Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004542.1 Hibiscus syriacus cultivar Beakdansim tig00010052_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: 98836
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Found at i:2087 original size:29 final size:28
Alignment explanation
Indices: 2037--2091 Score: 65
Period size: 29 Copynumber: 1.9 Consensus size: 28
2027 TGAGAAAGGA
2037 TATGAACTATATGAGAACATGTATATGAT
1 TATGAACTATATGAGAACATGT-TATGAT
* * * *
2066 TATGAGCTATGTGATAAGATGTTATG
1 TATGAACTATATGAGAACATGTTATG
2092 TTAAATGATC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 4 0.18
29 18 0.82
ACGTcount: A:0.36, C:0.05, G:0.22, T:0.36
Consensus pattern (28 bp):
TATGAACTATATGAGAACATGTTATGAT
Found at i:2384 original size:7 final size:7
Alignment explanation
Indices: 2372--2399 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
2362 CCTTCGAGAC
2372 ATATGTG
1 ATATGTG
2379 ATATGTG
1 ATATGTG
2386 ATATGTG
1 ATATGTG
2393 ATATGTG
1 ATATGTG
2400 GTCCTTCGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.43
Consensus pattern (7 bp):
ATATGTG
Found at i:11733 original size:66 final size:62
Alignment explanation
Indices: 11645--11798 Score: 191
Period size: 66 Copynumber: 2.4 Consensus size: 62
11635 TACACTAGGG
* * *
11645 GTGCATCTGTACACTAATTGCATTCGATGTTTCAAAAAAAACCAGGAGTGCATCGATGCATGGTC
1 GTGCATC-GTACACAAAATGCATTCGATGTTTC-AAAAAAACCAAGAGTGCATCGATGCATGG--
11710 T
62 T
** **
11711 GTGCATCGATACACAAAATGCATTCGATGTTTCAATGAATTCAAGAGTGCATCGATGCATGGT
1 GTGCATCG-TACACAAAATGCATTCGATGTTTCAAAAAAACCAAGAGTGCATCGATGCATGGT
11774 GTGCATCGGTACACAAAATGCATTC
1 GTGCATC-GTACACAAAATGCATTC
11799 CAAATAGGGT
Statistics
Matches: 79, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
63 24 0.30
64 1 0.01
65 25 0.32
66 29 0.37
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.28
Consensus pattern (62 bp):
GTGCATCGTACACAAAATGCATTCGATGTTTCAAAAAAACCAAGAGTGCATCGATGCATGGT
Found at i:11835 original size:12 final size:9
Alignment explanation
Indices: 11809--11872 Score: 53
Period size: 8 Copynumber: 6.8 Consensus size: 9
11799 CAAATAGGGT
11809 GTGCATCGA
1 GTGCATCGA
11818 -TGCATCATGAA
1 GTGCATC--G-A
11829 GTGCATCGA
1 GTGCATCGA
11838 GTGCATCGA
1 GTGCATCGA
11847 -TGCATCATGAA
1 GTGCATC--G-A
11858 GTGCATCG-
1 GTGCATCGA
11866 GTGCATC
1 GTGCATC
11873 CCTTCATAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 17
0.73 0.00 0.27
Matches are distributed among these distances:
8 19 0.40
9 10 0.21
10 4 0.09
11 2 0.04
12 12 0.26
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (9 bp):
GTGCATCGA
Found at i:11843 original size:29 final size:28
Alignment explanation
Indices: 11809--11872 Score: 119
Period size: 29 Copynumber: 2.2 Consensus size: 28
11799 CAAATAGGGT
11809 GTGCATCGATGCATCATGAAGTGCATCG
1 GTGCATCGATGCATCATGAAGTGCATCG
11837 AGTGCATCGATGCATCATGAAGTGCATCG
1 -GTGCATCGATGCATCATGAAGTGCATCG
11866 GTGCATC
1 GTGCATC
11873 CCTTCATAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 7 0.20
29 28 0.80
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (28 bp):
GTGCATCGATGCATCATGAAGTGCATCG
Found at i:14505 original size:23 final size:22
Alignment explanation
Indices: 14471--14544 Score: 87
Period size: 23 Copynumber: 3.3 Consensus size: 22
14461 CATAGTAGGG
*
14471 TGCATCGATGCACATTCAAGGAA
1 TGCATCGATGCACATTCATGG-A
* *
14494 TGCATCGGTGCACCTTCATGG-
