Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000308.1 Hibiscus syriacus cultivar Beakdansim tig00000578_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: 95325
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:846 original size:3 final size:3
Alignment explanation
Indices: 840--914 Score: 55
Period size: 3 Copynumber: 25.3 Consensus size: 3
830 TTTTTTATTT
* * * *
840 TAA TAA TAA TTA T-A TAA TAA TTA TAA TAA TAA TAC TAA TATT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
* * **
885 TAT TAA TAA TAG TAA TCT TAA -AA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
915 TTAAGTAAAT
Statistics
Matches: 54, Mismatches: 15, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
2 4 0.07
3 48 0.89
4 2 0.04
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:858 original size:11 final size:12
Alignment explanation
Indices: 840--872 Score: 59
Period size: 11 Copynumber: 2.8 Consensus size: 12
830 TTTTTTATTT
840 TAATAATAATTA
1 TAATAATAATTA
852 T-ATAATAATTA
1 TAATAATAATTA
863 TAATAATAAT
1 TAATAATAAT
873 ACTAATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TAATAATAATTA
Found at i:3316 original size:169 final size:170
Alignment explanation
Indices: 3036--3358 Score: 540
Period size: 169 Copynumber: 1.9 Consensus size: 170
3026 CTGATCCCAA
*
3036 TTTTAATGATTAAACGGTTAAAGGAGCGGAGGAGGGCAACCCATGAACATATAGATATATCTAGG
1 TTTTAATGATTAAACGGTTAAAGGAGCGGAGGAGGGCAACCCATGAACACATAGATATATCTAGG
* *
3101 ATGAACTAGTTTAACAATCACTCCTAAAATTTTTAAATTCTTATATAATTTAAGAATTATACATC
66 ATGAACTAGTTGAACAATCACTCCTAAAAATTTTAAATTCTTATATAATTTAAGAATTATACATC
*
3166 ACTAAATTATTTAATCTTTTTATTATCAATTTTTTAGATT
131 ACTAAATTATTTAATCCTTTTATTATCAATTTTTTAGATT
* * * *
3206 TTTTAATGATTAAATGGTTAAAGGAGCGGATGA-GGCAACCCATGAACACATAGATATATTTCGG
1 TTTTAATGATTAAACGGTTAAAGGAGCGGAGGAGGGCAACCCATGAACACATAGATATATCTAGG
* *
3270 ATGAGCTGGTTGAACAATCACTCCTAAAAATTTTAAATTCTTATATAATTTAAGAATTATACATC
66 ATGAACTAGTTGAACAATCACTCCTAAAAATTTTAAATTCTTATATAATTTAAGAATTATACATC
*
3335 ACTCAATTATTTAATCCTTTTATT
131 ACTAAATTATTTAATCCTTTTATT
3359 TTTATTATCA
Statistics
Matches: 142, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
169 111 0.78
170 31 0.22
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (170 bp):
TTTTAATGATTAAACGGTTAAAGGAGCGGAGGAGGGCAACCCATGAACACATAGATATATCTAGG
ATGAACTAGTTGAACAATCACTCCTAAAAATTTTAAATTCTTATATAATTTAAGAATTATACATC
ACTAAATTATTTAATCCTTTTATTATCAATTTTTTAGATT
Found at i:3652 original size:34 final size:34
Alignment explanation
Indices: 3608--3688 Score: 103
Period size: 35 Copynumber: 2.4 Consensus size: 34
3598 TATTATAATT
* *
3608 ATATATATATATATAACTC-AATTATTTTTATTA
1 ATATATATATATATAAATCAAATTACTTTTATTA
*
3641 A-ATATAAATATACTTAAATCAAATTACTTTTATTA
1 ATATATATATATA--TAAATCAAATTACTTTTATTA
3676 ATATATATATATA
1 ATATATATATATA
3689 ATTATTTATA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
32 10 0.25
33 1 0.03
34 5 0.12
35 14 0.35
36 10 0.25
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (34 bp):
ATATATATATATATAAATCAAATTACTTTTATTA
Found at i:18269 original size:54 final size:54
Alignment explanation
Indices: 18206--18313 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
18196 GATAAAATCT
18206 CACTATACGGAGGTGGTACTTGGTCTTCTGTTGTGTGAAGTAGAAGATGTCACA
1 CACTATACGGAGGTGGTACTTGGTCTTCTGTTGTGTGAAGTAGAAGATGTCACA
18260 CACTATACGGAGGTGGTACTTGGTCTTCTGTTGTGTGAAGTAGAAGATGTCACA
1 CACTATACGGAGGTGGTACTTGGTCTTCTGTTGTGTGAAGTAGAAGATGTCACA
18314 GTAATGGGTC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.24, C:0.15, G:0.30, T:0.31
Consensus pattern (54 bp):
CACTATACGGAGGTGGTACTTGGTCTTCTGTTGTGTGAAGTAGAAGATGTCACA
Found at i:18628 original size:29 final size:29
Alignment explanation
Indices: 18575--18647 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
18565 AACCCAACCA
* **
18575 TAGGTCGCCATGCACTCCCAACGACCTCC
1 TAGGTCGCCATGCACGCCCAACGACCAAC
** *
18604 TAGGTCGCCATGCACGCCCGGCGACCAAG
1 TAGGTCGCCATGCACGCCCAACGACCAAC
*
18633 GAGGTCGCCATGCAC
1 TAGGTCGCCATGCAC
18648 TCGGGGAGAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.21, C:0.40, G:0.26, T:0.14
Consensus pattern (29 bp):
TAGGTCGCCATGCACGCCCAACGACCAAC
Found at i:18658 original size:29 final size:29
Alignment explanation
Indices: 18605--18663 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
18595 ACGACCTCCT
*
18605 AGGTCGCCATGCACGCCCGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGAGACCAAGG
* **
18634 AGGTCGCCATGCACTCGGGGAGACCAAGG
1 AGGTCGCCATGCACGCCCGGAGACCAAGG
18663 A
1 A
18664 TTCATTCATG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.24, C:0.32, G:0.36, T:0.08
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGAGACCAAGG
Found at i:18938 original size:29 final size:29
