Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004540.1 Hibiscus syriacus cultivar Beakdansim tig00010050_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: 429677
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:334015 original size:14 final size:14
Alignment explanation
Indices: 333996--334031 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
333986 ATTGTTTAAT
333996 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
* *
334010 TGATTTGTAGAAGT
1 TGATTTGTAAAAGG
334024 TGATTTGT
1 TGATTTGT
334032 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:334162 original size:19 final size:18
Alignment explanation
Indices: 334138--334194 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
334128 AAAAAGTACT
334138 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
334157 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
334171 ATCGCAACGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
334190 ATCGC
1 ATCGC
334195 GTTGCGATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
14 10 0.32
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 15 0.48
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:334213 original size:19 final size:19
Alignment explanation
Indices: 334191--334274 Score: 61
Period size: 19 Copynumber: 4.6 Consensus size: 19
334181 GAAATGAAAA
334191 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
334210 TCGCATTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
334224 TCTCGTTTCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* ** *
334243 TCGCATTGCGATAGTAATTT
1 TCGCGTTGCGATTTTCA-TT
334263 TCGCGTTGCGAT
1 TCGCGTTGCGAT
334275 AGACATTAAG
Statistics
Matches: 48, Mismatches: 11, Indels: 11
0.69 0.16 0.16
Matches are distributed among these distances:
14 8 0.17
16 3 0.06
17 3 0.06
19 21 0.44
20 13 0.27
ACGTcount: A:0.14, C:0.21, G:0.20, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:336558 original size:12 final size:12
Alignment explanation
Indices: 336541--336577 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
336531 TCTTCGGGGA
336541 CTTTTTCTTCTT
1 CTTTTTCTTCTT
336553 CTTTTTCTTCTT
1 CTTTTTCTTCTT
336565 CTTTTTCTTCTT
1 CTTTTTCTTCTT
336577 C
1 C
336578 AGGATTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:336816 original size:24 final size:24
Alignment explanation
Indices: 336765--336819 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
336755 AAAATCTGAG
* **
336765 TATTGACCAATATCAAAGTCCGGG
1 TATTGACCAAGATCAAAGTCCGAA
* *
336789 TATTGACCAAGATCAAATTTCGAA
1 TATTGACCAAGATCAAAGTCCGAA
336813 TATTGAC
1 TATTGAC
336820 TAGTACTCAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.29
Consensus pattern (24 bp):
TATTGACCAAGATCAAAGTCCGAA
Found at i:337615 original size:20 final size:21
Alignment explanation
Indices: 337590--337641 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
337580 TTTTCCTAAT
*
337590 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
337610 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
337631 TCGCAATGCGA
1 TCGCAATGCGA
337642 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:337663 original size:20 final size:20
Alignment explanation
Indices: 337630--337708 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 20
337620 AATTTGGAAA
* *
337630 ATCGCAATGCGATACTGACT
1 ATCGCAACGAGATACTGACT
* *
337650 ATCGCAACGAGATAAT-ACAAA
1 ATCGCAACGAGATACTGAC--T
*
337671 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATACTGACT
* *
337691 TTCGCAACGAGATTCTGA
1 ATCGCAACGAGATACTGA
337709 AAATCACAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
19 2 0.04
20 30 0.62
21 14 0.29
22 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGAGATACTGACT
Found at i:338025 original size:20 final size:20
Alignment explanation
Indices: 337931--338018 Score: 106
Period size: 20 Copynumber: 4.4 Consensus size: 20
337921 TAACGGGGAA
337931 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
*
337951 ATCGCAACGCGAAAATGTCT
1 ATCGCAACGCGAAAATGGCT
** ***
337971 ATCGCAATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
337991 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
338011 ATCGCAAC
1 ATCGCAAC
338019 TAGAAAACCG
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
19 5 0.09
20 45 0.82
21 5 0.09
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:338069 original size:14 final size:14
Alignment explanation
Indices: 338050--338103 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
338040 GAAAATCGCA
338050 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
338064 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
338081 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
338097 TTGCGAT
1 TTGCGAT
338104 AGTCAGTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:338069 original size:33 final size:33
Alignment explanation
Indices: 338032--338102 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
338022 AAAACCGTAA
338032 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
338065 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
338098 TGCGA
1 TGCGA
338103 TAGTCAGTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:338249 original size:14 final size:15
Alignment explanation
Indices: 338230--338267 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
338220 CATCAATTAA
338230 ACAAATCAAT-ATTT
1 ACAAATCAATCATTT
*
338244 ACAAATC-ATCTTTT
1 ACAAATCAATCATTT
338258 ACAAATCAAT
1 ACAAATCAAT
338268 TAAACAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 2 0.10
14 17 0.81
15 2 0.10
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.34
Consensus pattern (15 bp):
ACAAATCAATCATTT
Found at i:340209 original size:14 final size:14
Alignment explanation
Indices: 340190--340247 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
340180 ATGCGAAATG
340190 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
340204 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
340220 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
340236 AAAATCGCAACG
1 AAAATCGCAACG
340248 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:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:340232 original size:32 final size:33
Alignment explanation
Indices: 340174--340252 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
340164 GGAAATGGCT
340174 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
340207 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
340239 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
