Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006569.1 Hibiscus syriacus cultivar Beakdansim tig00016071_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: 45847
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:5357 original size:2 final size:2
Alignment explanation
Indices: 5350--5387 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5340 TATACCCATA
5350 AT 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 AT
5388 TAATAAAGCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6567 original size:22 final size:21
Alignment explanation
Indices: 6515--6593 Score: 74
Period size: 21 Copynumber: 3.8 Consensus size: 21
6505 CGGTGTTTGA
6515 GTGCATGGATGCAC-TGCATG
1 GTGCATGGATGCACTTGCATG
* *
6535 GAGCATCGATGCACTAGTGCA-G
1 GTGCATGGATGCACT--TGCATG
*
6557 GTGCATGGATGCAC-TGCAGGG
1 GTGCATGGATGCACTTGCA-TG
*
6578 GTGCATGGATACACTT
1 GTGCATGGATGCACTT
6594 TGACACCCTT
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
19 4 0.08
20 12 0.25
21 14 0.29
22 14 0.29
23 4 0.08
ACGTcount: A:0.23, C:0.20, G:0.34, T:0.23
Consensus pattern (21 bp):
GTGCATGGATGCACTTGCATG
Found at i:6693 original size:29 final size:29
Alignment explanation
Indices: 6672--6729 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
6662 AAACTTTGAA
6672 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
6701 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
6730 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:6719 original size:30 final size:30
Alignment explanation
Indices: 6672--6731 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
6662 AAACTTTGAA
6672 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
6701 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
6732 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:10312 original size:38 final size:39
Alignment explanation
Indices: 10270--10404 Score: 138
Period size: 38 Copynumber: 3.6 Consensus size: 39
10260 TTGGGTGTTG
* *
10270 TTTCTCTTGAAACA-AAATGTCATCTCACTTGAGACATT
1 TTTCTCTTGAAACACAAATTTCGTCTCACTTGAGACATT
* * * *
10308 TTTCTCTT-AAAAACAAATTTTGTCTAACTTGAGTCATTT
1 TTTCTCTTGAAACACAAATTTCGTCTCACTTGAGACA-TT
* *
10347 TTTCTCTT-AAA-ACAAATTTCGTTTCACTTGAGCCA-T
1 TTTCTCTTGAAACACAAATTTCGTCTCACTTGAGACATT
10383 TTTC-CTTCGAAACACAAATTTC
1 TTTCTCTT-GAAACACAAATTTC
10405 AAAGTTGTTT
Statistics
Matches: 82, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
35 3 0.04
36 5 0.06
37 7 0.09
38 54 0.66
39 13 0.16
ACGTcount: A:0.30, C:0.21, G:0.08, T:0.41
Consensus pattern (39 bp):
TTTCTCTTGAAACACAAATTTCGTCTCACTTGAGACATT
Found at i:10480 original size:37 final size:38
Alignment explanation
Indices: 10415--10487 Score: 112
Period size: 37 Copynumber: 1.9 Consensus size: 38
10405 AAAGTTGTTT
*
10415 TCTTAAAATCAAATTTTGTATCACTTGAGACATTTTTC
1 TCTTAAAATCAAATTTCGTATCACTTGAGACATTTTTC
* *
10453 TCTTAAAA-CAAATTTCGTTTCATTTGAGACATTTT
1 TCTTAAAATCAAATTTCGTATCACTTGAGACATTTT
10488 CCTTCGGAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
