Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009301.1 Hibiscus syriacus cultivar Beakdansim tig00113023_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: 91293
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:457 original size:19 final size:18
Alignment explanation
Indices: 421--471 Score: 50
Period size: 19 Copynumber: 2.8 Consensus size: 18
411 ATTAAATTGC
** *
421 ATAAATAAAAGTATTAAT
1 ATAAATAAAAAAAATAAT
439 ATTAAA-AAAATAAAATAAT
1 A-TAAATAAAA-AAAATAAT
458 ATAAATAAAAAAAA
1 ATAAATAAAAAAAA
472 GGGCACAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (18 bp):
ATAAATAAAAAAAATAAT
Found at i:1173 original size:28 final size:28
Alignment explanation
Indices: 1136--1210 Score: 114
Period size: 28 Copynumber: 2.6 Consensus size: 28
1126 ATTTGTTGTG
1136 GTGGAGGGGGCTGCTGGGTTACTTGAAAC
1 GTGGA-GGGGCTGCTGGGTTACTTGAAAC
* **
1165 GTGGAGGGGCTACTGGGTTTTTTGAAAC
1 GTGGAGGGGCTGCTGGGTTACTTGAAAC
1193 GTGGAGGGGCTGCTGGGT
1 GTGGAGGGGCTGCTGGGT
1211 ATGAAAGGTA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 37 0.88
29 5 0.12
ACGTcount: A:0.15, C:0.12, G:0.47, T:0.27
Consensus pattern (28 bp):
GTGGAGGGGCTGCTGGGTTACTTGAAAC
Found at i:1870 original size:95 final size:94
Alignment explanation
Indices: 1754--1939 Score: 320
Period size: 95 Copynumber: 2.0 Consensus size: 94
1744 TAAAATCTCA
* *
1754 TTTGAAAACATCCTGCCCTGAAGGTCTTATGGATGAACCGAAGGCTTTTTGAAAACATCC-TGTA
1 TTTGAAAACATCCTGCACTGAAGGTCTTATGGATGAACCGAAGGCTTTTTGAAAACA-CCTTGCA
1818 CTGAAGGTCTTATGGATGACCCGAAGGCTT
65 CTGAAGGTCTTATGGATGACCCGAAGGCTT
*
1848 TTTGAAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGAAGGCTTTTTGAAAACACCTTGCA
1 TTTG-AAAACATCCTGCACTGAAGGTCTTATGGATGAACCGAAGGCTTTTTGAAAACACCTTGCA
1913 CTGAAGGTCTTATGGATGACCCGAAGG
65 CTGAAGGTCTTATGGATGACCCGAAGG
1940 TTTAATTACT
Statistics
Matches: 87, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
94 6 0.07
95 81 0.93
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.27
Consensus pattern (94 bp):
TTTGAAAACATCCTGCACTGAAGGTCTTATGGATGAACCGAAGGCTTTTTGAAAACACCTTGCAC
TGAAGGTCTTATGGATGACCCGAAGGCTT
Found at i:1876 original size:48 final size:47
Alignment explanation
Indices: 1754--1939 Score: 320
Period size: 47 Copynumber: 3.9 Consensus size: 47
1744 TAAAATCTCA
* *
1754 TTTGAAAACATCCTGCCCTGAAGGTCTTATGGATGAACCGAAGGCTT
1 TTTGAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGAAGGCTT
*
1801 TTTGAAAACATCCTGTACTGAAGGTCTTATGGATGACCCGAAGGCTT
1 TTTGAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGAAGGCTT
1848 TTTGAAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGAAGGCTT
1 TTTG-AAAACATCCTGCACTGAAGGTCTTATGGATGACCCGAAGGCTT
1896 TTTGAAAACA-CCTTGCACTGAAGGTCTTATGGATGACCCGAAGG
1 TTTGAAAACATCC-TGCACTGAAGGTCTTATGGATGACCCGAAGG
1940 TTTAATTACT
Statistics
Matches: 133, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
46 2 0.02
47 85 0.64
48 46 0.35
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.27
Consensus pattern (47 bp):
TTTGAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGAAGGCTT
Found at i:2551 original size:246 final size:246
Alignment explanation
Indices: 2072--2938 Score: 1411
Period size: 246 Copynumber: 3.5 Consensus size: 246
2062 AAGGACTTAT
* * * *
2072 CATCTTGCTCAAAAGACTAACAGATGACCCGAAGGATTTACAAATTTGTGGGAAATACTTTACTA
1 CATCATGCTCGAAAGACTAACAGATGACCCGAAAGATTTACAAATTTGTGGGAAATACTTTACTG
* *
2137 GGTAAGAAACTTCTTACTTTTCAAGAATTTGATTTTCTAGAACATTAAATGAGAAACTTTGAAAA
66 GGTAAGAAACTTCTTACTTTTCAAGAATTTCATTTTCTAAAACATTAAATGAGAAACTTTGAAAA
* *
2202 TCG-TATCTCATTTTCATGCGAAAATCATA-TGAACATCCTACCCAAAAGCTTTACGGATGGCCT
131 TCGCTATCTCATTTTCATGCGAAAATCATATTGAACATCCTACCCAAAGGCTTTACGGATGGCCC
*
2265 TAAAGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGAAGGTTTTAAG
196 TAAGGACTTATCATCTTGCTCGAAAGAC-GACA-ATGACCCGAAGGTTTTAAG
* * *
2318 CATCATGTTCGAAAGACTAACAGATGACCCGAAAGATTTACTAATTTATGGGAAATACTTTACTG
1 CATCATGCTCGAAAGACTAACAGATGACCCGAAAGATTTACAAATTTGTGGGAAATACTTTACTG
2383 GGTAAGAAACTTCTTACTTTTCAAGAATTTCATTTTCTAAAACATTAAATGAGAAACTTTGAAAA
66 GGTAAGAAACTTCTTACTTTTCAAGAATTTCATTTTCTAAAACATTAAATGAGAAACTTTGAAAA
*
2448 TCGCTATCTCATTTTCATACGAAAATCATATGTGAACATCCTACCCAAAGGCTTTACGGATGGCC
131 TCGCTATCTCATTTTCATGCGAAAATCATAT-TGAACATCCTACCCAAAGGCTTTACGGATGGCC
2513 CTAAGGACTTATCATCTTGCTCGAAGAGA-GAC-ATGACCCGAAGGTTTTAAG
195 CTAAGGACTTATCATCTTGCTCGAA-AGACGACAATGACCCGAAGGTTTTAAG
* * * *
2564 CATCATGCTCGAAAGACTAACAAATGACCCGAAGGATTTACAAATTTGTGGGAAATATTTTATTG
1 CATCATGCTCGAAAGACTAACAGATGACCCGAAAGATTTACAAATTTGTGGGAAATACTTTACTG
* *
2629 GGTAAGAAACTTCTTACTTTTCAAGAATTTGATTTTCTAGAACATTAAATGAGAAACTTTGAAAA
66 GGTAAGAAACTTCTTACTTTTCAAGAATTTCATTTTCTAAAACATTAAATGAGAAACTTTGAAAA
2694 TCGCTATCTCATTTTCATGCGAAAATCATATATGAACATCCTACCCAAAGGCTTTACGGATGGCC
131 TCGCTATCTCATTTTCATGCGAAAATCATAT-TGAACATCCTACCCAAAGGCTTTACGGATGGCC
*
2759 CTAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCAAAGGTTTTAAG
195 CTAAGGACTTATCATCTTGCTCGAAAGAC-GACA-ATGACCCGAAGGTTTTAAG
*
2813 CATCATGCTCGAAAGACTAACAGATGACCC-AAAGGATTTATAAATTTGTGGGAAATACTTTACT
1 CATCATGCTCGAAAGACTAACAGATGACCCGAAA-GATTTACAAATTTGTGGGAAATACTTTACT
*
2877 GGGTAAGAAACTTCTTACTTTTCAAGAATTTCATTTTCTAAAAAAGATTAAATGAGAAACTT
