Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004214.1 Hibiscus syriacus cultivar Beakdansim tig00009230_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: 290190
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
File 2 of 2
Found at i:219563 original size:42 final size:41
Alignment explanation
Indices: 219483--219579 Score: 101
Period size: 42 Copynumber: 2.4 Consensus size: 41
219473 GCATTTTAGA
* * *
219483 TATAAAAGCCGCTAATTTACCACTATATTACGGCGTTTGTGG
1 TATAAACGCCGCTAATTTAACACTATATTACGGCGTTTG-GC
* *
219525 TATAAACGCCGCTACA-TTAACACTTTATTGA-GGTGTTTGGC
1 TATAAACGCCGCTA-ATTTAACACTATATT-ACGGCGTTTGGC
219566 TA-AAACGCCGCTAA
1 TATAAACGCCGCTAA
219580 ATGTCTACTC
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
39 1 0.02
40 11 0.23
41 3 0.06
42 31 0.65
43 2 0.04
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.31
Consensus pattern (41 bp):
TATAAACGCCGCTAATTTAACACTATATTACGGCGTTTGGC
Found at i:220297 original size:20 final size:20
Alignment explanation
Indices: 220254--220300 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
220244 TTGTTTGGCT
* * *
220254 CTGAATGAAATTATTCGGCT
1 CTGAATGAAATAATTCAGCA
*
220274 CTGAATGAAATAATTTAGCA
1 CTGAATGAAATAATTCAGCA
220294 CTGAATG
1 CTGAATG
220301 CTGAACAGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (20 bp):
CTGAATGAAATAATTCAGCA
Found at i:223556 original size:28 final size:28
Alignment explanation
Indices: 223500--223589 Score: 117
Period size: 28 Copynumber: 3.2 Consensus size: 28
223490 CAAGGCTGAT
* * * *
223500 CATATATCATTCAGGCGACAGAGCTGAC
1 CATATATCAATCAGGCGATAGAACCGAC
* *
223528 CATATATCAATCAGGCGGTATAACCGAC
1 CATATATCAATCAGGCGATAGAACCGAC
*
223556 CATATATCAATCAGGCGATAGAACCGGC
1 CATATATCAATCAGGCGATAGAACCGAC
223584 CATATA
1 CATATA
223590 ATAGAACTAA
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 53 1.00
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (28 bp):
CATATATCAATCAGGCGATAGAACCGAC
Found at i:228605 original size:28 final size:28
Alignment explanation
Indices: 228546--228610 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
228536 CAACAGAGTC
* * *
228546 GACCATATATCAATCAGGCGGTAAAACC
1 GACCATATATCAATCAGACGGCAAAACA
* * *
228574 GACCATATGTCAATCAGACGGCAGAGCA
1 GACCATATATCAATCAGACGGCAAAACA
228602 GACCATATA
1 GACCATATA
228611 ACAAAACTAA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.38, C:0.25, G:0.20, T:0.17
Consensus pattern (28 bp):
GACCATATATCAATCAGACGGCAAAACA
Found at i:229051 original size:2 final size:2
Alignment explanation
Indices: 229044--229081 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
229034 GTCTTCTAAC
229044 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
229082 GGGTTAAAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:234343 original size:45 final size:44
Alignment explanation
Indices: 234242--234344 Score: 118
Period size: 44 Copynumber: 2.3 Consensus size: 44
234232 GGCAAGGTGT
* *
234242 CGATGTTGTGTGACCCGAACCTAGCCTAAGGTATTGGGAGGTGC
1 CGATGTTGTGTGACCCGAACCTAGCCTAAGATATTGGGAGATGC
* * * *
234286 CGATGCTATGTGACCC-AGACCTCGCCTGAGATACTTGGGAGATGC
1 CGATGTTGTGTGACCCGA-ACCTAGCCTAAGATA-TTGGGAGATGC
*
234331 TGATGTTGTGTGAC
1 CGATGTTGTGTGAC
234345 GTAGGTCTAC
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
43 1 0.02
44 26 0.54
45 21 0.44
ACGTcount: A:0.20, C:0.21, G:0.32, T:0.26
Consensus pattern (44 bp):
CGATGTTGTGTGACCCGAACCTAGCCTAAGATATTGGGAGATGC
Found at i:238921 original size:39 final size:39
Alignment explanation
Indices: 238897--238990 Score: 161
Period size: 39 Copynumber: 2.4 Consensus size: 39
238887 GCCAAACTTA
*
238897 AAGACTCCAGGAGTGCACGGCGTCTTTAGATCAATGGAT
1 AAGACTCCAGGAGTGCACGGCGTCTTTAGACCAATGGAT
* *
238936 AAGACTCCAGGAGTGCACGGCGTTTTTAGATCAATGGAT
1 AAGACTCCAGGAGTGCACGGCGTCTTTAGACCAATGGAT
238975 AAGACTCCAGGAGTGC
1 AAGACTCCAGGAGTGC
