Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003768.1 Hibiscus syriacus cultivar Beakdansim tig00008070_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: 65158
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Found at i:15901 original size:27 final size:27
Alignment explanation
Indices: 15810--15899 Score: 101
Period size: 27 Copynumber: 3.3 Consensus size: 27
15800 ACAACACCAT
* *
15810 CATTACTACAATTTACATCCACTACAAC
1 CATTACTACAATTAACATCCACTGC-AC
* * *
15838 C-TTGCTACAATTAACATCCTCTGCAA
1 CATTACTACAATTAACATCCACTGCAC
*
15864 CATTACTACTATTAACATCCACTGCAC
1 CATTACTACAATTAACATCCACTGCAC
*
15891 CATTGCTAC
1 CATTACTAC
15900 TAATATTTAG
Statistics
Matches: 51, Mismatches: 10, Indels: 3
0.80 0.16 0.05
Matches are distributed among these distances:
26 2 0.04
27 48 0.94
28 1 0.02
ACGTcount: A:0.33, C:0.32, G:0.04, T:0.30
Consensus pattern (27 bp):
CATTACTACAATTAACATCCACTGCAC
Found at i:18281 original size:23 final size:20
Alignment explanation
Indices: 18254--18294 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
18244 CTCTAAGAAA
18254 TTGATCTTGAAGATGATTGTTCT
1 TTGAT-TTGAA-ATG-TTGTTCT
18277 TTGATTTGAAATGTTGTT
1 TTGATTTGAAATGTTGTT
18295 AACAATAGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 3 0.17
22 5 0.28
23 5 0.28
ACGTcount: A:0.22, C:0.05, G:0.22, T:0.51
Consensus pattern (20 bp):
TTGATTTGAAATGTTGTTCT
Found at i:19079 original size:35 final size:35
Alignment explanation
Indices: 19033--19104 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
19023 GAAAGAAGAT
19033 TAATTGAATTCCATTACAGTTGATTGGAATATAAG
1 TAATTGAATTCCATTACAGTTGATTGGAATATAAG
** *
19068 TAATTGAATTCCATTAGTGTTGATTGGAATATTAG
1 TAATTGAATTCCATTACAGTTGATTGGAATATAAG
19103 TA
1 TA
19105 GTTTAAGGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.35, C:0.07, G:0.18, T:0.40
Consensus pattern (35 bp):
TAATTGAATTCCATTACAGTTGATTGGAATATAAG
Found at i:26565 original size:68 final size:69
Alignment explanation
Indices: 26472--26606 Score: 218
Period size: 68 Copynumber: 2.0 Consensus size: 69
26462 GTCTTTCTGT
* *
26472 TGATTAAATGACTGGATAATGATGTTCATACCATGAGCTGTTTCAATTGGCACAAAATCAAAAGG
1 TGATTAAATGACTGGATAATAATGTTCATACAATGAGCTGTTTCAATTGGCACAAAATCAAAAGG
26537 TGTG
66 TGTG
* * *
26541 TGATTAAATG-CTGGATAATAATGTTCATACAATGTGTTGTTTCAATTGTCACAAAATCAAAAGG
1 TGATTAAATGACTGGATAATAATGTTCATACAATGAGCTGTTTCAATTGGCACAAAATCAAAAGG
26605 TG
66 TG
26607 GGATTTAAAG
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
68 51 0.84
69 10 0.16
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.33
Consensus pattern (69 bp):
TGATTAAATGACTGGATAATAATGTTCATACAATGAGCTGTTTCAATTGGCACAAAATCAAAAGG
TGTG
Found at i:26704 original size:31 final size:31
Alignment explanation
Indices: 26669--26730 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
26659 CTGCTACTTG
26669 ATAGTACTCTGCGAGTAACTATACTAGTTAT
1 ATAGTACTCTGCGAGTAACTATACTAGTTAT
* *
26700 ATAGTACTCTGCTAGTAACTATGCTAGTTAT
1 ATAGTACTCTGCGAGTAACTATACTAGTTAT
26731 TGATAGTCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (31 bp):
ATAGTACTCTGCGAGTAACTATACTAGTTAT
Found at i:27447 original size:41 final size:41
Alignment explanation
Indices: 27401--27525 Score: 234
Period size: 40 Copynumber: 3.0 Consensus size: 41
27391 TGTTGAAAAG
27401 AAAACTTATGAATACAACACAAAATATTCATAAAAAAATAT
1 AAAACTTATGAATACAACACAAAATATTCATAAAAAAATAT
27442 AAAACTTATGAATACAACACAAAATATTCAT-AAAAAATAT
1 AAAACTTATGAATACAACACAAAATATTCATAAAAAAATAT
27482 AAAACTTATGAATACAACACAAAATATTCATAAAAAAAATAT
1 AAAACTTATGAATACAACACAAAATATTCAT-AAAAAAATAT
27524 AA
1 AA
27526 CCGATAGAGC
Statistics
Matches: 82, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
40 40 0.49
41 31 0.38
42 11 0.13
ACGTcount: A:0.62, C:0.12, G:0.02, T:0.24
Consensus pattern (41 bp):
AAAACTTATGAATACAACACAAAATATTCATAAAAAAATAT
Found at i:29975 original size:31 final size:31
Alignment explanation
Indices: 29910--29975 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
29900 TAACATTTGA
* * *
29910 TCACTTTTGTTTTTATTTAATTAAGATTTAG
1 TCACATTTATTTTTATTTAATTAAGATGTAG
*
29941 TCACATTTATTTTTATTTAATTAAGATGTGG
1 TCACATTTATTTTTATTTAATTAAGATGTAG
29972 TCAC
1 TCAC
29976 TGATGGTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.27, C:0.09, G:0.11, T:0.53
Consensus pattern (31 bp):
TCACATTTATTTTTATTTAATTAAGATGTAG
Found at i:30151 original size:20 final size:20
Alignment explanation
Indices: 30109--30151 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
30099 TTAAGTTTCA
*
30109 AAAATAACAAACAGTTCCCT
1 AAAATAACAAACAGGTCCCT
* * *
30129 AAAATATCAAATAGGTCCTT
1 AAAATAACAAACAGGTCCCT
30149 AAA
1 AAA
30152 CAATGATTCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.51, C:0.19, G:0.07, T:0.23
Consensus pattern (20 bp):
AAAATAACAAACAGGTCCCT
Found at i:30276 original size:2 final size:2
Alignment explanation
Indices: 30269--30328 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
30259 ATTTAAAAAG
30269 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 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
30311 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
30329 AATTGGAAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:32543 original size:182 final size:181