Alignment explanation
Indices: 18887--18962 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
18877 TGTCGCCGCA
* **
18887 AGTGCATGGCGACCTCCTTGGTCG-TCGGG
1 AGTGCATGGCGACCTACGAGGTCGCT-GGG
* *
18916 CGTGCATGGCGACCTAGGAGGTCGCTGGG
1 AGTGCATGGCGACCTACGAGGTCGCTGGG
18945 AGTGCATGGCGACCTACG
1 AGTGCATGGCGACCTACG
18963 GCCACTGTTG
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
29 38 0.97
30 1 0.03
ACGTcount: A:0.14, C:0.26, G:0.39, T:0.20
Consensus pattern (29 bp):
AGTGCATGGCGACCTACGAGGTCGCTGGG
Found at i:20237 original size:21 final size:21
Alignment explanation
Indices: 20208--20247 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
20198 TTTTTATTAT
* *
20208 TTTATTAAAAGAATTGGTATG
1 TTTAGTAAAACAATTGGTATG
*
20229 TTTAGTAAAACACTTGGTA
1 TTTAGTAAAACAATTGGTA
20248 CATTTAGACT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.05, G:0.17, T:0.40
Consensus pattern (21 bp):
TTTAGTAAAACAATTGGTATG
Found at i:24166 original size:57 final size:57
Alignment explanation
Indices: 24105--24323 Score: 332
Period size: 57 Copynumber: 3.8 Consensus size: 57
24095 TTCGTATACC
* * * * *
24105 GGAACTGGTGGAGGCAA-TGGTTTATTATATACGGGAACTGGCGGAGGCTTGTAGATT
1 GGAACTGGAGGAGG-AAGTGGCTTCTTATACACCGGAACTGGCGGAGGCTTGTAGATT
*
24162 GGAACTGGAGGGGGAAGTGGCTTCTTATACACCGGAACTGGCGGAGGCTTGTAGATT
1 GGAACTGGAGGAGGAAGTGGCTTCTTATACACCGGAACTGGCGGAGGCTTGTAGATT
* *
24219 GGAACTGGAGGAGGAAGTGGTTTCTTATACACCGGAACTGGTGGAGGCTTGTAGATT
1 GGAACTGGAGGAGGAAGTGGCTTCTTATACACCGGAACTGGCGGAGGCTTGTAGATT
* *
24276 GGAACTGGAGGAGGAAGTGGCTTCTTATACACTGGAACTGGTGGAGGC
1 GGAACTGGAGGAGGAAGTGGCTTCTTATACACCGGAACTGGCGGAGGC
24324 AATGGCTTCT
Statistics
Matches: 150, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
56 2 0.01
57 148 0.99
ACGTcount: A:0.24, C:0.13, G:0.38, T:0.25
Consensus pattern (57 bp):
GGAACTGGAGGAGGAAGTGGCTTCTTATACACCGGAACTGGCGGAGGCTTGTAGATT
Found at i:24312 original size:33 final size:33
Alignment explanation
Indices: 24275--24478 Score: 194
Period size: 33 Copynumber: 6.5 Consensus size: 33
24265 GCTTGTAGAT
24275 TGGAACTGGAGGAGGAAGTGGCTTCTTATACAC
1 TGGAACTGGAGGAGGAAGTGGCTTCTTATACAC
* *
24308 TGGAACTGGTGGAGGCAA-TGGCTTCTTATATAC
1 TGGAACTGGAGGAGG-AAGTGGCTTCTTATACAC
* * * *
24341 GGGAACTGGAGGA-G-A-------CTTGTAGAT
1 TGGAACTGGAGGAGGAAGTGGCTTCTTATACAC
* * *
24365 TGGAACTGGTGGAGGAAGTGGTTTCTTATATAC
1 TGGAACTGGAGGAGGAAGTGGCTTCTTATACAC
* * *
24398 TGGAACCGGAGGAGGATGTGGCTTCTTGTACAC
1 TGGAACTGGAGGAGGAAGTGGCTTCTTATACAC
*
24431 TGGAACTGGAGGAGGAAGTGGTTTCTTATACAC
1 TGGAACTGGAGGAGGAAGTGGCTTCTTATACAC
* *
24464 CGGAACTGGTGGAGG
1 TGGAACTGGAGGAGG
24479 TTTATAGATT
Statistics
Matches: 137, Mismatches: 24, Indels: 20
0.76 0.13 0.11
Matches are distributed among these distances:
24 17 0.12
25 1 0.01
26 1 0.01
30 1 0.01
32 1 0.01
33 114 0.83
34 2 0.01
ACGTcount: A:0.25, C:0.13, G:0.36, T:0.26
Consensus pattern (33 bp):
TGGAACTGGAGGAGGAAGTGGCTTCTTATACAC
Found at i:24322 original size:90 final size:90
Alignment explanation
Indices: 24218--24763 Score: 329
Period size: 90 Copynumber: 6.2 Consensus size: 90
24208 GCTTGTAGAT
*
24218 TGGAACTGGAGGAGGAAGTGGTTTCTTATACACCGGAACTGGTGGAGGCTTGTAGATTGGAACTG
1 TGGAACTGGTGGAGGAAGTGGTTTCTTATACACCGGAACTGGTGGAGGCTTGTAGATTGGAACTG
24283 GAGGAGGAAGTGGCTTCTTATACAC
66 GAGGAGGAAGTGGCTTCTTATACAC
* * * * *
24308 TGGAACTGGTGGAGGCAA-TGGCTTCTTATATACGGGAACTGGAGGAGACTTGTAGATTGGAACT
1 TGGAACTGGTGGAGG-AAGTGGTTTCTTATACACCGGAACTGGTGGAGGCTTGTAGATTGGAACT
* * *
24372 GGTGGAGGAAGTGGTTTCTTATATAC
65 GGAGGAGGAAGTGGCTTCTTATACAC
* * * * * * * * * *** **
24398 TGGAACCGGAGGAGGATGTGGCTTCTTGTACACTGGAACTGGAGGAGGAAGTGGTTTCTTATACA
1 TGGAACTGGTGGAGGAAGTGGTTTCTTATACACCGGAACTGGTGGAGG--CTTGTAGATTGGA-A
* *** ** * * *
24463 CCGGAACTGGTGGAGG--T-TTATAGAT
63 CTGGAGGAGGAAGTGGCTTCTTATACAC
* * * * * *
24488 TGGAACTGGTGGAGGAAGTGGCTTT-TTGTATACTGGAACTGGCGGAGGCTTATAGATTGGAACA
1 TGGAACTGGTGGAGGAAGTGG-TTTCTTATACACCGGAACTGGTGGAGGCTTGTAGATTGGAACT
* * *
24552 GGTGGAGGAAGTGGCTTCTTGTATAC
65 GGAGGAGGAAGTGGCTTCTTATACAC
* * * ** * *
24578 TGGAAC---TGGCGG-A--GG---CTTATAGATCGGAACTGGTGGAGG-AAGTGGCTTCTGGTAT
1 TGGAACTGGTGGAGGAAGTGGTTTCTTATACACCGGAACTGGTGGAGGCTTGTAG-AT-TGG-A-
* *** *
24633 ACTGGA--ACCG--GTGGAGGCTTATAGAC
62 ACTGGAGGA-GGAAGTGGCTTCTTATACAC
* * * *
24659 CGGAACTGGAGGAGGAAGTGGTTTCTTATACACCGGAACTGGTGGAGGTTTATAGATTGGAACTG
1 TGGAACTGGTGGAGGAAGTGGTTTCTTATACACCGGAACTGGTGGAGGCTTGTAGATTGGAACTG
* *
24724 GTGGAGGAAGTGGTTTCTTATACAC
66 GAGGAGGAAGTGGCTTCTTATACAC
*
24749 CGGAACTGGTGGAGG
1 TGGAACTGGTGGAGG
24764 TTTATAGATT
Statistics
Matches: 333, Mismatches: 94, Indels: 58
0.69 0.19 0.12
Matches are distributed among these distances:
80 2 0.01
81 35 0.11
82 4 0.01
