Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000470.1 Hibiscus syriacus cultivar Beakdansim tig00000874_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: 60432
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:3743 original size:20 final size:20
Alignment explanation
Indices: 3714--3751 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3704 AGAACCCCAG
*
3714 GGGGGTATCGATTCCCCTGT
1 GGGGGAATCGATTCCCCTGT
*
3734 GGGGGAATCGGTTCCCCT
1 GGGGGAATCGATTCCCCT
3752 TCAAAGGGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.26, G:0.37, T:0.26
Consensus pattern (20 bp):
GGGGGAATCGATTCCCCTGT
Found at i:10786 original size:22 final size:22
Alignment explanation
Indices: 10747--10807 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
10737 TTTTTTATTA
* *
10747 TGGGGGAATCGGTT-CCCCCCC
1 TGGGGGTATCGATTCCCCCCCC
10768 TGGGGGTATCGATTCCCCCCCC
1 TGGGGGTATCGATTCCCCCCCC
10790 TGGGGGTATCGATTCCCC
1 TGGGGGTATCGATTCCCC
10808 TCTAGCATTC
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
21 12 0.32
22 25 0.68
ACGTcount: A:0.10, C:0.36, G:0.31, T:0.23
Consensus pattern (22 bp):
TGGGGGTATCGATTCCCCCCCC
Found at i:10858 original size:21 final size:21
Alignment explanation
Indices: 10834--10876 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
10824 TTCATATTCG
* *
10834 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
10855 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
10876 T
1 T
10877 AGCCCATAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:16900 original size:23 final size:22
Alignment explanation
Indices: 16874--16937 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 22
16864 CAGCTCATAT
16874 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCT-AGTGCCACGTAG
* * *
16897 AATTACACCGGAGTGCCGCGTAG
1 AATTGCACC-TAGTGCCACGTAG
16920 AATTGCACCGTAGTGCCA
1 AATTGCACC-TAGTGCCA
16938 TATAATAATG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.28, C:0.27, G:0.25, T:0.20
Consensus pattern (22 bp):
AATTGCACCTAGTGCCACGTAG
Found at i:17586 original size:19 final size:20
Alignment explanation
Indices: 17549--17586 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
17539 TTTTTCATTA
*
17549 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
17569 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
17587 TCTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:17637 original size:21 final size:21
Alignment explanation
Indices: 17613--17653 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
17603 TTCATATTCG
* *
17613 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
17634 TTGAATGGGTACCGATTCCC
1 TTGAAGGGGTACCGATTCCC
17654 TTAGCCCAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.24, G:0.29, T:0.29
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:20774 original size:2 final size:2
Alignment explanation
Indices: 20767--20799 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
20757 ATCACAAGTA
20767 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20800 CACACACACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23756 original size:29 final size:29
Alignment explanation
Indices: 23706--23769 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
23696 ATTTAGTATT
*
23706 TTTTTATTGTTTATTAGAAAAT-TAATAAA
1 TTTTTATTGTTTATTACAAAATGTAAT-AA
*
23735 TTTTTATT-TTTATTATCTAAATGTAATAA
1 TTTTTATTGTTTATTA-CAAAATGTAATAA
23764 TTTTTA
1 TTTTTA
23770 AAGATGACTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 7 0.23
29 20 0.65
30 4 0.13