Alignment explanation
Indices: 32248--32664 Score: 604
Period size: 182 Copynumber: 2.3 Consensus size: 181
32238 GATACAAATG
* * * * *
32248 AAAAATATATCGCTCCATAGCAATATTACAGGTAAAAATATGACAAAACCGGTCTCGAAATGAAA
1 AAAAATGTATCGATCCATAACAATATAACA-GTAAAAATATGACAAAACCGGTCTCAAAATGAAA
* * *
32313 AAACCGGTAAAACGCTACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTT
65 AAACAGGTAAAACACTACCGAATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTT
*
32378 CT-GAATTTAAAACAGAAGAAGTTATAGCGCCTAAAAAGTATCGATACTTTAT
130 -TGGAATTTAAAACAGAAGAAGTTATAGCGCCTAAAAAGTATCGATACTTTAA
* * * *
32430 GAAAATGTATCGATTCATAACAATATAACAGCTAAAAATATGACAAAACTGGTCTCAAAATGACA
1 AAAAATGTATCGATCCATAACAATATAACAG-TAAAAATATGACAAAACCGGTCTCAAAATGAAA
* *
32495 AAACAGGTAAATA-ACTACCGAATATTTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTT
65 AAACAGGTAAA-ACACTACCGAATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTT
* * *
32559 TTGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAA
129 TTGGAATTTAAAACAGAAGAAGTTATAGCGCCTAAAAAGTATCGATACTTTAA
*
32612 AAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGAAAAAACCGGT
1 AAAAATGTATCGATCCATAACAATATAACA-GTAAAAATATGACAAAACCGGT
32665 AAAAAGATAT
Statistics
Matches: 209, Mismatches: 22, Indels: 8
0.87 0.09 0.03
Matches are distributed among these distances:
181 2 0.01
182 205 0.98
183 2 0.01
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (181 bp):
AAAAATGTATCGATCCATAACAATATAACAGTAAAAATATGACAAAACCGGTCTCAAAATGAAAA
AACAGGTAAAACACTACCGAATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTT
GGAATTTAAAACAGAAGAAGTTATAGCGCCTAAAAAGTATCGATACTTTAA
Found at i:33366 original size:21 final size:19
Alignment explanation
Indices: 33312--33379 Score: 118
Period size: 19 Copynumber: 3.6 Consensus size: 19
33302 CTTTTATTTA
33312 ATATTATAGGTAAAAAATG
1 ATATTATAGGTAAAAAATG
33331 ATATTATAGGTAAAAAATG
1 ATATTATAGGTAAAAAATG
*
33350 ATATTATAGGTAGAAAATG
1 ATATTATAGGTAAAAAATG
*
33369 ATATTTTAGGT
1 ATATTATAGGT
33380 TGTATAAATG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 47 1.00
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.35
Consensus pattern (19 bp):
ATATTATAGGTAAAAAATG
Found at i:34649 original size:22 final size:22
Alignment explanation
Indices: 34621--34671 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 22
34611 TTTATTTTTT
34621 TTATATAAAATGATAATATAGTTA
1 TTATATAAAATGATAA-AT-GTTA
*
34645 TTATATAAAATGATAAATTTTA
1 TTATATAAAATGATAAATGTTA
34667 TTATA
1 TTATA
34672 AATGCATGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 8 0.31
23 2 0.08
24 16 0.62
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (22 bp):
TTATATAAAATGATAAATGTTA
Found at i:36861 original size:19 final size:19
Alignment explanation
Indices: 36837--36886 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
36827 AAATGTAGGG
36837 TTAATTTTGTATAAAATTT
1 TTAATTTTGTATAAAATTT
**
36856 TTAATTTTGTATACGATTT
1 TTAATTTTGTATAAAATTT
*
36875 ATAATTTTGTAT
1 TTAATTTTGTAT
36887 GTAAATGTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.32, C:0.02, G:0.08, T:0.58
Consensus pattern (19 bp):
TTAATTTTGTATAAAATTT
Found at i:37550 original size:199 final size:199
Alignment explanation
Indices: 37210--38235 Score: 1660
Period size: 199 Copynumber: 5.2 Consensus size: 199
37200 GTAAACTTAT
37210 GTGTCGATACATTTATAACAAGTATCGATCCCAAAAATATCGAAACCCATAATTATAATCTAATA
1 GTGTCGATACATTTATAACAAGTATCGATCCCAAAAATATCGAAACCCATAATTATAATCTAATA
* *
37275 GGTAAATTAACAATGTAACCGGTCTAAATATACCGGTTTTTGAGAAGAA-GGGTGTACAAAAAAT
66 GGTAAATTAACAATGTAACCGGTCTAAATATACCGGTTTTTGAGAA-AACAGGTGTACAAAAAGT
* *
37339 ATCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAAAATGAATTTCTAAACCAAGTGTACG
130 ATCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGAATTTCTAAACCAAGTGCACG
37404 AAAAA
195 AAAAA
*
37409 GTGTCGATACATTTATATCAAGTATCGATCCCAAAAATATCGAAACCCATAATTATAATCTAATA
1 GTGTCGATACATTTATAACAAGTATCGATCCCAAAAATATCGAAACCCATAATTATAATCTAATA
*
37474 GGTAAATTAACAATGTAACCGGTCTAAATATACCGGTTTTTGAGAAAATAGGTGTACAAAAAGTA
66 GGTAAATTAACAATGTAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGTA
* * *
37539 TCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCATAATGAATTTCTGAACCAAGTGCAGGA
131 TCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGAATTTCTAAACCAAGTGCACGA
37604 AAAA
196 AAAA
* * *
37608 GTATCGATACATTTATAACAAGTATCGATCCCAAAAATATCGAAACCCATAATTATAATGTAATT
1 GTGTCGATACATTTATAACAAGTATCGATCCCAAAAATATCGAAACCCATAATTATAATCTAATA
* * * *
37673 GGTAAATTAACAATGTAACCGGTCTAAATATACCGTTTTTTTAGAAAACAAGTGTAAAAAAAGTA
66 GGTAAATTAACAATGTAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGTA
* * *
37738 TCGACACAAATAAAACAAGTGTCGATAATGTTGGTCTAGAATGAATTTCTAAACCAAGTGCACGA
131 TCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGAATTTCTAAACCAAGTGCACGA
37803 AAAA
196 AAAA
* *
37807 GTGTCGATACATTTATAACAAGTATCGATCCCAAAAACATCGAAACTCATAATTATAATCTAATA
1 GTGTCGATACATTTATAACAAGTATCGATCCCAAAAATATCGAAACCCATAATTATAATCTAATA
* *
37872 GGTAAATTAAAAATGTAACCGGTCTAAATATACCAGTTTTTGAGAAAACAGGTGTACAAAAAGTA
66 GGTAAATTAACAATGTAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGTA
* * *
37937 -CAGACACAAATAAAATAAGTGTCGATACTTTTGGTCCATAATGAATTTCTAAAACAAGTGCACG
