Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005425.1 Hibiscus syriacus cultivar Beakdansim tig00012441_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: 61413
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:2093 original size:9 final size:9
Alignment explanation
Indices: 2081--2114 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
2071 TATTATTTTG
2081 TATTTAATT
1 TATTTAATT
*
2090 TATTTAA-G
1 TATTTAATT
2098 TATTTAATT
1 TATTTAATT
2107 TATTTAAT
1 TATTTAAT
2115 ATTTTTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (9 bp):
TATTTAATT
Found at i:2102 original size:17 final size:17
Alignment explanation
Indices: 2080--2118 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
2070 TTATTATTTT
2080 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
2097 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
2114 -TATTT
1 GTATTT
2119 TTTTTAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:2124 original size:16 final size:16
Alignment explanation
Indices: 2064--2136 Score: 58
Period size: 16 Copynumber: 4.6 Consensus size: 16
2054 ATATTTTATT
* *
2064 ATATTTTTATTATTTT
1 ATATTTTTTTTATTTA
* **
2080 GTATTTAATTTATTTA
1 ATATTTTTTTTATTTA
**
2096 AGTATTTAATTTATTTA
1 A-TATTTTTTTTATTTA
*
2113 ATATTTTTTTTAATTA
1 ATATTTTTTTTATTTA
2129 AT-TTTTTT
1 ATATTTTTT
2137 GCAGATATAA
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
15 6 0.13
16 25 0.53
17 16 0.34
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
ATATTTTTTTTATTTA
Found at i:6967 original size:3 final size:3
Alignment explanation
Indices: 6959--7038 Score: 119
Period size: 3 Copynumber: 27.3 Consensus size: 3
6949 CCATTTTAAA
* * *
6959 ATT ATT ATT ATT ATT ATT ATT ATT ATA ATT ATA AGT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
7007 ATT ATT ATT A-T ATT ATT ATT A-T ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
7039 ATAAATAATT
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
2 4 0.06
3 65 0.94
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:8289 original size:22 final size:22
Alignment explanation
Indices: 8264--8305 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
8254 TAGTTTGATA
* *
8264 ATTTTTATTTAATATATTTTGC
1 ATTTTAATTTAATAAATTTTGC
*
8286 ATTTTAATTTTATAAATTTT
1 ATTTTAATTTAATAAATTTT
8306 AATTTCTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (22 bp):
ATTTTAATTTAATAAATTTTGC
Found at i:8398 original size:23 final size:22
Alignment explanation
Indices: 8340--8406 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 22
8330 TTATTTGCAA
8340 TATTATTTTATTATTACTTT-T
1 TATTATTTTATTATTACTTTCT
*
8361 TATATATTTAAATTATTACTTTCGT
1 TAT-TATTT-TATTATTACTTTC-T
*
8386 TATTATTTTATTATTATTTTC
1 TATTATTTTATTATTACTTTC
8407 ATCTTAGTCA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
21 3 0.08
22 5 0.13
23 22 0.56
24 5 0.13
25 4 0.10
ACGTcount: A:0.27, C:0.06, G:0.01, T:0.66
Consensus pattern (22 bp):
TATTATTTTATTATTACTTTCT
Found at i:8687 original size:23 final size:22
Alignment explanation
Indices: 8661--8706 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
8651 ATATTTAAAA
8661 ATAAATAAATAAATATCCTACTT
1 ATAAATAAATAAATAT-CTACTT
** *
8684 ATAAATGTATATATATCTACTT
1 ATAAATAAATAAATATCTACTT
8706 A
1 A
8707 GTTTTTATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (22 bp):
