Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009618.1 Hibiscus syriacus cultivar Beakdansim tig00117007_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: 1135495
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:209009 original size:23 final size:23
Alignment explanation
Indices: 208960--209011 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
208950 GGTCGGGTCG
* *
208960 GGTCAACGGGTCGGGTCGGTTCG
1 GGTCAACGGGTCGGGTCGGTACC
208983 GGTCAACGGGTCGGGTC-GTGACC
1 GGTCAACGGGTCGGGTCGGT-ACC
209006 GGTCAA
1 GGTCAA
209012 ACCGGTCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 2 0.08
23 24 0.92
ACGTcount: A:0.13, C:0.23, G:0.44, T:0.19
Consensus pattern (23 bp):
GGTCAACGGGTCGGGTCGGTACC
Found at i:210609 original size:2 final size:2
Alignment explanation
Indices: 210602--210689 Score: 167
Period size: 2 Copynumber: 44.0 Consensus size: 2
210592 CTATTAAGTG
210602 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
*
210644 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
210686 AT AT
1 AT AT
210690 GACATAAGTT
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 84 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:213272 original size:20 final size:20
Alignment explanation
Indices: 213227--213272 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
213217 TACTATACTA
*
213227 TATGAATAATACGGATATTG
1 TATGAATAATACGGATAATG
213247 TATGAATAATATC-GATAATG
1 TATGAATAATA-CGGATAATG
*
213267 TGTGAA
1 TATGAA
213273 CAGTAATGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.41, C:0.04, G:0.20, T:0.35
Consensus pattern (20 bp):
TATGAATAATACGGATAATG
Found at i:214669 original size:19 final size:20
Alignment explanation
Indices: 214645--214691 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
214635 AACAATTTTC
* *
214645 TTTTGAAAGCAAAAATGGA-
1 TTTTGAAAACAAAAATGAAT
*
214664 TTTTGAAAACCAAAATGAAT
1 TTTTGAAAACAAAAATGAAT
214684 TTTTGAAA
1 TTTTGAAA
214692 TATGATTTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.47, C:0.06, G:0.15, T:0.32
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAT
Found at i:216928 original size:11 final size:11
Alignment explanation
Indices: 216912--216952 Score: 82
Period size: 11 Copynumber: 3.7 Consensus size: 11
216902 TATTATTTTT
216912 GAATTCTTCTA
1 GAATTCTTCTA
216923 GAATTCTTCTA
1 GAATTCTTCTA
216934 GAATTCTTCTA
1 GAATTCTTCTA
216945 GAATTCTT
1 GAATTCTT
216953 TTTAACTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.46
Consensus pattern (11 bp):
GAATTCTTCTA
Found at i:230692 original size:32 final size:32
Alignment explanation
Indices: 230655--230730 Score: 152
Period size: 32 Copynumber: 2.4 Consensus size: 32
230645 GATCTTCATC
230655 TAGTTTCTCTCGAACACTAAAGATCTTTAACT
1 TAGTTTCTCTCGAACACTAAAGATCTTTAACT
230687 TAGTTTCTCTCGAACACTAAAGATCTTTAACT
1 TAGTTTCTCTCGAACACTAAAGATCTTTAACT
230719 TAGTTTCTCTCG
1 TAGTTTCTCTCG
230731 TACATTATGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (32 bp):
TAGTTTCTCTCGAACACTAAAGATCTTTAACT
Found at i:231778 original size:11 final size:11
Alignment explanation
Indices: 231762--231788 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
231752 GTTTACATGA
231762 AATTTCTAGTT
1 AATTTCTAGTT
231773 AATTTCTAGTT
1 AATTTCTAGTT
231784 AATTT
1 AATTT
231789 GTCATTTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.56
Consensus pattern (11 bp):
AATTTCTAGTT
Found at i:238858 original size:17 final size:17
Alignment explanation
Indices: 238836--238870 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
238826 ATGCATAAAT
238836 GTTTAGAATTTTGTGAG
1 GTTTAGAATTTTGTGAG
238853 GTTTAGAATTTTGTGAG
1 GTTTAGAATTTTGTGAG
238870 G
1 G
238871 AGGTCTGGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (17 bp):
GTTTAGAATTTTGTGAG
Found at i:241446 original size:14 final size:14
Alignment explanation
Indices: 241412--241447 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
241402 ATATAATGAT
*
241412 TAATTTAAGTACAA
1 TAATTTAAATACAA
241426 TAA-TTAAATACAA
1 TAATTTAAATACAA
241439 TAATTTAAA
1 TAATTTAAA
241448 GTAACTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.36
Consensus pattern (14 bp):
TAATTTAAATACAA
Found at i:242781 original size:16 final size:16
Alignment explanation
Indices: 242757--242806 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
242747 TTTTTTAAAA
* *
242757 TTTAAAATAAACATAT
1 TTTATAATAAATATAT
242773 TTTATAAT-AATAT-T
1 TTTATAATAAATATAT
*
242787 TTTATAATAATTATAT
1 TTTATAATAAATATAT
242803 TTTA
1 TTTA
242807 AACAATTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 9 0.31
15 8 0.28
16 12 0.41
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTATAATAAATATAT
Found at i:242820 original size:38 final size:37
Alignment explanation
Indices: 242778--242871 Score: 102
Period size: 38 Copynumber: 2.5 Consensus size: 37
242768 CATATTTTAT
242778 AATAATATTTTTATAATAA-TTATATTTTAAACAATTAA
1 AATAATATTTTTATAATAATTTATATTTT-AACAA-TAA
* * *
242816 AATAATATATTTATATTAATTTTATATTTTAATAATAA
1 AATAATATTTTTATAATAA-TTTATATTTTAACAATAA
*
242854 AATAA-ATTATTTAGAATA
1 AATAATATT-TTTATAATA
242872 TTAAATATTA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
37 2 0.04
38 32 0.68
39 4 0.09
40 9 0.19
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (37 bp):
AATAATATTTTTATAATAATTTATATTTTAACAATAA
Found at i:245451 original size:17 final size:17
Alignment explanation
Indices: 245422--245471 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
245412 TAATAGTTAA
*
245422 TTTAATAAATGAACTAG
1 TTTAATGAATGAACTAG
*
245439 TTTGATGAATGAACTAG
1 TTTAATGAATGAACTAG
*
245456 TTTAATTAATGAACTA
1 TTTAATGAATGAACTA
245472 CTTCCCTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.42, C:0.06, G:0.14, T:0.38
Consensus pattern (17 bp):
TTTAATGAATGAACTAG
Found at i:250047 original size:29 final size:29
Alignment explanation
Indices: 249971--250047 Score: 145
Period size: 29 Copynumber: 2.7 Consensus size: 29
249961 CTTCCCAGCA
*
249971 TAGGTCGCCATGCACTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCTGGCGACCTTG
250000 TAGGTCGCCATGCACTCCTGGCGACCTTG
1 TAGGTCGCCATGCACTCCTGGCGACCTTG
250029 TAGGTCGCCATGCACTCCT
1 TAGGTCGCCATGCACTCCT
250048 CCTGCTCCTC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.14, C:0.35, G:0.27, T:0.23
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCTGGCGACCTTG
Found at i:250140 original size:14 final size:14
Alignment explanation
Indices: 250103--250140 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
250093 GCTCGCTCGA
250103 ATGGCCTCGGTCGG
1 ATGGCCTCGGTCGG
*
250117 ATGCCCTCGGTCGG
1 ATGGCCTCGGTCGG
*
250131 ATGGCTTCGG
1 ATGGCCTCGG
250141 ATGCCCAACG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.08, C:0.29, G:0.39, T:0.24
Consensus pattern (14 bp):
ATGGCCTCGGTCGG
