Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006403.1 Hibiscus syriacus cultivar Beakdansim tig00015439_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: 87546
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:3730 original size:187 final size:190
Alignment explanation
Indices: 3418--3798 Score: 632
Period size: 187 Copynumber: 2.0 Consensus size: 190
3408 GCATAATTTG
*
3418 GTAAAAACTGGGACTCCAATAAGACATCTTTTGAACATATATCTGCTTAGCTGTTCTTTTTAATA
1 GTAAAAACTGGGACTCCAATAAGACATCTTTTGAACATATATCTGCTTAGCTGTTATTTTTAATA
* *
3483 AGATTCGCAGTGAAATAAAACAATGGTTAATACAGGGTTCGATAATGAAGCCCCTTCTCAAAATA
66 AGATTCGAAGTGAAATAAAACAATGGGTAATACAGGGTTCGATAATGAAGCCCCTTCTCAAAATA
*
3548 C-A-A-TATCCAGGTTATCAGT-AAA-ATAAGAATATTGCAATATCTCATTTT-AACATA
131 CAATATTATACAGGTTATCAGTAAAACATAAGAATATTGCAATATCTCATTTTAAACATA
3602 GTAAAAACTGGGACTCCAATAAGACATCTTTTGAACATATATAATCTGCTTAGCTGTTATTTTTA
1 GTAAAAACTGGGACTCCAATAAGACATCTTTTGAAC--ATAT-ATCTGCTTAGCTGTTATTTTTA
3667 ATAAGATTCGAAGTGAAAATAAAACAATGGGTAATACAGGGTTCGATAATGAAG-CCCTTCTCAA
63 ATAAGATTCGAAGTG-AAATAAAACAATGGGTAATACAGGGTTCGATAATGAAGCCCCTTCTCAA
3731 AATACAATATTATACAGGTTATCAGTAAAACCATAAGAATATTGCAATATCTCATTTTAAACATA
127 AATACAATATTATACAGGTTATCAGTAAAA-CATAAGAATATTGCAATATCTCATTTTAAACATA
3796 GTA
1 GTA
3799 TATCTTATTT
Statistics
Matches: 182, Mismatches: 4, Indels: 12
0.92 0.02 0.06
Matches are distributed among these distances:
184 36 0.20
186 4 0.02
187 50 0.27
188 38 0.21
189 1 0.01
190 15 0.08
191 3 0.02
193 26 0.14
194 9 0.05
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.31
Consensus pattern (190 bp):
GTAAAAACTGGGACTCCAATAAGACATCTTTTGAACATATATCTGCTTAGCTGTTATTTTTAATA
AGATTCGAAGTGAAATAAAACAATGGGTAATACAGGGTTCGATAATGAAGCCCCTTCTCAAAATA
CAATATTATACAGGTTATCAGTAAAACATAAGAATATTGCAATATCTCATTTTAAACATA
Found at i:6696 original size:2 final size:2
Alignment explanation
Indices: 6691--6721 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6681 AAAAATAGAT
6691 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
6722 TAAAAAAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:8208 original size:28 final size:28
Alignment explanation
Indices: 8176--8230 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
8166 CTGTTTTTAC
* * *
8176 TTTCAAGCACTATCTTGATGACATAATA
1 TTTCAAGCACTAGCTCGACGACATAATA
*
8204 TTTCATGCACTAGCTCGACGACATAAT
1 TTTCAAGCACTAGCTCGACGACATAAT
8231 GTAAATAAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.33
Consensus pattern (28 bp):
TTTCAAGCACTAGCTCGACGACATAATA
Found at i:13619 original size:14 final size:14
Alignment explanation
Indices: 13581--13611 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
13571 ATTATTAATC
*
13581 TCAATCGTCTATTT
1 TCAATAGTCTATTT
13595 TCAATAGTCTATTT
1 TCAATAGTCTATTT
13609 TCA
1 TCA
13612 CTTATCTAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.19, G:0.06, T:0.48
Consensus pattern (14 bp):
TCAATAGTCTATTT
Found at i:14029 original size:36 final size:36
Alignment explanation
Indices: 13987--14058 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
13977 GCAGGTTTAA
13987 AAATATAAATATATTTTTTAATATATTTAGAAATAT
1 AAATATAAATATATTTTTTAATATATTTAGAAATAT
* *
14023 AAATATAAATATATTTTTTAGTATGTTTAGAAATAT
1 AAATATAAATATATTTTTTAATATATTTAGAAATAT
14059 TTGTGGCCCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (36 bp):
AAATATAAATATATTTTTTAATATATTTAGAAATAT
Found at i:20106 original size:17 final size:18
Alignment explanation
Indices: 20074--20119 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