131 TC-GACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGAATTTCTAAACCAAGTGCACG
38001 AAAAA
195 AAAAA
* * * * * *
38006 GTGTCGATACATTTATAATAAGTGTCGATCCCAAAAATATCAAAACCCTTAATTAGAATGTAATA
1 GTGTCGATACATTTATAACAAGTATCGATCCCAAAAATATCGAAACCCATAATTATAATCTAATA
* * *** *
38071 TGTTAATTAACAATGTAATTAGTCTAAATATACCGGTTTTTGAGAAAACAAGTGTACAAAAAGTA
66 GGTAAATTAACAATGTAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGTA
38136 TCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGAATTTCTAAACCAAGTGCACGA
131 TCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGAATTTCTAAACCAAGTGCACGA
38201 AAAA
196 AAAA
* *
38205 GTGTCAATACATTTATAACAAGTATAGATCC
1 GTGTCGATACATTTATAACAAGTATCGATCC
38236 TAAGAACATT
Statistics
Matches: 762, Mismatches: 62, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
198 3 0.00
199 758 0.99
200 1 0.00
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.28
Consensus pattern (199 bp):
GTGTCGATACATTTATAACAAGTATCGATCCCAAAAATATCGAAACCCATAATTATAATCTAATA
GGTAAATTAACAATGTAACCGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGTA
TCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGAATTTCTAAACCAAGTGCACGA
AAAA
Found at i:39115 original size:64 final size:63
Alignment explanation
Indices: 39030--39190 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 63
39020 TTGTTTAAGG
* * * *
39030 TGCATCGATGCACATGCAGTGCATCGATGCAT-TAATTTAAAAAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCAA-TTAAAAA-AAAACATCGAATAGGATTTA
* * *
39094 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCAT-CCAATTAAAAAAAAACATCGAATAGGATTTA
*
39158 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
39191 ACCACCATTA
Statistics
Matches: 85, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
63 1 0.01
64 62 0.73
65 21 0.25
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (63 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCAATTAAAAAAAAACATCGAATAGGATTTA
Found at i:39871 original size:103 final size:103
Alignment explanation
Indices: 39646--39863 Score: 418
Period size: 103 Copynumber: 2.1 Consensus size: 103
39636 GTAGAGGGTC
*
39646 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTATGGTGAGACACATAC
*
39711 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
39749 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTATGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTATGGTGAGACACATAC
39814 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
39852 TATGTGGTCCTT
1 TATGTGGTCCTT
39864 ATGGACATTA
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 113 1.00
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTATGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:39938 original size:23 final size:23
Alignment explanation
Indices: 39879--39942 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
39869 CATTATTATA
39879 TGGCAC-TACGGTGCAATTCTACG
1 TGGCACTTA-GGTGCAATTCTACG
* *
39902 CGGCACTCCA-GTGCAATTCTACG
1 TGGCACT-TAGGTGCAATTCTACG
39925 TGGCACTTAGGTGCAATT
1 TGGCACTTAGGTGCAATT
39943 ATATGAGCTG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
22 1 0.03
23 32 0.94
25 1 0.03
ACGTcount: A:0.22, C:0.27, G:0.25, T:0.27
Consensus pattern (23 bp):
TGGCACTTAGGTGCAATTCTACG
Found at i:41332 original size:2 final size:2
Alignment explanation
Indices: 41319--41352 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
41309 ATGGGGAATG
*
41319 AT AT AC 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
41353 CTCAGGAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:42190 original size:3 final size:3
Alignment explanation
Indices: 42159--42208 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
42149 CAAGCGGTCA
* * * * *
42159 ATG AAG ATG ACG ATG AAG ATG AAG ATG ATG ATA ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
42207 AT
1 AT
42209 CCAAACAAGT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.42, C:0.02, G:0.30, T:0.26
Consensus pattern (3 bp):
ATG
Found at i:44631 original size:199 final size:200
Alignment explanation
Indices: 43958--44642 Score: 1104
Period size: 201 Copynumber: 3.4 Consensus size: 200
43948 TAGATATAAT
* * *
43958 ATGTAATAGGCCACTTTACAATGTAACCGGTTTAAACTTACCGGTTTTATGAGAAAATGGGTCTA
1 ATGTAATAGGTCACTTTACAATGTAACCGGTTTAAATTTACCGGTTTTATGAGAAAATAGGTCTA
*
44023 AATAATGTATCGACACTTTATTTATTTGTGTCGATACTTTTTATCCCTAATGAATTCCCAAACTA
66 AATAATGTATCGACACTTTATTTATTTGTGTCGATACTTTTTATCCATAATGAATTCCCAAACTA
* *
44088 TGTGCACACATAAAGTGTCGATACATTTATAAAAAGTGTCGACCCCAAATACATCGAGACCGAAA
131 TGTGCACACATAAAGTGTCGATACAATTATAAAAAGT-TCGACCCCAAATACATCGAGACCAAAA
44153 ATTATA
195 ATTATA
* * *
44159 ATGTAATAGGTCACTTTACAATGTTACTGGTTTAAATTTATCGGTTTTATGAGAAAATAGGTCTA
1 ATGTAATAGGTCACTTTACAATGTAACCGGTTTAAATTTACCGGTTTTATGAGAAAATAGGTCTA
* *
44224 AATAATGTATTGACACTTTATTTATTTGTGTCGATACTTTTTATCCATAATGAATTCTCAAACTA
66 AATAATGTATCGACACTTTATTTATTTGTGTCGATACTTTTTATCCATAATGAATTCCCAAACTA
* * *
44289 TGTGCACGCATAAAGTGTCGATATAATTATAAAAAGCTTCAACCCCAAATACATCGAGACCAAAA
131 TGTGCACACATAAAGTGTCGATACAATTATAAAAAG-TTCGACCCCAAATACATCGAGACCAAAA
44354 ATTATA
195 ATTATA
*
44360 ATGTAATAGGTCACTTTACAATGTAACCGGTTTAAATTTACCGGTTTTATGAGAAAATATGTCTA
