Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008446.1 Hibiscus syriacus cultivar Beakdansim tig00111251_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: 251382
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:161123 original size:14 final size:16
Alignment explanation
Indices: 161103--161176 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
161093 TGAAAATCGC
161103 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
161118 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
161135 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
161154 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
161170 -TTGCGAT
1 ATTGCGAT
161177 AGCCATTTCG
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 18 0.33
16 3 0.06
17 3 0.06
19 30 0.56
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:161140 original size:19 final size:19
Alignment explanation
Indices: 161099--161166 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
161089 GAAATGAAAA
161099 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
161115 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
161132 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
161151 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
161167 TCGTTGCGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.23
16 3 0.06
17 3 0.06
19 30 0.64
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:161300 original size:14 final size:14
Alignment explanation
Indices: 161281--161317 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
161271 CATCAATTAA
161281 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
161295 ACAAATCATCTTTT
1 ACAAATCAACATTT
161309 ACAAATCAA
1 ACAAATCAA
161318 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:163204 original size:20 final size:20
Alignment explanation
Indices: 163179--163231 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
163169 CGAAACTTAA
163179 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
163199 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGAAAATGACT
*
163219 ATCGCAATGCGAA
1 ATCGCAACGCGAA
163232 TGAAAATCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.36, C:0.25, G:0.25, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:163240 original size:18 final size:17
Alignment explanation
Indices: 163219--163295 Score: 51
Period size: 14 Copynumber: 4.7 Consensus size: 17
163209 GGAAATGGCT
163219 ATCGCAATGCGAATGAAA
1 ATCGCAA-GCGAATGAAA
*
163237 ATCGCAA-CG-A-CAAA
1 ATCGCAAGCGAATGAAA
163251 ATCGCAACGCGAAATG-AA
1 ATCGCAA-GCG-AATGAAA
*
163269 ATCGCAA-CG-A-CAAA
1 ATCGCAAGCGAATGAAA
163283 ATCGCAACGCGAA
1 ATCGCAA-GCGAA
163296 ACACAAATCG
Statistics
Matches: 47, Mismatches: 3, Indels: 19
0.68 0.04 0.28
Matches are distributed among these distances:
14 20 0.43
15 1 0.02
16 8 0.17
17 1 0.02
18 17 0.36
ACGTcount: A:0.45, C:0.25, G:0.19, T:0.10
Consensus pattern (17 bp):
ATCGCAAGCGAATGAAA
Found at i:163253 original size:14 final size:14
Alignment explanation
Indices: 163234--163291 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
163224 AATGCGAATG
163234 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
163248 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
163264 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
163280 AAAATCGCAACG
1 AAAATCGCAACG
163292 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:163296 original size:32 final size:33