65 GGGTAAGAAACTTCTTACTTTTCAAGAATTTCATTTTCT--AAAACATTAAATGAGAAACTT
2939 GTTGGTTGGG
Statistics
Matches: 577, Mismatches: 33, Indels: 17
0.92 0.05 0.03
Matches are distributed among these distances:
245 3 0.01
246 352 0.61
247 28 0.05
248 5 0.01
249 167 0.29
250 3 0.01
251 19 0.03
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (246 bp):
CATCATGCTCGAAAGACTAACAGATGACCCGAAAGATTTACAAATTTGTGGGAAATACTTTACTG
GGTAAGAAACTTCTTACTTTTCAAGAATTTCATTTTCTAAAACATTAAATGAGAAACTTTGAAAA
TCGCTATCTCATTTTCATGCGAAAATCATATTGAACATCCTACCCAAAGGCTTTACGGATGGCCC
TAAGGACTTATCATCTTGCTCGAAAGACGACAATGACCCGAAGGTTTTAAG
Found at i:2836 original size:42 final size:42
Alignment explanation
Indices: 2771--2852 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 42
2761 AAGGACTTAT
* * *
2771 CATCTTGCTCGAAAGACTGACAGATGACCCAAAGGTTTTAAG
1 CATCATGCTCGAAAGACTAACAGATGACCCAAAGGATTTAAG
2813 CATCATGCTCGAAAGACTAACAGATGACCCAAAGGATTTA
1 CATCATGCTCGAAAGACTAACAGATGACCCAAAGGATTTA
2853 TAAATTTGTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (42 bp):
CATCATGCTCGAAAGACTAACAGATGACCCAAAGGATTTAAG
Found at i:4948 original size:2 final size:2
Alignment explanation
Indices: 4941--4982 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
4931 ATGATGGACC
4941 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4982 T
1 T
4983 GATAAGACAT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7156 original size:18 final size:18
Alignment explanation
Indices: 7133--7170 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
7123 CATTTGATCT
*
7133 TCTGGTCGTGCTTGTTCC
1 TCTGGTCGAGCTTGTTCC
*
7151 TCTGGTGGAGCTTGTTCC
1 TCTGGTCGAGCTTGTTCC
7169 TC
1 TC
7171 GTGCTTTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.03, C:0.26, G:0.29, T:0.42
Consensus pattern (18 bp):
TCTGGTCGAGCTTGTTCC
Found at i:8808 original size:22 final size:23
Alignment explanation
Indices: 8761--8822 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
8751 ATTCCCATAT
8761 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
8784 AGGGGGAATCGGTTCCCCTTC-A
1 AGGGGGAATCGGTTCCCCTTCAA
* *
8806 AGGGGGCATCGATTCCC
1 AGGGGGAATCGGTTCCC
8823 TCTGCACCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
22 16 0.43
23 21 0.57
ACGTcount: A:0.19, C:0.27, G:0.32, T:0.21
Consensus pattern (23 bp):
AGGGGGAATCGGTTCCCCTTCAA
Found at i:12667 original size:22 final size:21
Alignment explanation
Indices: 12625--12664 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
12615 GTCTTTATTT
*
12625 TCATTTTTCAATTTTTAAACA
1 TCATTTTTCAATTTTAAAACA
12646 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
12665 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:14995 original size:23 final size:23
Alignment explanation
Indices: 14957--15038 Score: 119
Period size: 23 Copynumber: 3.6 Consensus size: 23
14947 CTTATATGGT
* * *
14957 ACTTCGGTGCATTTCTACGCGAC
1 ACTTCGGTGCAATTCTACGTGGC
*
14980 ACTACGGTGCAATTCTACGTGGC
1 ACTTCGGTGCAATTCTACGTGGC
*
15003 ACTTCGGTGCAATTCTGCGTGGC
1 ACTTCGGTGCAATTCTACGTGGC
15026 ACTTCGGTGCAAT
1 ACTTCGGTGCAAT
15039 ATATACGAGC
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 53 1.00
ACGTcount: A:0.18, C:0.27, G:0.26, T:0.29
Consensus pattern (23 bp):
ACTTCGGTGCAATTCTACGTGGC
Found at i:17813 original size:541 final size:541
Alignment explanation
Indices: 16791--17870 Score: 2052
Period size: 541 Copynumber: 2.0 Consensus size: 541
16781 TATGATTGGC
16791 TGACTAGGGCTTGTGCCCTAGATTGAACAAATGTTATTGACTAGTTGTCAGAGTAAAGGTGATAG
1 TGACTAGGGCTTGTGCCCTAGATTGAACAAATGTTATTGACTAGTTGTCAGAGTAAAGGTGATAG
*
16856 AGTTATAAGATTGAAGGAAAAGATAAAGTTGAGTTAATTGATTATGAAGTGAATCTGAATATAGT
66 AGTTATAAGATTGAAGGAAAAGATAAAGTTGAGTTAATTGATTATGAAGCGAATCTGAATATAGT
16921 TGTGTATTCTGATCAGATAGCTATGATGTAGAAAAGGAGATAAGTATTTGCATGGAACCTTAAAG
131 TGTGTATTCTGATCAGATAGCTATGATGTAGAAAAGGAGATAAGTATTTGCATGGAACCTTAAAG
16986 AACAAAAATACAAGTATAAGAAATGATAAAGAATGAAGTTCTATATAGGTAAATGGATTATCAAA
196 AACAAAAATACAAGTATAAGAAATGATAAAGAATGAAGTTCTATATAGGTAAATGGATTATCAAA
17051 GTTATGAGGATGCAATGAAGATTGATACATAGAGATGAGTATAGATGATAAGACAAGAGTATGTG
261 GTTATGAGGATGCAATGAAGATTGATACATAGAGATGAGTATAGATGATAAGACAAGAGTATGTG
*
17116 AACATGAAAGGAAATATATGATTTGGATATAAGGAATAAATATAGGAATAATGAAATAAAGAAAT
326 AACATGAAAGGAAAGATATGATTTGGATATAAGGAATAAATATAGGAATAATGAAATAAAGAAAT
17181 GAAAGGGATGAGTTAAAGGATCAGATATGATAAAGGTTATATGGAAGTGTAGATGATAATTTTGA
391 GAAAGGGATGAGTTAAAGGATCAGATATGATAAAGGTTATATGGAAGTGTAGATGATAATTTTGA
*
17246 TATAGAAGTAAGAAAAGTGTGCAAGGTGATGTGAAAAGATTCTTTAAAGTGTATGTTAATTATAT
456 TATAGAAGTAAAAAAAGTGTGCAAGGTGATGTGAAAAGATTCTTTAAAGTGTATGTTAATTATAT
17311 TTAAAGAAGATCTAATGTTAT
521 TTAAAGAAGATCTAATGTTAT
* *
17332 TGACTAGGGCTTGTGCCCTAGATTGAACAGATGTTATTGACTAGTTTTCAGAGTAAAGGTGATAG
1 TGACTAGGGCTTGTGCCCTAGATTGAACAAATGTTATTGACTAGTTGTCAGAGTAAAGGTGATAG
*
17397 AGTTATAAGATTGGAGGAAAAGATAAAGTTGAGTTAATTGATTATGAAGCGAATCTGAATATAGT
66 AGTTATAAGATTGAAGGAAAAGATAAAGTTGAGTTAATTGATTATGAAGCGAATCTGAATATAGT
*
17462 TGTGTATTCTGATCAGATAGCTATGATGTAGAAAAGGAGATAAGTATTTGCATGGAACCTTAAGG
131 TGTGTATTCTGATCAGATAGCTATGATGTAGAAAAGGAGATAAGTATTTGCATGGAACCTTAAAG
*
17527 AAGAAAAATACAAGTATAAGAAATGATAAAGAATGAAGTTCTATATAGGTAAATGGATTATCAAA
196 AACAAAAATACAAGTATAAGAAATGATAAAGAATGAAGTTCTATATAGGTAAATGGATTATCAAA