ATAAATAAATAAATATCTACTT
Found at i:8854 original size:2 final size:2
Alignment explanation
Indices: 8847--8884 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
8837 AAAACTCTAA
8847 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8885 CCTTATAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8854 original size:155 final size:152
Alignment explanation
Indices: 8557--8852 Score: 341
Period size: 155 Copynumber: 1.9 Consensus size: 152
8547 TTTTATTTAA
* * *
8557 ATTATTTTTTAGGAAAGATTATCACATTTTCAATATTTATTTATTTTTTAATATTAAGAAAGGAC
1 ATTATTTTTTAGGAAAGATTATCACATTTTCAATATATATTTATTTATTAATATTAAGAAAAGAC
*
8622 AGTCTTAATATAACTAGATGTCTATTCTGATATTTAAAAATAAATAAATAAATATCCTACTTATA
66 AGTCTTAATATAACTAGATGTCTATTCTGATATTT----ATAAATAAATAAATATCCTACTTAAA
*
8687 AATGTATATATATCTACTTAGTTTTT
127 AATCTATATATATCTACTTAGTTTTT
* * * *
8713 ATTATTTTTTAGGAAA-ATTATTATATTCTT-ATTA-ATATTTATTTATTAATATTAAAGAAAAT
1 ATTATTTTTTAGGAAAGATTATCACATT-TTCAATATATATTTATTTATTAATATT-AAGAAAAG
* * * *
8775 ACAGTCTTAA-AGTAACTAGATGTCTTTTTCTGATATTT-TAAATAAATAAATGTCTTATTTACA
64 ACAGTCTTAATA-TAACTAGATGTC-TATTCTGATATTTATAAATAAATAAATATCCTACTTA-A
*
8838 AAACTCTAAATATAT
126 AAA-TCTATATATAT
8853 ATATATATAT
Statistics
Matches: 120, Mismatches: 14, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
151 20 0.17
152 3 0.03
153 9 0.08
154 18 0.15
155 40 0.33
156 30 0.25
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.45
Consensus pattern (152 bp):
ATTATTTTTTAGGAAAGATTATCACATTTTCAATATATATTTATTTATTAATATTAAGAAAAGAC
AGTCTTAATATAACTAGATGTCTATTCTGATATTTATAAATAAATAAATATCCTACTTAAAAATC
TATATATATCTACTTAGTTTTT
Found at i:11242 original size:49 final size:49
Alignment explanation
Indices: 11189--11282 Score: 188
Period size: 49 Copynumber: 1.9 Consensus size: 49
11179 ACTATGGCCA
11189 AGAACAAGACATTGAAGAAATGTTTAGATGATTATGGAGATCTTGTACG
1 AGAACAAGACATTGAAGAAATGTTTAGATGATTATGGAGATCTTGTACG
11238 AGAACAAGACATTGAAGAAATGTTTAGATGATTATGGAGATCTTG
1 AGAACAAGACATTGAAGAAATGTTTAGATGATTATGGAGATCTTG
11283 AACATAAAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.39, C:0.07, G:0.24, T:0.29
Consensus pattern (49 bp):
AGAACAAGACATTGAAGAAATGTTTAGATGATTATGGAGATCTTGTACG
Found at i:11685 original size:21 final size:20
Alignment explanation
Indices: 11661--11713 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
11651 TTTTTCATTA
11661 CATTTGCATTTTT-TATGTTT
1 CATTTGCATTTTTATAT-TTT
11681 GCATTTGCATTTTTATATTTT
1 -CATTTGCATTTTTATATTTT
*
11702 CATTTACATTTT
1 CATTTGCATTTT
11714 CATTTTATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 11 0.37
21 16 0.53
22 3 0.10
ACGTcount: A:0.19, C:0.11, G:0.08, T:0.62
Consensus pattern (20 bp):
CATTTGCATTTTTATATTTT
Found at i:11695 original size:20 final size:20
Alignment explanation
Indices: 11661--11713 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
11651 TTTTTCATTA
*
11661 CATTTGCATTTTTTATGTTTG
1 CATTTGCA-TTTTTATATTTG
*
11682 CATTTGCATTTTTATATTTT
1 CATTTGCATTTTTATATTTG
*
11702 CATTTACATTTT
1 CATTTGCATTTT
11714 CATTTTATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 21 0.72
21 8 0.28
ACGTcount: A:0.19, C:0.11, G:0.08, T:0.62
Consensus pattern (20 bp):
CATTTGCATTTTTATATTTG
Found at i:17316 original size:22 final size:22
Alignment explanation