Alignment explanation
Indices: 163219--163296 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
163209 GGAAATGGCT
*
163219 ATCGCAATGCG-AATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
163251 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
163283 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
163297 CACAAATCGC
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
32 40 0.91
33 4 0.09
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:163389 original size:33 final size:33
Alignment explanation
Indices: 163306--163394 Score: 126
Period size: 32 Copynumber: 2.7 Consensus size: 33
163296 ACACAAATCG
* *
163306 CATTGCGATTTTTATTTCGCGTTGCGATTTTGT
1 CATTGCGATTTTCATTTCGCATTGCGATTTTGT
* *
163339 CGTTGCGA-TTTCATTTCGCATTGCGCTTTTGT
1 CATTGCGATTTTCATTTCGCATTGCGATTTTGT
*
163371 CATTGTGATTTTCATTTCGCATTG
1 CATTGCGATTTTCATTTCGCATTG
163395 TGATAGCCAT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
32 27 0.55
33 22 0.45
ACGTcount: A:0.12, C:0.18, G:0.20, T:0.49
Consensus pattern (33 bp):
CATTGCGATTTTCATTTCGCATTGCGATTTTGT
Found at i:163434 original size:20 final size:20
Alignment explanation
Indices: 163385--163437 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
163375 GTGATTTTCA
* *
163385 TTTCGCATTGTGATAGCCAT
1 TTTCGCGTTGCGATAGCCAT
*
163405 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGCCAT
*
163425 TTTCGTGTTGCGA
1 TTTCGCGTTGCGA
163438 AAGTAAACTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.15, C:0.19, G:0.25, T:0.42
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGCCAT
Found at i:163943 original size:18 final size:18
Alignment explanation
Indices: 163917--163961 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
163907 GTCGATCAGA
*
163917 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
163935 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
163953 TGATGGCTC
1 TGATGGCTC
163962 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:165300 original size:20 final size:20
Alignment explanation
Indices: 165275--165328 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
165265 AATAGTTTCT
165275 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
** *
165295 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACAC
*
165315 GAAACT-AAAATCGC
1 GAAAATGAAAATCGC
165329 GTTGCGATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:165589 original size:22 final size:22
Alignment explanation
Indices: 165562--165605 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
165552 GATGGAGATA
165562 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
* *
165584 GACGGATTTTGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
165606 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.18, C:0.14, G:0.45, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:165813 original size:20 final size:20
Alignment explanation
Indices: 165787--165859 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
165777 GATTATGTAT
165787 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
165807 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
165827 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
*
165847 TATCTCGTTGCGA
1 TATCGCGTTGCGA
165860 TTTTGTATTA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:165914 original size:20 final size:20
Alignment explanation