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.58
Consensus pattern (29 bp):
TTTTTATTGTTTATTACAAAATGTAATAA
Found at i:24051 original size:3 final size:3
Alignment explanation
Indices: 24036--24119 Score: 123
Period size: 3 Copynumber: 28.0 Consensus size: 3
24026 CCATTTTGAT
* * * *
24036 TTA TTA CTA TTA TTA TTA TAA TTA TTA TTA TTA TTA TAA TTA TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
24084 ATA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
24120 AAAATAATTA
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:26154 original size:17 final size:16
Alignment explanation
Indices: 26132--26180 Score: 73
Period size: 17 Copynumber: 3.0 Consensus size: 16
26122 TTTCTTTTAA
26132 ATTTTTTATTACTTATT
1 ATTTTTTATTA-TTATT
26149 ATTTTTTATATATTATT
1 ATTTTTTAT-TATTATT
26166 ATTTTTTATT-TTATT
1 ATTTTTTATTATTATT
26181 TATGTATTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.16
16 1 0.03
17 23 0.74
18 2 0.06
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (16 bp):
ATTTTTTATTATTATT
Found at i:27856 original size:14 final size:14
Alignment explanation
Indices: 27837--27879 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
27827 TTTTAAATAA
27837 TTTACATTTACATT
1 TTTACATTTACATT
* *
27851 TTTACATTCACATA
1 TTTACATTTACATT
*
27865 TTTACATTTGCATT
1 TTTACATTTACATT
27879 T
1 T
27880 GGCATCTTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.28, C:0.16, G:0.02, T:0.53
Consensus pattern (14 bp):
TTTACATTTACATT
Found at i:30787 original size:2 final size:2
Alignment explanation
Indices: 30780--30813 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
30770 TTATCCTTTA
30780 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
30814 CCTTTGTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33570 original size:114 final size:113
Alignment explanation
Indices: 33370--33593 Score: 376
Period size: 114 Copynumber: 2.0 Consensus size: 113
33360 TGCCAGGTGA
33370 TCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
1 TCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
* * *
33435 TTTGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATTTGC
66 TTCGGTAGGAACCCCAAAACC-ATCATTGGAATTAAAAGATGAATTTGC
* *
33484 TCATAGTAGAAATAAGGAGACTCGATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
1 TCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
* *
33549 TTCGGTAGGAACCCCAGAACCATCATTGGAATTAAAGGATGAATT
66 TTCGGTAGGAACCCCAAAACCATCATTGGAATTAAAAGATGAATT
33594 GCATGATCGT
Statistics
Matches: 103, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
113 22 0.21
114 81 0.79
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (113 bp):
TCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
TTCGGTAGGAACCCCAAAACCATCATTGGAATTAAAAGATGAATTTGC
Found at i:36198 original size:22 final size:22
Alignment explanation
Indices: 36168--36246 Score: 106
Period size: 22 Copynumber: 3.6 Consensus size: 22
36158 ACATCTACAT
*
36168 TCTTCAAAGATGATAGATTCTC
1 TCTTTAAAGATGATAGATTCTC
*
36190 TCTTTAAAGATGATAGATTCCC
1 TCTTTAAAGATGATAGATTCTC
* *
36212 TTTTTAAAGATGACAGATTCTC
1 TCTTTAAAGATGATAGATTCTC
36234 T-TTTCAAAGATGA
1 TCTTT-AAAGATGA
36247 AAGCTTTATC
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
21 3 0.06
22 48 0.94
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (22 bp):
TCTTTAAAGATGATAGATTCTC
Found at i:37042 original size:112 final size:112
Alignment explanation
Indices: 36685--37639 Score: 1507
Period size: 112 Copynumber: 8.5 Consensus size: 112
36675 TACCAGTTCG
* * *
