Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004362.1 Hibiscus syriacus cultivar Beakdansim tig00009555_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: 82266
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:2746 original size:90 final size:90
Alignment explanation
Indices: 2635--2807 Score: 303
Period size: 90 Copynumber: 1.9 Consensus size: 90
2625 TAATCTCGAA
*
2635 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATA-AAATCCCTAATATGA
1 TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAGAAA-CCCTAATATGA
2699 TTAGGGTAACTTGGATATATAAGGAT
65 TTAGGGTAACTTGGATATATAAGGAT
*
2725 TATTAAATTTTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAGAAACCCTAATATGAT
1 TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAGAAACCCTAATATGAT
*
2790 TAGGGTAACTTGGCTATA
66 TAGGGTAACTTGGATATA
2808 AAATGGTGTG
Statistics
Matches: 79, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
90 76 0.96
91 3 0.04
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (90 bp):
TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAGAAACCCTAATATGAT
TAGGGTAACTTGGATATATAAGGAT
Found at i:5516 original size:18 final size:18
Alignment explanation
Indices: 5493--5528 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
5483 GTGGACCTAC
5493 GAGTGGGAAATGGAGCAA
1 GAGTGGGAAATGGAGCAA
5511 GAGTGGGAAATGGAGCAA
1 GAGTGGGAAATGGAGCAA
5529 AAGTTTATGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.44, T:0.11
Consensus pattern (18 bp):
GAGTGGGAAATGGAGCAA
Found at i:9630 original size:86 final size:87
Alignment explanation
Indices: 9466--9630 Score: 262
Period size: 86 Copynumber: 1.9 Consensus size: 87
9456 TCCTGAATTT
9466 AATTTCAATTAATTAAATATAAATTTAAGTAATTTGAAATAATAAAATCCCTAATATGATTAGGG
1 AATTTCAATTAATTAAATATAAATTTAAGTAATTTGAAATAATAAAATCCCTAATATGATTAGGG
*
9531 TAACTTGGATATAAGATTATTA
66 TAACTTCGATATAAGATTATTA
* * *
9553 AATTTTAATTAATT-AATATAGATTTAATTAATTTGAAATAATAGAAA-CCCTAATATGATTAGG
1 AATTTCAATTAATTAAATATAAATTTAAGTAATTTGAAATAATA-AAATCCCTAATATGATTAGG
*
9616 GTAACTTCGCTATAA
65 GTAACTTCGATATAA
9631 AAGGGTGTTT
Statistics
Matches: 72, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
86 56 0.78
87 16 0.22
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (87 bp):
AATTTCAATTAATTAAATATAAATTTAAGTAATTTGAAATAATAAAATCCCTAATATGATTAGGG
TAACTTCGATATAAGATTATTA
Found at i:13299 original size:13 final size:11
Alignment explanation
Indices: 13272--13296 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
13262 GAATGAGAGC
13272 TTTGTGTGGTG
1 TTTGTGTGGTG
13283 TTTGTGTGGTG
1 TTTGTGTGGTG
13294 TTT
1 TTT
13297 TTGATGTAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.40, T:0.60
Consensus pattern (11 bp):
TTTGTGTGGTG
Found at i:22017 original size:20 final size:20
Alignment explanation
Indices: 21994--22036 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
21984 AATTCACCAC
*
21994 ATGCAACTAAATGCTTCTAA
1 ATGCAACTAAATGCTCCTAA
* *
22014 ATGCATCTATATGCTCCTAA
1 ATGCAACTAAATGCTCCTAA
22034 ATG
1 ATG