1 ATGTAATAGGTCACTTTACAATGTAACCGGTTTAAATTTACCGGTTTTATGAGAAAATAGGTCTA
* * * * *
44425 AATAATGTATCGACACTTTATTTATTTGTATTGATGCTTTTTATCCATAATGAATTCCCGAAGTA
66 AATAATGTATCGACACTTTATTTATTTGTGTCGATACTTTTTATCCATAATGAATTCCCAAACTA
*
44490 TGTGCACACATAAAGTGTCGATACAATTATAAAAAGTT-GACCCCAAATACATCGAGTCCAAAAA
131 TGTGCACACATAAAGTGTCGATACAATTATAAAAAGTTCGACCCCAAATACATCGAGACCAAAAA
44554 TTATA
196 TTATA
* * *
44559 ATGTAATAGGTCACTTTACAATGTAACCGGTTTAAATTTATCGATTTTATGAGAAAATCGGTC-A
1 ATGTAATAGGTCACTTTACAATGTAACCGGTTTAAATTTACCGGTTTTATGAGAAAATAGGTCTA
*
44623 ACATAATGTATCGAAACTTT
66 A-ATAATGTATCGACACTTT
44643 TTAAATTCAT
Statistics
Matches: 448, Mismatches: 34, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
198 2 0.00
199 105 0.23
200 2 0.00
201 338 0.75
202 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.34
Consensus pattern (200 bp):
ATGTAATAGGTCACTTTACAATGTAACCGGTTTAAATTTACCGGTTTTATGAGAAAATAGGTCTA
AATAATGTATCGACACTTTATTTATTTGTGTCGATACTTTTTATCCATAATGAATTCCCAAACTA
TGTGCACACATAAAGTGTCGATACAATTATAAAAAGTTCGACCCCAAATACATCGAGACCAAAAA
TTATA
Found at i:48412 original size:200 final size:198
Alignment explanation
Indices: 48041--49343 Score: 853
Period size: 201 Copynumber: 6.4 Consensus size: 198
48031 ACATTTTCCA
* * ** *
48041 AAAAACATCGAAACAAATA-ATTATAATATAATAGGTAAATTAACAATGTAACCAATATACATAT
1 AAAAACATCGAAACACATAGA-TATAATGTAATAGGTAAATTAACAATGTAACCGGTATAAATAT
* * * * * *
48105 ATCGGTTAATTATAAAACTGGTCA-ACATAATGTATCGACACTATTAGAATTTGTGTCGATACTT
65 ACCGGTTTATGAGAAAACAGGT-ATACATAATGTATCGACAC-ATTACAATTTGTGTCGATACTT
* * ** * *
48169 ATTGTCTAGAATGAATGGCCAAACGACAG-GCACGCATAAAGTGTCGATACATTTATAACAAGTG
128 ATTTTCCAGAATGAATTCCCAAACCA-AGTGCACG-ACAAAGTGTCGATACATTTATAACAAGTG
48233 TCGATACT
191 TCGATACT
* ** *
48241 AAAAACATCGAAACACATAGATATAATGTAATAGGTAAAATAACAATGTAACCGGCCTAAATACA
1 AAAAACATCGAAACACATAGATATAATGTAATAGGTAAATTAACAATGTAACCGGTATAAATATA
* * ***
48306 CCGGTTTATGAGAAAACAGGTATACATAAAGTATCGACACAACTACAACAAGTGTCGATACTTAT
66 CCGGTTTATGAGAAAACAGGTATACATAATGTATCGACAC-ATTACAATTTGTGTCGATACTTAT
* *
48371 TTTCCAGAATGTATTTTCCAAACCAAGTGCACGACAAAGTGTCGATACATTTATAACAAGTGTCG
130 TTTCCAGAATG-AATTCCCAAACCAAGTGCACGACAAAGTGTCGATACATTTATAACAAGTGTCG
48436 ATACT
194 ATACT
* * * * *
48441 AAAAACATCGAAACACATAGATATAATATGTAATAGGTCACTTTACAATGTAACCGGTTTAAATT
1 AAAAACATCGAAACACATAGATAT-A-ATGTAATAGGTAAATTAACAATGTAACCGGTATAAATA
* * * * **
48506 TACCGGTTTTATGAGAAAATAGGTCTAAATAATGTATCGACACTTTATTTATTTGTGTCGATACT
64 TACCGG-TTTATGAGAAAACAGGTATACATAATGTATCGACACATTA-CAATTTGTGTCGATACT
* * * *
48571 T-TTTATCCATAATGAATTCCCAAACTATGTGCAC-ACATAAAGTGTCGATACATTTATAAAAAG
127 TATTT-TCCAGAATGAATTCCCAAACCAAGTGCACGAC--AAAGTGTCGATACATTTATAACAAG
** *
48634 TGTCGACCCC
189 TGTCGATACT
* * * * * * * * * * *
48644 AAATACATTGAGAC-CGA-AAATTATAATATAATAGGTCACTTTACAATGTAATCGGTTTAAATT
1 AAAAACATCGAAACAC-ATAGA-TATAATGTAATAGGTAAATTAACAATGTAACCGGTATAAATA
* * * * * **
48707 TACCGGTTTTATGAGAAAATAAGTCTAAATAATGTATCGACACTTTATTTATTTGTGTCGATACT
64 TACCGG-TTTATGAGAAAACAGGTATACATAATGTATCGACACATTA-CAATTTGTGTCGATACT
* * * * * *
48772 T-TTTATCCATAATGAATTCCCAAACTATGTGCACGCATAAAGTGTCAATACATTTATAAAAAGT
127 TATTT-TCCAGAATGAATTCCCAAACCAAGTGCACG-ACAAAGTGTCGATACATTTATAACAAGT
** *
48836 GTCGACCCC
190 GTCGATACT
* * * * * * * * * *
48845 AAATACATCGAGAC-CGA-AAATTATAATGTAATAGGTCACTTTACAATATAACTGGTTTAAATT
1 AAAAACATCGAAACAC-ATAGA-TATAATGTAATAGGTAAATTAACAATGTAACCGGTATAAATA
* * * * **
48908 TACCGGTTTTATGAGAAAATAGGTCTAAATAATGTATCGACACTTTATTTATTTGTGTCGATACT
64 TACCGG-TTTATGAGAAAACAGGTATACATAATGTATCGACACATTA-CAATTTGTGTCGATACT
* * * * * * * *
48973 T-TTTATCCATAATGAATTCCCATACTATGTGCACGCATAAAATGTCGACACATTTATAAAAAGT
127 TATTT-TCCAGAATGAATTCCCAAACCAAGTGCACG-ACAAAGTGTCGATACATTTATAACAAGT
** *
49037 GTCGACCCC
190 GTCGATACT
* * * * * * * * * *
49046 AAATACATCGAGAC-CGA-AAATTATAATGTAATAGATCACTTTACAATGTAACCGATTTAAATT
1 AAAAACATCGAAACAC-ATAGA-TATAATGTAATAGGTAAATTAACAATGTAACCGGTATAAATA
* * * *
49109 TACCGATTTTATGAGAAAACCA-GTCA-ACATAACGTATCGACACTTTTTA-AATTCGTGTCGAC
64 TACCG-GTTTATGAGAAAA-CAGGT-ATACATAATGTATCGACAC--ATTACAATTTGTGTCG--
* * *
49171 ACTTTTTAAAATTACCCTTCATTATTTTCCAGAATGTATTTTCCAAACTAAGTGCACGACAAAGT
122 ----------A-TA-----C-TTATTTTCCAGAATG-AATTCCCAAACCAAGTGCACGACAAAGT
49236 GTCGATACATTTATAACAAGTGTCGATACT
169 GTCGATACATTTATAACAAGTGTCGATACT
* * * * *
49266 -AAAACATCGATAC-CGATA-ATTATAATGTAATAGGTATATTTACAATGTAAACGGTAGAAATA
1 AAAAACATCGAAACAC-ATAGA-TATAATGTAATAGGTAAATTAACAATGTAACCGGTATAAATA
* *
49328 TATCGGGTTAATGAGA
64 TA-CCGGTTTATGAGA
49344 GAATATGTTA
Statistics
Matches: 948, Mismatches: 112, Indels: 67
0.84 0.10 0.06
Matches are distributed among these distances:
199 1 0.00
200 176 0.19
201 479 0.51
202 62 0.07
203 104 0.11
213 1 0.00
214 2 0.00
219 60 0.06
220 43 0.05
221 20 0.02
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (198 bp):
AAAAACATCGAAACACATAGATATAATGTAATAGGTAAATTAACAATGTAACCGGTATAAATATA
CCGGTTTATGAGAAAACAGGTATACATAATGTATCGACACATTACAATTTGTGTCGATACTTATT
TTCCAGAATGAATTCCCAAACCAAGTGCACGACAAAGTGTCGATACATTTATAACAAGTGTCGAT
ACT
Found at i:48735 original size:201 final size:201
Alignment explanation
Indices: 48131--49178 Score: 1213
Period size: 201 Copynumber: 5.2 Consensus size: 201
48121 ACTGGTCAAC
