score: 246
Period size: 75 Copynumber: 2.5 Consensus size: 75
57726 CAAAGCCAAA
* * * * **
57736 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGATT--CCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
57801 TTTGGCTCCGAG
64 TTTGGCTCCGAG
* *
57813 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACATTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
* *
57878 TTGTTCCGAG
66 TGGCTCCGAG
* *
57888 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCC
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCC
57922 CCTGTTCAAC
Statistics
Matches: 96, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
75 71 0.74
77 25 0.26
ACGTcount: A:0.25, C:0.31, G:0.23, T:0.22
Consensus pattern (75 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
TGGCTCCGAG
Found at i:61617 original size:183 final size:184
Alignment explanation
Indices: 61288--61673 Score: 620
Period size: 183 Copynumber: 2.1 Consensus size: 184
61278 TTTTCTAATT
* * *
61288 TATATAAAAT-TA-AATATTTTTTAATTCAAAAAAGGTTTATAATTAATTTAAATAATAAATAAT
1 TATATAATATATATAATATTTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATAAATAAT
*
61351 TATAAAATAAAAATTTTAGATAAATTTTTTAATTAATTAATATTAATTTAAGTTTAAAATTTATT
66 TATAAAATAAAAATTTTAGATAAATTTTTTAATTAATTAATATTAATTTAAGTTTAAAAGTTATT
* *
61416 GGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTT-AGCCCATATGTTA
131 AGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGG-TTGAGCCCATATGTTA
*
61470 TATATAATATATATAATATTTTTTAATT-AAAAAACAGTTTACAATTAATTTAAATAATATATAA
1 TATATAATATATATAATATTTTTTAATTCAAAAAA-AGTTTACAATTAATTTAAATAATAAATAA
* *
61534 TTATAAAATAAAAATTTTATAT-AATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
65 TTATAAAATAAAAATTTTAGATAAATTTTTTAATTAATTAATATTAATTTAAGTTTAAAAGTTAT
*
61598 TAGATCTTAAATTATTAATTGGGTTTTTAATGATTTGGGTTGAGCCCATATGTTA
130 TAGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTGAGCCCATATGTTA
*
61653 TATATAATATATTTAATATTT
1 TATATAATATATATAATATTT
61674 AAAATTTAAT
Statistics
Matches: 189, Mismatches: 11, Indels: 7
0.91 0.05 0.03
Matches are distributed among these distances:
182 11 0.06
183 117 0.62
184 61 0.32
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.46
Consensus pattern (184 bp):
TATATAATATATATAATATTTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATAAATAAT
TATAAAATAAAAATTTTAGATAAATTTTTTAATTAATTAATATTAATTTAAGTTTAAAAGTTATT
AGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTGAGCCCATATGTTA
Found at i:63746 original size:3 final size:3
Alignment explanation
Indices: 63738--63767 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
63728 TTATTTTGAA
63738 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
63768 TATGCAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:72080 original size:3 final size:3
Alignment explanation
Indices: 72072--72147 Score: 53
Period size: 3 Copynumber: 24.0 Consensus size: 3
72062 CCATTTTTAT
* * * * * * *
72072 TTA TTA TTA TTA TAA TAA TAA TAA TAA TAA TTA TTA TTA TTA TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
72120 TATA TATA TATA TATA TTA TTA TTA TTA
1 T-TA T-TA T-TA T-TA TTA TTA TTA TTA
72148 AAAAAATAAT
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
3 54 0.79
4 14 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (3 bp):
TTA
Found at i:72139 original size:25 final size:21
Alignment explanation
Indices: 72095--72142 Score: 60
Period size: 25 Copynumber: 2.1 Consensus size: 21
72085 AATAATAATA
72095 ATAATAATTATTATTATTATT
1 ATAATAATTATTATTATTATT
72116 ATAATATATATATATATATATTATT
1 ATAATA-AT-TAT-TAT-TATTATT
72141 AT
1 AT
72143 TATTAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 6 0.26
22 2 0.09
23 3 0.13
24 3 0.13
25 9 0.39
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATAATAATTATTATTATTATT
Found at i:84869 original size:1 final size:1
