Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004701.1 Hibiscus syriacus cultivar Beakdansim tig00010561_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: 35791
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:754 original size:74 final size:75
Alignment explanation
Indices: 629--814 Score: 270
Period size: 75 Copynumber: 2.5 Consensus size: 75
619 ACCGTTGTAC
* * *
629 AGGGGGAATCGGTACCCCCT-TGGGGGGATCGGTTCCCTCCGAGCATACTGG-AATCTCGGAG-C
1 AGGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGCC
**
691 AAAACTGTTT
66 AAAACCATTT
* *
701 AGGGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGGC
1 A-GGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGC
766 CAAAACCATTT
65 CAAAACCATTT
777 AGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCC
1 AGGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCC
815 TGAGCAATCT
Statistics
Matches: 102, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
72 1 0.01
73 17 0.17
74 29 0.28
75 30 0.29
76 25 0.25
ACGTcount: A:0.20, C:0.24, G:0.33, T:0.23
Consensus pattern (75 bp):
AGGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAGCC
AAAACCATTT
Found at i:1423 original size:23 final size:23
Alignment explanation
Indices: 1377--1424 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1367 CACTATTCAT
*
1377 AAATCCAAAATCCAAAATCCCCA
1 AAATCCAAAATCCAAAATACCCA
*
1400 AAAT-CAACAATCCAAAATATCCA
1 AAATCCAA-AATCCAAAATACCCA
1423 AA
1 AA
1425 TGTTGAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 3 0.14
23 19 0.86
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (23 bp):
AAATCCAAAATCCAAAATACCCA
Found at i:9263 original size:75 final size:76
Alignment explanation
Indices: 9136--9344 Score: 287
Period size: 75 Copynumber: 2.8 Consensus size: 76
9126 CCGTTGTACA
* * * *
9136 AGGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG-
1 AGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAGC
**
9199 CAAAACTGTTT
66 CAAAACCATTT
* *
9210 AGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGGC
1 AGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAGC
9275 CAAAACCATTT
66 CAAAACCATTT
* * *
9286 AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCAATCTGTAATT
1 A-GGGGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATT
9345 TTTGGCTTTG
Statistics
Matches: 119, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
74 18 0.15
75 39 0.33
76 10 0.08
77 21 0.18
78 31 0.26
ACGTcount: A:0.20, C:0.23, G:0.32, T:0.24
Consensus pattern (76 bp):
AGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAGC
CAAAACCATTT
Found at i:9627 original size:23 final size:23
Alignment explanation
Indices: 9594--9656 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 23
9584 ATTATTATAT
9594 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
9617 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
