Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001386.1 Hibiscus syriacus cultivar Beakdansim tig00002705_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: 60823
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:1686 original size:80 final size:78
Alignment explanation
Indices: 1537--1700 Score: 265
Period size: 80 Copynumber: 2.1 Consensus size: 78
1527 TATCCTTCGG
**
1537 CCATCAGTAAGTCTGTCGAGCATGATGATTAATCCTTCGGTAATTTGTAAGCCTTCACAGAAGAG
1 CCATCAGTAAGTCTGTCGAGCATGATGATTAATCCTTCGGTAATTCATAAGCCTTCACAGAAGAG
1602 TAGTGAAGCAAGT
66 TAGTGAAGCAAGT
* * *
1615 CCATCAGTAAGTCTTTTGAGCATGATGATTAAATCCTTCAGGTAATTCATAAGCCTTCACGGAAG
1 CCATCAGTAAGTCTGTCGAGCATGATGATT-AATCCTTC-GGTAATTCATAAGCCTTCACAGAAG
1680 AGTAGTGAAGCAAGT
64 AGTAGTGAAGCAAGT
1695 CCATCA
1 CCATCA
1701 AGCCTTCCAA
Statistics
Matches: 79, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
78 28 0.35
79 8 0.10
80 43 0.54
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (78 bp):
CCATCAGTAAGTCTGTCGAGCATGATGATTAATCCTTCGGTAATTCATAAGCCTTCACAGAAGAG
TAGTGAAGCAAGT
Found at i:1720 original size:80 final size:76
Alignment explanation
Indices: 1555--1768 Score: 236
Period size: 80 Copynumber: 2.8 Consensus size: 76
1545 AAGTCTGTCG
**
1555 AGCATGATGATTAATCCTTCGGTAATTTGTAAGCCTTCACAGAAGAGTAGTGAAGCAAGTCCATC
1 AGCATGATGATTAATCCTTCGGTAATTCATAAGCCTTCACAGAAGAGTAGTGAAGCAAGTCCATC
* ***
1620 AGTAAGTCTTTTG
66 A--AAGCCTTCCA
*
1633 AGCATGATGATTAAATCCTTCAGGTAATTCATAAGCCTTCACGGAAGAGTAGTGAAGCAAGTCCA
1 AGCATGATGATT-AATCCTTC-GGTAATTCATAAGCCTTCACAGAAGAGTAGTGAAGCAAGTCCA
1698 TC-AAGCCTTCCA
64 TCAAAGCCTTCCA
* ** * *
1710 AGCATGATGATTAACTCCTCCGAGCCA-TCTTAAGCCTTCACCA-AAAAGTAGTGAAGCAA
1 AGCATGATGATTAA-TCCTTCG-GTAATTCATAAGCCTTCA-CAGAAGAGTAGTGAAGCAA
1769 ATCAATCTTA
Statistics
Matches: 118, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
76 30 0.25
77 26 0.22
78 12 0.10
79 8 0.07
80 42 0.36
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (76 bp):
AGCATGATGATTAATCCTTCGGTAATTCATAAGCCTTCACAGAAGAGTAGTGAAGCAAGTCCATC
AAAGCCTTCCA
Found at i:1780 original size:37 final size:37
Alignment explanation
Indices: 1736--1850 Score: 185
Period size: 37 Copynumber: 3.1 Consensus size: 37
1726 CCTCCGAGCC
* *
1736 ATCTTAAGCCTTCACCAAAAAGTAGTGAAGCAAATCA
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCA
1773 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCA
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCA
* * *
1810 ATCTTAAGCCTTCATCGAAGAGTAGTGGAGCAAATCG
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCA
1847 ATCT
1 ATCT
1851 CGAGTCCTAT
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 73 1.00
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.23
Consensus pattern (37 bp):
ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCA
Found at i:2053 original size:3 final size:3
Alignment explanation
Indices: 2047--2095 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
2037 ATAATAATAA
*
2047 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2095 T
1 T
2096 TTTTTATTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:4205 original size:2 final size:2
Alignment explanation
Indices: 4198--4315 Score: 236
