Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003943.1 Hibiscus syriacus cultivar Beakdansim tig00008523_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: 61989
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:2179 original size:17 final size:17
Alignment explanation
Indices: 2157--2193 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
2147 GATTGGGTAA
2157 GGTCAATTTTTGAGTCG
1 GGTCAATTTTTGAGTCG
*
2174 GGTCAATTTTTGGGTCG
1 GGTCAATTTTTGAGTCG
2191 GGT
1 GGT
2194 GCTTTTTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.14, C:0.11, G:0.35, T:0.41
Consensus pattern (17 bp):
GGTCAATTTTTGAGTCG
Found at i:3068 original size:16 final size:16
Alignment explanation
Indices: 3047--3090 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
3037 GTTGCTTTGA
3047 TTCGGGTTAATTTCAG
1 TTCGGGTTAATTTCAG
**
3063 TTCGGGTTGCTTTCAG
1 TTCGGGTTAATTTCAG
*
3079 TT-AGGTTAATTT
1 TTCGGGTTAATTT
3091 TGGTTCTTGT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
15 7 0.30
16 16 0.70
ACGTcount: A:0.16, C:0.11, G:0.25, T:0.48
Consensus pattern (16 bp):
TTCGGGTTAATTTCAG
Found at i:3872 original size:15 final size:16
Alignment explanation
Indices: 3852--3884 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
3842 TAATAGTGAG
3852 TTATTATAAATAT-TT
1 TTATTATAAATATATT
3867 TTATTATAAATATATT
1 TTATTATAAATATATT
3883 TT
1 TT
3885 TATTTGTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTATTATAAATATATT
Found at i:4968 original size:20 final size:20
Alignment explanation
Indices: 4909--4968 Score: 52
Period size: 20 Copynumber: 2.9 Consensus size: 20
4899 AATTTTTAAA
4909 AATAGAAAAATTTATAAAATTTT
1 AATA-AAAAA-TTA-AAAATTTT
*
4932 AACAAACAAA--AACAAATTTT
1 AATAAA-AAATTAA-AAATTTT
4952 AATAAAAAATTAAAAAT
1 AATAAAAAATTAAAAAT
4969 ATGAGATAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 11
0.70 0.05 0.25
Matches are distributed among these distances:
19 4 0.13
20 17 0.55
21 2 0.06
22 2 0.06
23 6 0.19
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.28
Consensus pattern (20 bp):
AATAAAAAATTAAAAATTTT
Found at i:7520 original size:16 final size:16
Alignment explanation
Indices: 7499--7530 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
7489 CGATGCACTC
7499 ATGTAAGGAACTAGAA
1 ATGTAAGGAACTAGAA
7515 ATGTAAGGAACTAGAA
1 ATGTAAGGAACTAGAA
7531 GATTAACGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.06, G:0.25, T:0.19
Consensus pattern (16 bp):
ATGTAAGGAACTAGAA
Found at i:11236 original size:107 final size:107
Alignment explanation
Indices: 11045--11250 Score: 369
Period size: 107 Copynumber: 1.9 Consensus size: 107
11035 CCGTAAACTC
*
11045 TGATTTCTTACTTACTAGACTTCTGATATGTGAGCATGTAACATTTTTGTAACACCCCCAAGCCG
1 TGATCTCTTACTTACTAGACTTCTGATATGTGAGCATGTAACATTTTTGTAACACCCCCAAGCCG
11110 TACCCGACCCGGATACGAATCCGAGGTGTCACATAAACCTGA
66 TACCCGACCCGGATACGAATCCGAGGTGTCACATAAACCTGA
* *
11152 TGATCTCTTACTTACTAGACTTTTGATATGTGAGCATGTAATATTTTTGTAACACCCCCAA-CTC
1 TGATCTCTTACTTACTAGACTTCTGATATGTGAGCATGTAACATTTTTGTAACACCCCCAAGC-C
11216 GTACCCGACCCGGATACGAATCCGAGGTGTCACAT
65 GTACCCGACCCGGATACGAATCCGAGGTGTCACAT