Indices: 165870--165941 Score: 99
Period size: 20 Copynumber: 3.5 Consensus size: 20
165860 TTTTGTATTA
* **
165870 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
165891 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
165911 TCGCATTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
165931 TCGCATTGCGA
1 TCGCATTGCGA
165942 ATTGGGAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 36 0.78
21 10 0.22
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:166665 original size:157 final size:157
Alignment explanation
Indices: 166379--166681 Score: 561
Period size: 157 Copynumber: 1.9 Consensus size: 157
166369 TGAATAATTT
166379 CTTTTAGGTCCCTGTGGTTTACGCATATTTTTGTATTTTGGTCCCTAATATTTTTTAAAATTTCA
1 CTTTTAGGTCCCTGTGGTTTACGCATATTTTTGTATTTTGGTCCCTAATATTTTTTAAAATTTCA
* *
166444 ATTTAGCCTTTGAATTTCGATTTGTTTTAATTCAGTCGTATTTAATGTTTAATTTATTCCCTTTT
66 ATTTAGCCATTGAATTTCGATTTGTTTTAATTCAGACGTATTTAATGTTTAATTTATTCCCTTTT
166509 GGTTTAGTAATTTAATTGTTTTGGTCC
131 GGTTTAGTAATTTAATTGTTTTGGTCC
**
166536 CTTTTAGGTCCCTGTGGTTTACGCATATTTTTGTATTTTGGTCCCTAATATTTTTTTTAATTTCA
1 CTTTTAGGTCCCTGTGGTTTACGCATATTTTTGTATTTTGGTCCCTAATATTTTTTAAAATTTCA
*
166601 ATTTAGCCATTGAATTTTGATTTGTTTTAATTCAGACGTATTTAATGTTTAATTTATTCCCTTTT
66 ATTTAGCCATTGAATTTCGATTTGTTTTAATTCAGACGTATTTAATGTTTAATTTATTCCCTTTT
166666 GGTTTAGTAATTTAAT
131 GGTTTAGTAATTTAAT
166682 AGTTATACAA
Statistics
Matches: 141, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
157 141 1.00
ACGTcount: A:0.21, C:0.12, G:0.14, T:0.53
Consensus pattern (157 bp):
CTTTTAGGTCCCTGTGGTTTACGCATATTTTTGTATTTTGGTCCCTAATATTTTTTAAAATTTCA
ATTTAGCCATTGAATTTCGATTTGTTTTAATTCAGACGTATTTAATGTTTAATTTATTCCCTTTT
GGTTTAGTAATTTAATTGTTTTGGTCC
Found at i:166735 original size:17 final size:18
Alignment explanation
Indices: 166705--166759 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 18
166695 GGTCCTTGTA
166705 TTTATGTTTATTTTTTAT
1 TTTATGTTTATTTTTTAT
*
166723 TTTATG-TTGTTTTTTA-
1 TTTATGTTTATTTTTTAT
* * *
166739 -CTATTTTTATTTGTTAT
1 TTTATGTTTATTTTTTAT
166756 TTTA
1 TTTA
166760 ATTATTTTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
15 3 0.11
16 8 0.29
17 9 0.32
18 8 0.29
ACGTcount: A:0.16, C:0.02, G:0.07, T:0.75
Consensus pattern (18 bp):
TTTATGTTTATTTTTTAT
Found at i:166767 original size:21 final size:21
Alignment explanation
Indices: 166705--166768 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
166695 GGTCCTTGTA
166705 TTTATG-T-TTATTTT-TTAT
1 TTTATGTTGTTATTTTATTAT
*
166723 TTTATGTTGTT-TTTTACTATT
1 TTTATGTTGTTATTTTATTA-T
166744 TTTAT-TTGTTATTTTAATTAT
1 TTTATGTTGTTATTTT-ATTAT
166765 TTTA
1 TTTA
166769 ATTAAGTTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
18 6 0.16
19 5 0.13
20 9 0.24
21 15 0.39
22 3 0.08
ACGTcount: A:0.19, C:0.02, G:0.06, T:0.73
Consensus pattern (21 bp):
TTTATGTTGTTATTTTATTAT
Found at i:169229 original size:22 final size:22
Alignment explanation
Indices: 169204--169256 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
169194 CTTCTAATTA
169204 TTTTATTTC-ATGTTTATTTTAT
1 TTTTATTTCAAT-TTTATTTTAT
*
169226 TTTTA-ATCAAATTTTATTTTAT
1 TTTTATTTC-AATTTTATTTTAT
169248 TATTTATTT
1 T-TTTATTT
169257 AAAATATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 2 0.08
22 16 0.64
23 6 0.24
24 1 0.04
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTTATTTCAATTTTATTTTAT
Found at i:170112 original size:2 final size:2