Period size: 2 Copynumber: 59.0 Consensus size: 2
4188 AAAGAATTTA
4198 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
4240 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
4282 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
4316 GTTGACCCTA
Statistics
Matches: 116, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 116 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6608 original size:18 final size:18
Alignment explanation
Indices: 6585--6641 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 18
6575 TTTTTATATC
6585 AAAGAAAAAAATAAAATA
1 AAAGAAAAAAATAAAATA
** *
6603 AAAGAACGAGATAAAATA
1 AAAGAAAAAAATAAAATA
* * *
6621 AAATAAAATAATAAGATA
1 AAAGAAAAAAATAAAATA
6639 AAA
1 AAA
6642 ATAAAGCAAA
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.75, C:0.02, G:0.09, T:0.14
Consensus pattern (18 bp):
AAAGAAAAAAATAAAATA
Found at i:6618 original size:23 final size:24
Alignment explanation
Indices: 6586--6646 Score: 79
Period size: 23 Copynumber: 2.6 Consensus size: 24
6576 TTTTATATCA
*
6586 AAGAAAAAAATAAAATAAAAGAAC
1 AAGATAAAAATAAAATAAAAGAAC
* * *
6610 GAGAT-AAAATAAAATAAAATAAT
1 AAGATAAAAATAAAATAAAAGAAC
6633 AAGATAAAAATAAA
1 AAGATAAAAATAAA
6647 GCAAAAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 20 0.65
24 11 0.35
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.15
Consensus pattern (24 bp):
AAGATAAAAATAAAATAAAAGAAC
Found at i:7230 original size:4 final size:4
Alignment explanation
Indices: 7221--7247 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
7211 AGTGCTGGAA
7221 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
7248 CATAAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:11046 original size:131 final size:131
Alignment explanation
Indices: 10842--11172 Score: 450
Period size: 131 Copynumber: 2.5 Consensus size: 131
10832 CCGATCAAAC
* * * * * *
10842 ATAAATGATCTCTCGTGCCTTAAATCAGCCATTTATTACTCTAATCGAAATGAAGAGATATCCCT
1 ATAAATGACCTCTCATGCCTTAAAGCAGTCATTTATTACTCCAATCGAAATGAAGAGATATCACT
* * * ** *
10907 ATTTCATCTT-AAAATTCAATATCGATTCGAGTGAAAACA-ATAATATGTAATGATTTTCAATTG
66 ATTCCATCTTAAAAATT-AATATCGATTCAAGAGAAAA-AGATAATATCAAATGATTTTCAATCG
10970 AGA
129 AGA
*
10973 ATAAATGACCTCTCATGCCTTAAAGCAGTCATTTATTACTCCAATTGAAATGAAGAGATATCACT
1 ATAAATGACCTCTCATGCCTTAAAGCAGTCATTTATTACTCCAATCGAAATGAAGAGATATCACT
* * *
11038 ATTCCATCTTAAAAATTAATATTGATTCAAGAGAAAAAGGTAATATCAAATTATTTTCAATCGAG
66 ATTCCATCTTAAAAATTAATATCGATTCAAGAGAAAAAGATAATATCAAATGATTTTCAATCGAG
11103 A
131 A
* * * *
11104 ATAAATGACCTCTCATGCCTTAAAGCAGTCATTTATTACTCCAACCGAAATAAAAAGATATTACT
1 ATAAATGACCTCTCATGCCTTAAAGCAGTCATTTATTACTCCAATCGAAATGAAGAGATATCACT
11169 ATTC
66 ATTC
11173 TCAACATCGA
Statistics
Matches: 177, Mismatches: 21, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
130 1 0.01
131 170 0.96
132 6 0.03
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (131 bp):
ATAAATGACCTCTCATGCCTTAAAGCAGTCATTTATTACTCCAATCGAAATGAAGAGATATCACT
ATTCCATCTTAAAAATTAATATCGATTCAAGAGAAAAAGATAATATCAAATGATTTTCAATCGAG
A
Found at i:14952 original size:21 final size:22
Alignment explanation
Indices: 14927--14975 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
14917 TTAAAGGTGC
* *