17592 GTTATGAGGATGCAATGAAGATTGATACATAGAGATGAGTATAGATGATAAGACAAGAGTATGTG
261 GTTATGAGGATGCAATGAAGATTGATACATAGAGATGAGTATAGATGATAAGACAAGAGTATGTG
* *
17657 AACATGAAAGGAAAGATATGATTTGGGTATAAGGAATAAATATAGGAATAATGGAATAAAGAAAT
326 AACATGAAAGGAAAGATATGATTTGGATATAAGGAATAAATATAGGAATAATGAAATAAAGAAAT
*
17722 GAAAGGGATGAGTTAAAGGATCGGATATGATAAAGGTTATATGGAAGTGTAGATGATAATTTTGA
391 GAAAGGGATGAGTTAAAGGATCAGATATGATAAAGGTTATATGGAAGTGTAGATGATAATTTTGA
17787 TATAGAAGTAAAAAAAGTGTGCAAGGTGATGTGAAAAGATTCTTTAAAGTGTATGTTAATTATAT
456 TATAGAAGTAAAAAAAGTGTGCAAGGTGATGTGAAAAGATTCTTTAAAGTGTATGTTAATTATAT
*
17852 TTAAAGAATATCTAATGTT
521 TTAAAGAAGATCTAATGTT
17871 GTTTTCTCGG
Statistics
Matches: 527, Mismatches: 12, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
541 527 1.00
ACGTcount: A:0.42, C:0.05, G:0.24, T:0.29
Consensus pattern (541 bp):
TGACTAGGGCTTGTGCCCTAGATTGAACAAATGTTATTGACTAGTTGTCAGAGTAAAGGTGATAG
AGTTATAAGATTGAAGGAAAAGATAAAGTTGAGTTAATTGATTATGAAGCGAATCTGAATATAGT
TGTGTATTCTGATCAGATAGCTATGATGTAGAAAAGGAGATAAGTATTTGCATGGAACCTTAAAG
AACAAAAATACAAGTATAAGAAATGATAAAGAATGAAGTTCTATATAGGTAAATGGATTATCAAA
GTTATGAGGATGCAATGAAGATTGATACATAGAGATGAGTATAGATGATAAGACAAGAGTATGTG
AACATGAAAGGAAAGATATGATTTGGATATAAGGAATAAATATAGGAATAATGAAATAAAGAAAT
GAAAGGGATGAGTTAAAGGATCAGATATGATAAAGGTTATATGGAAGTGTAGATGATAATTTTGA
TATAGAAGTAAAAAAAGTGTGCAAGGTGATGTGAAAAGATTCTTTAAAGTGTATGTTAATTATAT
TTAAAGAAGATCTAATGTTAT
Found at i:18980 original size:21 final size:21
Alignment explanation
Indices: 18956--19004 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
18946 CTATGTGCAT
18956 CGATGCACATTCAATGTGTAC
1 CGATGCACATTCAATGTGTAC
18977 CGATGCACATTCAATGTGTAC
1 CGATGCACATTCAATGTGTAC
18998 CGATGCA
1 CGATGCA
19005 TCAACGGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (21 bp):
CGATGCACATTCAATGTGTAC
Found at i:19850 original size:23 final size:23
Alignment explanation
Indices: 19824--19882 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
19814 TGGCACTTTG
19824 GTGCATTTCTACGCGGCACTACA
1 GTGCATTTCTACGCGGCACTACA
* * * *
19847 GTGCAATTCTACGTGGCACTTCG
1 GTGCATTTCTACGCGGCACTACA
*
19870 GTGCATTTATACG
1 GTGCATTTCTACG
19883 AGCTGTGGTG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.20, C:0.25, G:0.24, T:0.31
Consensus pattern (23 bp):
GTGCATTTCTACGCGGCACTACA
Found at i:21603 original size:159 final size:159
Alignment explanation
Indices: 21314--21627 Score: 549
Period size: 159 Copynumber: 2.0 Consensus size: 159
21304 TAATGCAACA
21314 GTATGATGAACAAAATGATCATATATGGTAATCTCCATTGTCACTATTTCACCATTTCCATTCTT
1 GTATGATGAACAAAATGATCATATATGGTAATCTCCATTGTCACTATTTCACCATTTCCATTCTT
*
21379 CATTCCTTTCTGTATCATTAGAAATATTTGTTCAAATCAATGATCTTTCTGAAGGATAATATGGG
66 CATACCTTTCTGTATCATTAGAAATATTTGTTCAAATCAATGATCTTTCTGAAGGATAATATGGG
*
21444 CTTTTAGCATACCCCAGTGTTTGCTAACC
131 CTTTTAGCATACCCCAGTATTTGCTAACC
* *
21473 GTATGATGAACAAAATGATCATATATGGTCATCTCCATTGTCACTATTTCACCATTTTCATTCTT
1 GTATGATGAACAAAATGATCATATATGGTAATCTCCATTGTCACTATTTCACCATTTCCATTCTT
*
21538 CATACCTTTCTGTATCATT-GTAAATATTTGTTCAAATCAATGATCTTTCTGAAGGATGATATGG
66 CATACCTTTCTGTATCATTAG-AAATATTTGTTCAAATCAATGATCTTTCTGAAGGATAATATGG
* *
21602 GCTTTTAGCATGCCCTAGTATTTGCT
130 GCTTTTAGCATACCCCAGTATTTGCT
21628 TCTTGTTGAT
Statistics
Matches: 147, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
158 1 0.01
159 146 0.99
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (159 bp):
GTATGATGAACAAAATGATCATATATGGTAATCTCCATTGTCACTATTTCACCATTTCCATTCTT
CATACCTTTCTGTATCATTAGAAATATTTGTTCAAATCAATGATCTTTCTGAAGGATAATATGGG
CTTTTAGCATACCCCAGTATTTGCTAACC
Found at i:23979 original size:450 final size:450
Alignment explanation
Indices: 23138--23981 Score: 1472
Period size: 450 Copynumber: 1.9 Consensus size: 450
23128 TGACGCCTTC
* *
23138 TGTAGGATCGAGTCATTCATTTCTAAACAACTTCCTAGTGGGTTACCCATCCCTGGATTGCCCTT
1 TGTAGGATCGAGTCATTCATTTCTAAACAACTTCCCAGTGGGTCACCCATCCCTGGATTGCCCTT
* *
23203 GTCCAAGCACGCTTAACTACAGAGTTCTGAAACGAATGGTCACCATTCCTTCTTAAAACCAATTG
66 GTCAAAGCACGCTTAACTACAGAGTTCTGAAACGAATGATCACCATTCCTTCTTAAAACCAATTG
23268 GTGATAAGTAGGTGGGCCATTTTAACCTTATATCTTTATAGTGGGTGATCACTGGGTTCCCCCAA
131 GTGATAAGTAGGTGGGCCATTTTAACCTTATATCTTTATAGTGGGTGATCACTGGGTTCCCCCAA
*
23333 GCCAAGGTGGATTCTTTTGGGGCACCCGACACAGTTCACCACGGCATTGCAAAGCCCCGCATCTA
196 GCCAAGGTAGATTCTTTTGGGGCACCCGACACAGTTCACCACGGCATTGCAAAGCCCCGCATCTA
*
23398 TAGCGTACTGCGGGCGGGCCTAGGGGCTTTATAAGGCACACGTGGGCGTCGACAGGTTGGACAGT
261 TAGCGTACTGCGGGCGGGCCTAGGGGCTTTATAAGGCACACGTGGGCCTCGACAGGTTGGACAGT
* * *
23463 CACGTACCAATATCATGCCCATACACAATAGAATCCCTAAGGGTGATCATTGGACCCTATAACCC
326 CACGTACCAATATCACGCCCATACACAATAGAATCCCTAAGGGTGATCACTGGACCCCATAACCC
23528 AACAATCACCCCCCAACGACACCTGGGGGATTCGAACCTGCAACCTGCTCTGATAACAAT
391 AACAATCACCCCCCAACGACACCTGGGGGATTCGAACCTGCAACCTGCTCTGATAACAAT
* * *
23588 TGTAGGATCGAGTCATTCATTTCTGAACAACTTCCCAGTGGGTCACCCATCCCTGGATTTCTCTT
1 TGTAGGATCGAGTCATTCATTTCTAAACAACTTCCCAGTGGGTCACCCATCCCTGGATTGCCCTT
* * *
23653 GTCAAATCACGCTTAACTATAGAGTTCTGAAGCGAATGATCACCATTCCTTCTTAAAACCAATTG
66 GTCAAAGCACGCTTAACTACAGAGTTCTGAAACGAATGATCACCATTCCTTCTTAAAACCAATTG
*
23718 GTGATAAGTAGGTGGGCCATTTTAACCTTATATCTTTGTAGTGGGTGATCACTGGGTTCCCCCAA