36685 AGTTCATAATGAGAATAACTCATCTGAAGAAGGAAGAAAAAATTCATAATGAGAAGAATTTGTCC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
* * * * * * ****
36750 AACCTTTTGTTCAAATCTATCACTTGATGGATTATCTTTTCCAGTTCG
66 AACCTTATGCT-GAATCCATCACTTGATGGATTAGCTTTGCCAGAGAA
* * * *
36798 AGTTCATAATGAGAAGAAATCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTCC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
* * * *
36863 AACCTTTTGTTCAAATCTATCACTTGATGGATTAGCTTTGCCAGAGAA
66 AACCTTATGCT-GAATCCATCACTTGATGGATTAGCTTTGCCAGAGAA
36911 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
*
36976 AACCTTATGCTGAATCCATCACTTGATGGATTAGATTTGCCAGAGAA
66 AACCTTATGCTGAATCCATCACTTGATGGATTAGCTTTGCCAGAGAA
37023 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
37088 AACCTTATGCTGAATCCATCACTTGATGGATTAGCTTTGCCAGAGAA
66 AACCTTATGCTGAATCCATCACTTGATGGATTAGCTTTGCCAGAGAA
* *
37135 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTCC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
* * * *
37200 AACCTTTTGTTCAAATCTATCACTTGATGGATTAGCTTTGCCAGAGAA
66 AACCTTATGCT-GAATCCATCACTTGATGGATTAGCTTTGCCAGAGAA
37248 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
*
37313 AACCTTATGCTGAATCCATCACTTGATGGATTAGCTTTGCTAGAGAA
66 AACCTTATGCTGAATCCATCACTTGATGGATTAGCTTTGCCAGAGAA
37360 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
37425 AACCTTATGCTGAATCCATCACTTGATGGATTAGCTTTGCCAGAGAA
66 AACCTTATGCTGAATCCATCACTTGATGGATTAGCTTTGCCAGAGAA
*
37472 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
* * * * * * *
37537 AGCCTTTTACCTGAATTCATCAATTGATGGATCAGCCTTT-CCAGAAAA
66 AACCTTAT-GCTGAATCCATCACTTGATGGATTAG-CTTTGCCAGAGAA
* *
37585 AGTTCATAATGAAAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAA
37640 AAACTCATCA
Statistics
Matches: 795, Mismatches: 44, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
112 430 0.54
113 361 0.45
114 4 0.01
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.28
Consensus pattern (112 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
AACCTTATGCTGAATCCATCACTTGATGGATTAGCTTTGCCAGAGAA
Found at i:37083 original size:225 final size:225
Alignment explanation
Indices: 36685--37639 Score: 1493
Period size: 225 Copynumber: 4.2 Consensus size: 225
36675 TACCAGTTCG
* *
36685 AGTTCATAATGAGAATAACTCATCTGAAGAAGGAAGAAAAAATTCATAATGAGAAGAATTTGTCC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTCC
* * * * * ****
36750 AACCTTTTGTTCAAATCTATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGA
66 AACCTTATGCTCAAATCCATCACTTGATGGATTAGCTTTGCCAGAGAAAGTTCATAATGAGAAGA
* * * * * *
36815 AATCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTCCAACCTTTTGTTCAAATC
131 ACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCT-AAATC
*
36880 TATCACTTGATGGATTAGCTTTGCCAGAGAA
195 CATCACTTGATGGATTAGCTTTGCCAGAGAA
*
36911 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTCC
* *
36976 AACCTTATGCT-GAATCCATCACTTGATGGATTAGATTTGCCAGAGAAAGTTCATAATGAGAAGA
66 AACCTTATGCTCAAATCCATCACTTGATGGATTAGCTTTGCCAGAGAAAGTTCATAATGAGAAGA
*
37040 ACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTGAATCC
131 ACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTAAATCC
37105 ATCACTTGATGGATTAGCTTTGCCAGAGAA
196 ATCACTTGATGGATTAGCTTTGCCAGAGAA
*
37135 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTCC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTCC
* * *
37200 AACCTTTTGTTCAAATCTATCACTTGATGGATTAGCTTTGCCAGAGAAAGTTCATAATGAGAAGA
66 AACCTTATGCTCAAATCCATCACTTGATGGATTAGCTTTGCCAGAGAAAGTTCATAATGAGAAGA
*
