Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005936.1 Hibiscus syriacus cultivar Beakdansim tig00013938_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: 100010
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:7224 original size:30 final size:30
Alignment explanation
Indices: 7165--7244 Score: 126
Period size: 30 Copynumber: 2.7 Consensus size: 30
7155 CCCAAAGGAC
*
7165 CTATCCAGAGGTCACAAAGA-CCCCGGTAA
1 CTATCCAGAGGTCATAAAGATCCCCGGTAA
*
7194 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCCCGGTAA
*
7224 CTGTCCAGAGGTCATAAAGAT
1 CTATCCAGAGGTCATAAAGAT
7245 GGGCTTATGC
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 19 0.40
30 28 0.60
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.20
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCCCGGTAA
Found at i:13089 original size:63 final size:64
Alignment explanation
Indices: 12888--13100 Score: 209
Period size: 64 Copynumber: 3.3 Consensus size: 64
12878 TCTTTTAATG
* * * ** * * * * *
12888 AAGGTATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGTATTTGATGTTTTATTATTAC
1 AAGG-ATGCATCGATGCACTACTTATTCATCGATGCACGAATTGCATTCGATGTTTCATTATTAA
** * * *
12953 TGGGATGCATCGATGCA-TGCCTTATTCATCGATGCACTAATTGCATTCGATGTTTCCTTATTAA
1 AAGGATGCATCGATGCACT-ACTTATTCATCGATGCACGAATTGCATTCGATGTTTCATTATTAA
* *
13017 TAGGATGCATCGATGCACTACTTA-TCATCGATGCACGAATTGCATTCGATGTATTTATT-TTAA
1 AAGGATGCATCGATGCACTACTTATTCATCGATGCACGAATTGCATTCGATGT-TTCATTATTAA
13080 AA-GAGTGCATCGATGCACTAC
1 AAGGA-TGCATCGATGCACTAC
13101 CAATGCATCG
Statistics
Matches: 124, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
62 2 0.02
63 49 0.40
64 70 0.56
65 3 0.02
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (64 bp):
AAGGATGCATCGATGCACTACTTATTCATCGATGCACGAATTGCATTCGATGTTTCATTATTAA
Found at i:16140 original size:25 final size:26
Alignment explanation
Indices: 16112--16161 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
16102 GAGAAACCAC
16112 TATGTCCCGAAGGA-CACATAGAACA
1 TATGTCCCGAAGGACCACATAGAACA
*
16137 TATGTCCCGAAGGACCACGTAGAAC
1 TATGTCCCGAAGGACCACATAGAAC
16162 CCTCGAATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.36, C:0.26, G:0.22, T:0.16
Consensus pattern (26 bp):
TATGTCCCGAAGGACCACATAGAACA
Found at i:17943 original size:15 final size:15
Alignment explanation
Indices: 17925--17953 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
17915 ATTTTTATGC
17925 TTGTCATTTATCTGT
1 TTGTCATTTATCTGT
17940 TTGTCATTTATCTG
1 TTGTCATTTATCTG
17954 CATGTCCTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.59
Consensus pattern (15 bp):
TTGTCATTTATCTGT
Found at i:17959 original size:15 final size:15
Alignment explanation
Indices: 17926--17959 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
17916 TTTTTATGCT
**
17926 TGTCATTTATCTGTT
1 TGTCATTTATCTGCA
17941 TGTCATTTATCTGCA
1 TGTCATTTATCTGCA
17956 TGTC
1 TGTC
17960 CTTCAGCATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.18, G:0.15, T:0.53
Consensus pattern (15 bp):
TGTCATTTATCTGCA
Found at i:28125 original size:32 final size:32
Alignment explanation
Indices: 28089--28153 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
28079 AGAAAAAAGA
*