** * * * * ** *
48131 ATAATGTATCGACACTATTA-GAATTTGTGTCGATACTTATTGTCTAGAATGAATGGCCAAACGA
1 ATAATGTATCGACACT-TTATTTATTTGTGTCGATACTTTTTATCCATAATGAATTCCCAAACTA
* * * ** * * *
48195 CAG-GCACGCATAAAGTGTCGATACATTTATAACAAGTGTCGATACTAAAAACATCGAAACAC-A
65 -TGTGCACACATAAAGTGTCGATACATTTATAAAAAGTGTCGACCCCAAATACATCGAGAC-CGA
* * * ** * ** **
48258 TAGA-TATAATGTAATAGGTAAAATAACAATGTAACCGGCCTAAATACACCGG-TTTATGAGAAA
128 -AAATTATAATATAATAGGTCACTTTACAATGTAACCGGTTTAAATTTACCGGTTTTATGAGAAA
* * * *
48321 ACAGGTATAC
192 ATAAGTCTAA
* ** ** *** * * *
48331 ATAAAGTATCGACACAACTA-CAACAAGTGTCGATACTTATTT-TCCAGAATGTATTTTCCAAAC
1 ATAATGTATCGACAC-TTTATTTATTTGTGTCGATACTT-TTTATCCATAATG-AATTCCCAAAC
* * * ** * * *
48394 CAAGTGCACGAC--AAAGTGTCGATACATTTATAACAAGTGTCGATACTAAAAACATCGAAACAC
63 TATGTGCAC-ACATAAAGTGTCGATACATTTATAAAAAGTGTCGACCCCAAATACATCGAGAC-C
*
48457 -ATAGA-TATAATATGTAATAGGTCACTTTACAATGTAACCGGTTTAAATTTACCGGTTTTATGA
126 GA-AAATTATAATA--TAATAGGTCACTTTACAATGTAACCGGTTTAAATTTACCGGTTTTATGA
*
48520 GAAAATAGGTCTAA
188 GAAAATAAGTCTAA
48534 ATAATGTATCGACACTTTATTTATTTGTGTCGATACTTTTTATCCATAATGAATTCCCAAACTAT
1 ATAATGTATCGACACTTTATTTATTTGTGTCGATACTTTTTATCCATAATGAATTCCCAAACTAT
*
48599 GTGCACACATAAAGTGTCGATACATTTATAAAAAGTGTCGACCCCAAATACATTGAGACCGAAAA
66 GTGCACACATAAAGTGTCGATACATTTATAAAAAGTGTCGACCCCAAATACATCGAGACCGAAAA
*
48664 TTATAATATAATAGGTCACTTTACAATGTAATCGGTTTAAATTTACCGGTTTTATGAGAAAATAA
131 TTATAATATAATAGGTCACTTTACAATGTAACCGGTTTAAATTTACCGGTTTTATGAGAAAATAA
48729 GTCTAA
196 GTCTAA
48735 ATAATGTATCGACACTTTATTTATTTGTGTCGATACTTTTTATCCATAATGAATTCCCAAACTAT
1 ATAATGTATCGACACTTTATTTATTTGTGTCGATACTTTTTATCCATAATGAATTCCCAAACTAT
* *
48800 GTGCACGCATAAAGTGTCAATACATTTATAAAAAGTGTCGACCCCAAATACATCGAGACCGAAAA
66 GTGCACACATAAAGTGTCGATACATTTATAAAAAGTGTCGACCCCAAATACATCGAGACCGAAAA
* * * *
48865 TTATAATGTAATAGGTCACTTTACAATATAACTGGTTTAAATTTACCGGTTTTATGAGAAAATAG
131 TTATAATATAATAGGTCACTTTACAATGTAACCGGTTTAAATTTACCGGTTTTATGAGAAAATAA
48930 GTCTAA
196 GTCTAA
*
48936 ATAATGTATCGACACTTTATTTATTTGTGTCGATACTTTTTATCCATAATGAATTCCCATACTAT
1 ATAATGTATCGACACTTTATTTATTTGTGTCGATACTTTTTATCCATAATGAATTCCCAAACTAT
* * *
49001 GTGCACGCATAAAATGTCGACACATTTATAAAAAGTGTCGACCCCAAATACATCGAGACCGAAAA
66 GTGCACACATAAAGTGTCGATACATTTATAAAAAGTGTCGACCCCAAATACATCGAGACCGAAAA
* * * * **
49066 TTATAATGTAATAGATCACTTTACAATGTAACCGATTTAAATTTACCGATTTTATGAGAAAACCA
131 TTATAATATAATAGGTCACTTTACAATGTAACCGGTTTAAATTTACCGGTTTTATGAGAAAATAA
49131 GTC-AA
196 GTCTAA
* * * *
49136 CATAACGTATCGACACTTT-TTAAATTCGTGTCGACACTTTTTA
1 -ATAATGTATCGACACTTTATT-TATTTGTGTCGATACTTTTTA
49179 AAATTACCCT
Statistics
Matches: 759, Mismatches: 73, Indels: 31
0.88 0.08 0.04
Matches are distributed among these distances:
200 106 0.14
201 492 0.65
202 58 0.08
203 103 0.14
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (201 bp):
ATAATGTATCGACACTTTATTTATTTGTGTCGATACTTTTTATCCATAATGAATTCCCAAACTAT
GTGCACACATAAAGTGTCGATACATTTATAAAAAGTGTCGACCCCAAATACATCGAGACCGAAAA
TTATAATATAATAGGTCACTTTACAATGTAACCGGTTTAAATTTACCGGTTTTATGAGAAAATAA
GTCTAA
Found at i:56572 original size:36 final size:34
Alignment explanation
Indices: 56510--56629 Score: 100
Period size: 35 Copynumber: 3.4 Consensus size: 34
56500 ATATTTTAAT
* *
56510 TATCTTTTAAT-TTGAATTATTTAAAAAGATATTGT
1 TATCTTTTAATATT-AA-AATTTAAAAAGATATTGA
* * **
56545 TATCGTTTTAATATTTAAATTTAAAAAAATAATAAA
1 TATC-TTTTAATATTAAAATTTAAAAAGAT-ATTGA
*
56581 TATCTTTTAAT-TTAAAATATTCGAAAAGATATTGA
1 TATCTTTTAATATTAAAAT-TT-AAAAAGATATTGA
56616 TATCCTTTTAATAT
1 TAT-CTTTTAATAT
56630 CTTTTAATAT
Statistics
Matches: 67, Mismatches: 11, Indels: 12
0.74 0.12 0.13
Matches are distributed among these distances:
34 6 0.09
35 30 0.45
36 28 0.42
37 3 0.04
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.47
Consensus pattern (34 bp):
TATCTTTTAATATTAAAATTTAAAAAGATATTGA
Found at i:56591 original size:71 final size:71
Alignment explanation
Indices: 56510--56741 Score: 203
Period size: 71 Copynumber: 3.1 Consensus size: 71
56500 ATATTTTAAT
*
56510 TATCTTTTAATTTGAATTATTTAAAAAGATATTGTTATCGTTTTAATATTTAAATTTAAAAAAAT
1 TATCTTTTAATTTGAAATATTTAAAAAGATATTGTTATCGTTTTAATATTTAAATTTAAAAAAAT
56575 AATAAA
66 AATAAA
* ** * * *
56581 TATCTTTTAATTTAAAATATTCGAAAAGATATTGATATCCTTTTAATATCTTTTAATATTCAAAT
1 TATCTTTTAATTTGAAATATTTAAAAAGATATTGTTATCGTTTTAATA---TTTAA-ATTTAAA-
*
56646 TTTTATAAAAAATAAA
61 ----A-AAATAATAAA
* * ** * * * ***
56662 TATCTTTTACTTTGAAATATTTAATAAGATATAATTATCGTATTAATATTCAAATGTAAAGGGAT
1 TATCTTTTAATTTGAAATATTTAAAAAGATATTGTTATCGTTTTAATATTTAAATTTAAAAAAAT
*
56727 GATAAA
66 AATAAA
56733 TATCTTTTA
1 TATCTTTTA
56742 GTTTAGAATA
Statistics
Matches: 125, Mismatches: 26, Indels: 20
0.73 0.15 0.12
Matches are distributed among these distances:
71 57 0.46
74 5 0.04
75 6 0.05
77 5 0.04
78 4 0.03
80 1 0.01
81 47 0.38
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (71 bp):
TATCTTTTAATTTGAAATATTTAAAAAGATATTGTTATCGTTTTAATATTTAAATTTAAAAAAAT
AATAAA
Found at i:56666 original size:35 final size:36
Alignment explanation
Indices: 56625--56716 Score: 98
Period size: 35 Copynumber: 2.6 Consensus size: 36
56615 ATATCCTTTT
*
56625 AATATCTTTTAATATTCAAAT-TTTTATAAAAAATA
1 AATATCTTTTAATATTCAAATATTTAATAAAAAATA
