Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007407.1 Hibiscus syriacus cultivar Beakdansim tig00020012_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: 67932
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:6194 original size:3 final size:3
Alignment explanation
Indices: 6186--6271 Score: 79
Period size: 3 Copynumber: 28.0 Consensus size: 3
6176 ATATTTTTAT
*
6186 TAA TAA TAA TAA TAA TAAA TAA TAA TAA TAA -ATA TTA TAA TAA -ATA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TA-A TAA TAA TAA TA-A
* *
6232 TAA TAA TAA T-A TAA TAGA TTAA TAA TAA AAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TA-A -TAA TAA TAA TAA TAA TAA TAA
6272 AAACAAATGG
Statistics
Matches: 69, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
2 4 0.06
3 57 0.83
4 6 0.09
5 2 0.03
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:6225 original size:25 final size:23
Alignment explanation
Indices: 6186--6265 Score: 92
Period size: 25 Copynumber: 3.4 Consensus size: 23
6176 ATATTTTTAT
6186 TAATAATAATA-ATAATAAATAA
1 TAATAATAATATATAATAAATAA
6208 TAATAATAAATATTATAATAAAT-A
1 TAATAAT-AATA-TATAATAAATAA
*
6232 TAATAATAATATAATAGATTAATAA
1 TAATAATAATAT-ATA-ATAAATAA
*
6257 TAAAAATAA
1 TAATAATAA
6266 AAATAAAAAC
Statistics
Matches: 50, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
22 8 0.16
23 11 0.22
24 13 0.26
25 18 0.36
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (23 bp):
TAATAATAATATATAATAAATAA
Found at i:6271 original size:43 final size:40
Alignment explanation
Indices: 6191--6272 Score: 110
Period size: 43 Copynumber: 2.0 Consensus size: 40
6181 TTTATTAATA
* * *
6191 ATAATAATAATAAATAATAATAATAAATATTATAATAAAT
1 ATAATAATAATAAATAATAATAATAAAAATAAAAATAAAT
6231 ATAATAATAATATAATAGATTAATAATAAAAATAAAAATAAA
1 ATAATAATAATA-AATA-A-TAATAATAAAAATAAAAATAAA
6273 AACAAATGGA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
40 12 0.33
41 4 0.11
42 1 0.03
43 19 0.53
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (40 bp):
ATAATAATAATAAATAATAATAATAAAAATAAAAATAAAT
Found at i:6951 original size:123 final size:123
Alignment explanation
Indices: 6601--7156 Score: 735
Period size: 123 Copynumber: 4.6 Consensus size: 123
6591 TTAAACAAAT
*
6601 TCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
1 TCTTCTCATTATGAACTTCTTC-TTCTTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGG
** *
6666 AAAAATTGATGTTGATCTACCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGC
65 AAATGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGC
*
6725 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
1 TCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGG
*
6790 AAAGGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGC
65 AAATGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGC
6849 TCTTCTCATTATGAACTTCTTC-TCATTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGG
1 TCTTCTCATTATGAACTTCTTCTTC-TTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGG
* * * *
6913 AAATGTTGGTGATGATTTATCTCCTTCTGCGATAGAGTCATGCAAAAGGTTGAACAAGC
65 AAATGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGC
* * *
6972 TCTTCTCATTATGAACTTTTTCTTCCTCTTCAGATAAGTTCTTCTTATTATGAACTTTCTCT-GA
1 TCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGA
* * ** * * * *
7036 AA-----A---TG-TCGATC-CATTGAGTGAT-GAATTCGA-GCAAAAAGTTAAACAAGT
66 AATGTTGATGTTGATCTATCTCCTTCTGTGATAG-AGTC-ATGCAAAAGGTTGAACAAGC
* * * * *
7084 TCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTATTCTCATTATGAACTTTATCTGAA
1 TCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGA
7149 AATGTTGA
66 AATGTTGA
7157 AAACATTCTG
Statistics
Matches: 390, Mismatches: 31, Indels: 28
0.87 0.07 0.06
Matches are distributed among these distances:
111 1 0.00
112 80 0.21
113 8 0.02
114 2 0.01
118 1 0.00
122 5 0.01
123 151 0.39
124 142 0.36
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (123 bp):
TCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGA
AATGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAGC
Found at i:7655 original size:19 final size:18
Alignment explanation
Indices: 7631--7691 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 18
7621 AGATGTATCA
7631 ATGCAATGCATGATCTGTT
1 ATGCAATGCATGAT-TGTT
*
7650 ATGCAAATG-ATG-TTCTT
1 ATGC-AATGCATGATTGTT
*
7667 ATG-AATGCATGAATGTT
1 ATGCAATGCATGATTGTT
7684 GATGCAAT
1 -ATGCAAT
7692 CTTCATTTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
15 4 0.12
16 3 0.09
17 9 0.26
18 4 0.12
19 10 0.29
20 4 0.12
ACGTcount: A:0.31, C:0.11, G:0.21, T:0.36
Consensus pattern (18 bp):
ATGCAATGCATGATTGTT
Found at i:8000 original size:22 final size:22
Alignment explanation
Indices: 7975--8025 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
7965 TAAAGCGTTT
7975 ATCTTTGAAAAGAGAATCTATC
1 ATCTTTGAAAAGAGAATCTATC
* * *
7997 ATCTTTGGAGAGTGAATCTATC
1 ATCTTTGAAAAGAGAATCTATC
8019 ATCTTTG
1 ATCTTTG
8026 TAGATGTAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (22 bp):
ATCTTTGAAAAGAGAATCTATC
Found at i:16748 original size:46 final size:49
Alignment explanation
Indices: 16681--16772 Score: 145
Period size: 46 Copynumber: 1.9 Consensus size: 49
16671 AGGTATAAAT
* *
16681 CCTAACCTCATGCTTTCTAGTTC-CATGC-TTTGTTT-GGAAAAATTAA
1 CCTAACCGCATGATTTCTAGTTCACATGCATTTGTTTAGGAAAAATTAA
16727 CCTAACCGCATGATTTCTAGTTCACATGCATTTGTTTAGGAAAAAT
1 CCTAACCGCATGATTTCTAGTTCACATGCATTTGTTTAGGAAAAAT
16773 AAAATAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
46 21 0.51
47 5 0.12
48 7 0.17
49 8 0.20
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (49 bp):
CCTAACCGCATGATTTCTAGTTCACATGCATTTGTTTAGGAAAAATTAA
Found at i:18060 original size:14 final size:14
Alignment explanation
Indices: 18037--18074 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
18027 TCTGTCTATA
*
18037 TGCAGAGATTT-TT
1 TGCAGGGATTTATT
18050 TCGCAGGGATTTATT
1 T-GCAGGGATTTATT
18065 TGCAGGGATT
1 TGCAGGGATT
18075 ACTTCCCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 1 0.05
14 18 0.82
15 3 0.14
ACGTcount: A:0.21, C:0.11, G:0.29, T:0.39
Consensus pattern (14 bp):
TGCAGGGATTTATT
Found at i:20277 original size:3 final size:3
Alignment explanation
Indices: 20271--20340 Score: 74
Period size: 3 Copynumber: 23.0 Consensus size: 3
20261 TTTTTATTAT
20271 TAA TAA TAA TAAA TAA TAA TAA TAA TAA -ATA TAA TAA TAA T-A TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA
*
20316 TAGA TTAA TAA TAA AAA TAA -AA TAA
1 TA-A -TAA TAA TAA TAA TAA TAA TAA
20341 AAACAAATAA
Statistics
Matches: 58, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
2 5 0.09
3 45 0.78
4 6 0.10
5 2 0.03
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:20309 original size:31 final size:31
Alignment explanation
Indices: 20271--20350 Score: 99
Period size: 33 Copynumber: 2.5 Consensus size: 31
20261 TTTTTATTAT
20271 TAATAATAATAAATAA-TAATAATAATAAATA
1 TAATAATAATAAATAATTAATAATAA-AAATA
20302 TAATAATAATATAATAGATTAATAATAAAAATA
1 TAATAATAATA-AATA-ATTAATAATAAAAATA
* * *
20335 AAATAAAAACAAATAA
1 TAATAATAATAAATAA
20351 AAACAAATGG
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
31 12 0.28
32 8 0.19
33 14 0.33
34 9 0.21
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.29
Consensus pattern (31 bp):
TAATAATAATAAATAATTAATAATAAAAATA
Found at i:20348 original size:10 final size:10
Alignment explanation
Indices: 20325--20358 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
20315 ATAGATTAAT
*
20325 AATAAAAATAA
1 AATAAAAA-CA
20336 AATAAAAACA