83 2 0.01
84 10 0.03
85 1 0.00
86 1 0.00
87 21 0.06
88 7 0.02
89 6 0.02
90 222 0.67
91 7 0.02
92 6 0.02
93 9 0.03
ACGTcount: A:0.25, C:0.13, G:0.36, T:0.27
Consensus pattern (90 bp):
TGGAACTGGTGGAGGAAGTGGTTTCTTATACACCGGAACTGGTGGAGGCTTGTAGATTGGAACTG
GAGGAGGAAGTGGCTTCTTATACAC
Found at i:24369 original size:57 final size:57
Alignment explanation
Indices: 24299--24991 Score: 796
Period size: 57 Copynumber: 12.0 Consensus size: 57
24289 GAAGTGGCTT
* * * * * *
24299 CTTATACACTGGAACTGGTGGAGGCAA-TGGCTTCTTATATACGGGAACTGGAGGAGA
1 CTTATAGATTGGAACTGGTGGAGG-AAGTGGCTTCTTGTATACTGGAACTGGTGGAGG
* * * * *
24356 CTTGTAGATTGGAACTGGTGGAGGAAGTGGTTTCTTATATACTGGAACCGGAGGAGGATGTGG
1 CTTATAGATTGGAACTGGTGGAGGAAGTGGCTTCTTGTATACTGGAA-C--TGGTGGA---GG
* * * * * * * *
24419 CTTCTTGTACACTGGAACTGGAGGAGGAAGTGGTTTCTTATACACCGGAACTGGTGGAGG
1 ---CTTATAGATTGGAACTGGTGGAGGAAGTGGCTTCTTGTATACTGGAACTGGTGGAGG
* * *
24479 TTTATAGATTGGAACTGGTGGAGGAAGTGGCTTTTTGTATACTGGAACTGGCGGAGG
1 CTTATAGATTGGAACTGGTGGAGGAAGTGGCTTCTTGTATACTGGAACTGGTGGAGG
* *
24536 CTTATAGATTGGAACAGGTGGAGGAAGTGGCTTCTTGTATACTGGAACTGGCGGAGG
1 CTTATAGATTGGAACTGGTGGAGGAAGTGGCTTCTTGTATACTGGAACTGGTGGAGG
* * *
24593 CTTATAGATCGGAACTGGTGGAGGAAGTGGCTTCTGGTATACTGGAACCGGTGGAGG
1 CTTATAGATTGGAACTGGTGGAGGAAGTGGCTTCTTGTATACTGGAACTGGTGGAGG
** * * * * *
24650 CTTATAGACCGGAACTGGAGGAGGAAGTGGTTTCTTATACACCGGAACTGGTGGAGG
1 CTTATAGATTGGAACTGGTGGAGGAAGTGGCTTCTTGTATACTGGAACTGGTGGAGG
* * * * *
24707 TTTATAGATTGGAACTGGTGGAGGAAGTGGTTTCTTATACACCGGAACTGGTGGAGG
1 CTTATAGATTGGAACTGGTGGAGGAAGTGGCTTCTTGTATACTGGAACTGGTGGAGG
* * *
24764 TTTATAGATTGGAACTGGTGGAGGAAGTGGCTTTTTGTATACTGGAACTGGCGGAGG
1 CTTATAGATTGGAACTGGTGGAGGAAGTGGCTTCTTGTATACTGGAACTGGTGGAGG
* *
24821 CTTATAGATTGGAACAGGTGGAGGAAGTGGCTTCTTGTATACTGGAACTGGCGGAGG
1 CTTATAGATTGGAACTGGTGGAGGAAGTGGCTTCTTGTATACTGGAACTGGTGGAGG
* *
24878 CTTATAGATCGGAACTGGTGGAGGAAGTGGCTTCTTGTATACTGGAACCGGTGGAGG
1 CTTATAGATTGGAACTGGTGGAGGAAGTGGCTTCTTGTATACTGGAACTGGTGGAGG
** * * * * *
24935 CTTATAGACCGGAACTGGTGGAGGGAGTGGATT-TTCGTAAACAGGAACAGGTGGAGG
1 CTTATAGATTGGAACTGGTGGAGGAAGTGGCTTCTT-GTATACTGGAACTGGTGGAGG
24992 AAGTGGTTTT
Statistics
Matches: 561, Mismatches: 64, Indels: 22
0.87 0.10 0.03
Matches are distributed among these distances:
56 4 0.01
57 499 0.89
58 1 0.00
60 8 0.01
63 6 0.01
65 1 0.00
66 42 0.07
ACGTcount: A:0.25, C:0.13, G:0.36, T:0.27
Consensus pattern (57 bp):
CTTATAGATTGGAACTGGTGGAGGAAGTGGCTTCTTGTATACTGGAACTGGTGGAGG
Found at i:24483 original size:24 final size:24
Alignment explanation
Indices: 24456--24502 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
24446 AAGTGGTTTC
24456 TTATACACCGGAACTGGTGGAGGT
1 TTATACACCGGAACTGGTGGAGGT
* **
24480 TTATAGATTGGAACTGGTGGAGG
1 TTATACACCGGAACTGGTGGAGG
24503 AAGTGGCTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.11, G:0.36, T:0.28
Consensus pattern (24 bp):
TTATACACCGGAACTGGTGGAGGT
Found at i:24535 original size:33 final size:33
Alignment explanation
Indices: 24488--24592 Score: 93
Period size: 33 Copynumber: 3.5 Consensus size: 33
24478 GTTTATAGAT
* *
24488 TGGAACTGGTGGAGGAAGTGGCTTTTTGTATAC
1 TGGAACTGGCGGAGGAAGTGGCTTATTGTATAC
*
24521 TGGAACTGGC---GG-A--GGCTTATAG-AT--
1 TGGAACTGGCGGAGGAAGTGGCTTATTGTATAC
* * *
24545 TGGAACAGGTGGAGGAAGTGGCTTCTTGTATAC
1 TGGAACTGGCGGAGGAAGTGGCTTATTGTATAC
24578 TGGAACTGGCGGAGG
1 TGGAACTGGCGGAGG
24593 CTTATAGATC
Statistics
Matches: 54, Mismatches: 9, Indels: 18
0.67 0.11 0.22
Matches are distributed among these distances:
24 8 0.15
26 2 0.04
27 9 0.17
28 1 0.02
29 1 0.02
30 9 0.17
31 2 0.04
33 22 0.41
ACGTcount: A:0.23, C:0.11, G:0.39, T:0.27
Consensus pattern (33 bp):
TGGAACTGGCGGAGGAAGTGGCTTATTGTATAC
Found at i:24688 original size:33 final size:33
Alignment explanation
Indices: 24650--24763 Score: 120
Period size: 33 Copynumber: 3.7 Consensus size: 33
24640 CCGGTGGAGG
* *
24650 CTTATAGACCGGAACTGGAGGAGGAAGTGGTTT
1 CTTATACACCGGAACTGGTGGAGGAAGTGGTTT
24683 CTTATACACCGGAACTGGT---GG-A--GG--T
1 CTTATACACCGGAACTGGTGGAGGAAGTGGTTT
* **
24708 -TTATAGATTGGAACTGGTGGAGGAAGTGGTTT
1 CTTATACACCGGAACTGGTGGAGGAAGTGGTTT
24740 CTTATACACCGGAACTGGTGGAGG
1 CTTATACACCGGAACTGGTGGAGG
24764 TTTATAGATT
Statistics
Matches: 64, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
24 15 0.23
25 1 0.02
27 4 0.06
28 1 0.02
29 1 0.02
30 4 0.06
32 1 0.02
33 37 0.58
ACGTcount: A:0.25, C:0.13, G:0.35, T:0.26
Consensus pattern (33 bp):
CTTATACACCGGAACTGGTGGAGGAAGTGGTTT
Found at i:24711 original size:24 final size:24
Alignment explanation
Indices: 24684--24730 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
24674 AAGTGGTTTC
24684 TTATACACCGGAACTGGTGGAGGT
1 TTATACACCGGAACTGGTGGAGGT
* **
