Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000465.1 Hibiscus syriacus cultivar Beakdansim tig00000862_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: 52865
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:24160 original size:16 final size:16
Alignment explanation
Indices: 24139--24179 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
24129 TCAGATGAGA
24139 AGGAATTTGGCAGATT
1 AGGAATTTGGCAGATT
*
24155 AGGAATTTGGCAGTTT
1 AGGAATTTGGCAGATT
*
24171 GGGAATTTG
1 AGGAATTTG
24180 AACAATGGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.27, C:0.05, G:0.34, T:0.34
Consensus pattern (16 bp):
AGGAATTTGGCAGATT
Found at i:28017 original size:21 final size:22
Alignment explanation
Indices: 27993--28034 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
27983 ACAGATTGCC
27993 GTAAAAAGCTTTCT-ATATATT
1 GTAAAAAGCTTTCTCATATATT
* *
28014 GTAAAGAGCTTTTTCATATAT
1 GTAAAAAGCTTTCTCATATAT
28035 ACTATACAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.43
Consensus pattern (22 bp):
GTAAAAAGCTTTCTCATATATT
Found at i:32513 original size:22 final size:21
Alignment explanation
Indices: 32461--32513 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
32451 ATAATTCAAC
*
32461 ATCCAAATACAAAATTTAAAA
1 ATCCAAATACAAAATCTAAAA
* *
32482 ATTCAAAATACAAAATCTAATA
1 A-TCCAAATACAAAATCTAAAA
32504 ATCCATAATA
1 ATCCA-AATA
32514 TAAATAAAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 4 0.15
22 22 0.85
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.26
Consensus pattern (21 bp):
ATCCAAATACAAAATCTAAAA
Found at i:33684 original size:20 final size:20
Alignment explanation
Indices: 33659--33696 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
33649 AACAAGGGGA
33659 GAAGAAAGAAGAGAAAAGGT
1 GAAGAAAGAAGAGAAAAGGT
33679 GAAGAAAGAAGAGAAAAG
1 GAAGAAAGAAGAGAAAAG
33697 AAAAAGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.34, T:0.03
Consensus pattern (20 bp):
GAAGAAAGAAGAGAAAAGGT
Found at i:33703 original size:20 final size:20
Alignment explanation
Indices: 33660--33719 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
33650 ACAAGGGGAG
***
33660 AAGAAAGAAGAGAAAAGGTG
1 AAGAAAGAAGAGAAAAGAAA
33680 AAGAAAGAAGAGAAAAGAAA
1 AAGAAAGAAGAGAAAAGAAA
*
33700 AAGAAA-AAGAAGAGAAGAAA
1 AAGAAAGAAG-AGAAAAGAAA
33720 GTTAAAGTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 3 0.09
20 32 0.91
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02
Consensus pattern (20 bp):
AAGAAAGAAGAGAAAAGAAA
Found at i:34685 original size:19 final size:19
Alignment explanation
Indices: 34663--34699 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
34653 GCATTGTATA
34663 TTTATATAATATATTTATG
1 TTTATATAATATATTTATG
* *
34682 TTTATATCATGTATTTAT
1 TTTATATAATATATTTAT
34700 TTTTTTACAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.59
Consensus pattern (19 bp):
TTTATATAATATATTTATG
