Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003568.1 Hibiscus syriacus cultivar Beakdansim tig00007534_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: 65013
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:892 original size:28 final size:28
Alignment explanation
Indices: 833--957 Score: 121
Period size: 28 Copynumber: 4.5 Consensus size: 28
823 CTCATTCATG
* * *
833 TTTTTTAAGCTAAGGTAAGACTAAAATA
1 TTTTTTAAGTTAAGATAAGAATAAAATA
*
861 -TTTTTAAGTTAAAATAAGAATAAAATA
1 TTTTTTAAGTTAAGATAAGAATAAAATA
* *
888 TTTTTTAGGTTAAGACAAGAATAAAATA
1 TTTTTTAAGTTAAGATAAGAATAAAATA
* *
916 TTTTGATT-AGTTAATATAAAAAT-AAATA
1 TTTT--TTAAGTTAAGATAAGAATAAAATA
*
944 TATTTTAATGTTAA
1 TTTTTTAA-GTTAA
958 TATGTAAAAT
Statistics
Matches: 80, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
26 2 0.03
27 24 0.30
28 41 0.51
29 11 0.14
30 2 0.03
ACGTcount: A:0.47, C:0.02, G:0.10, T:0.40
Consensus pattern (28 bp):
TTTTTTAAGTTAAGATAAGAATAAAATA
Found at i:894 original size:55 final size:57
Alignment explanation
Indices: 833--949 Score: 139
Period size: 55 Copynumber: 2.1 Consensus size: 57
823 CTCATTCATG
** * *
833 TTTTTTAAGCTAAGGTAAGACTAAAATATTTT-TAAGTTAAAATAAGAATAAA-ATA
1 TTTTTTAAGCTAAGACAAGAATAAAATATTTTATAAGTTAAAATAAAAATAAATATA
* * * *
888 TTTTTTAGGTTAAGACAAGAATAAAATATTTTGATTAGTTAATATAAAAATAAATATA
1 TTTTTTAAGCTAAGACAAGAATAAAATATTTT-ATAAGTTAAAATAAAAATAAATATA
946 TTTT
1 TTTT
950 AATGTTAATA
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
55 27 0.53
57 17 0.33
58 7 0.14
ACGTcount: A:0.47, C:0.03, G:0.10, T:0.40
Consensus pattern (57 bp):
TTTTTTAAGCTAAGACAAGAATAAAATATTTTATAAGTTAAAATAAAAATAAATATA
Found at i:957 original size:57 final size:55
Alignment explanation
Indices: 849--957 Score: 130
Period size: 57 Copynumber: 1.9 Consensus size: 55
839 AAGCTAAGGT
* * *
849 AAGACTAAAATATTTTTAAGTTAAAATAAGAATAAAATATTTTTTAGGTTAAGAC
1 AAGAATAAAATATTTTTAAGTTAAAATAAAAATAAAATATTTTTAAGGTTAAGAC
* * *
904 AAGAATAAAATATTTTGATTAGTTAATATAAAAAT-AAATATATTTTAATGTTAA
1 AAGAATAAAATATTTT--TAAGTTAAAATAAAAATAAAATAT-TTTTAAGGTTAA
958 TATGTAAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
55 15 0.33
56 6 0.13
57 24 0.53
ACGTcount: A:0.50, C:0.02, G:0.09, T:0.39
Consensus pattern (55 bp):
AAGAATAAAATATTTTTAAGTTAAAATAAAAATAAAATATTTTTAAGGTTAAGAC
Found at i:988 original size:18 final size:18
Alignment explanation
Indices: 947--993 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
937 ATAAATATAT
947 TTTAATGTTAATATGTAAA
1 TTTAAT-TTAATATGTAAA
* *
966 ATTAATTTAATATGTGAA
1 TTTAATTTAATATGTAAA
*
984 TTTAAGTTAA
1 TTTAATTTAA
994 GATATATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 19 0.79
19 5 0.21
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.47
Consensus pattern (18 bp):
TTTAATTTAATATGTAAA
Found at i:3066 original size:30 final size:30
Alignment explanation
Indices: 3030--3105 Score: 116
Period size: 30 Copynumber: 2.5 Consensus size: 30
3020 AGGGTAAGGT
*
3030 GCATTTGGTGCACCGCGCCTCCCATAAGAC
1 GCATTTGGTGCACCGCACCTCCCATAAGAC
* *
3060 GCATTTGGTGCACCACACCTCCCATAAGGC
1 GCATTTGGTGCACCGCACCTCCCATAAGAC
*
3090 GCGTTTGGTGCACCGC
1 GCATTTGGTGCACCGC
3106 TTTCGATTGC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.18, C:0.36, G:0.25, T:0.21
Consensus pattern (30 bp):
GCATTTGGTGCACCGCACCTCCCATAAGAC