14927 ATAAAATTAAATAACAA-AAAA
1 ATAAAATAAAAGAACAATAAAA
*
14948 AT-AAATAAAAGAGCAATAAAA
1 ATAAAATAAAAGAACAATAAAA
14969 ATAAAAT
1 ATAAAAT
14976 GTTCGTGTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 11 0.48
21 8 0.35
22 4 0.17
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.18
Consensus pattern (22 bp):
ATAAAATAAAAGAACAATAAAA
Found at i:15109 original size:16 final size:16
Alignment explanation
Indices: 15088--15118 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
15078 TAAATAAATA
15088 AAAAGTTAGTTGTTAG
1 AAAAGTTAGTTGTTAG
15104 AAAAGTTAGTTGTTA
1 AAAAGTTAGTTGTTA
15119 ACAGTCCGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.23, T:0.39
Consensus pattern (16 bp):
AAAAGTTAGTTGTTAG
Found at i:15199 original size:17 final size:17
Alignment explanation
Indices: 15177--15226 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
15167 CAAGGTCATA
15177 TAATAATTCAAACAAAT
1 TAATAATTCAAACAAAT
15194 TAATAA---AAA-AAA-
1 TAATAATTCAAACAAAT
15206 T--TAATTCAAACAAAT
1 TAATAATTCAAACAAAT
15221 TAATAA
1 TAATAA
15227 AAATATTAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 14
0.65 0.00 0.35
Matches are distributed among these distances:
10 3 0.12
12 1 0.04
13 6 0.23
14 6 0.23
15 1 0.04
17 9 0.35
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (17 bp):
TAATAATTCAAACAAAT
Found at i:15222 original size:14 final size:14
Alignment explanation
Indices: 15180--15224 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
15170 GGTCATATAA
15180 TAATTCAAACAAAT
1 TAATTCAAACAAAT
* *
15194 TAA-TAAAAAAAAT
1 TAATTCAAACAAAT
15207 TAATTCAAACAAAT
1 TAATTCAAACAAAT
15221 TAAT
1 TAAT
15225 AAAAATATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
13 11 0.42
14 15 0.58
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (14 bp):
TAATTCAAACAAAT
Found at i:24166 original size:172 final size:175
Alignment explanation
Indices: 23864--24203 Score: 562
Period size: 172 Copynumber: 2.0 Consensus size: 175
23854 AAATTTACCC
23864 CTAACATAAAATCTACATCTGTTATTGATTAGGTCCGATCATAACTTTGCGGACTGTTTTTTGGA
1 CTAACATAAAATCTA-ATCTGTTATTGATTAGGTCCGATCATAACTTTGCGGACTGTTTTTTGGA
* *
23929 TGCTCATACGTTAGCTCAATAAGGTTTGACATAGGTTGATATAAAATAATAAAAGCAATATATA-
65 TGCTCATACGTTAGCTCAAGAAGGTTTGACATAGGTTGATATAAAACAATAAAAGCAATATATAT
23993 T-TATGATAAGGTTTGTCGTCATCTATACCTTCATTTTTAAAATCA
130 TATATGATAAGGTTTGTCGTCATCTATACCTTCATTTTTAAAATCA
* * *
24038 CTAACATAAAATCT-ATCTGTTATTGATTAGGTCTGATTATAACTTTGCGGAGT-TTTTTTGGGA
1 CTAACATAAAATCTAATCTGTTATTGATTAGGTCCGATCATAACTTTGCGGACTGTTTTTT-GGA
* * *
24101 TGTTCATACGTTAGCTCGAGAAGGTTTGACATAGGTTGATATAAAACAATAAAAGCAGTATATAT
65 TGCTCATACGTTAGCTCAAGAAGGTTTGACATAGGTTGATATAAAACAATAAAAGCAATATATAT
24166 TATATGATAAGGTTTGTCGTCATCTATACCTTCATTTT
130 TATATGATAAGGTTTGTCGTCATCTATACCTTCATTTT
24204 ATTATAACTT
Statistics
Matches: 155, Mismatches: 8, Indels: 6
0.92 0.05 0.04
Matches are distributed among these distances:
171 6 0.04
172 98 0.63
173 1 0.01
174 50 0.32
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.38
Consensus pattern (175 bp):
CTAACATAAAATCTAATCTGTTATTGATTAGGTCCGATCATAACTTTGCGGACTGTTTTTTGGAT
GCTCATACGTTAGCTCAAGAAGGTTTGACATAGGTTGATATAAAACAATAAAAGCAATATATATT
ATATGATAAGGTTTGTCGTCATCTATACCTTCATTTTTAAAATCA