11251 TAACTATTCA
Statistics
Matches: 95, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
106 1 0.01
107 94 0.99
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (107 bp):
TGATCTCTTACTTACTAGACTTCTGATATGTGAGCATGTAACATTTTTGTAACACCCCCAAGCCG
TACCCGACCCGGATACGAATCCGAGGTGTCACATAAACCTGA
Found at i:12232 original size:64 final size:64
Alignment explanation
Indices: 12159--12382 Score: 213
Period size: 64 Copynumber: 3.5 Consensus size: 64
12149 TGTTTGAATG
* * * **
12159 TGCACCGATGCATTGGTAATGCATCGATGCA-CTCTTTTAA-AATAAAGACATCGAATGCAATTC
1 TGCATCGATGCATAGGTAGTGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATGCAATTC
12222 A
64 A
* * * **
12223 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAGTGAAACATCGAATGCAATTGG
1 TGCATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
** ** * ** *
12287 TGCATCGATGCATAAGG-AGTGCATCGATGCATCCCAGCAATAATACTACATCGAATACCTTTTA
1 TGCATCGATGCAT-AGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
*
12351 TGCACCGATGCATCA-GTAGTGCATCGATGCAT
1 TGCATCGATGCAT-AGGTAGTGCATCGATGCAT
12383 ACCTTCATTA
Statistics
Matches: 132, Mismatches: 24, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
63 1 0.01
64 124 0.94
65 7 0.05
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (64 bp):
TGCATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
Found at i:12706 original size:12 final size:12
Alignment explanation
Indices: 12688--12723 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
12678 TATATATGTT
12688 CATGTGATATGA
1 CATGTGATATGA
*
12700 TATGTGATATGA
1 CATGTGATATGA
*
12712 CCTGTGATATGA
1 CATGTGATATGA
12724 GAACATGATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36
Consensus pattern (12 bp):
CATGTGATATGA
Found at i:12785 original size:29 final size:29
Alignment explanation
Indices: 12743--12812 Score: 106
Period size: 29 Copynumber: 2.4 Consensus size: 29
12733 ATGAAGTGAT
*
12743 ATGAGCTACATGATCACAAAAGAAATGAC
1 ATGAGCTACATGATCACAAAAGAAAGGAC
**
12772 ATGAGCTACATGATCACAAGTGAAAGGAC
1 ATGAGCTACATGATCACAAAAGAAAGGAC
12801 ATGAG-TACATGA
1 ATGAGCTACATGA
12813 ATATATGAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
28 7 0.18
29 31 0.82
ACGTcount: A:0.44, C:0.16, G:0.21, T:0.19
Consensus pattern (29 bp):
ATGAGCTACATGATCACAAAAGAAAGGAC
Found at i:12923 original size:15 final size:15
Alignment explanation
Indices: 12897--12944 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
12887 GAGGGTATGA
12897 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
* * *
12912 TATTCTTTCGGGACG
1 TAGTCCTTCGGGATG
*
12927 TAGTCCTTCGAGATG
1 TAGTCCTTCGGGATG
12942 TAG
1 TAG
12945 GAGTCCTACG
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.17, C:0.19, G:0.29, T:0.35
Consensus pattern (15 bp):
TAGTCCTTCGGGATG
Found at i:19156 original size:64 final size:64
Alignment explanation
Indices: 19088--19272 Score: 176
Period size: 64 Copynumber: 2.9 Consensus size: 64
19078 TTGTTTGAAT
* ** * **
19088 GTGCACCGATGCATTGGTAATGCATCGATGCA-CTCTTTTAA-AATAAAGACATCGAATGCAATT
1 GTGCATCGATGCATAAGTAATACATCGATGCATC-CCATTAATAATAAA-ACATCGAATGCAATT