* * * *
56660 AATATCTTTTACT-TTGAAATATTTAATAAGATATA
1 AATATCTTTTAATATTCAAATATTTAATAAAAAATA
* *
56695 ATTATCGTATTAATATTCAAAT
1 AATATC-TTTTAATATTCAAAT
56717 GTAAAGGGAT
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
34 6 0.13
35 28 0.62
36 5 0.11
37 6 0.13
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.46
Consensus pattern (36 bp):
AATATCTTTTAATATTCAAATATTTAATAAAAAATA
Found at i:56708 original size:81 final size:82
Alignment explanation
Indices: 56545--56710 Score: 196
Period size: 81 Copynumber: 2.0 Consensus size: 82
56535 AAGATATTGT
*
56545 TATCGTTTTAATATTTAAATTTAAAAAAATAATAAATATCTTTTAATTTAAAATATTCGAAAAGA
1 TATCGTTTTAATATTCAAATTTAAAAAAATAATAAATATCTTTTAATTTAAAATATTCGAAAAGA
* *
56610 TATTGATATCCTTTTAA
66 TATTAATATCCTATTAA
* * * * *
56627 TATC-TTTTAATATTCAAATTTTTATAAAA-AATAAATATCTTTTACTTTGAAATATT-TAATAA
1 TATCGTTTTAATATTCAAA-TTTAAAAAAATAATAAATATCTTTTAATTTAAAATATTCGAA-AA
*
56689 GATA-TAATTATCGTATTAA
64 GATATTAA-TATCCTATTAA
56708 TAT
1 TAT
56711 TCAAATGTAA
Statistics
Matches: 72, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
80 4 0.06
81 56 0.78
82 12 0.17
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (82 bp):
TATCGTTTTAATATTCAAATTTAAAAAAATAATAAATATCTTTTAATTTAAAATATTCGAAAAGA
TATTAATATCCTATTAA
Found at i:59729 original size:17 final size:17
Alignment explanation
Indices: 59707--59754 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
59697 AAAAATAATA
59707 TATATATAATA-TAAATT
1 TATATATAA-ACTAAATT
*
59724 TATATATAAACTATATT
1 TATATATAAACTAAATT
59741 TATATTATAAACTA
1 TATA-TATAAACTA
59755 TATAATTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 1 0.04
17 18 0.64
18 9 0.32
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (17 bp):
TATATATAAACTAAATT
Found at i:59751 original size:18 final size:18
Alignment explanation
Indices: 59721--59780 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
59711 TATAATATAA
59721 ATTTATA-TATAAACTAT
1 ATTTATATTATAAACTAT
59738 ATTTATATTATAAACTAT
1 ATTTATATTATAAACTAT
* *
59756 A-TAATTATTATAAGCTAT
1 ATTTA-TATTATAAACTAT
*
59774 ATATATA
1 ATTTATA
59781 AATTATGTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 9 0.25
18 26 0.72
19 1 0.03
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (18 bp):
ATTTATATTATAAACTAT
Found at i:59785 original size:20 final size:18
Alignment explanation
Indices: 59728--59786 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
59718 TAAATTTATA
*
59728 TATAAACTATAT-TTATAT
1 TATAAACTATATAATA-AT
*
59746 TATAAACTATATAATTAT
1 TATAAACTATATAATAAT
*
59764 TATAAGCTATATATATAAAT
1 TATAAACTATATA-AT-AAT
59784 TAT
1 TAT
59787 GTTTATGTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
18 26 0.76
19 3 0.09
20 5 0.15
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (18 bp):
TATAAACTATATAATAAT
Found at i:59863 original size:2 final size:2
Alignment explanation
Indices: 59856--59884 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
59846 TATATTAATT
59856 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
59885 TATTCAAAGT
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:60015 original size:46 final size:45
Alignment explanation
Indices: 59958--60047 Score: 121
Period size: 46 Copynumber: 2.0 Consensus size: 45
59948 ATTTTATTTA
* *
59958 GGAATTTAGAGGGAAATT-GAGAAATTTTGAGA-ATATAGAGAAATTG
1 GGAATTAAGAGGGAAATTGGA-AAATTTAGAGAGA-ATAGA-AAATTG
60004 GGAATTAAGAGGGAAATTGGAAAATTTAGAGAGAATAGAAAATT
1 GGAATTAAGAGGGAAATTGGAAAATTTAGAGAGAATAGAAAATT
60048 TTGGGAAGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
45 5 0.12
46 32 0.80
47 3 0.08
ACGTcount: A:0.47, C:0.00, G:0.28, T:0.26
Consensus pattern (45 bp):
GGAATTAAGAGGGAAATTGGAAAATTTAGAGAGAATAGAAAATTG
Found at i:60254 original size:2 final size:2
Alignment explanation
Indices: 60247--60417 Score: 121
Period size: 2 Copynumber: 89.0 Consensus size: 2
60237 TACTTTTAAT
* * *
60247 TA TA TA TA TA TA TA TA TA TA TA AA CTA TA TG TA TA -A AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* * * * *
60289 TA GTT TA TA AA T- TA TA T- TA -A TA TA -A TA TA CA TA TG TA TG
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
60328 T- TA -A CTA -A TA TA -A GTA -A TC TA TA GA -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
*
60366 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
60408 TA AA TA TA TA
1 TA TA TA TA TA
60418 AACACTATGC
Statistics
Matches: 133, Mismatches: 21, Indels: 30
0.72 0.11 0.16
Matches are distributed among these distances:
1 11 0.08
2 118 0.89
3 4 0.03
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (2 bp):
TA
Found at i:60704 original size:21 final size:20
Alignment explanation
Indices: 60659--60697 Score: 62
Period size: 19 Copynumber: 1.9 Consensus size: 20
60649 ACATGTAACT
60659 TATATGTATGTATAAACTATG
1 TATATGTA-GTATAAACTATG
60680 TATATGTA-TATAAACTAT
1 TATATGTAGTATAAACTAT
60698 AGGTATAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
21 8 0.44
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (20 bp):
TATATGTAGTATAAACTATG
Found at i:60820 original size:35 final size:36
Alignment explanation
Indices: 60781--60868 Score: 112
Period size: 35 Copynumber: 2.5 Consensus size: 36
60771 ATAGAAATCT