24708 TTATAGATTGGAACTGGTGGAGG
1 TTATACACCGGAACTGGTGGAGG
24731 AAGTGGTTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.11, G:0.36, T:0.28
Consensus pattern (24 bp):
TTATACACCGGAACTGGTGGAGGT
Found at i:24768 original size:24 final size:24
Alignment explanation
Indices: 24741--24787 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
24731 AAGTGGTTTC
24741 TTATACACCGGAACTGGTGGAGGT
1 TTATACACCGGAACTGGTGGAGGT
* **
24765 TTATAGATTGGAACTGGTGGAGG
1 TTATACACCGGAACTGGTGGAGG
24788 AAGTGGCTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.11, G:0.36, T:0.28
Consensus pattern (24 bp):
TTATACACCGGAACTGGTGGAGGT
Found at i:24820 original size:33 final size:33
Alignment explanation
Indices: 24773--24934 Score: 99
Period size: 33 Copynumber: 5.5 Consensus size: 33
24763 GTTTATAGAT
* *
24773 TGGAACTGGTGGAGGAAGTGGCTTTTTGTATAC
1 TGGAACTGGCGGAGGAAGTGGCTTATTGTATAC
*
24806 TGGAACTGGC---GG-A--GGCTTATAG-AT--
1 TGGAACTGGCGGAGGAAGTGGCTTATTGTATAC
* * *
24830 TGGAACAGGTGGAGGAAGTGGCTTCTTGTATAC
1 TGGAACTGGCGGAGGAAGTGGCTTATTGTATAC
*
24863 TGGAACTGGC---GG-A--GGCTTATAG-AT-C
1 TGGAACTGGCGGAGGAAGTGGCTTATTGTATAC
* *
24888 -GGAACTGGTGGAGGAAGTGGCTTCTTGTATAC
1 TGGAACTGGCGGAGGAAGTGGCTTATTGTATAC
* *
24920 TGGAACCGGTGGAGG
1 TGGAACTGGCGGAGG
24935 CTTATAGACC
Statistics
Matches: 96, Mismatches: 15, Indels: 36
0.65 0.10 0.24
Matches are distributed among these distances:
24 16 0.17
25 1 0.01
26 4 0.04
27 18 0.19
28 2 0.02
29 2 0.02
30 18 0.19
31 4 0.04
32 1 0.01
33 30 0.31
ACGTcount: A:0.23, C:0.12, G:0.38, T:0.27
Consensus pattern (33 bp):
TGGAACTGGCGGAGGAAGTGGCTTATTGTATAC
Found at i:24982 original size:33 final size:33
Alignment explanation
Indices: 24945--25015 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 33
24935 CTTATAGACC
* * *
24945 GGAACTGGTGGAGGGAGTGGATTTTCGTAAACA
1 GGAACAGGTGGAGGAAGTGGATTTTCATAAACA
* *
24978 GGAACAGGTGGAGGAAGTGGTTTTTCATATACA
1 GGAACAGGTGGAGGAAGTGGATTTTCATAAACA
25011 GGAAC
1 GGAAC
25016 CGGCGGGGGC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.30, C:0.10, G:0.37, T:0.24
Consensus pattern (33 bp):
GGAACAGGTGGAGGAAGTGGATTTTCATAAACA
Found at i:25070 original size:90 final size:90
Alignment explanation
Indices: 24888--25054 Score: 210
Period size: 90 Copynumber: 1.9 Consensus size: 90
24878 CTTATAGATC
* * * * * *
24888 GGAACTGGTGGAGGAAGTGGCTTCTTGTATACTGGAACCGGTGGAGGCTTATAGACCGGAACTGG
1 GGAACAGGTGGAGGAAGTGGCTTCTTATATACAGGAACCGGCGGAGGCTTATACACCGGAACCGG
* *
24953 TGGAGGGAGTGGATTTTCGTAAACA
66 TGGAGGAAGAGGATTTTCGTAAACA
* * *
24978 GGAACAGGTGGAGGAAGTGG-TTTTTCATATACAGGAACCGGCGGGGGCTTGTACACCGGAACCG
1 GGAACAGGTGGAGGAAGTGGCTTCTT-ATATACAGGAACCGGCGGAGGCTTATACACCGGAACCG
*
25042 GTGGCGGAAGAGG
65 GTGGAGGAAGAGG
25055 TTTCTTGTAG
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
89 4 0.06
90 60 0.94
ACGTcount: A:0.25, C:0.15, G:0.40, T:0.21
Consensus pattern (90 bp):
GGAACAGGTGGAGGAAGTGGCTTCTTATATACAGGAACCGGCGGAGGCTTATACACCGGAACCGG
TGGAGGAAGAGGATTTTCGTAAACA
Found at i:25158 original size:24 final size:24
Alignment explanation
Indices: 25125--25183 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
25115 AGGAAACGTT
* *
25125 GGCAAAGGAGGATGGTTCCACTTA
1 GGCAATGGAGGATGGTGCCACTTA
*
25149 GGCAATGGAGGATGGTGCCACTTG
1 GGCAATGGAGGATGGTGCCACTTA
25173 GGCAATGGAGG
1 GGCAATGGAGG
25184 GAACTTAAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.25, C:0.15, G:0.41, T:0.19
Consensus pattern (24 bp):
GGCAATGGAGGATGGTGCCACTTA
Found at i:35126 original size:25 final size:25
Alignment explanation
Indices: 35097--35155 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
35087 TTGAAAAGTG
*
35097 ACTTTTAAAAGTATGGTAGAAAATA
1 ACTTTTAAAAGTATAGTAGAAAATA
35122 ACTTTTAAAAGTATAGTAGAAAATA
1 ACTTTTAAAAGTATAGTAGAAAATA
35147 ACTTTTAAA
1 ACTTTTAAA
35156 CGTGTTGTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.49, C:0.05, G:0.12, T:0.34
Consensus pattern (25 bp):
ACTTTTAAAAGTATAGTAGAAAATA
Found at i:35342 original size:34 final size:30
Alignment explanation
Indices: 35304--35372 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 30
35294 TCGATATAAC
*
35304 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTATTTGGACTT-AATTG
35338 AATTT-ACAAAATGTATTTGGACTTAATTG
1 AATTTAACAAAATGTATTTGGACTTAATTG
35367 AATTTA
1 AATTTA
35373 TTCAAAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 10 0.30
30 11 0.33
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.36, C:0.06, G:0.17, T:0.41
Consensus pattern (30 bp):
AATTTAACAAAATGTATTTGGACTTAATTG
Found at i:35380 original size:31 final size:31
Alignment explanation
Indices: 35313--35372 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
35303 CAATTTAAGG
*