19151 G
64 G
* * * *
19152 GTGCATCAATGCATAAGTAGTACATCGATGCATCCCATTAATAGTGAAACATCGAATGCAATTG
1 GTGCATCGATGCATAAGTAATACATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTG
* * * * ** **
19216 GTGCATCGATGTATAAGGAGTGCATCGATGCATCCCAGCAATAATACTACATCGAAT
1 GTGCATCGATGCATAAGTAATACATCGATGCATCCCATTAATAATAAAACATCGAAT
19273 ACCTTTTATG
Statistics
Matches: 99, Mismatches: 20, Indels: 4
0.80 0.16 0.03
Matches are distributed among these distances:
64 94 0.95
65 5 0.05
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.26
Consensus pattern (64 bp):
GTGCATCGATGCATAAGTAATACATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTG
Found at i:19603 original size:27 final size:24
Alignment explanation
Indices: 19565--19613 Score: 71
Period size: 27 Copynumber: 1.9 Consensus size: 24
19555 AATACAGTAG
19565 TTGTGAACATGCATACATGATAATTA
1 TTGTGAACATGCATA-A-GATAATTA
19591 TTGTGATACATGCATAAGATAAT
1 TTGTGA-ACATGCATAAGATAAT
19614 ATGTTCATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 6 0.27
26 7 0.32
27 9 0.41
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (24 bp):
TTGTGAACATGCATAAGATAATTA
Found at i:19637 original size:12 final size:12
Alignment explanation
Indices: 19619--19654 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
19609 ATAATATGTT
19619 CATGTGATATGA
1 CATGTGATATGA
*
19631 TATGTGATATGA
1 CATGTGATATGA
*
19643 CCTGTGATATGA
1 CATGTGATATGA
19655 GAACATGATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36
Consensus pattern (12 bp):
CATGTGATATGA
Found at i:19712 original size:29 final size:29
Alignment explanation
Indices: 19670--19743 Score: 114
Period size: 29 Copynumber: 2.6 Consensus size: 29
19660 TGATATGAAG
19670 TGACATGAGCTACATGATCACAAAAGAAA
1 TGACATGAGCTACATGATCACAAAAGAAA
**
19699 TGACATGAGCTACATGATCACAAGTGAAA
1 TGACATGAGCTACATGATCACAAAAGAAA
*
19728 GGACATGAG-TACATGA
1 TGACATGAGCTACATGA
19744 ATATATGAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 7 0.17
29 35 0.83
ACGTcount: A:0.43, C:0.16, G:0.22, T:0.19
Consensus pattern (29 bp):
TGACATGAGCTACATGATCACAAAAGAAA
Found at i:19863 original size:15 final size:15
Alignment explanation
Indices: 19828--19891 Score: 92
Period size: 15 Copynumber: 4.2 Consensus size: 15
19818 GAGGGTATGA
19828 TAGTCCTTCGGGACCG
1 TAGTCCTTCGGGA-CG
*
19844 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGACG
19859 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
* *
19874 TAGTCCTTTGGGATG
1 TAGTCCTTCGGGACG
19889 TAG
1 TAG
19892 GAGTCCTACG
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
15 31 0.70
16 13 0.30
ACGTcount: A:0.14, C:0.22, G:0.33, T:0.31
Consensus pattern (15 bp):
TAGTCCTTCGGGACG
Found at i:19878 original size:30 final size:31
Alignment explanation
Indices: 19828--19891 Score: 112
Period size: 30 Copynumber: 2.1 Consensus size: 31
19818 GAGGGTATGA
19828 TAGTCCTTCGGGACCGTAGTCCTTCGGGATG
1 TAGTCCTTCGGGACCGTAGTCCTTCGGGATG
*
19859 TAGTCCTTCGGGA-CGTAGTCCTTTGGGATG
1 TAGTCCTTCGGGACCGTAGTCCTTCGGGATG
19889 TAG
1 TAG
19892 GAGTCCTACG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 19 0.59