Found at i:35107 original size:23 final size:24
Alignment explanation
Indices: 35068--35112 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
35058 AGAAAGGGAT
*
35068 GAAAAAATCACACGAAA-ATTTCA
1 GAAAAAATCACAAGAAATATTTCA
35091 GAAAAAAT-AGCAAGAAATATTT
1 GAAAAAATCA-CAAGAAATATTT
35113 GTAATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 1 0.05
23 14 0.74
24 4 0.21
ACGTcount: A:0.58, C:0.11, G:0.11, T:0.20
Consensus pattern (24 bp):
GAAAAAATCACAAGAAATATTTCA
Found at i:35983 original size:17 final size:18
Alignment explanation
Indices: 35969--36002 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35959 ACTATTATAT
35969 TATTT-TTACTTTTATTA
1 TATTTATTACTTTTATTA
*
35986 TATTTATTATTTTTATT
1 TATTTATTACTTTTATT
36003 TGTTTGTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (18 bp):
TATTTATTACTTTTATTA
Found at i:36002 original size:30 final size:29
Alignment explanation
Indices: 35968--36109 Score: 87
Period size: 30 Copynumber: 4.6 Consensus size: 29
35958 TACTATTATA
35968 TTATTTTTACTTTTATTATATTTATTATTT
1 TTATTTTTA-TTTTATTATATTTATTATTT
35998 TTATTTGTT-TGTTTATTAT-TATTATTATTT
1 TTATTT-TTAT-TTTATTATAT-TTATTATTT
* *
36028 CTT-TTTTTATTTAAATATCATTATATATATTT
1 -TTATTTTTATTTTATTAT-ATT-TAT-TATTT
* * *
36060 TTAGTTTTTTTATTCTATT-TTTTTACTATTT
1 TTA---TTTTTATTTTATTATATTTATTATTT
36091 TT-TATTTTATTTTACTTAT
1 TTAT-TTTTATTTTA-TTAT
36110 TTAATACTAT
Statistics
Matches: 88, Mismatches: 8, Indels: 32
0.69 0.06 0.25
Matches are distributed among these distances:
27 1 0.01
28 9 0.10
29 12 0.14
30 29 0.33
31 17 0.19
32 7 0.08
33 2 0.02
34 1 0.01
35 10 0.11
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.71
Consensus pattern (29 bp):
TTATTTTTATTTTATTATATTTATTATTT
Found at i:36016 original size:24 final size:24
Alignment explanation
Indices: 35989--36038 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
35979 TTTATTATAT
* *
35989 TTATTATTTTTATTTGTTTGTTTA
1 TTATTATTATTATTTCTTTGTTTA
*
36013 TTATTATTATTATTTCTTTTTTTA
1 TTATTATTATTATTTCTTTGTTTA
36037 TT
1 TT
36039 TAAATATCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.76
Consensus pattern (24 bp):
TTATTATTATTATTTCTTTGTTTA
Found at i:36082 original size:12 final size:12
Alignment explanation
Indices: 36065--36103 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
36055 TATTTTTAGT
36065 TTTTTTATTCTA
1 TTTTTTATTCTA
*
36077 TTTTTT-TACTA
1 TTTTTTATTCTA
*
36088 TTTTTTATTTTA
1 TTTTTTATTCTA
36100 TTTT
1 TTTT
36104 ACTTATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTTTATTCTA
Found at i:36364 original size:7 final size:7
Alignment explanation
Indices: 36347--36393 Score: 71
Period size: 7 Copynumber: 6.9 Consensus size: 7
36337 ACTATTTATT
36347 TTTTTTG
1 TTTTTTG
36354 -TTTTTG
1 TTTTTTG
36360 TTTTTTG
1 TTTTTTG
36367 TTTTTTG
1 TTTTTTG
36374 TATTTTTG
1 T-TTTTTG
36382 -TTTTTG
1 TTTTTTG
36388 TTTTTT
1 TTTTTT
36394 AATTTTATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