Found at i:24396 original size:198 final size:197
Alignment explanation
Indices: 24038--24408 Score: 593
Period size: 198 Copynumber: 1.9 Consensus size: 197
24028 TTTAAAATCA
* * * * *
24038 CTAACATAAAATCTATCTGTTATTGATTAGGTCTGATTATAACTTTGCGGAGTTTTTTTGGGATG
1 CTAACATAAAATCTATCTATTATTGATTAGGTCCGATCATAACTTTACGGAGTATTTTTGGGATG
*
24103 TTCATACGTTAGCTCGAGAAGGTTTGACATAGGTTGATATAAAACAATAAAAGCAGTATATATTA
66 CTCATACGTTAGCTCGAGAAGGTTTGACATAGGTTGATATAAAACAATAAAAGCAGTATATATTA
*
24168 TATGATAAGGTTTGTCGTCATCTATACCTTCATTTTATTATAACTTATTAAAATATAAAATTTAC
131 TATGATAAAGTTTGTCGTCATCTATACCTTCATTTTATTATAACTTATTAAAATATAAAATTTAC
24233 CC
196 CC
* *
24235 CTAACATAAAATCTAAATCTATTATTGATTAGGTCCGATCATTA-TATTATGGAGTATTTTT-GG
1 CTAACATAAAATCT--ATCTATTATTGATTAGGTCCGATCATAACT-TTACGGAGTATTTTTGGG
* * *
24298 ATGCTCATACGTTAGCTCGAGAAGGTTTGATATAGGTTGATATAAAATAATAAAATCAGTATATA
63 ATGCTCATACGTTAGCTCGAGAAGGTTTGACATAGGTTGATATAAAACAATAAAAGCAGTATATA
24363 TTATATGATAAAGTTTGTCGTCATCTATACCTTCATTTTATTATAA
128 TTATATGATAAAGTTTGTCGTCATCTATACCTTCATTTTATTATAA
24409 ATTTGTAACA
Statistics
Matches: 159, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
197 14 0.09
198 109 0.69
199 36 0.23
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (197 bp):
CTAACATAAAATCTATCTATTATTGATTAGGTCCGATCATAACTTTACGGAGTATTTTTGGGATG
CTCATACGTTAGCTCGAGAAGGTTTGACATAGGTTGATATAAAACAATAAAAGCAGTATATATTA
TATGATAAAGTTTGTCGTCATCTATACCTTCATTTTATTATAACTTATTAAAATATAAAATTTAC
CC
Found at i:25797 original size:23 final size:23
Alignment explanation
Indices: 25769--25827 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 23
25759 CTTGAGACTC
*
25769 AAACTCGACTGAAGCCCAATTTT
1 AAACTCGACTCAAGCCCAATTTT
* * * *
25792 AAACTCAATTCAAGCTCGATTTT
1 AAACTCGACTCAAGCCCAATTTT
*
25815 AAACTCGATTCAA
1 AAACTCGACTCAA
25828 ACTAGATTCA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.37, C:0.24, G:0.10, T:0.29
Consensus pattern (23 bp):
AAACTCGACTCAAGCCCAATTTT
Found at i:25835 original size:23 final size:23
Alignment explanation
Indices: 25787--25835 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
25777 CTGAAGCCCA
* *
25787 ATTTTAAACTCAATTCAAGCTCG
1 ATTTTAAACTCAATTCAAACTAG
*
25810 ATTTTAAACTCGATTCAAACTAG
1 ATTTTAAACTCAATTCAAACTAG
25833 ATT
1 ATT
25836 CAAGCTCGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (23 bp):
ATTTTAAACTCAATTCAAACTAG
Found at i:25846 original size:11 final size:11
Alignment explanation
Indices: 25799--25868 Score: 59
Period size: 11 Copynumber: 6.2 Consensus size: 11
25789 TTTAAACTCA
25799 ATTCAAGCTCG
1 ATTCAAGCTCG
* *
25810 ATTTTAAACTCG
1 A-TTCAAGCTCG
* *
25822 ATTCAAACTAG
1 ATTCAAGCTCG
25833 ATTCAAGCTCG
1 ATTCAAGCTCG
** *
25844 ATTTTGAGCTTG
1 A-TTCAAGCTCG
25856 ATTCAAGCTCG
1 ATTCAAGCTCG
25867 AT
1 AT
25869 GGGTTTTAAT
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
11 28 0.62
12 17 0.38
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (11 bp):
ATTCAAGCTCG
Found at i:28014 original size:7 final size:7
Alignment explanation
Indices: 28002--28056 Score: 83
Period size: 7 Copynumber: 7.9 Consensus size: 7
27992 CATAATCAGA
28002 TTTAGGG
1 TTTAGGG
28009 TTTAGGG
1 TTTAGGG
*
28016 TTTAGGA
1 TTTAGGG
*