31 13 0.41
ACGTcount: A:0.14, C:0.22, G:0.33, T:0.31
Consensus pattern (31 bp):
TAGTCCTTCGGGACCGTAGTCCTTCGGGATG
Found at i:21007 original size:22 final size:22
Alignment explanation
Indices: 20977--21021 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
20967 GGTATGTGAA
20977 ATTTATCCCGAAGGACCTATGT
1 ATTTATCCCGAAGGACCTATGT
*
20999 ATTTGTCCCGAAGGACCTATGT
1 ATTTATCCCGAAGGACCTATGT
21021 A
1 A
21022 ACCCTCGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (22 bp):
ATTTATCCCGAAGGACCTATGT
Found at i:21788 original size:21 final size:21
Alignment explanation
Indices: 21762--21809 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
21752 TTGGTCTTAA
*
21762 GGTATCGGTACCCATTTATAG
1 GGTATCGGTACCCATTCATAG
21783 GGTATCGGTACCCATTCATAG
1 GGTATCGGTACCCATTCATAG
21804 GGTATC
1 GGTATC
21810 AATACCACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.31
Consensus pattern (21 bp):
GGTATCGGTACCCATTCATAG
Found at i:21815 original size:21 final size:21
Alignment explanation
Indices: 21770--21815 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
21760 AAGGTATCGG
* **
21770 TACCCATTTATAGGGTATCGG
1 TACCCATTCATAGGGTATCAA
21791 TACCCATTCATAGGGTATCAA
1 TACCCATTCATAGGGTATCAA
21812 TACC
1 TACC
21816 ACTTGCCCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.30
Consensus pattern (21 bp):
TACCCATTCATAGGGTATCAA
Found at i:25548 original size:22 final size:22
Alignment explanation
Indices: 25520--25561 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
25510 ATGTGAAATT
*
25520 TGTCCCGAATGACCTATGTATA
1 TGTCCCGAAGGACCTATGTATA
25542 TGTCCCGAAGGACCTATGTA
1 TGTCCCGAAGGACCTATGTA
25562 ACCCTCGACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (22 bp):
TGTCCCGAAGGACCTATGTATA
Found at i:29263 original size:23 final size:23
Alignment explanation
Indices: 29232--29277 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
29222 CACCACATCT
* *
29232 CGTATAAATACACTGAAGTGCCA
1 CGTAGAAATACACCGAAGTGCCA
*
29255 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATACACCGAAGTGCCA
29278 TATAAAATGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (23 bp):
CGTAGAAATACACCGAAGTGCCA
Found at i:29308 original size:23 final size:21
Alignment explanation
Indices: 29282--29343 Score: 52
Period size: 23 Copynumber: 2.8 Consensus size: 21
29272 GTGCCATATA
*
29282 AAATGTCCATAAGGACCACATAG
1 AAAT-TCC-TAAGGACCACATAC
* *
29305 AAATCTCCTTAAGAACCATATAC
1 AAAT-TCC-TAAGGACCACATAC
*
29328 ATATTCCTAAGGACCA
1 AAATTCCTAAGGACCA
29344 ATTATGTGTC
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
21 8 0.25
22 3 0.09
23 21 0.66
ACGTcount: A:0.42, C:0.24, G:0.11, T:0.23
Consensus pattern (21 bp):
AAATTCCTAAGGACCACATAC
Found at i:29389 original size:21 final size:21
Alignment explanation
Indices: 29364--29412 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
29354 TCGAAAGACC
* *
29364 ACATATATGTTCCAAAGGATT
1 ACATATATGTCCCAAAGGACT
*
29385 ACATATATGTCCCGAAGGACT
1 ACATATATGTCCCAAAGGACT
*
29406 ACGTATA
1 ACATATA
29413 CCCTCGACTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (21 bp):
