Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004332.1 Hibiscus syriacus cultivar Beakdansim tig00009499_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: 82127
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:30 original size:2 final size:2
Alignment explanation
Indices: 23--53 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
13 CTACCCAACA
23 AG AG AG AG AG AG AG AG AG AG AG AG -G AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
54 TAATCATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:7434 original size:22 final size:22
Alignment explanation
Indices: 7409--7455 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
7399 TATATTATTT
7409 AAATTATTTACGTTTATGTGTA
1 AAATTATTTACGTTTATGTGTA
7431 AAATTATTTACGTTTATGTGTA
1 AAATTATTTACGTTTATGTGTA
7453 AAA
1 AAA
7456 AAATTTATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (22 bp):
AAATTATTTACGTTTATGTGTA
Found at i:7461 original size:22 final size:22
Alignment explanation
Indices: 7414--7462 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
7404 TATTTAAATT
**
7414 ATTTACGTTTATGTGTAAAATT
1 ATTTACGTTTATGTGTAAAAAA
7436 ATTTACGTTTATGTGTAAAAAA
1 ATTTACGTTTATGTGTAAAAAA
7458 ATTTA
1 ATTTA
7463 TTGTGTTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.12, T:0.47
Consensus pattern (22 bp):
ATTTACGTTTATGTGTAAAAAA
Found at i:10757 original size:34 final size:35
Alignment explanation
Indices: 10718--10804 Score: 99
Period size: 35 Copynumber: 2.5 Consensus size: 35
10708 AATATAATTT
*
10718 TAAATACAACAAACTTACAATAA-G-TATTAAATGG
1 TAAATA-AACAAAATTACAATAATGATATTAAATGG
*
10752 TAAATAATAAAAAAATTACAATAATTGATATTAAATGG
1 TAAAT-A-AACAAAATTACAATAA-TGATATTAAATGG
10790 T-AATAAACAAAATTA
1 TAAATAAACAAAATTA
10805 ACAAAATAAA
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 4 0.09
38 11 0.24
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (35 bp):
TAAATAAACAAAATTACAATAATGATATTAAATGG
Found at i:10817 original size:13 final size:13
Alignment explanation
Indices: 10799--10823 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10789 GTAATAAACA
10799 AAATTAACAAAAT
1 AAATTAACAAAAT
10812 AAATTAACAAAA
1 AAATTAACAAAA
10824 AGTCCAACAA
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:0.08, G:0.00, T:0.20
Consensus pattern (13 bp):
AAATTAACAAAAT
Found at i:10840 original size:34 final size:32
Alignment explanation
Indices: 10799--10883 Score: 116
Period size: 34 Copynumber: 2.5 Consensus size: 32
10789 GTAATAAACA
*
10799 AAATTAACAAAATAAATTAACAAAAAGTCCAAC
1 AAATTAACAAAATAAATTAA-AAAAAATCCAAC
*
10832 AAATTTAACAAAAAAAATTTAAAAAAAATCCAACC
1 AAA-TTAACAAAATAAA-TTAAAAAAAATCCAA-C
10867 AAATTAACAAAATAAAT
1 AAATTAACAAAATAAAT
10884 AAAGTATTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
33 4 0.09
34 34 0.74
35 8 0.17
ACGTcount: A:0.66, C:0.13, G:0.01, T:0.20
Consensus pattern (32 bp):
AAATTAACAAAATAAATTAAAAAAAATCCAAC
Found at i:10922 original size:13 final size:13
Alignment explanation
Indices: 10904--10946 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
10894 ATGATAAATA
*
10904 AAAAAATTACAAT
1 AAAAAAGTACAAT
*
10917 AAAAAAGTCCAAT
1 AAAAAAGTACAAT
*
10930 AAACAAGTA-AAT
1 AAAAAAGTACAAT
10942 AAAAA
1 AAAAA
10947 TATAATAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 7 0.28