131 GTGATAAGTAGGTGGGCCATTTTAACCTTATATCTTTATAGTGGGTGATCACTGGGTTCCCCCAA
*
23783 GCCAAGGTAGATTCTTTTGGGGCACCCGCCACAGTTCACCACGGCATTGCAAAGCCCCGCATCTA
196 GCCAAGGTAGATTCTTTTGGGGCACCCGACACAGTTCACCACGGCATTGCAAAGCCCCGCATCTA
*
23848 TAGCGTACTGCGGGCGGGCCTAGGGGCTTTATAAGGCACACGTGGGCCTCGGCAGGTTGGACAGT
261 TAGCGTACTGCGGGCGGGCCTAGGGGCTTTATAAGGCACACGTGGGCCTCGACAGGTTGGACAGT
* * * * * *
23913 CACGTACCGATATCGCGCTCATACACGATAGAATCCCTAAGGGTGATCGCTGGGCCCCATAACCC
326 CACGTACCAATATCACGCCCATACACAATAGAATCCCTAAGGGTGATCACTGGACCCCATAACCC
23978 AACA
391 AACA
23982 TTATGCATGG
Statistics
Matches: 370, Mismatches: 24, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
450 370 1.00
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (450 bp):
TGTAGGATCGAGTCATTCATTTCTAAACAACTTCCCAGTGGGTCACCCATCCCTGGATTGCCCTT
GTCAAAGCACGCTTAACTACAGAGTTCTGAAACGAATGATCACCATTCCTTCTTAAAACCAATTG
GTGATAAGTAGGTGGGCCATTTTAACCTTATATCTTTATAGTGGGTGATCACTGGGTTCCCCCAA
GCCAAGGTAGATTCTTTTGGGGCACCCGACACAGTTCACCACGGCATTGCAAAGCCCCGCATCTA
TAGCGTACTGCGGGCGGGCCTAGGGGCTTTATAAGGCACACGTGGGCCTCGACAGGTTGGACAGT
CACGTACCAATATCACGCCCATACACAATAGAATCCCTAAGGGTGATCACTGGACCCCATAACCC
AACAATCACCCCCCAACGACACCTGGGGGATTCGAACCTGCAACCTGCTCTGATAACAAT
Found at i:25894 original size:30 final size:31
Alignment explanation
Indices: 25855--25921 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 31
25845 GAAAGACCTA
* * * *
25855 TCCAGAGGTCATAAAGAACCTCGG-CAACTG
1 TCCATAGGTCACAAAGAACCTAGGTAAACTG
* *
25885 TCCATAGGTCCCGAAGAACCTAGGTAAACTG
1 TCCATAGGTCACAAAGAACCTAGGTAAACTG
25916 TCCATA
1 TCCATA
25922 TGTTCCTTAG
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
30 19 0.63
31 11 0.37
ACGTcount: A:0.33, C:0.27, G:0.21, T:0.19
Consensus pattern (31 bp):
TCCATAGGTCACAAAGAACCTAGGTAAACTG
Found at i:25918 original size:31 final size:31
Alignment explanation
Indices: 25880--26099 Score: 189
Period size: 31 Copynumber: 7.0 Consensus size: 31
25870 GAACCTCGGC
* *
25880 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* ** *
25911 AACTGTCCATATGTTCCTTAGAACATAGTTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* * *
25942 TACTGTCCATAAGTCCCG-AGAAACATATGTA
1 AACTGTCCATATGTCCCGAAG-AACATAGGTA
* * *
25973 ATTCTATCCATATGTTCCGAAGAACATAGGTA
1 A-ACTGTCCATATGTCCCGAAGAACATAGGTA
*
26005 TACTGTCCATATGTCCCGAA-AGACATAGGTA
1 AACTGTCCATATGTCCCGAAGA-ACATAGGTA
*
26036 ATTA-TGTCCATATGGT-CCGTAGAACATAGGTA
1 A--ACTGTCCATAT-GTCCCGAAGAACATAGGTA
* **
26068 TACTGTCCATATGTCTTG-AGAGACATAGGTA
1 AACTGTCCATATGTCCCGAAGA-ACATAGGTA
26099 A
1 A
26100 TTCCTCGACT
Statistics
Matches: 150, Mismatches: 28, Indels: 22
0.75 0.14 0.11
Matches are distributed among these distances:
30 9 0.06
31 91 0.61
32 44 0.29
33 6 0.04
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.29
Consensus pattern (31 bp):
AACTGTCCATATGTCCCGAAGAACATAGGTA
Found at i:25997 original size:63 final size:62
Alignment explanation
Indices: 25881--26102 Score: 275
Period size: 63 Copynumber: 3.5 Consensus size: 62
25871 AACCTCGGCA
* * * * *
25881 ACTGTCCATAGGTCCCGAAGAACCTAGGTAA-ACTGTCCATATGTTCCTTAGAACATAGTTAT
1 ACTGTCCATATGTCCCGAA-AACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTAT
* * * *
25943 ACTGTCCATAAGTCCCGAGAAACATATGTAATTCTATCCATATGTTCCGAAGAACATAGGTAT
1 ACTGTCCATATGTCCCGA-AAACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTAT
* *
26006 ACTGTCCATATGTCCCGAAAGACATAGGTAATTATGTCCATATGGTCCGTAGAACATAGGTAT
1 ACTGTCCATATGTCCCGAAA-ACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTAT
** *
26069 ACTGTCCATATGTCTTGAGAGACATAGGTAATTC
1 ACTGTCCATATGTCCCGA-AAACATAGGTAATTC
26103 CTCGACTCTT
Statistics
Matches: 138, Mismatches: 18, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
62 28 0.20
63 109 0.79
64 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.29
Consensus pattern (62 bp):
ACTGTCCATATGTCCCGAAAACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTAT
Found at i:26077 original size:94 final size:94
Alignment explanation
Indices: 25881--26099 Score: 216
Period size: 94 Copynumber: 2.3 Consensus size: 94
25871 AACCTCGGCA
* * * ** *
25881 ACTGTCCATAGGTCCCGAAGAACCTAGGTAAACTGTCCATATGTTCCTTAGAACATAGTTATACT
1 ACTGTCCATATGTCCCGAAGAACATAGGTAAACTGTCCATATGTCCCAAAGAACATAGTAATACT
*
25946 GTCCATAAGTCCCGAGAAACATATGTAAT
66 GTCCATAAGTCCCGAGAAACATAGGTAAT
* * * *
25975 TCTATCCATATGTTCCGAAGAACATAGGTATACTGTCCATATGTCCCGAAAG-ACATAGGTAATT
1 ACTGTCCATATGTCCCGAAGAACATAGGTAAACTGTCCATATGTCCC-AAAGAACATA-GTAA-T
*
26039 A-TGTCCATATGGT-CCGTAG-AACATAGGT-AT
63 ACTGTCCATA-AGTCCCG-AGAAACATAGGTAAT
**
26069 ACTGTCCATATGTCTTG-AGAGACATAGGTAA
1 ACTGTCCATATGTCCCGAAGA-ACATAGGTAA
26100 TTCCTCGACT
Statistics
Matches: 101, Mismatches: 18, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
93 3 0.03
94 68 0.67
95 24 0.24
96 6 0.06
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (94 bp):
ACTGTCCATATGTCCCGAAGAACATAGGTAAACTGTCCATATGTCCCAAAGAACATAGTAATACT
GTCCATAAGTCCCGAGAAACATAGGTAAT
Found at i:30707 original size:4 final size:4
Alignment explanation
Indices: 30698--30738 Score: 50
Period size: 4 Copynumber: 10.5 Consensus size: 4
30688 AAAAAACATG
*
30698 AAAT AAAT AAAT -ATT AAAT AAAT AAAAT AAAT AAA- AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AA