Found at i:4039 original size:60 final size:58
Alignment explanation
Indices: 3935--4103 Score: 169
Period size: 60 Copynumber: 2.8 Consensus size: 58
3925 CATTCCATCA
** ** *
3935 AGTTCAATAGGGAGACATTCATCTGCCAACTTCTTTGATGTCAATATAGATATGTCTTCC
1 AGTTCAAT-GGGAGACATTCATCTGCCAACTTCTTAAACCTCAATATAGATATCT-TTCC
* *
3995 AGTTCCAATGGGAGACATTCATCTGCCAACTTCTTCAACCTCAATATGGATATCTTTCC
1 AGTT-CAATGGGAGACATTCATCTGCCAACTTCTTAAACCTCAATATAGATATCTTTCC
* ** * * *
4054 TGTTTCAGGGGGAGATATTCATCTGTCAACTT-TTAAAACCCCAATATAGA
1 AG-TTCAATGGGAGACATTCATCTGCCAACTTCTT-AAACCTCAATATAGA
4104 GATGCATTCA
Statistics
Matches: 92, Mismatches: 14, Indels: 7
0.81 0.12 0.06
Matches are distributed among these distances:
58 2 0.02
59 40 0.43
60 46 0.50
61 4 0.04
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (58 bp):
AGTTCAATGGGAGACATTCATCTGCCAACTTCTTAAACCTCAATATAGATATCTTTCC
Found at i:6680 original size:12 final size:12
Alignment explanation
Indices: 6650--6728 Score: 52
Period size: 12 Copynumber: 6.6 Consensus size: 12
6640 CTTTTCACTC
*
6650 TCATCATCGTCG
1 TCATCATCATCG
* *
6662 TCGTCATC-TTG
1 TCATCATCATCG
*
6673 ATCATCATCATCT
1 -TCATCATCATCG
* *
6686 TGATCGTCATCG
1 TCATCATCATCG
*
6698 TCATCATCATTG
1 TCATCATCATCG
* * *
6710 TTATCGTCATCA
1 TCATCATCATCG
6722 TCATCAT
1 TCATCAT
6729 TACTCTCAGC
Statistics
Matches: 48, Mismatches: 17, Indels: 4
0.70 0.25 0.06
Matches are distributed among these distances:
11 2 0.04
12 45 0.94
13 1 0.02
ACGTcount: A:0.22, C:0.28, G:0.11, T:0.39
Consensus pattern (12 bp):
TCATCATCATCG
Found at i:6683 original size:15 final size:15
Alignment explanation
Indices: 6665--6696 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
6655 ATCGTCGTCG
6665 TCATCTTGATCATCA
1 TCATCTTGATCATCA
*
6680 TCATCTTGATCGTCA
1 TCATCTTGATCATCA
6695 TC
1 TC
6697 GTCATCATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.28, G:0.09, T:0.41
Consensus pattern (15 bp):
TCATCTTGATCATCA
Found at i:6701 original size:24 final size:24
Alignment explanation
Indices: 6673--6728 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
6663 CGTCATCTTG
6673 ATCATCATCATCT-TGATCGTCATC
1 ATCATCATCAT-TGTGATCGTCATC
* *
6697 GTCATCATCATTGTTATCGTCATC
1 ATCATCATCATTGTGATCGTCATC
6721 ATCATCAT
1 ATCATCAT
6729 TACTCTCAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 1 0.04
24 27 0.96
ACGTcount: A:0.25, C:0.27, G:0.09, T:0.39
Consensus pattern (24 bp):
ATCATCATCATTGTGATCGTCATC
Found at i:7696 original size:15 final size:16
Alignment explanation
Indices: 7678--7708 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
7668 ATATAAAGAC
7678 AATT-AAATTAAAAAA
1 AATTAAAATTAAAAAA
7693 AATTAAAATTAAAAAA
1 AATTAAAATTAAAAAA
7709 CGTACCTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AATTAAAATTAAAAAA
Found at i:17736 original size:4 final size:4
Alignment explanation
Indices: 17722--17751 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
17712 ATATTTGCTG
17722 CTTT C-TT CTTT CTTT CTTT CTTT CTTT CTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTT
17752 GTTTTCCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (4 bp):
CTTT
Found at i:25848 original size:23 final size:23
Alignment explanation
Indices: 25816--25874 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
25806 GTGTTCGTTT