340253 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 29 0.64
33 16 0.36
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:340300 original size:14 final size:14
Alignment explanation
Indices: 340281--340338 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
340271 TTTCATTTCG
340281 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
340295 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
340311 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
340327 CGTTGCGATTTT
1 CGTTGCGATTTT
340339 CATTTCGCAT
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:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:340345 original size:33 final size:33
Alignment explanation
Indices: 340264--340354 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
340254 ACAAATCGCA
*
340264 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
340297 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
340329 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
340355 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:340390 original size:20 final size:20
Alignment explanation
Indices: 340339--340382 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
340329 TTGCGATTTT
* *
340339 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGTGATAGC
*
340358 CATTTCCGCGTTGTGATAGT
1 CATTTCCGCGTTGTGATAGC
340378 CATTT
1 CATTT
340383 TCGTGTTGCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.39
Consensus pattern (20 bp):
CATTTCCGCGTTGTGATAGC
Found at i:340901 original size:18 final size:18
Alignment explanation
Indices: 340875--340919 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
340865 GTCGATCAGA
*
340875 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
340893 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
340911 TGATGGCTC
1 TGATGGCTC
340920 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:342287 original size:20 final size:20
Alignment explanation
Indices: 342239--342297 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
342229 AATAGTTTCT
* *
342239 GAAAATGAAAATCGCAACAC
1 GAAAATGACAATCGCAACGC
342259 GAAAATGACAATCGCAACGC
1 GAAAATGACAATCGCAACGC
** *
342279 GAATTTGACTATCGCAACG
1 GAAAATGACAATCGCAACG
342298 AGAGAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (20 bp):
GAAAATGACAATCGCAACGC
Found at i:342573 original size:22 final size:22
Alignment explanation
Indices: 342546--342589 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
342536 GATGGAGATA
342546 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
342568 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
342590 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:342863 original size:61 final size:61
Alignment explanation
Indices: 342757--342894 Score: 186
Period size: 61 Copynumber: 2.3 Consensus size: 61
342747 CGCTTTGAAA
* * * *
342757 ATCGCATTGCGATTATGTATTATCGCGTTACGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTACGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * * *
342818 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTACGAAAGTAAGAATCGCATTGCGAAAGTCAGT
342879 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
342895 CCCAATTCGC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTACGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:342891 original size:20 final size:20
Alignment explanation
Indices: 342757--342891 Score: 112
Period size: 20 Copynumber: 6.7 Consensus size: 20
342747 CGCTTTGAAA
*
342757 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * * *
342778 ATCGCGTTACGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
342798 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
342818 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
342839 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
342859 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
342879 ATCGCATTGCGAT
1 ATCGCATTGCGAT
342892 TTTCCCAATT
Statistics
Matches: 94, Mismatches: 16, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
19 5 0.05
20 65 0.69
21 22 0.23
22 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:342910 original size:61 final size:61
Alignment explanation
Indices: 342757--342912 Score: 152
Period size: 61 Copynumber: 2.6 Consensus size: 61
342747 CGCTTTGAAA
* ** * * * * *
342757 ATCGCATTGCGATTATGTATTATCGCGTTACGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
* * ** * * * *
342818 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
342879 ATCGCATTGCGATTTTCCCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGATTTT-CCAATATCGCGTTGCGAT
342913 TTACTTATTC
Statistics
Matches: 78, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
61 76 0.97
62 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (61 bp):
ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:342981 original size:21 final size:21
Alignment explanation
Indices: 342941--342981 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
342931 AATTGGGAAA
** *
342941 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
342962 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
342982 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:346707 original size:21 final size:22
Alignment explanation
Indices: 346683--346727 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
346673 TAAGGATTTT
346683 TATT-TTTATATTATT-AAAATA
1 TATTCTTTA-ATTATTAAAAATA
346704 TATTCTTTAATTATTAAAAATA
1 TATTCTTTAATTATTAAAAATA
346726 TA
1 TA
346728 AAAATATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
TATTCTTTAATTATTAAAAATA
Found at i:346765 original size:40 final size:42
Alignment explanation
Indices: 346699--346795 Score: 121
Period size: 40 Copynumber: 2.4 Consensus size: 42
346689 TATATTATTA
* *
346699 AAATATATT-CTTTAATTATTAAAAATATAA-AAATATAATAT
1 AAATATATTATTTTAATAATTAAAAATATAATAAATA-AATAT
* *
346740 -AAT-TATTATTTTAATAATTACAAATATAATAAATAATTAT
1 AAATATATTATTTTAATAATTAAAAATATAATAAATAAATAT
346780 AAATATATTATTTTAA
1 AAATATATTATTTTAA
346796 AATATTAATA
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
39 4 0.08
40 25 0.52
41 8 0.17
42 11 0.23
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (42 bp):
AAATATATTATTTTAATAATTAAAAATATAATAAATAAATAT
Found at i:347969 original size:23 final size:23
Alignment explanation
Indices: 347937--347990 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
347927 TAATTATTAA
*
347937 GTGGGGATATATATGGGTTACAC
1 GTGGGAATATATATGGGTTACAC
347960 GTGGGAATATATATGGGTTACAC
1 GTGGGAATATATATGGGTTACAC
347983 GTGGGAAT
1 GTGGGAAT