ACATATATGTCCCAAAGGACT
Found at i:34607 original size:23 final size:23
Alignment explanation
Indices: 34576--34643 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 23
34566 CACCACAGCT
*
34576 CGTATAAATGCACCAAAGTGCCA
1 CGTAGAAATGCACCAAAGTGCCA
* * * * *
34599 CGTAGAAATGGACCGAATTACCG
1 CGTAGAAATGCACCAAAGTGCCA
*
34622 CGTAGAAAT-CAACAAAGTGCCA
1 CGTAGAAATGCACCAAAGTGCCA
34644 TATAAAATAT
Statistics
Matches: 33, Mismatches: 12, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
22 7 0.21
23 26 0.79
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.16
Consensus pattern (23 bp):
CGTAGAAATGCACCAAAGTGCCA
Found at i:36367 original size:43 final size:41
Alignment explanation
Indices: 36276--36368 Score: 107
Period size: 43 Copynumber: 2.2 Consensus size: 41
36266 TCAATACCCT
* * *
36276 CAGTATCGATATTACTCCTTTGGTATCGATACTCCTTGAAC
1 CAGTATCGAAATTACTCCTTTGGTATCGATACTCATTCAAC
* *
36317 AATTATCGAAATTTA-TGCCTTATGGTATCGATACTCATTCAAC
1 CAGTATCGAAA-TTACT-CCTT-TGGTATCGATACTCATTCAAC
36360 CAGTATCGA
1 CAGTATCGA
36369 TACCCATGCT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
41 9 0.21
42 7 0.17
43 26 0.62
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (41 bp):
CAGTATCGAAATTACTCCTTTGGTATCGATACTCATTCAAC
Found at i:37771 original size:32 final size:33
Alignment explanation
Indices: 37727--37788 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
37717 ATGAATCTCG
* *
37727 ATTGAAAAATATCAAGCCATGAGTTTCATGATA
1 ATTGAAAAATATCAAGACATGAATTTCATGATA
37760 ATTG-AAAATATCAAGACATGAATTTCATG
1 ATTGAAAAATATCAAGACATGAATTTCATG
37789 GTATACTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 23 0.85
33 4 0.15
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.31
Consensus pattern (33 bp):
ATTGAAAAATATCAAGACATGAATTTCATGATA
Found at i:47195 original size:15 final size:15
Alignment explanation
Indices: 47175--47204 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
47165 GGTGGAGAGA
47175 TTATATGATACATAT
1 TTATATGATACATAT
*
47190 TTATATGGTACATAT
1 TTATATGATACATAT
47205 GGTGCAATTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.47
Consensus pattern (15 bp):
TTATATGATACATAT
Found at i:47262 original size:24 final size:25
Alignment explanation
Indices: 47206--47307 Score: 134
Period size: 25 Copynumber: 4.1 Consensus size: 25
47196 GGTACATATG
47206 GTGCAATTCTACGAGGCATTTTCGA
1 GTGCAATTCTACGAGGCATTTTCGA
* ** *
47231 GTGCAATTCTATGAGGTGTTTT-TA
1 GTGCAATTCTACGAGGCATTTTCGA
*
47255 GTGCAATTCTACGAGGCACTTTCGA
1 GTGCAATTCTACGAGGCATTTTCGA
* *
47280 GTGCAATTTTACGAGGCACTTTCGA
1 GTGCAATTCTACGAGGCATTTTCGA
47305 GTG
1 GTG
47308 AAAATATTTC
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
24 19 0.29
25 47 0.71
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (25 bp):
GTGCAATTCTACGAGGCATTTTCGA
Found at i:47328 original size:29 final size:26
Alignment explanation
Indices: 47212--47330 Score: 93
Period size: 25 Copynumber: 4.6 Consensus size: 26
47202 TATGGTGCAA
* *
47212 TTCTACGAGGCATTTTCGAGTGCAA-
1 TTCTACGAGGCACTTTCGAGTGAAAT
* ** ** *
47237 TTCTATGAGG-TGTTTTTAGTGCAA-
1 TTCTACGAGGCACTTTCGAGTGAAAT