*
25816 ATTTATTGTTCACGAACATGTTC
1 ATTTAATGTTCACGAACATGTTC
* *
25839 ATTTAATGTTCGCGAACGTGTTC
1 ATTTAATGTTCACGAACATGTTC
*
25862 GTTTATATGTTCA
1 ATTTA-ATGTTCA
25875 TGAAGATGAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 24 0.80
24 6 0.20
ACGTcount: A:0.24, C:0.15, G:0.17, T:0.44
Consensus pattern (23 bp):
ATTTAATGTTCACGAACATGTTC
Found at i:30440 original size:29 final size:30
Alignment explanation
Indices: 30390--30446 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
30380 AAATGCTAAT
***
30390 AATTAAAATTAGTGACTAAATT-ATAATAA
1 AATTAAAATTAAAAACTAAATTCATAATAA
*
30419 AATTAAAATTAAAAACTTAATTCATAAT
1 AATTAAAATTAAAAACTAAATTCATAAT
30447 TAATTAGAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 18 0.78
30 5 0.22
ACGTcount: A:0.56, C:0.05, G:0.04, T:0.35
Consensus pattern (30 bp):
AATTAAAATTAAAAACTAAATTCATAATAA
Found at i:31179 original size:15 final size:14
Alignment explanation
Indices: 31155--31196 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
31145 CCTCGGTAAG
*
31155 TTTCTCTTCTTTCTT
1 TTTCTTTTCTTTC-T
31170 TTTCTTTTCTTTCT
1 TTTCTTTTCTTTCT
31184 TTTCTGTTTCTTT
1 TTTCT-TTTCTTT
31197 TCTGCTGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 6 0.24
15 19 0.76
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.76
Consensus pattern (14 bp):
TTTCTTTTCTTTCT
Found at i:31187 original size:20 final size:20
Alignment explanation
Indices: 31155--31199 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
31145 CCTCGGTAAG
*
31155 TTTCTCTTCTTTCTTTTTCT
1 TTTCTCTTCTTTCTGTTTCT
31175 TTTCT-TTCTTTTCTGTTTCT
1 TTTCTCTTC-TTTCTGTTTCT
31195 TTTCT
1 TTTCT
31200 GCTGAGATCG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76
Consensus pattern (20 bp):
TTTCTCTTCTTTCTGTTTCT
Found at i:31200 original size:11 final size:11
Alignment explanation
Indices: 31164--31200 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
31154 GTTTCTCTTC
*
31164 TTTCTTTTTCT
1 TTTCTGTTTCT
31175 TTTC--TTTCT
1 TTTCTGTTTCT
31184 TTTCTGTTTCT
1 TTTCTGTTTCT
31195 TTTCTG
1 TTTCTG
31201 CTGAGATCGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 9 0.38
11 15 0.62
ACGTcount: A:0.00, C:0.19, G:0.05, T:0.76
Consensus pattern (11 bp):
TTTCTGTTTCT
Found at i:31753 original size:3 final size:3
Alignment explanation
Indices: 31745--31804 Score: 102
Period size: 3 Copynumber: 20.0 Consensus size: 3
31735 TAATAGTATA
* *
31745 AAT AAT AAT AAT AAT GAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
31793 AAT AAT AAT AAT
1 AAT AAT AAT AAT
31805 GAATCAATAT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:32332 original size:116 final size:116
Alignment explanation
Indices: 32132--32814 Score: 915
Period size: 116 Copynumber: 6.0 Consensus size: 116
32122 TAGAATTATG
* ** *
32132 CAAAAAGTTGAACAAGCTCTTCTTATTATGAAC---TTCTT-CTTCTTCAGATGACGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGACGAGTTCTTC
* *
32193 TAATTATGGACTCTACCTGGCAATGTTAATCCATCGAATGATGGATTTAAA
66 TTATTATGAACTCTACCTGGCAATGTTAATCCATCGAATGATGGATTTAAA
32244 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGACGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGACGAGTTCTTC
*
32309 TTATTATGAACTCTACCTGGCAATGTTAATCCATTGAATGATGGATTTAAA
66 TTATTATGAACTCTACCTGGCAATGTTAATCCATCGAATGATGGATTTAAA