Found at i:263841 original size:31 final size:32
Alignment explanation
Indices: 263788--263855 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 32
263778 GTGTGAAAGT
* *** *
263788 AGTAATAAAGGGTTTTGGTAAAAAGTGATT-A
1 AGTAATAAAGAGTTTAAATAAAAAGTAATTAA
*
263819 AGTAATAAAGAGTTTAAATAAAAGGTAATTAA
1 AGTAATAAAGAGTTTAAATAAAAAGTAATTAA
263851 AGTAA
1 AGTAA
263856 AAAAATTAAG
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
31 24 0.80
32 6 0.20
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (32 bp):
AGTAATAAAGAGTTTAAATAAAAAGTAATTAA
Found at i:270397 original size:24 final size:24
Alignment explanation
Indices: 270367--270413 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
270357 AACTGGTTAT
*
270367 TATATATGATGTTTATCATGAATA
1 TATATATGATATTTATCATGAATA
270391 TATATATGATATTTATCATGAAT
1 TATATATGATATTTATCATGAAT
270414 GTTATTGTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.47
Consensus pattern (24 bp):
TATATATGATATTTATCATGAATA
Found at i:277646 original size:111 final size:109
Alignment explanation
Indices: 277427--277660 Score: 319
Period size: 111 Copynumber: 2.1 Consensus size: 109
277417 TAAACGTCTA
* * *
277427 CATGG-ACGGCTTGCGGGACCAGTTTGTTGTGAGAAGAAGAAAAAACTGAAGAAGAGACATTCTT
1 CATGGAAC-GCTTGCAGGACCAGTTTGTTGTGAGAAGAAGAAAAAACTGAAGAAGACACATGCTT
* * * * *
277491 GTGGTTCCTAAATTTCAACCATTTTTAAGATTAATTTGATGTGTG
65 GTGGTTCCAAAAATTCAAACATCTTTAAGATTAATTTGACGTGTG
* *
277536 CATGGAACGCTTGCAGGACCAGTTTGTTGTGAGAAGAAG-CAAAATTGAAGAAGACACATGCTTT
1 CATGGAACGCTTGCAGGACCAGTTTGTTGTGAGAAGAAGAAAAAACTGAAGAAGACACATGC-TT
277600 ACGTGGTTCCAAAAATTCAAACATCTTTAAGATTAATTTGACGTGTG
65 --GTGGTTCCAAAAATTCAAACATCTTTAAGATTAATTTGACGTGTG
*
277647 CATGGACCGCTTGC
1 CATGGAACGCTTGC
277661 TGTCATAAAA
Statistics
Matches: 110, Mismatches: 11, Indels: 6
0.87 0.09 0.05
Matches are distributed among these distances:
108 18 0.16
109 37 0.34
110 2 0.02
111 53 0.48
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (109 bp):
CATGGAACGCTTGCAGGACCAGTTTGTTGTGAGAAGAAGAAAAAACTGAAGAAGACACATGCTTG
TGGTTCCAAAAATTCAAACATCTTTAAGATTAATTTGACGTGTG
Found at i:278677 original size:16 final size:16
Alignment explanation
Indices: 278656--278688 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
278646 TAATAAATAA
278656 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
278672 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
278688 A
1 A
278689 AAATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:278769 original size:10 final size:10
Alignment explanation
Indices: 278754--278828 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
278744 CATTTAATAA
278754 ATAAACGAAC
1 ATAAACGAAC
278764 ATAAACGAAC
1 ATAAACGAAC
278774 ----ACGAAC
1 ATAAACGAAC
278780 ATAAACGAAC
1 ATAAACGAAC
** *
278790 ACGAAC-ATAA
1 ATAAACGA-AC
278800 ATGAACACGAAC
1 AT-AA-ACGAAC
278812 ATAAACGAAC
1 ATAAACGAAC
278822 ATAAACG
1 ATAAACG
278829 TTGGAGACCC
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 35 0.69
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.57, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:278779 original size:16 final size:16
Alignment explanation
Indices: 278758--278822 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
278748 TAATAAATAA
278758 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
278774 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
278790 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
278806 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
278822 A
1 A
278823 TAAACGTTGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:279585 original size:14 final size:14
Alignment explanation
Indices: 279568--279623 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
279558 AATGAACATA
*
279568 AACGAACATAATCG
1 AACGAACATAACCG
279582 AACGAACAT-A---
1 AACGAACATAACCG
*
279592 AACGAACATAACCA
1 AACGAACATAACCG
279606 AACGAACATAACCG
1 AACGAACATAACCG
279620 AACG
1 AACG
279624 TTCACGAACC
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 26 0.70
ACGTcount: A:0.54, C:0.25, G:0.12, T:0.09
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:279588 original size:24 final size:24
Alignment explanation
Indices: 279548--279622 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
279538 GATTGGGTTA
*
279548 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
279572 AACATAATCGAACGAACATAAACG
1 AACATAATCGAACGAACATAAACG
* * *
279596 AACATAACCAAACGAACATAACCG
1 AACATAATCGAACGAACATAAACG
279620 AAC
1 AAC
279623 GTTCACGAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
23 3 0.07
24 43 0.93
ACGTcount: A:0.56, C:0.21, G:0.11, T:0.12
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:287002 original size:13 final size:13
Alignment explanation
Indices: 286984--287009 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
286974 ATGAGGTTTA
286984 GGTTATGAAAAAT
1 GGTTATGAAAAAT
286997 GGTTATGAAAAAT
1 GGTTATGAAAAAT
287010 AGTGATTACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (13 bp):
GGTTATGAAAAAT
Found at i:287239 original size:20 final size:20
Alignment explanation
Indices: 287214--287269 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
287204 ATTCGCGTTG
*
287214 CATTTCGTGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
287234 CATTTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
287254 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
287270 AGTCTACAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.45
Consensus pattern (20 bp):
CATTTCGCGTTGCGATTTTC
Found at i:287305 original size:40 final size:41
Alignment explanation
Indices: 287241--287371 Score: 185
Period size: 41 Copynumber: 3.2 Consensus size: 41
287231 TTCCATTTCG
*
287241 CGTTGCGATTTTCC-ATTTCGCGTTGCGATAGTCTACA-ATGT
1 CGTTGCGATTTTCCAAATT--CGTTGCGATAGTCTACAGATGT
*
287282 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGATGT
* *
287323 CGTTGCGATTTTCCAAATTCGTTACGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGATGT
*
287364 TGTTGCGA
1 CGTTGCGA
287372 AAGTCTACAG
Statistics
Matches: 84, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
40 17 0.20
41 64 0.76
42 3 0.04
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (41 bp):
CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGATGT
Found at i:287328 original size:22 final size:22
Alignment explanation
Indices: 287261--287394 Score: 111
Period size: 22 Copynumber: 6.4 Consensus size: 22
287251 TTCCATTTCG
287261 CGTTGCGATAGTCTACA-ATGT
1 CGTTGCGATAGTCTACAGATGT
* * *
287282 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGATGT
*
287301 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGATGT
* * *
287323 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGATGT
* *
287342 CGTTACGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGATGT
* * *
287364 TGTTGCGAAAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGATGT
287386 CGTTGCGAT
1 CGTTGCGAT
287395 TTTCCAAATT
Statistics
Matches: 86, Mismatches: 20, Indels: 13
0.72 0.17 0.11
Matches are distributed among these distances:
19 23 0.27
20 7 0.08
21 19 0.22
22 37 0.43
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGATGT
Found at i:287505 original size:6 final size:6
Alignment explanation
Indices: 287494--287532 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
287484 GACACGTATT
287494 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
287533 CGAGACGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.33, C:0.51, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:287543 original size:5 final size:5
Alignment explanation
Indices: 287533--287573 Score: 75
Period size: 5 Copynumber: 8.4 Consensus size: 5
287523 GACCACGACC
287533 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CG-GA CG
1 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CG
287574 GCGGCGGCGG
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.11
5 32 0.89
ACGTcount: A:0.37, C:0.22, G:0.41, T:0.00
Consensus pattern (5 bp):
CGAGA
Found at i:288066 original size:5 final size:5
Alignment explanation
Indices: 288058--288107 Score: 73
Period size: 5 Copynumber: 9.6 Consensus size: 5
288048 CCGTCTCGTC
*
288058 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGT TCGGGG TCGTGG TCG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TC-GGG TCG-GG TCG
288108 TGGTTGTGGT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
5 32 0.78
6 9 0.22
ACGTcount: A:0.00, C:0.20, G:0.56, T:0.24
Consensus pattern (5 bp):
TCGGG
Found at i:288261 original size:22 final size:22
Alignment explanation
Indices: 288235--288328 Score: 97
Period size: 22 Copynumber: 4.4 Consensus size: 22
288225 AATTTGGAAA
288235 ATCGCAACGAAAACTGTAGACT
1 ATCGCAACGAAAACTGTAGACT
288257 ATCGCAAC-AACAACTGTAGACT
1 ATCGCAACGAA-AACTGTAGACT
* * **
288279 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGAAAACTGTAGACT
* *
288298 ATCGCAATGACAACTGTAGACT
1 ATCGCAACGAAAACTGTAGACT
288320 ATCGCAACG
1 ATCGCAACG
288329 CGATTTTCAA
Statistics
Matches: 57, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
19 12 0.21
20 2 0.04
21 4 0.07
22 39 0.68
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.19
Consensus pattern (22 bp):
ATCGCAACGAAAACTGTAGACT
Found at i:289038 original size:135 final size:136
Alignment explanation
Indices: 288798--289136 Score: 444
Period size: 135 Copynumber: 2.6 Consensus size: 136
288788 AGGAACAATT
* *
288798 TCTTCTCATTATGAAC-T-TTCT-CCT-T-TAAGATGAGTTCTTCTCATTATGAACTCT--TCTT
1 TCTTCTCATTATGAACTTCTTCTCCCTCTGTCAGATGAGTTCTTCTCATTATGAACTCTCCACTT
* ** * * *
288856 GAAACGTTGATCCCTCAAGAAAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGATAGGTCGA
66 AAAATATTGATCCCTCAAGAAAGGCGTCACTGATTCGAAATGCCATGAATCGAGCGATAGGTCGA
288921 ACAAGC
131 ACAAGC
* *
288927 TCTTCTCATTATG-ACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCCACTC
1 TCTTCTCATTATGAACTTCTTCTCCCTCTGTCAGATGAGTTCTTCTCATTATGAACTCTCCACTT
* ** * *
288991 AAAATATTGATCCCTCGAGCGAGGCGTCGCTGATTCGAAATGCCATGAATCGAGCGATAGGTTGA
66 AAAATATTGATCCCTCAAGAAAGGCGTCACTGATTCGAAATGCCATGAATCGAGCGATAGGTCGA
289056 ACAAGC
131 ACAAGC
* * *
289062 TCTTCTCATTATGAACTTCTTCTCCCTCTGTCAGATAAGTTCTTCCCACTATGAACTCTCCA-TT
1 TCTTCTCATTATGAACTTCTTCTCCCTCTGTCAGATGAGTTCTTCTCATTATGAACTCTCCACTT
289126 AGAAATATTGA
66 A-AAATATTGA
289137 CCGATTTATT
Statistics
Matches: 181, Mismatches: 20, Indels: 11
0.85 0.09 0.05
Matches are distributed among these distances:
128 2 0.01
129 14 0.08
130 4 0.02
131 3 0.02
132 1 0.01
133 27 0.15
135 77 0.43
136 53 0.29
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.34
Consensus pattern (136 bp):
TCTTCTCATTATGAACTTCTTCTCCCTCTGTCAGATGAGTTCTTCTCATTATGAACTCTCCACTT
AAAATATTGATCCCTCAAGAAAGGCGTCACTGATTCGAAATGCCATGAATCGAGCGATAGGTCGA
ACAAGC
Found at i:290138 original size:19 final size:20
Alignment explanation
Indices: 290111--290185 Score: 73
Period size: 19 Copynumber: 3.8 Consensus size: 20
290101 ATCATGCTCA
290111 AAAGACTTACTGATGGCCCG
1 AAAGACTTACTGATGGCCCG
* * * *
290131 -AGGACTTACTCATCATGCTCG
1 AAAGACTTACTGAT--GGCCCG
290152 AAAGACTTACTGATGGCCCG
1 AAAGACTTACTGATGGCCCG
*
290172 AATGACTTA-TGATG
1 AAAGACTTACTGATG
290186 ATTCAAAGTG
Statistics
Matches: 43, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
19 16 0.37
20 12 0.28
21 4 0.09
22 11 0.26
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (20 bp):
AAAGACTTACTGATGGCCCG
Found at i:290156 original size:41 final size:40
Alignment explanation
Indices: 290051--290181 Score: 147
Period size: 41 Copynumber: 3.2 Consensus size: 40
290041 TGGCCCAAAA
* * *
290051 GACTTATCATCTTGCTCGAAAGACTTA-TAGATGACCTGAAG
1 GACTTATCATCATGCTCGAAAGACTTACT-GATGGCCCG-AG
* * *
290092 GATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAG
1 GACTT-ATCATCATGCTCGAAAGACTTACTGATGGCCCGAG
*
290133 GACTTACTCATCATGCTCGAAAGACTTACTGATGGCCCGAAT
1 GACTTA-TCATCATGCTCGAAAGACTTACTGATGGCCCG-AG
290175 GACTTAT
1 GACTTAT
290182 GATGATTCAA
Statistics
Matches: 76, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
40 1 0.01
41 41 0.54
42 33 0.43
43 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (40 bp):
GACTTATCATCATGCTCGAAAGACTTACTGATGGCCCGAG
Found at i:290161 original size:22 final size:22
Alignment explanation
Indices: 290100--290162 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 22
290090 AGGATTTAAG
*
290100 CATCATGCTCAAAAGACTTACT
1 CATCATGCTCGAAAGACTTACT
* * * *
290122 GAT--GGCCCG-AGGACTTACT
1 CATCATGCTCGAAAGACTTACT
290141 CATCATGCTCGAAAGACTTACT
1 CATCATGCTCGAAAGACTTACT
290163 GATGGCCCGA
Statistics
Matches: 29, Mismatches: 9, Indels: 6
0.66 0.20 0.14
Matches are distributed among these distances:
19 11 0.38
20 3 0.10
21 4 0.14
22 11 0.38
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.25
Consensus pattern (22 bp):
CATCATGCTCGAAAGACTTACT
Found at i:290360 original size:42 final size:42
Alignment explanation
Indices: 290314--290415 Score: 152
Period size: 42 Copynumber: 2.4 Consensus size: 42
290304 ATGGATGACA
290314 CGAAGGACTTACACATCATGCTCGAAAGACCTACTGATGGCC
1 CGAAGGACTTACACATCATGCTCGAAAGACCTACTGATGGCC
* * *
290356 CGAAGGATTTA-AGCATCATGTTCGAAAGACTTACTGATGGCC
1 CGAAGGACTTACA-CATCATGCTCGAAAGACCTACTGATGGCC
*
290398 CGAAGGACTTACTCATCA
1 CGAAGGACTTACACATCA
290416 AGAAACCCTT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
41 1 0.02
42 52 0.98
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.23
Consensus pattern (42 bp):
CGAAGGACTTACACATCATGCTCGAAAGACCTACTGATGGCC
Found at i:290629 original size:53 final size:53
Alignment explanation
Indices: 290458--290700 Score: 240