20064 TTTTTTTATT
*
20074 AAAATTAAATTAATCAAA
1 AAAAATAAATTAATCAAA
*
20092 AAAAATAAATT-ATCAAT
1 AAAAATAAATTAATCAAA
*
20109 TAAAATAAATT
1 AAAAATAAATT
20120 CTTTTTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 15 0.60
18 10 0.40
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAAATAAATTAATCAAA
Found at i:30318 original size:19 final size:20
Alignment explanation
Indices: 30294--30332 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
30284 AGGGTTAATA
*
30294 TATATTGTGT-TTAATGTAT
1 TATATTATGTATTAATGTAT
30313 TATATTATGTAGTTAATGTA
1 TATATTATGTA-TTAATGTA
30333 GGATATTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
21 8 0.47
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (20 bp):
TATATTATGTATTAATGTAT
Found at i:31360 original size:173 final size:173
Alignment explanation
Indices: 31071--31418 Score: 660
Period size: 173 Copynumber: 2.0 Consensus size: 173
31061 TATGACAGGC
*
31071 AATCCCAGTTTACTTTCTGATTTTCATCACCATAAGTCTATCACCCTGTAACTTTAGCCAATGGG
1 AATCCCAGTTTACTTTCTGATTTTCATCACCACAAGTCTATCACCCTGTAACTTTAGCCAATGGG
31136 TCAACAGCCAAAGTTATTGGGTCAGGAACCGCTAATCTTACTCCATCCCTTTATTTATCATCGAT
66 TCAACAGCCAAAGTTATTGGGTCAGGAACCGCTAATCTTACTCCATCCCTTTATTTATCATCGAT
31201 TCTTAGTCTACCGCAACTATGGGAAAGTCAACAATGGGACTGT
131 TCTTAGTCTACCGCAACTATGGGAAAGTCAACAATGGGACTGT
31244 AATCCCAGTTTACTTTCTGATTTTCATCACCACAAGTCTATCACCCTGTAACTTTAGCCAATGGG
1 AATCCCAGTTTACTTTCTGATTTTCATCACCACAAGTCTATCACCCTGTAACTTTAGCCAATGGG
* * *
31309 TCAACAGCCGAAGTTATTGGGTCTGGAACCGCTAATCTTACTCCATCCCTTTATTTATCATTGAT
66 TCAACAGCCAAAGTTATTGGGTCAGGAACCGCTAATCTTACTCCATCCCTTTATTTATCATCGAT
31374 TCTTAGTCTACCGCAACTATGGGAAAGTCAACAATGGGACTGT
131 TCTTAGTCTACCGCAACTATGGGAAAGTCAACAATGGGACTGT
31417 AA
1 AA
31419 AACTAAATTA
Statistics
Matches: 171, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
173 171 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.32
Consensus pattern (173 bp):
AATCCCAGTTTACTTTCTGATTTTCATCACCACAAGTCTATCACCCTGTAACTTTAGCCAATGGG
TCAACAGCCAAAGTTATTGGGTCAGGAACCGCTAATCTTACTCCATCCCTTTATTTATCATCGAT
TCTTAGTCTACCGCAACTATGGGAAAGTCAACAATGGGACTGT
Found at i:35271 original size:17 final size:17
Alignment explanation
Indices: 35246--35283 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
35236 CTGATCCCAT
35246 TTCCGATACATTAGAAG
1 TTCCGATACATTAGAAG
*
35263 TTCCTATACATTAGAAG
1 TTCCGATACATTAGAAG
35280 TTCC
1 TTCC
35284 AAAACTTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (17 bp):
TTCCGATACATTAGAAG
Found at i:38504 original size:24 final size:24
Alignment explanation
Indices: 38472--38518 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
38462 GAAAGAGAAC
38472 AATAAGAGATCTAAGATATTGCAA
1 AATAAGAGATCTAAGATATTGCAA
38496 AATAAGAGATCTAAGATATTGCA
1 AATAAGAGATCTAAGATATTGCA
38519 GTTATCAGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.49, C:0.09, G:0.17, T:0.26
Consensus pattern (24 bp):
AATAAGAGATCTAAGATATTGCAA
Found at i:39200 original size:35 final size:34
Alignment explanation
Indices: 39141--39252 Score: 136
Period size: 35 Copynumber: 3.2 Consensus size: 34
39131 AAAACATTCC
* *
39141 TCAATTTCATTATAAATCCCAAATTTCAAAGTAAT
1 TCAATTTCATTCTAAA-CCCAAATTTCAAAATAAT
*
39176 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCC-AAATTTCAAAATAAT
* *
39211 TCAATTACATTCTAAACCCCAAA-TTCTAAAATACT
1 TCAATTTCATTCTAAA-CCCAAATTTC-AAAATAAT
39246 TCAATTT
1 TCAATTT
39253 AAGGAGAAAT
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
34 5 0.07
35 59 0.88
36 3 0.04
ACGTcount: A:0.42, C:0.21, G:0.01, T:0.36