32360 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGACGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGACGAGTTCTTC
*
32425 TTATTATGAACTCTACCTGGCAATGTTGATCCATCGAATGATGGATTTAAA
66 TTATTATGAACTCTACCTGGCAATGTTAATCCATCGAATGATGGATTTAAA
32476 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGACGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGACGAGTTCTTC
* * * *
32541 TTATTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAA
66 TTATTATGAACTCTACCTGGCAATGTTAATCCATCGAATGATGGATTTAAA
* * * * *
32592 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGAT---GAGTTCTAC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGACGAGTTCTTC
* * * * * * * *
32654 TCATTATGAACT-TTCTCTGGAAAAGATAATCCATC-AAGTGATAGATTTGAG
66 TTATTATGAACTCTAC-CTGGCAATGTTAATCCATCGAA-TGATGGATTTAAA
* * * * *
32705 TAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTATTC--AT-ATGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGACGAGTTCTTC
* * * * * * *
32767 TCATTATGAACT-TCCTCTGGAAAGGCTGATCCATCAAATGATGGATTT
66 TTATTATGAACTCTAC-CTGGCAATGTTAATCCATCGAATGATGGATTT
32815 GAATCTTTGC
Statistics
Matches: 522, Mismatches: 40, Indels: 17
0.90 0.07 0.03
Matches are distributed among these distances:
111 2 0.00
112 33 0.06
113 133 0.25
114 2 0.00
115 5 0.01
116 347 0.66
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (116 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGACGAGTTCTTC
TTATTATGAACTCTACCTGGCAATGTTAATCCATCGAATGATGGATTTAAA
Found at i:33243 original size:22 final size:22
Alignment explanation
Indices: 33218--33272 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
33208 CATAAAGTTT
*
33218 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
*
33240 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
33262 TCATCTTTGAA
1 TCATCTTTGAA
33273 GAGTGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:36130 original size:114 final size:115
Alignment explanation
Indices: 35699--36156 Score: 783
Period size: 115 Copynumber: 4.0 Consensus size: 115
35689 ATGATCATGC
* * * * * *
35699 AATTCATCTTTCAATTCCAATGATCGGTTCTGGGGTTCCTACCAAATCAGATCAGATAACTCAAA
1 AATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATAACTCAAA
* *
35764 GAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAA
66 GAACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACTATGAGCAA
35814 AATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATAACTCAAA
1 AATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATAACTCAAA
35879 GAACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACTATGAGCAA
66 GAACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACTATGAGCAA
35929 AATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATAACTCAAA
1 AATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATAACTCAAA
*
35994 GAACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACCATGAGC-A
66 GAACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACTATGAGCAA
36043 AATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATAACTCAAA
1 AATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATAACTCAAA
* * * * *
36108 GAACACTTTCAGAAGATACTATTGGGTCTTCTTATTTCTACTATGAGCA
66 GAACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACTATGAGCA
36157 CATGACACTT
Statistics
Matches: 327, Mismatches: 15, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