28023 TTTAGGA
1 TTTAGGG
*
28030 TTTAGGA
1 TTTAGGG
28037 TTTAGGG
1 TTTAGGG
28044 TTTAGGG
1 TTTAGGG
28051 TTTAGG
1 TTTAGG
28057 ATTCATTACA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 46 1.00
ACGTcount: A:0.20, C:0.00, G:0.36, T:0.44
Consensus pattern (7 bp):
TTTAGGG
Found at i:28182 original size:11 final size:11
Alignment explanation
Indices: 28166--28228 Score: 60
Period size: 11 Copynumber: 5.9 Consensus size: 11
28156 ATATTATAGA
28166 ATTTTTAATAT
1 ATTTTTAATAT
28177 ATTTTTAA-A-
1 ATTTTTAATAT
28186 ATTTTATAAT-T
1 ATTTT-TAATAT
*** *
28197 ATCAATAATGT
1 ATTTTTAATAT
28208 ATTTTTAATAT
1 ATTTTTAATAT
28219 ATTTTTAATA
1 ATTTTTAATA
28229 ATGTAATTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
9 5 0.12
10 8 0.20
11 28 0.68
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:34493 original size:3 final size:3
Alignment explanation
Indices: 34485--34556 Score: 63
Period size: 3 Copynumber: 23.7 Consensus size: 3
34475 CCATTCGATT
* * *
34485 TTA TTA TTA TTA TTA TTA TTA CTA TTG TTA TTG TTA TTA TTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
* * * * *
34531 TGA ATA TTT TTA TTT TTA TTT TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
34557 TTTCAGGTCC
Statistics
Matches: 52, Mismatches: 16, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
3 49 0.94
4 3 0.06
ACGTcount: A:0.26, C:0.01, G:0.04, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:34557 original size:6 final size:6
Alignment explanation
Indices: 34535--34559 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
34525 TATTTATGAA
34535 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
34560 CAGGTCCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:34981 original size:13 final size:12
Alignment explanation
Indices: 34965--35027 Score: 56
Period size: 13 Copynumber: 5.1 Consensus size: 12
34955 ATTTTGTTTC
34965 AGAAAAAGTAAAA
1 AGAAAAAG-AAAA
34978 AGAAAAAGGAAAA
1 AGAAAAA-GAAAA
* *
34991 GGAAAAGGAAAA
1 AGAAAAAGAAAA
*
35003 AG-AAAAGCAAA
1 AGAAAAAGAAAA
*
35014 AGTAAAAGTAAAA
1 AGAAAAAG-AAAA
35027 A
1 A
35028 AATAAGCAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
11 9 0.22
12 11 0.27
13 20 0.49
14 1 0.02
ACGTcount: A:0.73, C:0.02, G:0.21, T:0.05
Consensus pattern (12 bp):
AGAAAAAGAAAA
Found at i:34983 original size:6 final size:6
Alignment explanation
Indices: 34965--35027 Score: 56
Period size: 6 Copynumber: 10.2 Consensus size: 6
34955 ATTTTGTTTC
* * *
34965 AGAAAA AGTAAAA AGAAAA AGGAAAA GGAAAA GGAAAA AG-AAA AGCAAA
1 AGAAAA AG-AAAA AGAAAA A-GAAAA AGAAAA AGAAAA AGAAAA AGAAAA
*
35014 AGTAAA AGTAAAA A
1 AGAAAA AG-AAAA A
35028 AATAAGCAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
5 5 0.10
6 29 0.59
7 15 0.31
ACGTcount: A:0.73, C:0.02, G:0.21, T:0.05
Consensus pattern (6 bp):
AGAAAA
Found at i:35034 original size:24 final size:24
Alignment explanation
Indices: 34968--35044 Score: 93
Period size: 24 Copynumber: 3.1 Consensus size: 24
34958 TTGTTTCAGA
* *
34968 AAAAGTAAAAAGAAAAAGGAAAAGG
1 AAAAGTAAAAAG-AAAAGCAAAAGT
*
34993 AAAAGGAAAAAGAAAAGCAAAAGT
1 AAAAGTAAAAAGAAAAGCAAAAGT
35017 AAAAGTAAAAA-AATAAGCAAAATGT
1 AAAAGTAAAAAGAA-AAGCAAAA-GT
35042 AAA
1 AAA