Indices: 17286--17345 Score: 86
Period size: 22 Copynumber: 2.7 Consensus size: 22
17276 TCTCCATCTA
*
17286 CATTCTTCAAAGATGATAGATT
1 CATTATTCAAAGATGATAGATT
17308 CATTATTCAAAGATGATAGATT
1 CATTATTCAAAGATGATAGATT
*
17330 C-TCTTTTCAAAGATGA
1 CAT-TATTCAAAGATGA
17346 AAGCTTTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 1 0.03
22 34 0.97
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (22 bp):
CATTATTCAAAGATGATAGATT
Found at i:18093 original size:45 final size:46
Alignment explanation
Indices: 18029--18119 Score: 141
Period size: 45 Copynumber: 2.0 Consensus size: 46
18019 CTATTTCCCA
*
18029 CATCTGTAAGCCCCTCAGTGCATGATGTTTTC-AAAGCCTTCGGGT
1 CATCTGTAAGCCCCTCAGTGCAGGATGTTTTCAAAAGCCTTCGGGT
18074 CATCTGTAAG-CCCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGG
1 CATCTGTAAGCCCCT-CAGTGCAGGATGTTTTC-AAAAGCCTTCGGG
18120 AGCTTTTTGA
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
44 4 0.10
45 26 0.62
47 12 0.29
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.29
Consensus pattern (46 bp):
CATCTGTAAGCCCCTCAGTGCAGGATGTTTTCAAAAGCCTTCGGGT
Found at i:18187 original size:76 final size:76
Alignment explanation
Indices: 18051--18420 Score: 584
Period size: 76 Copynumber: 4.9 Consensus size: 76
18041 CCTCAGTGCA
* *
18051 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTACAGTGCAGGATGTTTTCAAAAAGCCTT
1 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTT
18116 CGGGAGCTTTT
66 CGGGAGCTTTT
* * *
18127 TGATATTTTTAAAGCCTTCGGGTCATCTGTAAGCCCTACAGTGCAGGACGTTTTCAAAAAGCCTT
1 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTT
18192 CGGGAGCTTTT
66 CGGGAGCTTTT
* *
18203 TGATA-TTTCAAAGCCTTCGGGTCATCTTTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTT
1 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTT
18267 CGGGAGCTTTT
66 CGGGAGCTTTT
* ** * *
18278 TGATATTTTCAAAACCTTCGGGTCATCCATAAAACCTACAGTGCAGGATGTTTTTAAAAAGCCTT
1 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTT
18343 CGGGAGCTTTT
66 CGGGAGCTTTT
* * *
18354 TGATATTTTCAAAGCCTTCGGGTCACCTGTAAGACCTTCAGTGCATGATGTTTTC-AAAA-CCTT
1 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTT
18417 CGGG
66 CGGG
18421 TCATCCATAA
Statistics
Matches: 271, Mismatches: 22, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
74 8 0.03
75 74 0.27
76 189 0.70
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (76 bp):
TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTT
CGGGAGCTTTT
Found at i:18331 original size:151 final size:152
Alignment explanation
Indices: 18051--18420 Score: 593
Period size: 151 Copynumber: 2.5 Consensus size: 152
18041 CCTCAGTGCA
* * *
18051 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTACAGTGCAGGATGTTTTCAAAAAGCCTT
1 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTT
* * ** **
18116 CGGGAGCTTTTTGATATTTTTAAAGCCTTCGGGTCATCTGTAAGCCCTACAGTGCAGGACGTTTT
66 CGGGAGCTTTTTGATATTTTCAAAACCTTCGGGTCATCCATAAAACCTACAGTGCAGGACGTTTT
18181 CAAAAAGCCTTCGGGAGCTTTT
131 CAAAAAGCCTTCGGGAGCTTTT
*
18203 TGATA-TTTCAAAGCCTTCGGGTCATCTTTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTT
1 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTT
*
18267 CGGGAGCTTTTTGATATTTTCAAAACCTTCGGGTCATCCATAAAACCTACAGTGCAGGATGTTTT
66 CGGGAGCTTTTTGATATTTTCAAAACCTTCGGGTCATCCATAAAACCTACAGTGCAGGACGTTTT