114 108 0.33
115 219 0.67
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.32
Consensus pattern (115 bp):
AATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACTATGAGCAA
Found at i:36151 original size:229 final size:230
Alignment explanation
Indices: 35699--36156 Score: 783
Period size: 229 Copynumber: 2.0 Consensus size: 230
35689 ATGATCATGC
* * * *
35699 AATTCATCTTTCAATTCCAATGATCGGTTCTGGGGTTCCTACCAAATCAGATCAGATAACTCAAA
1 AATTCATCTTTCAAATCCAATGATCGATTCTGGAGTTCATACCAAATCAGATCAGATAACTCAAA
* * *
35764 GAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAAATTCATCTTTCAAA
66 GAACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACCATGAGCAAAATTCATCTTTCAAA
35829 TCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAG
131 TCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAG
*
35894 ATGCTATTGAGCCTCCTTATTTCTACTATGAGCAA
196 ATACTATTGAGCCTCCTTATTTCTACTATGAGCAA
* *
35929 AATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATAACTCAAA
1 AATTCATCTTTCAAATCCAATGATCGATTCTGGAGTTCATACCAAATCAGATCAGATAACTCAAA
35994 GAACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACCATGAGC-AAATTCATCTTTCAAA
66 GAACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACCATGAGCAAAATTCATCTTTCAAA
*
36058 TCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATAACTCAAAGAACACTTTCAGAAG
131 TCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAG
* * *
36123 ATACTATTGGGTCTTCTTATTTCTACTATGAGCA
196 ATACTATTGAGCCTCCTTATTTCTACTATGAGCA
36157 CATGACACTT
Statistics
Matches: 214, Mismatches: 14, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
229 110 0.51
230 104 0.49
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.32
Consensus pattern (230 bp):
AATTCATCTTTCAAATCCAATGATCGATTCTGGAGTTCATACCAAATCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACCATGAGCAAAATTCATCTTTCAAA
TCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAG
ATACTATTGAGCCTCCTTATTTCTACTATGAGCAA
Found at i:38239 original size:11 final size:11
Alignment explanation
Indices: 38223--38252 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
38213 TCAATTTTCC
38223 TTTTTCTTTTT
1 TTTTTCTTTTT
*
38234 TTTTTCCTTTT
1 TTTTTCTTTTT
38245 TTTTTCTT
1 TTTTTCTT
38253 GTTTCTTTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:38257 original size:18 final size:18
Alignment explanation
Indices: 38218--38257 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
38208 TTGATTCAAT
*
38218 TTTCCTTTTTCTTTTTTT
1 TTTCCTTTTTCTTTTTTG
38236 TTTCCTTTTT-TTTTCTTG
1 TTTCCTTTTTCTTTT-TTG
38254 TTTC
1 TTTC
38258 TTTGCTGGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (18 bp):
TTTCCTTTTTCTTTTTTG
Found at i:38561 original size:2 final size:2
Alignment explanation
Indices: 38554--38579 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
38544 ACAACAAAGG
38554 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
38580 TAAAGGATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41707 original size:18 final size:19
Alignment explanation
Indices: 41671--41708 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
41661 ATACGAACGT
41671 AAAAATGCAAATATGAAAA
1 AAAAATGCAAATATGAAAA
41690 AAAAATGCAAATAT-AAAA
1 AAAAATGCAAATATGAAAA
41708 A
1 A