22037 AGCTCTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (20 bp):
ATGCAACTAAATGCTCCTAA
Found at i:26451 original size:93 final size:92
Alignment explanation
Indices: 26286--26471 Score: 243
Period size: 93 Copynumber: 2.0 Consensus size: 92
26276 CATGTTATAT
*
26286 TATTATATATATATATATATAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAATCAACCC
1 TATTATATATATATATATATAATAAAGCTTGAGTTGTCCCTATAAAGCAATTGGTTAATCAACCC
26351 GGCTTTATGGATAA-TATTCAACTAGCC
66 GGCTTTATGGATAAGT-TTCAACTAGCC
* * * ***
26378 TATTATAT-TAT-TATTATATGCAATAGAGCTTGAGTTGTCCCTATAGAGCAGTTGGTTAATTGC
1 TATTATATATATATA-TATAT--AATAAAGCTTGAGTTGTCCCTATAAAGCAATTGGTTAATCAA
*
26441 CCCGGTTTTATGGATAAGTTTCAACTAGCC
63 CCCGGCTTTATGGATAAGTTTCAACTAGCC
26471 T
1 T
26472 GATAAATGTG
Statistics
Matches: 82, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
90 2 0.02
91 8 0.10
92 8 0.10
93 63 0.77
94 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.38
Consensus pattern (92 bp):
TATTATATATATATATATATAATAAAGCTTGAGTTGTCCCTATAAAGCAATTGGTTAATCAACCC
GGCTTTATGGATAAGTTTCAACTAGCC
Found at i:29247 original size:42 final size:43
Alignment explanation
Indices: 29182--29309 Score: 122
Period size: 42 Copynumber: 3.0 Consensus size: 43
29172 CCCAAATTTA
*
29182 TAAATCCTTCGGTTCAT-TAGTAAG-TCTTTCGAGCATGATGTT
1 TAAATCCTTCGGGTCATCT-GTAAGATCTTTCGAGCATGATGTT
* * * * *
29224 TAAATCCTTCGGGTCATCTGTAAGCTTTTTTGAGCAAGATG-A
1 TAAATCCTTCGGGTCATCTGTAAGATCTTTCGAGCATGATGTT
* * *
29266 TAATTCCTTCAGGTCATCCGTAAGATC-TTC-AGGCATGATGTT
1 TAAATCCTTCGGGTCATCTGTAAGATCTTTCGA-GCATGATGTT
29308 TA
1 TA
29310 CACATGATTT
Statistics
Matches: 69, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
40 1 0.01
41 9 0.13
42 45 0.65
43 14 0.20
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.38
Consensus pattern (43 bp):
TAAATCCTTCGGGTCATCTGTAAGATCTTTCGAGCATGATGTT
Found at i:29517 original size:20 final size:20
Alignment explanation
Indices: 29438--29517 Score: 56
Period size: 20 Copynumber: 3.9 Consensus size: 20
29428 TATTTCCCAA
* *
29438 ATTTGTAAATCATTCGGGTC
1 ATTTGTAAATCTTTCGAGTC
* *
29458 ATTAGTAAGTCTTTCGAG-C
1 ATTTGTAAATCTTTCGAGTC
*
29477 ATAATACT-TAAATCCTTCGAGTC
1 AT--T--TGTAAATCTTTCGAGTC
*
29500 ATTTGTAAGTCTTTCGAG
1 ATTTGTAAATCTTTCGAG
29518 CAAGATGATA
Statistics
Matches: 45, Mismatches: 9, Indels: 12
0.68 0.14 0.18
Matches are distributed among these distances:
19 4 0.09
20 25 0.56
21 2 0.04
22 11 0.24
23 3 0.07
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (20 bp):
ATTTGTAAATCTTTCGAGTC
Found at i:29771 original size:36 final size:36
Alignment explanation
Indices: 29730--29813 Score: 123
Period size: 36 Copynumber: 2.3 Consensus size: 36
29720 AATAGATTTA
* * *
29730 TCTCACTCGAGATTGTTTTTCTTAAAACAAAATTCT
1 TCTCACTAGAGATGGTTTTTCTTAAAACAAAATTCG
*
29766 TCTCACTAGAGATGGTTTTTCTTAAAACAAACTTCG
1 TCTCACTAGAGATGGTTTTTCTTAAAACAAAATTCG
*
29802 TCTCACTTGAGA
1 TCTCACTAGAGA
29814 CAATTTTCCC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (36 bp):