238991 TTAGCGTCCT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 54 1.00
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (39 bp):
AAGACTCCAGGAGTGCACGGCGTCTTTAGACCAATGGAT
Found at i:239085 original size:13 final size:13
Alignment explanation
Indices: 239067--239093 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
239057 AATATTAAAG
239067 TATTGATTTTTTA
1 TATTGATTTTTTA
239080 TATTGATTTTTTA
1 TATTGATTTTTTA
239093 T
1 T
239094 GTAACCACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.70
Consensus pattern (13 bp):
TATTGATTTTTTA
Found at i:239340 original size:60 final size:60
Alignment explanation
Indices: 239276--239393 Score: 191
Period size: 60 Copynumber: 2.0 Consensus size: 60
239266 TATTTTTATC
* *
239276 TTGATAGTTGATCGTCCATATTCATCTTTATTATTATTTTTAGTTTGTTATCTTTTCATG
1 TTGATAGTTAATCGTCCATATTCATCTTTATTATCATTTTTAGTTTGTTATCTTTTCATG
** *
239336 TTGATAGTTAATCGTCTGTATTTATCTTTATTATCATTTTTAGTTTGTTATCTTTTCA
1 TTGATAGTTAATCGTCCATATTCATCTTTATTATCATTTTTAGTTTGTTATCTTTTCA
239394 GTTTTTATTC
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 53 1.00
ACGTcount: A:0.20, C:0.11, G:0.11, T:0.58
Consensus pattern (60 bp):
TTGATAGTTAATCGTCCATATTCATCTTTATTATCATTTTTAGTTTGTTATCTTTTCATG
Found at i:241754 original size:20 final size:20
Alignment explanation
Indices: 241705--241758 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
241695 GCGTAGCTAG
* *
241705 GCACTGAAGATGACGCTCAA
1 GCACTGAAGGTGGCGCTCAA
241725 GCACTGAAGGTGGCGCTCAA
1 GCACTGAAGGTGGCGCTCAA
241745 GCACTGAAGGTGGC
1 GCACTGAAGGTGGC
241759 ATCCGCCTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.28, C:0.24, G:0.33, T:0.15
Consensus pattern (20 bp):
GCACTGAAGGTGGCGCTCAA
Found at i:242884 original size:12 final size:12
Alignment explanation
Indices: 242867--242902 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
242857 TTGATATTAA
242867 AAAATAAATATT
1 AAAATAAATATT
242879 AAAATAAATATT
1 AAAATAAATATT
242891 AAAATAAATATT
1 AAAATAAATATT
242903 TATTTATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATAAATATT
Found at i:242899 original size:16 final size:14
Alignment explanation
Indices: 242860--242902 Score: 58
Period size: 12 Copynumber: 3.4 Consensus size: 14
242850 CTTTTCTTTG
242860 ATATTAAAAAATAA
1 ATATTAAAAAATAA
242874 ATATT--AAAATAA
1 ATATTAAAAAATAA
242886 ATATT--AAAATAA
1 ATATTAAAAAATAA
242898 ATATT
1 ATATT
242903 TATTTATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 24 0.83
14 5 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
ATATTAAAAAATAA
Found at i:243633 original size:12 final size:12
Alignment explanation
Indices: 243616--243641 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
243606 GGAAAATACC
243616 TTCGGTGTTATT
1 TTCGGTGTTATT
243628 TTCGGTGTTATT
1 TTCGGTGTTATT
243640 TT
1 TT
243642 TCTAAAAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.23, T:0.62
Consensus pattern (12 bp):
TTCGGTGTTATT
Found at i:244356 original size:3 final size:3
Alignment explanation
Indices: 244348--244398 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
244338 TTAATATATT
* * * *
244348 TAA TAA TAA TAA TTA TTA TTA TTA TAA TAA TAA TAA TAA TAA TAA TTAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA
244397 TA
1 TA
244399 TGGGTAAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 42 0.93
4 3 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (3 bp):
TAA
Found at i:244937 original size:113 final size:113
Alignment explanation
Indices: 244725--245470 Score: 1196
Period size: 113 Copynumber: 6.6 Consensus size: 113
244715 CAAAAAGTTG
* *
244725 TCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTCTCT-GAAAATGTTGATCCATCA
1 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAA-GATGATCCATCA
* * ** *
244788 ATTGATGAATTCATGTAAAAGGTTGAACAAGCTCTTCGCATTATGAACT
65 AATGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACT
244837 T-TCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCA
1 TCT-TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCA
* *
244901 AGTGATGAATTCAGGTAAAAGGTTGATCAAATTCTTCTCATTATGAACT
65 AATGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACT
*
244950 TCTTCTTCCTTCTTTAGATGAGTTCTTCTCATTATGAAC-TTCTCTGGAAAAGATGATCCATCAA
1 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCAA
*
245014 ATGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACT
66 ATGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACT
245062 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCAA
1 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCAA
*
245127 ATGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACT
66 ATGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACT
*
245175 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGAAAAAGATGATCCATCAA
1 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCAA
*
245240 ATGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACT
66 ATGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACT
* * * *
245288 TCTTCTTCCTTCTTCAAATGAATTCTTCTCATTATGAACTTTCTCTGGAAAAAATAATCCATCAA
1 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCAA
* * ** *
245353 GTAATGAATTCAGACAAAAGGTTGAACAAGTTCTTCTCATTATGAACT
66 ATGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACT
* * *
245401 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGG-AAATATCAATCCATCA
1 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGAT-GATCCATCA
245465 AATGAT
65 AATGAT
245471 AGATTTGAAT
Statistics
Matches: 597, Mismatches: 31, Indels: 11
0.93 0.05 0.02
Matches are distributed among these distances:
111 1 0.00
112 149 0.25
113 441 0.74
114 6 0.01
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (113 bp):
TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCAA
ATGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACT
Found at i:245116 original size:225 final size:225
Alignment explanation
Indices: 244725--245475 Score: 1220
Period size: 225 Copynumber: 3.3 Consensus size: 225
244715 CAAAAAGTTG
* *
244725 TCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCT-GAAAATGTTGATCCATCAA
1 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAAAA-GATGATCCATCAA
* * * ** *
244789 TTGATGAATTCATGTAAAAGGTTGAACAAGCTCTTCGCATTATGAACTT-TCTCTTCCTTCTTCA
65 ATGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCT-TCTTCCTTCTTCA
244853 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGTA
129 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGTA
*
244918 AAAGGTTGATCAAATTCTTCTCATTATGAACT
194 AAAGGTTGAACAAATTCTTCTCATTATGAACT
*
244950 TCTTCTTCCTTCTTTAGATGAGTTCTTCTCATTATGAACTTCTCTGGAAAAGATGATCCATCAAA
1 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAAAAGATGATCCATCAAA
245015 TGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
66 TGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
* *
245080 TGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGTAAA
131 TGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGTAAA
245145 AGGTTGAACAAATTCTTCTCATTATGAACT
196 AGGTTGAACAAATTCTTCTCATTATGAACT
*
245175 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGAAAAAGATGATCCATCAA
1 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTCTCTGGAAAAGATGATCCATCAA
*
245240 ATGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAA
65 ATGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
* * * * **
245305 ATGAATTCTTCTCATTATGAACTTTCTCTGGAAAAAATAATCCATCAAGTAATGAATTCAGACAA
130 ATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGTAA
*
245370 AAGGTTGAACAAGTTCTTCTCATTATGAACT
195 AAGGTTGAACAAATTCTTCTCATTATGAACT
* *
245401 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGG-AAATATCAATCCATCA
1 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA-CTTCTCTGGAAAAGAT-GATCCATCA
*
245465 AATGATAGATT
64 AATGATGGATT