Period size: 52 Copynumber: 4.5 Consensus size: 53
290448 GTTGTAAAGG
*
290458 AACCCTTAAAAATTAGGCTTAGTTTCCTTTTAAAAACTCA-TTGAAAACCATCATCAAGA
1 AACCCCTAAAAATTAGGCTTAGTTT-C-TTT-AAAACTCATTTG-AAA--A-CATCAAGA
* * * *
290517 AATCCCTGAAAATCAGGCTTAGTTTC-TAAAAACTCATTTGAAAACATCAAGA
1 AACCCCTAAAAATTAGGCTTAGTTTCTTTAAAACTCATTTGAAAACATCAAGA
* * * * * *
290569 TATCCCTAAAAATTAGGCTTAATTTCTTTGAAATTCATTTGAAAACATTAAGA
1 AACCCCTAAAAATTAGGCTTAGTTTCTTTAAAACTCATTTGAAAACATCAAGA
* * * *
290622 AACCCCT-AAAATTAGGCTTAGCTTCTTTCAAATTCATTTGAAAACATCGAGA
1 AACCCCTAAAAATTAGGCTTAGTTTCTTTAAAACTCATTTGAAAACATCAAGA
* * *
290674 AACCCTTGAAAATCAGGCTTAGTTTCT
1 AACCCCTAAAAATTAGGCTTAGTTTCT
290701 AAAAATCTTT
Statistics
Matches: 158, Mismatches: 23, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
52 76 0.48
53 45 0.28
55 11 0.07
56 4 0.03
58 1 0.01
59 21 0.13
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.32
Consensus pattern (53 bp):
AACCCCTAAAAATTAGGCTTAGTTTCTTTAAAACTCATTTGAAAACATCAAGA
Found at i:290663 original size:105 final size:108
Alignment explanation
Indices: 290458--290700 Score: 273
Period size: 105 Copynumber: 2.2 Consensus size: 108
290448 GTTGTAAAGG
*
290458 AACCCTTAAAAATTAGGCTTAGTTTCCTTTTAAAAACTCATTGAAAACCATCATCAAGAAATCCC
1 AACCCTTAAAAATTAGGCTTAGTTT-C-TTTAAAAACTCATTGAAAACCAT-ATCAAGAAACCCC
*
290523 TGAAAATCAGGCTTAGTTTCTAAAAACTCATTTGAAAACATCAAGA
63 TGAAAATCAGGCTTAGCTTCTAAAAACTCATTTGAAAACATCAAGA
* * * *
290569 TATCCC-TAAAAATTAGGCTTAATTTCTTT-GAAATTCATTTGAAAA-CAT-T-AAGAAACCCCT
1 -AACCCTTAAAAATTAGGCTTAGTTTCTTTAAAAACTCA-TTGAAAACCATATCAAGAAACCCCT
* ** * *
290629 -AAAATTAGGCTTAGCTTCTTTCAAATTCATTTGAAAACATCGAGA
64 GAAAATCAGGCTTAGCTTC-TAAAAACTCATTTGAAAACATCAAGA
* *
290674 AACCCTTGAAAATCAGGCTTAGTTTCT
1 AACCCTTAAAAATTAGGCTTAGTTTCT
290701 AAAAATCTTT
Statistics
Matches: 113, Mismatches: 15, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
104 20 0.18
105 50 0.44
106 1 0.01
108 9 0.08
109 10 0.09
110 1 0.01
111 18 0.16
112 4 0.04
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.32
Consensus pattern (108 bp):
AACCCTTAAAAATTAGGCTTAGTTTCTTTAAAAACTCATTGAAAACCATATCAAGAAACCCCTGA
AAATCAGGCTTAGCTTCTAAAAACTCATTTGAAAACATCAAGA
Found at i:290762 original size:39 final size:39
Alignment explanation
Indices: 290702--290859 Score: 205
Period size: 39 Copynumber: 4.1 Consensus size: 39
290692 TTAGTTTCTA
* * * *
290702 AAAATCTTTTGTTTTGGGCGAAACTATCTCAAGTGAGAT
1 AAAATCTTATGTTTCGAGCGAAACTATCTCAAGCGAGAT
*
290741 AAAATCTTATGTTTCGAGCGAAACTATCTCAAGGGAGAT
1 AAAATCTTATGTTTCGAGCGAAACTATCTCAAGCGAGAT
* *
290780 AAAATCTTATGTTCCGAGTGAAACTATCTCAAGCGAGAT
1 AAAATCTTATGTTTCGAGCGAAACTATCTCAAGCGAGAT
* * *
290819 AAAAT-TCA--TTTCAAGGGAAACTATCTCAAGCGAGAT
1 AAAATCTTATGTTTCGAGCGAAACTATCTCAAGCGAGAT
290855 AAAAT
1 AAAAT
290860 TCGTTTGAAG
Statistics
Matches: 108, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
36 30 0.28
38 2 0.02
39 76 0.70
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.29
Consensus pattern (39 bp):
AAAATCTTATGTTTCGAGCGAAACTATCTCAAGCGAGAT
Found at i:290846 original size:36 final size:37
Alignment explanation
Indices: 290721--290889 Score: 171
Period size: 39 Copynumber: 4.5 Consensus size: 37
290711 TGTTTTGGGC
* * * *
290721 GAAACTATCTCAAGTGAGATAAAATCTTATGTTTCGAGC
1 GAAACTATCTCAAGCGAGATAAAATCTCA--TTTCAAGA
* * * *
290760 GAAACTATCTCAAGGGAGATAAAATCTTATGTTCCGAGT
1 GAAACTATCTCAAGCGAGATAAAATCTCAT-TT-CAAGA
*
290799 GAAACTATCTCAAGCGAGATAAAAT-TCATTTCAAGG
1 GAAACTATCTCAAGCGAGATAAAATCTCATTTCAAGA
* *
290835 GAAACTATCTCAAGCGAGATAAAAT-TCGTTTGAAGA
1 GAAACTATCTCAAGCGAGATAAAATCTCATTTCAAGA
* *
290871 GAAACTGTCTCAAGGGAGA
1 GAAACTATCTCAAGCGAGA
290890 CGATCAACTA
Statistics
Matches: 117, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
36 53 0.45
37 3 0.03
38 5 0.04
39 56 0.48
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.26
Consensus pattern (37 bp):
GAAACTATCTCAAGCGAGATAAAATCTCATTTCAAGA
Found at i:292625 original size:22 final size:22
Alignment explanation
Indices: 292599--292641 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
292589 CACTGGTTAT
*
292599 TATATGATGTTTATCATGAATA
1 TATATGATATTTATCATGAATA
292621 TATATGATATTTATCATGAAT
1 TATATGATATTTATCATGAAT
292642 GTTATTGTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.47
Consensus pattern (22 bp):
TATATGATATTTATCATGAATA
Found at i:303507 original size:388 final size:386
Alignment explanation
Indices: 302618--303545 Score: 1523
Period size: 386 Copynumber: 2.4 Consensus size: 386
302608 AGCATTTCCT
* *
302618 TTGGCTAAGCTATACTTATTAACCTGGGAAGTCGAAAACAAGAGATCCAAGTATAATCCTAAAAG
1 TTGGCTAAGCTATACTTGTTAACCTGGGAAGTCGAAAACAAGAGATCCAAGTATATTCCTAAAAG
* * * *
302683 TTGAGTGATGGGGCAAAAACAACACCTATAACCCTTCCACTCCTACACTAACTCTGCCACCAAAG
66 TAGAGTGATGGGACAAAAACAACACCTATAAGCCTTCCACTCCTACACTGACTCTGCCACCAAAG
* *
302748 ACTACACAACCTACGAATAGTCAACGATTTTCTGACAGAAATTGCAACGATACTGTTGAAGAATT
131 ACTACACAACCTACGAGTAGTCAACGATTCTCTGACAGAAATTGCAACGATACTGTTGAAGAATT
* *
302813 TAATAAACTAACTCAGGGAGGTTCAGTGGAGGATTATCATGAAAATTTTGAGGAATTGTAATCAT
196 TAATAAACTAACTCAGGGAGGTTCAGTGGAGGACTATCATGAAAAATTTGAGGAATTGTAATCAT
* * *
302878 TTATGCTTCGGTGCAATCTATTGTTAGATGAGGGTTTCTTGTTTCAAGTTTTTGAGCGGATTGAA
261 TTATGCTTCAGTGCAATCTATTGTTAGATGAGGGTTACTTGTATCAAGTTTTTGAGCGGATTGAA
* * ** *
302943 GGAGGAAGTTAAGCACAGAGTCAAATCTCATGAACCACAAACATTGGTTGTTGCCTTCAAG
326 GGAGAAAGTTAAGCACAGAGTCAAATCTCATGAACCACAAACATTGGCTACTACCTTCAAG
303004 TTGGCTAAGCTATACTTGTTAACCTGGGAAGTCGAAAACAAGAGATCCAAGTATATTCCTAAAAG
1 TTGGCTAAGCTATACTTGTTAACCTGGGAAGTCGAAAACAAGAGATCCAAGTATATTCCTAAAAG
* * * *
303069 TGGAGTGATAGGACAAAAACAACACTTATAAGCCTTCCACTCCTACACTGACGCTGCCACCAAAG
66 TAGAGTGATGGGACAAAAACAACACCTATAAGCCTTCCACTCCTACACTGACTCTGCCACCAAAG
*
303134 ACTACACAACCTACGAGTAGTCAACGATTCTCTGACAGGAATTGCAACGATACTGTTGAAGAATT
131 ACTACACAACCTACGAGTAGTCAACGATTCTCTGACAGAAATTGCAACGATACTGTTGAAGAATT
*
303199 TAATAAACTTACTCAGGGAGGTTCAGTGGAGGACTATCATGAAAAATTTGAGGAATTGTAATCAT
196 TAATAAACTAACTCAGGGAGGTTCAGTGGAGGACTATCATGAAAAATTTGAGGAATTGTAATCAT
* *
303264 TTATGCTTCATTGTAATCTATTGTTAGATGAGGGTTACTTTGTATCAAGTTTTTTGAGCGGATTG
261 TTATGCTTCAGTGCAATCTATTGTTAGATGAGGGTTAC-TTGTATCAAG-TTTTTGAGCGGATTG
* *
303329 AAGGAGAAAGTTAAGCACATAGTCAAATCTCATGAACCACAAACATTGGCTACTACCTTGAAG
324 AAGGAGAAAGTTAAGCACAGAGTCAAATCTCATGAACCACAAACATTGGCTACTACCTTCAAG
303392 TTGGCTAAGCTATACTTGTTAACCTGGGAAGTCGAAAACAAGAGATCCAAGTATATTCCTAAAAG
1 TTGGCTAAGCTATACTTGTTAACCTGGGAAGTCGAAAACAAGAGATCCAAGTATATTCCTAAAAG
* * * ** *
303457 TAGAGTGATGGGACAAAAACGACACCTATAAGCATTCCACTCCAACACTGACTCTTTCACCATAG
66 TAGAGTGATGGGACAAAAACAACACCTATAAGCCTTCCACTCCTACACTGACTCTGCCACCAAAG
*
303522 AATACACAACCTACGAGTAGTCAA
131 ACTACACAACCTACGAGTAGTCAA
303546 ACTAAACAGC
Statistics