TCTCACTAGAGATGGTTTTTCTTAAAACAAAATTCG
Found at i:30101 original size:17 final size:17
Alignment explanation
Indices: 30053--30103 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
30043 TCCAATGAGT
30053 AGTTCATAATGAGAAGA
1 AGTTCATAATGAGAAGA
**
30070 A-TTCAT-CCGATGAAGA
1 AGTTCATAATGA-GAAGA
30086 AGTTCATAATGAGAAGA
1 AGTTCATAATGAGAAGA
30103 A
1 A
30104 CTTGTTCAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
15 2 0.07
16 11 0.41
17 12 0.44
18 2 0.07
ACGTcount: A:0.45, C:0.10, G:0.22, T:0.24
Consensus pattern (17 bp):
AGTTCATAATGAGAAGA
Found at i:30390 original size:118 final size:119
Alignment explanation
Indices: 30181--30495 Score: 499
Period size: 118 Copynumber: 2.7 Consensus size: 119
30171 ACATTTTCAA
* * * *
30181 TGGAAGAGTTCATAATGATAAGAACTCGTCCGAAGAGGAAGAAGAAGTTCAT-ATGAGAAGAGCT
1 TGGAAGAGTTCATAATAAGAAGAACTCATCCAAAGAGGAAGAAGAAGTTCATAATGAGAAGAGCT
30245 TGTTCAACCTTTTGATAGATTCCATCACAGAAGGAGATGGATCGTCATT-CCAG
66 TGTTCAACCTTTTGATAGATTCCATCACAGAAGGAGATGGATCGTCATTCCCAG
* * *
30298 TTGAAGAGTTCACAATAAGAAGAACTCATCCAAAAAGGAAGAAGAAGTTCATAATGAGAAGAGCT
1 TGGAAGAGTTCATAATAAGAAGAACTCATCCAAAGAGGAAGAAGAAGTTCATAATGAGAAGAGCT
*
30363 TGTTCAACCTTTTGATAGATTCCATCACATAAGGAGATGGATCGTCATTCCCAG
66 TGTTCAACCTTTTGATAGATTCCATCACAGAAGGAGATGGATCGTCATTCCCAG
* *
30417 TGGAAGAGTTCATAATAAGAAGAACTCATCCAAAGAGGAAGAAAAAAGTTCATAATGAGAAGAAC
1 TGGAAGAGTTCATAATAAGAAGAACTCATCCAAAGAGGAAG-AAGAAGTTCATAATGAGAAGAGC
* *
30482 TTGTTTAACATTTT
65 TTGTTCAACCTTTT
30496 TGTCTTAATC
Statistics
Matches: 180, Mismatches: 15, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
117 45 0.25
118 60 0.33
119 42 0.23
120 33 0.18
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.25
Consensus pattern (119 bp):
TGGAAGAGTTCATAATAAGAAGAACTCATCCAAAGAGGAAGAAGAAGTTCATAATGAGAAGAGCT
TGTTCAACCTTTTGATAGATTCCATCACAGAAGGAGATGGATCGTCATTCCCAG
Found at i:30630 original size:3 final size:3
Alignment explanation
Indices: 30617--30678 Score: 81
Period size: 3 Copynumber: 21.0 Consensus size: 3
30607 TTGTCTCATT
* * * *
30617 TTA TT- TTA TTA TTA TTA TTT TTT TTA TTT TTA TTA TCA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
30664 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
30679 CATGCCCGAA
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
2 2 0.04
3 50 0.96
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:32988 original size:15 final size:13
Alignment explanation
Indices: 32954--32987 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
32944 ACTAAATTAG
32954 ATATATATCCTAA
1 ATATATATCCTAA
32967 ATATATATCCTAA
1 ATATATATCCTAA
32980 ATATATAT
1 ATATATAT
32988 AAATACTGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (13 bp):
ATATATATCCTAA
Found at i:34670 original size:41 final size:42
Alignment explanation
Indices: 34589--34670 Score: 105
Period size: 41 Copynumber: 2.0 Consensus size: 42
34579 TGGGTCATTA
* * * *
34589 GTAAGTCTTTCGAACATGATGCTTAAATCCTTCGGGTCATCT
1 GTAAGTCTTTCGAACAAGATGCATAAAACCTTCGGATCATCT