9640 GGCACTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
9657 ATATGAGCTG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 35 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:11245 original size:39 final size:39
Alignment explanation
Indices: 11202--11288 Score: 122
Period size: 39 Copynumber: 2.2 Consensus size: 39
11192 CAGTCAAACC
* *
11202 TTCTAAATTCCTACTTTATTAAATT-TTATCCCCTTAACA
1 TTCTAAATTCCTACTTTATTAAATTATT-TCACATTAACA
* *
11241 TTCTAAATTCTTACTTTCTTAAATTATTTCACATTAACA
1 TTCTAAATTCCTACTTTATTAAATTATTTCACATTAACA
11280 TTCTAAATT
1 TTCTAAATT
11289 ATTTTTTAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
39 41 0.95
40 2 0.05
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (39 bp):
TTCTAAATTCCTACTTTATTAAATTATTTCACATTAACA
Found at i:16547 original size:13 final size:13
Alignment explanation
Indices: 16529--16553 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16519 AGCAGTACCT
16529 TGTTTCTAAATTG
1 TGTTTCTAAATTG
16542 TGTTTCTAAATT
1 TGTTTCTAAATT
16554 CCTTGACCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.12, T:0.56
Consensus pattern (13 bp):
TGTTTCTAAATTG
Found at i:16891 original size:20 final size:20
Alignment explanation
Indices: 16859--16896 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
16849 TCCATATAAA
*
16859 TTGGTTACAAGAATGTTTTG
1 TTGGTTACAAGAAGGTTTTG
16879 TTGGTTAGC-AGAAGGTTT
1 TTGGTTA-CAAGAAGGTTT
16897 CTGCTATTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.94
21 1 0.06
ACGTcount: A:0.24, C:0.05, G:0.29, T:0.42
Consensus pattern (20 bp):
TTGGTTACAAGAAGGTTTTG
Found at i:20167 original size:42 final size:41
Alignment explanation
Indices: 20078--20173 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 41
20068 AATTGATACT
* * * * *
20078 TTAGCGGCGTTTGTTGTAAAAATGCTGCAATAGATTTGACA
1 TTAGCGGCGTTTGTTATAAAAATGCCGCAATAGAGTGGAAA
20119 TATAGCGGCGTTT-TTATAAAAAATGCCGCAATAGAGTGGTAAA
1 T-TAGCGGCGTTTGTTAT-AAAAATGCCGCAATAGAGTGG-AAA
20162 TTAGCGGCGTTT
1 TTAGCGGCGTTT
20174 ATACCACAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
41 4 0.09
42 40 0.85
43 3 0.06
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.32
Consensus pattern (41 bp):
TTAGCGGCGTTTGTTATAAAAATGCCGCAATAGAGTGGAAA
Found at i:20253 original size:41 final size:41
Alignment explanation
Indices: 20144--20278 Score: 170
Period size: 42 Copynumber: 3.3 Consensus size: 41
20134 ATAAAAAATG
20144 CCGCAATAGAGTGGTAAATTAGCGGCGTTTATACCACAAACA
1 CCGCAATAGA-TGGTAAATTAGCGGCGTTTATACCACAAACA
*
20186 CCGCAATAGAT--TAACATATAGTGGCGTTT-TAGCCA-AAACA
1 CCGCAATAGATGGTAA-AT-TAGCGGCGTTTATA-CCACAAACA
* *
20226 CCACAATAGATCGGTAAATTAGCGGCGTTTATACCACAAACG
1 CCGCAATAGAT-GGTAAATTAGCGGCGTTTATACCACAAACA
20268 CCGCAATAGAT
1 CCGCAATAGAT
20279 TACACATATA
Statistics
Matches: 80, Mismatches: 5, Indels: 16
0.79 0.05 0.16