347991 GAAGGAGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.28, C:0.07, G:0.35, T:0.30
Consensus pattern (23 bp):
GTGGGAATATATATGGGTTACAC
Found at i:348560 original size:21 final size:21
Alignment explanation
Indices: 348497--348553 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
348487 TTTATGGGTT
*
348497 ATGTGCATCGATGCATCTTCA
1 ATGTGTATCGATGCATCTTCA
348518 ATGTGTATCGATGCATCTTCA
1 ATGTGTATCGATGCATCTTCA
348539 ATGTGTATCGATGCA
1 ATGTGTATCGATGCA
348554 CTCTCAAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (21 bp):
ATGTGTATCGATGCATCTTCA
Found at i:348595 original size:44 final size:44
Alignment explanation
Indices: 348545--348641 Score: 108
Period size: 44 Copynumber: 2.2 Consensus size: 44
348535 TTCAATGTGT
*
348545 ATCGATGCA-CTCTCA-AATAAATGAACATCGAATGCAATTAGTGC
1 ATCGATGCACCCCTCAGAATAAA--AACATCGAATGCAATTAGTGC
* ** * *
348589 ATCGATGCACCCCTTAGAATAAAAACATCGAATGTGATTTGTGT
1 ATCGATGCACCCCTCAGAATAAAAACATCGAATGCAATTAGTGC
348633 ATCGATGCA
1 ATCGATGCA
348642 TAGTTAGTGC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
44 35 0.78
45 4 0.09
46 6 0.13
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.27
Consensus pattern (44 bp):
ATCGATGCACCCCTCAGAATAAAAACATCGAATGCAATTAGTGC
Found at i:348774 original size:14 final size:14
Alignment explanation
Indices: 348755--348793 Score: 78
Period size: 14 Copynumber: 2.8 Consensus size: 14
348745 AAGGAGTGAG
348755 CAATTAGAATATAT
1 CAATTAGAATATAT
348769 CAATTAGAATATAT
1 CAATTAGAATATAT
348783 CAATTAGAATA
1 CAATTAGAATA
348794 CTAATATGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.33
Consensus pattern (14 bp):
CAATTAGAATATAT
Found at i:349455 original size:18 final size:18
Alignment explanation
Indices: 349432--349480 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
349422 TTTTACGTGA
*
349432 TCCTTCAGGACATAGTGG
1 TCCTTCGGGACATAGTGG
349450 TCCTTCGGGACATAGTGG
1 TCCTTCGGGACATAGTGG
349468 TCCTTCGGGACAT
1 TCCTTCGGGACAT
349481 TTCATAGTGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.18, C:0.24, G:0.29, T:0.29
Consensus pattern (18 bp):
TCCTTCGGGACATAGTGG
Found at i:349490 original size:23 final size:20
Alignment explanation
Indices: 349441--349502 Score: 83
Period size: 23 Copynumber: 3.0 Consensus size: 20
349431 ATCCTTCAGG
349441 ACATAGTGGTCCTTCGGG--
1 ACATAGTGGTCCTTCGGGAC
349459 ACATAGTGGTCCTTCGGGAC
1 ACATAGTGGTCCTTCGGGAC
349479 ATTTCATAGTGGTCCTTCGGGAC
1 A---CATAGTGGTCCTTCGGGAC
349502 A
1 A
349503 AATTCATATG
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
18 18 0.46
20 1 0.03
23 20 0.51
ACGTcount: A:0.19, C:0.23, G:0.29, T:0.29
Consensus pattern (20 bp):
ACATAGTGGTCCTTCGGGAC
Found at i:360322 original size:62 final size:62
Alignment explanation
Indices: 360202--360326 Score: 198
Period size: 62 Copynumber: 2.0 Consensus size: 62
360192 AGGGTCGAGG
* * *
360202 GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACTGATTACCTAGGTTCTTCGGAACATATGGACT
*
360264 GTTTACCTATGTTCTTCGGGACATATGGACTGATTACCTAGGTTCTTTGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACTGATTACCTAGGTTCTTCGGAA-CATATGGACT
360326 G
1 G
360327 GTCCTTCGGG
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
62 57 0.98
63 1 0.02
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.38
Consensus pattern (62 bp):
GTTTACCTATGTTCTTCGGGACATATGGACTGATTACCTAGGTTCTTCGGAACATATGGACT
Found at i:360326 original size:31 final size:31
Alignment explanation
Indices: 360202--360310 Score: 200
Period size: 31 Copynumber: 3.5 Consensus size: 31
360192 AGGGTCGAGG
360202 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
360233 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
360264 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
360295 GATTACCTAGGTTCTT
1 GTTTACCTATGTTCTT
360311 TGGAATCTAT
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 76 1.00
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:369074 original size:2 final size:2
Alignment explanation
Indices: 369067--369120 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
369057 TAATGGAGGT
369067 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
369109 TA TA TA TA TA TA
1 TA TA TA TA TA TA
369121 GTCATCGACA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:369207 original size:2 final size:2
Alignment explanation
Indices: 369200--369225 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
369190 ATTTATGTGG
369200 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
369226 GAATTGTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:371870 original size:99 final size:99
Alignment explanation
Indices: 371752--371950 Score: 398
Period size: 99 Copynumber: 2.0 Consensus size: 99
371742 TGTGTTCGAG
371752 ACTCTTTATCTATATGCTGAAAAGATAAGCTAAATACACCCGGAAATAACACATTAGATACGAGT
1 ACTCTTTATCTATATGCTGAAAAGATAAGCTAAATACACCCGGAAATAACACATTAGATACGAGT
371817 TAACTGTTTTTAACGGTAAGAATAATCACTACGA
66 TAACTGTTTTTAACGGTAAGAATAATCACTACGA
371851 ACTCTTTATCTATATGCTGAAAAGATAAGCTAAATACACCCGGAAATAACACATTAGATACGAGT
1 ACTCTTTATCTATATGCTGAAAAGATAAGCTAAATACACCCGGAAATAACACATTAGATACGAGT
371916 TAACTGTTTTTAACGGTAAGAATAATCACTACGA
66 TAACTGTTTTTAACGGTAAGAATAATCACTACGA
371950 A
1 A
371951 GTTACATTGA
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
99 100 1.00
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (99 bp):
ACTCTTTATCTATATGCTGAAAAGATAAGCTAAATACACCCGGAAATAACACATTAGATACGAGT
TAACTGTTTTTAACGGTAAGAATAATCACTACGA
Found at i:377298 original size:32 final size:32
Alignment explanation
Indices: 377252--377315 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
377242 GAAAGACCGT
*
377252 TGATGAATCGGATTAATGGCGGTCACTACCAC
1 TGATGAATCAGATTAATGGCGGTCACTACCAC
*
377284 TGATGAATCAGATTAATGGTGGTCACTACCAC
1 TGATGAATCAGATTAATGGCGGTCACTACCAC
377316 AACCATGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (32 bp):
TGATGAATCAGATTAATGGCGGTCACTACCAC
Found at i:380058 original size:27 final size:27
Alignment explanation
Indices: 380018--380091 Score: 139
Period size: 27 Copynumber: 2.7 Consensus size: 27
380008 CTTAACCTAC
380018 TTTTACTTTCTCTTTATCATTATTTAG
1 TTTTACTTTCTCTTTATCATTATTTAG
*
380045 TTTTACTTTTTCTTTATCATTATTTAG
1 TTTTACTTTCTCTTTATCATTATTTAG
380072 TTTTACTTTCTCTTTATCAT
1 TTTTACTTTCTCTTTATCAT
380092 ATATATATAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.18, C:0.15, G:0.03, T:0.65
Consensus pattern (27 bp):
TTTTACTTTCTCTTTATCATTATTTAG
Found at i:381328 original size:15 final size:14
Alignment explanation
Indices: 381304--381356 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 14