*
60781 TAAATCCCTAAACCCTAAATAGT-ATATATAAACCC
1 TAAATCCCTAAACCCTAAATAGTAAAATATAAACCC
* *
60816 TAAAT-CCTAAATCCTAAATATTAAAATATAAACCC
1 TAAATCCCTAAACCCTAAATAGTAAAATATAAACCC
60851 TAAA-CCCT-AACCCATAAA
1 TAAATCCCTAAACCC-TAAA
60869 CTCTAAACCC
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
34 19 0.41
35 27 0.59
ACGTcount: A:0.49, C:0.25, G:0.01, T:0.25
Consensus pattern (36 bp):
TAAATCCCTAAACCCTAAATAGTAAAATATAAACCC
Found at i:60836 original size:27 final size:28
Alignment explanation
Indices: 60781--60836 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
60771 ATAGAAATCT
* *
60781 TAAATCCCTAAACCCTAAATAGTATATA
1 TAAATCCCTAAACCCTAAATACTAAATA
* *
60809 TAAA-CCCTAAATCCTAAATCCTAAATA
1 TAAATCCCTAAACCCTAAATACTAAATA
60836 T
1 T
60837 TAAAATATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.46, C:0.23, G:0.02, T:0.29
Consensus pattern (28 bp):
TAAATCCCTAAACCCTAAATACTAAATA
Found at i:60854 original size:7 final size:7
Alignment explanation
Indices: 60844--60883 Score: 55
Period size: 7 Copynumber: 5.7 Consensus size: 7
60834 TATTAAAATA
60844 TAAACCC
1 TAAACCC
60851 TAAACCC
1 TAAACCC
60858 T-AACCC
1 TAAACCC
*
60864 ATAAACTC
1 -TAAACCC
60872 TAAACCC
1 TAAACCC
60879 TAAAC
1 TAAAC
60884 ATTATGCATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 5 0.17
7 20 0.69
8 4 0.14
ACGTcount: A:0.45, C:0.38, G:0.00, T:0.17
Consensus pattern (7 bp):
TAAACCC
Found at i:60980 original size:15 final size:15
Alignment explanation
Indices: 60962--61018 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
60952 CTTATAGTAC
*
60962 ATGTATGTATAAACT
1 ATGTATATATAAACT
60977 ATGTATATATAAACT
1 ATGTATATATAAACT
* *
60992 ATATATATATAACCT
1 ATGTATATATAAACT
*
61007 ATAGTATGTATA
1 AT-GTATATATA
61019 CACAATCTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
15 29 0.81
16 7 0.19
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (15 bp):
ATGTATATATAAACT
Found at i:60984 original size:37 final size:36
Alignment explanation
Indices: 60905--60978 Score: 96
Period size: 37 Copynumber: 2.1 Consensus size: 36
60895 ACAATAGTTA
* *
60905 ATATATGTAACATATAGTATATGTATACATGTAAACT
1 ATATATGTAACATATAGTACATGTATA-ATATAAACT
* *
60942 ATATATGTAACTTATAGTACATGTAT-GTATAAACT
1 ATATATGTAACATATAGTACATGTATAATATAAACT
60977 AT
1 AT
60979 GTATATATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 9 0.27
37 24 0.73
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (36 bp):
ATATATGTAACATATAGTACATGTATAATATAAACT
Found at i:61191 original size:15 final size:14
Alignment explanation
Indices: 61154--61442 Score: 86
Period size: 15 Copynumber: 19.8 Consensus size: 14
61144 TTAATGTACT
61154 ATATAATTTATATTA
1 ATATAA-TTATATTA
* *
61169 ATGTTAATTATCTTA
1 AT-ATAATTATATTA
61184 ACTATAATTATATTA
1 A-TATAATTATATTA
* *
61199 ATATAGTATATAGTTT
1 ATATAAT-TATA-TTA
*
61215 ATA-AACTATA-TA
1 ATATAATTATATTA
*
61227 ATATTAATTATATGA
1 ATA-TAATTATATTA
*
61242 ATTATAGTTTATAAACTATA
1 A-TATA-ATTAT--A-T-TA
*
61262 TATATAATT-TATAA
1 -ATATAATTATATTA
*
61276 CATATAGTTTATATTA
1 -ATATA-ATTATATTA
*
61292 ATATTAATTTTA-TA
1 ATA-TAATTATATTA
*
61306 GACTATATTTTATATTA
1 -A-TATA-ATTATATTA
*
61323 ATATTAATTACAATT-
1 ATA-TAATTA-TATTA
*
61338 ATA-AACTATATT-
1 ATATAATTATATTA
61350 ATATTAA-TATAAGTTA
1 ATA-TAATTAT-A-TTA
*
61366 ATATTAATTAAATTA
1 ATA-TAATTATATTA
*
61381 ATATAATTATAAT-
1 ATATAATTATATTA
61394 ATATAA-T-TATT-
1 ATATAATTATATTA
61405 -TAT-ATTATA-TA
1 ATATAATTATATTA
*
61416 ATATATATTATTTTA
1 ATATA-ATTATATTA
61431 ATATTAATTATA
1 ATA-TAATTATA
61443 AATACTTTAT
Statistics
Matches: 205, Mismatches: 32, Indels: 74
0.66 0.10 0.24
Matches are distributed among these distances:
9 1 0.00
10 5 0.02
11 5 0.02
12 14 0.07
13 13 0.06
14 39 0.19
15 69 0.34
16 44 0.21
17 4 0.02
18 2 0.01
19 3 0.01
20 5 0.02
21 1 0.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (14 bp):
ATATAATTATATTA
Found at i:61248 original size:37 final size:35
Alignment explanation
Indices: 61183--61288 Score: 121
Period size: 34 Copynumber: 3.0 Consensus size: 35
61173 TAATTATCTT
*
61183 AACTATAATTATATTAA-TATA-GTATATAGTTTATA
1 AACTAT-A-TATATTAATTATATGAATATAGTTTATA
61218 AACTATATAATATTAATTATATGAATTATAGTTTATA
1 AACTATAT-ATATTAATTATATGAA-TATAGTTTATA
*
61255 AACTATATATA-TAATT-TATAACATATAGTTTATA
1 AACTATATATATTAATTATATGA-ATATAGTTTATA
61289 TTAATATTAA
Statistics
Matches: 64, Mismatches: 2, Indels: 11
0.83 0.03 0.14
Matches are distributed among these distances:
33 1 0.02
34 23 0.36
35 16 0.25
36 5 0.08
37 19 0.30
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (35 bp):
AACTATATATATTAATTATATGAATATAGTTTATA
Found at i:61281 original size:20 final size:20
Alignment explanation
Indices: 61186--61275 Score: 59
Period size: 20 Copynumber: 4.6 Consensus size: 20
61176 TTATCTTAAC
*
61186 TATAATTATATTAA-TATAGTA
1 TATAATT-TATAAACTATA-TA
*
61207 TATAGTTTATAAACTATATAA
1 TATAATTTATAAACTATAT-A
61228 TATTAA-TTAT--A-TGA-AT-
1 TA-TAATTTATAAACT-ATATA
*
61244 TATAGTTTATAAACTATATA
1 TATAATTTATAAACTATATA
61264 TATAATTTATAA
1 TATAATTTATAA
61276 CATATAGTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 21
0.68 0.06 0.26
Matches are distributed among these distances:
15 2 0.04
16 6 0.11
18 5 0.09