*
18332 TAAAAAGCCTTCGGGAGCTTTT
131 CAAAAAGCCTTCGGGAGCTTTT
* *
18354 TGATATTTTCAAAGCCTTCGGGTCACCTGTAAGACCTTCAGTGCATGATGTTTTC-AAAA-CCTT
1 TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTT
18417 CGGG
66 CGGG
18421 TCATCCATAA
Statistics
Matches: 202, Mismatches: 15, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
150 8 0.04
151 144 0.71
152 50 0.25
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (152 bp):
TGATATTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTT
CGGGAGCTTTTTGATATTTTCAAAACCTTCGGGTCATCCATAAAACCTACAGTGCAGGACGTTTT
CAAAAAGCCTTCGGGAGCTTTT
Found at i:18410 original size:45 final size:45
Alignment explanation
Indices: 18354--18467 Score: 158
Period size: 45 Copynumber: 2.5 Consensus size: 45
18344 GGGAGCTTTT
* * *
18354 TGATATTTTCAAAGCCTTCGGGTCA-CCTGTAAGACCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCC-ATAAGACCTACAGTGCA
*
18399 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCCATAAGACCTACAGTGCA
18444 TGATGTTTTCAAAAAGCCTTCGGG
1 TGATGTTTTC--AAAGCCTTCGGG
18468 AGCTTTTTGA
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
45 48 0.79
46 2 0.03
47 11 0.18
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (45 bp):
TGATGTTTTCAAAGCCTTCGGGTCATCCATAAGACCTACAGTGCA
Found at i:18430 original size:121 final size:121
Alignment explanation
Indices: 18278--18566 Score: 424
Period size: 121 Copynumber: 2.4 Consensus size: 121
18268 GGGAGCTTTT
* * * *
18278 TGATATTTTCAAAACCTTCGGGTCATCCATAAAACCTACAGTGCAGGATGTTTTTAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAAGATGTTTTCAAAAAGCCTT
* *
18343 CGGGAGCTTTTTGATATTTTCAAAGCCTTCGGGTCACCTGTAAGACCTTCAGTGCA
66 CGGGAGCTTTTTGATATTTTCAAAGCCTTCGGGTCACCTGTAAGACCTACAATGCA
*
18399 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAAGATGTTTTCAAAAAGCCTT
* *
18464 CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAATGCA
66 CGGGAGCTTTTTGATATTTTCAAAGCCTTCGGGTCACCTGTAAGACCTACAATGCA
* * * *
18520 AGATG--AT-AAGACC-TCAGGGCCATCCATAAGACCTACAGTGCAAGATG
1 TGATGTTTTCAAAACCTTC-GGGTCATCCATAAGACCTACAGTGCAAGATG
18567 AGGTTTTAAC
Statistics
Matches: 154, Mismatches: 13, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
117 2 0.01
118 34 0.22
119 1 0.01
121 117 0.76
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (121 bp):
TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTGCAAGATGTTTTCAAAAAGCCTT
CGGGAGCTTTTTGATATTTTCAAAGCCTTCGGGTCACCTGTAAGACCTACAATGCA
Found at i:18717 original size:3 final size:3
Alignment explanation
Indices: 18709--18761 Score: 81
Period size: 3 Copynumber: 18.0 Consensus size: 3
18699 TATAAATTTG
* *
18709 TTA TTA TTA TTA TTA TTA TAA GTA TTA TTA TTA TTA TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
18756 TTA TTA
1 TTA TTA
18762 ATAAAAAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
2 2 0.04
3 43 0.96
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:19926 original size:22 final size:22
Alignment explanation
Indices: 19901--19942 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
19891 TAGTTTGATA
* *
19901 ATTTTTATTTAATATATTTTGC
1 ATTTTAATTTAATAAATTTTGC
*
19923 ATTTTAATTTTATAAATTTT
1 ATTTTAATTTAATAAATTTT
19943 AATTTCTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (22 bp):
ATTTTAATTTAATAAATTTTGC