381294 ATCTTAAATC
*
381304 AATTTCAATATAAA
1 AATTTAAATATAAA
381318 ATATTTAAATATTCAAA
1 A-ATTTAAATA-T-AAA
*
381335 AAATTAAATATAAA
1 AATTTAAATATAAA
381349 AA-TTAAAT
1 AATTTAAAT
381357 TACAAAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
13 6 0.18
14 6 0.18
15 9 0.26
16 9 0.26
17 4 0.12
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (14 bp):
AATTTAAATATAAA
Found at i:381348 original size:31 final size:27
Alignment explanation
Indices: 381310--381371 Score: 79
Period size: 31 Copynumber: 2.1 Consensus size: 27
381300 AATCAATTTC
*
381310 AATATAAAATATTTAAATATTCAAAAAATTA
1 AATATAAAA-A-TTAAAT-TACAAAAAA-TA
381341 AATATAAAAATTAAATTACAAAAAATA
1 AATATAAAAATTAAATTACAAAAAATA
381368 AATA
1 AATA
381372 CATATTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 6 0.20
28 8 0.27
29 6 0.20
30 1 0.03
31 9 0.30
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (27 bp):
AATATAAAAATTAAATTACAAAAAATA
Found at i:381351 original size:13 final size:13
Alignment explanation
Indices: 381310--381371 Score: 52
Period size: 13 Copynumber: 4.3 Consensus size: 13
381300 AATCAATTTC
381310 AATATAAAATATTTA
1 AATATAAAA-A-TTA
381325 AATATTCAAAAAATTA
1 AATA-T--AAAAATTA
381341 AATATAAAAATTA
1 AATATAAAAATTA
* *
381354 AATTACAAAAAATA
1 AA-TATAAAAATTA
381368 AATA
1 AATA
381372 CATATTAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
13 12 0.29
14 11 0.27
15 5 0.12
16 8 0.20
17 1 0.02
18 4 0.10
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (13 bp):
AATATAAAAATTA
Found at i:381363 original size:14 final size:14
Alignment explanation
Indices: 381333--381370 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
381323 TAAATATTCA
*
381333 AAAAATTAAA-TAT
1 AAAAATTAAATTAC
381346 AAAAATTAAATTAC
1 AAAAATTAAATTAC
*
381360 AAAAAATAAAT
1 AAAAATTAAAT
381371 ACATATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAAATTAAATTAC
Found at i:381373 original size:13 final size:13
Alignment explanation
Indices: 381331--381373 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
381321 TTTAAATATT
381331 CAAAAAATTAAATA
1 CAAAAAA-TAAATA
* *
381345 TAAAAATTAAATTA
1 CAAAAAATAAA-TA
381359 CAAAAAATAAATA
1 CAAAAAATAAATA
381372 CA
1 CA
381374 TATTAAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
13 8 0.33
14 16 0.67
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (13 bp):
CAAAAAATAAATA
Found at i:381843 original size:31 final size:30
Alignment explanation
Indices: 381755--381845 Score: 80
Period size: 36 Copynumber: 2.9 Consensus size: 30
381745 TATCTACAAA
*
381755 TTTAT-AAATAAAAAT-ATA-AGATTATAT
1 TTTATAAAATAAAAATAATATATATTATAT
*
381782 TTTATTAAAATAAAATTATTATAAACTATATTAGTAT
1 TTTA-TAAAATAAAA--A-TA-ATA-TATATTA-TAT
381819 TTTATAAAATAAAAATAATATATATTA
1 TTTATAAAATAAAAATAATATATATTA
381846 ATTATATTAA
Statistics
Matches: 51, Mismatches: 3, Indels: 16
0.73 0.04 0.23
Matches are distributed among these distances:
27 4 0.08
28 1 0.02
29 8 0.16
31 8 0.16
32 3 0.06
33 2 0.04
34 3 0.06
36 15 0.29
37 7 0.14
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (30 bp):
TTTATAAAATAAAAATAATATATATTATAT
Found at i:381884 original size:19 final size:19
Alignment explanation
Indices: 381860--381914 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
381850 TATTAATTAC
381860 TTATTAAAATAAAAAATAA
1 TTATTAAAATAAAAAATAA
* *
381879 TTATTAAAATATTAAAATTA
1 TTATTAAAATA-AAAAATAA
381899 TATATTAAAATAAAAA
1 T-TATTAAAATAAAAA
381915 TATTATATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 11 0.35
20 10 0.32
21 10 0.32
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
TTATTAAAATAAAAAATAA
Found at i:381921 original size:19 final size:19
Alignment explanation
Indices: 381861--381924 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
381851 ATTAATTACT
*
381861 TATTAAAATAAAAA-ATAA
1 TATTAAAATAAAAATATTA
381879 TTATTAAAATATTAAAAT-TATA
1 -TATTAAAATA--AAAATAT-TA
381901 TATTAAAATAAAAATATTA
1 TATTAAAATAAAAATATTA
381920 TATTA
1 TATTA
381925 TATTTTAAGG
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
19 22 0.56
20 1 0.03
21 15 0.38
22 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TATTAAAATAAAAATATTA
Found at i:381924 original size:40 final size:39
Alignment explanation
Indices: 381783--381924 Score: 113
Period size: 40 Copynumber: 3.6 Consensus size: 39
381773 AGATTATATT
*
381783 TTATTAAAATAAAATTATTATA--AACT-ATATTAGTATT--
1 TTATTAAAATAAAAATATTATATTAA-TAATATTA--ATTAC
*
381820 TTA-TAAAATAAAAATAATATATATTAATTATATTAATTAC
1 TTATTAAAATAAAAAT-AT-TATATTAATAATATTAATTAC
*
381860 TTATTAAAATAAAAA-ATAATTATTAA-AATATTAAAATTA-
1 TTATTAAAATAAAAATATTA-TATTAATAATATT--AATTAC
381899 TATATTAAAATAAAAATATTATATTA
1 T-TATTAAAATAAAAATATTATATTA
381925 TATTTTAAGG
Statistics
Matches: 88, Mismatches: 4, Indels: 23
0.77 0.03 0.20
Matches are distributed among these distances:
36 11 0.12
37 5 0.06
38 13 0.15
39 10 0.11
40 35 0.40
41 14 0.16
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (39 bp):
TTATTAAAATAAAAATATTATATTAATAATATTAATTAC
Found at i:382005 original size:22 final size:22
Alignment explanation
Indices: 381980--382090 Score: 92
Period size: 22 Copynumber: 5.2 Consensus size: 22
381970 ATTTTATGAA
*
381980 ATTAATAAATAATAT-TAATTTT
1 ATTAATAAATAATATAT-ATTAT
* *
382002 ATTAATAATTATTATATATTAT
1 ATTAATAAATAATATATATTAT
**
382024 AAAAATAAA-AATATTATATTAT
1 ATTAATAAATAATA-TATATTAT
382046 ATT-AT-AATAATATA-ATTAT
1 ATTAATAAATAATATATATTAT
*
382065 ATCAAT-AA-AATATAATATTAT
1 ATTAATAAATAATAT-ATATTAT
382086 ATTAA
1 ATTAA
382091 AAAGTATCAA
Statistics
Matches: 72, Mismatches: 11, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
19 12 0.17
20 9 0.12
21 18 0.25
22 32 0.44
23 1 0.01
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (22 bp):
ATTAATAAATAATATATATTAT
Found at i:382059 original size:40 final size:43
Alignment explanation
Indices: 381983--382089 Score: 116
Period size: 40 Copynumber: 2.5 Consensus size: 43
381973 TTATGAAATT
*
381983 AATAAATAATATTA-ATTTTATTAATAATTAT-TATATATTATAAA
1 AATAAA-AATATTATATTATATT-ATAATTATATATA-ATTATAAA
**
382027 AATAAAAATATTATATTATATTATAA-TA-ATATAATTATATC
1 AATAAAAATATTATATTATATTATAATTATATATAATTATAAA
*
382068 AAT-AAAATATAATATTATATTA
1 AATAAAAATATTATATTATATTA
382090 AAAAGTATCA
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
40 18 0.32
41 9 0.16
42 6 0.11
43 11 0.19
44 13 0.23
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (43 bp):
AATAAAAATATTATATTATATTATAATTATATATAATTATAAA
Found at i:382065 original size:19 final size:19