Matches are distributed among these distances:
39 3 0.04
40 19 0.24
41 27 0.34
42 28 0.35
43 3 0.04
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.22
Consensus pattern (41 bp):
CCGCAATAGATGGTAAATTAGCGGCGTTTATACCACAAACA
Found at i:20299 original size:42 final size:41
Alignment explanation
Indices: 20167--20299 Score: 157
Period size: 42 Copynumber: 3.2 Consensus size: 41
20157 GTAAATTAGC
20167 GGCGTTTATACCACAAACACCGCAATAGATTAACATATAGT
1 GGCGTTTATACCACAAACACCGCAATAGATTAACATATAGT
* *
20208 GGCGTTT-TAGCCA-AAACACCACAATAGATCGGTAA-AT-TAGC
1 GGCGTTTATA-CCACAAACACCGCAATAGAT---TAACATATAGT
*
20249 GGCGTTTATACCACAAACGCCGCAATAGATTACACATATAGT
1 GGCGTTTATACCACAAACACCGCAATAGATTA-ACATATAGT
*
20291 GGCATTTAT
1 GGCGTTTAT
20300 TCTTAAAATG
Statistics
Matches: 77, Mismatches: 6, Indels: 17
0.77 0.06 0.17
Matches are distributed among these distances:
39 2 0.03
40 18 0.23
41 25 0.32
42 29 0.38
43 3 0.04
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (41 bp):
GGCGTTTATACCACAAACACCGCAATAGATTAACATATAGT
Found at i:20332 original size:42 final size:41
Alignment explanation
Indices: 20261--20475 Score: 195
Period size: 41 Copynumber: 5.2 Consensus size: 41
20251 CGTTTATACC
* *
20261 ACAAACGCCGCAATAG-ATTACA-CATATAGTGGCATTTATTCTT
1 ACAAACGCCACAATAGTGTTA-ATCA-ATAGTGGCATTT-TT-TT
* * * * **
20304 A-AAATGCCGCAATAGTGATAATAAATAGTGGCATTTTTAG
1 ACAAACGCCACAATAGTGTTAATCAATAGTGGCATTTTTTT
* **
20344 ACAAACGCCACAATAGTGTTAATCAATAGTGGCGTTTTTAG
1 ACAAACGCCACAATAGTGTTAATCAATAGTGGCATTTTTTT
* * * *
20385 AAAAACGTCGCAATAGTTTTAATCAATAGTGGCATTTTTTT
1 ACAAACGCCACAATAGTGTTAATCAATAGTGGCATTTTTTT
* *
20426 ACAAACGCCACAATAGTG-TAATCAATAGTGTCGTTTTTTGT
1 ACAAACGCCACAATAGTGTTAATCAATAGTGGCATTTTTT-T
*
20467 ATAAACGCC
1 ACAAACGCC
20476 GCAAAATGTT
Statistics
Matches: 143, Mismatches: 25, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
40 20 0.14
41 93 0.65
42 26 0.18
43 4 0.03
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (41 bp):
ACAAACGCCACAATAGTGTTAATCAATAGTGGCATTTTTTT
Found at i:20372 original size:41 final size:41
Alignment explanation
Indices: 20313--20455 Score: 198
Period size: 41 Copynumber: 3.5 Consensus size: 41
20303 TAAAATGCCG
* *
20313 CAATAGTGATAATAAATAGTGGCATTTTTAGACAAACGCCA
1 CAATAGTGTTAATCAATAGTGGCATTTTTAGACAAACGCCA
* * * *
20354 CAATAGTGTTAATCAATAGTGGCGTTTTTAGAAAAACGTCG
1 CAATAGTGTTAATCAATAGTGGCATTTTTAGACAAACGCCA
* **
20395 CAATAGTTTTAATCAATAGTGGCATTTTTTTACAAACGCCA
1 CAATAGTGTTAATCAATAGTGGCATTTTTAGACAAACGCCA
20436 CAATAGTG-TAATCAATAGTG
1 CAATAGTGTTAATCAATAGTG
20456 TCGTTTTTTG
Statistics
Matches: 88, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
40 12 0.14
41 76 0.86
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.31
Consensus pattern (41 bp):
CAATAGTGTTAATCAATAGTGGCATTTTTAGACAAACGCCA
Found at i:20473 original size:82 final size:82
Alignment explanation