6 12 0.32
7 19 0.51
8 6 0.16
ACGTcount: A:0.02, C:0.00, G:0.13, T:0.85
Consensus pattern (7 bp):
TTTTTTG
Found at i:36399 original size:14 final size:13
Alignment explanation
Indices: 36320--36399 Score: 54
Period size: 13 Copynumber: 5.8 Consensus size: 13
36310 TAGTTATATA
*
36320 TTTTTATTTTTAT
1 TTTTTATTTTTGT
*
36333 TATTACTATTTATT-T
1 T-TT-TTATTT-TTGT
*
36348 TTTTTGTTTTTGT
1 TTTTTATTTTTGT
*
36361 TTTTTGTTTTTTGT
1 TTTTT-ATTTTTGT
*
36375 ATTTTTGTTTTTGT
1 -TTTTTATTTTTGT
*
36389 TTTTTAATTTT
1 TTTTTATTTTT
36400 ATTTAATTTA
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
12 2 0.04
13 20 0.37
14 18 0.33
15 12 0.22
16 2 0.04
ACGTcount: A:0.11, C:0.01, G:0.07, T:0.80
Consensus pattern (13 bp):
TTTTTATTTTTGT
Found at i:40272 original size:95 final size:95
Alignment explanation
Indices: 40102--40300 Score: 303
Period size: 95 Copynumber: 2.1 Consensus size: 95
40092 CGTATACCCA
* * *
40102 GATTAT-A-ATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGCTAAACGCCCCGGCTTTA
1 GATTATAATATACAATAAAGCTTGAGCTGTCACTCTAAAACAATTGGCTAAACGCCCCGGCTTTA
40165 TGGATAAGATTCAGCTAGCCTGATAAAGGT
66 TGGATAAGATTCAGCTAGCCTGATAAAGGT
* *
40195 GATTATAATATACAATAAAGCTTGAGCTGTCACTTTAAAACAATTGGTTAAACGCCCCGGCTTTA
1 GATTATAATATACAATAAAGCTTGAGCTGTCACTCTAAAACAATTGGCTAAACGCCCCGGCTTTA
* * * *
40260 TGGATAAGATTCATCTATCTTGATAGAGGT
66 TGGATAAGATTCAGCTAGCCTGATAAAGGT
40290 GATTATAATAT
1 GATTATAATAT
40301 TGAACTGTCC
Statistics
Matches: 95, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
93 6 0.06
94 1 0.01
95 88 0.93
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.31
Consensus pattern (95 bp):
GATTATAATATACAATAAAGCTTGAGCTGTCACTCTAAAACAATTGGCTAAACGCCCCGGCTTTA
TGGATAAGATTCAGCTAGCCTGATAAAGGT
Found at i:41705 original size:85 final size:85
Alignment explanation
Indices: 41561--42658 Score: 1426
Period size: 85 Copynumber: 13.0 Consensus size: 85
41551 TGAACTATTG
**
41561 ACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAAGAAAGACCTTCGAGTTCGATTACACTCAG
1 ACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAG
*
41626 CTCAAAGGCATATCAAGTTT
66 CTCAAAGGCATATCAAATTT
* * * * * *
41646 GCAGCATAGCTCAAGGCAAAAAGGGCTATCTGTTAACCAAGACCTTCGAGTTAGATTACACTCAG
1 ACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAG
41711 CTCAAAGGCATATCAAATTT
66 CTCAAAGGCATATCAAATTT
* * *
41731 ACAGCATAACTCATGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCAATTACACTCAG
1 ACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAG
*
41796 CTCAAAGGCACATCAAATTT
66 CTCAAAGGCATATCAAATTT
* * *
41816 ACAGCATAGCTCAAGGCGATAAGGGCTATCTGTCAACCAAGAACTTCGAGTTCGATTACACTCAG
1 ACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAG
*
41881 CTCAAAAGC--AT---ATTT
66 CTCAAAGGCATATCAAATTT
* * *
41896 ACAGCATAACTCAAGGCGAGAAGGTTTATCTGTCAACCAAGACCTTCGAGTTCAATTACACTCAG
1 ACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAG
41961 CTCAAAGGCATATCAAATTT
66 CTCAAAGGCATATCAAATTT
* * *
41981 ACAGCATACCTCAAGGCGAGAAGGGATATCTATCAACCAAGACCTTCGAGTTCGATTACACTCAG
1 ACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAG
* *
42046 TTTAAAGGCATATCAAATTT
66 CTCAAAGGCATATCAAATTT
* * **
42066 ACAGTATAGCTCAAGGCGAGAAGGGTTATATGTCAACCAAGACCTTCGAGTTCGATTACACAAAG
1 ACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAG
*
42131 CTCAAAGGCACATCAAATTT
66 CTCAAAGGCATATCAAATTT
* * * * * *
42151 ATAGTATAGCACAAGGCGAAAAGGGTTATTTGTCAACCAAGACCTTTGAGTTCGATTACACTCAG
1 ACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAG
42216 CTCAAAGGC--AT---ATTT
66 CTCAAAGGCATATCAAATTT
* * * *
42231 ACAACATAACTCAAAGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTTGATTACACTCAG
1 ACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAG
* *
42296 TTCAAAGACATATCAAATTT
66 CTCAAAGGCATATCAAATTT
* * * *
42316 ACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAGACCTTCAAGTTCGATTACATTCAG
1 ACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAG
*
42381 CTCAAAGGCATATCCAATTT
66 CTCAAAGGCATATCAAATTT
* * * *** * *
42401 ACAACATAACTCAAGGCGAGAAGGGTTATTTGTCAGTAAAGACCTTTGAGTTCGATTACATTCAG
1 ACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAG
42466 CTCAAAGGCATATCAAATTT
66 CTCAAAGGCATATCAAATTT
* ** * * * * *
42486 ACAGCATAACTCAAGATGAAAAGGGTTATCTGTCAACAAAGACCTTCGAGTTTGATTACATTTAG
1 ACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAG
* *
42551 CTCAAAGGCGTATAAAATTT
66 CTCAAAGGCATATCAAATTT
* * * * * * ** * * *
42571 ATAGCATAGGTCAAGGCGAGAAGGGCTATATGTCAGCAAAGACCTTTTAGTTTGATTACATTTAG
1 ACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAG
42636 CTC-AAGGACATATCAAATTT
66 CTCAAAGG-CATATCAAATTT
42656 ACA
1 ACA
42659 ATATAACTTA
Statistics
Matches: 889, Mismatches: 113, Indels: 22
0.87 0.11 0.02
Matches are distributed among these distances:
80 137 0.15
82 4 0.00
83 4 0.00
84 4 0.00
85 740 0.83
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (85 bp):
ACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAG
CTCAAAGGCATATCAAATTT
Found at i:42187 original size:335 final size:335
Alignment explanation
Indices: 41556--42712 Score: 1526
Period size: 335 Copynumber: 3.4 Consensus size: 335
41546 TTAAATGAAC
* * *
41556 TATTGACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAAGAAAGACCTTCGAGTTCGATTACA
1 TATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACA
* * * * * * *
41621 CTCAGCTCAAAGGCATATCAAGTTTGCAGCATAGCTCAAGGCAAAAAGGGCTATCTGTTAACCAA
66 CTCAGCTCAAAGGCATATCAAATTTACAACATAGCTCAAGGCGAGAAGGGCTATCTATCAACCAA
* *
41686 GACCTTCGAGTTAGATTACACTCAGCTCAAAGGCATATCAAATTTACAGCATAACTCATGGCGAG
131 GACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCAAATTTACAGCATAACTCAAGGCGAG
* *
41751 AAGGGTTATCTGTCAACCAAGACCTTCGAGTTCAATTACACTCAGCTCAAAGGCACATCAAATTT
196 AAGGGTTATATGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTT
* * *