Found at i:20035 original size:23 final size:22
Alignment explanation
Indices: 19977--20043 Score: 71
Period size: 23 Copynumber: 3.0 Consensus size: 22
19967 TTATTTGCAA
*
19977 TATTATTTTATTATTACTTTTG
1 TATTATTTTATTATTACTTTCG
* * *
19999 AAATATTTAAATTATTACTTTCG
1 TATTATTT-TATTATTACTTTCG
*
20022 TTATTATTTTATTATTATTTTC
1 -TATTATTTTATTATTACTTTC
20044 ATCTTAGTCA
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
22 6 0.17
23 23 0.66
24 6 0.17
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.63
Consensus pattern (22 bp):
TATTATTTTATTATTACTTTCG
Found at i:20060 original size:2 final size:2
Alignment explanation
Indices: 20053--20119 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
20043 CATCTTAGTC
20053 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20095 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 A
20120 AATAATAATA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20219 original size:151 final size:152
Alignment explanation
Indices: 20064--20369 Score: 336
Period size: 151 Copynumber: 2.0 Consensus size: 152
20054 TATATATATA
* * * *
20064 TATATATATATA--TATATATATATATATATATATATATATATATA-TATATATATAT-AAATAA
1 TATATATATATACTTATAT-TATATATAAAT-TAT-TATAT-TATAGGAGAGAT-TATCAAATAA
* * * *
20125 T-AATATTTATTTATTTTTTAATATTAAGAATGGGCAGTCTTAATATAACTAGATGTCTTATTCT
61 TAAATATCTATTTATTTTTTAATATTAAGAAAGGGCAATCTTAATATAACTAGATGTCCTATTCT
**
20189 GGTA-TTTAAAATAAATAAATAAAAAT
126 AATATTTTAAAATAAATAAATAAAAAT
* * * * * * * * **
20215 TATATATATTTACTTTTATTTTATTTAAATTATTTTCTTTTAGGAGAGATTATCACATTTTAAAT
1 TATATATATATACTTATATTATATATAAATTATTATATTATAGGAGAGATTATCAAATAATAAAT
20280 ATCTATTTATTTTTTAATATTAAGAAAGGGCAATCTTAATATAACTAGATGTCCTATTCTAATAT
66 ATCTATTTATTTTTTAATATTAAGAAAGGGCAATCTTAATATAACTAGATGTCCTATTCTAATAT
*
20345 TTTAAAATAAATAAATAAATAT
131 TTTAAAATAAATAAATAAAAAT
20367 TAT
1 TAT
20370 GCTTATAAAT
Statistics
Matches: 128, Mismatches: 21, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
149 6 0.05
150 11 0.09
151 75 0.59
152 32 0.25
153 4 0.03
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.46
Consensus pattern (152 bp):
TATATATATATACTTATATTATATATAAATTATTATATTATAGGAGAGATTATCAAATAATAAAT
ATCTATTTATTTTTTAATATTAAGAAAGGGCAATCTTAATATAACTAGATGTCCTATTCTAATAT
TTTAAAATAAATAAATAAAAAT
Found at i:30369 original size:13 final size:13
Alignment explanation
Indices: 30351--30384 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
30341 TATTTAGTTG
*
30351 TTTATTATACTTT
1 TTTATTATAATTT
*
30364 TTTATTGTAATTT
1 TTTATTATAATTT
30377 TTTATTAT
1 TTTATTAT
30385 TTATCATTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (13 bp):
TTTATTATAATTT
Found at i:30440 original size:33 final size:35
Alignment explanation
Indices: 30398--30484 Score: 108
Period size: 33 Copynumber: 2.5 Consensus size: 35
30388 TCATTTAATA
*
30398 TTTACTTTATTTTGTTAATA-TGGTTGGA-TTTTT
1 TTTAATTTATTTTGTTAATATTGGTTGGACTTTTT
*
30431 TTTAATTTATTTTGTTAA-ATTTGTTGGACTTTTT
1 TTTAATTTATTTTGTTAATATTGGTTGGACTTTTT
* *
30465 GTTAATGTATTTTGGTTAAT
1 TTTAATTTATTTT-GTTAAT
30485 TTTGTTTATT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
32 1 0.02
33 24 0.52
34 16 0.35
35 5 0.11
ACGTcount: A:0.21, C:0.02, G:0.15, T:0.62
Consensus pattern (35 bp):
TTTAATTTATTTTGTTAATATTGGTTGGACTTTTT
Found at i:30470 original size:34 final size:33