28089 TAGAATGGAAAGCAAAAAAGGATGCTCCTATG
1 TAGAATGGAAACCAAAAAAGGATGCTCCTATG
*
28121 TAGAATGGAAACCAAAAAAGGATGCTTCTATG
1 TAGAATGGAAACCAAAAAAGGATGCTCCTATG
28153 T
1 T
28154 TGGTGGAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.43, C:0.12, G:0.23, T:0.22
Consensus pattern (32 bp):
TAGAATGGAAACCAAAAAAGGATGCTCCTATG
Found at i:29132 original size:20 final size:20
Alignment explanation
Indices: 29120--29159 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
29110 AAACTTTAGG
29120 GAAAGTTTTGAAACTCTTGA
1 GAAAGTTTTGAAACTCTTGA
*
29140 GATAGTTTTGAAACTCTTGA
1 GAAAGTTTTGAAACTCTTGA
29160 AAATATCGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.38
Consensus pattern (20 bp):
GAAAGTTTTGAAACTCTTGA
Found at i:29954 original size:21 final size:20
Alignment explanation
Indices: 29930--29968 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
29920 CAAATTCAAA
*
29930 TTAGGATTTATTTTATTTTTT
1 TTAGGAATTATTTT-TTTTTT
29951 TTAGGAATTATTTTTTTT
1 TTAGGAATTATTTTTTTT
29969 AATTTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (20 bp):
TTAGGAATTATTTTTTTTTT
Found at i:30912 original size:12 final size:12
Alignment explanation
Indices: 30892--30930 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
30882 CTTTATACTA
*
30892 TTATATTTATAT
1 TTATATTTATTT
* *
30904 TTATTTTTATTA
1 TTATATTTATTT
30916 TTATATTTATTT
1 TTATATTTATTT
30928 TTA
1 TTA
30931 ATGAGATTAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
TTATATTTATTT
Found at i:39930 original size:5 final size:5
Alignment explanation
Indices: 39920--39945 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
39910 TATTATTATT
39920 TCGGG TCGGG TCGGG TCGGG TCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG T
39946 TTTTAAGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.58, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:48975 original size:12 final size:12
Alignment explanation
Indices: 48958--49004 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
48948 AAAACCCTAG
48958 AATACTAAAAAT
1 AATACTAAAAAT
*
48970 AATACTAAGAA-
1 AATACTAAAAAT
*
48981 AATACAAAAAAT
1 AATACTAAAAAT
*
48993 AAATCCTAAAAA
1 -AATACTAAAAA
49005 GATAATTCCT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
11 9 0.32
12 10 0.36
13 9 0.32
ACGTcount: A:0.68, C:0.11, G:0.02, T:0.19
Consensus pattern (12 bp):
AATACTAAAAAT
Found at i:54204 original size:13 final size:13
Alignment explanation
Indices: 54160--54206 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
54150 CCTTTTCTTG
*
54160 ATATTGAAAACTAA
1 ATATTTAAAA-TAA
54174 ATA-TTAAAATAA
1 ATATTTAAAATAA
*
54186 TTTATTTAAAATAA
1 -ATATTTAAAATAA
54200 ATATTTA
1 ATATTTA
54207 TTTATTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 3 0.11
13 13 0.46
14 12 0.43
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (13 bp):
ATATTTAAAATAA
Found at i:55648 original size:3 final size:3
Alignment explanation
Indices: 55640--55731 Score: 166
Period size: 3 Copynumber: 30.7 Consensus size: 3
55630 AATATATATT
* *
55640 TAA TAA TAA TAA TAA TGA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
55688 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
55732 TGGGTAAAAA