Matches: 502, Mismatches: 38, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
386 279 0.56
387 9 0.02
388 214 0.43
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (386 bp):
TTGGCTAAGCTATACTTGTTAACCTGGGAAGTCGAAAACAAGAGATCCAAGTATATTCCTAAAAG
TAGAGTGATGGGACAAAAACAACACCTATAAGCCTTCCACTCCTACACTGACTCTGCCACCAAAG
ACTACACAACCTACGAGTAGTCAACGATTCTCTGACAGAAATTGCAACGATACTGTTGAAGAATT
TAATAAACTAACTCAGGGAGGTTCAGTGGAGGACTATCATGAAAAATTTGAGGAATTGTAATCAT
TTATGCTTCAGTGCAATCTATTGTTAGATGAGGGTTACTTGTATCAAGTTTTTGAGCGGATTGAA
GGAGAAAGTTAAGCACAGAGTCAAATCTCATGAACCACAAACATTGGCTACTACCTTCAAG
Found at i:307844 original size:13 final size:13
Alignment explanation
Indices: 307826--307851 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
307816 ATGAGGTTTA
307826 GGTTATGAAAAAT
1 GGTTATGAAAAAT
307839 GGTTATGAAAAAT
1 GGTTATGAAAAAT
307852 AGTGATTACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (13 bp):
GGTTATGAAAAAT
Found at i:308098 original size:20 final size:20
Alignment explanation
Indices: 308073--308122 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
308063 GTTGAAAATT
308073 GCGTTGCGATTTTCCATTTC
1 GCGTTGCGATTTTCCATTTC
308093 GCGTTGCGATTTTCCATTTC
1 GCGTTGCGATTTTCCATTTC
308113 GCGTTGCGAT
1 GCGTTGCGAT
308123 AGTCTACAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.10, C:0.24, G:0.24, T:0.42
Consensus pattern (20 bp):
GCGTTGCGATTTTCCATTTC
Found at i:308158 original size:40 final size:41
Alignment explanation
Indices: 308094--308224 Score: 185
Period size: 41 Copynumber: 3.2 Consensus size: 41
308084 TTCCATTTCG
*
308094 CGTTGCGATTTTCC-ATTTCGCGTTGCGATAGTCTACA-ATGT
1 CGTTGCGATTTTCCAAATT--CGTTGCGATAGTCTACAGATGT
*
308135 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGATGT
* *
308176 CGTTGCGATTTTCCAAATTCGTTACGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGATGT
*
308217 TGTTGCGA
1 CGTTGCGA
308225 AAGTCTACAG
Statistics
Matches: 84, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
40 17 0.20
41 64 0.76
42 3 0.04
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (41 bp):
CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGATGT
Found at i:308181 original size:22 final size:22
Alignment explanation
Indices: 308114--308247 Score: 111
Period size: 22 Copynumber: 6.4 Consensus size: 22
308104 TTCCATTTCG
308114 CGTTGCGATAGTCTACA-ATGT
1 CGTTGCGATAGTCTACAGATGT
* * *
308135 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGATGT
*
308154 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGATGT
* * *
308176 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGATGT
* *
308195 CGTTACGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGATGT
* * *
308217 TGTTGCGAAAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGATGT
308239 CGTTGCGAT
1 CGTTGCGAT
308248 TTTCCAAATT
Statistics
Matches: 86, Mismatches: 20, Indels: 13
0.72 0.17 0.11
Matches are distributed among these distances:
19 23 0.27
20 7 0.08
21 19 0.22
22 37 0.43
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGATGT
Found at i:308357 original size:6 final size:6
Alignment explanation
Indices: 308346--308400 Score: 69
Period size: 6 Copynumber: 9.5 Consensus size: 6
308336 GACACGTATT
* * *
308346 ACCACG ACCACG ACCACG ACCATG ACCATG ACCATG ACCACG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
308393 ACC-CG ACC
1 ACCACG ACC
308401 CGAGACGAGA
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
5 10 0.21
6 37 0.79
ACGTcount: A:0.31, C:0.47, G:0.16, T:0.05
Consensus pattern (6 bp):
ACCACG
Found at i:309106 original size:22 final size:22
Alignment explanation
Indices: 309080--309173 Score: 113
Period size: 22 Copynumber: 4.4 Consensus size: 22
309070 AATTTGGAAA
309080 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
*
309102 ATCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
309124 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
*
309143 ATCGCAATGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
309165 ATCGCAACG
1 ATCGCAACG
309174 CGAACTGGAA
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
19 12 0.21
20 2 0.04
21 2 0.04
22 41 0.72
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.19
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:309156 original size:41 final size:41
Alignment explanation
Indices: 309102--309192 Score: 130
Period size: 41 Copynumber: 2.2 Consensus size: 41
309092 ACTGTAGACT
*
309102 ATCGCAACAACAACTGTAGACTATCGCAA-CGAATTTGGAAA
1 ATCGCAACAACAACTGTAGACTATCGCAACCGAA-CTGGAAA
**
309143 ATCGCAATGACAACTGTAGACTATCGCAACGCGAACTGGAAA
1 ATCGCAACAACAACTGTAGACTATCGCAAC-CGAACTGGAAA
309185 ATCGCAAC
1 ATCGCAAC
309193 GCGATTTTCA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
41 27 0.61
42 13 0.30
43 4 0.09
ACGTcount: A:0.40, C:0.24, G:0.19, T:0.18
Consensus pattern (41 bp):
ATCGCAACAACAACTGTAGACTATCGCAACCGAACTGGAAA
Found at i:309212 original size:63 final size:62
Alignment explanation
Indices: 309066--309193 Score: 170
Period size: 63 Copynumber: 2.1 Consensus size: 62
309056 GAATTTTCGT
* **
309066 AACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACAACAACTGTAGACTATCGC
1 AACGAATTTGCAAAATCGCAACGACAACTGTAGACTATCGCAACAACAACTG-AGAAAATCGC
* * *
309129 AACGAATTTGGAAAATCGCAATGACAACTGTAGACTATCGCAAC-GCGAACTG-GAAAATCGC
1 AACGAATTTGCAAAATCGCAACGACAACTGTAGACTATCGCAACAAC-AACTGAGAAAATCGC
309190 AACG
1 AACG
309194 CGATTTTCAA
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
61 11 0.18
62 1 0.02
63 48 0.80
ACGTcount: A:0.40, C:0.23, G:0.20, T:0.18
Consensus pattern (62 bp):
AACGAATTTGCAAAATCGCAACGACAACTGTAGACTATCGCAACAACAACTGAGAAAATCGC
Found at i:309904 original size:136 final size:136
Alignment explanation
Indices: 309663--310002 Score: 462
Period size: 136 Copynumber: 2.6 Consensus size: 136
309653 AGGAACAATT
* *
309663 TCTTCTCATTATGAAC-T-TTCT-CCT-T-TAAGATGAGTTCTTCTCATTATGAACTCT--TCTT
1 TCTTCTCATTATGAACTTCTTCTCCCTCTGTCAGATGAGTTCTTCTCATTATGAACTCTCCACTT
* ** * * *
309721 GAAACGTTGATCCCTCAAGAAAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGATAGGTCGA
66 AAAATATTGATCCCTCAAGAAAGGCGTCACTGATTCGAAATGCCATGAATCGAGCGATAGGTCGA
309786 ACAAGC
131 ACAAGC
* *
309792 TCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCCACTC
1 TCTTCTCATTATGAACTTCTTCTCCCTCTGTCAGATGAGTTCTTCTCATTATGAACTCTCCACTT
* ** * *
309857 AAAATATTGATCCCTCGAGCGAGGCGTCGCTGATTCGAAATGCCATGAATCGAGCGATAGGTTGA
66 AAAATATTGATCCCTCAAGAAAGGCGTCACTGATTCGAAATGCCATGAATCGAGCGATAGGTCGA
309922 ACAAGC
131 ACAAGC
* *
309928 TCTTCTCATTATGAACTTCTTCTCCCTCTGTCAGATAAGTTCTTCCCATTATGAACTCTCCA-TT
1 TCTTCTCATTATGAACTTCTTCTCCCTCTGTCAGATGAGTTCTTCTCATTATGAACTCTCCACTT
309992 AGAAATATTGA
66 A-AAATATTGA
310003 CCGATTTATT
Statistics
Matches: 184, Mismatches: 19, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
129 16 0.09
130 1 0.01
131 4 0.02