35313 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
35344 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
35373 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:38102 original size:21 final size:21
Alignment explanation
Indices: 38076--38117 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
38066 ATTTGAATAT
*
38076 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
38097 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
38118 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:38179 original size:21 final size:21
Alignment explanation
Indices: 38146--38185 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
38136 TTTTTGCAGA
*
38146 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
38168 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
38186 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:39867 original size:13 final size:13
Alignment explanation
Indices: 39846--39875 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
39836 ATTTTCTATG
39846 TTCTATTTTTGTT
1 TTCTATTTTTGTT
*
39859 TTCTTTTTTTGTT
1 TTCTATTTTTGTT
39872 TTCT
1 TTCT
39876 GAAAATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.03, C:0.10, G:0.07, T:0.80
Consensus pattern (13 bp):
TTCTATTTTTGTT
Found at i:39952 original size:13 final size:14
Alignment explanation
Indices: 39933--39969 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
39923 GTTAATTGAA
39933 ATTAAAAATAAAAT
1 ATTAAAAATAAAAT
39947 -TTAAAAATAAAAT
1 ATTAAAAATAAAAT
*
39960 ATTGAAAATA
1 ATTAAAAATA
39970 TATTTTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 13 0.62
14 8 0.38
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (14 bp):
ATTAAAAATAAAAT
Found at i:44436 original size:3 final size:3
Alignment explanation
Indices: 44428--44547 Score: 151
Period size: 3 Copynumber: 41.0 Consensus size: 3
44418 CCATTTGTTT
* *
44428 TTA TTA TTA -TA TTA TTA TTG TTA TTA TTA -TA TTA TTA TTG TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
44474 TTA TT- TTA TTTA TTA CTA TTA CTA TTA TTA TT- TTA -TA TTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
44517 TTA TTA TTA TTA TTTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
44548 CATTTCAGGC
Statistics
Matches: 102, Mismatches: 8, Indels: 14
0.82 0.06 0.11
Matches are distributed among these distances:
2 10 0.10
3 86 0.84
4 6 0.06
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:44999 original size:21 final size:22
Alignment explanation
Indices: 44974--45014 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
44964 AACGAAAGGG
* *
44974 GAGAGGAAGCAATA-AAAAACA
1 GAGAGAAAACAATATAAAAACA
44995 GAGAGAAAACAATATAAAAA
1 GAGAGAAAACAATATAAAAA
45015 AAACTACTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.66, C:0.07, G:0.20, T:0.07
Consensus pattern (22 bp):
GAGAGAAAACAATATAAAAACA
Found at i:45717 original size:21 final size:20
Alignment explanation
Indices: 45676--45724 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
45666 ATTTAGTCAC
*
45676 TAATTTTAATACTTTCATTT
1 TAATTTTAATACTATCATTT
45696 TATATTTTAATACTAT-AGTTT
1 TA-ATTTTAATACTATCA-TTT
45717 TAATTTTA
1 TAATTTTA
45725 TTTATTTTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.59
Consensus pattern (20 bp):
TAATTTTAATACTATCATTT
Found at i:45766 original size:17 final size:17
Alignment explanation
Indices: 45740--45777 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
45730 TTTAGTCTCT
*
45740 ATTTATTTA-TATTTTA
1 ATTTATTTATTATTTAA
45756 ATTTAATTTATTATTTAA
1 ATTT-ATTTATTATTTAA
45774 ATTT
1 ATTT
45778 CAATATGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 4 0.21
17 5 0.26
18 10 0.53
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
ATTTATTTATTATTTAA
Found at i:45795 original size:14 final size:14
Alignment explanation
Indices: 45776--45805 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
45766 TTATTTAAAT
45776 TTCAATATGTTTAA
1 TTCAATATGTTTAA
45790 TTCAATATGTTTAA
1 TTCAATATGTTTAA
45804 TT
1 TT
45806 ATTATTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (14 bp):
TTCAATATGTTTAA
Found at i:50139 original size:15 final size:15
Alignment explanation
Indices: 50116--50147 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
50106 GATCAATACC
50116 TTTTACATACATTCA
1 TTTTACATACATTCA
*
50131 TTTTGCATACATTCA
1 TTTTACATACATTCA
50146 TT
1 TT
50148 GCATTATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.19, G:0.03, T:0.50
Consensus pattern (15 bp):
TTTTACATACATTCA
Found at i:57528 original size:23 final size:24
Alignment explanation
Indices: 57486--57542 Score: 66
Period size: 23 Copynumber: 2.4 Consensus size: 24
57476 ATGCTTGGAG
57486 AAGAAAAAAATAATAAGAAAA-AA
1 AAGAAAAAAATAATAAGAAAAGAA