245476 TGAATCTTTG
Statistics
Matches: 493, Mismatches: 28, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
225 248 0.50
226 244 0.49
227 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (225 bp):
TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAAAAGATGATCCATCAAA
TGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
TGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGTAAA
AGGTTGAACAAATTCTTCTCATTATGAACT
Found at i:246941 original size:83 final size:83
Alignment explanation
Indices: 246262--246929 Score: 1142
Period size: 83 Copynumber: 8.0 Consensus size: 83
246252 CTTATTTCTA
* *
246262 CTATGAGCAAATTCATCTTCCAAATTTAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
246327 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
*
246345 CTATGAGTACATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
246410 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
**
246428 CTATGAGCACATTCATCTTCCCCATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
246493 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* * *
246511 CTATGAGTACATTCATCTTCCCAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCACA
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
246576 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* * *
246594 CTATGAGTACATTCATCTTCCCAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCACA
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
246659 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
*
246677 CTATGAGTACATTCATCTTCCAAATTCAATGATTGGTTCTG-CCAAACCAGATCAGATAACTCAA
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGTCC-AACCAGATCAGATAACTCAA
*
246741 AGAAAACTTCCAGAAGATG
65 AGAACACTTCCAGAAGATG
* * *
246760 CTATGAACACATTCATCTTCTAAATTCAATGATTGGTTATG-CCAAACCAGATCAGATAACTCAA
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGTCC-AACCAGATCAGATAACTCAA
246824 AGAACACTTCCAGAAGATG
65 AGAACACTTCCAGAAGATG
**
246843 CTATGAGCACATTCATCTTCCCCATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
246908 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
246926 CTAT
1 CTAT
246930 TGGCAAATTC
Statistics
Matches: 561, Mismatches: 22, Indels: 4
0.96 0.04 0.01
Matches are distributed among these distances:
82 2 0.00
83 557 0.99
84 2 0.00
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.27
Consensus pattern (83 bp):
CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATG
Found at i:248099 original size:9 final size:9
Alignment explanation
Indices: 248081--248124 Score: 63
Period size: 9 Copynumber: 4.9 Consensus size: 9
248071 TTGACCCTCC
248081 TTTTTC-TT
1 TTTTTCTTT
248089 TTTTTCTTT
1 TTTTTCTTT
248098 TTTTTCTTTT
1 TTTTTC-TTT
248108 TTTTTCTTT
1 TTTTTCTTT
*
248117 CTTTTCTT
1 TTTTTCTT
248125 CAAGCATAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
8 6 0.18
9 18 0.55
10 9 0.27
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:248100 original size:10 final size:10
Alignment explanation
Indices: 248087--248121 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
248077 CTCCTTTTTC
248087 TTTTTTTC-T
1 TTTTTTTCTT
248096 TTTTTTTCTT
1 TTTTTTTCTT
248106 TTTTTTTCTT
1 TTTTTTTCTT
248116 TCTTTT
1 T-TTTT
248122 CTTCAAGCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 8 0.33
10 12 0.50
11 4 0.17
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:248111 original size:19 final size:19
Alignment explanation
Indices: 248087--248124 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
248077 CTCCTTTTTC
*
248087 TTTTTTTCTTTTTTTTCTT
1 TTTTTTTCTTTCTTTTCTT
248106 TTTTTTTCTTTCTTTTCTT
1 TTTTTTTCTTTCTTTTCTT
248125 CAAGCATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (19 bp):
TTTTTTTCTTTCTTTTCTT
Found at i:259372 original size:13 final size:13
Alignment explanation
Indices: 259335--259374 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