41816 ACAGCATAGCTCAAGGCGATAAGGGCTATCTGTCAACCAAGAACTTCGAGTTCGATTACACTCAG
261 ACAGCATAGCTCAAGGCGAAAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAG
*
41881 CTCAAAAGCA
326 CTCAAAGGCA
* * *
41891 TATTTACAGCATAACTCAAGGCGAGAAGGTTTATCTGTCAACCAAGACCTTCGAGTTCAATTACA
1 TATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACA
* * *
41956 CTCAGCTCAAAGGCATATCAAATTTACAGCATACCTCAAGGCGAGAAGGGATATCTATCAACCAA
66 CTCAGCTCAAAGGCATATCAAATTTACAACATAGCTCAAGGCGAGAAGGGCTATCTATCAACCAA
* * * *
42021 GACCTTCGAGTTCGATTACACTCAGTTTAAAGGCATATCAAATTTACAGTATAGCTCAAGGCGAG
131 GACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCAAATTTACAGCATAACTCAAGGCGAG
**
42086 AAGGGTTATATGTCAACCAAGACCTTCGAGTTCGATTACACAAAGCTCAAAGGCACATCAAATTT
196 AAGGGTTATATGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTT
* * * * *
42151 ATAGTATAGCACAAGGCGAAAAGGGTTATTTGTCAACCAAGACCTTTGAGTTCGATTACACTCAG
261 ACAGCATAGCTCAAGGCGAAAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAG
42216 CTCAAAGGCA
326 CTCAAAGGCA
* * * *
42226 TATTTACAACATAACTCAAAGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTTGATTACA
1 TATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACA
* * *
42291 CTCAGTTCAAAGACATATCAAATTTACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAA
66 CTCAGCTCAAAGGCATATCAAATTTACAACATAGCTCAAGGCGAGAAGGGCTATCTATCAACCAA
* * * *
42356 GACCTTCAAGTTCGATTACATTCAGCTCAAAGGCATATCCAATTTACAACATAACTCAAGGCGAG
131 GACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCAAATTTACAGCATAACTCAAGGCGAG
* *** * * *
42421 AAGGGTTATTTGTCAGTAAAGACCTTTGAGTTCGATTACATTCAGCTCAAAGGCATATCAAATTT
196 AAGGGTTATATGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTT
* ** * * * *
42486 ACAGCATAACTCAAGATGAAAAGGGTTATCTGTCAACAAAGACCTTCGAGTTTGATTACATTTAG
261 ACAGCATAGCTCAAGGCGAAAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAG
42551 CTCAAAGGCGTA
326 CTCAAAGGC--A
* ** * * * ** *
42563 TAAAATTTATAGCATAGGTCAAGGCGAGAAGGGCTATATGTCAGCAAAGACCTTTTAGTTTGATT
1 T---ATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATT
* * * * * * **
42628 ACATTTAGCTC-AAGGACATATCAAATTTACAATATAACTTAAGTCGAGAAAAGCTATCTATC-A
63 ACACTCAGCTCAAAGG-CATATCAAATTTACAACATAGCTCAAGGCGAGAAGGGCTATCTATCAA
* *
42691 CCAATAACTATCGAGTTCGATT
127 CCAAGACCT-TCGAGTTCGATT
42713 CCATTCACCT
Statistics
Matches: 717, Mismatches: 98, Indels: 9
0.87 0.12 0.01
Matches are distributed among these distances:
335 596 0.83
337 2 0.00
339 11 0.02
340 108 0.15
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (335 bp):
TATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACA
CTCAGCTCAAAGGCATATCAAATTTACAACATAGCTCAAGGCGAGAAGGGCTATCTATCAACCAA
GACCTTCGAGTTCGATTACACTCAGCTCAAAGGCATATCAAATTTACAGCATAACTCAAGGCGAG
AAGGGTTATATGTCAACCAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTT
ACAGCATAGCTCAAGGCGAAAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACACTCAG
CTCAAAGGCA
Found at i:44529 original size:3 final size:3