Indices: 20304--20479 Score: 246
Period size: 82 Copynumber: 2.1 Consensus size: 82
20294 ATTTATTCTT
*
20304 AAAATGCCGCAATAGTGATAATAAATAGTGGCATTTTTAGACAAACGCCACAATAGTGTTAATCA
1 AAAACGCCGCAATAGTGATAATAAATAGTGGCATTTTTAGACAAACGCCACAATAGTGTTAATCA
20369 ATAGTGGCGTTTTTAGA
66 ATAGTGGCGTTTTTAGA
* ** * **
20386 AAAACGTCGCAATAGTTTTAATCAATAGTGGCATTTTTTTACAAACGCCACAATAGTG-TAATCA
1 AAAACGCCGCAATAGTGATAATAAATAGTGGCATTTTTAGACAAACGCCACAATAGTGTTAATCA
* *
20450 ATAGTGTCGTTTTTTGTA
66 ATAGTGGCGTTTTTAG-A
*
20468 TAAACGCCGCAA
1 AAAACGCCGCAA
20480 AATGTTAAAT
Statistics
Matches: 82, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
81 20 0.24
82 62 0.76
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (82 bp):
AAAACGCCGCAATAGTGATAATAAATAGTGGCATTTTTAGACAAACGCCACAATAGTGTTAATCA
ATAGTGGCGTTTTTAGA
Found at i:21805 original size:43 final size:44
Alignment explanation
Indices: 21711--21808 Score: 110
Period size: 43 Copynumber: 2.3 Consensus size: 44
21701 TAAAAGGTAA
* * * * * *
21711 TTAGCGGCGTTTGTATCTAGAAACGCCGCTATAGATCTGACATT
1 TTAGTGGCGTTTGTATCCAAAAACGCCGCTAAAGATCTAACACT
* *
21755 TTA-TGGCGTTTGTATCCAAAAACGCCGCTAAAGA-GTAATACT
1 TTAGTGGCGTTTGTATCCAAAAACGCCGCTAAAGATCTAACACT
21797 TTAGTGGCGTTT
1 TTAGTGGCGTTT
21809 TTGAAACAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
42 7 0.16
43 35 0.78
44 3 0.07
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (44 bp):
TTAGTGGCGTTTGTATCCAAAAACGCCGCTAAAGATCTAACACT
Found at i:22170 original size:41 final size:41
Alignment explanation
Indices: 21867--22177 Score: 349
Period size: 41 Copynumber: 7.5 Consensus size: 41
21857 TTTTTCCAAT
*
21867 AAACGCCGCTATAG-GTACGTACTTTAGTGGCGTTTTTATAC
1 AAACGCCGCTATAGACTA-GTACTTTAGTGGCGTTTTTATAC
* * * *
21908 AAACGTCGCTATATACTAGTACTTTAGTGGCATTTCTATAC
1 AAACGCCGCTATAGACTAGTACTTTAGTGGCGTTTTTATAC
* ** *
21949 AAACGCCGCTATATACTAGTACTTTAGTGGTATTTCTATAC
1 AAACGCCGCTATAGACTAGTACTTTAGTGGCGTTTTTATAC
* * * *
21990 AAACGCCGCTATATACTCA-TACTTTAGTGGCATTTTGAATCC
1 AAACGCCGCTATAGACT-AGTACTTTAGTGGCGTTTT-TATAC
* * *
22032 AAACGCCGCTATAAACTCGTACTTTAGTGGCGTTTTGAATGA-
1 AAACGCCGCTATAGACTAGTACTTTAGTGGCGTTTT-TAT-AC
* * * * * *
22074 ATACGCCGCTAAAGACTCGTACTTTAATAGCGTTTTTATAT
1 AAACGCCGCTATAGACTAGTACTTTAGTGGCGTTTTTATAC
22115 AAACGCCGCTATAGACTAGTACTTTAGTGGCGTTTTTATAC
1 AAACGCCGCTATAGACTAGTACTTTAGTGGCGTTTTTATAC
*
22156 AAACGCCGCTATAGACTCGTAC
1 AAACGCCGCTATAGACTAGTAC
22178 CAGAAGCAAC
Statistics
Matches: 236, Mismatches: 28, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
40 1 0.00
41 162 0.69
42 73 0.31
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.33
Consensus pattern (41 bp):
AAACGCCGCTATAGACTAGTACTTTAGTGGCGTTTTTATAC
Found at i:28556 original size:55 final size:55
Alignment explanation
Indices: 28497--28950 Score: 233
Period size: 51 Copynumber: 8.6 Consensus size: 55
28487 AATGACGAGC