13 18 0.72
ACGTcount: A:0.70, C:0.09, G:0.05, T:0.16
Consensus pattern (13 bp):
AAAAAAGTACAAT
Found at i:13111 original size:12 final size:12
Alignment explanation
Indices: 13088--13157 Score: 61
Period size: 13 Copynumber: 5.5 Consensus size: 12
13078 AACTACAAAA
13088 AAAATAATTAAAT
1 AAAAT-ATTAAAT
13101 AAAATATTAAAAAAT
1 AAAATATT---AAAT
*
13116 TAAATAGTTAAAT
1 AAAATA-TTAAAT
*
13129 AAAATACT-AAT
1 AAAATATTAAAT
13140 AAAATATTAAAT
1 AAAATATTAAAT
*
13152 ATAATA
1 AAAATA
13158 AAATATACCC
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
11 10 0.21
12 12 0.26
13 14 0.30
15 9 0.19
16 2 0.04
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (12 bp):
AAAATATTAAAT
Found at i:13112 original size:23 final size:23
Alignment explanation
Indices: 13086--13157 Score: 65
Period size: 23 Copynumber: 2.9 Consensus size: 23
13076 ATAACTACAA
*
13086 AAAAAATAATTAAATAAAATATT
1 AAAAAATAATTAAATAAAATACT
13109 AAAAAATTAAATAGTTAAATAAAATACT
1 AAAAAA-T--A-A-TTAAATAAAATACT
*
13137 AATAAAAT-ATTAAATATAATA
1 AA-AAAATAATTAAATAAAATA
13158 AAATATACCC
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
23 17 0.41
24 2 0.05
26 1 0.02
27 1 0.02
28 16 0.39
29 4 0.10
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.31
Consensus pattern (23 bp):
AAAAAATAATTAAATAAAATACT
Found at i:13126 original size:28 final size:29
Alignment explanation
Indices: 13089--13144 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
13079 ACTACAAAAA
*
13089 AAATAATTAAATAAAATATTAA-AAAATT
1 AAATAATTAAATAAAATACTAATAAAATT
*
13117 AAATAGTTAAATAAAATACTAATAAAAT
1 AAATAATTAAATAAAATACTAATAAAAT
13145 ATTAAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 20 0.80
29 5 0.20
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (29 bp):
AAATAATTAAATAAAATACTAATAAAATT
Found at i:13158 original size:17 final size:18
Alignment explanation
Indices: 13130--13163 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
13120 TAGTTAAATA
13130 AAATACTAATAAAATATT
1 AAATACTAATAAAATATT
13148 AAATA-TAATAAAATAT
1 AAATACTAATAAAATAT
13164 ACCCTAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (18 bp):
AAATACTAATAAAATATT
Found at i:18542 original size:12 final size:12
Alignment explanation
Indices: 18499--18560 Score: 58
Period size: 11 Copynumber: 5.4 Consensus size: 12
18489 CTCAAACTCA
18499 ATTG-AAGCTCG
1 ATTGTAAGCTCG
* * *
18510 ATTTTGAGCTTG
1 ATTGTAAGCTCG
18522 ATTGT-AGCTCG
1 ATTGTAAGCTCG
18533 ATTGTAAGCTCG
1 ATTGTAAGCTCG
* *
18545 ATT-CAAGCTCA
1 ATTGTAAGCTCG
18556 ATTGT
1 ATTGT
18561 GAACTCAATT
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
11 22 0.55
12 18 0.45
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.37
Consensus pattern (12 bp):
ATTGTAAGCTCG
Found at i:18542 original size:23 final size:23
Alignment explanation
Indices: 18499--18590 Score: 71
Period size: 23 Copynumber: 4.0 Consensus size: 23
18489 CTCAAACTCA
* * *
18499 ATTGAAGCTCGATTTTGAGCTTG
1 ATTGAAGCTCGATTGTAAGCTCG
*
18522 ATTGTAGCTCGATTGTAAGCTCG
1 ATTGAAGCTCGATTGTAAGCTCG
* * *
18545 ATTCAAGCTCAATTGTGAA-CTCA
1 ATTGAAGCTCGATTGT-AAGCTCG
* * *
18568 ATTCAAACTCGACT-TAAGCTCG
1 ATTGAAGCTCGATTGTAAGCTCG
18590 A
1 A
18591 GGATGGGTTA
Statistics
Matches: 55, Mismatches: 12, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