34631 GTAAGTCTTTC-AAGCAAGATG-ATAAAACCTTCGGATCATC
1 GTAAGTCTTTCGAA-CAAGATGCATAAAACCTTCGGATCATC
34671 CATAAAACCT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
41 18 0.51
42 17 0.49
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (42 bp):
GTAAGTCTTTCGAACAAGATGCATAAAACCTTCGGATCATCT
Found at i:34933 original size:74 final size:75
Alignment explanation
Indices: 34822--35018 Score: 260
Period size: 74 Copynumber: 2.7 Consensus size: 75
34812 CAAAGATTTG
* * *
34822 TCTCGCTTGAGACAA-TTTCACTCG-AAACAGAAATTTATCTCACTTGAGATTGTTTTTATTAAA
1 TCTCACTTGAGACAATTTTCACTTGAAAACATAAATTTATCTCACTTGAGATTGTTTTTATTAAA
34885 AC-AACTTCA
66 ACAAACTTCA
* *
34894 TTTCACTTGAGACAATTTTCACTTGAAAACATAAATTTATCTCACTTGAGATTGTTTTTTTTAAA
1 TCTCACTTGAGACAATTTTCACTTGAAAACATAAATTTATCTCACTTGAGATTGTTTTTATTAAA
34959 ACAAACTTCA
66 ACAAACTTCA
* * * * * *
34969 TCTCACTTGAAACTATTTTC-CCTCAAAACAT-ATTTTATCTCACCTGAGAT
1 TCTCACTTGAGACAATTTTCACTTGAAAACATAAATTTATCTCACTTGAGAT
35019 AGTTCCTCTT
Statistics
Matches: 110, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
72 13 0.12
73 25 0.23
74 48 0.44
75 24 0.22
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.39
Consensus pattern (75 bp):
TCTCACTTGAGACAATTTTCACTTGAAAACATAAATTTATCTCACTTGAGATTGTTTTTATTAAA
ACAAACTTCA
Found at i:34940 original size:39 final size:38
Alignment explanation
Indices: 34812--34944 Score: 114
Period size: 37 Copynumber: 3.6 Consensus size: 38
34802 AATTTCAAAG
* * *
34812 CAAAGATTTGTCTCGCTTGAGACAA-TTTCACTCG-AAA
1 CAAA-ATTTATCTCACTTGAGACAATTTTCACTTGAAAA
*** *
34849 CAGAAATTTATCTCACTTGAGATTGTTTTTA-TT-AAAA
1 CA-AAATTTATCTCACTTGAGACAATTTTCACTTGAAAA
* * *
34886 C-AACTTCATTTCACTTGAGACAATTTTCACTTGAAAA
1 CAAAATTTATCTCACTTGAGACAATTTTCACTTGAAAA
34923 CATAAATTTATCTCACTTGAGA
1 CA-AAATTTATCTCACTTGAGA
34945 TTGTTTTTTT
Statistics
Matches: 72, Mismatches: 17, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
35 21 0.29
36 2 0.03
37 27 0.38
38 6 0.08
39 16 0.22
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (38 bp):
CAAAATTTATCTCACTTGAGACAATTTTCACTTGAAAA
Found at i:35545 original size:20 final size:20
Alignment explanation
Indices: 35482--35546 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
35472 CTAAAGAAAG
35482 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
* ** **
35502 CG-TCCGAA-GAGGAAGAAGA
1 AGTTCATAATGA-GAAGAACT
35521 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
*
35541 TGTTCA
1 AGTTCA
35547 ACATTTCCTT
Statistics
Matches: 31, Mismatches: 11, Indels: 6
0.65 0.23 0.12
Matches are distributed among these distances:
18 2 0.06
19 11 0.35
20 16 0.52
21 2 0.06
ACGTcount: A:0.42, C:0.12, G:0.25, T:0.22
Consensus pattern (20 bp):
AGTTCATAATGAGAAGAACT
Found at i:36766 original size:21 final size:22
Alignment explanation
Indices: 36731--36771 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
36721 TTTTTGTGTC
*
36731 TTTTAATTTGTTATTCTAGTTT
1 TTTTAATTTGATATTCTAGTTT
*
36753 TTTTAATTT-ATATTTTAGT
1 TTTTAATTTGATATTCTAGT