37 24 0.75
38 8 0.25
ACGTcount: A:0.32, C:0.15, G:0.08, T:0.45
Consensus pattern (38 bp):
TCTTAAAATCAAATTTCGTATCACTTGAGACATTTTTC
Found at i:10489 original size:102 final size:101
Alignment explanation
Indices: 10312--10586 Score: 358
Period size: 102 Copynumber: 2.7 Consensus size: 101
10302 GACATTTTTC
* *
10312 TCTTAAAAACAAATTTTGTCTAACTTGAGTCATTTTTTCTCTTAAAACAAATTTCGTTTCACTTG
1 TCTT-AAAACAAATTTTGTCTCACTTGAGACA-TTTTTCTCTTAAAACAAATTTCGTTTCACTTG
* *
10377 AGCCATTTTCCTTCGAAACACAAATTTCAAAGTTGTTT
64 AGACATTTTCCTTCGAAACACAAATTTCAAAGTTATTT
* *
10415 TCTTAAAATCAAATTTTGTATCACTTGAGACATTTTTCTCTTAAAACAAATTTCGTTTCATTTGA
1 TCTTAAAA-CAAATTTTGTCTCACTTGAGACATTTTTCTCTTAAAACAAATTTCGTTTCACTTGA
* *
10480 GACATTTTCCTTCGGAGCACAAATTTCAAAGTTATTT
65 GACATTTTCCTTCGAAACACAAATTTCAAAGTTATTT
* * * * *
10517 TACTT-GAACAAAATTTTGTCTCACTTGAGACA-ATTTCTCTCAAAACAAATATAGTCTT-ACTT
1 T-CTTAAAAC-AAATTTTGTCTCACTTGAGACATTTTTCTCTTAAAACAAATTTCGT-TTCACTT
10579 GAGACATT
63 GAGACATT
10587 CTCCCAAAAT
Statistics
Matches: 153, Mismatches: 15, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
101 31 0.20
102 95 0.62
103 27 0.18
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.40
Consensus pattern (101 bp):
TCTTAAAACAAATTTTGTCTCACTTGAGACATTTTTCTCTTAAAACAAATTTCGTTTCACTTGAG
ACATTTTCCTTCGAAACACAAATTTCAAAGTTATTT
Found at i:10751 original size:63 final size:65
Alignment explanation
Indices: 10632--10793 Score: 188
Period size: 63 Copynumber: 2.5 Consensus size: 65
10622 AAGAACAAAT
* * *
10632 TTTGTCT-TCCTTGAGACAATTTCTCTTGAAACAATATCTTTGAATATGTTTCCCTTGAAAAAAA
1 TTTGTCTCT-CTTGAGACAGTTTCTCTTGAAACAATATCTTTGAACATATTTCCCTTGAAAAAAA
10696 A
65 A
* **
10697 TTTGTCTCTCTTGAGAC-GTTTCTCTTGAAACCA-ATCTTT-AACATCATTTCCCTTGAAATGAA
1 TTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAATATCTTTGAACAT-ATTTCCCTTGAAAAAAA
*
10759 T
65 A
* * *
10760 TTTGTCTCCCTTGAGACAGTTTCCCTTTAAACAA
1 TTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAA
10794 AATTTTGTCT
Statistics
Matches: 83, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
62 4 0.05
63 36 0.43
64 27 0.33
65 15 0.18
66 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.40
Consensus pattern (65 bp):
TTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAATATCTTTGAACATATTTCCCTTGAAAAAAAA
Found at i:10847 original size:36 final size:36
Alignment explanation
Indices: 10743--10959 Score: 182
Period size: 36 Copynumber: 5.9 Consensus size: 36
10733 TTTAACATCA
**
10743 TTTCCCTTGAAATGAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
* * *
10779 TTTCCCTTTAAACAAAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAG
* * * *
10816 TTTCTCTTGAAACACATCTCGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
* * * * * *
10852 TTTCTCTTCAAACGAATTTTATCTCGCTTGAGATAG
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
** * * *
10888 TTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAG
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
* * * *
10924 TTTCACTCGGAACATAAGATTTTATCTCCCTTGAGA
1 TTTCCCT-TGAA-ACAA-ATTTTGTCTCCCTTGAGA
10960 TATTTTCGCT
Statistics
Matches: 150, Mismatches: 27, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
36 96 0.64
37 34 0.23
38 3 0.02
39 17 0.11
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
Found at i:10918 original size:72 final size:73
Alignment explanation
Indices: 10743--10966 Score: 247
Period size: 72 Copynumber: 3.1 Consensus size: 73
10733 TTTAACATCA
* * *
10743 TTTCCCTTGAAATGAATTTTGTCTCCCTTGAGACAGTTTCCCTTTAAACAAAATTTTGTCTCTCT
1 TTTCCCTTGAAATGAATTTTGTCTCCCTTGAGACAGTTTCCCTTCAAACAAAATTTTATCTCGCT
10808 TGAGATAG
66 TGAGATAG
* * * * * *
10816 TTTCTCTTGAAA-CACATCTCGTCTCCCTTGAGACAGTTTCTCTTCAAAC-GAATTTTATCTCGC
1 TTTCCCTTGAAATGA-ATTTTGTCTCCCTTGAGACAGTTTCCCTTCAAACAAAATTTTATCTCGC
10879 TTGAGATAG
65 TTGAGATAG
* * * * *
10888 TTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAGTTTCAC-TCGGAACATAAGATTTTATCTC
1 TTTCCCTTGAAATGAATTTTGTCTCCCTTGAGACAGTTTCCCTTC-AAACA-AA-ATTTTATCTC
* *
10952 CCTTGAGATAT
63 GCTTGAGATAG
10963 TTTC
1 TTTC
10967 GCTCAAAACA
Statistics
Matches: 124, Mismatches: 21, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
71 2 0.02
72 56 0.45
73 42 0.34
74 1 0.01
75 23 0.19
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (73 bp):
TTTCCCTTGAAATGAATTTTGTCTCCCTTGAGACAGTTTCCCTTCAAACAAAATTTTATCTCGCT
TGAGATAG
Found at i:10957 original size:39 final size:39
Alignment explanation
Indices: 10867--11024 Score: 178
Period size: 39 Copynumber: 4.1 Consensus size: 39
10857 CTTCAAACGA
* * *
10867 ATTTTATCTCGCTTGAGATAGTTTCCCT-TGAA-ATGA-
1 ATTTTATCTCGCTTGAGATAGTTTCACTCAGAACATAAG
*
10903 ATTTTATCTCGCTTGAGATAGTTTCACTCGGAACATAAG
1 ATTTTATCTCGCTTGAGATAGTTTCACTCAGAACATAAG
* * * *
10942 ATTTTATCTCCCTTGAGATATTTTCGCTCAAAACATAAG
1 ATTTTATCTCGCTTGAGATAGTTTCACTCAGAACATAAG
* * * * *
10981 ATTTTATCTCACTTGAGATAGTTTCGCCCAAAACAAAAG
1 ATTTTATCTCGCTTGAGATAGTTTCACTCAGAACATAAG
11020 ATTTT
1 ATTTT
11025 TAGAAACTAA
Statistics
Matches: 107, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
36 27 0.25
37 3 0.03
38 3 0.03
39 74 0.69
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (39 bp):
ATTTTATCTCGCTTGAGATAGTTTCACTCAGAACATAAG
Found at i:11114 original size:52 final size:52
Alignment explanation
Indices: 11026--11217 Score: 242
Period size: 52 Copynumber: 3.7 Consensus size: 52
11016 AAAGATTTTT
* * *
11026 AGAAACTAAGCCTGATTTTCAGGGGTTTCTCGATGTTTTCAAATGAATTTGAA
1 AGAAACTAAGCCTAATTTTCAGGGATTTCTTGATGTTTTCAAATGAATTT-AA
* * *
11079 AGAAGCTAAGCCTAATTTT-AGGGGTTTCTTAATGTTTTCAAATGAATTTCAA
1 AGAAACTAAGCCTAATTTTCAGGGATTTCTTGATGTTTTCAAATGAATTT-AA
* * * * **
11131 AGAAATTAAGCCTAATTTTTAGGGATATCTTGATGTTTTCAAATGAGTTTTT
1 AGAAACTAAGCCTAATTTTCAGGGATTTCTTGATGTTTTCAAATGAATTTAA
*
11183 AGAAACTAAGCCTGATTTTCAGGGATTTCTTGATG
1 AGAAACTAAGCCTAATTTTCAGGGATTTCTTGATG
11218 ATGGTTTTCA
Statistics
Matches: 121, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