132 3 0.02
133 1 0.01
134 27 0.15
135 2 0.01
136 130 0.71
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (136 bp):
TCTTCTCATTATGAACTTCTTCTCCCTCTGTCAGATGAGTTCTTCTCATTATGAACTCTCCACTT
AAAATATTGATCCCTCAAGAAAGGCGTCACTGATTCGAAATGCCATGAATCGAGCGATAGGTCGA
ACAAGC
Found at i:310763 original size:41 final size:40
Alignment explanation
Indices: 310658--310788 Score: 129
Period size: 41 Copynumber: 3.2 Consensus size: 40
310648 TGGCCCAAAA
* * *
310658 GACTTATCATCTTGCTCGAAAGACTTA-TAGATGACCTGAAG
1 GACTTATCATCATGCTCGAAAGACTTACT-GATGGCCCG-AG
* * * *
310699 GATTTAAGCAGCATGCTCAAAAGACTTACTGATGGCCCGAG
1 GACTT-ATCATCATGCTCGAAAGACTTACTGATGGCCCGAG
* *
310740 GACTTACTCATCATGCTCGAAAGACTTACTAATGGCCCGAAT
1 GACTTA-TCATCATGCTCGAAAGACTTACTGATGGCCCG-AG
310782 GACTTAT
1 GACTTAT
310789 GATGATTCAA
Statistics
Matches: 73, Mismatches: 13, Indels: 8
0.78 0.14 0.09
Matches are distributed among these distances:
40 1 0.01
41 39 0.53
42 32 0.44
43 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (40 bp):
GACTTATCATCATGCTCGAAAGACTTACTGATGGCCCGAG
Found at i:310968 original size:42 final size:42
Alignment explanation
Indices: 310922--311023 Score: 152
Period size: 42 Copynumber: 2.4 Consensus size: 42
310912 ATGGATGACA
310922 CGAAGGACTTACACATCATGCTCGAAAGACCTACTGATGGCC
1 CGAAGGACTTACACATCATGCTCGAAAGACCTACTGATGGCC
* * *
310964 CGAAGGATTTA-AGCATCATGTTCGAAAGACTTACTGATGGCC
1 CGAAGGACTTACA-CATCATGCTCGAAAGACCTACTGATGGCC
*
311006 CGAAGGACTTACTCATCA
1 CGAAGGACTTACACATCA
311024 AGAAACCCTT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
41 1 0.02
42 52 0.98
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.23
Consensus pattern (42 bp):
CGAAGGACTTACACATCATGCTCGAAAGACCTACTGATGGCC
Found at i:311237 original size:53 final size:53
Alignment explanation
Indices: 311117--311308 Score: 230
Period size: 52 Copynumber: 3.7 Consensus size: 53
311107 TGAAAACCAT
* * *
311117 CATCAAGAAATCCCTGAAAATCAGGCTTAGTTTC--TGAAAACTCATTTGAAAA
1 CATCAAGATACCCCTGAAAATCAGGCTTAGTTTCTTTG-AAATTCATTTGAAAA
* * * *
311169 CATCAAGATATCCCTAAAAATTAGGCTTAATTTCTTTGAAATTCATTTGAAAA
1 CATCAAGATACCCCTGAAAATCAGGCTTAGTTTCTTTGAAATTCATTTGAAAA
* * *
311222 CATTAAGATACCCCT-AAAATTAGGCTTAGCTTT-TTTCAAATTCATTTGAAAA
1 CATCAAGATACCCCTGAAAATCAGGCTTAG-TTTCTTTGAAATTCATTTGAAAA
* *
311274 CATCGAGAAACCCCTGAAAATCAGGCTTAGTTTCT
1 CATCAAGATACCCCTGAAAATCAGGCTTAGTTTCT
311309 AAAAATCTTT
Statistics
Matches: 122, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
52 76 0.62
53 44 0.36
54 2 0.02
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.32
Consensus pattern (53 bp):
CATCAAGATACCCCTGAAAATCAGGCTTAGTTTCTTTGAAATTCATTTGAAAA
Found at i:311372 original size:39 final size:39
Alignment explanation
Indices: 311329--311467 Score: 194
Period size: 39 Copynumber: 3.6 Consensus size: 39
311319 TATTTTGGGT
*
311329 GAAACTATCTCAAGTGAGATAAAATCTTATGTTTCGAGC
1 GAAACTATCTCAAGCGAGATAAAATCTTATGTTTCGAGC
* * *
311368 GAAACTATCTCAAGGGAGATAAAATCTTATGTTCCGAGT
1 GAAACTATCTCAAGCGAGATAAAATCTTATGTTTCGAGC
* * *
311407 GAAACTATCTCAAGCGAGATAAAAT-TCA--TTTCAAGG
1 GAAACTATCTCAAGCGAGATAAAATCTTATGTTTCGAGC
311443 GAAACTATCTCAAGCGAGATAAAAT
1 GAAACTATCTCAAGCGAGATAAAAT
311468 TCGTTTGAAG
Statistics
Matches: 92, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
36 30 0.33
38 2 0.02
39 60 0.65
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.27
Consensus pattern (39 bp):
GAAACTATCTCAAGCGAGATAAAATCTTATGTTTCGAGC
Found at i:311454 original size:36 final size:36
Alignment explanation
Indices: 311329--311591 Score: 213
Period size: 36 Copynumber: 7.1 Consensus size: 36
311319 TATTTTGGGT
* * * *
311329 GAAACTATCTCAAGTGAGATAAAATCTTATGTTTCGAGC
1 GAAACTATCTCAAGGGAGATAAAAT-TCA--TTTCAAGG
* * *
311368 GAAACTATCTCAAGGGAGATAAAATCTTATGTTCCGAGT
1 GAAACTATCTCAAGGGAGATAAAAT-TCAT-TT-CAAGG
*
311407 GAAACTATCTCAAGCGAGATAAAATTCATTTCAAGG
1 GAAACTATCTCAAGGGAGATAAAATTCATTTCAAGG
* * * *
311443 GAAACTATCTCAAGCGAGATAAAATTCGTTTGAAGA
1 GAAACTATCTCAAGGGAGATAAAATTCATTTCAAGG
* ** * * *
311479 GAAACTGTCTCAAGGGAGACGAGATGT-GTTTCAAGA
1 GAAACTATCTCAAGGGAGATAAAAT-TCATTTCAAGG
* * ** *
311515 GAAACTATCTCAAGAGAGACAAAATTTTGTTTAAAGG
1 GAAACTATCTCAAGGGAGATAAAA-TTCATTTCAAGG
* * *
311552 GAAAATGTCTCAAGGGAGACAAAATTCATTTCAAGG
1 GAAACTATCTCAAGGGAGATAAAATTCATTTCAAGG
311588 GAAA
1 GAAA
311592 TGATGTTAAA
Statistics
Matches: 192, Mismatches: 27, Indels: 13
0.83 0.12 0.06
Matches are distributed among these distances:
36 98 0.51
37 33 0.17
38 5 0.03
39 56 0.29
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (36 bp):
GAAACTATCTCAAGGGAGATAAAATTCATTTCAAGG
Found at i:311701 original size:65 final size:63
Alignment explanation
Indices: 311540--311703 Score: 179
Period size: 64 Copynumber: 2.6 Consensus size: 63
311530 GAGACAAAAT
* * * * *
311540 TTTGTTTAAAGGGAAAATGTCTCAAGGGAGACAAAATTCATTTCAAGGGAAATGATGTTAAAGA
1 TTTGTTTCAAGAGAAAATGTCTCAAGGAAGAC-AAATTCATTTCAAGGGAAATCATATTAAAGA
* ** *
311604 TTGGTTTCAAGAGAAACCGTCTCAA-GAGAGACAAATTCTTTTTCAAGGGAAA-CATATTCAAAG
1 TTTGTTTCAAGAGAAAATGTCTCAAGGA-AGACAAATTC-ATTTCAAGGGAAATCATATT-AAAG
311667 A
63 A
*
311668 TATTGTTTCAAGAGAAATTGTCTCAAGGAAGACAAA
1 T-TTGTTTCAAGAGAAAATGTCTCAAGGAAGACAAA
311704 ATTTGTTCTT
Statistics
Matches: 83, Mismatches: 12, Indels: 9
0.80 0.12 0.09
Matches are distributed among these distances:
63 11 0.13
64 42 0.51
65 28 0.34
66 2 0.02
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.27
Consensus pattern (63 bp):
TTTGTTTCAAGAGAAAATGTCTCAAGGAAGACAAATTCATTTCAAGGGAAATCATATTAAAGA
Found at i:311891 original size:37 final size:38
Alignment explanation
Indices: 311848--311920 Score: 121
Period size: 37 Copynumber: 1.9 Consensus size: 38
311838 GCTCCGAAGG
*
311848 AAAATGTCTCAAGTGAAACGAAA-TTTATTTTAAGAGA
1 AAAATGTCTCAAGTGAAACAAAATTTTATTTTAAGAGA
*
311885 AAAATGTCTCAAGTGATACAAAATTTTATTTTAAGA
1 AAAATGTCTCAAGTGAAACAAAATTTTATTTTAAGA
311921 AAACAACTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
37 21 0.64
38 12 0.36
ACGTcount: A:0.45, C:0.08, G:0.14, T:0.33
Consensus pattern (38 bp):
AAAATGTCTCAAGTGAAACAAAATTTTATTTTAAGAGA
Found at i:311929 original size:102 final size:100
Alignment explanation
Indices: 311749--312021 Score: 327
Period size: 102 Copynumber: 2.7 Consensus size: 100
311739 ATTTTGGGAG
* * * * * **
311749 AATGTCTCAAGT-AAGACTATATTTGTTTTGAGAG-AAATTGTCTCAAGCGAGACAAAATTTGGT
1 AATGTCTCAAGTGAA-ACGAAATTT-TTTTAAGAGAAAAATGTCTCAAGTGAGACAAAATTTTTT
* *
311812 TCAAGTAAAATAACTTTGAAATTTGTGCTCCGAAGGAA
64 TTAAG-AAAACAACTTTGAAATTTGTGCTCCGAAGGAA
*
311850 AATGTCTCAAGTGAAACGAAATTTATTTTAAGAGAAAAATGTCTCAAGTGATACAAAATTTTATT
1 AATGTCTCAAGTGAAACGAAATTT-TTTTAAGAGAAAAATGTCTCAAGTGAGACAAAATTTT-TT
* *
311915 TTAAGAAAACAACTTTGAAATTTGTGTTTCGAAGGAA
64 TTAAGAAAACAACTTTGAAATTTGTGCTCCGAAGGAA
* * *