30739 CAACATACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
3 5 0.16
4 23 0.72
5 4 0.12
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:31917 original size:21 final size:19
Alignment explanation
Indices: 31879--31921 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
31869 CAAAGGTAAC
31879 CTCATTTTCCTTATTTTCT
1 CTCATTTTCCTTATTTTCT
*
31898 CTCATATTTCGTTATGTTTCT
1 CTCAT-TTTCCTTAT-TTTCT
31919 CTC
1 CTC
31922 TATCTTTTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
20 8 0.38
21 8 0.38
ACGTcount: A:0.12, C:0.26, G:0.05, T:0.58
Consensus pattern (19 bp):
CTCATTTTCCTTATTTTCT
Found at i:34449 original size:14 final size:14
Alignment explanation
Indices: 34430--34464 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
34420 CTCTGGTTGT
34430 GTTACTTTCTTAGA
1 GTTACTTTCTTAGA
34444 GTTACTTTCTTAGA
1 GTTACTTTCTTAGA
*
34458 GTAACTT
1 GTTACTT
34465 GTGAGGTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.23, C:0.14, G:0.14, T:0.49
Consensus pattern (14 bp):
GTTACTTTCTTAGA
Found at i:38298 original size:3 final size:3
Alignment explanation
Indices: 38290--38351 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
38280 ATATTTTTGT
38290 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
38338 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
38352 TTTTTTCGAC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:38449 original size:63 final size:64
Alignment explanation
Indices: 38350--38473 Score: 187
Period size: 63 Copynumber: 2.0 Consensus size: 64
38340 ATAATAATAA
** * *
38350 TATTTTTTCGACTTGGACAAAAATATATTTCAACAATATAAAGATAT-AAATTAACATAACTAG
1 TATTTTTTCGACCCGGACAAAAACATATTTCAACAATATAAAGATATAAAAATAACATAACTAG
* *
38413 TATTTTTTCGACCCGGACAAAAACATGTTTCTACAATATAAAGATATAAAAATAACATAAC
1 TATTTTTTCGACCCGGACAAAAACATATTTCAACAATATAAAGATATAAAAATAACATAAC
38474 CGATTACATT
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
63 42 0.78
64 12 0.22
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.32
Consensus pattern (64 bp):
TATTTTTTCGACCCGGACAAAAACATATTTCAACAATATAAAGATATAAAAATAACATAACTAG
Found at i:48218 original size:21 final size:21
Alignment explanation
Indices: 48169--48220 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
48159 GTTTCCAGAT
* **
48169 TCGCAACGCGGACTTTGACTA
1 TCGCAATGCGGACTTCAACTA
48190 TCGCAATGCGGACTTCAACTA
1 TCGCAATGCGGACTTCAACTA
*
48211 TCGTAATGCG
1 TCGCAATGCG
48221 AACGTATCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (21 bp):
TCGCAATGCGGACTTCAACTA
Found at i:48253 original size:6 final size:6
Alignment explanation
Indices: 48242--48274 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
48232 GACACGTATT
48242 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
48275 CGAGACGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:48783 original size:6 final size:6
Alignment explanation
Indices: 48774--48798 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
48764 GCCGCCCGTC
48774 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
48799 AATACGTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.36
Consensus pattern (6 bp):
TCGTGG
Found at i:48940 original size:21 final size:21
Alignment explanation
Indices: 48888--49031 Score: 127
Period size: 21 Copynumber: 6.9 Consensus size: 21
48878 CGTTGCGATT
*
48888 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAATGCGAAC
* *
48907 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAATGCGAAC
48930 TTGGACTATCGCAATGCGAA-
1 TTGGACTATCGCAATGCGAAC
* *
48950 TATGTA-AATCGCAATGCGATA-
1 T-TGGACTATCGCAATGCGA-AC
* *
48971 GTCGACTATCGCAATGCGAAC
1 TTGGACTATCGCAATGCGAAC
*
48992 TTGGACTATCGCAACGCGAAC
1 TTGGACTATCGCAATGCGAAC
* *
49013 TTCGACTATCGCATTGCGA
1 TTGGACTATCGCAATGCGA
49032 TTTACATATT
Statistics
Matches: 101, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
19 6 0.06
20 16 0.16
21 69 0.68
23 10 0.10
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (21 bp):
TTGGACTATCGCAATGCGAAC
Found at i:49119 original size:41 final size:41
Alignment explanation
Indices: 49062--49147 Score: 129
Period size: 41 Copynumber: 2.1 Consensus size: 41
49052 TAGTTGATTA
* *
49062 CGATTTACATATTCGCATTGCGATAGT-CGACTATCGCATTG
1 CGATTTACATATTCGCATTACGATAGTCCAACT-TCGCATTG
*
49103 CGATTTACATATTCGCATTACGATAGTCCAAGTTCGCATTG
1 CGATTTACATATTCGCATTACGATAGTCCAACTTCGCATTG
49144 CGAT
1 CGAT
49148 AGTCGACTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
41 38 0.93
42 3 0.07
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.34
Consensus pattern (41 bp):
CGATTTACATATTCGCATTACGATAGTCCAACTTCGCATTG
Found at i:49154 original size:62 final size:62
Alignment explanation
Indices: 49073--49215 Score: 259
Period size: 62 Copynumber: 2.3 Consensus size: 62
49063 GATTTACATA
*
49073 TTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATATTCGCATTACGATAGTCCAAG
1 TTCGCATTGCGATAGTCGACTATCGCATTACGATTTACATATTCGCATTACGATAGTCCAAG
* *
49135 TTCGCATTGCGATAGTCGACTATCGCATTACGATTTACATATTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCGACTATCGCATTACGATTTACATATTCGCATTACGATAGTCCAAG
49197 TTCGCATTGCGATAGTCGA
1 TTCGCATTGCGATAGTCGA
49216 AGTTCGCGTT
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 78 1.00