1 AATAAAAACA
20346 AATAAAAACA
1 AATAAAAACA
20356 AAT
1 AAT
20359 GGATAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 14 0.64
11 8 0.36
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (10 bp):
AATAAAAACA
Found at i:28155 original size:58 final size:59
Alignment explanation
Indices: 28019--28159 Score: 169
Period size: 58 Copynumber: 2.4 Consensus size: 59
28009 TCCTTAATTT
* * * *
28019 TTTTGAATATTCTAATTTCATTCCTAAATTATGACTTTCATTCTAAATTAGTTTTTAAAA
1 TTTTGAATATTCTAATTTCATCCCTAAACTATGACCTT-ATTCTAAATTAGTTTCTAAAA
* * * *
28079 TTTTGGACATTCTAATTTCATCCCTAAACTATGACACTT-TT-TAAATTGGTTTCTAAAG
1 TTTTGAATATTCTAATTTCATCCCTAAACTATGAC-CTTATTCTAAATTAGTTTCTAAAA
*
28137 TTTTGAATATTCTCATTTCATCC
1 TTTTGAATATTCTAATTTCATCC
28160 TGAATTTCAC
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
58 34 0.49
59 2 0.03
60 31 0.45
61 2 0.03
ACGTcount: A:0.30, C:0.16, G:0.07, T:0.48
Consensus pattern (59 bp):
TTTTGAATATTCTAATTTCATCCCTAAACTATGACCTTATTCTAAATTAGTTTCTAAAA
Found at i:28379 original size:60 final size:59
Alignment explanation
Indices: 28286--28452 Score: 160
Period size: 60 Copynumber: 2.8 Consensus size: 59
28276 GTATATACAT
* * * *
28286 ATAGTTTGAGATGGAATTGGAATGTTCAAAAAGTTTGGGGACCAATATAGAATGA-ATGTC
1 ATAGTTTGGGATGAAATTGAAATGTT-TAAAAGTTTGGGGACCAATATAGAATGATA-GTC
** * *
28346 ATAGTTTGGGGATGAAATTGAAATGTTTAAAAGTTTGGGGATTAGTTTAGAATGATAGTC
1 ATAGTTT-GGGATGAAATTGAAATGTTTAAAAGTTTGGGGACCAATATAGAATGATAGTC
* * * *
28406 ATGGTTTAGGGATGAAATT-AGAGTATTTAAAAGTTT-AGGACCAATAT
1 ATAGTTT-GGGATGAAATTGA-AATGTTTAAAAGTTTGGGGACCAATAT
28453 GAAATGAGGA
Statistics
Matches: 87, Mismatches: 17, Indels: 7
0.78 0.15 0.06
Matches are distributed among these distances:
59 7 0.08
60 63 0.72
61 17 0.20
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (59 bp):
ATAGTTTGGGATGAAATTGAAATGTTTAAAAGTTTGGGGACCAATATAGAATGATAGTC
Found at i:29212 original size:42 final size:41
Alignment explanation
Indices: 29127--29215 Score: 117
Period size: 42 Copynumber: 2.1 Consensus size: 41
29117 TTAATGAGCA
*
29127 CATGCATCTATGGGTACCCATCCATCCATCCATTTCTCCAT
1 CATGCATCTATGGGTACCCATCCATCCATCCATGTCTCCAT
* * *
29168 CATGCATCTATGGGTA-TCATGCACTGCCATCCATGTCTCTAT
1 CATGCATCTATGGGTACCCATCCA-T-CCATCCATGTCTCCAT
29210 CATGCA
1 CATGCA
29216 CAAATGTTGC
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
40 5 0.12
41 17 0.40
42 20 0.48
ACGTcount: A:0.22, C:0.33, G:0.13, T:0.31
Consensus pattern (41 bp):
CATGCATCTATGGGTACCCATCCATCCATCCATGTCTCCAT
Found at i:34887 original size:32 final size:31
Alignment explanation
Indices: 34851--34927 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
34841 CGGGGCCGTG
*
34851 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
34883 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
34914 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
34928 GTCACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:34910 original size:63 final size:63
Alignment explanation
Indices: 34804--34927 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
34794 CCCTAAGGGA
* * ** *
34804 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
34867 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
34928 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 50 0.96
ACGTcount: A:0.26, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:35819 original size:5 final size:5
Alignment explanation
Indices: 35809--35888 Score: 79
Period size: 5 Copynumber: 14.8 Consensus size: 5
35799 AACGGTCAAC
* *
35809 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
*
35858 GGTCG GGTCG GGTCAAT GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTC
35889 AGACCGGTCA
Statistics
Matches: 63, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