37265 ACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTGAATCC
131 ACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTAAATCC
*
37330 ATCACTTGATGGATTAGCTTTGCTAGAGAA
196 ATCACTTGATGGATTAGCTTTGCCAGAGAA
*
37360 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTCC
*
37425 AACCTTATGCT-GAATCCATCACTTGATGGATTAGCTTTGCCAGAGAAAGTTCATAATGAGAAGA
66 AACCTTATGCTCAAATCCATCACTTGATGGATTAGCTTTGCCAGAGAAAGTTCATAATGAGAAGA
* * * * * *
37489 ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAGCCTTTTACCTGAATT
131 ACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTAT-GCTAAATC
* * *
37554 CATCAATTGATGGATCAGCCTTT-CCAGAAAA
195 CATCACTTGATGGATTAG-CTTTGCCAGAGAA
* *
37585 AGTTCATAATGAAAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAA
37640 AAACTCATCA
Statistics
Matches: 679, Mismatches: 47, Indels: 7
0.93 0.06 0.01
Matches are distributed among these distances:
224 210 0.31
225 394 0.58
226 75 0.11
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.28
Consensus pattern (225 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTCC
AACCTTATGCTCAAATCCATCACTTGATGGATTAGCTTTGCCAGAGAAAGTTCATAATGAGAAGA
ACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTAAATCC
ATCACTTGATGGATTAGCTTTGCCAGAGAA
Found at i:37266 original size:337 final size:337
Alignment explanation
Indices: 36685--37639 Score: 1617
Period size: 337 Copynumber: 2.8 Consensus size: 337
36675 TACCAGTTCG
* * *
36685 AGTTCATAATGAGAATAACTCATCTGAAGAAGGAAGAAAAAATTCATAATGAGAAGAATTTGTCC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
* * * * * * ****
36750 AACCTTTTGTTCAAATCTATCACTTGATGGATTATCTTTTCCAGTTCGAGTTCATAATGAGAAGA
66 AACCTTATGCT-GAATCCATCACTTGATGGATTAGCTTTGCCAGAGAAAGTTCATAATGAGAAGA
* *
36815 AATCATCTGAAGAAGGATGAAGAAGTTCATAATGAGAAGAATTTGTCCAACCTTTTGTTCAAATC
130 ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTCCAACCTTTTGTTCAAATC
36880 TATCACTTGATGGATTAGCTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
195 TATCACTTGATGGATTAGCTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
36945 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTGAATCCATCACTTGATGGATTAG
260 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTGAATCCATCACTTGATGGATTAG
37010 ATTTGCCAGAGAA
325 ATTTGCCAGAGAA
37023 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
37088 AACCTTATGCTGAATCCATCACTTGATGGATTAGCTTTGCCAGAGAAAGTTCATAATGAGAAGAA
66 AACCTTATGCTGAATCCATCACTTGATGGATTAGCTTTGCCAGAGAAAGTTCATAATGAGAAGAA
37153 CTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTCCAACCTTTTGTTCAAATCT
131 CTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTCCAACCTTTTGTTCAAATCT
37218 ATCACTTGATGGATTAGCTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
196 ATCACTTGATGGATTAGCTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
*
37283 GAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTGAATCCATCACTTGATGGATTAGC
261 GAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTGAATCCATCACTTGATGGATTAGA
*
37348 TTTGCTAGAGAA
326 TTTGCCAGAGAA
37360 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
37425 AACCTTATGCTGAATCCATCACTTGATGGATTAGCTTTGCCAGAGAAAGTTCATAATGAGAAGAA
66 AACCTTATGCTGAATCCATCACTTGATGGATTAGCTTTGCCAGAGAAAGTTCATAATGAGAAGAA
* * ** * *
37490 CTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAGCCTTTTACCTGAATTC
131 CTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTCCAACCTTTT-GTTCAAATC
* * * *
37555 -ATCAATTGATGGATCAGCCTTT-CCAGAAAAAGTTCATAATGAAAAGAACTCATCTGAAGAAGG
195 TATCACTTGATGGATTAG-CTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