52 78 0.64
53 43 0.36
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (52 bp):
AGAAACTAAGCCTAATTTTCAGGGATTTCTTGATGTTTTCAAATGAATTTAA
Found at i:11212 original size:105 final size:108
Alignment explanation
Indices: 11026--11262 Score: 268
Period size: 105 Copynumber: 2.2 Consensus size: 108
11016 AAAGATTTTT
* * * * *
11026 AGAAACTAAGCCTGATTTTCAGGGGTTTCTCGATGTTTTCAAATGAATTTGAAAGAAGCTAAGCC
1 AGAAACTAAGCCTAATTTTTAGGGATATCTCGATGTTTTCAAATGAATTTGAAAGAAACTAAGCC
* *
11091 TAATTTTAGGGGTTTCTT-A-AT-GTTTTCAAATGA-ATTTCAA
66 TAATTTTAGGGATTTCTTGAGATGGTTTTC-AATGAGATTTAAA
* * * **
11131 AGAAATTAAGCCTAATTTTTAGGGATATCTTGATGTTTTCAAATGAGTTT-TTAGAAACTAAGCC
1 AGAAACTAAGCCTAATTTTTAGGGATATCTCGATGTTTTCAAATGAATTTGAAAGAAACTAAGCC
* *
11195 TGATTTTCAGGGATTTCTTGATGATGGTTTTCAATGAGTTTTTAAA
66 TAATTTT-AGGGATTTCTTGA-GATGGTTTTCAATGAG-ATTTAAA
11241 AGGAAACTAAGCCTAATTTTTA
1 A-GAAACTAAGCCTAATTTTTA
11263 TGGGTTCCTT
Statistics
Matches: 109, Mismatches: 15, Indels: 10
0.81 0.11 0.07
Matches are distributed among these distances:
104 17 0.16
105 53 0.49
106 1 0.01
108 7 0.06
109 6 0.06
110 6 0.06
111 19 0.17
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.39
Consensus pattern (108 bp):
AGAAACTAAGCCTAATTTTTAGGGATATCTCGATGTTTTCAAATGAATTTGAAAGAAACTAAGCC
TAATTTTAGGGATTTCTTGAGATGGTTTTCAATGAGATTTAAA
Found at i:11397 original size:42 final size:42
Alignment explanation
Indices: 11311--11412 Score: 125
Period size: 42 Copynumber: 2.4 Consensus size: 42
11301 AAGGGTTTCT
* *
11311 TGATGAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCAAACA
1 TGATGTGTAAATCCTTCGGGCCATCAGTAAGTCTTTCAAACA
* ** *
11353 TGATGCT-TAAATCCTTCGGGCCATCAGTAGGTCTTTTGAGCA
1 TGATG-TGTAAATCCTTCGGGCCATCAGTAAGTCTTTCAAACA
*
11395 TGATGTGTAAGTCCTTCG
1 TGATGTGTAAATCCTTCG
11413 TGTCATCCAT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
41 1 0.02
42 50 0.98
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.32
Consensus pattern (42 bp):
TGATGTGTAAATCCTTCGGGCCATCAGTAAGTCTTTCAAACA
Found at i:11592 original size:22 final size:22
Alignment explanation
Indices: 11565--11627 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 22
11555 TCGGGCCATC
11565 AGTAAGTCTTTCGAGCATGATG
1 AGTAAGTCTTTCGAGCATGATG
* * * *
11587 AGTAAGTC-CTCGGGC--CATC
1 AGTAAGTCTTTCGAGCATGATG
*
11606 AGTAAGTCTTTTGAGCATGATG
1 AGTAAGTCTTTCGAGCATGATG
11628 CTTAAATCCT
Statistics
Matches: 29, Mismatches: 9, Indels: 6
0.66 0.20 0.14
Matches are distributed among these distances:
19 10 0.34
20 4 0.14
21 5 0.17
22 10 0.34
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.30
Consensus pattern (22 bp):
AGTAAGTCTTTCGAGCATGATG
Found at i:11605 original size:41 final size:41
Alignment explanation
Indices: 11546--11688 Score: 164
Period size: 41 Copynumber: 3.5 Consensus size: 41
11536 TTGAATCATC
*
11546 ATAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATGATG
1 ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATG
*
11587 AGTAAGTCC-TCGGGCCATCAGTAAGTCTTTTGAGCATGATG
1 A-TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATG
* * * * *
11628 CTTAAATCCTTCAGGTCATCTA-TAAGTCTTTCGAGCAAGATG
1 -ATAAGTCCTTCGGGCCATC-AGTAAGTCTTTCGAGCATGATG
* *
11670 ATAAGTCTTTTGGGCCATC
1 ATAAGTCCTTCGGGCCATC
11689 TATAAGATCT
Statistics
Matches: 84, Mismatches: 14, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
41 51 0.61
42 32 0.38
43 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.31
Consensus pattern (41 bp):
ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATG
Found at i:11611 original size:19 final size:20
Alignment explanation
Indices: 11542--11613 Score: 67
Period size: 19 Copynumber: 3.6 Consensus size: 20
11532 CACTTTGAAT
11542 CATCA-TAAGTCATTCGGGC
1 CATCAGTAAGTCATTCGGGC
* *
11561 CATCAGTAAGTCTTTCGAGC
1 CATCAGTAAGTCATTCGGGC
* * *
11581 ATGATGAGTAAGTC-CTCGGGC
1 --CATCAGTAAGTCATTCGGGC
11602 CATCAGTAAGTC
1 CATCAGTAAGTC
11614 TTTTGAGCAT
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
19 15 0.36
20 12 0.29
21 5 0.12
22 10 0.24
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (20 bp):
CATCAGTAAGTCATTCGGGC
Found at i:12844 original size:136 final size:134
Alignment explanation
Indices: 12598--12939 Score: 433
Period size: 136 Copynumber: 2.6 Consensus size: 134
12588 AGAATAAATC
* *
12598 GATCAATATTTCTAATGGAGAGTTCATAATGGGAAGAACTTATCTGACAGAGGGAGAAGAAGTTC
1 GATCAATATTT-T-ATGGAGAGTTCATAATGAGAAGAACTCATCTGACAGAGGGAGAAGAAGTTC
* * *
12663 ATAATGAGAAGAGCTTGTTCAACCTATCGCTCGATTCATGGCATTTCAAATCAGCGACGCCTCGC
64 ATAATGAGAAGAGCTTGTTCAACCTATCACTCGATTCATGACATTTCAAATCAGCGACACCTCGC
12728 TCAAGG
129 TCAAGG
*
12734 GATCAATATTTTGAGTGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTC
1 GATCAATATTTT-A-TGGAGAGTTCATAATGAGAAGAACTCATCTGACAGAGGGAGAAGAAGTTC
* ** * **
12799 ATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGACATTTTGAATCAGTGACACCTTTC
64 ATAATGAGAAGAGCTTGTTCAACCTATCACTCGATTCATGACATTTCAAATCAGCGACACCTCGC
**
12864 TTGAGG
129 TCAAGG
** * * * *
12870 GATCAACGTTTCAAGAAGAGTTCATAATGAGAAGAACTCATCTTA-A-A-GGAG-A-AAGTTCAT
1 GATCAATATTTTATGGAGAGTTCATAATGAGAAGAACTCATCTGACAGAGGGAGAAGAAGTTCAT
12930 AATGAGAAGA
66 AATGAGAAGA
12940 AATTGTTCCT
Statistics
Matches: 183, Mismatches: 22, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
129 18 0.10
130 1 0.01
131 4 0.02
132 1 0.01
133 1 0.01
134 28 0.15
135 3 0.02
136 127 0.69
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (134 bp):
GATCAATATTTTATGGAGAGTTCATAATGAGAAGAACTCATCTGACAGAGGGAGAAGAAGTTCAT
AATGAGAAGAGCTTGTTCAACCTATCACTCGATTCATGACATTTCAAATCAGCGACACCTCGCTC
AAGG
Found at i:13671 original size:6 final size:5
Alignment explanation
Indices: 13601--13667 Score: 98
Period size: 5 Copynumber: 12.6 Consensus size: 5
13591 CCGTCTCGTC
13601 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGTGG TCGTGG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG
13653 TCGTGG TCGTGG TCG
1 TCG-GG TCG-GG TCG