5 51 0.81
7 12 0.19
ACGTcount: A:0.07, C:0.21, G:0.51, T:0.20
Consensus pattern (5 bp):
GGTCG
Found at i:35846 original size:27 final size:22
Alignment explanation
Indices: 35802--35888 Score: 165
Period size: 22 Copynumber: 4.0 Consensus size: 22
35792 GAAAGTCAAC
35802 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
35824 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
35846 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
*
35868 GGTCAATGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
35889 AGACCGGTCA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 64 1.00
ACGTcount: A:0.09, C:0.22, G:0.49, T:0.20
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:35903 original size:9 final size:9
Alignment explanation
Indices: 35885--35983 Score: 90
Period size: 9 Copynumber: 10.3 Consensus size: 9
35875 GGTCGGGTCG
*
35885 GGTCAGACC
1 GGTCAAACC
35894 GGTCAAACC
1 GGTCAAACC
* *
35903 GATTCAGACC
1 G-GTCAAACC
35913 GGTCAAACC
1 GGTCAAACC
*
35922 GGTTCGAACC
1 GG-TCAAACC
*
35932 GGTTGAAACC
1 GG-TCAAACC
35942 GGTCAAACC
1 GGTCAAACC
35951 GGTCAGAACC
1 GGTCA-AACC
*
35961 GGTTGAAAACC
1 GG-T-CAAACC
35972 GGTCAAACC
1 GGTCAAACC
35981 GGT
1 GGT
35984 TTCCAGCAGC
Statistics
Matches: 74, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
9 36 0.49
10 30 0.41
11 7 0.09
12 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:35909 original size:19 final size:19
Alignment explanation
Indices: 35887--35984 Score: 101
Period size: 19 Copynumber: 5.1 Consensus size: 19
35877 TCGGGTCGGG
*
35887 TCAGACCGGTCAAACCGAT
1 TCAGACCGGTCAAACCGGT
35906 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
35925 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
*
35944 TCAAACCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
* *
35964 TGAAAACCGGTCAAACCGGT
1 T-CAGACCGGTCAAACCGGT
35984 T
1 T
35985 TCCAGCAGCC
Statistics
Matches: 68, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
18 3 0.04
19 38 0.56
20 17 0.25
21 10 0.15
ACGTcount: A:0.30, C:0.29, G:0.26, T:0.16
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:35942 original size:29 final size:31
Alignment explanation
Indices: 35910--35984 Score: 129
Period size: 29 Copynumber: 2.5 Consensus size: 31
35900 ACCGATTCAG
35910 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
35939 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
35969 ACCGGTCAAACCGGTT
1 ACCGGTCAAACCGGTT
35985 TCCAGCAGCC
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.56
30 16 0.37
31 1 0.02
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.16
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:42253 original size:32 final size:31
Alignment explanation
Indices: 42215--42291 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
42205 CGGGGTCGTG
*
42215 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
42247 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
42278 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
42292 GTCACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:43204 original size:27 final size:27
Alignment explanation
Indices: 43174--43264 Score: 128
Period size: 27 Copynumber: 3.2 Consensus size: 27
43164 AACGGTCAAC
43174 GGTCAACGGTCGGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCGGGTCG
43201 GGTCAACGGTCGGGTCGGGTCGGGTCGGGTCG
1 GGTCAA----C-GGTCGGGTCGGGTCGGGTCG
*
43233 GGTCAACGGTCGGGTCGGGTCGGGTCA
1 GGTCAACGGTCGGGTCGGGTCGGGTCG
43260 GGTCA
1 GGTCA
43265 GACCGGTCAA
Statistics
Matches: 58, Mismatches: 1, Indels: 10
0.84 0.01 0.14
Matches are distributed among these distances:
27 30 0.52
28 1 0.02
31 1 0.02
32 26 0.45
ACGTcount: A:0.09, C:0.22, G:0.51, T:0.19