Alignment explanation
Indices: 382031--382080 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 19
382021 TATAAAAATA
*
382031 AAAATATTATATTATAT-TAT
1 AAAATA-TA-ATTATATCAAT
382051 AATAATATAATTATATCAAT
1 AA-AATATAATTATATCAAT
382071 AAAATATAAT
1 AAAATATAAT
382081 ATTATATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 15 0.56
20 8 0.30
21 4 0.15
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAATATAATTATATCAAT
Found at i:382102 original size:21 final size:21
Alignment explanation
Indices: 382017--382087 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
382007 TAATTATTAT
** *
382017 ATATTATAAAAATAAAAATATT
1 ATATTATATCAAT-AAAATATA
*
382039 ATATTATAT-TATAATAATAT-
1 ATATTATATCAATAA-AATATA
382059 A-ATTATATCAATAAAATATA
1 ATATTATATCAATAAAATATA
382079 ATATTATAT
1 ATATTATAT
382088 TAAAAAGTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
19 12 0.29
20 8 0.19
21 14 0.33
22 8 0.19
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (21 bp):
ATATTATATCAATAAAATATA
Found at i:382563 original size:17 final size:17
Alignment explanation
Indices: 382543--382576 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
382533 GATGATATGA
382543 ATATATATATAATATAT
1 ATATATATATAATATAT
*
382560 ATATATGTATAATATAT
1 ATATATATATAATATAT
382577 TTTAAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
ATATATATATAATATAT
Found at i:382617 original size:20 final size:20
Alignment explanation
Indices: 382567--382640 Score: 57
Period size: 19 Copynumber: 3.9 Consensus size: 20
382557 TATATATATG
* *
382567 TATAATATATTTTAAAAATA
1 TATAATATATTTTAATAATT
* *
382587 T-TGAT-TTTTTTAATAATT
1 TATAATATATTTTAATAATT
* *
382605 TAT-TTATCATTTT-ATAGTT
1 TATAATAT-ATTTTAATAATT
382624 TATAATATATTTTAATA
1 TATAATATATTTTAATA
382641 TCTAAAATTA
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
18 12 0.29
19 18 0.44
20 11 0.27
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (20 bp):
TATAATATATTTTAATAATT
Found at i:382849 original size:22 final size:23
Alignment explanation
Indices: 382810--382852 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
382800 AGTAATTTAA
**
382810 TTTTTAATTTTATATTTTATAAT
1 TTTTTAATACTATATTTTATAAT
382833 TTTTTAATACTAT-TTTTATA
1 TTTTTAATACTATATTTTATA
382853 TTTAACTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTTTAATACTATATTTTATAAT
Found at i:392742 original size:68 final size:69
Alignment explanation
Indices: 392621--392748 Score: 161
Period size: 68 Copynumber: 1.9 Consensus size: 69
392611 GGTAAGGACC
* *
392621 CCATCTTGTTTACTATTTTGAGTTCATCTATGGAGGTTAACTCGAACTCCTCTTC-GGAGGGTTA
1 CCATCATGTTTACTATTTTGAGTTCATCTATCGAGGTTAACTCGAACTCCTCTTCAGGAGGGTTA
392685 GTCT
66 GTCT
* * * ** *
392689 CCATCATGTTTACTGTTTTGAGTTCCTCTA-CGATGGTTAATTCGGGCTTCTCTTCAGGAG
1 CCATCATGTTTACTATTTTGAGTTCATCTATCGA-GGTTAACTCGAACTCCTCTTCAGGAG
392749 ATTAATTTTC
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
67 2 0.04
68 44 0.88
69 4 0.08
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.40
Consensus pattern (69 bp):
CCATCATGTTTACTATTTTGAGTTCATCTATCGAGGTTAACTCGAACTCCTCTTCAGGAGGGTTA
GTCT
Found at i:397292 original size:60 final size:60
Alignment explanation
Indices: 397214--397402 Score: 186
Period size: 60 Copynumber: 3.1 Consensus size: 60
397204 CACATTTTCT
* * * * * **
397214 CAAAAGTATGACTTTTATTTTAAATTGGTCCTTAAATTTTTAAATATTTTAATTTTATCC
1 CAAAACTATGACTATTATTCTAAATTGGTCCTTAAATTTTTGAATATTTCAATTCCATCC
* ** *
397274 TTAAAA-TATGACTATTATTCTAAATTAAT-CTTCAAACTTTTGAATATTTCAATTCCATCC
1 -CAAAACTATGACTATTATTCTAAATTGGTCCTT-AAATTTTTGAATATTTCAATTCCATCC
* * * * *
397334 CAAAACTATGACCATCATTCTAAATTGGTCCCTAAACTTTTTGAATATTCCAATTTCATCC
1 CAAAACTATGACTATTATTCTAAATTGGTCCTTAAA-TTTTTGAATATTTCAATTCCATCC
397395 C-AAACTAT
1 CAAAACTAT
397403 ACATATATAC
Statistics
Matches: 105, Mismatches: 19, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
59 7 0.07
60 70 0.67
61 28 0.27
ACGTcount: A:0.35, C:0.17, G:0.05, T:0.42
Consensus pattern (60 bp):
CAAAACTATGACTATTATTCTAAATTGGTCCTTAAATTTTTGAATATTTCAATTCCATCC
Found at i:397644 original size:59 final size:57
Alignment explanation
Indices: 397534--397692 Score: 158
Period size: 59 Copynumber: 2.7 Consensus size: 57
397524 ATATTTGGGG
* ** * * *
397534 ATGAAATTGGAACATTCAAAAGTTTTGGGAATAATTTAGAAAGAGGGCATAGTTTAGGA
1 ATGAAATT-GAATATTC-AAAGTTTAAGGATTAATTTAGAAAAAAGGCATAGTTTAGGA
* *
397593 ATGAAATTAGAATATTCAAAGTTTAAGGATTAATTTAGAATAAAAGTCATAGTTTATGA
1 ATGAAATT-GAATATTCAAAGTTTAAGGATTAATTTAGAA-AAAAGGCATAGTTTAGGA
* * *
397652 ATGAAATTGAAATATTTAAAAATTTAAGGATCAATTT-GAAA
1 ATGAAATTG-AATA-TTCAAAGTTTAAGGATTAATTTAGAAA
397693 TGAGAGTTAT
Statistics
Matches: 85, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
58 22 0.26
59 44 0.52
60 19 0.22
ACGTcount: A:0.45, C:0.04, G:0.18, T:0.33
Consensus pattern (57 bp):
ATGAAATTGAATATTCAAAGTTTAAGGATTAATTTAGAAAAAAGGCATAGTTTAGGA
Found at i:398303 original size:23 final size:23
Alignment explanation
Indices: 398249--398309 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
398239 TTTGTATTCA
*
398249 ATTCATTTAGTGTTCGTGAAGAT
1 ATTCATTTAATGTTCGTGAAGAT
*
398272 GTTCATTTAATGTTCGTGAATG-T
1 ATTCATTTAATGTTCGTGAA-GAT
*
398295 ATTCGTTTATATGTT
1 ATTCATTTA-ATGTT
398310 TTTCAATATG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
23 26 0.81
24 6 0.19
ACGTcount: A:0.23, C:0.08, G:0.20, T:0.49
Consensus pattern (23 bp):
ATTCATTTAATGTTCGTGAAGAT
Found at i:404261 original size:27 final size:27
Alignment explanation
Indices: 404210--404260 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
404200 TAATTTCATT
404210 TAAAAAAACCCAAAGCTTTTGAAAATC
1 TAAAAAAACCCAAAGCTTTTGAAAATC
*
404237 TAAAAAAGCCCCAAA-C-TTTGAAAA
1 TAAAAAA-ACCCAAAGCTTTTGAAAA
404261 AAATTATTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 8 0.36
27 8 0.36
28 6 0.27
ACGTcount: A:0.53, C:0.20, G:0.08, T:0.20
Consensus pattern (27 bp):
TAAAAAAACCCAAAGCTTTTGAAAATC
Found at i:405780 original size:9 final size:9
Alignment explanation
Indices: 405768--405826 Score: 55
Period size: 9 Copynumber: 6.2 Consensus size: 9
405758 CCTCCACCAG
*
405768 CACCGCCTC
1 CACCACCTC
*
405777 CACCACCTA
1 CACCACCTC
405786 CACCACCTC
1 CACCACCTC
*
405795 CAAAGCCACCAC
1 C--A-CCACCTC
*
405807 CACCACCTG
1 CACCACCTC
405816 CACCACCTC
1 CACCACCTC
405825 CA
1 CA
405827 TGTCCTCCAC
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
9 31 0.77
10 1 0.03
11 1 0.03
12 7 0.17
ACGTcount: A:0.27, C:0.59, G:0.05, T:0.08
Consensus pattern (9 bp):
CACCACCTC
Found at i:405836 original size:24 final size:24