*
57509 AAGAAAAAAATTAA-ATGAAAAGAA
1 AAGAAAAAAA-TAATAAGAAAAGAA
57533 AA-ACAAAAAA
1 AAGA-AAAAAA
57543 CAAAATAGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
23 17 0.57
24 13 0.43
ACGTcount: A:0.81, C:0.02, G:0.09, T:0.09
Consensus pattern (24 bp):
AAGAAAAAAATAATAAGAAAAGAA
Found at i:58223 original size:54 final size:54
Alignment explanation
Indices: 58142--58245 Score: 181
Period size: 54 Copynumber: 1.9 Consensus size: 54
58132 AGAGAACAAA
58142 ATCTGTGCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATATTTTACGAAC
1 ATCTGTGCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATATTTTACGAAC
* * *
58196 ATCTGTGCAGAAGCCACATGAATGGATGAATGTGTTGTCAAATGTTTTAC
1 ATCTGTGCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATATTTTAC
58246 AAACCAGCGA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (54 bp):
ATCTGTGCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATATTTTACGAAC
Found at i:58641 original size:22 final size:22
Alignment explanation
Indices: 58613--58697 Score: 116
Period size: 22 Copynumber: 3.9 Consensus size: 22
58603 ACATCTACAT
*
58613 TCTTCAAAGATGATAAATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
58635 TCTTCAAAGATGACAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
58657 TATTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
* * *
58679 TTTTCAAAGAAGAAAGATT
1 TCTTCAAAGATGATAGATT
58698 TATTGGATTT
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 56 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:59507 original size:244 final size:239
Alignment explanation
Indices: 59074--59723 Score: 790
Period size: 244 Copynumber: 2.7 Consensus size: 239
59064 TCAATGGATA
59074 AACATTTCCAAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATA
1 AACATTTCCAAAA-AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATA
* * *
59139 AGAAGAACTTGTTTAACCTTTTGCTCGAATTC-ATCACTAG-A-TG--AATCAG---CA-TTGCC
65 AGAAGAACTTGTTCAACCTTTTGCTCG-ATTCTATCA-TAGAAGAGATAATCAGCATCACTTTCC
* * * *
59195 AGAAGAGTTCATAATGAGAAGAACTCATCTAAAGAGGAAGAAGAAGTTCATAATGAGAAGAGCTT
128 AGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATAAGAAGAACTT
*
59260 GTTCAAAC-TTTTGCAT-GACTCTATCACAAAATGAGATAGATCAACATT
193 GTTC-AACTTTTTGC-TCGACTCTATCACAAAAGGAGATAGATCAACA-T
* *
59308 AACATTTCCAGAGAAAGTTCATAATGAGAAAAACTTATCTGAAGAAGG-AGAAGAAGTTCATAAT
1 AACATTTCCA-A-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
* *
59372 AAGAAGAACTTATTCAA-CTTTTGCTCGATTCTATTATAGAAGGAGATAGATCAGCATACACTTT
64 AAGAAGAACTTGTTCAACCTTTTGCTCGATTCTATCATAGAA-GAGATA-ATCAGCAT-CAC-TT
*
59436 TCCAAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATAAGAAGAA
125 TCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATAAGAAGAA
* * *
59501 CTTGTTCAACTTTTTGCTCGACTCTATTACAGAAGGAGATAGATCAGCAT
190 CTTGTTCAACTTTTTGCTCGACTCTATCACAAAAGGAGATAGATCAACAT
* *
59551 ACACTTTTCCATAAGAGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAAT
1 A-ACATTTCCA-AAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
* ** * * *
59615 GAGAAGAGTTTGTTCAACCTTTTGCAT-GACTCTATCACAGAATGAGATAAATCATCATCAACAT
64 AAGAAGAACTTGTTCAACCTTTTGC-TCGATTCTATCATAGAA-GAGAT-AATCAGCATC-AC-T
* *
59679 TTCTAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGA
124 TTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGA
59724 TAAATTGTTC
Statistics
Matches: 359, Mismatches: 34, Indels: 36
0.84 0.08 0.08
Matches are distributed among these distances:
232 7 0.02
233 14 0.04
234 41 0.11
235 33 0.09
236 2 0.01
237 1 0.00
238 5 0.01
242 5 0.01
243 64 0.18
244 185 0.52
245 2 0.01
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (239 bp):
AACATTTCCAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAA
GAAGAACTTGTTCAACCTTTTGCTCGATTCTATCATAGAAGAGATAATCAGCATCACTTTCCAGA
AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATAAGAAGAACTTGTT
CAACTTTTTGCTCGACTCTATCACAAAAGGAGATAGATCAACAT
Found at i:59557 original size:122 final size:121
Alignment explanation
Indices: 59188--59723 Score: 686
Period size: 122 Copynumber: 4.4 Consensus size: 121
59178 GATGAATCAG
* * * * *
59188 CATTGCCAGAAGAGTTCATAATGAGAAGAACTCATCTAAAGAGGAAGAAGAAGTTCATAATGAGA
1 CATTTCCAAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATAAGA
* * * *
59253 AGAGCTTGTTCAAACTTTTGCATGACTCTATCACAAAATGAGATAGATCAACATTA-A
66 AGAACTTGTTC-AACTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGCA-TACA
* * *
59310 CATTTCCAGAGAA-AGTTCATAATGAGAAAAACTTATCTGAAGAAGGAGAAGAAGTTCATAATAA
1 CATTTCCA-A-AAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATAA
* * * *
59374 GAAGAACTTATTCAACTTTTGC-TCGATTCTATTATAGAAGGAGATAGATCAGCATACA
64 GAAGAACTTGTTCAACTTTTGCAT-GACTCTATCACAGAAGGAGATAGATCAGCATACA
*