Alignment explanation
Indices: 44504--44572 Score: 58
Period size: 3 Copynumber: 23.3 Consensus size: 3
44494 TATTAAATAC
*
44504 TAT TA- TAT TAT TTT TACT T-T TAT TA- TATT TAT TATT TAT TAT T-T
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TA-T TAT TA-T TAT TAT TAT
44548 GT-T TAT TAT TAT TAT TAT TAT TAT T
1 -TAT TAT TAT TAT TAT TAT TAT TAT T
44573 TCCTTTTTTA
Statistics
Matches: 56, Mismatches: 2, Indels: 16
0.76 0.03 0.22
Matches are distributed among these distances:
2 8 0.14
3 41 0.73
4 7 0.12
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:44583 original size:27 final size:26
Alignment explanation
Indices: 44504--44584 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 26
44494 TATTAAATAC
44504 TATTA-TATTATT-TTTACTTTTATTA-
1 TATTATTATTATTATTT-CTTTT-TTAT
* *
44529 TATTTATTATTTATTATTTGTTTATTAT
1 TA-TTATTA-TTATTATTTCTTTTTTAT
44557 TATTATTATTATTATTTCCTTTTTTAT
1 TATTATTATTATTATTT-CTTTTTTAT
44584 T
1 T
44585 TATATATCGT
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
25 2 0.04
26 12 0.26
27 19 0.41
28 10 0.22
29 3 0.07
ACGTcount: A:0.25, C:0.04, G:0.01, T:0.70
Consensus pattern (26 bp):
TATTATTATTATTATTTCTTTTTTAT
Found at i:44900 original size:8 final size:8
Alignment explanation
Indices: 44865--44934 Score: 61
Period size: 8 Copynumber: 8.2 Consensus size: 8
44855 TAGTTATATA
44865 TTTTTATT
1 TTTTTATT
44873 TTTATTATT
1 TTT-TTATT
*
44882 TTTTTCTT
1 TTTTTATT
44890 TTTTTAGTTT
1 TTTTTA--TT
44900 TTGTTTATT
1 TT-TTTATT
*
44909 TATTTATT
1 TTTTTATT
*
44917 GTTTTT-TC
1 -TTTTTATT
44925 TTTTTATT
1 TTTTTATT
44933 TT
1 TT
44935 CTTCATTTTA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
7 5 0.10
8 22 0.44
9 15 0.30
10 4 0.08
11 4 0.08
ACGTcount: A:0.11, C:0.03, G:0.04, T:0.81
Consensus pattern (8 bp):
TTTTTATT
Found at i:44929 original size:35 final size:35
Alignment explanation
Indices: 44867--44934 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 35
44857 GTTATATATT
* *
44867 TTTATTTTTATTATTTTTTTCTTTTTTTAGTTTTTG
1 TTTATTTATATTATTTTTTTCTCTTTTTA-TTTTTG
44903 TTTATTTAT-TTATTGTTTTT-TCTTTTTATTTT
1 TTTATTTATATTATT-TTTTTCTCTTTTTATTTT
44935 CTTCATTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 4 0.14
35 12 0.41
36 13 0.45
ACGTcount: A:0.12, C:0.03, G:0.04, T:0.81
Consensus pattern (35 bp):
TTTATTTATATTATTTTTTTCTCTTTTTATTTTTG
Found at i:45655 original size:13 final size:13
Alignment explanation
Indices: 45637--45671 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
45627 TATAACTCGG
45637 AATTGACTGTT-AA
1 AATTGA-TGTTGAA
45650 AATTGATGTTGAA
1 AATTGATGTTGAA
45663 AATTGATGT
1 AATTGATGT
45672 GGAGAAATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 4 0.19
13 17 0.81
ACGTcount: A:0.37, C:0.03, G:0.20, T:0.40
Consensus pattern (13 bp):
AATTGATGTTGAA
Found at i:47756 original size:20 final size:19
Alignment explanation
Indices: 47731--47816 Score: 76