Alignment explanation
Indices: 170105--170147 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
170095 AAAATATTTC
170105 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
170147 A
1 A
170148 GAGACACACA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:170466 original size:14 final size:14
Alignment explanation
Indices: 170444--170477 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
170434 TATTTAAAAT
170444 TTTTATTTTT-ATA
1 TTTTATTTTTAATA
170457 TTTTATTTTTAATA
1 TTTTATTTTTAATA
170471 -TTTATTT
1 TTTTATTT
170478 ACGTATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 17 0.85
14 3 0.15
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTATTTTTAATA
Found at i:170527 original size:25 final size:25
Alignment explanation
Indices: 170463--170527 Score: 58
Period size: 25 Copynumber: 2.5 Consensus size: 25
170453 TATATTTTAT
** *
170463 TTTTAATATTTATTTACGTATAAATAT
1 TTTTAA-ATTT-TTTAAATATAAATAA
** *
170490 TTTTTGATATTTTAAATATAAATAA
1 TTTTAAATTTTTTAAATATAAATAA
170515 TTTTAAATTTTTT
1 TTTTAAATTTTTT
170528 TTGTTTAAAA
Statistics
Matches: 29, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
25 22 0.76
26 3 0.10
27 4 0.14
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (25 bp):
TTTTAAATTTTTTAAATATAAATAA
Found at i:174498 original size:25 final size:26
Alignment explanation
Indices: 174443--174498 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
174433 TATGATATTT
*
174443 GTTTCATGTGGAAATAGAAATTATTA
1 GTTTCATGTGGAAATAGAAATTATCA
* * * *
174469 TTTTCATGTGGGAGTA-AGATTATCA
1 GTTTCATGTGGAAATAGAAATTATCA
174494 GTTTC
1 GTTTC
174499 TGAAATTAGT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
25 11 0.46
26 13 0.54
ACGTcount: A:0.30, C:0.07, G:0.21, T:0.41
Consensus pattern (26 bp):
GTTTCATGTGGAAATAGAAATTATCA
Found at i:179420 original size:42 final size:42
Alignment explanation
Indices: 179366--179663 Score: 206
Period size: 43 Copynumber: 7.0 Consensus size: 42
179356 CGTTTTCTGA
* * * *
179366 CAAAAAATGCCGCAATCGGTTTTGTTATTTAGCGGCGTTTTT
1 CAAAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTT
* * *
179408 CAAAAAACGCCGCAATAGGTGTTGATGTTTAGCGGCATTTTCC
1 CAAAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTT-T
* * * * *
179451 CTACAAACGCCGCAGTAGGTGTTGAGATTTAGCGGCGTTTTA
1 CAAAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTT
* * *
179493 CTTACAAACGCCGCAGA-AGGTTTTGATATTTTA-CGGCGTTTTT
1 C-AAAAAACGCCGCA-ATAGGTGTTGATA-TTTAGCGGCGTTTTT
* * * * * * * *
179536 CCCACAAATGTCGCAGTAGGTTTTTAGATTTAGCGGCGTTTGTAT
1 -CAAAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTT-T-T
* * * * * * *
179581 C-GAAAACGACGCAGTAAGTGTTGAGAATTAGTGGCGTTTTT
1 CAAAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTT
* *
179622 CAATAAAAATGCCGCAATATGTGTTGATATTTAGCGGCGTTT
1 C-A-AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTT
179664 CCATACAAAC
Statistics
Matches: 203, Mismatches: 41, Indels: 22
0.76 0.15 0.08
Matches are distributed among these distances:
41 2 0.01
42 41 0.20
43 122 0.60
44 37 0.18
45 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (42 bp):
CAAAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTT
Found at i:179588 original size:86 final size:87
Alignment explanation
Indices: 179392--179663 Score: 229
Period size: 86 Copynumber: 3.2 Consensus size: 87
179382 CGGTTTTGTT