*
37618 AAGAAGAAGTTCATAATGAGAA
259 AAGAAGAAATTCATAATGAGAA
37640 AAACTCATCA
Statistics
Matches: 587, Mismatches: 28, Indels: 5
0.95 0.05 0.01
Matches are distributed among these distances:
337 507 0.86
338 80 0.14
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.28
Consensus pattern (337 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
AACCTTATGCTGAATCCATCACTTGATGGATTAGCTTTGCCAGAGAAAGTTCATAATGAGAAGAA
CTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTCCAACCTTTTGTTCAAATCT
ATCACTTGATGGATTAGCTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
GAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTATGCTGAATCCATCACTTGATGGATTAGA
TTTGCCAGAGAA
Found at i:37918 original size:3 final size:3
Alignment explanation
Indices: 37903--37983 Score: 126
Period size: 3 Copynumber: 27.0 Consensus size: 3
37893 CCATTTTGAT
* *
37903 TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
37951 TAA ATA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
37984 AAATAATTAC
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:44683 original size:20 final size:20
Alignment explanation
Indices: 44648--44685 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
44638 TCTAAATCAT
**
44648 TTTTCAAAATTTAATTTTGA
1 TTTTCAAAATCAAATTTTGA
44668 TTTTCAAAATCAAATTTT
1 TTTTCAAAATCAAATTTT
44686 TCTTTCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.08, G:0.03, T:0.53
Consensus pattern (20 bp):
TTTTCAAAATCAAATTTTGA
Found at i:45623 original size:53 final size:53
Alignment explanation
Indices: 45560--45662 Score: 197
Period size: 53 Copynumber: 1.9 Consensus size: 53
45550 GATCATATGA
*
45560 CCCTTTTACTCACCATGCATACACATCATATAGTACATATATAGCTATACATT
1 CCCTTTTACTCACCATGCATACACATCATATAGCACATATATAGCTATACATT
45613 CCCTTTTACTCACCATGCATACACATCATATAGCACATATATAGCTATAC
1 CCCTTTTACTCACCATGCATACACATCATATAGCACATATATAGCTATAC
45663 CAATTAACAA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.34, C:0.28, G:0.06, T:0.32
Consensus pattern (53 bp):
CCCTTTTACTCACCATGCATACACATCATATAGCACATATATAGCTATACATT
Found at i:45868 original size:23 final size:23
Alignment explanation
Indices: 45832--45991 Score: 230
Period size: 23 Copynumber: 7.0 Consensus size: 23
45822 CACCACAGCT
* * * * *
45832 CGTATAAATACACCGAAGTTCCA
1 CGTAGAAATGCACCGTAGTGCCG
*
45855 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGTAGTGCCG
*
45878 CATAGAAATGCACCGTAGTGCCG
1 CGTAGAAATGCACCGTAGTGCCG
*
45901 CATAGAAATGCACCGTAGTGCCG
1 CGTAGAAATGCACCGTAGTGCCG
*
45924 CGTAGAAATGCACCGTAGTGTCG
1 CGTAGAAATGCACCGTAGTGCCG
45947 CGTAGAAATGCACCGTAGTGCCG
1 CGTAGAAATGCACCGTAGTGCCG
*
45970 CGTAGAAATGCACCGAAGTGCC
1 CGTAGAAATGCACCGTAGTGCC
45992 ATATAATATT
Statistics
Matches: 125, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 125 1.00
ACGTcount: A:0.29, C:0.26, G:0.26, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGTAGTGCCG
Found at i:46625 original size:22 final size:21
Alignment explanation
Indices: 46574--46626 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
46564 GTACTCATTT
46574 TTCCTATAATTGATACATTAA
1 TTCCTATAATTGATACATTAA
* * **
46595 TGCCATATAATTTATATTTCTAA
1 TTCC-TATAATTGATACAT-TAA
46618 TTCCTATAA
1 TTCCTATAA
46627 CATCCTCATA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 3 0.12
22 16 0.64
23 6 0.24
ACGTcount: A:0.36, C:0.15, G:0.04, T:0.45
Consensus pattern (21 bp):
TTCCTATAATTGATACATTAA
Found at i:48314 original size:23 final size:22
Alignment explanation
Indices: 48272--48316 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