259325 TTGATATTAA
259335 AAAATAAATA-TT
1 AAAATAAATATTT
*
259347 AAAATAATTTATTT
1 AAAATAA-ATATTT
259361 AAAATAAATATTT
1 AAAATAAATATTT
259374 A
1 A
259375 TTTATTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 7 0.29
13 8 0.33
14 9 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATAAATATTT
Found at i:260364 original size:22 final size:22
Alignment explanation
Indices: 260338--260399 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
260328 TATTATTGTT
260338 TCTCTGTTTTTTTCTTTCTCCGG
1 TCTCTGTTTTTTTCTTTCT-CGG
* *
260361 -CTCTGTCTTTTCTCTTT-TTGG
1 TCTCTGT-TTTTTTCTTTCTCGG
*
260382 TCTCTGTTTTTTTTTTTC
1 TCTCTGTTTTTTTCTTTC
260400 AGGTTCGGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
21 10 0.31
22 13 0.41
23 9 0.28
ACGTcount: A:0.00, C:0.23, G:0.11, T:0.66
Consensus pattern (22 bp):
TCTCTGTTTTTTTCTTTCTCGG
Found at i:260826 original size:3 final size:3
Alignment explanation
Indices: 260818--260863 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
260808 TTAATATATT
*
260818 TAA TAA TAA TAA TAA TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
260864 TAATTAATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:261675 original size:28 final size:25
Alignment explanation
Indices: 261644--261706 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 25
261634 ATTTTAATTT
261644 TTAAAATAATAAAATATTAAATTAAATA
1 TTAAAATAAT-AAAT-TT-AATTAAATA
*
261672 TTAATTACATAATAAATTTTATTAAATA
1 TTAA--A-ATAATAAATTTAATTAAATA
261700 TTAAAAT
1 TTAAAAT
261707 TATTTTTATA
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
25 2 0.06
26 1 0.03
28 16 0.52
29 2 0.06
30 5 0.16
31 5 0.16
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (25 bp):
TTAAAATAATAAATTTAATTAAATA
Found at i:261728 original size:22 final size:23
Alignment explanation
Indices: 261673--261729 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 23
261663 AATTAAATAT
*
261673 TAATTACATAATAAATTTTATTAA
1 TAATTACA-AATTAATTTTATTAA
*
261697 -ATATTA-AAATTATTTTTA-TAA
1 TA-ATTACAAATTAATTTTATTAA
261718 TAATTACAAATT
1 TAATTACAAATT
261730 TTAAATTGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
21 7 0.25
22 15 0.54
23 2 0.07
24 4 0.14
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (23 bp):
TAATTACAAATTAATTTTATTAA
Found at i:262934 original size:12 final size:12
Alignment explanation
Indices: 262917--262963 Score: 94
Period size: 12 Copynumber: 3.9 Consensus size: 12
262907 GAAATGAAAA
262917 TGACAGTGGATG
1 TGACAGTGGATG
262929 TGACAGTGGATG
1 TGACAGTGGATG
262941 TGACAGTGGATG
1 TGACAGTGGATG
262953 TGACAGTGGAT
1 TGACAGTGGAT
262964 AGTGCACATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.26, C:0.09, G:0.40, T:0.26
Consensus pattern (12 bp):
TGACAGTGGATG
Found at i:265117 original size:24 final size:24
Alignment explanation
Indices: 265045--265118 Score: 94
Period size: 24 Copynumber: 3.1 Consensus size: 24
265035 CAACGACTCA
*
265045 ACTGGAAGAAACAGTTATGTCAGC
1 ACTGGAAGAAACAGTCATGTCAGC
* *
265069 ACTGGAAGAAACAGTCACGTAAGC
1 ACTGGAAGAAACAGTCATGTCAGC
* * *
265093 ACTGGAAGAAGCAGCCATGGCAGC
1 ACTGGAAGAAACAGTCATGTCAGC
265117 AC
1 AC
265119 AATTACACTT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.38, C:0.22, G:0.27, T:0.14
Consensus pattern (24 bp):
ACTGGAAGAAACAGTCATGTCAGC
Found at i:280646 original size:23 final size:23
Alignment explanation
Indices: 280616--280743 Score: 217
Period size: 23 Copynumber: 5.7 Consensus size: 23
280606 GCAGCAACCG
* *
280616 ACAAGCATCACTGTATCAATTCA
1 ACAAGCATCATTGCATCAATTCA
280639 ACAAGCATCATTGCATCAATTCA
1 ACAAGCATCATTGCATCAATTCA
280662 ACAAGCATCATTGCATCAATTC-
1 ACAAGCATCATTGCATCAATTCA
280684 ACAAGCATCATTGCATCAATTCA
1 ACAAGCATCATTGCATCAATTCA
280707 ACAAGCATCATTGCATCAATTCA
1 ACAAGCATCATTGCATCAATTCA
280730 AC-AGCATCA-TGCAT
1 ACAAGCATCATTGCAT
280744 TCAGAAAACA
Statistics
Matches: 102, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