36772 CCTTGCTACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.22, C:0.02, G:0.07, T:0.68
Consensus pattern (22 bp):
TTTTAATTTGATATTCTAGTTT
Found at i:44011 original size:20 final size:22
Alignment explanation
Indices: 43972--44022 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
43962 CTTATGGCTG
*
43972 CAAATATGAGGGGAAAATATCA
1 CAAATATTAGGGGAAAATATCA
*
43994 CAAATATTA-GGG-AAATATGA
1 CAAATATTAGGGGAAAATATCA
*
44014 AAAATATTA
1 CAAATATTA
44023 ATCCACTCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 15 0.58
21 3 0.12
22 8 0.31
ACGTcount: A:0.53, C:0.06, G:0.18, T:0.24
Consensus pattern (22 bp):
CAAATATTAGGGGAAAATATCA
Found at i:45884 original size:131 final size:132
Alignment explanation
Indices: 45700--46068 Score: 343
Period size: 131 Copynumber: 2.8 Consensus size: 132
45690 ATAATTTTAA
* * * * * * * *
45700 GAGAGAAAACGATAGTA-CCTAATTATTTTCAATCGAGAATAAATGACATTTCATGCGTTAAAAC
1 GAGAGAAAACAATAATATCC-AATAATTTCCAATCGATAATAAATGACCTTTCATGCCTTAAAGC
* ** * * * *
45764 AATCATTTATTACCCCAATTGAAATGAAGAGATATTACTATTTCGTC-TTAAAATTTAATATTGA
65 AATCATTTATTACTCCAATTGAAATGAAGAGATATTACTATTTCCACATTAAAAATCAATACTAA
45828 TTC
130 TTC
* * * * * *
45831 GAGTGAAAACAATAATATCTAATAATTTCCAATC-TTAAATAAATAACCTTTCATACCATAAAGC
1 GAGAGAAAACAATAATATCCAATAATTTCCAATCGAT-AATAAATGACCTTTCATGCCTTAAAGC
* * * * * *
45895 ATTCATTTATTACTCCTATCGAAATGAAGAAATGTCACTA-TTCCACATTAAAAATCAATACTAA
65 AATCATTTATTACTCCAATTGAAATGAAGAGATATTACTATTTCCACATTAAAAATCAATACTAA
*
45959 TTT
130 TTC
* ** * * *
45962 GAGAGAGAACGGTAATATCCAATTATTTCCAATCGATAATAAATGACCTCTCATGCCTTAAAGTA
1 GAGAGAAAACAATAATATCCAATAATTTCCAATCGATAATAAATGACCTTTCATGCCTTAAAGCA
* * *
46027 GTCATTTATTACTCCAACAT-AAATGAAAAGATATTACTATTT
66 ATCATTTATTACTCCAA-TTGAAATGAAGAGATATTACTATTT
46069 TCAATATTGA
Statistics
Matches: 184, Mismatches: 48, Indels: 11
0.76 0.20 0.05
Matches are distributed among these distances:
130 4 0.02
131 176 0.96
132 4 0.02
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (132 bp):
GAGAGAAAACAATAATATCCAATAATTTCCAATCGATAATAAATGACCTTTCATGCCTTAAAGCA
ATCATTTATTACTCCAATTGAAATGAAGAGATATTACTATTTCCACATTAAAAATCAATACTAAT
TC
Found at i:46766 original size:6 final size:6
Alignment explanation
Indices: 46755--46866 Score: 88
Period size: 6 Copynumber: 18.2 Consensus size: 6
46745 TTATTTGTTC
* *
46755 TCTTTT TCTTTTT CTCTTTT TCTCTT TCTTTT TCTTCTT CTCTTTT TATTTT
1 TCTTTT TC-TTTT -TCTTTT TCTTTT TCTTTT TCTT-TT -TCTTTT TCTTTT
* *
46807 T-TTTT TATTTT TCCTTT TC--TT TCTTTAT T-TATTT TCTTTTT TCTTTT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTT-T TCT-TTT TC-TTTT TCTTTT
*
46854 TCTTGT TCTTTT T
1 TCTTTT TCTTTT T
46867 TCATTCTTCA
Statistics
Matches: 88, Mismatches: 7, Indels: 22
0.75 0.06 0.19
Matches are distributed among these distances:
4 4 0.05
5 5 0.06
6 51 0.58
7 21 0.24
8 7 0.08
ACGTcount: A:0.04, C:0.17, G:0.01, T:0.79
Consensus pattern (6 bp):
TCTTTT
Found at i:46789 original size:26 final size:26
Alignment explanation
Indices: 46755--46866 Score: 103
