Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004051.1 Hibiscus syriacus cultivar Beakdansim tig00008853_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: 64749
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4405 original size:74 final size:73
Alignment explanation
Indices: 4321--4534 Score: 260
Period size: 74 Copynumber: 2.9 Consensus size: 73
4311 AAAACATCTT
*
4321 AAATCCTAATTAAAATACTTCAAA-CTATTTAAACTAAAATACCTAAAAAAAATATAATTTAAAA
1 AAATCCTAATTAAAATAC-TAAAACCTA-TTAAACTAAAATACCTAAAAAAAATATAATTTAAAA
*
4385 TAATAT-TCTA
64 TAATATAT-GA
*
4395 AAATCCTAATTAAAATACTAAAACCTATTAAACTAAAATACCTAAAACAAAGATA-AATATAAAA
1 AAATCCTAATTAAAATACTAAAACCTATTAAACTAAAATACCTAAAA-AAA-ATATAATTTAAAA
4459 TAATATATGA
64 TAATATATGA
* *
4469 AAA-CTTAATTAAAATACTAAAACCTACTTAAACTAAAATA-C-AAAGATAAATATAATGTTTAA
1 AAATCCTAATTAAAATACTAAAACCTA-TTAAACTAAAATACCTAAA-AAAAATATAA--TTTAA
4531 AATA
62 AATA
4535 TTATCCATAA
Statistics
Matches: 125, Mismatches: 6, Indels: 18
0.84 0.04 0.12
Matches are distributed among these distances:
71 3 0.02
72 7 0.06
73 48 0.38
74 63 0.50
75 4 0.03
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.29
Consensus pattern (73 bp):
AAATCCTAATTAAAATACTAAAACCTATTAAACTAAAATACCTAAAAAAAATATAATTTAAAATA
ATATATGA
Found at i:4478 original size:73 final size:74
Alignment explanation
Indices: 4321--4509 Score: 262
Period size: 74 Copynumber: 2.6 Consensus size: 74
4311 AAAACATCTT
* * *
4321 AAATCCTAATTAAAATACTTCAAA-CTATTTAAACTAAAATACCTAAAAAAAATATAATTTAAAA
1 AAATCCTAATTAAAATAC-TAAAACCTACTTAAACTAAAATACCTAAAAAAAATATAATATAAAA
*
4385 TAATATTCTA
65 TAATATTCGA
4395 AAATCCTAATTAAAATACTAAAACCTA-TTAAACTAAAATACCTAAAACAAAGATA-AATATAAA
1 AAATCCTAATTAAAATACTAAAACCTACTTAAACTAAAATACCTAAAA-AAA-ATATAATATAAA
4458 ATAATATAT-GA
64 ATAATAT-TCGA
*
4469 AAA-CTTAATTAAAATACTAAAACCTACTTAAACTAAAATAC
1 AAATCCTAATTAAAATACTAAAACCTACTTAAACTAAAATAC
4510 AAAGATAAAT
Statistics
Matches: 106, Mismatches: 4, Indels: 10
0.88 0.03 0.08
Matches are distributed among these distances:
73 46 0.43
74 56 0.53
75 4 0.04
ACGTcount: A:0.57, C:0.13, G:0.01, T:0.29
Consensus pattern (74 bp):
AAATCCTAATTAAAATACTAAAACCTACTTAAACTAAAATACCTAAAAAAAATATAATATAAAAT
AATATTCGA
Found at i:5308 original size:2 final size:2
Alignment explanation
Indices: 5301--5329 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5291 CCATATTAAT
5301 TA 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 TA T
5330 TGGTCTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6349 original size:15 final size:15
Alignment explanation
Indices: 6326--6366 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
6316 ATCTCATCCT
*
6326 ATTTCTCTTCTTTCC
1 ATTTATCTTCTTTCC
*
6341 ATTTTTCTTC-TTCC
1 ATTTATCTTCTTTCC
6355 -TTTATCTTCTTT
1 ATTTATCTTCTTT