21 5 0.05
22 29 0.28
23 68 0.67
ACGTcount: A:0.38, C:0.27, G:0.09, T:0.26
Consensus pattern (23 bp):
ACAAGCATCATTGCATCAATTCA
Found at i:280692 original size:68 final size:66
Alignment explanation
Indices: 280616--280743 Score: 220
Period size: 68 Copynumber: 1.9 Consensus size: 66
280606 GCAGCAACCG
*
280616 ACAAGCATCACTGTATCAATTCAACAAGCATCATTGCATCAATTCAACAAGCATCATTGCATCAA
1 ACAAGCATCACTGCATCAATTCAACAAGCATCATTGCATCAATTCAAC-AGCATCA-TGCATCAA
280681 TTC
64 TTC
*
280684 ACAAGCATCATTGCATCAATTCAACAAGCATCATTGCATCAATTCAACAGCATCATGCAT
1 ACAAGCATCACTGCATCAATTCAACAAGCATCATTGCATCAATTCAACAGCATCATGCAT
280744 TCAGAAAACA
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
66 5 0.09
67 7 0.12
68 46 0.79
ACGTcount: A:0.38, C:0.27, G:0.09, T:0.26
Consensus pattern (66 bp):
ACAAGCATCACTGCATCAATTCAACAAGCATCATTGCATCAATTCAACAGCATCATGCATCAATT
C
Found at i:280702 original size:45 final size:45
Alignment explanation
Indices: 280616--280743 Score: 206
Period size: 45 Copynumber: 2.8 Consensus size: 45
280606 GCAGCAACCG
* *
280616 ACAAGCATCACTGTATCAATTCAACAAGCATCATTGCATCAATTCA
1 ACAAGCATCATTGCATCAATTC-ACAAGCATCATTGCATCAATTCA
280662 ACAAGCATCATTGCATCAATTCACAAGCATCATTGCATCAATTCA
1 ACAAGCATCATTGCATCAATTCACAAGCATCATTGCATCAATTCA
280707 ACAAGCATCATTGCATCAATTCA-ACAGCATCA-TGCAT
1 ACAAGCATCATTGCATCAATTCACA-AGCATCATTGCAT
280744 TCAGAAAACA
Statistics
Matches: 79, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
44 6 0.08
45 53 0.67
46 20 0.25
ACGTcount: A:0.38, C:0.27, G:0.09, T:0.26
Consensus pattern (45 bp):
ACAAGCATCATTGCATCAATTCACAAGCATCATTGCATCAATTCA
Found at i:280857 original size:19 final size:20
Alignment explanation
Indices: 280825--280874 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
280815 CAACCTTACA
** *
280825 AATATCAAGTAGAAG-AAGC
1 AATATCAAACAGAAGCAAAC
280844 AATATCAAACAGAAGCAAAC
1 AATATCAAACAGAAGCAAAC
*
280864 AATATAAAACA
1 AATATCAAACA
280875 TAATCAAGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.60, C:0.14, G:0.12, T:0.14
Consensus pattern (20 bp):
AATATCAAACAGAAGCAAAC
Found at i:280894 original size:18 final size:17
Alignment explanation
Indices: 280873--280906 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
280863 CAATATAAAA
280873 CATAATCAAGATATCAAG
1 CATAATCAAG-TATCAAG
280891 CATAATCAAGTATCAA
1 CATAATCAAGTATCAA
280907 CTATTGCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.50, C:0.18, G:0.09, T:0.24
Consensus pattern (17 bp):
CATAATCAAGTATCAAG
Found at i:283448 original size:17 final size:17
Alignment explanation
Indices: 283426--283497 Score: 81
Period size: 17 Copynumber: 4.1 Consensus size: 17
283416 ATAGTTTTGA
283426 TTCGGGTTTGGATTGGG
1 TTCGGGTTTGGATTGGG
* *
283443 TTCGGGTTTGGATTTAGA
1 TTCGGGTTTGGA-TTGGG
**
283461 TTCAAGTTTGGATTGGG
1 TTCGGGTTTGGATTGGG
*
283478 TTCGGGTTTAGATTCGGG
1 TTCGGGTTTGGATT-GGG
283496 TT
1 TT
283498 TAGGTTGGGT
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
17 26 0.59
18 18 0.41
ACGTcount: A:0.12, C:0.07, G:0.38, T:0.43
Consensus pattern (17 bp):
TTCGGGTTTGGATTGGG
Found at i:283498 original size:29 final size:29
Alignment explanation
Indices: 283419--283525 Score: 85
Period size: 35 Copynumber: 3.5 Consensus size: 29
283409 GTTTCGAATA
*
283419 GTTTTGATTCGGGTTTGGATTGGGTTCGGGTTTG
1 GTTTAGATTCGGGTTTGGATTGGGTTC--G---G
**
283453 GATTTAGATTCAAGTTTGGATTGGGTTCGG
1 G-TTTAGATTCGGGTTTGGATTGGGTTCGG
283483 GTTTAGATTCGGGTTTAGG-TTGGGTT--G
1 GTTTAGATTCGGGTTT-GGATTGGGTTCGG
*
283510 GTTTCAGGTTCGGGTT
1 GTTT-AGATTCGGGTT
283526 CGAGTTTGGA
Statistics
Matches: 64, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
27 5 0.08
28 10 0.16
29 20 0.31
30 4 0.06
33 1 0.02
34 1 0.02
35 23 0.36
ACGTcount: A:0.11, C:0.07, G:0.38, T:0.44
Consensus pattern (29 bp):
GTTTAGATTCGGGTTTGGATTGGGTTCGG
Found at i:284024 original size:101 final size:102