Consensus pattern (34 bp):
TCAATTTCATTCTAAACCCAAATTTCAAAATAAT
Found at i:40320 original size:35 final size:34
Alignment explanation
Indices: 40269--40381 Score: 154
Period size: 35 Copynumber: 3.2 Consensus size: 34
40259 AAAAAAGACA
*
40269 GAAATTGAAGTATTTTAGAATTTGGGTTTTAGAAT
1 GAAATTGAATTATTTTAGAATTTGGG-TTTAGAAT
* *
40304 GTAATTGAATTGTTTTAGAATTTAGGGTTTAGAAT
1 GAAATTGAATTATTTTAGAATTT-GGGTTTAGAAT
* *
40339 GAAATTGAATTACTTTGGAATTTGTGGTTTAGAAT
1 GAAATTGAATTATTTTAGAATTTG-GGTTTAGAAT
40374 GAAATTGA
1 GAAATTGA
40382 GAATTGTTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
34 1 0.01
35 65 0.94
36 3 0.04
ACGTcount: A:0.34, C:0.01, G:0.23, T:0.42
Consensus pattern (34 bp):
GAAATTGAATTATTTTAGAATTTGGGTTTAGAAT
Found at i:40727 original size:16 final size:18
Alignment explanation
Indices: 40706--40749 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
40696 ACATTATCAG
40706 TAATCTTATT-CC-CTGA
1 TAATCTTATTCCCACTGA
40722 TAATCTTACATTCCCACTGA
1 TAATCTT--ATTCCCACTGA
40742 TAATCTTA
1 TAATCTTA
40750 CATTCCATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
16 7 0.29
18 4 0.17
19 2 0.08
20 11 0.46
ACGTcount: A:0.30, C:0.25, G:0.05, T:0.41
Consensus pattern (18 bp):
TAATCTTATTCCCACTGA
Found at i:40736 original size:18 final size:19
Alignment explanation
Indices: 40713--40756 Score: 72
Period size: 20 Copynumber: 2.3 Consensus size: 19
40703 CAGTAATCTT
40713 ATTCC-CTGATAATCTTAC
1 ATTCCACTGATAATCTTAC
40731 ATTCCCACTGATAATCTTAC
1 ATT-CCACTGATAATCTTAC
40751 ATTCCA
1 ATTCCA
40757 TAAACCAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.12
19 5 0.21
20 16 0.67
ACGTcount: A:0.30, C:0.30, G:0.05, T:0.36
Consensus pattern (19 bp):
ATTCCACTGATAATCTTAC
Found at i:40743 original size:20 final size:20
Alignment explanation
Indices: 40718--40755 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
40708 ATCTTATTCC
40718 CTGATAATCTTACATTCCCA
1 CTGATAATCTTACATTCCCA
40738 CTGATAATCTTACATTCC
1 CTGATAATCTTACATTCC
40756 ATAAACCAAA
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:0.29, C:0.29, G:0.05, T:0.37
Consensus pattern (20 bp):
CTGATAATCTTACATTCCCA
Found at i:41186 original size:21 final size:21
Alignment explanation
Indices: 41160--41234 Score: 105
Period size: 21 Copynumber: 3.6 Consensus size: 21
41150 GATTCCAGAT
* *
41160 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTAGACTA
41181 TCGCAATGCGAACTTAGACTA
1 TCGCAATGCGAACTTAGACTA
* *
41202 TCGCAATGAGAACTTGGACTA
1 TCGCAATGCGAACTTAGACTA
*
41223 TCGCAATACGAA
1 TCGCAATGCGAA
41235 TATGTAAATC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAACTTAGACTA
Found at i:41273 original size:21 final size:21
Alignment explanation
Indices: 41243--41296 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
41233 AATATGTAAA
*
41243 TCGCAATGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
41264 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
*
41285 TCGCGTTGCGAT
1 TCGCATTGCGAT
41297 TTATTACAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (21 bp):
TCGCATTGCGATAGTCGAAGT
Found at i:41384 original size:21 final size:21
Alignment explanation
Indices: 41336--41465 Score: 90
Period size: 21 Copynumber: 6.2 Consensus size: 21
41326 ACTTCAACTA
* * *
41336 TCGCATTGCGAT-TTACATAT
1 TCGCATTGCGATAGTCCAAAT
*
41356 TTGCATTGCGATAGTCCAAAT
1 TCGCATTGCGATAGTCCAAAT
*
41377 TCGCATTGCGATTTATTCCAAAT
1 TCGCATTGCGA--TAGTCCAAAT
* *
41400 TCG--TTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCCAAAT
* * *
41419 TTGCGTTGCGATTTATTCCAAAT
1 TCGCATTGCGA--TAGTCCAAAT