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 85 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:56186 original size:116 final size:113
Alignment explanation
Indices: 56048--56691 Score: 887
Period size: 116 Copynumber: 5.6 Consensus size: 113
56038 TGATAGAATT
* * *
56048 ATTGAACAAGTTCTTCTTATTATAAACTTCTTCTTTCTTCTTCAGATGACGAGTTCTTCTCATTA
1 ATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTA
*
56113 TGAACTCTACTTAGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAG
63 TGAACTCTACTTGGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAG
56164 ATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAACGAGTTCTTCTCATTA
1 ATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTA
* *
56229 TGAACTCTACCTGGCAATGTCGATCCATCAAATGATGAATTCAAGCAAAAG
63 TGAACTCTACTTGGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAG
56280 ATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 ATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
* * * * * * * * *
56345 AC-CTTCTCTGGAAAAGCTAATCCATCAATTTAATGAATTCAGGTAAAAG
66 ACTCTACT-TGGCAATGTTGATCCATCAA-ATGATGAATTCAAGCAAAAG
* * * *
56394 GTTGAATAAATTCTTCTCATTATGAACTTCTTCTTCCTTTTTCAGATGACGAGTTCTTCTCATTA
1 ATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTA
56459 TGAACTCTACTTGGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAG
63 TGAACTCTACTTGGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAG
56510 ATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 ATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
* * * * * * * *
56575 AC-CTTCTCTGGAAAAGCTAATCCATCAATTTGATGAATTCAGGTAAAAG
66 ACTCTACT-TGGCAATGTTGATCCATCAA-ATGATGAATTCAAGCAAAAG
* * *
56624 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTTTTCAGATGAGTTCTTCTCATTATGA
1 ATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
56689 ACT
66 ACT
56692 TTCTCTGGAA
Statistics
Matches: 473, Mismatches: 46, Indels: 19
0.88 0.09 0.04
Matches are distributed among these distances:
112 7 0.01
113 71 0.15
114 140 0.30
116 215 0.45
117 36 0.08
118 4 0.01
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (113 bp):
ATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
ACTCTACTTGGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAG
Found at i:56440 original size:230 final size:229
Alignment explanation
Indices: 56048--56691 Score: 1035
Period size: 230 Copynumber: 2.8 Consensus size: 229
56038 TGATAGAATT
* * *
56048 ATTGAACAAGTTCTTCTTATTATAAACTTCTTCTTTCTTCTTCAGATGACGAGTTCTTCTCATTA
1 ATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTA
* * * * * * * * * * *
56113 TGAACTCTACT-TAGCAATGTTGATCCATCAA-ATGATGAATTCAAGCAAAAGATTGAACAAGTT
63 TGAAC-CTTCTCTGGAAAAGCTAATCCATCAATTTGATGAATTCAGGTAAAAGGTTGAACAAATT
*
56176 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAACGAGTTCTTCTCATTATGAACTCTACCT
127 CTTCTCATTATGAACTTCTTCTTCCTTTTTCAGAT-ACGAGTTCTTCTCATTATGAACTCTACCT
56241 GGCAATGTCGATCCATCAAATGATGAATTCAAGCAAAAG
191 GGCAATGTCGATCCATCAAATGATGAATTCAAGCAAAAG
56280 ATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 ATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
* *
56345 ACCTTCTCTGGAAAAGCTAATCCATCAATTTAATGAATTCAGGTAAAAGGTTGAATAAATTCTTC