1 TGCATCGATGCACATTCATGGA
*
14515 TGTATCGATGCACATTCATGGGA
1 TGCATCGATGCACATTCAT-GGA
14538 TGCATCG
1 TGCATCG
14545 GTACACTCTC
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
21 16 0.38
22 2 0.05
23 24 0.57
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (22 bp):
TGCATCGATGCACATTCATGGA
Found at i:20862 original size:93 final size:89
Alignment explanation
Indices: 20704--20910 Score: 245
Period size: 93 Copynumber: 2.3 Consensus size: 89
20694 CAACAATTTG
*
20704 TTTTAGTACTTAAACTTTCAATTTTTAAAACTATACATAACGTTTAGTTTTTGTTTCATTCTAGT
1 TTTTAGTACTTAAACTTTCAATTTTTAAAACTATACATAACGTTTAGTTATTGTTTCATTCTAGT
20769 ACCCCACAGTTAAAAAATTAACGA
66 ACCCCACAGTTAAAAAATTAACGA
* * **
20793 TTTTAGTACCTAAACTTTTAATTTTTCCCCAAAA-TCATACATATTGTTTAGTTATTGTTTCATT
1 TTTTAGTACTTAAACTTTCAATTTTT----AAAACT-ATACATAACGTTTAGTTATTGTTTCATT
* * * * * *
20857 TTAGTACTCTACCGTTAAAAACTTAATGA
61 CTAGTACCCCACAGTTAAAAAATTAACGA
* *
20886 TTTTTGTACTTAAACTATCAATTTT
1 TTTTAGTACTTAAACTTTCAATTTT
20911 GATTAATTTT
Statistics
Matches: 98, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
89 24 0.24
92 1 0.01
93 73 0.74
ACGTcount: A:0.32, C:0.15, G:0.07, T:0.45
Consensus pattern (89 bp):
TTTTAGTACTTAAACTTTCAATTTTTAAAACTATACATAACGTTTAGTTATTGTTTCATTCTAGT
ACCCCACAGTTAAAAAATTAACGA
Found at i:30738 original size:35 final size:34
Alignment explanation
Indices: 30653--30739 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
30643 ATTTGGTATT
*
30653 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
30687 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
30725 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
30740 ACTGAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:30966 original size:12 final size:12
Alignment explanation
Indices: 30949--30987 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
30939 ACTCCTCGCT
*
30949 GTCATCATCGTC
1 GTCATCGTCGTC
* *
30961 GTCATCGTCATT
1 GTCATCGTCGTC
30973 GTCATCGTCGTC
1 GTCATCGTCGTC
30985 GTC
1 GTC
30988 CTAAGCAGGT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.13, C:0.31, G:0.21, T:0.36
Consensus pattern (12 bp):
GTCATCGTCGTC
Found at i:32975 original size:111 final size:111
Alignment explanation
Indices: 32835--33165 Score: 592
Period size: 111 Copynumber: 3.0 Consensus size: 111
32825 ATTACAAAAA
32835 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
32900 AATTAAAATGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
* * *
32946 TTAATTCTTAATCTAATAATCATGTATTAAATAAATCAACTAATTATGACTAAAAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
33011 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
*
33057 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATT-
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* *
33121 AATTAAAACGTTAAAATGTTACCGTATTAGCAAAGTGTAGAGATA
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATA
33166 ATGATTTCCA
Statistics
Matches: 210, Mismatches: 10, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
110 43 0.20
111 167 0.80
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
Found at i:43588 original size:19 final size:17
Alignment explanation
Indices: 43546--43591 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 17
43536 AAAAATATTC
43546 TTTTTATTTTATTCCTT
1 TTTTTATTTTATTCCTT
*
43563 TCATTTATTTTATTTCCTT
1 T-TTTTATTTTA-TTCCTT
43582 ATTTTTATTT
1 -TTTTTATTT