48262 GACTCCTTCA
48272 AATCATATATACATCATCATATC
1 AATCATATATACAT-ATCATATC
48295 AATCATATAATACAGT-TCATAT
1 AATCATAT-ATACA-TATCATAT
48317 TACCAAGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 14 0.70
24 5 0.25
25 1 0.05
ACGTcount: A:0.44, C:0.18, G:0.02, T:0.36
Consensus pattern (22 bp):
AATCATATATACATATCATATC
Found at i:48560 original size:30 final size:31
Alignment explanation
Indices: 48526--48583 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 31
48516 ACCTATCCAG
* *
48526 AGGTCATAAAGAACCTCGGT-AACTGTCTAT
1 AGGTCACAAAGAACCTAGGTAAACTGTCTAT
* *
48556 AGGTCCCGAAGAACCTAGGTAAACTGTC
1 AGGTCACAAAGAACCTAGGTAAACTGTC
48584 CATATGTTCC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
30 16 0.70
31 7 0.30
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (31 bp):
AGGTCACAAAGAACCTAGGTAAACTGTCTAT
Found at i:48653 original size:32 final size:31
Alignment explanation
Indices: 48548--48733 Score: 175
Period size: 31 Copynumber: 5.9 Consensus size: 31
48538 ACCTCGGTAA
* * * *
48548 CTGTCTATAGGTCCCGAAGAACCTAGGTAA-A
1 CTGTCCATATGTCCCG-AGAACATAGGTAATT
**
48579 CTGTCCATATGTTCCTTAGAACATAGGTATATT
1 CTGTCCATATG-TCCCGAGAACATAGGTA-ATT
48612 -T-TCCATATGTCCCGAGAGACATAGGTAATT
1 CTGTCCATATGTCCCGAGA-ACATAGGTAATT
*
48642 CTGTCCATATGTTCCGTAGAACATAGGT-ATAT
1 CTGTCCATATGTCCCG-AGAACATAGGTAAT-T
*
48674 -TGTCCATATGTCCCGAAAGACATAGGTAATT
1 CTGTCCATATGTCCCGAGA-ACATAGGTAATT
* *
48705 CTGTACATATGTTCCGTAGAACATAGGTA
1 CTGTCCATATGTCCCG-AGAACATAGGTA
48734 TTTCCTCGAC
Statistics
Matches: 129, Mismatches: 14, Indels: 23
0.78 0.08 0.14
Matches are distributed among these distances:
30 11 0.09
31 63 0.49
32 50 0.39
33 5 0.04
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.31
Consensus pattern (31 bp):
CTGTCCATATGTCCCGAGAACATAGGTAATT
Found at i:48655 original size:63 final size:62
Alignment explanation
Indices: 48549--48734 Score: 275
Period size: 63 Copynumber: 3.0 Consensus size: 62
48539 CCTCGGTAAC
* * * * *
48549 TGTCTATAGGTCCCGAAGAACCTAGGTAA-ACTGTCCATATGTTCCTTAGAACATAGGTATAT
1 TGTCCATATGTCCCGAAG-ACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATAT
*
48611 TTTCCATATGTCCCGAGAGACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATAT
1 TGTCCATATGTCCCGA-AGACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATAT
*
48674 TGTCCATATGTCCCGAAAGACATAGGTAATTCTGTACATATGTTCCGTAGAACATAGGTAT
1 TGTCCATATGTCCCG-AAGACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTAT
48735 TTCCTCGACT
Statistics
Matches: 113, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
62 22 0.19
63 90 0.80
64 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (62 bp):
TGTCCATATGTCCCGAAGACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATAT
Found at i:50810 original size:46 final size:45
Alignment explanation
Indices: 50708--50810 Score: 122
Period size: 44 Copynumber: 2.3 Consensus size: 45
50698 ACCTTACTAG
*
50708 GGGTATCGGTA-CCCTCATGACATTCTATAATTTTTCGTTCAAGG
1 GGGTATCGGTACCCCTCATGACATTCTATAATTTTTCGTTCAAGA
**
50752 GGGTATCGGTACCCCT-ATGACATTCTGA-AATTTTTCTCGTTTGAGA
1 GGGTATCGGTACCCCTCATGACATTCT-ATAA-TTTT-TCGTTCAAGA
*
50798 GGGTATCAGTACC
1 GGGTATCGGTACC
50811 TATTGAATGG
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
44 23 0.45
45 9 0.18
46 19 0.37
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.35
Consensus pattern (45 bp):
GGGTATCGGTACCCCTCATGACATTCTATAATTTTTCGTTCAAGA
Found at i:53227 original size:30 final size:30
Alignment explanation