Alignment explanation
Indices: 405809--405910 Score: 71
Period size: 24 Copynumber: 4.2 Consensus size: 24
405799 GCCACCACCA
*
405809 CCACCTGCACCACCTCCATGTCCT
1 CCACCTGCACCACCTCCATGACCT
* *
405833 CCACCTACACCACCACCAAT-ACCT
1 CCACCTGCACCACCTCC-ATGACCT
*** * ** *
405857 CCACCTTTTCCTCCTCCAAAACCA
1 CCACCTGCACCACCTCCATGACCT
* * *
405881 CCGCCAGCACCACCTCCATGTCCT
1 CCACCTGCACCACCTCCATGACCT
405905 CCACCT
1 CCACCT
405911 ATGCCGCCTC
Statistics
Matches: 54, Mismatches: 22, Indels: 4
0.68 0.28 0.05
Matches are distributed among these distances:
23 1 0.02
24 51 0.94
25 2 0.04
ACGTcount: A:0.23, C:0.54, G:0.05, T:0.19
Consensus pattern (24 bp):
CCACCTGCACCACCTCCATGACCT
Found at i:405892 original size:48 final size:48
Alignment explanation
Indices: 405840--405993 Score: 148
Period size: 54 Copynumber: 3.1 Consensus size: 48
405830 CCTCCACCTA
* * *
405840 CACCACCACCAAT-ACCTCCACCTTTTCCTCCTCCAAAACCACCGCCAG
1 CACCACCACC-ATGACCTCCACCTATGCCGCCTCCAAAACCACCGCCAG
* * *
405888 CACCACCTCCATGTCCTCCACCTATGCCGCCTCCAAAGCCGCCGCCACCGCCAG
1 CACCACCACCATGACCTCCACCTATGCCGCCTCCAAA------ACCACCGCCAG
* * * *
405942 CACCACCTCCATGTCCTCCACCTATGCCGCCTCCAAAGCCACCGCCAC
1 CACCACCACCATGACCTCCACCTATGCCGCCTCCAAAACCACCGCCAG
405990 CACC
1 CACC
405994 TGCACCACCT
Statistics
Matches: 92, Mismatches: 7, Indels: 14
0.81 0.06 0.12
Matches are distributed among these distances:
47 2 0.02
48 43 0.47
54 47 0.51
ACGTcount: A:0.22, C:0.54, G:0.10, T:0.14
Consensus pattern (48 bp):
CACCACCACCATGACCTCCACCTATGCCGCCTCCAAAACCACCGCCAG
Found at i:405905 original size:36 final size:36
Alignment explanation
Indices: 405805--405909 Score: 111
Period size: 36 Copynumber: 2.9 Consensus size: 36
405795 CAAAGCCACC
* * *
405805 ACCACCACCTGCACCACCTCCATGTCCTCCACCTAC
1 ACCACCACCAGCACCACCTCCATGTCCTCCACCAAA
** * * * * *
405841 ACCACCACCAATACCTCCACCTTTTCCTCCTCCAAA
1 ACCACCACCAGCACCACCTCCATGTCCTCCACCAAA
*
405877 ACCACCGCCAGCACCACCTCCATGTCCTCCACC
1 ACCACCACCAGCACCACCTCCATGTCCTCCACC
405910 TATGCCGCCT
Statistics
Matches: 51, Mismatches: 18, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.24, C:0.54, G:0.05, T:0.17
Consensus pattern (36 bp):
ACCACCACCAGCACCACCTCCATGTCCTCCACCAAA
Found at i:405941 original size:54 final size:54
Alignment explanation
Indices: 405878--406019 Score: 257
Period size: 54 Copynumber: 2.6 Consensus size: 54
405868 TCCTCCAAAA
*
405878 CCACCGCCAGCACCACCTCCATGTCCTCCACCTATGCCGCCTCCAAAGCCGCCG
1 CCACCGCCAGCACCACCTCCATGTCCTCCACCTATGCCGCCTCCAAAGCCACCG
405932 CCACCGCCAGCACCACCTCCATGTCCTCCACCTATGCCGCCTCCAAAGCCACCG
1 CCACCGCCAGCACCACCTCCATGTCCTCCACCTATGCCGCCTCCAAAGCCACCG
* *
405986 CCACCACCTGCACCACCTCCATGTCCTCCACCTA
1 CCACCGCCAGCACCACCTCCATGTCCTCCACCTA
406020 CACCACCACC
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 85 1.00
ACGTcount: A:0.20, C:0.54, G:0.12, T:0.14
Consensus pattern (54 bp):
CCACCGCCAGCACCACCTCCATGTCCTCCACCTATGCCGCCTCCAAAGCCACCG
Found at i:406023 original size:24 final size:24
Alignment explanation
Indices: 405989--406582 Score: 269
Period size: 24 Copynumber: 24.6 Consensus size: 24
405979 GCCACCGCCA
*
405989 CCACCTGCACCACCTCCATGTCCT
1 CCACCTACACCACCTCCATGTCCT
*
406013 CCACCTACACCACCACCAATG-CCT
1 CCACCTACACCACCTCC-ATGTCCT
** * *** *
406037 CCACC-ATTTCCTCCTCCAAAACCA
1 CCACCTA-CACCACCTCCATGTCCT
*
406061 CCGCC-ACACCACCTCCATGTCCT
1 CCACCTACACCACCTCCATGTCCT
** * * *
406084 CCACCTATGCCGCCTCCAAAG-CCA
1 CCACCTACACCACCTCC-ATGTCCT
* *
406108 CCGCCTGCACCACCTCCATGTCCT
1 CCACCTACACCACCTCCATGTCCT
*
406132 CCACCTACACCACCACCAATG-CCT
1 CCACCTACACCACCTCC-ATGTCCT
** * *** *
406156 CCACCT-TTCCTCCTCCAAAACCA
1 CCACCTACACCACCTCCATGTCCT
* *
406179 CCGCCAACACCACCTCCATGTCCT
1 CCACCTACACCACCTCCATGTCCT
** * * *
406203 CCACCTATGCCGCCTCCAAAG-CCA
1 CCACCTACACCACCTCC-ATGTCCT
* *
406227 CCGCCTGCACCACCTCCATGTCCT
1 CCACCTACACCACCTCCATGTCCT
*
406251 CCACCTACACCACCACCAATG-CCT
1 CCACCTACACCACCTCC-ATGTCCT
*** * *** *
406275 CCACCTTTTCCTCCTCCAAAACCA
1 CCACCTACACCACCTCCATGTCCT
* *
406299 CCGCCAACACCACCTCCATGTCCT
1 CCACCTACACCACCTCCATGTCCT
** * * *
406323 CCACCTATGCCGCCTCCAAAG-CCA
1 CCACCTACACCACCTCC-ATGTCCT
* *
406347 CCGCCTGCACCACCTCCATGTCCT
1 CCACCTACACCACCTCCATGTCCT
*
406371 CCACCTACACCACCACCAATG-CCT
1 CCACCTACACCACCTCC-ATGTCCT
*** * *** *
406395 CCACCTTTTCCTCCTCCAAAACCA
1 CCACCTACACCACCTCCATGTCCT
*
406419 CCGCC-AGCACCACCTCCATGTCCT
1 CCACCTA-CACCACCTCCATGTCCT
* *
406443 CCACCTACACCACCACCAAT-ACCT
1 CCACCTACACCACCTCC-ATGTCCT
*** * *
406467 CCACCTTTTCCTCCTCCAAT-ACCT
1 CCACCTACACCACCTCC-ATGTCCT
* *
406491 CCACCAACTCCACCTCCATGTCCT
1 CCACCTACACCACCTCCATGTCCT
* *
406515 CCACCTACACCACCACCAATACCTCCT
1 CCACCTACACCACCTCC-AT--GTCCT
* *
406542 CCACCACCTGCACCACCTCCGTGTCCT
1 ---CCACCTACACCACCTCCATGTCCT
406569 CCACCTACACCACC
1 CCACCTACACCACC
406583 GCCAGCTCCG
Statistics
Matches: 403, Mismatches: 140, Indels: 54
0.68 0.23 0.09
Matches are distributed among these distances:
22 1 0.00
23 38 0.09
24 317 0.79
25 23 0.06
27 8 0.02
29 1 0.00
30 15 0.04
ACGTcount: A:0.23, C:0.53, G:0.06, T:0.18
Consensus pattern (24 bp):
CCACCTACACCACCTCCATGTCCT
Found at i:406374 original size:120 final size:120
Alignment explanation
Indices: 405932--406449 Score: 941
Period size: 120 Copynumber: 4.3 Consensus size: 120
405922 AAAGCCGCCG
*
405932 CCACCGCCAGCACCACCTCCATGTCCTCCACCTATGCCGCCTCCAAAGCCACCGCCACCACCTGC
1 CCACCGCCAACACCACCTCCATGTCCTCCACCTATGCCGCCTCCAAAGCCACCG------CCTGC
*
405997 ACCACCTCCATGTCCTCCACCTACACCACCACCAATGCCTCCACCATTTCCTCCTCCAAAA
60 ACCACCTCCATGTCCTCCACCTACACCACCACCAATGCCTCCACCTTTTCCTCCTCCAAAA
406058 CCACCGCC-ACACCACCTCCATGTCCTCCACCTATGCCGCCTCCAAAGCCACCGCCTGCACCACC
1 CCACCGCCAACACCACCTCCATGTCCTCCACCTATGCCGCCTCCAAAGCCACCGCCTGCACCACC
406122 TCCATGTCCTCCACCTACACCACCACCAATGCCTCCACC-TTTCCTCCTCCAAAA
66 TCCATGTCCTCCACCTACACCACCACCAATGCCTCCACCTTTTCCTCCTCCAAAA
406176 CCACCGCCAACACCACCTCCATGTCCTCCACCTATGCCGCCTCCAAAGCCACCGCCTGCACCACC
1 CCACCGCCAACACCACCTCCATGTCCTCCACCTATGCCGCCTCCAAAGCCACCGCCTGCACCACC
406241 TCCATGTCCTCCACCTACACCACCACCAATGCCTCCACCTTTTCCTCCTCCAAAA
66 TCCATGTCCTCCACCTACACCACCACCAATGCCTCCACCTTTTCCTCCTCCAAAA
406296 CCACCGCCAACACCACCTCCATGTCCTCCACCTATGCCGCCTCCAAAGCCACCGCCTGCACCACC
1 CCACCGCCAACACCACCTCCATGTCCTCCACCTATGCCGCCTCCAAAGCCACCGCCTGCACCACC
406361 TCCATGTCCTCCACCTACACCACCACCAATGCCTCCACCTTTTCCTCCTCCAAAA
66 TCCATGTCCTCCACCTACACCACCACCAATGCCTCCACCTTTTCCTCCTCCAAAA
*
406416 CCACCGCCAGCACCACCTCCATGTCCTCCACCTA
1 CCACCGCCAACACCACCTCCATGTCCTCCACCTA
406450 CACCACCACC
Statistics
Matches: 388, Mismatches: 2, Indels: 10