35045 TTGGGGCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
23 2 0.04
24 28 0.61
25 16 0.35
ACGTcount: A:0.71, C:0.03, G:0.18, T:0.08
Consensus pattern (24 bp):
AAAAGTAAAAAGAAAAGCAAAAGT
Found at i:45504 original size:23 final size:24
Alignment explanation
Indices: 45466--45547 Score: 103
Period size: 24 Copynumber: 3.5 Consensus size: 24
45456 AATTATGTTA
* *
45466 TGATACCTGACCTGGATTCTGATC
1 TGATACATGACATGGATTCTGATC
* *
45490 TAATACA-GACATGGATTCTGATA
1 TGATACATGACATGGATTCTGATC
*
45513 TGATACATGACTTGGATTCTGATC
1 TGATACATGACATGGATTCTGATC
*
45537 TGATACTTGAC
1 TGATACATGAC
45548 CTAAATTATG
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
23 20 0.41
24 29 0.59
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (24 bp):
TGATACATGACATGGATTCTGATC
Found at i:45690 original size:57 final size:57
Alignment explanation
Indices: 45622--45793 Score: 263
Period size: 57 Copynumber: 3.0 Consensus size: 57
45612 GTTGGAGGAA
* * *
45622 GAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGGGCCTTATTGTTCGTGACGGGGTT
1 GAATACTTGCAGGTTCCTCGACTTTGTGCTCAGGGCCTTAATGTTCGTGACGGGGTT
* *
45679 GAATACTTGCAGGTTCCTCGACTTTGTGCTCAGGGCCTTAATGTTTGTGACGTGGTT
1 GAATACTTGCAGGTTCCTCGACTTTGTGCTCAGGGCCTTAATGTTCGTGACGGGGTT
* * * *
45736 GAATACTTGCAGGTTCCTCGACTTTTTGTTCAAGGCCTTACTGTTCGTGACGGGGTT
1 GAATACTTGCAGGTTCCTCGACTTTGTGCTCAGGGCCTTAATGTTCGTGACGGGGTT
45793 G
1 G
45794 TATGGTTCGG
Statistics
Matches: 104, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 104 1.00
ACGTcount: A:0.15, C:0.20, G:0.30, T:0.36
Consensus pattern (57 bp):
GAATACTTGCAGGTTCCTCGACTTTGTGCTCAGGGCCTTAATGTTCGTGACGGGGTT
Found at i:46316 original size:20 final size:21
Alignment explanation
Indices: 46276--46318 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
46266 AGAAAACCTG
46276 TTTTATTTTGAATACTGATAAA
1 TTTTATTTTG-ATACTGATAAA
*
46298 TTTTATTTTG-TACTTATAAA
1 TTTTATTTTGATACTGATAAA
46318 T
1 T
46319 GATTTTATGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
22 10 0.50
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.56
Consensus pattern (21 bp):
TTTTATTTTGATACTGATAAA
Found at i:48236 original size:17 final size:17
Alignment explanation
Indices: 48193--48244 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
48183 AATACAATAG
*
48193 AAACTCTTTAAATTAAT
1 AAACTCTCTAAATTAAT
**
48210 --ACTCGGTAAATTAAT
1 AAACTCTCTAAATTAAT
*
48225 AAACTCTCTAAAATAAT
1 AAACTCTCTAAATTAAT
48242 AAA
1 AAA
48245 TTTGTCCGGT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.50, C:0.13, G:0.04, T:0.33
Consensus pattern (17 bp):
AAACTCTCTAAATTAAT
Found at i:48723 original size:34 final size:34
Alignment explanation
Indices: 48675--48740 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
48665 TCATATTTGT
48675 CTGTCACAAATTTCAATTAATATTTGTTAGTTGA
1 CTGTCACAAATTTCAATTAATATTTGTTAGTTGA
*
48709 CTGTCACAATTTTCAATTAATATTTGTTAGTT
1 CTGTCACAAATTTCAATTAATATTTGTTAGTT
48741 TAGTCAATAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.47
Consensus pattern (34 bp):
CTGTCACAAATTTCAATTAATATTTGTTAGTTGA
Found at i:49903 original size:25 final size:25
Alignment explanation
Indices: 49875--49957 Score: 60
Period size: 27 Copynumber: 3.2 Consensus size: 25