*
47261 TTCTACGAGGCACTTTCGAGTGCAAT
1 TTCTACGAGGCACTTTCGAGTGAAAT
47287 TT-TACGAGGCACTTTCGAGTGAAAATAT
1 TTCTACGAGGCACTTTCGAGTG--AA-AT
*
47315 TTCTACGAGACACTTT
1 TTCTACGAGGCACTTT
47331 TAAGTGCATA
Statistics
Matches: 76, Mismatches: 12, Indels: 8
0.79 0.12 0.08
Matches are distributed among these distances:
24 19 0.25
25 38 0.50
26 2 0.03
27 1 0.01
28 4 0.05
29 12 0.16
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (26 bp):
TTCTACGAGGCACTTTCGAGTGAAAT
Found at i:52847 original size:16 final size:17
Alignment explanation
Indices: 52819--52850 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
52809 ATCGCCGACA
52819 AAATTTCACTATTCACG
1 AAATTTCACTATTCACG
52836 AAATTT-ACTATTCAC
1 AAATTTCACTATTCAC
52851 ATGAATAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.38, C:0.22, G:0.03, T:0.38
Consensus pattern (17 bp):
AAATTTCACTATTCACG
Found at i:56030 original size:185 final size:184
Alignment explanation
Indices: 55698--56139 Score: 403
Period size: 185 Copynumber: 2.4 Consensus size: 184
55688 TTGAGAAATT
* ** *
55698 ATAATTTAATCATTTTTTTATAATTTGTTAATGTAATATTAAATTAACTGTTTAAAATAATATAG
1 ATAATTTAATCATTTTTCTATAATTCATTAATGTAATATTAAATTAACTGTTTAAAATAATATAA
* * * * *
55763 TCTATTTTCGTTCTATAAGGTCTATTTTTGAGTTTTCGCTCAAGTTTTATAACTAAGGATCCTAA
66 TATATTTTCGTTCTATAAGGTCTATTTTTGAGTTTTCGATCAAGGTTGATAACTAAGGACCCTAA
*
55828 CTTTTTTTCAATTTTATAAAATAGTTCTTACATTCTACTTTTATAACTAAAGGCCC
131 --TTTTTTAAATTTTATAAAATAGTTCTTACATTCTACTTTTATAACTAAAGGCCC
** ** *
55884 ATAATTTAATCA-TTTTCTATGGTTCATTAATGTAATATTAAATTAGTTTTTTTCAAAATAATAT
1 ATAATTTAATCATTTTTCTATAATTCATTAATGTAATATTAAATTA-ACTGTTT-AAAATAATAT
* * * * * * * * *
55948 AATATATTTTTGTTCTATAGGGTCTTTTTTTTGAGTTTTTGATCGAGGTTGATTATTAGGGCCCC
64 AATATATTTTCGTTCTATAAGGTC-TATTTTTGAGTTTTCGATCAAGGTTGATAACTAAGGACCC
* * * * * * * **
56013 TAA-TTTTTAAATTTTATAAAATAATACATACTTTCTA-TCTTTATAAATGAGGGATC
128 TAATTTTTTAAATTTTATAAAATAGTTCTTACATTCTACT-TTTATAACTAAAGGCCC
* * * * * * * *
56069 GTGATTTAAACAATTTTCTATGATAT-ATTAA--T-ATATTAAATTAATTGTTCAAAATAATAAA
1 ATAATTTAATCATTTTTCTATAAT-TCATTAATGTAATATTAAATTAACTGTTTAAAATAATATA
56130 ATATATTTTC
65 ATATATTTTC
56140 ATTATATATG
Statistics
Matches: 208, Mismatches: 42, Indels: 17
0.78 0.16 0.06
Matches are distributed among these distances:
181 19 0.09
182 4 0.02
183 11 0.05
184 2 0.01
185 78 0.38
186 31 0.15
187 31 0.15
188 32 0.15
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.47
Consensus pattern (184 bp):
ATAATTTAATCATTTTTCTATAATTCATTAATGTAATATTAAATTAACTGTTTAAAATAATATAA
TATATTTTCGTTCTATAAGGTCTATTTTTGAGTTTTCGATCAAGGTTGATAACTAAGGACCCTAA
TTTTTTAAATTTTATAAAATAGTTCTTACATTCTACTTTTATAACTAAAGGCCC
Found at i:58137 original size:20 final size:20
Alignment explanation
Indices: 58050--58142 Score: 89
Period size: 20 Copynumber: 4.6 Consensus size: 20
58040 AACATGTTGA
*
58050 AATTTGA-AAAATTCGGTTTC
1 AATTTGACAAAA-CCGGTTTC
* **
58070 AATTTGACAAAACAGGTAAC
1 AATTTGACAAAACCGGTTTC
* **
58090 GAATTTGACAAAACCGATTGG
1 -AATTTGACAAAACCGGTTTC
*
58111 AAATTGACAAAACCGGTTTC
1 AATTTGACAAAACCGGTTTC
58131 AATTTGACAAAA
1 AATTTGACAAAA