43592 CTCTCTTTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 1 0.04
18 9 0.38
19 13 0.54
20 1 0.04
ACGTcount: A:0.15, C:0.11, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTTATTTTATTCCTT
Found at i:53867 original size:2 final size:2
Alignment explanation
Indices: 53862--53888 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
53852 TTCGATTCTT
53862 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
53889 TCTCACCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:55814 original size:29 final size:30
Alignment explanation
Indices: 55764--55824 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 30
55754 TGAGAAAGGA
55764 TATGAACTATATGAGAACATG-TATATGAT
1 TATGAACTATATGAGAACATGTTATATGAT
* * * * *
55793 TATGAGCTATGTGATAAGATGTTATGTGAT
1 TATGAACTATATGAGAACATGTTATATGAT
55823 TA
1 TA
55825 AATGATCAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (30 bp):
TATGAACTATATGAGAACATGTTATATGAT
Found at i:61119 original size:16 final size:17
Alignment explanation
Indices: 61095--61137 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
61085 TGATTCAGTT
61095 ACAGATCAGGTTT-ATA
1 ACAGATCAGGTTTGATA
*
61111 ACAGGTCA-GTTTGATA
1 ACAGATCAGGTTTGATA
*
61127 ATAGATCAGGT
1 ACAGATCAGGT
61138 AATATTAGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
15 4 0.18
16 16 0.73
17 2 0.09
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (17 bp):
ACAGATCAGGTTTGATA
Found at i:65423 original size:65 final size:65
Alignment explanation
Indices: 65345--65471 Score: 164
Period size: 65 Copynumber: 2.0 Consensus size: 65
65335 TACACTAGGG
** * * *
65345 GTGCATCGGTACACTAATTACATTCGATGTTTCAAAAAAGCCAAGAGTCCATCGATGCATGGTTT
1 GTGCATCAATACACAAAATACATTCGATGTTTCAAAAAAGCCAAGAGTACATCGATGCATGGTTT
* ** **
65410 GTGCATCAATACACAAAATGCATTCGATGTTTCAATGAATTCAAGAGTACATCGATGCATGG
1 GTGCATCAATACACAAAATACATTCGATGTTTCAAAAAAGCCAAGAGTACATCGATGCATGG
65472 CTATGCACGG
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
65 52 1.00
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (65 bp):
GTGCATCAATACACAAAATACATTCGATGTTTCAAAAAAGCCAAGAGTACATCGATGCATGGTTT
Found at i:70443 original size:31 final size:31
Alignment explanation
Indices: 70403--70621 Score: 372
Period size: 31 Copynumber: 7.1 Consensus size: 31
70393 GAGGTCAATA
*
70403 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAATTGTTCATATGTGCCTTTAAACATATG
*
70434 TAGAA-TGTTCATATGTGCCTTTAAACATATA
1 TA-AATTGTTCATATGTGCCTTTAAACATATG
*
70465 T-AACTGTTCATATGTGCCTTTAAACATAT-
1 TAAATTGTTCATATGTGCCTTTAAACATATG
*
70494 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAATTGTTCATATGTGCCTTTAAACATATG
70525 TAAATTGTTCATATGTGCCTTTAAACATATG
1 TAAATTGTTCATATGTGCCTTTAAACATATG
70556 TAAATTGTTCATATGTGCCTTTAAACATATG
1 TAAATTGTTCATATGTGCCTTTAAACATATG
70587 TAAATTGTTCATATGTGCCTTTAAACATATG
1 TAAATTGTTCATATGTGCCTTTAAACATATG
70618 TAAA
1 TAAA
70622 CCCTCGACTC
Statistics
Matches: 182, Mismatches: 2, Indels: 8
0.95 0.01 0.04
Matches are distributed among these distances:
29 3 0.02
30 53 0.29
31 124 0.68
32 2 0.01
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.40
Consensus pattern (31 bp):
TAAATTGTTCATATGTGCCTTTAAACATATG
Found at i:71245 original size:64 final size:64
Alignment explanation
Indices: 71138--71297 Score: 214
Period size: 64 Copynumber: 2.5 Consensus size: 64
71128 CAATAAGGGT
* * * *