*
41442 TCG--TTGCGATAGTCCAAAA
1 TCGCATTGCGATAGTCCAAAT
41461 TCGCA
1 TCGCA
41466 ACGACTGGTG
Statistics
Matches: 85, Mismatches: 16, Indels: 17
0.72 0.14 0.14
Matches are distributed among these distances:
19 20 0.24
20 11 0.13
21 33 0.39
23 21 0.25
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.35
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAAT
Found at i:41428 original size:42 final size:42
Alignment explanation
Indices: 41361--41465 Score: 165
Period size: 42 Copynumber: 2.5 Consensus size: 42
41351 CATATTTGCA
41361 TTGCGATAGTCCAAATTCGCATTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAATTCGCATTGCGATTTATTCCAAATTCG
* * * *
41403 TTGCGATAGTCGAAGTTTGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAATTCGCATTGCGATTTATTCCAAATTCG
*
41445 TTGCGATAGTCCAAAATCGCA
1 TTGCGATAGTCCAAATTCGCA
41466 ACGACTGGTG
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (42 bp):
TTGCGATAGTCCAAATTCGCATTGCGATTTATTCCAAATTCG
Found at i:42147 original size:19 final size:19
Alignment explanation
Indices: 42123--42186 Score: 65
Period size: 21 Copynumber: 3.2 Consensus size: 19
42113 TCGTTGCGAT
42123 TTTGGACTATCGCAACGAA
1 TTTGGACTATCGCAACGAA
*
42142 TTTGGAATAAATCGCAACGCGAA
1 TTTGGACT--ATCGCAA--CGAA
* *
42165 CTTCGACTATCGCAACGAA
1 TTTGGACTATCGCAACGAA
42184 TTT
1 TTT
42187 AGAATAAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
19 13 0.36
21 14 0.39
23 9 0.25
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.27
Consensus pattern (19 bp):
TTTGGACTATCGCAACGAA
Found at i:42157 original size:21 final size:21
Alignment explanation
Indices: 42131--42200 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
42121 ATTTTGGACT
*
42131 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTAGAATAA
* * *
42152 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAATTTAGAATAA
42173 ATCGCAACGAATTTAGAATAA
1 ATCGCAACGAATTTAGAATAA
*
42194 ATTGCAA
1 ATCGCAA
42201 TGCGAATATG
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
19 9 0.24
21 20 0.53
23 9 0.24
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (21 bp):
ATCGCAACGAATTTAGAATAA
Found at i:42186 original size:42 final size:42
Alignment explanation
Indices: 42127--42206 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
42117 TGCGATTTTG
*
42127 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTAGAATAAATCGCAACGCGAACTTC
* *
42169 GACTATCGCAACGAATTTAGAATAAATTGCAATGCGAA
1 GACTATCGCAACGAATTTAGAATAAATCGCAACGCGAA
42207 TATGTAAATC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.23
Consensus pattern (42 bp):
GACTATCGCAACGAATTTAGAATAAATCGCAACGCGAACTTC
Found at i:42338 original size:21 final size:21
Alignment explanation
Indices: 42273--42339 Score: 107
Period size: 21 Copynumber: 3.2 Consensus size: 21
42263 AAATCACAAC
*
42273 GCGAACTTCGACTATCGCAAT
1 GCGAACTTGGACTATCGCAAT
*
42294 GCAAACTTGGACTATCGCAAT
1 GCGAACTTGGACTATCGCAAT
*
42315 GCGAACTTGGACTATCGCATT
1 GCGAACTTGGACTATCGCAAT
42336 GCGA
1 GCGA
42340 TTTACATATT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.24
Consensus pattern (21 bp):
GCGAACTTGGACTATCGCAAT
Found at i:42352 original size:113 final size:112
Alignment explanation
Indices: 42138--42364 Score: 255
Period size: 113 Copynumber: 2.0 Consensus size: 112
42128 ACTATCGCAA
* * * *
42138 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTAGAATAAATTGCAATG
1 CGAATTTGGAATAAATCACAACGCGAACTTCGACTATCGCAACAAACTTAGAAT-AATCGCAATG
* * *
42203 CGAATATGTAAATCTCAATGCGATAGACGAAGTTCGCGTTGCGATAGT