179392 ATTTAGCGGCGTTTT-TCAAAAAACGCCGCA-ATAGGTGTTGATGTTTAGCGGCATTTTCCCTAC
1 ATTTAGCGGCGTTTTATCAAAAAACGCCGCAGATAGGTGTTGATGTTTAGCGGCATTTTCCCTAC
179455 AAACGCCGCAGTAGGTGTTGAG
66 AAACGCCGCAGTAGGTGTTGAG
* * * * *
179477 ATTTAGCGGCGTTTTA-CTTACAAACGCCGCAGA-AGGTTTTGATATTTTA-CGGCGTTTTTCCC
1 ATTTAGCGGCGTTTTATC-AAAAAACGCCGCAGATAGGTGTTGAT-GTTTAGCGGC-ATTTTCCC
* * * *
179539 -ACAAATGTCGCAGTAGGTTTTTAG
63 TACAAACGCCGCAGTAGGTGTTGAG
* * * * * * **
179563 ATTTAGCGGCGTTTGTATC-GAAAACGACGCAG-TAAGTGTTGA-GAATTAGTGGCGTTTTTCAA
1 ATTTAGCGGCGTTT-TATCAAAAAACGCCGCAGATAGGTGTTGATG-TTTAGCGGC-ATTTTCCC
* * * * *
179625 TAAAAATGCCGCAATATGTGTTGAT
63 TACAAACGCCGCAGTAGGTGTTGAG
179650 ATTTAGCGGCGTTT
1 ATTTAGCGGCGTTT
179664 CCATACAAAC
Statistics
Matches: 150, Mismatches: 26, Indels: 20
0.77 0.13 0.10
Matches are distributed among these distances:
85 19 0.13
86 85 0.57
87 45 0.30
88 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (87 bp):
ATTTAGCGGCGTTTTATCAAAAAACGCCGCAGATAGGTGTTGATGTTTAGCGGCATTTTCCCTAC
AAACGCCGCAGTAGGTGTTGAG
Found at i:180104 original size:21 final size:21
Alignment explanation
Indices: 180080--180152 Score: 78
Period size: 21 Copynumber: 3.5 Consensus size: 21
180070 CTTTGTGATG
*
180080 CCGCTGCTTCTTTCTCTGCTT
1 CCGCTGCTTCTCTCTCTGCTT
**
180101 CCGCTG-TTGCTCTGGCTGCTT
1 CCGCTGCTT-CTCTCTCTGCTT
*
180122 CCGCTGCTGCTCTCTCTGCTT
1 CCGCTGCTTCTCTCTCTGCTT
180143 CC-CTTGCTTC
1 CCGC-TGCTTC
180153 ATTTTCCGCT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
20 3 0.07
21 38 0.90
22 1 0.02
ACGTcount: A:0.00, C:0.40, G:0.19, T:0.41
Consensus pattern (21 bp):
CCGCTGCTTCTCTCTCTGCTT
Found at i:183780 original size:42 final size:41
Alignment explanation
Indices: 183684--183782 Score: 128
Period size: 42 Copynumber: 2.4 Consensus size: 41
183674 GTACTAGTAT
* * *
183684 TTAGCGGCGTTTATGTTAAAAACGTCACTAAATTACGTGTAA
1 TTAGCGGCGTTTGTGTTAAAAACG-CACAAAAATACGTGTAA
*
183726 TTAGCGACGTTTGTGTGTAAAATAC-CACAAAAATACGTGTAA
1 TTAGCGGCGTTTGTGT-TAAAA-ACGCACAAAAATACGTGTAA
183768 TTAGCGGCGTTTGTG
1 TTAGCGGCGTTTGTG
183783 CTTGCAATGC
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
42 43 0.86
43 5 0.10
44 2 0.04
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.32
Consensus pattern (41 bp):
TTAGCGGCGTTTGTGTTAAAAACGCACAAAAATACGTGTAA
Found at i:184024 original size:42 final size:42
Alignment explanation
Indices: 183873--184241 Score: 301
Period size: 42 Copynumber: 8.9 Consensus size: 42
183863 ATAAAAATGC
* * * * * *
183873 TTAGCGGCATTTTTGCATAAAATGCCACTAAAGAACGTGTAA
1 TTAGCGGCGTTTGTACATAAAACGCCACTATAGTACGTGTAA
* * * * **
183915 TTATCGGCGTTTGTACTTAAAACGCCACTA-AATACAT-TCT
1 TTAGCGGCGTTTGTACATAAAACGCCACTATAGTACGTGTAA
* *
183955 TTAGCGGCGTTTGTATAAAAACGACGCCACTATAGTACGTGTAA
1 TTAGCGGCGTTTGTACATAAA--ACGCCACTATAGTACGTGTAA
183999 TTCA-CGGCGTTTGTACATAAAACGCCACGTAT-GTACGTGTAA
1 TT-AGCGGCGTTTGTACATAAAACGCCAC-TATAGTACGTGTAA
* * * * *
184041 TTAGCGGAGTTTGTGCTTAAAATGCCACGCAT-GTACGTGTAA
1 TTAGCGGCGTTTGTACATAAAACGCCAC-TATAGTACGTGTAA
* * *
184083 TTAGCGACGTTTGT--ATAAAACGCCAC-ATATGTAC-AGTAT
1 TTAGCGGCGTTTGTACATAAAACGCCACTATA-GTACGTGTAA
* * * *
184122 TTATCGGCGTTTATATA-AAAACGCCACTATAGTGCGTGTAA
1 TTAGCGGCGTTTGTACATAAAACGCCACTATAGTACGTGTAA
* * *
184163 TTAGCGGCGTTTGTACGTTAAACGCCACTGA-AGTACGTGGAA
1 TTAGCGGCGTTTGTACATAAAACGCCACT-ATAGTACGTGTAA
* * * *
184205 TTAGCGACGTTTGTACTTAAAATGCCACTAAAGTACG
1 TTAGCGGCGTTTGTACATAAAACGCCACTATAGTACG