Alignment explanation
Indices: 283879--284068 Score: 337
Period size: 101 Copynumber: 1.9 Consensus size: 102
283869 GATGAATTTT
*
283879 TGGGTGTTTGATCCAAAAAAACACTAAATGATTTGGGTTTTGGTGTTTGTGAAGATCAAATGAGG
1 TGGGTGTTTGATCC-AAAAAACACGAAATGATTTGGGTTTTGGTGTTTGTGAAGATCAAATGAGG
*
283944 GTTTTTGGGATCAACACGGATGAACATGGTTGAAATTA
65 GGTTTTGGGATCAACACGGATGAACATGGTTGAAATTA
283982 TGGGTGTTTGATCC-AAAAACACGAAATGATTTGGGTTTTGGTGTTTGTGAAGATCAAATGAGGG
1 TGGGTGTTTGATCCAAAAAACACGAAATGATTTGGGTTTTGGTGTTTGTGAAGATCAAATGAGGG
*
284046 GTTTTGGGATGAACACGGATGAA
66 GTTTTGGGATCAACACGGATGAA
284069 AACTTATGAA
Statistics
Matches: 84, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
101 70 0.83
103 14 0.17
ACGTcount: A:0.30, C:0.08, G:0.29, T:0.32
Consensus pattern (102 bp):
TGGGTGTTTGATCCAAAAAACACGAAATGATTTGGGTTTTGGTGTTTGTGAAGATCAAATGAGGG
GTTTTGGGATCAACACGGATGAACATGGTTGAAATTA
Found at i:284354 original size:29 final size:29
Alignment explanation
Indices: 284316--284415 Score: 82
Period size: 28 Copynumber: 3.4 Consensus size: 29
284306 CAATGCAATG
284316 TATT-AATTTAAGCTTCATATTTAAAATT
1 TATTCAATTTAAGCTTCATATTTAAAATT
* * *
284344 TCTTCAATTT-AG-TCCAAATATAATGTTACAATT
1 TATTCAATTTAAGCTTC----AT-AT-TTAAAATT
284377 TATT-AATTTAAGCTTCATATTTAAAATT
1 TATTCAATTTAAGCTTCATATTTAAAATT
*
284405 TGTTCAATTTA
1 TATTCAATTTA
284416 TCCTTATATA
Statistics
Matches: 55, Mismatches: 7, Indels: 19
0.68 0.09 0.23
Matches are distributed among these distances:
27 2 0.04
28 15 0.27
29 13 0.24
30 2 0.04
31 2 0.04
32 7 0.13
33 12 0.22
34 2 0.04
ACGTcount: A:0.37, C:0.10, G:0.05, T:0.48
Consensus pattern (29 bp):
TATTCAATTTAAGCTTCATATTTAAAATT
Found at i:284381 original size:61 final size:60
Alignment explanation
Indices: 284276--284415 Score: 201
Period size: 61 Copynumber: 2.3 Consensus size: 60
284266 TGTTCTTACT
* *
284276 TTTAAAA-TTTTCAATTTAGTCCAAATTTAACAATGCAATGTATTAATTTAAGCTTCATA
1 TTTAAAATTTTTCAATTTAGTCCAAATATAACAATACAATGTATTAATTTAAGCTTCATA
*** *
284335 TTTAAAATTTCTTCAATTTAGTCCAAATATAATGTTACAATTTATTAATTTAAGCTTCATA
1 TTTAAAATTT-TTCAATTTAGTCCAAATATAACAATACAATGTATTAATTTAAGCTTCATA
284396 TTTAAAATTTGTTCAATTTA
1 TTTAAAATTT-TTCAATTTA
284416 TCCTTATATA
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
59 7 0.10
60 2 0.03
61 63 0.88
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.46
Consensus pattern (60 bp):
TTTAAAATTTTTCAATTTAGTCCAAATATAACAATACAATGTATTAATTTAAGCTTCATA
Found at i:284539 original size:13 final size:13
Alignment explanation
Indices: 284523--284553 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
284513 TGTATATACC
284523 ATATACTTTATAT
1 ATATACTTTATAT
284536 ATATACTTTATAT
1 ATATACTTTATAT
284549 ATATA
1 ATATA
284554 GTTAATATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (13 bp):
ATATACTTTATAT
Found at i:284561 original size:13 final size:13
Alignment explanation
Indices: 284523--284561 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
284513 TGTATATACC
*
284523 ATATACTTTATAT
1 ATATACTTAATAT
*
284536 ATATACTTTATAT
1 ATATACTTAATAT
*
284549 ATATAGTTAATAT
1 ATATACTTAATAT
284562 GTAAACTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (13 bp):
ATATACTTAATAT
Found at i:284705 original size:18 final size:18
Alignment explanation
Indices: 284665--284698 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
284655 TATATACTTT
284665 GAAT-TTATATAGTATAA
1 GAATATTATATAGTATAA
*
284682 GTATATTATATAGTATA
1 GAATATTATATAGTATA
284699 TAAATATCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 3 0.20
18 12 0.80
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (18 bp):
GAATATTATATAGTATAA
Found at i:284714 original size:28 final size:27
Alignment explanation
Indices: 284683--284756 Score: 112
Period size: 28 Copynumber: 2.7 Consensus size: 27
284673 ATAGTATAAG
*
284683 TATATTATATAGTATATAAATATCAAAC
1 TATAGTATATAGTATATAAATATC-AAC