41709 TATGAATGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.71, C:0.05, G:0.08, T:0.16
Consensus pattern (19 bp):
AAAAATGCAAATATGAAAA
Found at i:43254 original size:19 final size:19
Alignment explanation
Indices: 43229--43272 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
43219 TATTAATAAA
43229 AAAAATATATAAATAT-TAT
1 AAAAATA-ATAAATATATAT
* *
43248 GAAAATAATAAGTATATAT
1 AAAAATAATAAATATATAT
43267 AAAAAT
1 AAAAAT
43273 TTTGAAAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (19 bp):
AAAAATAATAAATATATAT
Found at i:43254 original size:28 final size:28
Alignment explanation
Indices: 43223--43280 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
43213 ATGAAATATT
*
43223 AATAAAAAAAATATATAAATATTATGAA
1 AATAAAAAAAATATATAAAAATTATGAA
* ** *
43251 AATAATAAGTATATATAAAAATTTTGAA
1 AATAAAAAAAATATATAAAAATTATGAA
43279 AA
1 AA
43281 GAAAGAATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (28 bp):
AATAAAAAAAATATATAAAAATTATGAA
Found at i:44119 original size:29 final size:30
Alignment explanation
Indices: 44069--44125 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
44059 AAATGCTAAT
***
44069 AATTAAAATTAGTGACTAAATT-ATAATAA
1 AATTAAAATTAAAAACTAAATTCATAATAA
*
44098 AATTAAAATTAAAAACTTAATTCATAAT
1 AATTAAAATTAAAAACTAAATTCATAAT
44126 TAATCAGAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 18 0.78
30 5 0.22
ACGTcount: A:0.56, C:0.05, G:0.04, T:0.35
Consensus pattern (30 bp):
AATTAAAATTAAAAACTAAATTCATAATAA
Found at i:44843 original size:15 final size:14
Alignment explanation
Indices: 44819--44860 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
44809 CCTCGGTAAG
*
44819 TTTCTCTTCTTTCTT
1 TTTCTTTTCTTTC-T
44834 TTTCTTTTCTTTCT
1 TTTCTTTTCTTTCT
44848 TTTCTGTTTCTTT
1 TTTCT-TTTCTTT
44861 TCTGCTGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 6 0.24
15 19 0.76
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.76
Consensus pattern (14 bp):
TTTCTTTTCTTTCT
Found at i:44851 original size:20 final size:20
Alignment explanation
Indices: 44819--44863 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
44809 CCTCGGTAAG
*
44819 TTTCTCTTCTTTCTTTTTCT
1 TTTCTCTTCTTTCTGTTTCT
44839 TTTCT-TTCTTTTCTGTTTCT
1 TTTCTCTTC-TTTCTGTTTCT
44859 TTTCT
1 TTTCT
44864 GCTGAGATCG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76
Consensus pattern (20 bp):
TTTCTCTTCTTTCTGTTTCT
Found at i:44864 original size:11 final size:11
Alignment explanation
Indices: 44828--44864 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
44818 GTTTCTCTTC
*
44828 TTTCTTTTTCT
1 TTTCTGTTTCT
44839 TTTC--TTTCT
1 TTTCTGTTTCT
44848 TTTCTGTTTCT
1 TTTCTGTTTCT
44859 TTTCTG
1 TTTCTG
44865 CTGAGATCGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 9 0.38
11 15 0.62
ACGTcount: A:0.00, C:0.19, G:0.05, T:0.76
Consensus pattern (11 bp):
TTTCTGTTTCT
Found at i:45402 original size:21 final size:21
Alignment explanation
Indices: 45361--45404 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
45351 ATTGGGCTTG
* *
45361 TATATATTTTTTATTATTATT
1 TATATATTATTTAATATTATT
45382 TATATATGTATTTAATA-TATT
1 TATATAT-TATTTAATATTATT
45403 TA
1 TA
45405 ATAGTAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
TATATATTATTTAATATTATT
Found at i:45417 original size:3 final size:3
Alignment explanation
Indices: 45403--45477 Score: 132