184242 ACCTTTAGCG
Statistics
Matches: 262, Mismatches: 49, Indels: 32
0.76 0.14 0.09
Matches are distributed among these distances:
38 2 0.01
39 14 0.05
40 45 0.17
41 26 0.10
42 147 0.56
43 9 0.03
44 18 0.07
45 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.30
Consensus pattern (42 bp):
TTAGCGGCGTTTGTACATAAAACGCCACTATAGTACGTGTAA
Found at i:184188 original size:164 final size:166
Alignment explanation
Indices: 183907--184232 Score: 430
Period size: 164 Copynumber: 2.0 Consensus size: 166
183897 CCACTAAAGA
* * * * *
183907 ACGTGTAATTATCGGCGTTTGTACTTAAAACGCCACTAAATACATTCTTTAGCGGCGTTTGTATA
1 ACGTGTAATTAGCGACGTTTGTAC-TAAAACGCCACTAAATACAGTATTTAGCGGCGTTTATATA
*
183972 AAAACGACGCCACTATAGTACGTGTAATTCACGGCGTTTGTACATAAAACGCCAC-GTATGTACG
65 AAAAC-ACGCCACTATAGTACGTGTAATTCACGGCGTTTGTACATAAAACGCCACTG-AAGTACG
* *
184036 TGTAATTAGCGGA-GTTTGTGCTTAAAATGCCACGCATGT
128 TGGAATTAGC-GACGTTTGTACTTAAAATGCCACGCATGT
** *
184075 ACGTGTAATTAGCGACGTTTGTA-TAAAACGCCACATATGTACAGTATTTATCGGCGTTTATAT-
1 ACGTGTAATTAGCGACGTTTGTACTAAAACGCCAC-TAAATACAGTATTTAGCGGCGTTTATATA
* * *
184138 AAAA-ACGCCACTATAGTGCGTGTAATT-AGCGGCGTTTGTACGTTAAACGCCACTGAAGTACGT
65 AAAACACGCCACTATAGTACGTGTAATTCA-CGGCGTTTGTACATAAAACGCCACTGAAGTACGT
184201 GGAATTAGCGACGTTTGTACTTAAAATGCCAC
129 GGAATTAGCGACGTTTGTACTTAAAATGCCAC
184233 TAAAGTACGA
Statistics
Matches: 140, Mismatches: 14, Indels: 12
0.84 0.08 0.07
Matches are distributed among these distances:
163 3 0.02
164 78 0.56
165 1 0.01
166 15 0.11
167 22 0.16
168 21 0.15
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (166 bp):
ACGTGTAATTAGCGACGTTTGTACTAAAACGCCACTAAATACAGTATTTAGCGGCGTTTATATAA
AAACACGCCACTATAGTACGTGTAATTCACGGCGTTTGTACATAAAACGCCACTGAAGTACGTGG
AATTAGCGACGTTTGTACTTAAAATGCCACGCATGT
Found at i:184305 original size:164 final size:163
Alignment explanation
Indices: 183932--184319 Score: 367
Period size: 164 Copynumber: 2.4 Consensus size: 163
183922 CGTTTGTACT
*** * * *
183932 TAAAACGCCAC-TAAATACATTCTTTAGCGGCGTTTGTATAAAAACGACGCCACTATAGTACGTG
1 TAAAACGCCACATAAATACAGAATTTATCGGCATTTATAT-AAAA--ACGCCACTATAGTACGTG
* * *
183996 TAATTCACGGCGTTTGTACATAAAACGCCACGTATGTACGTGTAATTAGCGGAGTTTGTGCTTAA
63 TAATTCACGGCGTTTGTACATAAAACGCCACGTAAGTACGTGGAATTAGCGGAGTTTGTACTTAA
* * ** *
184061 AATGCCACGCATGTACGTGTAATTAGCGACGTTTGTA
128 AATGCCACGAAAGTACGCCT-ATTAGCGACGTTTATA
** * * *
184098 TAAAACGCCACATATGTACAGTATTTATCGGCGTTTATATAAAAACGCCACTATAGTGCGTGTAA
1 TAAAACGCCACATAAATACAGAATTTATCGGCATTTATATAAAAACGCCACTATAGTACGTGTAA
* *
184163 TT-AGCGGCGTTTGTACGTTAAACGCCAC-TGAAGTACGTGGAATTAGC-GACGTTTGTACTTAA
66 TTCA-CGGCGTTTGTACATAAAACGCCACGT-AAGTACGTGGAATTAGCGGA-GTTTGTACTTAA
* **
184225 AATGCCACTAAAGTACGACCT-TTAGCGTTGTTTATA
128 AATGCCACGAAAGTACG-CCTATTAGCGACGTTTATA
* * * * *
184261 TAAAAATGCCAC-TAAAATATAGAATTTAGT-GGCATTTTTATAAAAACACCACTAAAGTA
1 T-AAAACGCCACAT-AAATACAGAATTTA-TCGGCATTTATATAAAAACGCCACTATAGTA
184320 AATTATTTTC
Statistics
Matches: 184, Mismatches: 30, Indels: 18
0.79 0.13 0.08
Matches are distributed among these distances:
163 18 0.10
164 127 0.69
165 2 0.01
166 15 0.08
167 22 0.12
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (163 bp):
TAAAACGCCACATAAATACAGAATTTATCGGCATTTATATAAAAACGCCACTATAGTACGTGTAA
TTCACGGCGTTTGTACATAAAACGCCACGTAAGTACGTGGAATTAGCGGAGTTTGTACTTAAAAT
GCCACGAAAGTACGCCTATTAGCGACGTTTATA
Found at i:185401 original size:6 final size:6