Consensus pattern (27 bp):
GGTCAACGGTCGGGTCGGGTCGGGTCG
Found at i:43222 original size:32 final size:32
Alignment explanation
Indices: 43167--43263 Score: 158
Period size: 32 Copynumber: 3.0 Consensus size: 32
43157 GAAAGTCAAC
*
43167 GGTCAACGGTCAACGGTCGGGTCGGGTCGGGTCG
1 GGTCAACGGTC--GGGTCGGGTCGGGTCGGGTCG
43201 GGTCAACGGTCGGGTCGGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCGGGTCGGGTCG
*
43233 GGTCAACGGTCGGGTCGGGTCGGGTCAGGTC
1 GGTCAACGGTCGGGTCGGGTCGGGTCGGGTC
43264 AGACCGGTCA
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
32 50 0.82
34 11 0.18
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.19
Consensus pattern (32 bp):
GGTCAACGGTCGGGTCGGGTCGGGTCGGGTCG
Found at i:43265 original size:5 final size:5
Alignment explanation
Indices: 43181--43263 Score: 103
Period size: 5 Copynumber: 15.8 Consensus size: 5
43171 AACGGTCAAC
*
43181 GGTCG GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCG GGTCG
1 GGTCG GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTCG GGTCG
* *
43233 GGTCAAC GGTCG GGTCG GGTCG GGTCA GGTC
1 GGTC--G GGTCG GGTCG GGTCG GGTCG GGTC
43264 AGACCGGTCA
Statistics
Matches: 69, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
5 61 0.88
7 8 0.12
ACGTcount: A:0.06, C:0.22, G:0.53, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:43278 original size:9 final size:9
Alignment explanation
Indices: 43260--43339 Score: 79
Period size: 9 Copynumber: 8.3 Consensus size: 9
43250 GGTCGGGTCA
*
43260 GGTCAGACC
1 GGTCAAACC
43269 GGTCAAACC
1 GGTCAAACC
*
43278 GGTTCGAACC
1 GG-TCAAACC
*
43288 GGTTGAAACC
1 GG-TCAAACC
43298 GGTCAAACC
1 GGTCAAACC
43307 GGTCAGAACC
1 GGTCA-AACC
*
43317 GGTTGAAAACC
1 GG-T-CAAACC
43328 GGTCAAACC
1 GGTCAAACC
43337 GGT
1 GGT
43340 TTCCAGCAGC
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
9 29 0.48
10 23 0.38
11 7 0.12
12 1 0.02
ACGTcount: A:0.29, C:0.28, G:0.29, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:43298 original size:29 final size:31
Alignment explanation
Indices: 43266--43340 Score: 129
Period size: 29 Copynumber: 2.5 Consensus size: 31
43256 GTCAGGTCAG
43266 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
43295 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
43325 ACCGGTCAAACCGGTT
1 ACCGGTCAAACCGGTT
43341 TCCAGCAGCC
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.56
30 16 0.37
31 1 0.02
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.16
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:43328 original size:21 final size:20
Alignment explanation
Indices: 43266--43340 Score: 77
Period size: 19 Copynumber: 3.8 Consensus size: 20
43256 GTCAGGTCAG
43266 ACCGGTCAAACCGGTTCG--A
1 ACCGGTCAAACCGGTT-GAAA
* *
43285 ACCGGTTGAAACCGG-T-CAA
1 ACCGG-TCAAACCGGTTGAAA
43304 ACCGGTCAGAACCGGTTGAAA
1 ACCGGTCA-AACCGGTTGAAA
43325 ACCGGTCAAACCGGTT
1 ACCGGTCAAACCGGTT
43341 TCCAGCAGCC
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
18 2 0.04
19 18 0.38
20 17 0.36
21 10 0.21
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.16
Consensus pattern (20 bp):
ACCGGTCAAACCGGTTGAAA
Found at i:44243 original size:31 final size:31
Alignment explanation
Indices: 44169--44257 Score: 90
Period size: 31 Copynumber: 2.9 Consensus size: 31
44159 CATCTACTTT
* * * *
44169 AATTTAATTTTTAAACTTTAAATAAAATATT
1 AATTTAATTATTAAATTTTAATTAAAATATC
**
44200 AATTTCTTTATTAAATTTTAATTAAAATATC
1 AATTTAATTATTAAATTTTAATTAAAATATC
* * *
44231 AATTTAACTATTAGATCTT-ATTAAAAT
1 AATTTAATTATTAAATTTTAATTAAAAT
44258 CTACAGTCTT
Statistics
Matches: 47, Mismatches: 11, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
30 8 0.17
31 39 0.83
ACGTcount: A:0.45, C:0.06, G:0.01, T:0.48
Consensus pattern (31 bp):
AATTTAATTATTAAATTTTAATTAAAATATC