311952 AATGGCTCAAGTGAAACGAAA-TTTTTTAAGAGAAAAAATGACTCAAGTTAGACAAAATTTGTTT
1 AATGTCTCAAGTGAAACGAAATTTTTTTAAGAG-AAAAATGTCTCAAGTGAGACAAAATTT-TTT
312016 TTAAGA
64 TTAAGA
312022 GAAAAATGTC
Statistics
Matches: 150, Mismatches: 17, Indels: 10
0.85 0.10 0.06
Matches are distributed among these distances:
100 9 0.06
101 61 0.41
102 75 0.50
103 5 0.03
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.32
Consensus pattern (100 bp):
AATGTCTCAAGTGAAACGAAATTTTTTTAAGAGAAAAATGTCTCAAGTGAGACAAAATTTTTTTT
AAGAAAACAACTTTGAAATTTGTGCTCCGAAGGAA
Found at i:312054 original size:39 final size:38
Alignment explanation
Indices: 311950--312041 Score: 109
Period size: 36 Copynumber: 2.5 Consensus size: 38
311940 GTTTCGAAGG
* * *
311950 AAAATGGCTCAAGTGAAACGAAA--T-TTTTTAAGAGAA
1 AAAATGACTCAAGTGAGACAAAATTTGTTTTTAAGAG-A
*
311986 AAAATGACTCAAGTTAGACAAAATTTGTTTTTAAGAGA
1 AAAATGACTCAAGTGAGACAAAATTTGTTTTTAAGAGA
*
312024 AAAATGTCTCAAGTGAGA
1 AAAATGACTCAAGTGAGA
312042 TGACATTTTG
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
36 19 0.40
38 18 0.38
39 10 0.21
ACGTcount: A:0.46, C:0.09, G:0.18, T:0.27
Consensus pattern (38 bp):
AAAATGACTCAAGTGAGACAAAATTTGTTTTTAAGAGA
Found at i:312060 original size:38 final size:36
Alignment explanation
Indices: 311950--312063 Score: 97
Period size: 38 Copynumber: 3.1 Consensus size: 36
311940 GTTTCGAAGG
* *
311950 AAAATGGCTCAAGTGAAACGAAATTT-TTT-AAGAGAA
1 AAAATGACTCAAGTGAGA-GAAATTTGTTTCAAGAG-A
* * *
311986 AAAATGACTCAAGTTAGACAAAATTTGTTTTTAAGAGA
1 AAAATGACTCAAGTGAGA-GAAATTTG-TTTCAAGAGA
* *
312024 AAAATGTCTCAAGTGAGATGACATTTTGTTTCAAGAGA
1 AAAATGACTCAAGTGAGA-GA-AATTTGTTTCAAGAGA
312062 AA
1 AA
312064 TAACACCCAA
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
36 22 0.34
38 32 0.50
39 10 0.16
ACGTcount: A:0.44, C:0.09, G:0.18, T:0.29
Consensus pattern (36 bp):
AAAATGACTCAAGTGAGAGAAATTTGTTTCAAGAGA
Found at i:315645 original size:34 final size:30
Alignment explanation
Indices: 315607--315675 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
315597 TTGATATAAC
315607 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
315641 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
315670 AATTTA
1 AATTTA
315676 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:315686 original size:29 final size:30
Alignment explanation
Indices: 315616--315675 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
315606 CAATTTAAGG
315616 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
315647 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
315676 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:317148 original size:2 final size:2
Alignment explanation
Indices: 317141--317172 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
317131 AGCTTTATTA
317141 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
317173 GGGTATACAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:323691 original size:14 final size:15
Alignment explanation
Indices: 323668--323699 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
323658 GTTGGGTTTT
323668 TGAGGTTTTGGGTTA
1 TGAGGTTTTGGGTTA
323683 TGAGG-TTTGGGTTA
1 TGAGGTTTTGGGTTA
323697 TGA
1 TGA
323700 AAAATGGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.16, C:0.00, G:0.41, T:0.44
Consensus pattern (15 bp):
TGAGGTTTTGGGTTA
Found at i:326066 original size:34 final size:35
Alignment explanation
Indices: 326027--326097 Score: 135
Period size: 34 Copynumber: 2.1 Consensus size: 35
326017 TATTATATTA
326027 TGCAAGGGGATTATGAGTCATGGATA-TTTGATTT
1 TGCAAGGGGATTATGAGTCATGGATATTTTGATTT
326061 TGCAAGGGGATTATGAGTCATGGATATTTTGATTT
1 TGCAAGGGGATTATGAGTCATGGATATTTTGATTT
326096 TG
1 TG
326098 ATTTCAGTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 26 0.72
35 10 0.28
ACGTcount: A:0.25, C:0.06, G:0.30, T:0.39
Consensus pattern (35 bp):
TGCAAGGGGATTATGAGTCATGGATATTTTGATTT
Found at i:327124 original size:2 final size:2
Alignment explanation
Indices: 327117--327172 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
327107 TGGTTATTAT
327117 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
327159 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
327173 AATAAATTAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:328351 original size:19 final size:19
Alignment explanation
Indices: 328327--328405 Score: 79
Period size: 19 Copynumber: 4.2 Consensus size: 19
328317 AAGTCAACCC
328327 GACCTGACCCATTGACTTT
1 GACCTGACCCATTGACTTT
*
328346 GACCTGACCCGTTGACTTT
1 GACCTGACCCATTGACTTT
* * * *
328365 AACCCGACCCGTTGGCTTT
1 GACCTGACCCATTGACTTT
* *
328384 GACAC-AACCCATTAACTTT
1 GAC-CTGACCCATTGACTTT
328403 GAC
1 GAC
328406 TCGAGTTGAT
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
19 49 0.98
20 1 0.02
ACGTcount: A:0.23, C:0.33, G:0.16, T:0.28
Consensus pattern (19 bp):
GACCTGACCCATTGACTTT
Found at i:332574 original size:19 final size:19
Alignment explanation
Indices: 332552--332612 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
332542 CGAGTCAACC
332552 GACCTGACCCATTGACTTT
1 GACCTGACCCATTGACTTT
* *
332571 GACCTAACCCTTTGACTTT
1 GACCTGACCCATTGACTTT
* *
332590 GA-ATCGACCTATTGACTTT
1 GACCT-GACCCATTGACTTT
332609 GACC
1 GACC
332613 AGAGTTGATC
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
18 1 0.03
19 32 0.97
ACGTcount: A:0.23, C:0.30, G:0.15, T:0.33
Consensus pattern (19 bp):
GACCTGACCCATTGACTTT
Found at i:332638 original size:13 final size:13
Alignment explanation
Indices: 332617--332646 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
332607 TTGACCAGAG
*
332617 TTGATCGTTGACT
1 TTGACCGTTGACT
332630 TTGACCGTTGACT
1 TTGACCGTTGACT
332643 TTGA
1 TTGA
332647 ACCAAAAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.17, G:0.23, T:0.43
Consensus pattern (13 bp):
TTGACCGTTGACT
Found at i:336938 original size:19 final size:18
Alignment explanation
Indices: 336913--336985 Score: 74
Period size: 19 Copynumber: 3.9 Consensus size: 18
336903 TCAACCCGAC
*
336913 CCATTGACTTTGACCCAA
1 CCATTGACTTTGACCAAA
*
336931 CTCGTTGACTTTGAACCAAA
1 C-CATTGACTTTG-ACCAAA
**
336951 CCATTGACTTTGACCTGA
1 CCATTGACTTTGACCAAA
*
336969 CCTATTGACTTTAACCA
1 CC-ATTGACTTTGACCA
336986 GAGTGTATCA
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
18 7 0.16
19 32 0.71
20 6 0.13
ACGTcount: A:0.27, C:0.29, G:0.12, T:0.32
Consensus pattern (18 bp):
CCATTGACTTTGACCAAA
Found at i:336977 original size:38 final size:37
Alignment explanation
Indices: 336913--336985 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 37
336903 TCAACCCGAC
*
336913 CCATTGACTTTGACCCAACTCGTTGACTTTGAACCAAA
1 CCATTGACTTTGACCCAACTCATTGACTTT-AACCAAA
**
336951 CCATTGACTTTGACCTGAC-CTATTGACTTTAACCA
1 CCATTGACTTTGACCCAACTC-ATTGACTTTAACCA
336986 GAGTGTATCA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