Indices: 53193--53251 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
53183 AAAACATAAT
*
53193 ATATGGTCACTTTTATTTTTATTTAATTAG
1 ATATGGTCACTTTCATTTTTATTTAATTAG
*
53223 ATATGGTCACTTTCGTTTTTATTTAATTA
1 ATATGGTCACTTTCATTTTTATTTAATTA
53252 AGACGTAGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.25, C:0.08, G:0.10, T:0.56
Consensus pattern (30 bp):
ATATGGTCACTTTCATTTTTATTTAATTAG
Found at i:53521 original size:24 final size:24
Alignment explanation
Indices: 53483--53588 Score: 85
Period size: 26 Copynumber: 4.2 Consensus size: 24
53473 TTAAACTCGT
53483 AATATTTTATATATATTAACTTTAAA
1 AATATTTTAT-TATATTAA-TTTAAA
*
53509 AATATTTT-TTATAATAACTTATTAAA
1 AATATTTTATTATATTAA--T-TTAAA
53535 TAA-ATTTTATTATTAACTTAATTTAAA
1 -AATATTTTATTA-T-A-TTAATTTAAA
*
53562 AATA-TTTATT-TTTTAATTTAAA
1 AATATTTTATTATATTAATTTAAA
53584 AATAT
1 AATAT
53589 ATATTTGGTT
Statistics
Matches: 67, Mismatches: 4, Indels: 21
0.73 0.04 0.23
Matches are distributed among these distances:
22 14 0.21
24 8 0.12
25 2 0.03
26 26 0.39
27 11 0.16
28 2 0.03
29 1 0.01
30 3 0.04
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (24 bp):
AATATTTTATTATATTAATTTAAA
Found at i:53567 original size:22 final size:21
Alignment explanation
Indices: 53542--53593 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
53532 AAATAAATTT
53542 TATTATTAACTTAATTTAAAAA
1 TATTATT-ACTTAATTTAAAAA
**
53564 TATTTATTTTTTAATTTAAAAA
1 TA-TTATTACTTAATTTAAAAA
53586 TATATATT
1 TAT-TATT
53594 TGGTTCTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 1 0.04
22 20 0.77
23 5 0.19
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (21 bp):
TATTATTACTTAATTTAAAAA
Found at i:53594 original size:22 final size:22
Alignment explanation
Indices: 53552--53594 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
53542 TATTATTAAC
*
53552 TTAATTTAAAAATATTTATTTT
1 TTAATTTAAAAATATATATTTT
53574 TTAATTTAAAAATATATATTT
1 TTAATTTAAAAATATATATTT
53595 GGTTCTTCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TTAATTTAAAAATATATATTTT
Found at i:55525 original size:16 final size:16
Alignment explanation
Indices: 55504--55536 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
55494 CATCACAAAA
55504 ACGGCGAAATGATCAC
1 ACGGCGAAATGATCAC
55520 ACGGCGAAATGATCAC
1 ACGGCGAAATGATCAC
55536 A
1 A
55537 TGAGATAGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.24, G:0.24, T:0.12
Consensus pattern (16 bp):
ACGGCGAAATGATCAC
Found at i:55691 original size:27 final size:28
Alignment explanation
Indices: 55630--55700 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 28
55620 AAACATTATT
* *
55630 ATTTCTACTGATTTTTTTATTATCGGACG
1 ATTT-TACTGATTTTGTTATTATCAGACG
*
55659 ATTTTTACTGATTTTGTTATTATTAGAC-
1 A-TTTTACTGATTTTGTTATTATCAGACG
55687 ATTTTACTGATTTT
1 ATTTTACTGATTTT
55701 ATTAACAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 13 0.34
28 1 0.03
29 21 0.55
30 3 0.08
ACGTcount: A:0.23, C:0.10, G:0.11, T:0.56
Consensus pattern (28 bp):
ATTTTACTGATTTTGTTATTATCAGACG
Found at i:60267 original size:31 final size:29
Alignment explanation
Indices: 60213--60285 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 29
60203 TTTCTGATTT
*
60213 TATTTTTTA-TTATTTATATATAATGTTTA
1 TATTTTTTATTTATTTATACATAAT-TTTA
*
60242 TATTTATTTATTTATTTTTACATAATTTTA
1 TATTT-TTTATTTATTTATACATAATTTTA
60272 TATTTCTATTATTT
1 TATTT-T-TTATTT
60286 TCCTATCGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 5 0.13
30 14 0.37
31 19 0.50
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (29 bp):
TATTTTTTATTTATTTATACATAATTTTA
Done.