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (62 bp):
TTCGCATTGCGATAGTCGACTATCGCATTACGATTTACATATTCGCATTACGATAGTCCAAG
Found at i:49216 original size:21 final size:21
Alignment explanation
Indices: 49073--49229 Score: 132
Period size: 21 Copynumber: 7.6 Consensus size: 21
49063 GATTTACATA
*
49073 TTCGCATTGCGATAGTCG-AC
1 TTCGCATTGCGATAGTCGAAG
*
49093 TATCGCATTGCGAT-TTAC-ATA-
1 T-TCGCATTGCGATAGT-CGA-AG
* *
49114 TTCGCATTACGATAGTCCAAG
1 TTCGCATTGCGATAGTCGAAG
*
49135 TTCGCATTGCGATAGTCG-AC
1 TTCGCATTGCGATAGTCGAAG
* *
49155 TATCGCATTACGAT-TTAC-ATA-
1 T-TCGCATTGCGATAGT-CGA-AG
49176 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCGAAG
49197 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCGAAG
*
49218 TTCGCGTTGCGA
1 TTCGCATTGCGA
49230 ATCTGGAAAC
Statistics
Matches: 112, Mismatches: 11, Indels: 27
0.75 0.07 0.18
Matches are distributed among these distances:
20 31 0.28
21 79 0.71
22 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCGAAG
Found at i:49490 original size:19 final size:20
Alignment explanation
Indices: 49453--49491 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
49443 AAATTAAATT
49453 ATTTATGAATAATAATAGTA
1 ATTTATGAATAATAATAGTA
* *
49473 ATTTATTAA-AATAGTAGTA
1 ATTTATGAATAATAATAGTA
49492 GTAAAGTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (20 bp):
ATTTATGAATAATAATAGTA
Found at i:51799 original size:20 final size:20
Alignment explanation
Indices: 51751--51812 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 20
51741 AACTTAAATC
*
51751 AAAATAATTAAAATAA-ATAT
1 AAAATAATT-TAATAATATAT
51771 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAATATAT
51789 AAAATAATTT-AT-ATGATAT
1 AAAATAATTTAATAAT-ATAT
51808 AAAAT
1 AAAAT
51813 TAAATATCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 5 0.14
18 13 0.35
19 11 0.30
20 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAATAATTTAATAATATAT
Found at i:51896 original size:62 final size:63
Alignment explanation
Indices: 51807--51961 Score: 230
Period size: 63 Copynumber: 2.5 Consensus size: 63
51797 TTATATGATA
*
51807 TAAAATTAAATATCTATAATATAATATTAAAAATTAATATTTAATTTATTT-AAAAATTAATAT
1 TAAAATT-AATATATATAATATAATATTAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
*
51870 TAAAATTAATATATATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTGATAT
1 TAAAATTAATATATATAATATAATATT-AAAAATTAATATTTAATTTATTTAAAAAATTAATAT
51934 TAAAATTAA-A-ATCA-AATATAATA-TAAAA
1 TAAAATTAATATAT-ATAATATAATATTAAAA
51962 CCTCTTTGAA
Statistics
Matches: 87, Mismatches: 2, Indels: 9
0.89 0.02 0.09
Matches are distributed among these distances:
60 4 0.05
61 1 0.01
62 30 0.34
63 32 0.37
64 20 0.23
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (63 bp):
TAAAATTAATATATATAATATAATATTAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
Found at i:51908 original size:40 final size:36
Alignment explanation
Indices: 51828--51910 Score: 105
Period size: 40 Copynumber: 2.2 Consensus size: 36
51818 ATCTATAATA
*
51828 TAATATTAAAAATTAATATTTAATTTATTTAAAAAT
1 TAATATTAAAAATTAATATTTAATTTATTAAAAAAT
51864 TAATATT-AAAATTAATATATATAATATAATATTAAAAAAT
1 TAATATTAAAAATTAATAT-T-TAAT-T--TATTAAAAAAT
51904 TAATATT
1 TAATATT
51911 TAATTTATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
35 11 0.27
36 8 0.20
37 4 0.10
38 1 0.02
40 17 0.41
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (36 bp):
TAATATTAAAAATTAATATTTAATTTATTAAAAAAT
Found at i:51914 original size:26 final size:26
Alignment explanation
Indices: 51861--51942 Score: 91
Period size: 24 Copynumber: 3.2 Consensus size: 26
51851 TTTATTTAAA
51861 AATTAATATT--AAAATTAATATATAT
1 AATTAATATTAAAAAATTAATAT-TAT
51886 AATATAATATTAAAAAATTAATATT-T
1 AAT-TAATATTAAAAAATTAATATTAT
* * *
51912 AATTTAT-TTAAAAAATTGATATTAA
1 AATTAATATTAAAAAATTAATATTAT
51937 AATTAA
1 AATTAA
51943 AATCAAATAT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
24 15 0.31
25 11 0.22
26 11 0.22
27 1 0.02
28 11 0.22
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (26 bp):
AATTAATATTAAAAAATTAATATTAT
Found at i:52396 original size:24 final size:24
Alignment explanation
Indices: 52369--52426 Score: 116
Period size: 24 Copynumber: 2.4 Consensus size: 24
52359 TGGAGTTATG
52369 GTATCGATACTACTATGTAAAGTA
1 GTATCGATACTACTATGTAAAGTA
52393 GTATCGATACTACTATGTAAAGTA
1 GTATCGATACTACTATGTAAAGTA
52417 GTATCGATAC
1 GTATCGATAC
52427 CCCTTTGAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (24 bp):
GTATCGATACTACTATGTAAAGTA
Found at i:53802 original size:19 final size:19
Alignment explanation
Indices: 53755--53804 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
53745 GATCACCAAT
*
53755 TCAATCAAAAAAGCAGACA
1 TCAATCAAAGAAGCAGACA
*
53774 TCAATCAAAGAAGCAGATA
1 TCAATCAAAGAAGCAGACA
53793 TCAATCAAAGAA
1 TCAATCAAAGAA
53805 ACCCCATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.56, C:0.18, G:0.12, T:0.14
Consensus pattern (19 bp):
TCAATCAAAGAAGCAGACA
Found at i:56450 original size:10 final size:10
Alignment explanation
Indices: 56435--56462 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
56425 TTTAAAGTGA
56435 AAAGAAAATT
1 AAAGAAAATT
56445 AAAGAAAATT
1 AAAGAAAATT
56455 AAAGAAAA
1 AAAGAAAA