Period size: 20 Copynumber: 4.6 Consensus size: 19
47721 TATTTGAATT
47731 TTTTATAATAATTAACTTGA
1 TTTTATAATAATTAA-TTGA
*
47751 TTTTATAATAATTTA-TGTA
1 TTTTATAATAATTAATTG-A
*
47770 TATGTAT-AT-A-T--TTGA
1 T-TTTATAATAATTAATTGA
47785 TTTTATAATAATTAACTTGA
1 TTTTATAATAATTAA-TTGA
47805 TTTTATAATAAT
1 TTTTATAATAAT
47817 GTATGCATAG
Statistics
Matches: 54, Mismatches: 3, Indels: 18
0.72 0.04 0.24
Matches are distributed among these distances:
14 4 0.07
15 4 0.07
16 3 0.06
17 2 0.04
18 3 0.06
19 4 0.07
20 34 0.63
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.53
Consensus pattern (19 bp):
TTTTATAATAATTAATTGA
Found at i:47794 original size:54 final size:54
Alignment explanation
Indices: 47731--47850 Score: 174
Period size: 54 Copynumber: 2.2 Consensus size: 54
47721 TATTTGAATT
* * *
47731 TTTTATAATAATTAACTTGATTTTATAATAATTTATGTATATGT-A-TATATTTGA
1 TTTTATAATAATTAACTTGATTTTATAATAATGTATGCATA-GTAATTAAATTT-A
47785 TTTTATAATAATTAACTTGATTTTATAATAATGTATGCATAGTAATTAAATTTA
1 TTTTATAATAATTAACTTGATTTTATAATAATGTATGCATAGTAATTAAATTTA
47839 -TTTATAATAATT
1 TTTTATAATAATT
47851 TATGTATTTT
Statistics
Matches: 61, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
53 14 0.23
54 41 0.67
55 6 0.10
ACGTcount: A:0.39, C:0.03, G:0.07, T:0.52
Consensus pattern (54 bp):
TTTTATAATAATTAACTTGATTTTATAATAATGTATGCATAGTAATTAAATTTA
Found at i:48943 original size:8 final size:8
Alignment explanation
Indices: 48930--48955 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
48920 ATTAGACAAG
48930 AAATTATA
1 AAATTATA
48938 AAATTATA
1 AAATTATA
48946 AAATTATA
1 AAATTATA
48954 AA
1 AA
48956 TAAATAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
AAATTATA
Found at i:51393 original size:32 final size:32
Alignment explanation
Indices: 51352--51507 Score: 156
Period size: 32 Copynumber: 4.9 Consensus size: 32
51342 AGTCGAGGGT
*
51352 TTACCTATGTTCTACGGAACATATGGACAGAA
1 TTACCTATGTTCTTCGGAACATATGGACAGAA
* * *
51384 TTACCTATGTTTTTCGGGACATATGAACAGAA
1 TTACCTATGTTCTTCGGAACATATGGACAGAA
* *
51416 TTACCTATG-TCTTCTGAGACATATGGACAGTA
1 TTACCTATGTTCTTCGGA-ACATATGGACAGAA
** * *
51448 -TACCTATGTTCTAAGGAACATATGAACA-AT
1 TTACCTATGTTCTTCGGAACATATGGACAGAA
* * * *
51478 TTACCTAGGTTTTTCGGGACCTATGGACAG
1 TTACCTATGTTCTTCGGAACATATGGACAG
51508 TTGTCGAGGT
Statistics
Matches: 98, Mismatches: 22, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
31 44 0.45
32 54 0.55
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (32 bp):
TTACCTATGTTCTTCGGAACATATGGACAGAA
Found at i:52212 original size:21 final size:21
Alignment explanation
Indices: 52188--52232 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
52178 ATGTAGCAAT
*
52188 ACTGTAGCAATGCATCGATGC
1 ACTGTAGCAATGCATCGATAC
* *
52209 ACTGTAGCAGTGCATTGATAC
1 ACTGTAGCAATGCATCGATAC
52230 ACT
1 ACT
52233 ATTGATATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (21 bp):
ACTGTAGCAATGCATCGATAC
Done.