49865 GATAAGTATA
49875 CATTGTAAGGACAACAAATATCGAC
1 CATTGTAAGGACAACAAATATCGAC
* * * * * *
49900 CATTTAGTTAGAAC-TCAAAGATAAGTATA
1 CA-TT-GTAAGGACAACAAATAT-CG-A-C
49929 CATTGTAAGGACAACAAATATCGAC
1 CATTGTAAGGACAACAAATATCGAC
49954 CATT
1 CATT
49958 TAGTTAGATA
Statistics
Matches: 40, Mismatches: 12, Indels: 12
0.62 0.19 0.19
Matches are distributed among these distances:
25 6 0.15
26 9 0.22
27 14 0.35
28 9 0.22
29 2 0.05
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.25
Consensus pattern (25 bp):
CATTGTAAGGACAACAAATATCGAC
Found at i:49938 original size:54 final size:55
Alignment explanation
Indices: 49855--49965 Score: 215
Period size: 54 Copynumber: 2.0 Consensus size: 55
49845 ATGTACTTTT
49855 GAACTCCAAAGATAAGTATACATTGTAAGGACAACAAATATCGACCATTTAGTTA
1 GAACTCCAAAGATAAGTATACATTGTAAGGACAACAAATATCGACCATTTAGTTA
49910 GAACT-CAAAGATAAGTATACATTGTAAGGACAACAAATATCGACCATTTAGTTA
1 GAACTCCAAAGATAAGTATACATTGTAAGGACAACAAATATCGACCATTTAGTTA
49964 GA
1 GA
49966 TAAGTAGAAG
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
54 51 0.91
55 5 0.09
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (55 bp):
GAACTCCAAAGATAAGTATACATTGTAAGGACAACAAATATCGACCATTTAGTTA
Found at i:53893 original size:19 final size:19
Alignment explanation
Indices: 53790--53901 Score: 111
Period size: 19 Copynumber: 5.9 Consensus size: 19
53780 ATTTCAAAAT
* * *
53790 TTATTTTCTGAATCAGAAC
1 TTATTTTCAGATTCATAAC
*
53809 TTA-TTTCTAGATTCAAAAC
1 TTATTTTC-AGATTCATAAC
* *
53828 TTATTTTCAGACTCATAGC
1 TTATTTTCAGATTCATAAC
*
53847 TTATTGTT-AGATTCATAGC
1 TTATT-TTCAGATTCATAAC
*
53866 TTATTTTCAAATTCATAAC
1 TTATTTTCAGATTCATAAC
*
53885 TTATTTTCAAATTCATA
1 TTATTTTCAGATTCATA
53902 GCCCAACGCA
Statistics
Matches: 80, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
18 6 0.08
19 68 0.85
20 6 0.08
ACGTcount: A:0.32, C:0.15, G:0.07, T:0.46
Consensus pattern (19 bp):
TTATTTTCAGATTCATAAC
Found at i:55169 original size:14 final size:14
Alignment explanation
Indices: 55150--55181 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
55140 CAATTTTGAT
55150 ATTATAATATTAAC
1 ATTATAATATTAAC
55164 ATTATAATATTAAC
1 ATTATAATATTAAC
55178 ATTA
1 ATTA
55182 ATAAAAACTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (14 bp):
ATTATAATATTAAC
Found at i:56420 original size:16 final size:16
Alignment explanation
Indices: 56369--56421 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
56359 ATAACTAATT
56369 AATATCATTATAATAA
1 AATATCATTATAATAA
* *
56385 AATAT-ACTA-AGATATT
1 AATATCATTATA-ATA-A
56401 AATATCATTATAATAA
1 AATATCATTATAATAA
56417 AATAT
1 AATAT
56422 TTAGTAGTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
14 1 0.03
15 6 0.21
16 15 0.52
17 6 0.21
18 1 0.03
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.38
Consensus pattern (16 bp):
AATATCATTATAATAA
Found at i:59942 original size:18 final size:18
Alignment explanation
Indices: 59904--59943 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
59894 ATAAAAAAAT
* *
59904 ATTATATATATTTATAAA
1 ATTATATATATTGACAAA
*
59922 ATTATATATATTGACATA
1 ATTATATATATTGACAAA
59940 ATTA
1 ATTA
59944 ATAAAGAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (18 bp):
ATTATATATATTGACAAA
Done.