65 CGAATATGGAAATCGCAATGCGATAGACGAAGTTCGCATTGCGATAGT
* *
42251 CGAATTTGGAATAAATCACAACGCGAACTTCGACTATCGCAATGCAAACTTGGACT-ATCGCAAT
1 CGAATTTGGAATAAATCACAACGCGAACTTCGACTATCGCAA--CAAACTTAGAATAATCGCAAT
* * **
42315 GCGAACT-TGGACTATCGCATTGCGATTTAC-ATA-TTCGCATTGCGATAGT
64 GCGAA-TATGGA-AATCGCAATGCGATAGACGA-AGTTCGCATTGCGATAGT
42364 C
1 C
42365 CAAGTTCGCG
Statistics
Matches: 96, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
113 73 0.76
114 15 0.16
115 8 0.08
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.26
Consensus pattern (112 bp):
CGAATTTGGAATAAATCACAACGCGAACTTCGACTATCGCAACAAACTTAGAATAATCGCAATGC
GAATATGGAAATCGCAATGCGATAGACGAAGTTCGCATTGCGATAGT
Found at i:45296 original size:159 final size:159
Alignment explanation
Indices: 45006--45308 Score: 525
Period size: 159 Copynumber: 1.9 Consensus size: 159
44996 AGAAATATTA
* * *
45006 AATTATAAAGTTGAATGAAGCCTCCTTTATATAGGGGTTGAGTTCTAAAAACCTTAGATAACTAA
1 AATTACAAAGTTGAATGAAACCTCCTTTATATAGGGGCTGAGTTCTAAAAACCTTAGATAACTAA
* *
45071 TAAATAAAATAATAATAAATTAAACATGTCTTAACTCTAATTCCTAATAAAATAATAATAACTAA
66 TAAATAAAATAATAATAAATTAAACATGTCTTAACCCTAATTCATAATAAAATAATAATAACTAA
45136 AGATAATATTTTAACCCAACCAAATCTTG
131 AGATAATATTTTAACCCAACCAAATCTTG
**
45165 AATTACAAAGTTGAATGAAACCTCCTTTATATAGGGGCTGAGTTCTAAAGGCCTTAGATAACTAA
1 AATTACAAAGTTGAATGAAACCTCCTTTATATAGGGGCTGAGTTCTAAAAACCTTAGATAACTAA
* *
45230 TGAATAAAATAATAATAAATTAAACATGTCTTAACCCTAATTCATAATAAAATAATAATAATTAA
66 TAAATAAAATAATAATAAATTAAACATGTCTTAACCCTAATTCATAATAAAATAATAATAACTAA
45295 AGATAATATTTTAA
131 AGATAATATTTTAA
45309 TCAAACCTTA
Statistics
Matches: 135, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
159 135 1.00
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.32
Consensus pattern (159 bp):
AATTACAAAGTTGAATGAAACCTCCTTTATATAGGGGCTGAGTTCTAAAAACCTTAGATAACTAA
TAAATAAAATAATAATAAATTAAACATGTCTTAACCCTAATTCATAATAAAATAATAATAACTAA
AGATAATATTTTAACCCAACCAAATCTTG
Found at i:49950 original size:13 final size:13
Alignment explanation
Indices: 49932--49956 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49922 TTTTATAATT
49932 AAATTTAAATAAA
1 AAATTTAAATAAA
49945 AAATTTAAATAA
1 AAATTTAAATAA
49957 CTCAATTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAATTTAAATAAA
Found at i:55585 original size:2 final size:2
Alignment explanation
Indices: 55578--55605 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
55568 GAATGTTAAT
55578 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
55606 TGGAGCATGC
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:56065 original size:16 final size:16
Alignment explanation
Indices: 55976--56068 Score: 50
Period size: 16 Copynumber: 5.7 Consensus size: 16
55966 TTAATATATT
*
55976 TAAAAATTATATTAAT-
1 TAAAATTTA-ATTAATA
*
55992 TAAAAATTATATATAA-A
1 TAAAATTTA-AT-TAATA
* * *
56009 TAATATTTATTTGATA
1 TAAAATTTAATTAATA
56025 TAATAAATTTAA--AACTA
1 T-A-AAATTTAATTAA-TA
*
56042 TAATATTTAATTAATA
1 TAAAATTTAATTAATA
56058 TAAAATTTAAT
1 TAAAATTTAAT
56069 AAAGTAAAGA
Statistics
Matches: 60, Mismatches: 9, Indels: 16
0.71 0.11 0.19
Matches are distributed among these distances:
15 9 0.15
16 29 0.48
17 16 0.27
18 6 0.10
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (16 bp):
TAAAATTTAATTAATA
Found at i:63945 original size:20 final size:20
Alignment explanation
Indices: 63920--63958 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
63910 TATATAATGA
63920 AAAGAAAATTTT-GTAGAAAG
1 AAAG-AAATTTTGGTAGAAAG
*
63940 AAAGAAGTTTTGGTAGAAA
1 AAAGAAATTTTGGTAGAAA