Period size: 26 Copynumber: 4.5 Consensus size: 26
46745 TTATTTGTTC
46755 TCTTTTTCTTTTTCTCTTTTTCTCTT
1 TCTTTTTCTTTTTCTCTTTTTCTCTT
* *
46781 TCTTTTTCTTCTTCTCTTTTTAT-TT
1 TCTTTTTCTTTTTCTCTTTTTCTCTT
* *
46806 TTTTTTTATTTTTC-C--TTT-TCTT
1 TCTTTTTCTTTTTCTCTTTTTCTCTT
*
46828 TCTTTATT-TATTTTCT-TTTTTCTTTT
1 TCTTT-TTCT-TTTTCTCTTTTTCTCTT
*
46854 TCTTGTTCTTTTT
1 TCTTTTTCTTTTT
46867 TCATTCTTCA
Statistics
Matches: 70, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
21 1 0.01
22 10 0.14
23 7 0.10
24 1 0.01
25 22 0.31
26 29 0.41
ACGTcount: A:0.04, C:0.17, G:0.01, T:0.79
Consensus pattern (26 bp):
TCTTTTTCTTTTTCTCTTTTTCTCTT
Found at i:46830 original size:67 final size:65
Alignment explanation
Indices: 46743--46867 Score: 148
Period size: 67 Copynumber: 1.9 Consensus size: 65
46733 TTGAACCCCC
*
46743 TTTTATTTGTTCTCTTTTTCTTT-TTCTCTTTT-TCTCTTTCTTTTTCTTCTTCTCTTTTTATTT
1 TTTTATTTGTTCTCTTTTTCTTTATT-TATTTTCT-TCTTTCTTTTTCTTCTTCT-TTTTTATTT
46806 TTT
63 TTT
* * *
46809 TTTTATTT-TTCCTTTTCTTTCTTTATTTATTTTCTTTTTTCTTTTTCTTGTTCTTTTTT
1 TTTTATTTGTT-CTCTT-TTTCTTTATTTATTTTCTTCTTTCTTTTTCTTCTTCTTTTTT
46868 CATTCTTCAG
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
65 2 0.04
66 17 0.33
67 29 0.57
68 3 0.06
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.78
Consensus pattern (65 bp):
TTTTATTTGTTCTCTTTTTCTTTATTTATTTTCTTCTTTCTTTTTCTTCTTCTTTTTTATTTTTT
Found at i:46866 original size:20 final size:19
Alignment explanation
Indices: 46758--46867 Score: 77
Period size: 20 Copynumber: 5.6 Consensus size: 19
46748 TTTGTTCTCT
*
46758 TTTTCTTTTTCTCTTTTTC
1 TTTTCTTTTTTTCTTTTTC
*
46777 TCTTTCTTTTTCTTC-TTCTC
1 T-TTTCTTTTT-TTCTTTTTC
46797 TTTT-TATTTTTT-TTTTAT-
1 TTTTCT-TTTTTTCTTTT-TC
*
46815 TTTTCCTTTTCTTTCTTTATTTA
1 TTTT-CTTTT-TTTC-TT-TTTC
46838 TTTTC-TTTTTTCTTTTTC
1 TTTTCTTTTTTTCTTTTTC
46856 TTGTTCTTTTTT
1 TT-TTCTTTTTT
46868 CATTCTTCAG
Statistics
Matches: 73, Mismatches: 4, Indels: 27
0.70 0.04 0.26
Matches are distributed among these distances:
18 14 0.19
19 17 0.23
20 27 0.37
21 5 0.07
22 4 0.05
23 6 0.08
ACGTcount: A:0.04, C:0.16, G:0.01, T:0.79
Consensus pattern (19 bp):
TTTTCTTTTTTTCTTTTTC
Found at i:46868 original size:26 final size:25
Alignment explanation
Indices: 46755--46865 Score: 104
Period size: 24 Copynumber: 4.5 Consensus size: 25
46745 TTATTTGTTC
*
46755 TCTTTTTCTTTTTCTCTTTTTCTCTT
1 TCTTTTTC-TTTTCTCTTTTTCTTTT
*
46781 TCTTTTTCTTCTTCTCTTTTTATTTT
1 TCTTTTTCTT-TTCTCTTTTTCTTTT
* *
46807 T-TTTTTATTTT-TCCTTTTCTTTCT
1 TCTTTTTCTTTTCTCTTTTTCTTT-T
* *
46831 T-TATTTATTTTCT-TTTTTCTTTT
1 TCTTTTTCTTTTCTCTTTTTCTTTT
*
46854 TCTTGTTCTTTT
1 TCTTTTTCTTTT
46866 TTCATTCTTC
Statistics
Matches: 71, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
23 11 0.15
24 28 0.39
25 10 0.14
26 22 0.31
ACGTcount: A:0.04, C:0.17, G:0.01, T:0.78
Consensus pattern (25 bp):
TCTTTTTCTTTTCTCTTTTTCTTTT
Found at i:64485 original size:127 final size:131
Alignment explanation
Indices: 64137--64502 Score: 402
Period size: 132 Copynumber: 2.8 Consensus size: 131