6367 GAGTAGCCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 8 0.35
14 6 0.26
15 9 0.39
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.66
Consensus pattern (15 bp):
ATTTATCTTCTTTCC
Found at i:9279 original size:4 final size:4
Alignment explanation
Indices: 9270--9297 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
9260 TGTGATTACA
9270 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
9298 TGATCTAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:9975 original size:131 final size:132
Alignment explanation
Indices: 9801--10070 Score: 366
Period size: 133 Copynumber: 2.1 Consensus size: 132
9791 TGAATAGTCA
* *
9801 GTTTGAAAGTTTAATGTTTTTTAAATTACATTTTAATATTTAATTTGTTTATGAT-TT-TATGTT
1 GTTTGAAAGTTTAATGTTTTTTAAATTACAGTTTAATATTTAATGTGTTTATGATATTCTATGTT
* * * * *
9864 TTATCTGACCATGCGTTATTACTGTCTAACTAAGTTGTACATAATGCGTTATTATTTTCATGCGT
66 TTATCTCACCATGCGATATTACTGTCTAACTAAGTTGTACATAACGCGTGATGATTTTCATGCGT
9929 AG
131 AG
* * *
9931 GTTTGACATTTTAATGTTTTATTTAAATTAC-GTTTAATTTTTAATGTGTTTATGATATTCTATG
1 GTTTGAAAGTTTAATG-TTT-TTTAAATTACAGTTTAATATTTAATGTGTTTATGATATTCTATG
* * * * *
9995 TTTTATCTCACCTTGTGATATTACTGTCTCACTAAGTTTTACTTAACGCGTGATGATTTTCATGC
64 TTTTATCTCACCATGCGATATTACTGTCTAACTAAGTTGTACATAACGCGTGATGATTTTCATGC
10060 GTAG
129 GTAG
10064 GTTTGAA
1 GTTTGAA
10071 TAAAAAATCG
Statistics
Matches: 120, Mismatches: 16, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
130 14 0.12
131 25 0.21
132 12 0.10
133 69 0.57
ACGTcount: A:0.26, C:0.10, G:0.14, T:0.50
Consensus pattern (132 bp):
GTTTGAAAGTTTAATGTTTTTTAAATTACAGTTTAATATTTAATGTGTTTATGATATTCTATGTT
TTATCTCACCATGCGATATTACTGTCTAACTAAGTTGTACATAACGCGTGATGATTTTCATGCGT
AG
Found at i:11146 original size:22 final size:22
Alignment explanation
Indices: 11118--11175 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
11108 TGTACAAGCT
11118 GTGCTAAGGCACTTTAGTATAA
1 GTGCTAAGGCACTTTAGTATAA
* *
11140 GTGCTAAGGCAGTTTAGTATCA
1 GTGCTAAGGCACTTTAGTATAA
*
11162 GTGCTAATGCACTT
1 GTGCTAAGGCACTT
11176 CCGTGAATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.33
Consensus pattern (22 bp):
GTGCTAAGGCACTTTAGTATAA
Found at i:14058 original size:15 final size:15
Alignment explanation
Indices: 14038--14078 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
14028 ATATCTCATC
*
14038 CCATTTCTCTTCTTT
1 CCATTTATCTTCTTT
*
14053 CCATTTTTCTTC-TT
1 CCATTTATCTTCTTT
14067 CC-TTTATCTTCT
1 CCATTTATCTTCT
14079 CTGAGTAGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 8 0.35
14 4 0.17
15 11 0.48
ACGTcount: A:0.07, C:0.32, G:0.00, T:0.61
Consensus pattern (15 bp):
CCATTTATCTTCTTT
Found at i:14564 original size:21 final size:20
Alignment explanation
Indices: 14538--14577 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
14528 TTCGAGTTCG
14538 AGTATCAATACTGGTATGAAA