66 ACCTTCTCTGGAAAAGCTAATCCATCAATTTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTC
*
56410 TCATTATGAACTTCTTCTTCCTTTTTCAGATGACGAGTTCTTCTCATTATGAACTCTACTTGGCA
131 TCATTATGAACTTCTTCTTCCTTTTTCAGAT-ACGAGTTCTTCTCATTATGAACTCTACCTGGCA
*
56475 ATGTTGATCCATCAAATGATGAATTCAAGCAAAAG
195 ATGTCGATCCATCAAATGATGAATTCAAGCAAAAG
56510 ATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 ATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
56575 ACCTTCTCTGGAAAAGCTAATCCATCAATTTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTC
66 ACCTTCTCTGGAAAAGCTAATCCATCAATTTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTC
56640 TCATTATGAACTTCTTCTTCCTTTTTCAGAT--GAGTTCTTCTCATTATGAACT
131 TCATTATGAACTTCTTCTTCCTTTTTCAGATACGAGTTCTTCTCATTATGAACT
56692 TTCTCTGGAA
Statistics
Matches: 388, Mismatches: 22, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
227 21 0.05
228 4 0.01
229 35 0.09
230 284 0.73
232 44 0.11
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (229 bp):
ATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
ACCTTCTCTGGAAAAGCTAATCCATCAATTTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTC
TCATTATGAACTTCTTCTTCCTTTTTCAGATACGAGTTCTTCTCATTATGAACTCTACCTGGCAA
TGTCGATCCATCAAATGATGAATTCAAGCAAAAG
Found at i:57535 original size:92 final size:91
Alignment explanation
Indices: 57420--58035 Score: 929
Period size: 92 Copynumber: 7.0 Consensus size: 91
57410 TTCATCTATT
*
57420 AATTCCAATAATTGGTTCTGTAGTTCTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAG
1 AATT-CAATGATTGGTT-TGTAGTTCTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAG
57485 AAGATGCTATTGGCAAATTCATCTTCAA
64 AAGATGCTATTGGCAAATTCATCTTCAA
*
57513 AATTCAATGATTGGTTATGTAGTTCTTACAAAACCAGATCAGATAACTCAAAGAACACTTCCAGA
1 AATTCAATGATTGGTT-TGTAGTTCTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGA
57578 AGATGCTATTGGCAAATTCATCTTCAA
65 AGATGCTATTGGCAAATTCATCTTCAA
57605 AATTCAATGATTGGTTCTGTAGTTCTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGA
1 AATTCAATGATTGGTT-TGTAGTTCTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGA
* *
57670 ATATGCTATTAGCAAATTCATCTTCAA
65 AGATGCTATTGGCAAATTCATCTTCAA
57697 AATTCAATGATTGGTTCTGTAGTTCTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGA
1 AATTCAATGATTGGTT-TGTAGTTCTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGA
* *
57762 AGATGCTATTAGCAAATTCATCTTCCA
65 AGATGCTATTGGCAAATTCATCTTCAA
*
57789 AATTCAATGATTGG-TTCT-G----T-CC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAA
1 AATTCAATGATTGGTTTGTAGTTCTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAA
57846 GATGCTATTGGCAAATTCATCTTCAA
66 GATGCTATTGGCAAATTCATCTTCAA
*
57872 AATTCAATGATTGG-TTCT-G----T-CC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAA
1 AATTCAATGATTGGTTTGTAGTTCTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAA
57929 GATGCTATTGGCAAATTCATCTTCAA
66 GATGCTATTGGCAAATTCATCTTCAA
* *
57955 AATTCAATGATTGG-TTCT-G----T-CC-AACCAGATCAGATAACTTAAAGAACACTTCCAGAA
1 AATTCAATGATTGGTTTGTAGTTCTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAA
58012 GATGCTATTGGCAAATTCATCTTC
66 GATGCTATTGGCAAATTCATCTTC
58036 TAATTAATGT
Statistics
Matches: 510, Mismatches: 13, Indels: 10
0.96 0.02 0.02
Matches are distributed among these distances:
83 222 0.44
84 2 0.00
85 1 0.00
89 1 0.00
90 2 0.00
91 1 0.00
92 277 0.54
93 4 0.01
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (91 bp):
AATTCAATGATTGGTTTGTAGTTCTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAA
GATGCTATTGGCAAATTCATCTTCAA
Found at i:59196 original size:9 final size:10
Alignment explanation
Indices: 59176--59206 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
59166 TTGACCCCCC
*
59176 TTTTTCCTTT
1 TTTTTTCTTT
59186 TTTTTTCTTT
1 TTTTTTCTTT
59196 TTTTTTCTTT
1 TTTTTTCTTT
59206 T
1 T
59207 CAAGCATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:67752 original size:71 final size:71
Alignment explanation
Indices: 67636--67779 Score: 288
Period size: 71 Copynumber: 2.0 Consensus size: 71
67626 TCCTGATGCT
67636 TTCCGGGATTTATATAACTCCTGGTAATTTTTCTGTAATGCTCTGAATTCATCATCAACTTTTTC
1 TTCCGGGATTTATATAACTCCTGGTAATTTTTCTGTAATGCTCTGAATTCATCATCAACTTTTTC
67701 TTTATC
66 TTTATC
67707 TTCCGGGATTTATATAACTCCTGGTAATTTTTCTGTAATGCTCTGAATTCATCATCAACTTTTTC
1 TTCCGGGATTTATATAACTCCTGGTAATTTTTCTGTAATGCTCTGAATTCATCATCAACTTTTTC
67772 TTTATC
66 TTTATC
67778 TT
1 TT
67780 TTCACAACAT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 73 1.00
ACGTcount: A:0.22, C:0.19, G:0.11, T:0.47
Consensus pattern (71 bp):
TTCCGGGATTTATATAACTCCTGGTAATTTTTCTGTAATGCTCTGAATTCATCATCAACTTTTTC
TTTATC
Found at i:69961 original size:18 final size:17
Alignment explanation
Indices: 69913--69963 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
69903 AAATACTTGC
*
69913 AAATAAAATAAAACATAT
1 AAAT-AAATAAAAAATAT
*
69931 AAAT-ATTATAAAAATAAT
1 AAATAAATA-AAAAAT-AT
69949 AAATAAATAAAAAAT
1 AAATAAATAAAAAAT
69964 TTGACAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
16 3 0.11
17 5 0.19
18 16 0.59
19 3 0.11
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (17 bp):
AAATAAATAAAAAATAT
Found at i:70662 original size:13 final size:13
Alignment explanation
Indices: 70618--70664 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
70608 CTTTTCTTTG
*
70618 ATATTGAAAACTAA
1 ATATTTAAAA-TAA
70632 ATA-TTAAAATAA
1 ATATTTAAAATAA
*
70644 TTTATTTAAAATAA
1 -ATATTTAAAATAA
70658 ATATTTA
1 ATATTTA
70665 TTTATTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 3 0.11
13 13 0.46
14 12 0.43
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (13 bp):
ATATTTAAAATAA
Found at i:72106 original size:3 final size:3
Alignment explanation
Indices: 72098--72165 Score: 127
Period size: 3 Copynumber: 22.7 Consensus size: 3
72088 AATATATATT
*
72098 TAA TAA TAA TAA TAA TGA 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
72146 TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA
72166 TGGGTAAAAA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:78437 original size:2 final size:2
Alignment explanation
Indices: 78430--78470 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
78420 ATTTGAAATC
78430 AT AT AT AT 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 AT AT AT AT A
78471 GATCTTTTCC
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:79276 original size:29 final size:30
Alignment explanation
Indices: 79225--79283 Score: 111
Period size: 29 Copynumber: 2.0 Consensus size: 30