63959 TATGGACTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.51, C:0.00, G:0.23, T:0.26
Consensus pattern (20 bp):
AAAGAAATTTTGGTAGAAAG
Found at i:67947 original size:7 final size:7
Alignment explanation
Indices: 67935--67964 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
67925 ATGTACTCAC
67935 AAAAATA
1 AAAAATA
67942 AAAAATA
1 AAAAATA
67949 AAAAATA
1 AAAAATA
*
67956 AAAATTA
1 AAAAATA
67963 AA
1 AA
67965 CACTAGCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (7 bp):
AAAAATA
Found at i:72558 original size:16 final size:16
Alignment explanation
Indices: 72539--72572 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
72529 CAATATACGA
72539 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
72555 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
72571 AT
1 AT
72573 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:73316 original size:130 final size:130
Alignment explanation
Indices: 73113--73359 Score: 404
Period size: 130 Copynumber: 1.9 Consensus size: 130
73103 ATTTTCTTCT
* * *
73113 AATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGATC
1 AATTAGGTGGTGACATGTGTCACAAATAACACATATCATGATCATGTGCTAACACATGTCAGATC
** * *
73178 CTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATACCATATATAAAC
66 CTAATTAAATGATTAATTTATTAAATTCTACTTAATTTAGGACCAAATTGATACCATATATAAAC
* * *
73243 AATTAGGTGGTGACATGTGTCACAAATGACACGTGTCATGATCATGTGCTAACACATGTCAGATC
1 AATTAGGTGGTGACATGTGTCACAAATAACACATATCATGATCATGTGCTAACACATGTCAGATC
73308 CTAATTAAATGATTAATTTATTAAATTCTACTTAATTTAGGACCAAATTGAT
66 CTAATTAAATGATTAATTTATTAAATTCTACTTAATTTAGGACCAAATTGAT
73360 TATATAAATA
Statistics
Matches: 107, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
130 107 1.00
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (130 bp):
AATTAGGTGGTGACATGTGTCACAAATAACACATATCATGATCATGTGCTAACACATGTCAGATC
CTAATTAAATGATTAATTTATTAAATTCTACTTAATTTAGGACCAAATTGATACCATATATAAAC
Found at i:73807 original size:35 final size:35
Alignment explanation
Indices: 73757--73832 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
73747 AATTGAATTG
* *
73757 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
73792 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
73827 AATTGA
1 AATTGA
73833 GGACTGTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:75724 original size:30 final size:28
Alignment explanation
Indices: 75668--75724 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
75658 TAAACAGATA
*
75668 ATATATAATATTCACCTCAAATTTAAAT
1 ATATATAATATTCAACTCAAATTTAAAT
75696 ATATATATATATATCAAC-CAAATGTTAAA
1 ATATATA-ATAT-TCAACTCAAAT-TTAAA
75725 AAGCGCAACG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 7 0.28
29 9 0.36
30 9 0.36
ACGTcount: A:0.49, C:0.12, G:0.02, T:0.37
Consensus pattern (28 bp):
ATATATAATATTCAACTCAAATTTAAAT
Found at i:76386 original size:29 final size:29
Alignment explanation
Indices: 76341--76408 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 29
76331 CCCTAAACCT
* *
76341 GAATCTGACCGAGCATCACCTTTTAAAAA
1 GAATCCGACCGAACATCACCTTTTAAAAA
76370 GAATCCGACCGAACATCACCTTTTAAAAA
1 GAATCCGACCGAACATCACCTTTTAAAAA
* *
76399 AAACCCGACC
1 GAATCCGACC
76409 CAACTTGAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.40, C:0.29, G:0.12, T:0.19
Consensus pattern (29 bp):
GAATCCGACCGAACATCACCTTTTAAAAA
Found at i:81249 original size:22 final size:21
Alignment explanation
Indices: 81216--81256 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
81206 ATAAACTTTG
81216 ATTTTTTGCATTGTGCATTTA
1 ATTTTTTGCATTGTGCATTTA
* *