64127 ATAATTTTAA
* * * * * **
64137 GAGAGAAAACAATAATTTCTAATTATTTCCTATTGAGAATAAATGACCTTTCATGCCTTAAAATA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACC-TTCATGACTTAAAGCA
* * * * ** * *
64202 GTCATTTATTACCCCAATTGAAATAAAGATATATTACTATTTTGCCTTTAAAATTTAATATAAAT
65 GTCATTTATTACTCCAATCGAAATGAAGAGATATTACTATTCAGCCTTTAAAAATCAATATAAAT
64267 TC
130 TC
* * * *
64269 AAGTGAAAACGATAATATCTAATGATTTCCAATCTA-AATTAAATGACCTTTCAT-ACCTTAAAG
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAA-TAAATGACC-TTCATGA-CTTAAAG
* *
64332 CAGTCATTTATTACTCCTATCGAAATGAAGAGATATCACTATTCAGCC-TTAAAAATCAAT-T-A
63 CAGTCATTTATTACTCCAATCGAAATGAAGAGATATTACTATTCAGCCTTTAAAAATCAATATAA
64394 ATTC
128 ATTC
* * * *
64398 GAGAGAAAACGGTAATATCAAATTATTTTCAATCGAGAATAAATTACC-TCATGACTTAAAGCAG
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTTCATGACTTAAAGCAG
* * *
64462 TCATTTATTACTCCAACCAAAATGAAAAGATATTACTATTC
66 TCATTTATTACTCCAATCGAAATGAAGAGATATTACTATTC
64503 TTAATATCGA
Statistics
Matches: 196, Mismatches: 34, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
127 50 0.26
128 1 0.01
129 42 0.21
130 3 0.02
131 12 0.06
132 88 0.45
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.34
Consensus pattern (131 bp):
GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTTCATGACTTAAAGCAG
TCATTTATTACTCCAATCGAAATGAAGAGATATTACTATTCAGCCTTTAAAAATCAATATAAATT
C
Found at i:67372 original size:21 final size:21
Alignment explanation
Indices: 67346--67389 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
67336 TGAGTTTTAA
*
67346 TTATTACTATTATCATTATAT
1 TTATTACTATTATCATTAAAT
* *
67367 TTATTATTATTATTATTAAAT
1 TTATTACTATTATCATTAAAT
67388 TT
1 TT
67390 TGCATGCCCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (21 bp):
TTATTACTATTATCATTAAAT
Found at i:70282 original size:17 final size:20
Alignment explanation
Indices: 70256--70297 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
70246 TTTTTATAAT
70256 AAAATCAT-AATTGTTTT-A
1 AAAATCATAAATTGTTTTCA
70274 AAAAT-ATAAATTGTTTTCA
1 AAAATCATAAATTGTTTTCA
70293 AAAAT
1 AAAAT
70298 GGTTATGACA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 2 0.09
18 14 0.64
19 6 0.27
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (20 bp):
AAAATCATAAATTGTTTTCA
Found at i:74093 original size:3 final size:3
Alignment explanation
Indices: 74069--74118 Score: 55
Period size: 3 Copynumber: 16.0 Consensus size: 3
74059 TAATCTGAAT
* * *
74069 ATA AAA ATA ATA TTA ATAA ATA ATA ATAA ATA ATA ATA ATA ATA GTA
1 ATA ATA ATA ATA ATA AT-A ATA ATA AT-A ATA ATA ATA ATA ATA ATA
74116 ATA
1 ATA
74119 TTAAATATTG
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
3 33 0.85
4 6 0.15
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:74095 original size:10 final size:10
Alignment explanation
Indices: 74077--74112 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
74067 ATATAAAAAT
*
74077 AATATTAATA
1 AATAATAATA
74087 AATAATAATA
1 AATAATAATA
74097 AATAATAAT-
1 AATAATAATA
74106 AATAATA
1 AATAATA