56463 AAAATAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.14
Consensus pattern (10 bp):
AAAGAAAATT
Found at i:57666 original size:14 final size:15
Alignment explanation
Indices: 57630--57667 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
57620 AAAGAACTTG
57630 AAAAGAAT-TCAATA
1 AAAAGAATCTCAATA
57644 AAAAGAATCT-AATA
1 AAAAGAATCTCAATA
57658 AAAAGAATCT
1 AAAAGAATCT
57668 TCAAAGGCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 22 0.96
15 1 0.04
ACGTcount: A:0.63, C:0.08, G:0.08, T:0.21
Consensus pattern (15 bp):
AAAAGAATCTCAATA
Found at i:64051 original size:126 final size:125
Alignment explanation
Indices: 63826--64082 Score: 417
Period size: 126 Copynumber: 2.0 Consensus size: 125
63816 AGAACTGCCT
* *
63826 ATCATATACACTCCGACAACCATTTTTTAGGCATATTTGAAGCCAACTTTGCAGTTTAATCAAGG
1 ATCATTTACACTCCGACAACCAATTTTTAGGCATATTTGAAGCCAACTTTGCAGTTTAATCAAGG
* *
63891 TATGAGACAATGTTAACCCTTCTCAAAGAAAACATTTCTTGATAAATACCTTCCACTAGTC
66 TATGAGACAATGCTAACCCTTCTCAAAGAAAACATTTCTTCATAAATACC-TCCACTAGTC
*
63952 ATCATTTACACTCTGACAACCAATTTTTAGGCATATTTGAAGCCAACTTTGCAGTTTAATCAAGG
1 ATCATTTACACTCCGACAACCAATTTTTAGGCATATTTGAAGCCAACTTTGCAGTTTAATCAAGG
* * *
64017 TATG-GAACAATGCTAACCCTTTTTAAAGAAAACATTTCTTCATAAATACCTCTACTAGTC
66 TATGAG-ACAATGCTAACCCTTCTCAAAGAAAACATTTCTTCATAAATACCTCCACTAGTC
64077 ATCATT
1 ATCATT
64083 GAACAGACTA
Statistics
Matches: 122, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
125 16 0.13
126 106 0.87
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.33
Consensus pattern (125 bp):
ATCATTTACACTCCGACAACCAATTTTTAGGCATATTTGAAGCCAACTTTGCAGTTTAATCAAGG
TATGAGACAATGCTAACCCTTCTCAAAGAAAACATTTCTTCATAAATACCTCCACTAGTC
Found at i:66678 original size:2 final size:2
Alignment explanation
Indices: 66673--66700 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
66663 GATTTAACTC
66673 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
66701 TAATAATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:71348 original size:30 final size:31
Alignment explanation
Indices: 71287--71357 Score: 108
Period size: 30 Copynumber: 2.3 Consensus size: 31
71277 GTTATATGAG
* *
71287 CTATGTGATAAAGGTATGGAAAATGATATGT
1 CTATGTGATAAAGGTATAGAAAATAATATGT
71318 CTATGTGATAAAGGTATAG-AAATAATATGT
1 CTATGTGATAAAGGTATAGAAAATAATATGT
*
71348 CTATGAGATA
1 CTATGTGATA
71358 CACTATGTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
30 19 0.51
31 18 0.49
ACGTcount: A:0.41, C:0.04, G:0.23, T:0.32
Consensus pattern (31 bp):
CTATGTGATAAAGGTATAGAAAATAATATGT
Found at i:71552 original size:20 final size:20
Alignment explanation
Indices: 71524--71571 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
71514 GACACCTATT
*
71524 TGATCCTTGGTATATGTATA
1 TGATTCTTGGTATATGTATA
71544 TGATTCTTGGTATATGTATA
1 TGATTCTTGGTATATGTATA
71564 TGATTCTT
1 TGATTCTT
71572 AAGGAATTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.23, C:0.08, G:0.19, T:0.50
Consensus pattern (20 bp):
TGATTCTTGGTATATGTATA
Found at i:71698 original size:24 final size:23
Alignment explanation
Indices: 71618--71695 Score: 70
Period size: 23 Copynumber: 3.3 Consensus size: 23
71608 TATGGCACCA
71618 CGGTGCAATTCTACGTGGCACTT
1 CGGTGCAATTCTACGTGGCACTT
* * *
71641 CGGTACATTTCTACGCGGTC-CTT
1 CGGTGCAATTCTACGTGG-CACTT
* *
71664 TGG-GATAAATTCTACGTGGCACTT
1 CGGTG--CAATTCTACGTGGCACTT
71688 CGGTGCAA
1 CGGTGCAA
71696 ATTTATACGA
Statistics
Matches: 40, Mismatches: 10, Indels: 10
0.67 0.17 0.17
Matches are distributed among these distances:
23 23 0.57
24 16 0.40
25 1 0.03
ACGTcount: A:0.19, C:0.24, G:0.26, T:0.31
Consensus pattern (23 bp):
CGGTGCAATTCTACGTGGCACTT
Found at i:73772 original size:20 final size:20
Alignment explanation
Indices: 73757--73823 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
73747 CATTCCATAT
73757 TCTTCCATAAGGTTCCACAC
1 TCTTCCATAAGGTTCCACAC
*
73777 TCTTCCATAAGGTTTCACAC
1 TCTTCCATAAGGTTCCACAC
*
73797 TCTTCCATAAGGTTTCACAC
1 TCTTCCATAAGGTTCCACAC
73817 TCTTCCA
1 TCTTCCA
73824 GAATATTCTA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.24, C:0.33, G:0.09, T:0.34
Consensus pattern (20 bp):
TCTTCCATAAGGTTCCACAC
Found at i:74578 original size:29 final size:29
Alignment explanation
Indices: 74545--74617 Score: 69
Period size: 29 Copynumber: 2.4 Consensus size: 29
74535 AAAATTTGAC
*
74545 TAGTA-ACTAAAATATAAATTTTGAAAATT
1 TAGTAGAC-AAAATATAAATTTGGAAAATT
* *
74574 TAGTAGGCAAAGTATAAATTTGGAAAAAGTT
1 TAGTAGACAAAATATAAATTTGG-AAAA-TT
74605 TAGT-GACCAAAAT
1 TAGTAGA-CAAAAT
74618 GATCATTTTC
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
29 18 0.51
30 6 0.17
31 11 0.31
ACGTcount: A:0.48, C:0.05, G:0.15, T:0.32
Consensus pattern (29 bp):
TAGTAGACAAAATATAAATTTGGAAAATT
Found at i:77228 original size:26 final size:26
Alignment explanation
Indices: 77199--77251 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
77189 TACATTTATA
*
77199 TATTTGGGATCATAGGTACATTGTTG
1 TATTCGGGATCATAGGTACATTGTTG
77225 TATTCGGGATCATAGGTACATTGTTG
1 TATTCGGGATCATAGGTACATTGTTG
77251 T
1 T
77252 TGTGTTCTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.09, G:0.26, T:0.42
Consensus pattern (26 bp):
TATTCGGGATCATAGGTACATTGTTG
Found at i:77296 original size:54 final size:54