1 AGTATCAATACTGGT-TGAAA
14559 AGTATCAATACTGGTTGAA
1 AGTATCAATACTGGTTGAA
14578 TTGGTGCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (20 bp):
AGTATCAATACTGGTTGAAA
Found at i:17149 original size:133 final size:134
Alignment explanation
Indices: 16892--17165 Score: 379
Period size: 133 Copynumber: 2.1 Consensus size: 134
16882 TGAATAGTCA
* * *
16892 GTTTGAAAGTTTAATGTTTTATTTAAATTACGTTTAATATTTTAATTTGTTTGTGATATTTTATG
1 GTTTGAAAGTTTAATGTTTTATTTAAATTACGTTTAATATTTTAATGTGTTTATGATATTCTATG
* * * * * * *
16957 TTTTATTTGACCATGCGTTATTAATGTCTAACTAAGTTGTACATAATACGTTATTATTTTCTTGC
66 TTTTATCTCACCATGCGATATTAATGTCTAACTAAGTTGTACATAACACGTGATGATTTTCATGC
17022 GTAG
131 GTAG
*
17026 GTTTGAAATTTTAATGTTTTATTTAAATTACGTTTAAT-TTTTAATGTGTTTATGATATTCTATG
1 GTTTGAAAGTTTAATGTTTTATTTAAATTACGTTTAATATTTTAATGTGTTTATGATATTCTATG
* * * * * * *
17090 TTTTATCTCACCTTGTGATATTACTGTCTTACTAAGTTTTACTTAACGCGTGATGATTTTCATGC
66 TTTTATCTCACCATGCGATATTAATGTCTAACTAAGTTGTACATAACACGTGATGATTTTCATGC
17155 GTAG
131 GTAG
17159 GTTTGAA
1 GTTTGAA
17166 TAAAAAATCG
Statistics
Matches: 122, Mismatches: 18, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
133 85 0.70
134 37 0.30
ACGTcount: A:0.26, C:0.09, G:0.15, T:0.51
Consensus pattern (134 bp):
GTTTGAAAGTTTAATGTTTTATTTAAATTACGTTTAATATTTTAATGTGTTTATGATATTCTATG
TTTTATCTCACCATGCGATATTAATGTCTAACTAAGTTGTACATAACACGTGATGATTTTCATGC
GTAG
Found at i:18267 original size:22 final size:22
Alignment explanation
Indices: 18235--18292 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
18225 TGTACCAGCT
*
18235 GTGCTATGGCACTTTAGTATAA
1 GTGCTAAGGCACTTTAGTATAA
*
18257 GTGCTAAGGCACTTTAGTATCA
1 GTGCTAAGGCACTTTAGTATAA
* *
18279 TTGCTAATGCACTT
1 GTGCTAAGGCACTT
18293 CCGTGAATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (22 bp):
GTGCTAAGGCACTTTAGTATAA
Found at i:20890 original size:19 final size:19
Alignment explanation
Indices: 20866--20908 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
20856 TACTTTTACA
*
20866 TTTCAGATTCATAACTCTT
1 TTTCAGATCCATAACTCTT
*
20885 TTTCAGATCCATAACTTTT
1 TTTCAGATCCATAACTCTT
20904 TTTCA
1 TTTCA
20909 TTGAAAACCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.26, C:0.21, G:0.05, T:0.49
Consensus pattern (19 bp):
TTTCAGATCCATAACTCTT
Found at i:25074 original size:13 final size:13
Alignment explanation
Indices: 25056--25085 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
25046 TATTTCTCTT
*
25056 TTCTTCATTTTTC
1 TTCTTCATTTATC
25069 TTCTTCATTTATC
1 TTCTTCATTTATC
25082 TTCT
1 TTCT
25086 CTTAGTAGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.10, C:0.23, G:0.00, T:0.67
Consensus pattern (13 bp):
TTCTTCATTTATC
Found at i:25645 original size:21 final size:21
Alignment explanation
Indices: 25619--25670 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