0.97 0.00 0.03
Matches are distributed among these distances:
118 23 0.06
119 145 0.37
120 168 0.43
125 44 0.11
126 8 0.02
ACGTcount: A:0.22, C:0.53, G:0.08, T:0.17
Consensus pattern (120 bp):
CCACCGCCAACACCACCTCCATGTCCTCCACCTATGCCGCCTCCAAAGCCACCGCCTGCACCACC
TCCATGTCCTCCACCTACACCACCACCAATGCCTCCACCTTTTCCTCCTCCAAAA
Found at i:406411 original size:48 final size:48
Alignment explanation
Indices: 405989--406582 Score: 303
Period size: 48 Copynumber: 12.3 Consensus size: 48
405979 GCCACCGCCA
* *
405989 CCACCTGCACCACCTCC-ATGTCCTCCACCTACACCACCACCAATG-CCT
1 CCACCTACACCACCTCCAATG-CCTCCACCTACACCACCTCC-ATGTCCT
** * ** * *
406037 CCACC-ATTTCCTCCTCCAAAACCACCGCC-ACACCACCTCCATGTCCT
1 CCACCTA-CACCACCTCCAATGCCTCCACCTACACCACCTCCATGTCCT
** * * * * *
406084 CCACCTATGCCGCCTCCAAAGCCACCGCCTGCACCACCTCCATGTCCT
1 CCACCTACACCACCTCCAATGCCTCCACCTACACCACCTCCATGTCCT
* ** * *** *
406132 CCACCTACACCACCACCAATGCCTCCACCT-TTCCTCCTCCAAAACCA
1 CCACCTACACCACCTCCAATGCCTCCACCTACACCACCTCCATGTCCT
* * ** * * *
406179 CCGCCAACACCACCTCC-ATGTCCTCCACCTATGCCGCCTCCAAAG-CCA
1 CCACCTACACCACCTCCAATG-CCTCCACCTACACCACCTCC-ATGTCCT
* * *
406227 CCGCCTGCACCACCTCC-ATGTCCTCCACCTACACCACCACCAATG-CCT
1 CCACCTACACCACCTCCAATG-CCTCCACCTACACCACCTCC-ATGTCCT
*** * ** * * *
406275 CCACCTTTTCCTCCTCCAAAACCACCGCCAACACCACCTCCATGTCCT
1 CCACCTACACCACCTCCAATGCCTCCACCTACACCACCTCCATGTCCT
** * * * * *
406323 CCACCTATGCCGCCTCCAAAGCCACCGCCTGCACCACCTCCATGTCCT
1 CCACCTACACCACCTCCAATGCCTCCACCTACACCACCTCCATGTCCT
* *** * *** *
406371 CCACCTACACCACCACCAATGCCTCCACCTTTTCCTCCTCCAAAACCA
1 CCACCTACACCACCTCCAATGCCTCCACCTACACCACCTCCATGTCCT
* * *
406419 CCGCC-AGCACCACCTCC-ATGTCCTCCACCTACACCACCACCAAT-ACCT
1 CCACCTA-CACCACCTCCAATG-CCTCCACCTACACCACCTCC-ATGTCCT
*** * * * *
406467 CCACCTTTTCCTCCTCCAATACCTCCACCAACTCCACCTCCATGTCCT
1 CCACCTACACCACCTCCAATGCCTCCACCTACACCACCTCCATGTCCT
* * * *
406515 CCACCTACACCACCACCAATACCTCCTCCACCACCTGCACCACCTCCGTGTCCT
1 CCACCTACACCACCTCCAAT---GCCT---CCACCTACACCACCTCCATGTCCT
406569 CCACCTACACCACC
1 CCACCTACACCACC
406583 GCCAGCTCCG
Statistics
Matches: 422, Mismatches: 102, Indels: 38
0.75 0.18 0.07
Matches are distributed among these distances:
46 6 0.01
47 79 0.19
48 293 0.69
49 7 0.02
51 3 0.01
54 34 0.08
ACGTcount: A:0.23, C:0.53, G:0.06, T:0.18
Consensus pattern (48 bp):
CCACCTACACCACCTCCAATGCCTCCACCTACACCACCTCCATGTCCT
Found at i:406437 original size:72 final size:72
Alignment explanation
Indices: 406320--406540 Score: 343
Period size: 72 Copynumber: 3.1 Consensus size: 72
406310 ACCTCCATGT
* * * * *
406320 CCTCCACCTATGCCGCCTCCAAAGCCACCGCCTGCACCACCTCCATGTCCTCCACCTACACCACC
1 CCTCCACCTTTTCCTCCTCCAAAACCACCGCCAGCACCACCTCCATGTCCTCCACCTACACCACC
*
406385 ACCAATG
66 ACCAATA
406392 CCTCCACCTTTTCCTCCTCCAAAACCACCGCCAGCACCACCTCCATGTCCTCCACCTACACCACC
1 CCTCCACCTTTTCCTCCTCCAAAACCACCGCCAGCACCACCTCCATGTCCTCCACCTACACCACC
406457 ACCAATA
66 ACCAATA
* * * * *
406464 CCTCCACCTTTTCCTCCTCCAATACCTCCACCAACTCCACCTCCATGTCCTCCACCTACACCACC
1 CCTCCACCTTTTCCTCCTCCAAAACCACCGCCAGCACCACCTCCATGTCCTCCACCTACACCACC
406529 ACCAATA
66 ACCAATA
406536 CCTCC
1 CCTCC
406541 TCCACCACCT
Statistics
Matches: 138, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 138 1.00
ACGTcount: A:0.23, C:0.53, G:0.05, T:0.19
Consensus pattern (72 bp):
CCTCCACCTTTTCCTCCTCCAAAACCACCGCCAGCACCACCTCCATGTCCTCCACCTACACCACC
ACCAATA
Found at i:406470 original size:12 final size:12
Alignment explanation
Indices: 406440--406497 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
406430 ACCTCCATGT
* *
406440 CCTCCACCTACA
1 CCTCCACCAATA
*
406452 CCACCACCAATA
1 CCTCCACCAATA
** *
406464 CCTCCACCTTTT
1 CCTCCACCAATA
*
406476 CCTCCTCCAATA
1 CCTCCACCAATA
406488 CCTCCACCAA
1 CCTCCACCAA
406498 CTCCACCTCC
Statistics
Matches: 34, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.26, C:0.53, G:0.00, T:0.21
Consensus pattern (12 bp):
CCTCCACCAATA
Found at i:406636 original size:12 final size:12
Alignment explanation
Indices: 406619--406707 Score: 79
Period size: 12 Copynumber: 7.4 Consensus size: 12
406609 CTCCACCTTT
*
406619 TCCAACTCCACC
1 TCCAACACCACC
406631 TCCAACACCACC
1 TCCAACACCACC
* * **
406643 ACCGATTCCACC
1 TCCAACACCACC
*
406655 TCCAAAACCACC
1 TCCAACACCACC
* *
406667 ACCACCACCACC
1 TCCAACACCACC
406679 TCCAACACCACC
1 TCCAACACCACC
* * *
406691 GCCAGCCCCACC
1 TCCAACACCACC
406703 TCCAA
1 TCCAA
406708 AACCTCCACC
Statistics
Matches: 58, Mismatches: 19, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
12 58 1.00
ACGTcount: A:0.30, C:0.57, G:0.03, T:0.09
Consensus pattern (12 bp):
TCCAACACCACC
Found at i:406652 original size:24 final size:24
Alignment explanation
Indices: 406624--406717 Score: 102
Period size: 24 Copynumber: 3.9 Consensus size: 24
406614 CCTTTTCCAA
406624 CTCCACCTCCAACACCACCACCGA-
1 CTCCACCTCCAACACCACCACC-AC
* *
406648 TTCCACCTCCAAAACCACCACCAC
1 CTCCACCTCCAACACCACCACCAC
* *
406672 CACCACCTCCAACACCACCGCCAGC
1 CTCCACCTCCAACACCACCACCA-C
* *
406697 C-CCACCTCCAAAACCTCCACC
1 CTCCACCTCCAACACCACCACC
406718 TAAACCACCA
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
23 1 0.02
24 56 0.95
25 2 0.03
ACGTcount: A:0.30, C:0.59, G:0.03, T:0.09
Consensus pattern (24 bp):
CTCCACCTCCAACACCACCACCAC
Found at i:406684 original size:48 final size:48
Alignment explanation
Indices: 406626--406717 Score: 132
Period size: 48 Copynumber: 1.9 Consensus size: 48
406616 TTTTCCAACT
**
406626 CCACCTCCAACACCACCACC-GATTCCACCTCCAAAACCACCACCACCA
1 CCACCTCCAACACCACCACCAG-CCCCACCTCCAAAACCACCACCACCA
* *
406674 CCACCTCCAACACCACCGCCAGCCCCACCTCCAAAACCTCCACC
1 CCACCTCCAACACCACCACCAGCCCCACCTCCAAAACCACCACC
406718 TAAACCACCA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
48 38 0.97
49 1 0.03
ACGTcount: A:0.30, C:0.59, G:0.03, T:0.08
Consensus pattern (48 bp):
CCACCTCCAACACCACCACCAGCCCCACCTCCAAAACCACCACCACCA
Found at i:408071 original size:2 final size:2
Alignment explanation
Indices: 408064--408109 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
408054 GGTAGTTTTA
408064 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
408106 AT AT
1 AT AT
408110 GTTTAAGTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:414536 original size:11 final size:11
Alignment explanation
Indices: 414520--414549 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
414510 AGAACTCAAA
414520 CTCCCTCCCCT
1 CTCCCTCCCCT
414531 CTCCCTCCCCT
1 CTCCCTCCCCT
414542 C-CCCTCCC
1 CTCCCTCCC
414550 TTATTTCCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.37
11 12 0.63