79215 AATTTCCCCC
79225 CTTCTATTCGTTTGATTCCATTCAACATAT
1 CTTCTATTCGTTTGATTCCATTCAACATAT
79255 CTTCTATTCG-TTGATTCCATTCAACATAT
1 CTTCTATTCGTTTGATTCCATTCAACATAT
79284 ATTTTCACTT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 19 0.66
30 10 0.34
ACGTcount: A:0.24, C:0.24, G:0.07, T:0.46
Consensus pattern (30 bp):
CTTCTATTCGTTTGATTCCATTCAACATAT
Found at i:88361 original size:21 final size:20
Alignment explanation
Indices: 88320--88361 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
88310 TGGTTGTGAT
*
88320 TTTGAGGTTATGGTTATGGA
1 TTTGAGGTTATGGGTATGGA
88340 TTTGAAGGTTGATGGGTA-GGA
1 TTTG-AGGTT-ATGGGTATGGA
88361 T
1 T
88362 GAGATGCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 9 0.47
22 6 0.32
ACGTcount: A:0.21, C:0.00, G:0.38, T:0.40
Consensus pattern (20 bp):
TTTGAGGTTATGGGTATGGA
Found at i:89041 original size:13 final size:13
Alignment explanation
Indices: 89019--89068 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
89009 TCCATGGTTA
89019 TATT-AATTTTAT
1 TATTAAATTTTAT
89031 TATTAAATTTTA-
1 TATTAAATTTTAT
* **
89043 AAAAACAATTTTAT
1 TATTA-AATTTTAT
89057 TATTAAATTTTA
1 TATTAAATTTTA
89069 AAAAATCAGA
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
12 6 0.21
13 21 0.72
14 2 0.07
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (13 bp):
TATTAAATTTTAT
Found at i:89054 original size:26 final size:26
Alignment explanation
Indices: 89023--89073 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
89013 TGGTTATATT
89023 AATTTTATTATTAAATTTTAAAAAAC
1 AATTTTATTATTAAATTTTAAAAAAC
89049 AATTTTATTATTAAATTTTAAAAAA
1 AATTTTATTATTAAATTTTAAAAAA
89074 TCAGAGATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (26 bp):
AATTTTATTATTAAATTTTAAAAAAC
Found at i:89313 original size:14 final size:15
Alignment explanation
Indices: 89294--89326 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
89284 CCTTTCTTAT
*
89294 TTTTTTCTT-TTTAA
1 TTTTTTATTCTTTAA
89308 TTTTTTATTCTTTAA
1 TTTTTTATTCTTTAA
89323 TTTT
1 TTTT
89327 ATTTAACTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTTATTCTTTAA
Found at i:90250 original size:29 final size:29
Alignment explanation
Indices: 90195--90261 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
90185 GGACAAAAGG
* *
90195 TTTTATAAATTATAATGAATTACAAAA-T
1 TTTTATAAATTATAATAAAGTACAAAACT
**
90223 TGTTTATAAATTATAATAAAGTGTAAAACT
1 T-TTTATAAATTATAATAAAGTACAAAACT
90253 TTTTATAAA
1 TTTTATAAA
90262 ATAAAATATC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 1 0.03
29 30 0.91
30 2 0.06
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.43
Consensus pattern (29 bp):
TTTTATAAATTATAATAAAGTACAAAACT
Found at i:90561 original size:22 final size:21
Alignment explanation
Indices: 90504--90564 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
90494 ACGGATGGTG
* *
90504 GAAGAAGGTTGCACGAATGCTG
1 GAAGTAGG-TGCACGAATGCTA
90526 GAAGTA-GTGCACGAATGCTA
1 GAAGTAGGTGCACGAATGCTA
90546 GAAGTAGGCTGCACGAATG
1 GAAGTAGG-TGCACGAATG
90565 TTGGAAGCGG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 18 0.51
21 2 0.06
22 15 0.43
ACGTcount: A:0.33, C:0.15, G:0.34, T:0.18
Consensus pattern (21 bp):
GAAGTAGGTGCACGAATGCTA