25609 GGCATAAAGC
25619 ATCGATACTGCCAAGGAGAGT
1 ATCGATACTGCCAAGGAGAGT
* *
25640 ATCGATACTACCAGGGAGAGT
1 ATCGATACTGCCAAGGAGAGT
25661 ATCGATACTG
1 ATCGATACTG
25671 TGCGGCAGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (21 bp):
ATCGATACTGCCAAGGAGAGT
Found at i:25682 original size:19 final size:21
Alignment explanation
Indices: 25658--25709 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 21
25648 TACCAGGGAG
25658 AGTATCGATACTGTGCG-G-C
1 AGTATCGATACTGTGCGTGAC
*
25677 AGTATC-ATACTGTGGGTGAC
1 AGTATCGATACTGTGCGTGAC
*
25697 AATATCGATACTG
1 AGTATCGATACTG
25710 GACCTCAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 9 0.32
19 7 0.25
20 6 0.21
21 6 0.21
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (21 bp):
AGTATCGATACTGTGCGTGAC
Found at i:28867 original size:39 final size:39
Alignment explanation
Indices: 28823--28916 Score: 134
Period size: 39 Copynumber: 2.4 Consensus size: 39
28813 TTCAATCAAT
* * *
28823 TGATTTATTTTATTTTTCAAAATAGAAAAATAAATCTAA
1 TGATTTATTTTCTTTTACAAAATAGAAAAATAAATCCAA
* *
28862 TGATTTATTTCCTTTTACAAAATAGGAAAATAAATCCAA
1 TGATTTATTTTCTTTTACAAAATAGAAAAATAAATCCAA
*
28901 CGATTTATTTTCTTTT
1 TGATTTATTTTCTTTT
28917 GCATATCAGA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 48 1.00
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (39 bp):
TGATTTATTTTCTTTTACAAAATAGAAAAATAAATCCAA
Found at i:29023 original size:38 final size:38
Alignment explanation
Indices: 28945--29023 Score: 108
Period size: 38 Copynumber: 2.1 Consensus size: 38
28935 AGATTCTTAG
* *
28945 GAAAATAAATTTATCGATTTATTTTCTTTTTAAAACAA
1 GAAAATAAATTTATCAATTTATTTTCTTTTTAAAAAAA
28983 GAAAATAAATTCTA-CAATTTATTTTC-TTTTACAAAAAA
1 GAAAATAAATT-TATCAATTTATTTTCTTTTTA-AAAAAA
29021 GAA
1 GAA
29024 TCATATAAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
37 5 0.14
38 30 0.81
39 2 0.05
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.41
Consensus pattern (38 bp):
GAAAATAAATTTATCAATTTATTTTCTTTTTAAAAAAA
Found at i:29024 original size:96 final size:96
Alignment explanation
Indices: 28849--29108 Score: 342
Period size: 96 Copynumber: 2.7 Consensus size: 96
28839 TCAAAATAGA
* *
28849 AAAATAAATCTAATGATTTATTTCCTTTTACAAAATAGGAAAATAAATCCAACGATTTATTTTCT
1 AAAATAAAT-TAATGATTTATTTTCTTTTACAAAATAGGAAAATAAATTCAACGATTTATTTTCT
* * ** **
28914 TTTGCATATCAGAATCATATAAGATTCTTAGG
65 TTTACAAAAAAGAATCATATAAGATTCAAAGG
* * * * * *
28946 AAAATAAATTTATCGATTTATTTTCTTTT-TAAAACAAGAAAATAAATTCTACAATTTATTTTCT
1 AAAATAAATTAAT-GATTTATTTTCTTTTACAAAATAGGAAAATAAATTCAACGATTTATTTTCT
29010 TTTACAAAAAAGAATCATATAAGATTCAAAGG
65 TTTACAAAAAAGAATCATATAAGATTCAAAGG
* *
29042 AAAATAAATTGAATAATTTATTTTCTTTTACAAAATAGGAAAATAAACTCAACGATTTATTTTCT
1 AAAATAAATT-AATGATTTATTTTCTTTTACAAAATAGGAAAATAAATTCAACGATTTATTTTCT
29107 TT
65 TT
29109 CATAAAATAG