21 2 0.04
22 5 0.09
23 46 0.84
24 2 0.04
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (23 bp):
ATTGAAGCTCGATTGTAAGCTCG
Found at i:26421 original size:30 final size:30
Alignment explanation
Indices: 26385--26480 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 30
26375 TTGACCTAAC
*
26385 TAACACCCTATAGATTTATAATTCCCGTTA
1 TAACACCCTATAGATCTATAATTCCCGTTA
* * * * * * *
26415 TAACACCGTTTA-ACCAATATTTCTC-TAA
1 TAACACCCTATAGATCTATAATTCCCGTTA
*
26443 CTAACACCTTATAGATCTATAATTCCCGTTA
1 -TAACACCCTATAGATCTATAATTCCCGTTA
26474 TAACACC
1 TAACACC
26481 GTTTGACAAA
Statistics
Matches: 48, Mismatches: 15, Indels: 6
0.70 0.22 0.09
Matches are distributed among these distances:
28 2 0.04
29 18 0.38
30 26 0.54
31 2 0.04
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.34
Consensus pattern (30 bp):
TAACACCCTATAGATCTATAATTCCCGTTA
Found at i:26447 original size:59 final size:59
Alignment explanation
Indices: 26380--26508 Score: 222
Period size: 59 Copynumber: 2.2 Consensus size: 59
26370 GAGTTTTGAC
* *
26380 CTAACTAACACCCTATAGATTTATAATTCCCGTTATAACACCGTTTAACCAATATTTCT
1 CTAACTAACACCCTATAGATCTATAATTCCCGTTATAACACCGTTTAACAAATATTTCT
* *
26439 CTAACTAACACCTTATAGATCTATAATTCCCGTTATAACACCGTTTGACAAATATTTCT
1 CTAACTAACACCCTATAGATCTATAATTCCCGTTATAACACCGTTTAACAAATATTTCT
26498 CTAACTAACAC
1 CTAACTAACAC
26509 TCTTTCGGCT
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
59 66 1.00
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.34
Consensus pattern (59 bp):
CTAACTAACACCCTATAGATCTATAATTCCCGTTATAACACCGTTTAACAAATATTTCT
Found at i:26450 original size:29 final size:29
Alignment explanation
Indices: 26415--26508 Score: 84
Period size: 29 Copynumber: 3.2 Consensus size: 29
26405 ATTCCCGTTA
26415 TAACACCGTTTAACCAATATTTCTCTAAC
1 TAACACCGTTTAACCAATATTTCTCTAAC
* * * * *
26444 TAACACC-TTATAGATCTATAATTCCCGTTA-
1 TAACACCGTT-TA-ACCAATATTTCTC-TAAC
* *
26474 TAACACCGTTTGACAAATATTTCTCTAAC
1 TAACACCGTTTAACCAATATTTCTCTAAC
26503 TAACAC
1 TAACAC
26509 TCTTTCGGCT
Statistics
Matches: 48, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
28 4 0.08
29 23 0.48
30 17 0.35
31 4 0.08
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.34
Consensus pattern (29 bp):
TAACACCGTTTAACCAATATTTCTCTAAC
Found at i:32129 original size:23 final size:23
Alignment explanation
Indices: 32096--32158 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
32086 AATGATTCAG
* *
32096 TGCTGACTGATTCAGCAAAATAT
1 TGCTGAATGATTCAGCAAAACAT
* *
32119 TGCTGAATGATTCAACATAACAT
1 TGCTGAATGATTCAGCAAAACAT
*
32142 TACTGAATGATTCAGCA
1 TGCTGAATGATTCAGCA
32159 CATAAGTACA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (23 bp):
TGCTGAATGATTCAGCAAAACAT
Found at i:33081 original size:40 final size:40
Alignment explanation
Indices: 33037--33119 Score: 157
Period size: 40 Copynumber: 2.1 Consensus size: 40
33027 ATTGAGAAAG
*
33037 TTGCAAGTAAACAAATTTCATGAAATTGTTAGATGAATAA
1 TTGCAAATAAACAAATTTCATGAAATTGTTAGATGAATAA
33077 TTGCAAATAAACAAATTTCATGAAATTGTTAGATGAATAA
1 TTGCAAATAAACAAATTTCATGAAATTGTTAGATGAATAA
33117 TTG
1 TTG
33120 GTAAATTTGT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.34
Consensus pattern (40 bp):
TTGCAAATAAACAAATTTCATGAAATTGTTAGATGAATAA
Found at i:36070 original size:17 final size:14