13668 TGGTAATACG
Statistics
Matches: 61, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 38 0.62
6 23 0.38
ACGTcount: A:0.00, C:0.19, G:0.55, T:0.25
Consensus pattern (5 bp):
TCGGG
Found at i:13805 original size:41 final size:40
Alignment explanation
Indices: 13748--13860 Score: 165
Period size: 41 Copynumber: 2.8 Consensus size: 40
13738 CTTTTTTTTA
13748 ACTATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAG
1 ACTATCGCAACGAATTTGGAAAATCGCAACGAC-ACTGTAG
* *
13789 ACTATCGCAACGAATTTGGAAAAGCGCAACGACATTGTAG
1 ACTATCGCAACGAATTTGGAAAATCGCAACGACACTGTAG
*
13829 ACTATCGCAACGCGAA-ATGGAAAATCGCAACG
1 ACTATCGCAA--CGAATTTGGAAAATCGCAACG
13861 CGAAATGGAA
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
40 16 0.24
41 46 0.70
42 4 0.06
ACGTcount: A:0.39, C:0.22, G:0.21, T:0.18
Consensus pattern (40 bp):
ACTATCGCAACGAATTTGGAAAATCGCAACGACACTGTAG
Found at i:13857 original size:20 final size:20
Alignment explanation
Indices: 13832--13883 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
13822 ATTGTAGACT
13832 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
13852 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*
13872 ATTGCAACGCGA
1 ATCGCAACGCGA
13884 TTTTCAACTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.42, C:0.21, G:0.25, T:0.12
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:14132 original size:13 final size:13
Alignment explanation
Indices: 14114--14139 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
14104 TGTAATCACT
14114 ATTTTTCATAACC
1 ATTTTTCATAACC
14127 ATTTTTCATAACC
1 ATTTTTCATAACC
14140 TAAACCTCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (13 bp):
ATTTTTCATAACC
Found at i:19113 original size:388 final size:388
Alignment explanation
Indices: 18395--19310 Score: 1526
Period size: 388 Copynumber: 2.4 Consensus size: 388
18385 TAACCCATGC
* * ** * * *
18395 GTTGTGTATTCTATGGTGAAAGAGTCAGTGTTGGAGTGGAATGCTTATAGGTGTCGTTTTTGTCC
1 GTTGTGTAGTCTTTGGTGGCAGAGTCAGTGTAGGAGTGGAAGGCTTATAGGTGTTGTTTTTGTCC
*
18460 CATCACTCTACTTTTAGGAATATACTTGGATCTCTTGTTTTCGACTTCCCAGGTTAACAAGTATA
66 CATCACTCAACTTTTAGGAATATACTTGGATCTCTTGTTTTCGACTTCCCAGGTTAACAAGTATA
* ** * *
18525 GCTTAGCCAACTTCAAGGTAGTAGCCAATGTTTGTGGTTCATGAGATTTGACTATGTGTTTAACT
131 GCTTAGCCAACTTCAAGGCAACAACCAATGTTTGTGGTTCATGAGATTTGACTATGTGCTTAACT
* * * *
18590 TTCTCCTTCAATCCGCTCAAAAAACTTGATACAAAGTAACCCTCATCTAACAATAGATTACAATG
196 TCCTCCTTCAATCCGCTCAAAAAACTTGAAACAAAGAAACCCTCATCTAACAATAGATTACAACG
*
18655 AAGCATAAATGATTACAATTCCTCAAATTTTTCATGATAGTCCTCCACTGAACCTCCCTGAGTAA
261 AAGCATAAATGATTACAATTCCTCAAATTTTTCATGATAATCCTCCACTGAACCTCCCTGAGTAA
* *
18720 GTTTATTAAATTCTTCAACAGTATTGTTGCAATTCCTGTCAGAGAATCGTTGACTACTCGTAG
326 GTTTATTAAATTCTTCAACAGTATCGTTGCAATTCCTGTCAGAAAATCGTTGACTACTCGTAG
18783 GTTGTGTAGTCTTTGGTGGCAGAGTCAGTGTAGGAGTGGAAGGCTTATAGGTGTTGTTTTTGTCC
1 GTTGTGTAGTCTTTGGTGGCAGAGTCAGTGTAGGAGTGGAAGGCTTATAGGTGTTGTTTTTGTCC
* *
18848 TATCACTCCACTTTTAGGAATATACTTGGATCTCTTGTTTTCGACTTCCCAGGTTAACAAGTATA