**
28497 CTGCTCCCTATTCCTTCAG-GAAGTATAAGACTCGAGCAATCTTC-ATAAAATGTGT
1 CTGCTCCCTATTCCTTCAGAG-AGTATAAGACTCGAAAAATCTTCAATAAAA-GTGT
* * * * *
28552 CTGCTCTCTATTCATTCAGAGAGTATAAGACTTGAATAATCTTCAATAAAACGAGT
1 CTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAAAAATCTTCAATAAAA-GTGT
* *
28608 ATGCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAAAAATCTTCAATAAACAGT-T
1 CTGCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAAAAATCTTCAATAAA-AGTGT
* * * * * * *
28663 CCGCTCCCTATTCCTTCAGAGAGTACAGGACTC----ACTCTTTAACAAACGTGT
1 CTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAAAAATCTTCAATAAAAGTGT
* * * **
28714 -TCGCTCCCTA-TCCGTTCAGGGAGTAT-AGAACTC----AATTTTCAACAAACTTGT
1 CT-GCTCCCTATTCC-TTCAGAGAGTATAAG-ACTCGAAAAATCTTCAATAAAAGTGT
* ** * ** **
28765 CCGCTCCCTATTTATTCAGAGAGTATAGGACTC----AATCTTCAACGAACTTGT
1 CTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAAAAATCTTCAATAAAAGTGT
* * * * ** **
28816 CCGCTCCCTATTCATTCAGAGAGTATAGGAC-C---CAATCTTCAACGAACTTGT
1 CTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAAAAATCTTCAATAAAAGTGT
* * * ** **
28867 CCGCTCCCTATTCATTCAGAGAGTATAGGACTC----AATCTTCAACGAACTTGT
1 CTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAAAAATCTTCAATAAAAGTGT
* *
28918 CCGCTCCCTATTCCTTCAGAGAGTATAGGACTC
1 CTGCTCCCTATTCCTTCAGAGAGTATAAGACTC
28951 AATCTTCAAC
Statistics
Matches: 347, Mismatches: 38, Indels: 32
0.83 0.09 0.08
Matches are distributed among these distances:
50 7 0.02
51 215 0.62
52 3 0.01
55 66 0.19
56 55 0.16
57 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (55 bp):
CTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAAAAATCTTCAATAAAAGTGT
Found at i:28626 original size:56 final size:55
Alignment explanation
Indices: 28498--28687 Score: 210
Period size: 55 Copynumber: 3.4 Consensus size: 55
28488 ATGACGAGCC
** * *
28498 TGCTCCCTATTCCTTCAG-GAAGTATAAGACTCGAGCAATCTTC-ATAAAATGTGT
1 TGCTCCCTATTCCTTCAGAG-AGTATAAGACTCGAAAAATCTTCAATAAAACGAGT
* * * *
28552 CTGCTCTCTATTCATTCAGAGAGTATAAGACTTGAATAATCTTCAATAAAACGAGT
1 -TGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAAAAATCTTCAATAAAACGAGT
*
28608 ATGCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAAAAATCTTCAAT-AAAC-AGT
1 -TGCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAAAAATCTTCAATAAAACGAGT
28662 TCCGCTCCCTATTCCTTCAGAGAGTA
1 T--GCTCCCTATTCCTTCAGAGAGTA
28688 CAGGACTCAC
Statistics
Matches: 118, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
53 1 0.01
54 3 0.03
55 64 0.54
56 50 0.42
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (55 bp):
TGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAAAAATCTTCAATAAAACGAGT
Found at i:28738 original size:51 final size:51
Alignment explanation
Indices: 28622--28965 Score: 424
Period size: 51 Copynumber: 6.7 Consensus size: 51
28612 TCTCTATTCC
* * *