Found at i:90571 original size:22 final size:22
Alignment explanation
Indices: 90502--90581 Score: 92
Period size: 22 Copynumber: 3.7 Consensus size: 22
90492 CTACGGATGG
* *
90502 TGGAAGAAGGTTGCACGAATGC
1 TGGAAGTAGGCTGCACGAATGC
90524 TGGAAGTA-G-TGCACGAATGC
1 TGGAAGTAGGCTGCACGAATGC
* *
90544 TAGAAGTAGGCTGCACGAATGT
1 TGGAAGTAGGCTGCACGAATGC
**
90566 TGGAAGCGGGCTGCAC
1 TGGAAGTAGGCTGCAC
90582 AGGCGCTGAT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
20 18 0.36
21 2 0.04
22 30 0.60
ACGTcount: A:0.29, C:0.16, G:0.36, T:0.19
Consensus pattern (22 bp):
TGGAAGTAGGCTGCACGAATGC
Found at i:91945 original size:12 final size:12
Alignment explanation
Indices: 91925--91956 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
91915 AAAAGACTCT
91925 TAAATATACATA
1 TAAATATACATA
*
91937 TACATATACATA
1 TAAATATACATA
91949 TAAATATA
1 TAAATATA
91957 TTTGAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.34
Consensus pattern (12 bp):
TAAATATACATA
Found at i:93637 original size:14 final size:14
Alignment explanation
Indices: 93632--93674 Score: 68
Period size: 14 Copynumber: 3.1 Consensus size: 14
93622 CGTTCATTTA
*
93632 CGTTCGTTTATGTT
1 CGTTCATTTATGTT
93646 CGTTCATTTATGTT
1 CGTTCATTTATGTT
*
93660 CGTTTATTTATGTT
1 CGTTCATTTATGTT
93674 C
1 C
93675 ATTTATGTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.12, C:0.14, G:0.16, T:0.58
Consensus pattern (14 bp):
CGTTCATTTATGTT
Found at i:93651 original size:24 final size:24
Alignment explanation
Indices: 93619--93685 Score: 100
Period size: 24 Copynumber: 2.8 Consensus size: 24
93609 CAAAGGGCTC
*
93619 GTTCGTTCATTTACGTTCGTTTAT
1 GTTCGTTCATTTATGTTCGTTTAT
93643 GTTCGTTCATTTATGTTCGTTTAT
1 GTTCGTTCATTTATGTTCGTTTAT
*
93667 -TTATGTTCATTTATGTTCG
1 GTT-CGTTCATTTATGTTCG
93686 AACAGAGAGC
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
23 2 0.05
24 38 0.95
ACGTcount: A:0.13, C:0.13, G:0.16, T:0.57
Consensus pattern (24 bp):
GTTCGTTCATTTATGTTCGTTTAT
Found at i:93679 original size:14 final size:14
Alignment explanation
Indices: 93638--93680 Score: 68
Period size: 14 Copynumber: 3.1 Consensus size: 14
93628 TTTACGTTCG
*
93638 TTTATGTTCGTTCA
1 TTTATGTTCGTTTA
93652 TTTATGTTCGTTTA
1 TTTATGTTCGTTTA
*
93666 TTTATGTTCATTTA
1 TTTATGTTCGTTTA
93680 T
1 T
93681 GTTCGAACAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.16, C:0.09, G:0.12, T:0.63
Consensus pattern (14 bp):
TTTATGTTCGTTTA
Found at i:95569 original size:9 final size:9
Alignment explanation
Indices: 95555--95646 Score: 76
Period size: 9 Copynumber: 9.7 Consensus size: 9
95545 GGCTGCTGGA
95555 AACCGGTTT
1 AACCGGTTT
95564 AACCGGTTTT
1 AACCGG-TTT
95574 CAACCGGTTCT
1 -AACCGGTT-T
*
95585 GACCGGTTT
1 AACCGGTTT
*
95594 GACCGGTTT
1 AACCGGTTT
*
95603 CAACCGGTTCG
1 -AACCGGTT-T
95614 AACCGGTTT
1 AACCGGTTT
* *
95623 GACCGGTTG
1 AACCGGTTT
*
95632 AATCGGTTT
1 AACCGGTTT
*
95641 GACCGG
1 AACCGG
95647 CTGACCCGAC
Statistics
Matches: 67, Mismatches: 11, Indels: 10
0.76 0.12 0.11
Matches are distributed among these distances:
9 33 0.49
10 27 0.40
11 7 0.10
ACGTcount: A:0.17, C:0.25, G:0.28, T:0.29
Consensus pattern (9 bp):
AACCGGTTT
Found at i:95591 original size:10 final size:9
Alignment explanation