Alignment explanation
Indices: 84858--84922 Score: 76
Period size: 1 Copynumber: 65.0 Consensus size: 1
84848 ATGCTTGAAG
* * * * * *
84858 AAAAAAGAAAAAAAAAAGAAAAGAAAAAAAAAAAAAAAAAAAAGAAAAGAAAAAGAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
84923 GGGGGTCAAG
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (1 bp):
A
Found at i:84874 original size:11 final size:11
Alignment explanation
Indices: 84855--84923 Score: 97
Period size: 11 Copynumber: 6.3 Consensus size: 11
84845 ATTATGCTTG
84855 AAGAAAAAAGAA
1 AAGAAAAAA-AA
84867 AA-AAAAAAGAA
1 AAGAAAAAA-AA
84878 AAGAAAAAAAA
1 AAGAAAAAAAA
84889 AA-AAAAAAAA
1 AAGAAAAAAAA
*
84899 AAGAAAAGAAA
1 AAGAAAAAAAA
84910 AAGAAAAAAAA
1 AAGAAAAAAAA
84921 AAG
1 AAG
84924 GGGGTCAAGA
Statistics
Matches: 53, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
10 10 0.19
11 35 0.66
12 8 0.15
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:84894 original size:26 final size:26
Alignment explanation
Indices: 84858--84922 Score: 112
Period size: 26 Copynumber: 2.5 Consensus size: 26
84848 ATGCTTGAAG
*
84858 AAAAAAGAAAAAAAAAAGAAAAGAAA
1 AAAAAAAAAAAAAAAAAGAAAAGAAA
84884 AAAAAAAAAAAAAAAAAGAAAAGAAA
1 AAAAAAAAAAAAAAAAAGAAAAGAAA
*
84910 AAGAAAAAAAAAA
1 AAAAAAAAAAAAA
84923 GGGGGTCAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (26 bp):
AAAAAAAAAAAAAAAAAGAAAAGAAA
Found at i:86044 original size:89 final size:89
Alignment explanation
Indices: 85893--86170 Score: 506
Period size: 89 Copynumber: 3.1 Consensus size: 89
85883 AAGTGCCATG
85893 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAA
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAA
85958 ACCATCATTGGATTTAAAGATGAA
66 ACCATCATTGGATTTAAAGATGAA
85982 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCC-AAA
1 TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAA
86046 ACCATCATT-GATTTAAAGATGAA
66 ACCATCATTGGATTTAAAGATGAA
86069 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAA
1 --TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAA
86134 AAACCAATCATTGGATTTGAAAGATGAA
64 AAACC-ATCATTGGATTT-AAAGATGAA
86162 TGCTCATAG
1 TGCTCATAG
86171 TAGAAATAAG
Statistics
Matches: 183, Mismatches: 0, Indels: 10
0.95 0.00 0.05
Matches are distributed among these distances:
87 14 0.08
88 12 0.07
89 122 0.67
90 6 0.03
91 15 0.08
92 5 0.03
93 9 0.05
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.35
Consensus pattern (89 bp):
TGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAA
ACCATCATTGGATTTAAAGATGAA
Found at i:86272 original size:111 final size:114
Alignment explanation
Indices: 86076--86383 Score: 495
Period size: 111 Copynumber: 2.8 Consensus size: 114
86066 GAATGTGCTC
86076 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAAACCAA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAAACCAA
86141 TCATTGGATTTGAAAGATGAA-TGCTCATAGTAGAAATAAGAAGACCC-
66 TCATTGGATTTGAAAGATGAAGTGCTCATAGTAGAAATAAGAAGACCCA
* *
86188 A-AGCATTTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATATGAACCCCAAAAACCAA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAAACCAA
*
86252 TCATTGGATTTGAAAGATGAATGTGCTCATAGTAGAGATAAGAAGACCCA
66 TCATTGGATTTGAAAGATGAA-GTGCTCATAGTAGAAATAAGAAGACCCA
* * *
86302 ATAGCATCTT-TGGAAGTGTTCTTTGAGTTATCTGATCTGGTTCGGTAGGAA--CCACAAACCAA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAAACCAA
*
86364 TCATTGGAATT-AAAGATGAA
66 TCATTGGATTTGAAAGATGAA
86384 CTGCATGATC
Statistics
Matches: 183, Mismatches: 9, Indels: 9
0.91 0.04 0.04
Matches are distributed among these distances:
111 91 0.50
112 21 0.11
113 25 0.14
114 39 0.21
115 7 0.04
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (114 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCCAAAAACCAA
TCATTGGATTTGAAAGATGAAGTGCTCATAGTAGAAATAAGAAGACCCA
Done.