81237 ATTTTTCTTCATTTTGCATT
1 ATTTTT-TGCATTGTGCATT
81257 GAACTGCAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.17, C:0.12, G:0.10, T:0.61
Consensus pattern (21 bp):
ATTTTTTGCATTGTGCATTTA
Found at i:82463 original size:18 final size:19
Alignment explanation
Indices: 82423--82463 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
82413 AGAATATTTA
82423 AACATTCATAATGGTCTGC
1 AACATTCATAATGGTCTGC
82442 -ACATCTCA-AATGGTCT-C
1 AACAT-TCATAATGGTCTGC
82459 AACAT
1 AACAT
82464 ATCTCAACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
17 1 0.05
18 16 0.80
19 3 0.15
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.29
Consensus pattern (19 bp):
AACATTCATAATGGTCTGC
Found at i:84344 original size:15 final size:15
Alignment explanation
Indices: 84320--84404 Score: 55
Period size: 15 Copynumber: 5.7 Consensus size: 15
84310 TTATTGTCCC
84320 TTTCAACATTACCCA
1 TTTCAACATTACCCA
* *
84335 TTTCAGCATTATCCA
1 TTTCAACATTACCCA
* ** *
84350 TTTCTACACCA-ACA
1 TTTCAACATTACCCA
** *
84364 CTTTCAACATTGTCCT
1 -TTTCAACATTACCCA
*
84380 TTTCAACACTACCCA
1 TTTCAACATTACCCA
*
84395 TTTCAGCATT
1 TTTCAACATT
84405 GTCTATTTTT
Statistics
Matches: 49, Mismatches: 19, Indels: 4
0.68 0.26 0.06
Matches are distributed among these distances:
14 2 0.04
15 46 0.94
16 1 0.02
ACGTcount: A:0.28, C:0.32, G:0.04, T:0.36
Consensus pattern (15 bp):
TTTCAACATTACCCA
Found at i:84384 original size:60 final size:60
Alignment explanation
Indices: 84312--84614 Score: 315
Period size: 60 Copynumber: 5.0 Consensus size: 60
84302 TGTCTTTCTT
* *
84312 ATTGTCCCTTTCAACATTACCCATTTCAGCATTATCCATTTCTACACCAACACTTTCAAC
1 ATTGTCCCTTTCAACACTACCCATTTCAGCATTATCCATTTCTACACCAACACTTTCAGC
* * * * * * *
84372 ATTGTCCTTTTCAACACTACCCATTTCAGCATTGTCTATTTTTACA-CTACCCATTTTAGC
1 ATTGTCCCTTTCAACACTACCCATTTCAGCATTATCCATTTCTACACCAACAC-TTTCAGC
* ** * * * * * *
84432 ATTATCAATTTCTACACCA-GCACTTTCAGCACTATCTATTTCTACACCACCACTTTCAGC
1 ATTGTCCCTTTCAACACTACCCA-TTTCAGCATTATCCATTTCTACACCAACACTTTCAGC
* * * * * *
84492 ATTGTCCCTTTCAACACTACCCATTTCAGCATTGTCCCTTTCAACA-CTACCCATTTCAAC
1 ATTGTCCCTTTCAACACTACCCATTTCAGCATTATCCATTTCTACACCAACAC-TTTCAGC
* * *
84552 ATTGTCCCTTTCTACACTACCCATTTCAGCAATATCCATTTCTACACCACCACTTTCAGC
1 ATTGTCCCTTTCAACACTACCCATTTCAGCATTATCCATTTCTACACCAACACTTTCAGC
84612 ATT
1 ATT
84615 ATCCACTTCT
Statistics
Matches: 191, Mismatches: 46, Indels: 12
0.77 0.18 0.05
Matches are distributed among these distances:
59 9 0.05
60 174 0.91
61 8 0.04
ACGTcount: A:0.26, C:0.33, G:0.05, T:0.36
Consensus pattern (60 bp):
ATTGTCCCTTTCAACACTACCCATTTCAGCATTATCCATTTCTACACCAACACTTTCAGC
Found at i:84502 original size:15 final size:15
Alignment explanation
Indices: 84484--84563 Score: 74
Period size: 15 Copynumber: 5.3 Consensus size: 15
84474 TACACCACCA
*
84484 CTTTCAGCATTGTCC
1 CTTTCAACATTGTCC
* *
84499 CTTTCAACACT-ACC
1 CTTTCAACATTGTCC
*
84513 CATTTCAGCATTGTCC
1 C-TTTCAACATTGTCC
* *
84529 CTTTCAACACT-ACC
1 CTTTCAACATTGTCC
84543 CATTTCAACATTGTCC
1 C-TTTCAACATTGTCC
84559 CTTTC
1 CTTTC
84564 TACACTACCC
Statistics
Matches: 50, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
14 6 0.12
15 38 0.76
16 6 0.12
ACGTcount: A:0.21, C:0.36, G:0.06, T:0.36
Consensus pattern (15 bp):
CTTTCAACATTGTCC
Found at i:84578 original size:15 final size:15
Alignment explanation
Indices: 84500--84598 Score: 76
Period size: 15 Copynumber: 6.6 Consensus size: 15
84490 GCATTGTCCC
84500 TTTCAACACTACCCA
1 TTTCAACACTACCCA
* * *
84515 TTTCAGCATTGTCCC-
1 TTTCAACACT-ACCCA
84530 TTTCAACACTACCCA