Indices: 95556--95646 Score: 76
Period size: 10 Copynumber: 9.6 Consensus size: 9
95546 GCTGCTGGAA
*
95556 ACCGGTTTA
1 ACCGGTTTG
*
95565 ACCGGTTTTCA
1 ACCGG-TTT-G
95576 ACCGGTTCTG
1 ACCGGTT-TG
95586 ACCGGTTTG
1 ACCGGTTTG
*
95595 ACCGGTTTCA
1 ACCGGTTT-G
*
95605 ACCGGTTCG
1 ACCGGTTTG
95614 AACCGGTTTG
1 -ACCGGTTTG
95624 ACCGG-TTG
1 ACCGGTTTG
*
95632 AATCGGTTTG
1 -ACCGGTTTG
95642 ACCGG
1 ACCGG
95647 CTGACCCGAC
Statistics
Matches: 68, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
8 3 0.04
9 28 0.41
10 30 0.44
11 7 0.10
ACGTcount: A:0.16, C:0.25, G:0.29, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:95618 original size:29 final size:30
Alignment explanation
Indices: 95555--95630 Score: 120
Period size: 29 Copynumber: 2.6 Consensus size: 30
95545 GGCTGCTGGA
*
95555 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
95586 -ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
95614 AACCGGTTTGACCGGTT
1 AACCGGTTTGACCGGTT
95631 GAATCGGTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
28 1 0.02
29 29 0.67
30 13 0.30
ACGTcount: A:0.17, C:0.26, G:0.26, T:0.30
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:95659 original size:5 final size:5
Alignment explanation
Indices: 95649--95705 Score: 53
Period size: 5 Copynumber: 10.8 Consensus size: 5
95639 TTGACCGGCT
* *
95649 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GA-CC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
95697 GACCC GACC
1 GACCC GACC
95706 GTTGACCGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
4 2 0.05
5 34 0.79
6 1 0.02
7 6 0.14
ACGTcount: A:0.19, C:0.51, G:0.23, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:95695 original size:21 final size:21
Alignment explanation
Indices: 95649--95713 Score: 121
Period size: 21 Copynumber: 3.0 Consensus size: 21
95639 TTGACCGGCT
95649 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGA-CC
95671 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
95692 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
95713 G
1 G
95714 TTGACCGTTG
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
21 24 0.56
22 19 0.44
ACGTcount: A:0.18, C:0.48, G:0.25, T:0.09
Consensus pattern (21 bp):
GACCCGACCCGACCGTTGACC
Found at i:95700 original size:26 final size:27
Alignment explanation
Indices: 95666--95720 Score: 85
Period size: 26 Copynumber: 2.0 Consensus size: 27
95656 CCCGACCGTT
95666 GACCCGACCCGACC-CGACCGTTGACC
1 GACCCGACCCGACCGCGACCGTTGACC
*
95692 GACCCGACCCGACCGTTGACCGTTGACC
1 GACCCGACCCGACCG-CGACCGTTGACC
95720 G
1 G
95721 TTGACCGTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 14 0.54
28 12 0.46
ACGTcount: A:0.18, C:0.45, G:0.25, T:0.11
Consensus pattern (27 bp):
GACCCGACCCGACCGCGACCGTTGACC
Found at i:95714 original size:7 final size:7
Alignment explanation
Indices: 95702--95739 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
95692 GACCCGACCC
95702 GACCGTT
1 GACCGTT
95709 GACCGTT
1 GACCGTT
95716 GACCGTT
1 GACCGTT
95723 GACCGTT
1 GACCGTT
*
95730 GACCATT
1 GACCGTT
95737 GAC
1 GAC
95740 TTTCTTTGAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.18, C:0.29, G:0.26, T:0.26
Consensus pattern (7 bp):
GACCGTT
Done.