28622 TTCAGAGAGTATAGAACTCGAAAAATCTTCAATAAAC-AGTTCCGCTCCCTATTCC-
1 TTCAGAGAGTATAGGACTC----AATCTTCAACAAACTTG-TCCGCTCCCTA-TCCA
* * * * * *
28677 TTCAGAGAGTACAGGACTCACTCTTTAACAAACGTGTTCGCTCCCTATCCG
1 TTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCCGCTCCCTATCCA
* * * **
28728 TTCAGGGAGTATAGAACTCAATTTTCAACAAACTTGTCCGCTCCCTATTTA
1 TTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCCGCTCCCTATCCA
* *
28779 TTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCA
1 TTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCCGCTCCCTATCCA
* * *
28830 TTCAGAGAGTATAGGACCCAATCTTCAACGAACTTGTCCGCTCCCTATTCA
1 TTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCCGCTCCCTATCCA
*
28881 TTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCC-
1 TTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCCGCTCCCTA-TCCA
28932 TTCAGAGAGTATAGGACTCAATCTTCAACAAACT
1 TTCAGAGAGTATAGGACTCAATCTTCAACAAACT
28966 AATTTGCTTC
Statistics
Matches: 259, Mismatches: 27, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
50 3 0.01
51 236 0.91
52 3 0.01
55 17 0.07
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (51 bp):
TTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCCGCTCCCTATCCA
Found at i:30300 original size:9 final size:8
Alignment explanation
Indices: 30276--30402 Score: 60
Period size: 9 Copynumber: 14.4 Consensus size: 8
30266 TTGAACCCTC
30276 CTTTTATTT
1 CTTTT-TTT
30285 CTCTTTTTT
1 CT-TTTTTT
*
30294 CATTTTTCT
1 C-TTTTTTT
30303 CTTTTTATT
1 CTTTTT-TT
* *
30312 CCTTTTTC
1 CTTTTTTT
*
30320 CATTTTTT
1 CTTTTTTT
*
30328 CTCTCTTTT
1 CT-TTTTTT
30337 -TTTTTTT
1 CTTTTTTT
30344 CGTTTTTTCCAT
1 C-TTTTTT---T
*
30356 CATTTTTT
1 CTTTTTTT
30364 C-TTTTTT
1 CTTTTTTT
30371 CTTATTTTTT
1 C-T-TTTTTT
30381 CTTCTTTTCT
1 CTT-TTTT-T
30391 CTTTTATTT
1 CTTTT-TTT
30400 CTT
1 CTT
30403 CTTCAAGCAA
Statistics
Matches: 93, Mismatches: 10, Indels: 30
0.70 0.08 0.23
Matches are distributed among these distances:
7 12 0.13
8 17 0.18
9 40 0.43
10 17 0.18
11 5 0.05
12 2 0.02
ACGTcount: A:0.06, C:0.19, G:0.01, T:0.74
Consensus pattern (8 bp):
CTTTTTTT
Found at i:30306 original size:27 final size:27
Alignment explanation
Indices: 30277--30336 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 27
30267 TGAACCCTCC
*
30277 TTTTATTTCTCTTTTTTCA-TTTTTCTCT
1 TTTTA-TTC-CTTTTTCCATTTTTTCTCT
30305 TTTTATTCCTTTTTCCATTTTTTCTCT
1 TTTTATTCCTTTTTCCATTTTTTCTCT
30332 CTTTT
1 -TTTT
30337 TTTTTTTCGT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 8 0.28
27 12 0.41
28 9 0.31
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.73
Consensus pattern (27 bp):
TTTTATTCCTTTTTCCATTTTTTCTCT
Found at i:30341 original size:33 final size:33
Alignment explanation
Indices: 30304--30376 Score: 80
Period size: 33 Copynumber: 2.2 Consensus size: 33
30294 CATTTTTCTC
30304 TTTTTATTC-CTTTTTCCAT--TTTTTCTCTCTTT
1 TTTTTATTCGCTTTTTCCATCATTTTT-TCT-TTT