Period size: 3 Copynumber: 24.7 Consensus size: 3
45393 TTAATATATT
*
45403 TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
45451 TAA TAA TAA TAA TAA TAA TAA TGAA TA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TA
45478 TGGGTAAAAA
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
3 66 0.96
4 3 0.04
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:54237 original size:12 final size:12
Alignment explanation
Indices: 54206--54243 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
54196 AGGCAACCTA
54206 TTTCGTTTTA-T
1 TTTCGTTTTATT
*
54217 TTTCATTTTATT
1 TTTCGTTTTATT
54229 TTTCGTTTTATT
1 TTTCGTTTTATT
54241 TTT
1 TTT
54244 AGCATGCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.11, C:0.08, G:0.05, T:0.76
Consensus pattern (12 bp):
TTTCGTTTTATT
Found at i:54277 original size:15 final size:15
Alignment explanation
Indices: 54254--54298 Score: 58
Period size: 14 Copynumber: 3.0 Consensus size: 15
54244 AGCATGCTTT
54254 ATTTCATTTCATTTTA
1 ATTTCATTT-ATTTTA
54270 ATTT-ATTTTATTTT-
1 ATTTCA-TTTATTTTA
54284 ATTTCATTTATTTTA
1 ATTTCATTTATTTTA
54299 TCAGATGCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 12 0.46
15 7 0.27
16 7 0.27
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (15 bp):
ATTTCATTTATTTTA
Found at i:54298 original size:5 final size:5
Alignment explanation
Indices: 54251--54299 Score: 55
Period size: 5 Copynumber: 10.0 Consensus size: 5
54241 TTTAGCATGC
* * * *
54251 TTTAT TTCAT TTCAT TTTAA TTTAT TTTAT TTTAT TTCA- TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
54300 CAGATGCTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
4 3 0.08
5 34 0.92
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.71
Consensus pattern (5 bp):
TTTAT
Found at i:54636 original size:32 final size:32
Alignment explanation
Indices: 54599--54669 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
54589 TTTTAAACTT
*
54599 AAAACCCCATGTTTATTCCTTTTATAACCGAC
1 AAAACCCCATGTTTATCCCTTTTATAACCGAC
*
54631 AAAACCCCATGTTTATCCCTTTTATAATCGAC
1 AAAACCCCATGTTTATCCCTTTTATAACCGAC
54663 AAAACCC
1 AAAACCC
54670 TTCTCCATCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.34, C:0.30, G:0.06, T:0.31
Consensus pattern (32 bp):
AAAACCCCATGTTTATCCCTTTTATAACCGAC
Found at i:55667 original size:8 final size:8
Alignment explanation
Indices: 55654--55684 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
55644 TATATGTTCT
55654 TTATTTTA
1 TTATTTTA
*
55662 TTATTTCA
1 TTATTTTA
55670 TTATTTTA
1 TTATTTTA
55678 TTATTTT
1 TTATTTT
55685 TGTCATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (8 bp):
TTATTTTA
Found at i:56464 original size:17 final size:17
Alignment explanation
Indices: 56442--56481 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
56432 TACCATGTAT
56442 GGGTAGTCAACCTGCGA
1 GGGTAGTCAACCTGCGA
56459 GGGTAGTCAACCTGCGA
1 GGGTAGTCAACCTGCGA
56476 GGGTAG
1 GGGTAG
56482 GTTTTATTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.23, C:0.20, G:0.40, T:0.17
Consensus pattern (17 bp):
GGGTAGTCAACCTGCGA
Found at i:58526 original size:21 final size:21
Alignment explanation
Indices: 58500--58586 Score: 70
Period size: 21 Copynumber: 4.0 Consensus size: 21
58490 AAAAAAAGAG
58500 AAAAGATAGAAAAAG-GAAAAA
1 AAAAGA-AGAAAAAGAGAAAAA
* *