Statistics
Matches: 138, Mismatches: 22, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
96 82 0.59
97 56 0.41
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.39
Consensus pattern (96 bp):
AAAATAAATTAATGATTTATTTTCTTTTACAAAATAGGAAAATAAATTCAACGATTTATTTTCTT
TTACAAAAAAGAATCATATAAGATTCAAAGG
Found at i:29100 original size:39 final size:39
Alignment explanation
Indices: 29039--29192 Score: 170
Period size: 39 Copynumber: 3.9 Consensus size: 39
29029 TAAGATTCAA
* * **
29039 AGGAAAATAAATTGAATAATTTATTTTCTTTTACAAAAT
1 AGGAAAATAAACTCAACGATTTATTTTCTTTTACAAAAT
* *
29078 AGGAAAATAAACTCAACGATTTATTTTCTTTCATAAAAT
1 AGGAAAATAAACTCAACGATTTATTTTCTTTTACAAAAT
* *
29117 AGGAAAACAAA-TCCAACGATTTA-TTGCATTTTACAAAAT
1 AGGAAAATAAACT-CAACGATTTATTTTC-TTTTACAAAAT
* *
29156 AAGAAAACAAAAC-CAACGATTTATTTTCTTTTACAAA
1 AGGAAAA-TAAACTCAACGATTTATTTTCTTTTACAAA
29193 TCAGAATCAT
Statistics
Matches: 97, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
38 4 0.04
39 87 0.90
40 6 0.06
ACGTcount: A:0.46, C:0.12, G:0.08, T:0.34
Consensus pattern (39 bp):
AGGAAAATAAACTCAACGATTTATTTTCTTTTACAAAAT
Found at i:29394 original size:58 final size:57
Alignment explanation
Indices: 29244--29542 Score: 243
Period size: 58 Copynumber: 5.2 Consensus size: 57
29234 TTATTTCTTT
* * * * *
29244 ATTCAAGATTC-CTAAGAAGATAAATTTAACAATTTATTTTTTTCA-AAAGATAGAATC
1 ATTCAAGATTCTC-AAGAAAATAAATTCAACTATTTATTTTCTT-ATAAAGTTAGAATC
* * ** *
29301 A-TCAACGATTCTCAAGAATATGAATTTGA-TAATTTATTTATCTTATGAAGTTAGAATC
1 ATTCAA-GATTCTCAAGAAAATAAATTCAACT-ATTTATTT-TCTTATAAAGTTAGAATC
* *
29359 ATTCAAGATTCTCAAGAAAATAAATTCAACTATTTATTTTCGTTACAAAGTTAGAATTG
1 ATTCAAGATTCTCAAGAAAATAAATTCAACTATTTATTTTC-TTATAAAGTTAGAA-TC
* * * * * *
29418 A-TGAATATCCTCAACG-AAATAAATTCAACTATTTGTTTTCCTTACAAAAGTTAGAACC
1 ATTCAAGATTCTCAA-GAAAATAAATTCAACTATTTATTTT-CTTA-TAAAGTTAGAATC
* * * *
29476 ATTCAAG-TTTTCAAGGAAATAAATTCAACAATTTATTTTCCTAATAAAGTTAGAATC
1 ATTCAAGATTCTCAAGAAAATAAATTCAACTATTTATTTT-CTTATAAAGTTAGAATC
*
29533 ATTCTAGATT
1 ATTCAAGATT
29543 ATTTTCCTCA
Statistics
Matches: 196, Mismatches: 31, Indels: 29
0.77 0.12 0.11
Matches are distributed among these distances:
56 4 0.02
57 48 0.24
58 122 0.62
59 22 0.11
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (57 bp):
ATTCAAGATTCTCAAGAAAATAAATTCAACTATTTATTTTCTTATAAAGTTAGAATC
Found at i:29616 original size:91 final size:91
Alignment explanation
Indices: 29453--29624 Score: 249
Period size: 91 Copynumber: 1.9 Consensus size: 91
29443 CAACTATTTG
* *
29453 TTTTCCTTACAAAAGTTAGAACCATTCAAGTTTTCAAGGAAATAAATTCAACAATTTATTTTCCT
1 TTTTCCTCACAAAAGTTAGAACCATTCAAGTTCTCAAGGAAATAAATTCAACAATTTATTTTCCT
*
29518 AATAAAGTTAGAATCATTCTAGATTA
66 AACAAAGTTAGAATCATTCTAGATTA
* * *
29544 TTTTCCTCAC-AAAGTTAGAATCATTTAAGATTCTCAAGTAAATAAATTCAACAATTTA-TTTCT