Alignment explanation
Indices: 36046--36082 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
36036 ACTATTAATT
*
36046 ATTTTAATAAAATA
1 ATTTTAATAATATA
36060 ATTTTAATAATATA
1 ATTTTAATAATATA
36074 ATTTTAATA
1 ATTTTAATA
36083 TTTTAAGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:36670 original size:24 final size:24
Alignment explanation
Indices: 36635--36683 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
36625 TTTTATTTTC
36635 TTAAAATAATTTTAAATTATAATTT
1 TTAAAATAATTTTAAATTA-AATTT
*
36660 TTAAAAT-ATTTTATATTAAATTT
1 TTAAAATAATTTTAAATTAAATTT
36683 T
1 T
36684 AAATTGATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.26
24 10 0.43
25 7 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TTAAAATAATTTTAAATTAAATTT
Found at i:39735 original size:17 final size:18
Alignment explanation
Indices: 39701--39736 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
39691 TTTTCTTTTG
39701 TCTTAATCAATTAATATT
1 TCTTAATCAATTAATATT
*
39719 TCTTAATC-ATTATTATT
1 TCTTAATCAATTAATATT
39736 T
1 T
39737 AACTATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.33, C:0.11, G:0.00, T:0.56
Consensus pattern (18 bp):
TCTTAATCAATTAATATT
Found at i:40624 original size:3 final size:3
Alignment explanation
Indices: 40616--40646 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
40606 CTGTTAACAT
*
40616 TTA TTA TTA TTA TTA TTT TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
40647 ACAGGTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:49175 original size:15 final size:17
Alignment explanation
Indices: 49145--49178 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
49135 CAAATTGATG
49145 TTTGGCTCTCCGTTTGA
1 TTTGGCTCTCCGTTTGA
49162 TTTGGCT-T-CGTTTGA
1 TTTGGCTCTCCGTTTGA
49177 TT
1 TT
49179 ACAATTAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 1 0.06
17 7 0.41
ACGTcount: A:0.06, C:0.18, G:0.24, T:0.53
Consensus pattern (17 bp):
TTTGGCTCTCCGTTTGA
Found at i:50094 original size:19 final size:19
Alignment explanation
Indices: 50043--50094 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
50033 TTTAAATAGA
50043 AATTCAAAAAATTAACTTG
1 AATTCAAAAAATTAACTTG
* *
50062 AATTTTATAAAATTAACTTG
1 AA-TTCAAAAAATTAACTTG
*
50082 AATTGAAAAAATT
1 AATTCAAAAAATT
50095 CCAAATCAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.37
Consensus pattern (19 bp):
AATTCAAAAAATTAACTTG
Found at i:50257 original size:33 final size:33
Alignment explanation
Indices: 50215--50314 Score: 173
Period size: 33 Copynumber: 3.0 Consensus size: 33
50205 AGGGTAGGAA
50215 TCATTTGACTCGGTTTGTATAACTTTTCTTAGC
1 TCATTTGACTCGGTTTGTATAACTTTTCTTAGC
*
50248 TCATTTGACTCGGTTTGTATAACTTTTCTTACC
1 TCATTTGACTCGGTTTGTATAACTTTTCTTAGC
*
50281 TCATTTGACTCGGTTTGTATGACTTTTTCTTAGC
1 TCATTTGACTCGGTTTGTATAAC-TTTTCTTAGC
50315 GTGTGTGTCG
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
33 54 0.86
34 9 0.14
ACGTcount: A:0.17, C:0.19, G:0.15, T:0.49
Consensus pattern (33 bp):
TCATTTGACTCGGTTTGTATAACTTTTCTTAGC
Found at i:52567 original size:37 final size:36
Alignment explanation
Indices: 52492--52563 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
52482 TTTTTATATT
*
52492 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATAAA
* *