Alignment explanation
Indices: 30403--30490 Score: 106
Period size: 34 Copynumber: 2.6 Consensus size: 33
30393 TAATATTTAC
* *
30403 TTTATTTTGTT-AATATGGTTGGATTTTTTTTAA
1 TTTATTTTGTTAAAT-TTGTTGGATTTTTGTTAA
30436 TTTATTTTGTTAAATTTGTTGGACTTTTTGTTAA
1 TTTATTTTGTTAAATTTGTTGGA-TTTTTGTTAA
* *
30470 TGTATTTTGGTTAATTTTGTT
1 TTTATTTT-GTTAAATTTGTT
30491 TATTACTATT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
33 18 0.38
34 19 0.40
35 11 0.23
ACGTcount: A:0.19, C:0.01, G:0.16, T:0.64
Consensus pattern (33 bp):
TTTATTTTGTTAAATTTGTTGGATTTTTGTTAA
Found at i:30520 original size:35 final size:33
Alignment explanation
Indices: 30481--30565 Score: 82
Period size: 35 Copynumber: 2.5 Consensus size: 33
30471 GTATTTTGGT
*
30481 TAATTTTGTT-TATTACTATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAATA-C--TTATTG
*
30516 TAATTTGGTTATCATTTACCATTTAATACTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATACTTATTG
* *
30551 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
30566 TAAAATTATA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.57
36 1 0.02
37 2 0.05
38 12 0.29
ACGTcount: A:0.27, C:0.07, G:0.11, T:0.55
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATACTTATTG
Found at i:33543 original size:16 final size:16
Alignment explanation
Indices: 33518--33548 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
33508 ATATTTTTCA
*
33518 AATAATTATAATAAAT
1 AATAAGTATAATAAAT
33534 AATAAGTATAATAAA
1 AATAAGTATAATAAA
33549 AAAACTTATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
AATAAGTATAATAAAT
Found at i:36242 original size:2 final size:2
Alignment explanation
Indices: 36235--36275 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
36225 AAATTATTTC
36235 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
36276 GTTAGTTAAG
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:39706 original size:2 final size:2
Alignment explanation
Indices: 39699--39747 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
39689 AAGTGAAGAA
39699 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39741 AT AT AT A
1 AT AT AT A
39748 AAGAATATCG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:40694 original size:15 final size:17
Alignment explanation
Indices: 40676--40708 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
40666 TTTTTTTTTT
40676 TTAAATT-TAAG-TAGA
1 TTAAATTGTAAGATAGA
40691 TTAAATTGTAAGATAGA
1 TTAAATTGTAAGATAGA
40708 T
1 T
40709 AAAAATACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 4 0.25
17 5 0.31
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.39
Consensus pattern (17 bp):
TTAAATTGTAAGATAGA
Found at i:41380 original size:23 final size:24
Alignment explanation
Indices: 41336--41382 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
41326 GGACTGGAGA
41336 TAATCTAAATAATTATATATATTT
1 TAATCTAAATAATTATATATATTT
*
41360 TAATTTAAA-AATTAATCATATAT
1 TAATCTAAATAATT-AT-ATATAT
41383 ATTTTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 10 0.50
25 6 0.30
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (24 bp):
TAATCTAAATAATTATATATATTT
Found at i:41650 original size:26 final size:26
Alignment explanation
Indices: 41601--41651 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
41591 TTTTTAAGAT