1 TTTTCCTCACAAAAGTTAGAACCATTCAAG-TTCTCAAGGAAATAAATTCAACAATTTATTTTC-
*
29607 CTTACAAAGTTAGAATCA
64 CTAACAAAGTTAGAATCA
29625 ACGCAAGATT
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
90 21 0.29
91 51 0.71
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.37
Consensus pattern (91 bp):
TTTTCCTCACAAAAGTTAGAACCATTCAAGTTCTCAAGGAAATAAATTCAACAATTTATTTTCCT
AACAAAGTTAGAATCATTCTAGATTA
Found at i:29856 original size:45 final size:45
Alignment explanation
Indices: 29786--30013 Score: 210
Period size: 45 Copynumber: 5.1 Consensus size: 45
29776 GAATTAGTCC
* * * * *
29786 TTTAACTTTAGCAACCCACTAATCAAAAGGAATTAATCCTTTGAT
1 TTTAATTTTTGCAATCCAATAATCAAAAGGAACTAATCCTTTGAT
* * *
29831 TTTAATTTTTGCAGTCCAATAATCAAAAGAAACTAATCTTTTGAT
1 TTTAATTTTTGCAATCCAATAATCAAAAGGAACTAATCCTTTGAT
** * * **
29876 TTTAATCCTTGCAATCCAAAAATTGAAAAGGAACTAAT-AATTGAT
1 TTTAATTTTTGCAATCCAATAA-TCAAAAGGAACTAATCCTTTGAT
** * * * *
29921 TTTAATTTCCGC--GCCTGAGTAATCAAAAGTAATTAATCCTTTGAT
1 TTTAATTTTTGCAATCC--AATAATCAAAAGGAACTAATCCTTTGAT
* *
29966 TTTAATTTTGGCAACCCAATAATCAAAAGGAACTAATCCTTTGAT
1 TTTAATTTTTGCAATCCAATAATCAAAAGGAACTAATCCTTTGAT
30011 TTT
1 TTT
30014 GCTTATGTAA
Statistics
Matches: 143, Mismatches: 34, Indels: 12
0.76 0.18 0.06
Matches are distributed among these distances:
43 2 0.01
44 12 0.08
45 114 0.80
46 13 0.09
47 2 0.01
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (45 bp):
TTTAATTTTTGCAATCCAATAATCAAAAGGAACTAATCCTTTGAT
Found at i:30010 original size:90 final size:89
Alignment explanation
Indices: 29786--30013 Score: 246
Period size: 90 Copynumber: 2.5 Consensus size: 89
29776 GAATTAGTCC
* * * **
29786 TTTAACTTTAGCAACCCACTAATCAAAAGGAATTAATCCTTTGATTTTAATTTTTGCAGTCCAAT
1 TTTAA-TTTTGCAACCCAATAATCAAAAGGAACTAATCCTTTGATTTTAATTTCCGCAGTCCAAT
*
29851 AATCAAAAGAAACTAATCTTTTGAT
65 AATCAAAAGAAACTAATCCTTTGAT
* * * * **
29876 TTTAATCCTTGCAATCCAAAAATTGAAAAGGAACTAAT-AATTGATTTTAATTTCCGC-G-CCTG
1 TTTAAT-TTTGCAACCCAATAA-TCAAAAGGAACTAATCCTTTGATTTTAATTTCCGCAGTCC--
* * *
29938 AGTAATCAAAAGTAATTAATCCTTTGAT
62 AATAATCAAAAGAAACTAATCCTTTGAT
29966 TTTAATTTTGGCAACCCAATAATCAAAAGGAACTAATCCTTTGATTTT
1 TTTAATTTT-GCAACCCAATAATCAAAAGGAACTAATCCTTTGATTTT
30014 GCTTATGTAA
Statistics
Matches: 111, Mismatches: 21, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
88 2 0.02
89 18 0.16
90 78 0.70
91 13 0.12
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (89 bp):
TTTAATTTTGCAACCCAATAATCAAAAGGAACTAATCCTTTGATTTTAATTTCCGCAGTCCAATA
ATCAAAAGAAACTAATCCTTTGAT
Found at i:30269 original size:12 final size:12
Alignment explanation
Indices: 30252--30281 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
30242 ATACCATATC
30252 AATAATATCATG
1 AATAATATCATG
30264 AATAATATCATG
1 AATAATATCATG
*
30276 ATTAAT
1 AATAAT
30282 GCTTACATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.37