52528 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTAAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTATAAA
52564 ATTTGTAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
36 28 0.88
37 4 0.12
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATAAA
Found at i:52590 original size:18 final size:17
Alignment explanation
Indices: 52543--52591 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
52533 TTTTTTAAAG
*
52543 AAAATATATAAATATTTT
1 AAAATATAT-AATATTAT
* *
52561 AAAATTTGTAATATTAT
1 AAAATATATAATATTAT
52578 ACAAATATATAATA
1 A-AAATATATAATA
52592 AGGACAATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (17 bp):
AAAATATATAATATTAT
Found at i:55646 original size:18 final size:20
Alignment explanation
Indices: 55623--55662 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
55613 TCTTAGATTA
55623 TATTTG-ATTT-ATAAAAAT
1 TATTTGTATTTGATAAAAAT
*
55641 TATTTGTATTTGATAAAGAT
1 TATTTGTATTTGATAAAAAT
55661 TA
1 TA
55663 AAAAGAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 4 0.21
20 9 0.47
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (20 bp):
TATTTGTATTTGATAAAAAT
Found at i:63659 original size:32 final size:32
Alignment explanation
Indices: 63621--63688 Score: 136
Period size: 32 Copynumber: 2.1 Consensus size: 32
63611 TTATAAAATA
63621 AAAATATTATTAAAAATTAGTTTTTATTAGGG
1 AAAATATTATTAAAAATTAGTTTTTATTAGGG
63653 AAAATATTATTAAAAATTAGTTTTTATTAGGG
1 AAAATATTATTAAAAATTAGTTTTTATTAGGG
63685 AAAA
1 AAAA
63689 AACTTATTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (32 bp):
AAAATATTATTAAAAATTAGTTTTTATTAGGG
Found at i:73811 original size:60 final size:60
Alignment explanation
Indices: 73742--73855 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
73732 CGGGTAACAT
* *
73742 TTTTGTAACTTTTAATAGTCGATGAACTCAACAAAGCAACT-TCCTATAGTCTGGATACTA
1 TTTTATAACTTTTAATAGTCGAGGAACTCAACAAAGCAA-TATCCTATAGTCTGGATACTA
* * * *
73802 TTTTATAACTTTTAATAGTTGAGGGACTCAACAAAGTAATATCTTATAGTCTGG
1 TTTTATAACTTTTAATAGTCGAGGAACTCAACAAAGCAATATCCTATAGTCTGG
73856 GGACCATTTG
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
59 1 0.02
60 46 0.98
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (60 bp):
TTTTATAACTTTTAATAGTCGAGGAACTCAACAAAGCAATATCCTATAGTCTGGATACTA
Found at i:73873 original size:60 final size:60
Alignment explanation
Indices: 73743--73873 Score: 151
Period size: 60 Copynumber: 2.2 Consensus size: 60
73733 GGGTAACATT
* * *
73743 TTTGTA-ACTTTTAATAGTCGATGAACTCAACAAAGCAACTTCCTATAGTCTGGATACTA
1 TTTGTATACTTTTAATAGTCGAGGAACTCAACAAAGCAACTTCCTATAGTCTGGAGACCA
* * * * *
73802 TTT-TATAACTTTTAATAGTTGAGGGACTCAACAAAGTAA-TATCTTATAGTCTGGGGACCA
1 TTTGTAT-ACTTTTAATAGTCGAGGAACTCAACAAAGCAACT-TCCTATAGTCTGGAGACCA
73862 TTTGTATACTTT
1 TTTGTATACTTT
73874 ACCCTATTTT
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
58 2 0.03
59 4 0.07
60 51 0.85
61 3 0.05
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.37
Consensus pattern (60 bp):
TTTGTATACTTTTAATAGTCGAGGAACTCAACAAAGCAACTTCCTATAGTCTGGAGACCA
Found at i:74425 original size:3 final size:3
Alignment explanation
Indices: 74419--74443 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
74409 TCAACTAATG
74419 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
74444 AGTTAAGGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Done.