66 CATCACTCAACTTTTAGGAATATACTTGGATCTCTTGTTTTCGACTTCCCAGGTTAACAAGTATA
* *
18913 GCTTAGCCAACTTGAAGGCAACAACCAATGTTTGTGGTTCATGAGATTTGACTCTGTGCTTAACT
131 GCTTAGCCAACTTCAAGGCAACAACCAATGTTTGTGGTTCATGAGATTTGACTATGTGCTTAACT
* *
18978 TCCTCCTTCAATCCGCTCAAAAAACTTGAAACAAAGAAACCCTCATCTAACAATAGATTGCACCG
196 TCCTCCTTCAATCCGCTCAAAAAACTTGAAACAAAGAAACCCTCATCTAACAATAGATTACAACG
*
19043 AAGCATAAATGATTACAATTCCTCAAATTTTTCATGATAATCCTCCACTGAACCTCCCTGAGTTA
261 AAGCATAAATGATTACAATTCCTCAAATTTTTCATGATAATCCTCCACTGAACCTCCCTGAGTAA
*
19108 GTTTATTAAATTCTTCAACAGTATCGTTGCAATTTCTGTCAGAAAATCGTTGACTACTCGTAG
326 GTTTATTAAATTCTTCAACAGTATCGTTGCAATTCCTGTCAGAAAATCGTTGACTACTCGTAG
* * * *
19171 GTTGTGTAGTCTTTGGTGGCAGAGTTAGTGTAGGAGTGGAAGGGTTATAGGTGTTTTTTTTGCCC
1 GTTGTGTAGTCTTTGGTGGCAGAGTCAGTGTAGGAGTGGAAGGCTTATAGGTGTTGTTTTTGTCC
* *
19236 CATCACTCAACTTTTAGGATTATACTTGGATCTCTTGTTTTCGACTTCCCAGGTTAATAAGTATA
66 CATCACTCAACTTTTAGGAATATACTTGGATCTCTTGTTTTCGACTTCCCAGGTTAACAAGTATA
19301 GCTTAGCCAA
131 GCTTAGCCAA
19311 AGGAAATGCT
Statistics
Matches: 493, Mismatches: 35, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
388 493 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (388 bp):
GTTGTGTAGTCTTTGGTGGCAGAGTCAGTGTAGGAGTGGAAGGCTTATAGGTGTTGTTTTTGTCC
CATCACTCAACTTTTAGGAATATACTTGGATCTCTTGTTTTCGACTTCCCAGGTTAACAAGTATA
GCTTAGCCAACTTCAAGGCAACAACCAATGTTTGTGGTTCATGAGATTTGACTATGTGCTTAACT
TCCTCCTTCAATCCGCTCAAAAAACTTGAAACAAAGAAACCCTCATCTAACAATAGATTACAACG
AAGCATAAATGATTACAATTCCTCAAATTTTTCATGATAATCCTCCACTGAACCTCCCTGAGTAA
GTTTATTAAATTCTTCAACAGTATCGTTGCAATTCCTGTCAGAAAATCGTTGACTACTCGTAG
Found at i:29737 original size:22 final size:22
Alignment explanation
Indices: 29709--29753 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
29699 CCACAATAAC
*
29709 ATTCATGATAAATATCATATAT
1 ATTCATGATAAACATCATATAT
29731 ATTCATGATAAACATCATATAT
1 ATTCATGATAAACATCATATAT
29753 A
1 A
29754 ATAACCAGTG
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:0.47, C:0.11, G:0.04, T:0.38
Consensus pattern (22 bp):
ATTCATGATAAACATCATATAT
Found at i:41766 original size:5 final size:5
Alignment explanation
Indices: 41758--41782 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
41748 TGATTAAGCA
41758 CATTT CATTT CATTT CATTT CATTT
1 CATTT CATTT CATTT CATTT CATTT
41783 TTATTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (5 bp):
CATTT
Found at i:44842 original size:20 final size:20
Alignment explanation
Indices: 44819--44882 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
44809 TCGTTCGAAA
**
44819 AAAAATGAGAAAAAGACATG
1 AAAAATGAGAAAAAGACAAC
* *
44839 AAAATTGA-AAACAAAACAAC
1 AAAAATGAGAAA-AAGACAAC
*
44859 AAAAATGTGAAAAAG-CAA-
1 AAAAATGAGAAAAAGACAAC
44877 AAAAAT
1 AAAAAT
44883 CAAATGCATT
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
18 6 0.17
19 6 0.17
20 20 0.57
21 3 0.09
ACGTcount: A:0.69, C:0.08, G:0.12, T:0.11
Consensus pattern (20 bp):
AAAAATGAGAAAAAGACAAC
Done.