ACGTcount: A:0.00, C:0.77, G:0.00, T:0.23
Consensus pattern (11 bp):
CTCCCTCCCCT
Found at i:415966 original size:22 final size:20
Alignment explanation
Indices: 415937--415977 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
415927 TACATATATG
*
415937 CATCATTTTTGTGTTGGTAAT
1 CATCATTTTGGTG-TGGTAAT
415958 CATCTATTTTGGTGTGGTAA
1 CATC-ATTTTGGTGTGGTAA
415978 CGAGTTTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.20, C:0.10, G:0.22, T:0.49
Consensus pattern (20 bp):
CATCATTTTGGTGTGGTAAT
Found at i:419916 original size:52 final size:52
Alignment explanation
Indices: 419838--419946 Score: 182
Period size: 52 Copynumber: 2.1 Consensus size: 52
419828 TCTTCAAAAA
*
419838 ATTAATATTAGATTTAAAATCTATCAAAAATAATTTTAATATTAAACATGAT
1 ATTAATATTAGATCTAAAATCTATCAAAAATAATTTTAATATTAAACATGAT
* * *
419890 ATTAATATTAGCTCTAAAATGTATCAAAAATAATTTTAATATTAAATATGAT
1 ATTAATATTAGATCTAAAATCTATCAAAAATAATTTTAATATTAAACATGAT
419942 ATTAA
1 ATTAA
419947 AAGGTTATAT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.50, C:0.06, G:0.05, T:0.40
Consensus pattern (52 bp):
ATTAATATTAGATCTAAAATCTATCAAAAATAATTTTAATATTAAACATGAT
Found at i:420668 original size:27 final size:27
Alignment explanation
Indices: 420586--420673 Score: 90
Period size: 27 Copynumber: 3.3 Consensus size: 27
420576 AATATAGAAT
*
420586 ATAAAAAGAATATATATGATGGTAAT-A
1 ATAAAAAG-ATATATATAATGGTAATAA
* * *
420613 ATAATAAAGATATAAACAATGGGAA-AA
1 ATAA-AAAGATATATATAATGGTAATAA
* *
420640 ATAAGAAGATATATATAATAGTAATAA
1 ATAAAAAGATATATATAATGGTAATAA
420667 ATAAAAA
1 ATAAAAA
420674 ACTAAAAAAC
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
26 15 0.31
27 29 0.60
28 4 0.08
ACGTcount: A:0.61, C:0.01, G:0.12, T:0.25
Consensus pattern (27 bp):
ATAAAAAGATATATATAATGGTAATAA
Found at i:421000 original size:37 final size:38
Alignment explanation
Indices: 420947--421034 Score: 94
Period size: 37 Copynumber: 2.4 Consensus size: 38
420937 TTATGTATAG
*
420947 AGATAAATAAAA-ATAAA-TACATACAGTAAAAAAATAAA
1 AGATAAA-AAAATATAAAGAACATACA-TAAAAAAATAAA
* * *
420985 A-ATAAAAAAATATAAAGAATATACATATAATAATAAA
1 AGATAAAAAAATATAAAGAACATACATAAAAAAATAAA
421022 AGA-AAAAAAATAT
1 AGATAAAAAAATAT
421035 TTTATATACG
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
36 4 0.09
37 31 0.72
38 8 0.19
ACGTcount: A:0.72, C:0.03, G:0.05, T:0.20
Consensus pattern (38 bp):
AGATAAAAAAATATAAAGAACATACATAAAAAAATAAA
Found at i:421141 original size:2 final size:2
Alignment explanation
Indices: 421134--421162 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
421124 ATACATAAAA
421134 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
421163 AATAAAGGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:421195 original size:21 final size:21
Alignment explanation
Indices: 421171--421210 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
421161 TAAATAAAGG
421171 AATAAACGTA-ATAATAATGAA
1 AATAAA-GTATATAATAATGAA
*
421192 AATATAGTATATAATAATG
1 AATAAAGTATATAATAATG
421211 GTAGGGACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.57, C:0.03, G:0.10, T:0.30
Consensus pattern (21 bp):
AATAAAGTATATAATAATGAA
Found at i:423014 original size:105 final size:105
Alignment explanation
Indices: 422587--423425 Score: 1413
Period size: 105 Copynumber: 8.0 Consensus size: 105
422577 CGTTGTGAAT
* *
422587 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT--G-TGT
1 TGAAATTGAGAAA-TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
422649 CTGGAGTCCAATATCCTTCGTTGTGACGTTGAAATTGGCTC
65 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* *
422690 TGAAATTGAGAAGTTGTTTGTTGACAACCA-C-GTCCCTTCGCCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGAGAA-ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* *
422753 CTTGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTC
65 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
*
422794 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGAGAA-ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
422859 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTA
65 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
*
422900 TGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
422965 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* * *
423005 TGAAATTGAGAAGTTGCTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 TGAAATTGAGAA-ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
423070 CTGGAGTCCAATATCCTTCGTTGTGAAGTTG-AATTGGCTC
65 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* * *
423110 TGTATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
423175 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* * *
423215 TGTATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
423280 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
*
423320 TGACATTGAGAAAT-TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
423384 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
423424 TG
1 TG
423426 GGTAAAACCT
Statistics
Matches: 700, Mismatches: 28, Indels: 15
0.94 0.04 0.02
Matches are distributed among these distances:
101 24 0.03
102 1 0.00
103 27 0.04
104 241 0.34
105 247 0.35
106 160 0.23
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.34
Consensus pattern (105 bp):
TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
Found at i:424246 original size:56 final size:59
Alignment explanation
Indices: 424160--424271 Score: 153
Period size: 57 Copynumber: 1.9 Consensus size: 59
424150 TTTTCTCTTC
*
424160 TTTTTTCTTTTTCTTTTTTTTTAATTTTAGG-CGCCCT-TCCGGGTTTTCACCCTAAACG
1 TTTTTTCTTTTTCTTTTTTTTTAATCTTAGGACGCCCTCT-CGGGTTTTCACCCTAAACG
*
424218 TTTTTT-TTTTT-TTTTTTTTTCAA-CTTAGGACGCCCTCTCGGGTTTTCATCCTAA
1 TTTTTTCTTTTTCTTTTTTTTT-AATCTTAGGACGCCCTCTCGGGTTTTCACCCTAA
424272 GCGAAGTATT
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
56 14 0.29
57 28 0.57
58 7 0.14
ACGTcount: A:0.12, C:0.21, G:0.12, T:0.54
Consensus pattern (59 bp):
TTTTTTCTTTTTCTTTTTTTTTAATCTTAGGACGCCCTCTCGGGTTTTCACCCTAAACG
Found at i:427853 original size:26 final size:27
Alignment explanation
Indices: 427824--427877 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
427814 AAAAGAAAAT
*
427824 TGTTTGCCAAAGAAAA-AAATGCATCC
1 TGTTTGCCAAAGAAAAGAAAAGCATCC
**
427850 TGTTTGCCATGGAAAAGAAAAGCATCC
1 TGTTTGCCAAAGAAAAGAAAAGCATCC
427877 T
1 T
427878 TTATTAAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 14 0.58
27 10 0.42
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.24
Consensus pattern (27 bp):
TGTTTGCCAAAGAAAAGAAAAGCATCC
Done.