58143 TCAGTAAAGA
Statistics
Matches: 57, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
20 38 0.67
21 19 0.33
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (20 bp):
AATTTGACAAAACCGGTTTC
Found at i:59250 original size:144 final size:145
Alignment explanation
Indices: 58981--59338 Score: 431
Period size: 144 Copynumber: 2.5 Consensus size: 145
58971 ATATCAATAC
* * *
58981 TTTTATTCCAGTATGTTTGTCAAACAATTTGCACGTCAAATGTATCGATACACATTATTAAAATA
1 TTTTATTCCAGTAT-TTTCTCAAACAATTTGCACGCCAAATGTATCGATACACATTATTAAAGTA
*
59046 AAGATATTTATAATTTCAAAAAAAATGTATGCAAAGTATCAAAATGTCCAAGTATCATACTT-TT
65 TAGATATTTATAATTTCAAAAAAAATGTATGCAAAGTATCAAAATGTCCAAGTATCATACTTCTT
59110 ATG-CGGTATGGATAA
130 ATGCCGGTATGGATAA
* * * * *
59125 TTTTATTCCAATATATTTTTCGAACAATGTGCACACCAAATGTATCGATACACATTATTAAAGTA
1 TTTTATTCCAGTAT-TTTCTCAAACAATTTGCACGCCAAATGTATCGATACACATTATTAAAGTA
* * ** * * * *
59190 TTGGTATTTATAATTT-TGAAACAATGTATGTAAAGTATGAAAATGTCCAAGTATTGATACTTCT
65 TAGATATTTATAATTTCAAAAAAAATGTATGCAAAGTATCAAAATGTCCAAGTA-TCATACTTCT
* *
59254 TATGCCGGTGTGGATAC
129 TATGCCGGTATGGATAA
* * *
59271 TTTCATT-CAGTATTATTCTCAAACAATTTGCATGCAAAATGTATCGATACACA-TA-TAAAGTA
1 TTTTATTCCAGTATT-TTCTCAAACAATTTGCACGCCAAATGTATCGATACACATTATTAAAGTA
*
59333 TCGATA
65 TAGATA
59339 CTTGGAATTT
Statistics
Matches: 181, Mismatches: 29, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
143 43 0.24
144 80 0.44
145 42 0.23
146 16 0.09
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.36
Consensus pattern (145 bp):
TTTTATTCCAGTATTTTCTCAAACAATTTGCACGCCAAATGTATCGATACACATTATTAAAGTAT
AGATATTTATAATTTCAAAAAAAATGTATGCAAAGTATCAAAATGTCCAAGTATCATACTTCTTA
TGCCGGTATGGATAA
Found at i:59570 original size:197 final size:195
Alignment explanation
Indices: 59236--59928 Score: 998
Period size: 197 Copynumber: 3.5 Consensus size: 195
59226 ATGAAAATGT
* *** * * **
59236 CCAAGTATTGATACTTCTTATGCCGGTGTGGATACTTTCATT-CAGTATTATTCTCAAACAATTT
1 CCAAGTATCGATACTT-TTATATAGGTATGGATACTTTTATTCCAGTATGCTTCTCAAACAATTT
*
59300 GCA-TGCAAAATGTATCGATACACATATAAAGTATCGATACTTGGAATTTGGAACCTATTACTTT
65 GCACT-CAAAATGTATCGATACACATATAAAGTATCGATACTTGGAATTTCGAACCTATTACTTT
*
59364 AAAGTAATAGGTAAATTAACAATGCAAACGGTAAAAGTCTACCGGTATAATGATAATAGGCATAA
129 AAAGTAATAGGTAAATTAACAATG-AAACGGTAAAAGTCTACCGGTATAATGATAATAGGCGTAA
59429 ATA
193 ATA
* *
59432 CCAAGTATTGATACTCTTTATATAGGTATGGATACTTTTATTCCAATATGCTTCTCAAACAATTT
1 CCAAGTATCGATACT-TTTATATAGGTATGGATACTTTTATTCCAGTATGCTTCTCAAACAATTT
* ** *
59497 GCACTCAAAATGTATTGATACATGTATAACGTATCGATACTTGGAATTTCGAACCTATTACTTTA
65 GCACTCAAAATGTATCGATACACATATAAAGTATCGATACTTGGAATTTCGAACCTATTACTTTA
* *
59562 AAGTAATAGGTAAATTAACAATGTAAATGGTAAAAGTCTACCAGTATAATGATAATAGGCGTAAA
130 AAGTAATAGGTAAATTAACAATG-AAACGGTAAAAGTCTACCGGTATAATGATAATAGGCGTAAA
59627 TA
194 TA
* *
59629 CCAAGTATCGATACTTTTATATAGGTATAGATACTTTTATTCCAGTATGCTTCTCAAATAATTTG
1 CCAAGTATCGATACTTTTATATAGGTATGGATACTTTTATTCCAGTATGCTTCTCAAACAATTTG
* * * * *
59694 CACGCAAAATGTATCGATACACATATAAAGTATCGATACTTGAAATTTTGAAACATATTATTTTA
66 CACTCAAAATGTATCGATACACATATAAAGTATCGATACTTGGAATTTCG-AACCTATTACTTTA