**
41601 ACATGACATCAATTAATTGGTTGAAA
1 ACATGACATCAATTAATTAATTGAAA
* *
41627 ACATGATATCAATTGATTAATTGAA
1 ACATGACATCAATTAATTAATTGAA
41652 GGTTATACAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (26 bp):
ACATGACATCAATTAATTAATTGAAA
Found at i:44496 original size:83 final size:83
Alignment explanation
Indices: 44357--44523 Score: 334
Period size: 83 Copynumber: 2.0 Consensus size: 83
44347 GCCACATGCA
44357 TCCGCCATTGTTATGTAGTGTGGTTAATAAGACCGCAAGTGCTCCTCTAGAGAGCCACGTACATC
1 TCCGCCATTGTTATGTAGTGTGGTTAATAAGACCGCAAGTGCTCCTCTAGAGAGCCACGTACATC
44422 CGCTATTGCTATATAGTT
66 CGCTATTGCTATATAGTT
44440 TCCGCCATTGTTATGTAGTGTGGTTAATAAGACCGCAAGTGCTCCTCTAGAGAGCCACGTACATC
1 TCCGCCATTGTTATGTAGTGTGGTTAATAAGACCGCAAGTGCTCCTCTAGAGAGCCACGTACATC
44505 CGCTATTGCTATATAGTT
66 CGCTATTGCTATATAGTT
44523 T
1 T
44524 GATTAATAGA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 84 1.00
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.32
Consensus pattern (83 bp):
TCCGCCATTGTTATGTAGTGTGGTTAATAAGACCGCAAGTGCTCCTCTAGAGAGCCACGTACATC
CGCTATTGCTATATAGTT
Found at i:45088 original size:3 final size:3
Alignment explanation
Indices: 45080--45112 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
45070 CCCATGTTAT
45080 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
45113 TGCATGTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:46362 original size:20 final size:20
Alignment explanation
Indices: 46337--46374 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
46327 TTTGGTTCAC
*
46337 GGAATATAAGATTACCAGTG
1 GGAATAAAAGATTACCAGTG
46357 GGAATAAAAGATTACCAG
1 GGAATAAAAGATTACCAG
46375 AGAATAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.11, G:0.24, T:0.21
Consensus pattern (20 bp):
GGAATAAAAGATTACCAGTG
Found at i:46379 original size:18 final size:19
Alignment explanation
Indices: 46338--46380 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
46328 TTGGTTCACG
* *
46338 GAATATAAGATTACCAGTGG
1 GAATAAAAGATTACCAG-GA
46358 GAATAAAAGATTACCA-GA
1 GAATAAAAGATTACCAGGA
46376 GAATA
1 GAATA
46381 GAATTACTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 6 0.29
20 15 0.71
ACGTcount: A:0.49, C:0.09, G:0.21, T:0.21
Consensus pattern (19 bp):
GAATAAAAGATTACCAGGA
Found at i:48540 original size:18 final size:18
Alignment explanation
Indices: 48517--48551 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
48507 AGCATTTTAA
48517 TTCATTT-AGAGTTAAAAT
1 TTCATTTCAGAG-TAAAAT
48535 TTCATTTCAGAGTAAAA
1 TTCATTTCAGAGTAAAA
48552 GATCAAGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (18 bp):
TTCATTTCAGAGTAAAAT
Found at i:57639 original size:2 final size:2
Alignment explanation
Indices: 57632--57664 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
57622 TAGAAAAGTA
57632 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
57665 ACACTATTAT
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:60759 original size:16 final size:16
Alignment explanation
Indices: 60738--60777 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
60728 CTCTCGTGAA
60738 GGAAGAAGTGAAGAAT
1 GGAAGAAGTGAAGAAT
60754 GGAAGAAGTGAAGAAT
1 GGAAGAAGTGAAGAAT
60770 GGAAGAAG
1 GGAAGAAG
60778 AAAGGTAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.40, T:0.10
Consensus pattern (16 bp):
GGAAGAAGTGAAGAAT
Done.