71138 ATGCATCGATGCACTACTGATGCATCGATGCATAAAATACATTCGATGTTGT-ATTATTATTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAAATACATTCGATGTT-TCACTATTAATGGG
* ** * *
71202 ATGCATCGATGCACTCCTTATGCATCGATGCACCGATTGCATTCGATGTTTCACTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAAATACATTCGATGTTTCACTATTAATGGG
*
71266 ATGCATCGATGCACTACTTATGCATCAATGCA
1 ATGCATCGATGCACTACTTATGCATCGATGCA
71298 TGAATTTATT
Statistics
Matches: 84, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
63 1 0.01
64 83 0.99
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACAAAATACATTCGATGTTTCACTATTAATGGG
Found at i:74585 original size:31 final size:31
Alignment explanation
Indices: 74543--74733 Score: 328
Period size: 31 Copynumber: 6.2 Consensus size: 31
74533 GGTCACAATA
*
74543 TAAACTATTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
* *
74574 TAGACTGTTCATATGTGCCTTTAAACATATA
1 TAAACTGTTCATATGTGCCTTTAAACATATG
74605 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
* *
74636 TAGACTGCTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
74667 TAAATTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
74698 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
74729 TAAAC
1 TAAAC
74734 CCTCGACTCT
Statistics
Matches: 149, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 149 1.00
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (31 bp):
TAAACTGTTCATATGTGCCTTTAAACATATG
Found at i:75452 original size:64 final size:63
Alignment explanation
Indices: 75248--75470 Score: 232
Period size: 64 Copynumber: 3.5 Consensus size: 63
75238 CAATAAGGGT
* * * * * * *
75248 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATACATTCGATGTTGTATTATTATTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTTTTATT-TTAATGGG
* * * *
75312 ATGCATCGATGCACTCCTTATGCATCGATGCACG-ATTGCATTCGATGTTTCACTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTTTTA-TTTTAATGGG
* * * ** *
75375 ATGTATCGATGCACTACTTATGCATCGATGCATGAATTGTATTCGATCTTTTTATTTTAAAAGA
1 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGAT-GTTTTATTTTAATGGG
** *
75439 ATGCATCGATGCACTACCAATGCATCGTTGCA
1 ATGCATCGATGCACTACTTATGCATCGATGCA
75471 CATTCAAACA
Statistics
Matches: 131, Mismatches: 25, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
63 52 0.40
64 75 0.57
65 4 0.03
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTTTTATTTTAATGGG
Found at i:77439 original size:23 final size:22
Alignment explanation
Indices: 77399--77478 Score: 72
Period size: 23 Copynumber: 3.6 Consensus size: 22
77389 CATAGTAGGG
* *
77399 TGCATCGATGCACATTCAAGGAA
1 TGCATCGATACACATTCATGG-A
* *
77422 TGCATCGGTACACCTTCATGG-
1 TGCATCGATACACATTCATGGA
* *
77443 TGTATCGATGCACATTCATGGGA
1 TGCATCGATACACATTCAT-GGA
*
77466 TGCATCGGTACAC
1 TGCATCGATACAC
77479 TCTCTAGTGT
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
21 15 0.34
22 2 0.05
23 27 0.61
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (22 bp):
TGCATCGATACACATTCATGGA
Found at i:83370 original size:65 final size:64
Alignment explanation
Indices: 83281--83436 Score: 224
Period size: 65 Copynumber: 2.4 Consensus size: 64
83271 TACACTAGGG
* * *
83281 GTGCATCGGTACACTAATTACATTCGATGTTTCAA-AAGAGCCAGGAGTACATCGATGCATGGTC
1 GTGCATCGGTACACAAAATGCATTCGATGTTTCAATAA-AGCCAGGAGTACATCGATGCATGGT-
83345 T
64 T
** * *
83346 GTGCATCGGTACACAAAATGCATTCGATGTTTCAATAAATTCATGAGTGCATCGATGCATGGTT
1 GTGCATCGGTACACAAAATGCATTCGATGTTTCAATAAAGCCAGGAGTACATCGATGCATGGTT