Consensus pattern (12 bp):
AATAATATCATG
Found at i:31882 original size:23 final size:23
Alignment explanation
Indices: 31852--31898 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
31842 TATATGTTGC
31852 TACTTATGTTACCTAGACTATTT
1 TACTTATGTTACCTAGACTATTT
31875 TACTTATGTTACCTAGACTATTT
1 TACTTATGTTACCTAGACTATTT
31898 T
1 T
31899 TTTCCTTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.17, G:0.09, T:0.49
Consensus pattern (23 bp):
TACTTATGTTACCTAGACTATTT
Found at i:35330 original size:13 final size:13
Alignment explanation
Indices: 35309--35360 Score: 77
Period size: 13 Copynumber: 4.0 Consensus size: 13
35299 AATGACGCTC
35309 AATGCGCGTCATA
1 AATGCGCGTCATA
*
35322 AATGAGCGTCATA
1 AATGCGCGTCATA
* *
35335 AATGTGTGTCATA
1 AATGCGCGTCATA
35348 AATGCGCGTCATA
1 AATGCGCGTCATA
35361 GATTTATGAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:35333 original size:85 final size:85
Alignment explanation
Indices: 35178--35333 Score: 197
Period size: 85 Copynumber: 1.8 Consensus size: 85
35168 TAAATTCCCA
* * * * *
35178 CAAATGTGTGTCATCTTCATTTATGACAGGGGCTTCAATGACATGCAATGTAAGTCATACATGCG
1 CAAATGTGTGCCATCTTCATTTATGACAGAGGCTTCAATGACATGCAATGCAAGTCATAAATGAG
*
35243 TGTCATTAATTTATGACACG
66 CGTCATTAATTTATGACACG
* * * **
35263 CAAATGTGTGCCATCTTTATTTATGACTGAGGCTTCAATGACGCT-CAATGCGCGTCATAAATGA
1 CAAATGTGTGCCATCTTCATTTATGACAGAGGCTTCAATGAC-ATGCAATGCAAGTCATAAATGA
35327 GCGTCAT
65 GCGTCAT
35334 AAATGTGTGT
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
85 58 0.98
86 1 0.02
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (85 bp):
CAAATGTGTGCCATCTTCATTTATGACAGAGGCTTCAATGACATGCAATGCAAGTCATAAATGAG
CGTCATTAATTTATGACACG
Found at i:38924 original size:3 final size:3
Alignment explanation
Indices: 38916--38944 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
38906 ATGATAAAGT
38916 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
38945 TTAGAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:40254 original size:45 final size:45
Alignment explanation
Indices: 40198--40431 Score: 326
Period size: 45 Copynumber: 5.2 Consensus size: 45
40188 AACTGAACTA
* * *
40198 ATAATTGAAATGCATAGCGGTGCATTATCGGCATGAAAGGATGCC
1 ATAAATGAAATGCATAACGGTGCATTATCGACATGAAAGGATGCC
* * *
40243 ATAAATGAAATGCATAATGGTGAATTATCGACATGCAAGGATGCC
1 ATAAATGAAATGCATAACGGTGCATTATCGACATGAAAGGATGCC
* *
40288 ATAAATGAAATGCATAAAGGTGCATTATCGACATGAAATGATGCC
1 ATAAATGAAATGCATAACGGTGCATTATCGACATGAAAGGATGCC
* * *
40333 ATAAATGAAATGCATAACAGTGCATCATCGACATGAAATGATGCC
1 ATAAATGAAATGCATAACGGTGCATTATCGACATGAAAGGATGCC
* * * *
40378 ATAAATGAAATGCATAACGGTGTA-CATCGACATGGAGGGATGCC
1 ATAAATGAAATGCATAACGGTGCATTATCGACATGAAAGGATGCC
40422 ATAAATGAAA
1 ATAAATGAAA
40432 ATAACGAATA
Statistics