*
284711 TATAGTATATACTATATAAATATCAAC
1 TATAGTATATAGTATATAAATATCAAC
284738 TATAGTATATAGTTATATA
1 TATAGTATATAG-TATATA
284757 TATGGTTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
27 14 0.33
28 28 0.67
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.41
Consensus pattern (27 bp):
TATAGTATATAGTATATAAATATCAAC
Found at i:284821 original size:18 final size:18
Alignment explanation
Indices: 284798--284833 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
284788 TATACTAGTA
* *
284798 AATATAGTTTATATATAT
1 AATATAGTATATAAATAT
284816 AATATAGTATATAAATAT
1 AATATAGTATATAAATAT
284834 CAACTATGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (18 bp):
AATATAGTATATAAATAT
Found at i:284926 original size:24 final size:24
Alignment explanation
Indices: 284899--284972 Score: 132
Period size: 24 Copynumber: 3.1 Consensus size: 24
284889 ATAAATAGTT
284899 TATATAGTTCACTATTAAACTATA
1 TATATAGTTCACTATTAAACTATA
284923 TATATAGTTCACTATTAAACTATA
1 TATATAGTTCACTATTAAACTATA
284947 TATATAGTTCA-TATATAAACTATA
1 TATATAGTTCACTAT-TAAACTATA
284971 TA
1 TA
284973 ATTTATATAA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
23 3 0.06
24 46 0.94
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.42
Consensus pattern (24 bp):
TATATAGTTCACTATTAAACTATA
Found at i:285007 original size:24 final size:23
Alignment explanation
Indices: 284899--285002 Score: 128
Period size: 24 Copynumber: 4.6 Consensus size: 23
284889 ATAAATAGTT
284899 TATATAGTTCACTATTAAACTATA
1 TATATAGTTCA-TATTAAACTATA
284923 TATATAGTTCACTATTAAACTATA
1 TATATAGTTCA-TATTAAACTATA
284947 TATATAGTTCATATATAAACTATA
1 TATATAGTTCATAT-TAAACTATA
**
284971 TA-AT--TT-ATA-TAATTTATA
1 TATATAGTTCATATTAAACTATA
284989 TATATAGTTCATAT
1 TATATAGTTCATAT
285003 GTAATAATGT
Statistics
Matches: 72, Mismatches: 2, Indels: 13
0.83 0.02 0.15
Matches are distributed among these distances:
18 9 0.12
19 2 0.03
20 3 0.04
21 4 0.06
22 3 0.04
23 5 0.07
24 46 0.64
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (23 bp):
TATATAGTTCATATTAAACTATA
Found at i:285024 original size:2 final size:2
Alignment explanation
Indices: 285017--285142 Score: 57
Period size: 2 Copynumber: 61.0 Consensus size: 2
285007 TAATGTAAAC
* *
285017 TA TA TA TA T- TA TA TA GTA TA TA AA TA TCA -A CTA TA GTA CA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA T-A TA -TA TA -TA TA TA
* * *
285059 GTT TA TA TA TA TA TA -A T- TCA TA TG TA AA T- TA TA TA GTA TA
1 -TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA -TA TA
* *
285099 TA TA CTT TA TA TA TA TA TA GTT TA TA TA TA TA T- TA TA TA CTA
1 TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA
285141 TA
1 TA
285143 AAAATAGTTT
Statistics
Matches: 94, Mismatches: 14, Indels: 32
0.67 0.10 0.23
Matches are distributed among these distances:
1 6 0.06
2 74 0.79
3 14 0.15
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.47
Consensus pattern (2 bp):
TA
Found at i:285038 original size:9 final size:8
Alignment explanation
Indices: 285017--285142 Score: 57
Period size: 9 Copynumber: 15.2 Consensus size: 8
285007 TAATGTAAAC
285017 TATATATA
1 TATATATA
285025 T-TATATA
1 TATATATA
*
285032 GTATATAAA
1 -TATATATA
285041 TATCA-ACTA
1 TAT-ATA-TA
*
285050 TAGTACATA
1 TA-TATATA
*
285059 GTTTATATA
1 -TATATATA
285068 TATATA-A
1 TATATATA
*
285075 T-TCATATG
1 TAT-ATATA
*
285083 TAAAT-TA
1 TATATATA
285090 TATAGTATA
1 TATA-TATA
*
285099 TATACTTTA
1 TATA-TATA
285108 TATATATA
1 TATATATA
*
285116 TAGTTTATA
1 TA-TATATA
285125 TATATAT-
1 TATATATA
285132 TATATACTA
1 TATATA-TA
285141 TA
1 TA
285143 AAAATAGTTT
Statistics
Matches: 89, Mismatches: 14, Indels: 29
0.67 0.11 0.22
Matches are distributed among these distances:
6 1 0.01
7 21 0.24
8 25 0.28
9 39 0.44
10 3 0.03
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.47
Consensus pattern (8 bp):
TATATATA
Done.