* *
30336 TTTTTTTTCGTTTTTTCCATCATTTTTTCTTTT
1 TTTTTATTCGCTTTTTCCATCATTTTTTCTTTT
*
30369 TTCTTATT
1 TTTTTATT
30377 TTTTCTTCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
32 8 0.24
33 18 0.53
34 3 0.09
35 5 0.15
ACGTcount: A:0.07, C:0.18, G:0.01, T:0.74
Consensus pattern (33 bp):
TTTTTATTCGCTTTTTCCATCATTTTTTCTTTT
Found at i:30342 original size:25 final size:24
Alignment explanation
Indices: 30288--30388 Score: 75
Period size: 27 Copynumber: 4.0 Consensus size: 24
30278 TTTATTTCTC
30288 TTTTTTCA-TTTTTCTCT-TTTTAT
1 TTTTTTCATTTTTTCTCTCTTTT-T
30311 TCCTTTTTCCATTTTTTCTCTCTTTTT
1 T--TTTTT-CATTTTTTCTCTCTTTTT
*
30338 TTTTTTCGTTTTTTC-CATCATTTTTT
1 TTTTTTCATTTTTTCTC-TC--TTTTT
30364 CTTTTTTCTTATTTTTTCT-TCTTTT
1 -TTTTTTC--ATTTTTTCTCTCTTTT
30389 CTCTTTTATT
Statistics
Matches: 64, Mismatches: 2, Indels: 21
0.74 0.02 0.24
Matches are distributed among these distances:
23 2 0.03
24 10 0.16
25 10 0.16
26 11 0.17
27 18 0.28
28 6 0.09
29 7 0.11
ACGTcount: A:0.06, C:0.18, G:0.01, T:0.75
Consensus pattern (24 bp):
TTTTTTCATTTTTTCTCTCTTTTT
Found at i:30379 original size:36 final size:32
Alignment explanation
Indices: 30288--30379 Score: 87
Period size: 35 Copynumber: 2.7 Consensus size: 32
30278 TTTATTTCTC
30288 TTTTTTCATTTTTCTCTTTTTATTCCTTTTTCCAT
1 TTTTTTC-TTTTT-TCTTTTT-TTCCTTTTTCCAT
* *
30323 TTTTTCTCTCTTTT-TTTTTTTCGTTTTTTCCAT
1 TTTTT-TCTTTTTTCTTTTTTTC-CTTTTTCCAT
30356 CATTTTTTCTTTTTTCTTATTTTT
1 --TTTTTTCTTTTTTCTT-TTTTT
30380 TCTTCTTTTC
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
32 3 0.06
33 14 0.29
34 8 0.17
35 16 0.33
36 7 0.15
ACGTcount: A:0.07, C:0.17, G:0.01, T:0.75
Consensus pattern (32 bp):
TTTTTTCTTTTTTCTTTTTTTCCTTTTTCCAT
Found at i:30388 original size:27 final size:26
Alignment explanation
Indices: 30286--30395 Score: 86
Period size: 25 Copynumber: 4.2 Consensus size: 26
30276 CTTTTATTTC
*
30286 TCTTTTTTC-ATTTTTCTCTT-TTTAT
1 TCTTTTTTCTATTTTT-TCTTCTTTTT
* *
30311 TCCTTTTTCCATTTTTTC-TCTCTTTT
1 TCTTTTTTCTATTTTTTCTTCT-TTTT
* *
30337 T-TTTTTTCGT-TTTTTCCATCATTTTT
1 TCTTTTTTC-TATTTTTTCTTC-TTTTT
*
30363 TCTTTTTTCTTATTTTTTCTTCTTTTC
1 TCTTTTTTC-TATTTTTTCTTCTTTTT
30390 TCTTTT
1 TCTTTT
30396 ATTTCTTCTT
Statistics
Matches: 68, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
24 1 0.01
25 23 0.34
26 17 0.25
27 19 0.28
28 8 0.12
ACGTcount: A:0.05, C:0.19, G:0.01, T:0.75
Consensus pattern (26 bp):
TCTTTTTTCTATTTTTTCTTCTTTTT
Found at i:30400 original size:19 final size:20
Alignment explanation
Indices: 30357--30405 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
30347 TTTTTCCATC
* *
30357 ATTTTTTCTTTTTTCTTATT
1 ATTTCTTCTTTTCTCTTATT
*
30377 TTTTCTTCTTTTCTCTT-TT
1 ATTTCTTCTTTTCTCTTATT
30396 ATTTCTTCTT
1 ATTTCTTCTT
30406 CAAGCAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (20 bp):
ATTTCTTCTTTTCTCTTATT
Done.