Alignment explanation
Indices: 77236--77340 Score: 183
Period size: 54 Copynumber: 1.9 Consensus size: 54
77226 ATTCGGGATC
* *
77236 ATAGGTACATTGTTGTTGTGTTCTATAGTACTTGTACATTCACAGGGCACTATT
1 ATAGGTACATTGTTGTTGTGTTCTACAATACTTGTACATTCACAGGGCACTATT
*
77290 ATAGGTACATTGTTGTTGTGTTCTACAATATTTGTACATTCACAGGGCACT
1 ATAGGTACATTGTTGTTGTGTTCTACAATACTTGTACATTCACAGGGCACT
77341 GAATATACCA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (54 bp):
ATAGGTACATTGTTGTTGTGTTCTACAATACTTGTACATTCACAGGGCACTATT
Found at i:77773 original size:17 final size:17
Alignment explanation
Indices: 77743--77787 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
77733 AAAGAATCAG
*
77743 TAAAAGAAACAATAGAA
1 TAAAAGAAATAATAGAA
* *
77760 TAAGAGAAATAATATAA
1 TAAAAGAAATAATAGAA
77777 TAAAAGAAATA
1 TAAAAGAAATA
77788 GTAAGGTGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.69, C:0.02, G:0.11, T:0.18
Consensus pattern (17 bp):
TAAAAGAAATAATAGAA
Found at i:81236 original size:97 final size:97
Alignment explanation
Indices: 81070--81266 Score: 394
Period size: 97 Copynumber: 2.0 Consensus size: 97
81060 TTCCTAGATC
81070 TATGTACTATGTTTTATATCACTTAAGAATTGAATCAGTTTTAAATCATCATTTCATTGAAACAT
1 TATGTACTATGTTTTATATCACTTAAGAATTGAATCAGTTTTAAATCATCATTTCATTGAAACAT
81135 CTGGAATTTTCTATACAACATATATATATATA
66 CTGGAATTTTCTATACAACATATATATATATA
81167 TATGTACTATGTTTTATATCACTTAAGAATTGAATCAGTTTTAAATCATCATTTCATTGAAACAT
1 TATGTACTATGTTTTATATCACTTAAGAATTGAATCAGTTTTAAATCATCATTTCATTGAAACAT
81232 CTGGAATTTTCTATACAACATATATATATATA
66 CTGGAATTTTCTATACAACATATATATATATA
81264 TAT
1 TAT
81267 ATATATATAT
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 100 1.00
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.43
Consensus pattern (97 bp):
TATGTACTATGTTTTATATCACTTAAGAATTGAATCAGTTTTAAATCATCATTTCATTGAAACAT
CTGGAATTTTCTATACAACATATATATATATA
Found at i:81258 original size:2 final size:2
Alignment explanation
Indices: 81251--81306 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
81241 TCTATACAAC
81251 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
81293 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
81307 CCCTATTTGA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:82643 original size:64 final size:63
Alignment explanation
Indices: 82520--82656 Score: 143
Period size: 64 Copynumber: 2.2 Consensus size: 63
82510 CCTTTAACAT
* * *
82520 GTGCATCGATGCACTACCCATGCATCAATACACCAATCACCTTCAATGTTTTCATTTTAAGGGG
1 GTGCATCGATGCACTACCCATGCATCAATACACCAATCACATTCAATGTTTTCATTTTAA-AGA
* * * * ** *
82584 GTGCATCGATGCACT-CCTTATGCATCGATGCACTAATTGCATTCAATG-TTTCTTCTTTAAAGA
1 GTGCATCGATGCACTACC-CATGCATCAATACACCAATCACATTCAATGTTTTCAT-TTTAAAGA
82647 GTGCATCGAT
1 GTGCATCGAT
82657 ACACCTTGCC
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
63 18 0.30
64 43 0.70
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTACCCATGCATCAATACACCAATCACATTCAATGTTTTCATTTTAAAGA
Found at i:86057 original size:234 final size:224
Alignment explanation
Indices: 85619--86074 Score: 668
Period size: 234 Copynumber: 2.0 Consensus size: 224
85609 CTTTATTTCA
* *
85619 GTCGGGTCGGGTCGGTTTTTTTAAGTGTGATATTCGGGTCGAGTTCGGGTTTAGGATGAAATATA
1 GTCGGGTCGGGTCGGTTTTTTTAAGTGTGATATTCGGGTCGAGTTCGAGTTTAGGATGAAAAATA
* * *
85684 CCCGACCCGAAAATATATAATTTACCTTATATATTTAGGAATAATTACAATAATACCGCTCTATA
66 ACCGACCCGAAAAAATATAATTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTATA
* *
85749 TATTTTTTTTCAATTAAGTCACTGTTTTTATTGAATAAAATATTTTTTTATTATTTCGGGTCGGG
131 TATTTTTTTTCAATTAAGTCAATATTTTTATTGAATAAAATATTTTTTTATTATTTCGGGTCGGG
85814 TCGGGTCGGATTTCTAATTCATATATTCG
196 TCGGGTCGGATTTCTAATTCATATATTCG
85843 GTCGGGTC-GGTCGGGTTTTTTTAAGTGTGATACTCGGTCGGGTCG-GTTCGAGTTTA-GAGTGA
1 GTCGGGTCGGGTC-GGTTTTTTTAAGTGTGATA-T---TCGGGTCGAGTTCGAGTTTAGGA-TG-
85905 AAAAATCAAACCGACCCGAAAAAAATATAATTTTACCTTATATATTTAGGAATAATTACAATAAT
59 AAAAAT--AACCGACCCG-AAAAAATATAA-TTTACCTTATATATTTAGGAATAATTACAATAAT
85970 ACCCCTCTATATATATTTTTTTCCAATTAAGTCAATATTTTTATTGAATAAAAGTATTTTTTTAT
120 ACCCCTCTATATAT-TTTTTTT-CAATTAAGTCAATATTTTTATTGAATAAAA-TATTTTTTTAT
* * *
86035 TATTTTGTGTCGTGTC-GGTCGGATTTCTAATTCATATATT
182 TATTTCGGGTCGGGTCGGGTCGGATTTCTAATTCATATATT
86075 GAATAAAATA
Statistics
Matches: 208, Mismatches: 10, Indels: 18
0.88 0.04 0.08
Matches are distributed among these distances:
223 4 0.02
224 27 0.13
225 1 0.00
226 2 0.01
227 12 0.06
228 13 0.06
230 9 0.04
231 10 0.05
232 47 0.23
233 7 0.03
234 52 0.25
235 24 0.12
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41
Consensus pattern (224 bp):
GTCGGGTCGGGTCGGTTTTTTTAAGTGTGATATTCGGGTCGAGTTCGAGTTTAGGATGAAAAATA
ACCGACCCGAAAAAATATAATTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTATA
TATTTTTTTTCAATTAAGTCAATATTTTTATTGAATAAAATATTTTTTTATTATTTCGGGTCGGG
TCGGGTCGGATTTCTAATTCATATATTCG
Found at i:87498 original size:15 final size:15
Alignment explanation
Indices: 87478--87507 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
87468 TTACTATTCA
87478 CGTGAATAGTGAATT
1 CGTGAATAGTGAATT
87493 CGTGAATAGTGAATT
1 CGTGAATAGTGAATT
87508 TGGTCGGCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.27, T:0.33
Consensus pattern (15 bp):
CGTGAATAGTGAATT
Done.