19 5 0.09
20 17 0.31
21 17 0.31
22 2 0.04
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (20 bp):
TATAATTTATAAACTATATA
Found at i:61318 original size:31 final size:31
Alignment explanation
Indices: 61221--61331 Score: 104
Period size: 31 Copynumber: 3.5 Consensus size: 31
61211 GTTTATAAAC
* *
61221 TATA-TAATATTAATTATATGAA-TTATAGTT
1 TATATTAATATTAATTTTAT-AACATATAGTT
*
61251 TATAAACTATATATATAA-TTTATAACATATAGTT
1 TAT--ATTA-ATAT-TAATTTTATAACATATAGTT
*
61285 TATATTAATATTAATTTTATAGAC-TATATTT
1 TATATTAATATTAATTTTATA-ACATATAGTT
61316 TATATTAATATTAATT
1 TATATTAATATTAATT
61332 ACAATTATAA
Statistics
Matches: 69, Mismatches: 4, Indels: 15
0.78 0.05 0.17
Matches are distributed among these distances:
30 6 0.09
31 32 0.46
32 6 0.09
33 4 0.06
34 18 0.26
35 3 0.04
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (31 bp):
TATATTAATATTAATTTTATAACATATAGTT
Found at i:61380 original size:25 final size:27
Alignment explanation
Indices: 61347--61422 Score: 81
Period size: 25 Copynumber: 3.0 Consensus size: 27
61337 TATAAACTAT
*
61347 ATTATATTAATATAAGT-TAATAT-TA
1 ATTAAATTAATATAAGTATAATATATA
*
61372 ATTAAATTAATATAATTATAATATATA
1 ATTAAATTAATATAAGTATAATATATA
* *
61399 ATT--ATTTATATTA-TATAATATATA
1 ATTAAATTAATATAAGTATAATATATA
61423 TTATTTTAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
24 11 0.24
25 23 0.51
26 6 0.13
27 5 0.11
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (27 bp):
ATTAAATTAATATAAGTATAATATATA
Found at i:61420 original size:24 final size:24
Alignment explanation
Indices: 61382--61465 Score: 88
Period size: 23 Copynumber: 3.7 Consensus size: 24
61372 ATTAAATTAA
61382 TATAAT-TATAATATATAATTATT
1 TATAATATATAATATATAATTATT
*
61405 TATATTATATAATATAT-ATTATT
1 TATAATATATAATATATAATTATT
*
61428 T-TAATAT-TAAT-TATAAATACTT
1 TATAATATATAATATATAATTA-TT
* *
61450 TATAATAAATTATATA
1 TATAATATATAATATA
61466 AGACGGTAGC
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
20 3 0.06
21 7 0.14
22 8 0.16
23 17 0.34
24 13 0.26
25 2 0.04
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (24 bp):
TATAATATATAATATATAATTATT
Found at i:61426 original size:36 final size:40
Alignment explanation
Indices: 61320--61426 Score: 109
Period size: 43 Copynumber: 2.7 Consensus size: 40
61310 ATATTTTATA
* *
61320 TTAATATTAATTACAATTATAAACTATATTATATTAATATAAG
1 TTAATATTAATTA-AATTA-ATA-TATATTATAATAATATAAG
61363 TTAATATTAATTAAATTAATATA-ATTATAAT-ATATAA-
1 TTAATATTAATTAAATTAATATATATTATAATAATATAAG
*
61400 TT-AT-TTATATTATA-TAATATATATTAT
1 TTAATATTA-ATTAAATTAATATATATTAT
61427 TTTAATATTA
Statistics
Matches: 59, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
35 10 0.17
36 12 0.20
37 2 0.03
38 6 0.10
39 7 0.12
40 2 0.03
41 2 0.03
42 5 0.08
43 13 0.22
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.49
Consensus pattern (40 bp):
TTAATATTAATTAAATTAATATATATTATAATAATATAAG
Found at i:61587 original size:99 final size:99
Alignment explanation
Indices: 61460--61657 Score: 301
Period size: 99 Copynumber: 2.0 Consensus size: 99
61450 TATAATAAAT
*
61460 TATATAAGACGGTAGCGCCAAATAACCAAACCAGAATTGTCATTTCCCTCCTATTTTATTTTTCT
1 TATATAAGACGGTAGCGCCAAATAACCAAACCAGAATTATCATTTCCC-CCTATTTTATTTTTCT
* *
61525 TTTGATCTTAATTGTTTCCCTCTCTCC-AACAACC
65 TCTGATATTAATTGTTTCCCTCTCTCCAAACAACC
* * *
61559 TATATAAGGCGGT-GACGCCAGATAACCAAACCAGAATTATCATTTCCCCCTATTTTCTTTTTCT
1 TATATAAGACGGTAG-CGCCAAATAACCAAACCAGAATTATCATTTCCCCCTATTTTATTTTTCT
*
61623 TCTGCTATTAATTGTTTCCCTCTCTCCAAACAACC
65 TCTGATATTAATTGTTTCCCTCTCTCCAAACAACC
61658 CATCGCTCCA
Statistics
Matches: 90, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
98 40 0.44
99 50 0.56
ACGTcount: A:0.27, C:0.27, G:0.10, T:0.36
Consensus pattern (99 bp):
TATATAAGACGGTAGCGCCAAATAACCAAACCAGAATTATCATTTCCCCCTATTTTATTTTTCTT
CTGATATTAATTGTTTCCCTCTCTCCAAACAACC
Found at i:63061 original size:19 final size:19
Alignment explanation
Indices: 63034--63070 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
63024 CATAAGTTAA
63034 AAAAACTTATAATTTTATT
1 AAAAACTTATAATTTTATT
*
63053 AAAATCTTATAATTTTAT
1 AAAAACTTATAATTTTAT
63071 CTATGGTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (19 bp):
AAAAACTTATAATTTTATT
Found at i:63165 original size:15 final size:16
Alignment explanation
Indices: 63135--63168 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
63125 TTATTTACAT
63135 GTCAGGTTAAAAACAG
1 GTCAGGTTAAAAACAG
*
63151 GTCAGGTT-GAAACAG
1 GTCAGGTTAAAAACAG
63166 GTC
1 GTC
63169 GGGTAATACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.35, C:0.15, G:0.29, T:0.21
Consensus pattern (16 bp):
GTCAGGTTAAAAACAG
Found at i:63267 original size:31 final size:32
Alignment explanation
Indices: 63192--63272 Score: 94
Period size: 31 Copynumber: 2.5 Consensus size: 32
63182 ATTTACCAGG
63192 TCAATCTCGGGTTCAGGTTCATATTAGTCAGAT
1 TCAAT-TCGGGTTCAGGTTCATATTAGTCAGAT
* * * *
63225 GCAGTTCGGGTTCAGGTATCATATT-TTC-GGT
1 TCAATTCGGGTTCAGGT-TCATATTAGTCAGAT
63256 TCAATTCGGGTTCAGGT
1 TCAATTCGGGTTCAGGT
63273 CGGGTTCGGA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
31 17 0.41
32 14 0.34
33 10 0.24
ACGTcount: A:0.20, C:0.17, G:0.26, T:0.37
Consensus pattern (32 bp):
TCAATTCGGGTTCAGGTTCATATTAGTCAGAT
Done.