58521 AAAAGAAAGAAAATGAGAAAAG
1 AAAAG-AAGAAAAAGAGAAAAA
* *
58543 AAAAGAAGAAGAAGA-ATAAGA
1 AAAAGAAGAAAAAGAGA-AAAA
* *
58564 AGAAGAAGAAGAAGAAGAAAAA
1 AAAAGAAGAAAAAG-AGAAAAA
58586 A
1 A
58587 GGAGAACATA
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
20 1 0.02
21 35 0.66
22 16 0.30
23 1 0.02
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.03
Consensus pattern (21 bp):
AAAAGAAGAAAAAGAGAAAAA
Found at i:58542 original size:28 final size:27
Alignment explanation
Indices: 58486--58541 Score: 69
Period size: 26 Copynumber: 2.0 Consensus size: 27
58476 ATTCATATTC
* *
58486 AAGGAAAAAAAGAG-AAAAGATAGAAA
1 AAGGAAAAAAAAAGAAAAAAATAGAAA
58512 AAGGAAAAAAAAAGAAAGAAAATGAGAAA
1 AAGGAAAAAAAAAGAAA-AAAAT-AGAAA
58541 A
1 A
58542 GAAAAGAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 13 0.52
27 2 0.08
28 4 0.16
29 6 0.24
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.04
Consensus pattern (27 bp):
AAGGAAAAAAAAAGAAAAAAATAGAAA
Found at i:58553 original size:3 final size:3
Alignment explanation
Indices: 58536--58582 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
58526 AAAGAAAATG
*
58536 AGA A-A AGA A-A AGA AGA AGA AGA ATA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
58582 A
1 A
58583 AAAAGGAGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 4 0.10
3 36 0.90
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02
Consensus pattern (3 bp):
AGA
Found at i:59207 original size:14 final size:14
Alignment explanation
Indices: 59181--59220 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
59171 AAATAAAAAG
*
59181 GAAAAATAATAAAT
1 GAAAAATAGTAAAT
*
59195 GATAAATAGTAAAT
1 GAAAAATAGTAAAT
*
59209 TAAAAATAGTAA
1 GAAAAATAGTAA
59221 TAAAGATAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.25
Consensus pattern (14 bp):
GAAAAATAGTAAAT
Found at i:60083 original size:75 final size:74
Alignment explanation
Indices: 59906--60108 Score: 263
Period size: 75 Copynumber: 2.8 Consensus size: 74
59896 ATCTTAAATA
* * * * *
59906 CTAATTAAAACACTTAAACCTATTTAAACTAAAATA-CTTAAA-AAATAATAT-TTAAATTAATA
1 CTAATTAAAATACTTAAACCTATTTAAACTAAAATACCTAAAACAAATAAAATATAAAAATAATA
* *
59968 TTCTAAATC
66 TCCTAAAAC
59977 CTAATT-AAATA-TTAAACCTATTTAAACTAAAATACCTAAAACAAGATAAAATATAAAAATAAT
1 CTAATTAAAATACTTAAACCTATTTAAACTAAAATACCTAAAACAA-ATAAAATATAAAAATAAT
60040 ATCCTAAAAC
65 ATCCTAAAAC
* *
60050 TTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAATATAAAATATAA
1 CTAATTAAAATACTTAAACCTATTTAAACTAAAATACCTAAAAC-AA-ATAAAATATAA
60109 TGTTTAAAAT
Statistics
Matches: 115, Mismatches: 10, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
69 23 0.20
70 9 0.08
71 8 0.07
72 6 0.05
73 21 0.18
74 5 0.04
75 30 0.26
76 13 0.11
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (74 bp):
CTAATTAAAATACTTAAACCTATTTAAACTAAAATACCTAAAACAAATAAAATATAAAAATAATA
TCCTAAAAC
Found at i:60102 original size:25 final size:24
Alignment explanation
Indices: 60055--60102 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
60045 AAAACTTAAT
** *
60055 TAAAATACTAAAACCTATTTAAAC
1 TAAAATACTAAAACAAATATAAAC
60079 TAAAATACCTAAAACAAATATAAA
1 TAAAATA-CTAAAACAAATATAAA
60103 ATATAATGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.60, C:0.15, G:0.00, T:0.25
Consensus pattern (24 bp):
TAAAATACTAAAACAAATATAAAC
Done.