59432 CTTTTCCAAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATAAGA
1 CATTTCCAAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATAAGA
*
59497 AGAACTTGTTCAACTTTTTGC-TCGACTCTATTACAGAAGGAGATAGATCAGCATACA
66 AGAACTTGTTCAAC-TTTTGCAT-GACTCTATCACAGAAGGAGATAGATCAGCATACA
* * * *
59554 CTTTTCCATAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGA
1 CATTTCCAAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATAAGA
** * * *
59619 AGAGTTTGTTCAACCTTTTGCATGACTCTATCACAGAATGAGATAAATCATCAT-CAA
66 AGAACTTGTTCAA-CTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGCATAC-A
* * *
59676 CATTTCTAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGA
1 CATTTCCAAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGA
59724 TAAATTGTTC
Statistics
Matches: 368, Mismatches: 37, Indels: 18
0.87 0.09 0.04
Matches are distributed among these distances:
120 2 0.01
121 68 0.18
122 238 0.65
123 58 0.16
124 2 0.01
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (121 bp):
CATTTCCAAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATAAGA
AGAACTTGTTCAACTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGCATACA
Found at i:60114 original size:3 final size:3
Alignment explanation
Indices: 60106--60205 Score: 122
Period size: 3 Copynumber: 35.0 Consensus size: 3
60096 CCATTTGTTT
* *
60106 TTA TTA TTA -TA TTA TTA TTG TTA TTA TTA TT- TTA TTTA TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
60150 TTA TTA TT- TTA -TA TTA TTA TT- TTA -TA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
60194 TTA TTA ATA TTA
1 TTA TTA TTA TTA
60206 CATTTCAGGC
Statistics
Matches: 84, Mismatches: 6, Indels: 14
0.81 0.06 0.13
Matches are distributed among these distances:
2 12 0.14
3 69 0.82
4 3 0.04
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:60186 original size:41 final size:46
Alignment explanation
Indices: 60106--60199 Score: 135
Period size: 41 Copynumber: 2.1 Consensus size: 46
60096 CCATTTGTTT
60106 TTATTATTATATTATTATTGTTATTATTATTTTATTTATTACTATTA
1 TTATTATTATATTATTATTGTTATTATTA-TTTATTTATTACTATTA
*
60153 TTATT-TTATATTATTATT-TTA-TATTA-TTA-TTATTATTATTA
1 TTATTATTATATTATTATTGTTATTATTATTTATTTATTACTATTA
60194 TTATTA
1 TTATTA
60200 ATATTACATT
Statistics
Matches: 45, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
41 16 0.36
42 3 0.07
44 5 0.11
45 3 0.07
46 13 0.29
47 5 0.11
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.67
Consensus pattern (46 bp):
TTATTATTATATTATTATTGTTATTATTATTTATTTATTACTATTA
Found at i:60236 original size:16 final size:16
Alignment explanation
Indices: 60227--60257 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
60217 CAATTCAGAT
60227 CCAACCCAATTACAAA
1 CCAACCCAATTACAAA
*
60243 CCAACCCAGTTACAA
1 CCAACCCAATTACAA
60258 GAGCCCAACT
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:0.45, C:0.39, G:0.03, T:0.13
Consensus pattern (16 bp):
CCAACCCAATTACAAA
Found at i:61369 original size:21 final size:20
Alignment explanation
Indices: 61343--61391 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
61333 ATTTAGTTAC
* *
61343 TAATTTTAATACTTTCATTT
1 TAATTTTAATACTATAATTT
61363 TATATTTTAATACTATAATTT
1 TA-ATTTTAATACTATAATTT
61384 TAATTTTA
1 TAATTTTA
61392 TTTATTTTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (20 bp):
TAATTTTAATACTATAATTT
Found at i:61437 original size:17 final size:17
Alignment explanation
Indices: 61411--61448 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
61401 GTCACTATTT
*
61411 ATTTATTTA-TATTTTA
1 ATTTATTTATTATTTAA
61427 ATTTAATTTATTATTTAA
1 ATTT-ATTTATTATTTAA
61445 ATTT
1 ATTT
61449 CAATATGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 4 0.21
17 5 0.26
18 10 0.53
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
ATTTATTTATTATTTAA
Found at i:61466 original size:14 final size:14
Alignment explanation
Indices: 61447--61476 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
61437 TTATTTAAAT
61447 TTCAATATGTTTAA
1 TTCAATATGTTTAA
61461 TTCAATATGTTTAA
1 TTCAATATGTTTAA
61475 TT
1 TT
61477 ATTATTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (14 bp):
TTCAATATGTTTAA
Found at i:64064 original size:26 final size:26
Alignment explanation
Indices: 64024--64075 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
64014 AATAGAACAA
*
64024 GGAGAAAAGATAAGGAAAACGGCAGC
1 GGAGAAAAGAGAAGGAAAACGGCAGC
* * *
64050 GGAGAGAAGAGAAGGAGAGCGGCAGC
1 GGAGAAAAGAGAAGGAAAACGGCAGC
64076 TACTTACCTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.44, C:0.12, G:0.42, T:0.02
Consensus pattern (26 bp):
GGAGAAAAGAGAAGGAAAACGGCAGC
Found at i:64263 original size:32 final size:27
Alignment explanation
Indices: 64238--64290 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