83410 GTGCATCGGTACACAAAATGCATTCGA
1 GTGCATCGGTACACAAAATGCATTCGA
83437 AATAGGGTGT
Statistics
Matches: 83, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
64 28 0.34
65 53 0.64
66 2 0.02
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.28
Consensus pattern (64 bp):
GTGCATCGGTACACAAAATGCATTCGATGTTTCAATAAAGCCAGGAGTACATCGATGCATGGTT
Found at i:83889 original size:93 final size:89
Alignment explanation
Indices: 83731--83937 Score: 245
Period size: 93 Copynumber: 2.3 Consensus size: 89
83721 CAACAATTTG
*
83731 TTTTAGTACTTAAACTTTCAATTTTTAAAACTATACATAACGTTTAGTTTTTGTTTCATTCTAGT
1 TTTTAGTACTTAAACTTTCAATTTTTAAAACTATACATAACGTTTAGTTATTGTTTCATTCTAGT
83796 ACCCCACAGTTAAAAAATTAACGA
66 ACCCCACAGTTAAAAAATTAACGA
* * **
83820 TTTTAGTACCTAAACTTTTAATTTTTCCCCAAAA-TCATACATATTGTTTAGTTATTGTTTCATT
1 TTTTAGTACTTAAACTTTCAATTTTT----AAAACT-ATACATAACGTTTAGTTATTGTTTCATT
* * * * * *
83884 TTAGTACTCTACCGTTAAAAACTTAATGA
61 CTAGTACCCCACAGTTAAAAAATTAACGA
* *
83913 TTTTTGTACTTAAACTATCAATTTT
1 TTTTAGTACTTAAACTTTCAATTTT
83938 GATTAATTTT
Statistics
Matches: 98, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
89 24 0.24
92 1 0.01
93 73 0.74
ACGTcount: A:0.32, C:0.15, G:0.07, T:0.45
Consensus pattern (89 bp):
TTTTAGTACTTAAACTTTCAATTTTTAAAACTATACATAACGTTTAGTTATTGTTTCATTCTAGT
ACCCCACAGTTAAAAAATTAACGA
Found at i:93874 original size:15 final size:15
Alignment explanation
Indices: 93846--93878 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
93836 TGACTTTGCT
93846 GTCATCGTCGTCGTC
1 GTCATCGTCGTCGTC
93861 GTCATTCGTC-TCGTC
1 GTCA-TCGTCGTCGTC
93876 GTC
1 GTC
93879 GTCCTGAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.06, C:0.33, G:0.24, T:0.36
Consensus pattern (15 bp):
GTCATCGTCGTCGTC
Found at i:95829 original size:110 final size:111
Alignment explanation
Indices: 95688--96013 Score: 549
Period size: 110 Copynumber: 3.0 Consensus size: 111
95678 ATTACAAAAA
95688 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
95753 AATTAAAATGTTAAAATGTTA-CGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAATGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
* * *
95798 TTAATTCTTAATCTAATAATCATGTATTAAATAAATCAACTAATTATGACTAAAAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
95863 AATT-AAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAATGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
95908 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAA-TATTACTAATAATTTAAATT-
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
95971 AATTAAAACT-TTAAAATGTTACCGTATC--CAAAGTGTAGAGATA
66 AATTAAAA-TGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATA
96014 ATGATTTCCA
Statistics
Matches: 204, Mismatches: 9, Indels: 9
0.92 0.04 0.04
Matches are distributed among these distances:
107 14 0.07
108 4 0.02
109 54 0.26
110 132 0.65
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.37
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAATGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
Found at i:96095 original size:15 final size:15
Alignment explanation
Indices: 96075--96104 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
96065 GAATTATATT
96075 AGTAAAATTAAATAA
1 AGTAAAATTAAATAA
96090 AGTAAAATTAAATAA
1 AGTAAAATTAAATAA
96105 TTAAATACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.27
Consensus pattern (15 bp):
AGTAAAATTAAATAA
Done.