Matches: 171, Mismatches: 18, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
44 27 0.16
45 144 0.84
ACGTcount: A:0.40, C:0.15, G:0.22, T:0.23
Consensus pattern (45 bp):
ATAAATGAAATGCATAACGGTGCATTATCGACATGAAAGGATGCC
Found at i:44424 original size:55 final size:55
Alignment explanation
Indices: 44266--44480 Score: 263
Period size: 55 Copynumber: 3.9 Consensus size: 55
44256 TGAATATTAC
* * ** * * *
44266 AACTCATTATAAATTGTGTGGTTTTGCACACATAGTGCCGATACGGTAATTCACA
1 AACTCATTATGAATTTTGTGGGGTTGCACACATAGTGCCAATACGGAAATTCATA
* * *
44321 AACTCATTATGAATTACT-T-AGGTTGCATACATAGTGCCAATACGGAAATTCATA
1 AACTCATTATGAATT-TTGTGGGGTTGCACACATAGTGCCAATACGGAAATTCATA
* *
44375 AACTCATTATGAATTTTGTGGGGTTGCACACATAGTGCCAATACAGAAATTAATA
1 AACTCATTATGAATTTTGTGGGGTTGCACACATAGTGCCAATACGGAAATTCATA
* * * *
44430 AATTCATTATGAATTTCGTGGGGTTGCACACATATTTCCAATACGGAAATT
1 AACTCATTATGAATTTTGTGGGGTTGCACACATAGTGCCAATACGGAAATT
44481 GCAATATATA
Statistics
Matches: 138, Mismatches: 19, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
53 1 0.01
54 44 0.32
55 92 0.67
56 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (55 bp):
AACTCATTATGAATTTTGTGGGGTTGCACACATAGTGCCAATACGGAAATTCATA
Found at i:55831 original size:2 final size:2
Alignment explanation
Indices: 55824--55897 Score: 148
Period size: 2 Copynumber: 37.0 Consensus size: 2
55814 AATTCCAGTG
55824 AT AT 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 AT AT
55866 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
55898 CAAACCAGAT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57948 original size:17 final size:17
Alignment explanation
Indices: 57926--57970 Score: 90
Period size: 17 Copynumber: 2.6 Consensus size: 17
57916 TTCGACACCT
57926 CTTGCACTATCGTGTTC
1 CTTGCACTATCGTGTTC
57943 CTTGCACTATCGTGTTC
1 CTTGCACTATCGTGTTC
57960 CTTGCACTATC
1 CTTGCACTATC
57971 CTATAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.13, C:0.31, G:0.16, T:0.40
Consensus pattern (17 bp):
CTTGCACTATCGTGTTC
Found at i:58559 original size:2 final size:2
Alignment explanation
Indices: 58552--58603 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
58542 ATATGGTCTA
58552 AT AT 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 AT AT
58594 AT AT AT AT AT
1 AT AT AT AT AT
58604 TCACTGGAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59339 original size:21 final size:21
Alignment explanation
Indices: 59313--59362 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
59303 ATTTTTCTTA
59313 TTTTATAATT-ACTATTTAAAC
1 TTTTATAATTAACTATTT-AAC
* *
59334 TTTTATAATTAATTATTTTAC
1 TTTTATAATTAACTATTTAAC
59355 TTTTATAA
1 TTTTATAA
59363 ATGTTAATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 20 0.77
22 6 0.23
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (21 bp):
TTTTATAATTAACTATTTAAC
Done.