Found at i:46189 original size:111 final size:111
Alignment explanation
Indices: 45995--46327 Score: 603
Period size: 111 Copynumber: 3.0 Consensus size: 111
45985 TGGAAATCAT
*
45995 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
46060 TATTTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
* *
46106 ATATCTCGACATTTTGCTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
46171 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
* *
46217 ATATCTCGACACTTTGCTGATACGGTGACATTTTAACATTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
46282 TAATTAGTTGATTTATTTAATGCATTATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
46328 TTTTTGTAAT
Statistics
Matches: 213, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 213 1.00
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:54360 original size:61 final size:60
Alignment explanation
Indices: 54280--54407 Score: 154
Period size: 60 Copynumber: 2.1 Consensus size: 60
54270 GTATATAAAT
* *
54280 ATAGTTTGGGATGAAAATTGGAATAT-TCAAAAAGTTTAGGGATC-AATTTAGAATGAAAGTC
1 ATAGTTTGGGATGAAAATT-GAA-ATGTCAAAAAGTTTAAGGA-CAAAATTAGAATGAAAGTC
* * *
54341 ATAGTTTGGGGATG-GAATTGAAATGTCTAAAAGTTTAAGGACAAAATTAGAATGATAGTC
1 ATAGTTT-GGGATGAAAATTGAAATGTCAAAAAGTTTAAGGACAAAATTAGAATGAAAGTC
54401 ATAGTTT
1 ATAGTTT
54408 ATAGATAAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
59 3 0.05
60 39 0.66
61 11 0.19
62 6 0.10
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.32
Consensus pattern (60 bp):
ATAGTTTGGGATGAAAATTGAAATGTCAAAAAGTTTAAGGACAAAATTAGAATGAAAGTC
Found at i:57913 original size:31 final size:30
Alignment explanation
Indices: 57827--57915 Score: 92
Period size: 31 Copynumber: 3.0 Consensus size: 30
57817 AAAATTGAAT
57827 ACTTTAGGTA-TCTATTTTGA-CAAAAAAAA
1 ACTTTAGGTACT-TATTTTGACCAAAAAAAA
* * ** * *
57856 ACTTTAGGCACCTATTTCAACTAAAAATATA
1 ACTTTAGGTACTTATTTTGACCAAAAA-AAA
57887 ACTTTAGGTACTTATTTTGACCAAAAAAA
1 ACTTTAGGTACTTATTTTGACCAAAAAAA
57916 CTTCAAGTAC
Statistics
Matches: 45, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
29 15 0.33
30 6 0.13
31 24 0.53
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.34
Consensus pattern (30 bp):
ACTTTAGGTACTTATTTTGACCAAAAAAAA
Found at i:58139 original size:60 final size:60
Alignment explanation
Indices: 57996--58176 Score: 213
Period size: 60 Copynumber: 3.0 Consensus size: 60
57986 GCATCATATG
* *
57996 TCCCCAAATTATGACCCTCATTCTAAATTAGTCCTTAAAC-TTTAAACATTCCAATTTCA
1 TCCCCAAACTATGACTCTCATTCTAAATTAGTCCTTAAACTTTTAAACATTCCAATTTCA
* * * * * * **
58055 GCCTCAAACTATGACTCTAATTCTAAATTAGTACTTAAACTTTTGAATATTTTAATTTCA
1 TCCCCAAACTATGACTCTCATTCTAAATTAGTCCTTAAACTTTTAAACATTCCAATTTCA
* * * *
58115 TCCCCAAACTATGAATCTCATTCTAGATTAGTCCCTAAACTTTTAGATC-TTCCAATTTCA
1 TCCCCAAACTATGACTCTCATTCTAAATTAGTCCTTAAACTTTTA-AACATTCCAATTTCA
58175 TC
1 TC
58177 TTCATCCAAA
Statistics
Matches: 98, Mismatches: 22, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
59 34 0.35
60 63 0.64
61 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.06, T:0.38
Consensus pattern (60 bp):
TCCCCAAACTATGACTCTCATTCTAAATTAGTCCTTAAACTTTTAAACATTCCAATTTCA
Found at i:64214 original size:23 final size:21
Alignment explanation
Indices: 64177--64248 Score: 67
Period size: 20 Copynumber: 3.4 Consensus size: 21
64167 AAAAATGTAA
*
64177 AAATAAAT-TTTATAATTAAT
1 AAATAACTATTTATAATTAAT
64197 AAATAAACCTATTTATAATTAAT
1 AAAT-AA-CTATTTATAATTAAT
* * *
64220 -CATTACTATATATAATTAAT
1 AAATAACTATTTATAATTAAT
64240 AAATGAACT
1 AAAT-AACT
64249 TTAAAAAATC
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
20 18 0.44
21 5 0.12
22 6 0.15
23 12 0.29
ACGTcount: A:0.51, C:0.07, G:0.01, T:0.40
Consensus pattern (21 bp):
AAATAACTATTTATAATTAAT
Done.