64228 AATACATATG
* *
64238 TAAATAAATTTAAATGAATAGAAATAAA
1 TAAATAAATATAAATAAAT-GAAATAAA
64266 TAAATAAATATAAATAAATGAAATA
1 TAAATAAATATAAATAAATGAAATA
64291 TTGAAAGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (27 bp):
TAAATAAATATAAATAAATGAAATAAA
Found at i:64265 original size:14 final size:14
Alignment explanation
Indices: 64248--64290 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
64238 TAAATAAATT
*
64248 TAAATGAATAGAAA
1 TAAATAAATAGAAA
64262 TAAATAAATA-AATA
1 TAAATAAATAGAA-A
64276 TAAATAAAT-GAAA
1 TAAATAAATAGAAA
64289 TA
1 TA
64291 TTGAAAGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 5 0.19
14 21 0.81
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (14 bp):
TAAATAAATAGAAA
Found at i:64275 original size:18 final size:18
Alignment explanation
Indices: 64248--64290 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
64238 TAAATAAATT
*
64248 TAAATGAATAGAAATAAA
1 TAAATAAATAGAAATAAA
*
64266 TAAATAAATATAAATAAA
1 TAAATAAATAGAAATAAA
64284 TGAAATA
1 T-AAATA
64291 TTGAAAGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (18 bp):
TAAATAAATAGAAATAAA
Found at i:69541 original size:3 final size:3
Alignment explanation
Indices: 69533--69585 Score: 97
Period size: 3 Copynumber: 17.3 Consensus size: 3
69523 ACCTACTAAT
69533 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
69579 TTA TTA T
1 TTA TTA T
69586 AAAAACGAAC
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 46 0.94
4 3 0.06
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:76960 original size:19 final size:19
Alignment explanation
Indices: 76921--76960 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
76911 AAATAGAGAT
*
76921 ATCAGAAATCAGAGCAAAA
1 ATCAGAAATCAGAACAAAA
* *
76940 ATCAGATATCAGAACAGAA
1 ATCAGAAATCAGAACAAAA
76959 AT
1 AT
76961 AAGAGAAAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.15, G:0.15, T:0.15
Consensus pattern (19 bp):
ATCAGAAATCAGAACAAAA
Found at i:78600 original size:15 final size:15
Alignment explanation
Indices: 78580--78617 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
78570 AACGGTCAAC
78580 GAGTTGACCTGGTCT
1 GAGTTGACCTGGTCT
78595 GAGTTGACCTGGTCT
1 GAGTTGACCTGGTCT
78610 GAGTTGAC
1 GAGTTGAC
78618 TCAGCTTCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.16, C:0.18, G:0.34, T:0.32
Consensus pattern (15 bp):
GAGTTGACCTGGTCT
Found at i:80039 original size:2 final size:2
Alignment explanation
Indices: 80032--80060 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
80022 ATTAGTTGCT
80032 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
80061 CAGAACCGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:81623 original size:18 final size:18
Alignment explanation
Indices: 81600--81651 Score: 104
Period size: 18 Copynumber: 2.9 Consensus size: 18
81590 ATCAACTCGC
81600 TGGTATCCAACCACTAGT
1 TGGTATCCAACCACTAGT
81618 TGGTATCCAACCACTAGT
1 TGGTATCCAACCACTAGT
81636 TGGTATCCAACCACTA
1 TGGTATCCAACCACTA
81652 CCAGTACTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (18 bp):
TGGTATCCAACCACTAGT
Found at i:81909 original size:25 final size:24
Alignment explanation
Indices: 81861--81910 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
81851 TTATTTATTT
81861 TAAATATTTTTAATTATTTAATAA
1 TAAATATTTTTAATTATTTAATAA
*
81885 TAAATATTTATTTATTATATT-ATAA
1 TAAATATTT-TTAATTAT-TTAATAA
81910 T
1 T
81911 TGTTGGTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 9 0.39
25 12 0.52
26 2 0.09
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
TAAATATTTTTAATTATTTAATAA
Found at i:82124 original size:15 final size:15
Alignment explanation
Indices: 82106--82143 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
82096 GATTTATAAA
*
82106 TAATTTATTATTATT
1 TAATTTATTATCATT
*
82121 TAATTTATAATCATT
1 TAATTTATTATCATT
82136 T-ATTTATT
1 TAATTTATT
82144 GAAATGGTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (15 bp):
TAATTTATTATCATT
Found at i:82168 original size:2 final size:2
Alignment explanation
Indices: 82161--82188 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
82151 TTTCTAGTGA
82161 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
82189 TATTCACAAA
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:83182 original size:25 final size:25
Alignment explanation
Indices: 83148--83199 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
83138 GTCTTGCTTT
83148 AAAGTTTTTGTGCTTATCTGGTGTG
1 AAAGTTTTTGTGCTTATCTGGTGTG
83173 AAAGTTTTTGTGCTTATCTGGTGTG
1 AAAGTTTTTGTGCTTATCTGGTGTG
83198 AA
1 AA
83200 CTCTTTTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.19, C:0.08, G:0.27, T:0.46
Consensus pattern (25 bp):
AAAGTTTTTGTGCTTATCTGGTGTG
Done.