* * * * *
59759 AAGTAATAGGTAAATTAACAATGTAACAGTAAAAGTCTACTGATACAATGATAATAGGCGTAAAT
130 AAGTAATAGGTAAATTAACAATGAAACGGTAAAAGTCTACCGGTATAATGATAATAGGCGTAAAT
59824 A
195 A
* *
59825 TCAAGTATCGATAC-TTT-TATAGGTATGGATACTTTTATTCCAGTATGCTTCTCAAACAATGTG
1 CCAAGTATCGATACTTTTATATAGGTATGGATACTTTTATTCCAGTATGCTTCTCAAACAATTTG
* *
59888 CACTCAAAATGTATCGATAGAAATATAAAGTATCGATACTT
66 CACTCAAAATGTATCGATACACATATAAAGTATCGATACTT
59929 TAAAATAATA
Statistics
Matches: 449, Mismatches: 44, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
194 81 0.18
195 3 0.01
196 174 0.39
197 190 0.42
198 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (195 bp):
CCAAGTATCGATACTTTTATATAGGTATGGATACTTTTATTCCAGTATGCTTCTCAAACAATTTG
CACTCAAAATGTATCGATACACATATAAAGTATCGATACTTGGAATTTCGAACCTATTACTTTAA
AGTAATAGGTAAATTAACAATGAAACGGTAAAAGTCTACCGGTATAATGATAATAGGCGTAAATA
Found at i:60701 original size:127 final size:128
Alignment explanation
Indices: 60454--60892 Score: 585
Period size: 127 Copynumber: 3.5 Consensus size: 128
60444 CACACAACTA
60454 TATCGATACTTATAATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTACACGG
1 TATCGATACTTATAATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTACACGG
* * *
60519 TAAACGTTTCTACCGGTATATGAATATAGGCGTAAATGTCCAAGTATCGATACTCATACAAAG
66 TAAACGTTTCTACCGATAAATGAAAATAGGCGTAAATGTCCAAGTATCGATACTCATACAAAG
* * * *
60582 TATCTATACTTATAATTTTAAAACCTATTACTTTAAAGTAATATGTAAATTAGC-ATGTACACGG
1 TATCGATACTTATAATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTACACGG
* * * *
60646 TAAA-GTTTTTACCGATAGAATGAAAATATGCGTAAATGTCCAAGTGTCGATACTCATATATAAA
66 TAAACGTTTCTACCGATA-AATGAAAATAGGCGTAAATGTCCAAGTATCGATACTC--ATACAAA
60710 G
128 G
*
60711 TATCGATACTTA-AATTTCGAAA-CTATTACTTTAAAGTAATAGGTAAATTAACAATGT--ACGG
1 TATCGATACTTATAATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTACACGG
* * * ** *
60772 TAAACATTTCTA-CTAGTATAATG-AAATAGGCGTAAATGTACAAGTATCGATA-TTGT-CATA-
66 TAAACGTTTCTACCGA-TA-AATGAAAATAGGCGTAAATGTCCAAGTATCGATACTCATACAAAG
*
60832 TATCGATACTTATAATTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTAC
1 TATCGATACTTATAATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTAC
60893 GCGATAATAT
Statistics
Matches: 274, Mismatches: 27, Indels: 23
0.85 0.08 0.07
Matches are distributed among these distances:
121 12 0.04
122 12 0.04
123 36 0.13
125 1 0.00
126 47 0.17
127 86 0.31
128 62 0.23
129 18 0.07
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (128 bp):
TATCGATACTTATAATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTACACGG
TAAACGTTTCTACCGATAAATGAAAATAGGCGTAAATGTCCAAGTATCGATACTCATACAAAG
Found at i:61934 original size:18 final size:19
Alignment explanation
Indices: 61911--61954 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
61901 CCAGTAATCC
* *
61911 TATTCC-CTGGTAATCTTT
1 TATTCCACTGATAATCTTA
61929 TATTCCCACTGATAATCTTA
1 TATT-CCACTGATAATCTTA
61949 TATTCC
1 TATTCC
61955 GTGAACCAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 4 0.18
19 4 0.18
20 14 0.64
ACGTcount: A:0.23, C:0.25, G:0.07, T:0.45
Consensus pattern (19 bp):
TATTCCACTGATAATCTTA
Done.