1 TTTCAACACTACCCA
* *
84545 TTTCAACATTGTCCC-
1 TTTCAACACT-ACCCA
*
84560 TTTCTACACTACCCA
1 TTTCAACACTACCCA
* * *
84575 TTTCAGCAATATCCA
1 TTTCAACACTACCCA
*
84590 TTTCTACAC
1 TTTCAACAC
84599 CACCACTTTC
Statistics
Matches: 62, Mismatches: 18, Indels: 8
0.70 0.20 0.09
Matches are distributed among these distances:
14 6 0.10
15 50 0.81
16 6 0.10
ACGTcount: A:0.26, C:0.35, G:0.04, T:0.34
Consensus pattern (15 bp):
TTTCAACACTACCCA
Found at i:84608 original size:15 final size:15
Alignment explanation
Indices: 84590--84653 Score: 53
Period size: 15 Copynumber: 4.3 Consensus size: 15
84580 GCAATATCCA
84590 TTTCTACACCACCAC
1 TTTCTACACCACCAC
**
84605 TTTC-AGCATTATCCAC
1 TTTCTA-CACCA-CCAC
84621 -TTCTACACCACCAC
1 TTTCTACACCACCAC
*
84635 TTTCATA-ACAACCAC
1 TTTC-TACACCACCAC
84650 TTTC
1 TTTC
84654 ATTTATACCC
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
14 5 0.13
15 27 0.69
16 7 0.18
ACGTcount: A:0.28, C:0.39, G:0.02, T:0.31
Consensus pattern (15 bp):
TTTCTACACCACCAC
Found at i:84639 original size:30 final size:30
Alignment explanation
Indices: 84330--84632 Score: 281
Period size: 30 Copynumber: 10.1 Consensus size: 30
84320 TTTCAACATT
84330 ACCCATTTCAGCATTATCCATTTCTACACC
1 ACCCATTTCAGCATTATCCATTTCTACACC
* * * * * *
84360 A-ACACTTTCAACATTGTCCTTTTCAACACT
1 ACCCA-TTTCAGCATTATCCATTTCTACACC
* * * *
84390 ACCCATTTCAGCATTGTCTATTTTTACACT
1 ACCCATTTCAGCATTATCCATTTCTACACC
* *
84420 ACCCATTTTAGCATTATCAATTTCTACACC
1 ACCCATTTCAGCATTATCCATTTCTACACC
* * *
84450 A-GCACTTTCAGCACTATCTATTTCTACACC
1 ACCCA-TTTCAGCATTATCCATTTCTACACC
* * * *
84480 A-CCACTTTCAGCATTGTCCCTTTCAACACT
1 ACCCA-TTTCAGCATTATCCATTTCTACACC
* * * *
84510 ACCCATTTCAGCATTGTCCCTTTCAACACT
1 ACCCATTTCAGCATTATCCATTTCTACACC
* * * *
84540 ACCCATTTCAACATTGTCCCTTTCTACACT
1 ACCCATTTCAGCATTATCCATTTCTACACC
*
84570 ACCCATTTCAGCAATATCCATTTCTACACC
1 ACCCATTTCAGCATTATCCATTTCTACACC
*
84600 A-CCACTTTCAGCATTATCCACTTCTACACC
1 ACCCA-TTTCAGCATTATCCATTTCTACACC
84630 ACC
1 ACC
84633 ACTTTCATAA
Statistics
Matches: 230, Mismatches: 37, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
29 7 0.03
30 217 0.94
31 6 0.03
ACGTcount: A:0.26, C:0.35, G:0.05, T:0.34
Consensus pattern (30 bp):
ACCCATTTCAGCATTATCCATTTCTACACC
Found at i:84639 original size:120 final size:119
Alignment explanation
Indices: 84312--84628 Score: 402
Period size: 120 Copynumber: 2.6 Consensus size: 119
84302 TGTCTTTCTT
* * * * *
84312 ATTGTCCCTTTCAACATTACCCATTTCAGCATTATCCATTTCTACACCAACACTTTCAACATTGT
1 ATTGTCCCTTTCTACACTACCCATTTCAGCAATATCCATTTCTACACCACCACTTTCAGCATTGT
* * ** * *
84377 CCTTTTCAACACTACCCATTTCAGCATTGTCTATTTTTACACTACCCATTTTAGC
66 CC-CTTCAACACTACCCATTTCAGCATTGTCCATTTCAACACTACCCATTTCAAC
* ** * * * *
84432 ATTATCAATTTCTACACCA-GCACTTTCAGCACTATCTATTTCTACACCACCACTTTCAGCATTG
1 ATTGTCCCTTTCTACACTACCCA-TTTCAGCAATATCCATTTCTACACCACCACTTTCAGCATTG
*
84496 TCCCTTTCAACACTACCCATTTCAGCATTGTCCCTTTCAACACTACCCATTTCAAC
65 TCCC-TTCAACACTACCCATTTCAGCATTGTCCATTTCAACACTACCCATTTCAAC
*
84552 ATTGTCCCTTTCTACACTACCCATTTCAGCAATATCCATTTCTACACCACCACTTTCAGCATTAT
1 ATTGTCCCTTTCTACACTACCCATTTCAGCAATATCCATTTCTACACCACCACTTTCAGCATTGT
*
84617 CCACTTCTACAC
66 CC-CTTCAACAC
84629 CACCACTTTC
Statistics
Matches: 166, Mismatches: 27, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
119 2 0.01
120 161 0.97
121 3 0.02
ACGTcount: A:0.26, C:0.34, G:0.05, T:0.35
Consensus pattern (119 bp):
ATTGTCCCTTTCTACACTACCCATTTCAGCAATATCCATTTCTACACCACCACTTTCAGCATTGT
CCCTTCAACACTACCCATTTCAGCATTGTCCATTTCAACACTACCCATTTCAAC
Done.