74113 GTAATATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 7 0.28
10 18 0.72
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
AATAATAATA
Found at i:74125 original size:13 final size:12
Alignment explanation
Indices: 74069--74118 Score: 55
Period size: 13 Copynumber: 4.0 Consensus size: 12
74059 TAATCTGAAT
*
74069 ATAAAAATAATA
1 ATAATAATAATA
*
74081 TTAATAAATAATA
1 ATAAT-AATAATA
74094 ATAAATAATAATA
1 AT-AATAATAATA
*
74107 ATAATAGTAATA
1 ATAATAATAATA
74119 TTAAATATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
12 12 0.38
13 17 0.53
14 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (12 bp):
ATAATAATAATA
Found at i:74771 original size:20 final size:19
Alignment explanation
Indices: 74744--74821 Score: 66
Period size: 20 Copynumber: 3.8 Consensus size: 19
74734 CTTATCATCT
74744 TGCTCGAAAGACTTACACA
1 TGCTCGAAAGACTTACACA
* *
74763 TGACTCGAAGGATTTAATCATCA
1 TG-CTCGAAAGACTT-A-CA-CA
**
74786 TGCTCGAAAGACTTACTGA
1 TGCTCGAAAGACTTACACA
*
74805 TGGCCCGAAAGACTTAC
1 T-GCTCGAAAGACTTAC
74822 CAATTTGGAA
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
19 4 0.09
20 25 0.53
21 2 0.04
22 12 0.26
23 4 0.09
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (19 bp):
TGCTCGAAAGACTTACACA
Found at i:75155 original size:17 final size:17
Alignment explanation
Indices: 75135--75193 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
75125 TTTAGGGAAG
75135 TAGTTCATTTATGCATC
1 TAGTTCATTTATGCATC
* *
75152 TAGTT-ATTTAAT-AAAC
1 TAGTTCATTT-ATGCATC
* * *
75168 TAATTCATTCATGCATT
1 TAGTTCATTTATGCATC
75185 TAGTTCATT
1 TAGTTCATT
75194 GAATAAAGTG
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
16 12 0.39
17 19 0.61
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (17 bp):
TAGTTCATTTATGCATC
Found at i:76504 original size:19 final size:20
Alignment explanation
Indices: 76480--76531 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
76470 AAAGAAGAAA
*
76480 TGAGAGTTGAAAAAGA-CAT
1 TGAGAGTTGAAAAAGATAAT
76499 TGAGAGCATTG-AAAAGATAAT
1 TGAGAG--TTGAAAAAGATAAT
76520 TGAGAG-TGAAAA
1 TGAGAGTTGAAAA
76532 TGAGCACATT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
18 2 0.07
19 9 0.32
20 6 0.21
21 11 0.39
ACGTcount: A:0.48, C:0.04, G:0.27, T:0.21
Consensus pattern (20 bp):
TGAGAGTTGAAAAAGATAAT
Found at i:77646 original size:17 final size:17
Alignment explanation
Indices: 77607--77648 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
77597 AAGTATGTTG
*
77607 TGCATTAAAGCATGCAT
1 TGCATTTAAGCATGCAT
*
77624 TGCATTTAAGCATGTAT
1 TGCATTTAAGCATGCAT
*
77641 TTCATTTA
1 TGCATTTA
77649 GGGAAGTAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.40
Consensus pattern (17 bp):
TGCATTTAAGCATGCAT
Found at i:80692 original size:2 final size:2
Alignment explanation
Indices: 80685--80725 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
80675 TTAGCTTTAT
80685 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
80726 ATTGCCTTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Done.