Alignment explanation
Indices: 185392--185419 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
185382 ATGTTTATGT
185392 TATAAA TATAAA TATAAA TATAAA TATA
1 TATAAA TATAAA TATAAA TATAAA TATA
185420 CATTTAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
TATAAA
Found at i:190167 original size:43 final size:43
Alignment explanation
Indices: 190120--190284 Score: 160
Period size: 43 Copynumber: 3.8 Consensus size: 43
190110 TCTAAATATA
190120 ATTATATTTTAAAATAATTAAAATAATATATTTATAATAATTT
1 ATTATATTTTAAAATAATTAAAATAATATATTTATAATAATTT
* * *
190163 ATTATATTTTAAAAT-ATGAAAATAATGTATTTTATAGTAATTT
1 ATTATATTTTAAAATAATTAAAATAATATA-TTTATAATAATTT
* * *
190206 -TTATATTTT-TAATAATT-AAACAATATATTT-TAATAAATATGAA
1 ATTATATTTTAAAATAATTAAAATAATATATTTATAAT-AAT-T--T
* * * *
190249 ATAATTTTTTTAAATAATTAAAATAATATATATATA
1 ATTATATTTTAAAATAATTAAAATAATATATTTATA
190285 TATATATATT
Statistics
Matches: 98, Mismatches: 14, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
39 3 0.03
40 6 0.06
41 12 0.12
42 23 0.23
43 27 0.28
44 7 0.07
45 7 0.07
46 11 0.11
47 2 0.02
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (43 bp):
ATTATATTTTAAAATAATTAAAATAATATATTTATAATAATTT
Found at i:191083 original size:15 final size:14
Alignment explanation
Indices: 191053--191081 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
191043 TTATTGATTC
191053 ATAAATTTTAAAAA
1 ATAAATTTTAAAAA
191067 ATAAATTTTAAAAA
1 ATAAATTTTAAAAA
191081 A
1 A
191082 ATTAAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
ATAAATTTTAAAAA
Found at i:195136 original size:14 final size:15
Alignment explanation
Indices: 195128--195160 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
195118 AAATTTATTG
*
195128 AATTGAATTAAATT-
1 AATTGAATTGAATTA
195142 AATTGAATTGAATTA
1 AATTGAATTGAATTA
195157 AATT
1 AATT
195161 AGGACTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (15 bp):
AATTGAATTGAATTA
Found at i:195137 original size:19 final size:19
Alignment explanation
Indices: 195113--195161 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
195103 CATGAATAGA
*
195113 GAATTAAATTTATTGAATT
1 GAATTAAATTAATTGAATT
195132 GAATTAAATTAATTGAATT
1 GAATTAAATTAATTGAATT
195151 GAATTAAATTA
1 GAATTAAATTA
195162 GGACTAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.43
Consensus pattern (19 bp):
GAATTAAATTAATTGAATT
Found at i:195385 original size:3 final size:3
Alignment explanation
Indices: 195341--195365 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
195331 AAAAAAGTAA
195341 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
195366 TTGTGTGAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:227997 original size:12 final size:12
Alignment explanation
Indices: 227980--228006 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
227970 AATGAAATTT
227980 TGATGAAGAAGA
1 TGATGAAGAAGA
227992 TGATGAAGAAGA
1 TGATGAAGAAGA
228004 TGA
1 TGA
228007 AAGATGGCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.33, T:0.19
Consensus pattern (12 bp):
TGATGAAGAAGA
Found at i:238919 original size:16 final size:15
Alignment explanation
Indices: 238900--238929 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
238890 TTTTTTGAAA
*
238900 TTTTGGTTTTTTTTG
1 TTTTTGTTTTTTTTG
238915 TTTTTGTTTTTTTTG
1 TTTTTGTTTTTTTTG
238930 GAAAAAAAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (15 bp):
TTTTTGTTTTTTTTG
Done.