37 6 0.19
38 25 0.81
ACGTcount: A:0.27, C:0.29, G:0.12, T:0.32
Consensus pattern (37 bp):
CCATTGACTTTGACCCAACTCATTGACTTTAACCAAA
Found at i:338712 original size:35 final size:35
Alignment explanation
Indices: 338591--338719 Score: 118
Period size: 35 Copynumber: 3.6 Consensus size: 35
338581 GTTCAGTTCT
* * * *
338591 GATCAAGCTGGTAAATCCTTATATATGCTCAGTACT
1 GATCAAGCTGGTAATTCCTTATATAAGTTCAG-ACC
* * *
338627 GATC-AGCTCGTAATTCCTTATTGTAGGTTCA-ACTTC
1 GATCAAGCTGGTAATTCCTTA-TATAAGTTCAGAC--C
* *
338663 GATCAAACTAGTAATTCCTTATATAAGTTCAGACC
1 GATCAAGCTGGTAATTCCTTATATAAGTTCAGACC
*
338698 GATCAAGTTGGTAATTCCTTAT
1 GATCAAGCTGGTAATTCCTTAT
338720 GGACCTAAAA
Statistics
Matches: 75, Mismatches: 13, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
34 2 0.03
35 34 0.45
36 23 0.31
37 16 0.21
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (35 bp):
GATCAAGCTGGTAATTCCTTATATAAGTTCAGACC
Found at i:340352 original size:95 final size:96
Alignment explanation
Indices: 340167--340356 Score: 253
Period size: 95 Copynumber: 2.0 Consensus size: 96
340157 TACCGTTAAG
*
340167 GTAGTATCGATACCATTGGAAAGGTATCGATACCAAGCAAACATCGAATCTAATTTTGGTAACGA
1 GTAGTATCGATACCATTGGAAAGGTATCGATACCAAGCAAACATCGAACCTAATTTTGGTAACGA
* * *
340232 TACCGTACGGAGGTATCGGTGCCATAGTATA
66 TACCGGACGGAAGTATCGGTACCATAGTATA
* * *
340263 GTAGTATTGATACCA-TGGTAAGGGTATCGATACCAGGC-AACATCGAACCTAATTTTGG-AATC
1 GTAGTATCGATACCATTGG-AAAGGTATCGATACCAAGCAAACATCGAACCTAATTTTGGTAA-C
*
340325 GATACCCGGA-GGAAGTATTGGTACCATAGTAT
64 GATA-CCGGACGGAAGTATCGGTACCATAGTAT
340357 TGAATTATCA
Statistics
Matches: 83, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
94 2 0.02
95 46 0.55
96 35 0.42
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (96 bp):
GTAGTATCGATACCATTGGAAAGGTATCGATACCAAGCAAACATCGAACCTAATTTTGGTAACGA
TACCGGACGGAAGTATCGGTACCATAGTATA
Found at i:340372 original size:95 final size:96
Alignment explanation
Indices: 340189--340390 Score: 225
Period size: 95 Copynumber: 2.1 Consensus size: 96
340179 CCATTGGAAA
* * * *
340189 GGTATCGATACCAAGCAAACATCGAATCTAATTTTGGTAACGATACCGTACGGAGGTATCGGTGC
1 GGTATCGATACCAAGCAAACATCGAACCTAATTTTGGTAACGATACCGGACGGAAGTATCGGTAC
* * *
340254 CATAGTATAGTAGTATTGATACCATGGTAAG-
66 CATAGTATAGAAGTATAGATACCAGGGT-AGT
* *
340285 GGTATCGATACCAGGC-AACATCGAACCTAATTTTGG-AATCGATACCCGGA-GGAAGTATTGGT
1 GGTATCGATACCAAGCAAACATCGAACCTAATTTTGGTAA-CGATA-CCGGACGGAAGTATCGGT
* *
340347 ACCATAGTATTGAATTATCAG-TACCAGGGTAGT
64 ACCATAGTATAGAAGTAT-AGATACCAGGGTAGT
*
340380 AGTATCGATAC
1 GGTATCGATAC
340391 TATTGATCTT
Statistics
Matches: 90, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
94 4 0.04
95 66 0.73
96 20 0.22
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (96 bp):
GGTATCGATACCAAGCAAACATCGAACCTAATTTTGGTAACGATACCGGACGGAAGTATCGGTAC
CATAGTATAGAAGTATAGATACCAGGGTAGT
Found at i:340908 original size:34 final size:34
Alignment explanation
Indices: 340849--340913 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
340839 TCATAGCTAA
*
340849 AATGCACATGGATGCTTTATCGGCATAAAAGAAT
1 AATGCACATGGATGCATTATCGGCATAAAAGAAT
* * * *
340883 AATGCATATGGGTGCATTATTGGCATGAAAG
1 AATGCACATGGATGCATTATCGGCATAAAAG
340914 GATGGCCTAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (34 bp):
AATGCACATGGATGCATTATCGGCATAAAAGAAT
Found at i:340931 original size:79 final size:79
Alignment explanation
Indices: 340794--340958 Score: 267
Period size: 79 Copynumber: 2.1 Consensus size: 79
340784 AAATGAATGA
* *
340794 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAGCTAAAATGCACATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGGCATACCTAAAATGCACATG
*
340859 GATGCTTTATCGGC
66 GATGCATTATCGGC
* * *
340873 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGGCCTACCTGAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGGCATACCTAAAATGCACATG
*
340938 GGTGCATTATCGGC
66 GATGCATTATCGGC
340952 ATAAAAG
1 ATAAAAG
340959 TATACCACAT
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.27
Consensus pattern (79 bp):
ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGGCATACCTAAAATGCACATG
GATGCATTATCGGC
Found at i:353219 original size:40 final size:41
Alignment explanation
Indices: 353175--353423 Score: 122
Period size: 37 Copynumber: 6.7 Consensus size: 41
353165 TATATATTAA
353175 AATATAATGTAGTTTTT-G-AAA-ATATTTTTTGAAAACATAT
1 AATATAA--TAGTTTTTAGAAAACATATTTTTTGAAAACATAT
* *
353215 AATAT-ATAGTTTTTAGAAAACATTTTTTTTGAAAGCATAT
1 AATATAATAGTTTTTAGAAAACATATTTTTTGAAAACATAT
* **
353255 AATAT-ATAG-TTTTA-AAAA-TTGGTTTTTG-AAA-ATAT
1 AATATAATAGTTTTTAGAAAACATATTTTTTGAAAACATAT
* ** *
353290 -A-AT-AT-GGTTTT-G-AAA-ATACGTTTTGAAACCATAT
1 AATATAATAGTTTTTAGAAAACATATTTTTTGAAAACATAT
* ** *
353324 ATTAT-ATAG-TTTT-GAAAACA-AAATTTTGAAAACATGT
1 AATATAATAGTTTTTAGAAAACATATTTTTTGAAAACATAT
**
353361 AATATAGATAG-TTTTA-AAAAC--GGTTTTTGAAAACATAT
1 AATATA-ATAGTTTTTAGAAAACATATTTTTTGAAAACATAT
*
353399 -ATA-ATATAG-TTTTGGAAAACATATT
1 AATATA-ATAGTTTTTAGAAAACATATT
353424 ATATATATAT
Statistics
Matches: 166, Mismatches: 25, Indels: 37
0.73 0.11 0.16
Matches are distributed among these distances:
32 10 0.06
33 10 0.06
34 5 0.03
35 4 0.02
36 20 0.12
37 44 0.27
38 19 0.11
39 23 0.14
40 31 0.19
ACGTcount: A:0.43, C:0.04, G:0.12, T:0.41
Consensus pattern (41 bp):
AATATAATAGTTTTTAGAAAACATATTTTTTGAAAACATAT
Found at i:353399 original size:109 final size:110
Alignment explanation
Indices: 353173--353417 Score: 284
Period size: 109 Copynumber: 2.2 Consensus size: 110
353163 TATATATATT
* **
353173 AAAATATAATGTAGTTTTTGAAAATATTTTTTGAAAACATATAATATATAGTTTTTAGAAAACAT
1 AAAATATAATATAG-TTTTGAAAATACGTTTTGAAAACATATAATATATAGTTTTTAGAAAACAT
*** * *
353238 TTTTTTTGAAAGCATATAATATATAGTTTTAAAAATTGGTTTTTG-
65 AAATTTTGAAAACATATAATATATAGTTTTAAAAATCGGTTTTTGA
* * *
353283 AAAATATAATATGGTTTTGAAAATACGTTTTGAAACCATATATTATATAG-TTTT-GAAAACA-A
1 AAAATATAATATAGTTTTGAAAATACGTTTTGAAAACATATAATATATAGTTTTTAGAAAACATA
*
353345 AATTTTGAAAACATGTAATATAGATAGTTTTAAAAA-CGGTTTTTGAA
66 AATTTTGAAAACATATAATAT--ATAGTTTTAAAAATCGGTTTTTG-A
353392 AACATATATAATATAGTTTTGGAAAA
1 AA-A-ATATAATATAGTTTT-GAAAA
353418 CATATTATAT
Statistics
Matches: 115, Mismatches: 13, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
106 17 0.15
107 15 0.13
108 17 0.15
109 34 0.30
110 13 0.11
111 14 0.12
112 5 0.04
ACGTcount: A:0.43, C:0.04, G:0.12, T:0.41
Consensus pattern (110 bp):
AAAATATAATATAGTTTTGAAAATACGTTTTGAAAACATATAATATATAGTTTTTAGAAAACATA
AATTTTGAAAACATATAATATATAGTTTTAAAAATCGGTTTTTGA
Found at i:353416 original size:24 final size:26
Alignment explanation
Indices: 353383--353432 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 26
353373 TTTAAAAACG
*
353383 GTTTTTGAAAACATA-TATA-ATATA
1 GTTTTGGAAAACATATTATATATATA
353407 GTTTTGGAAAACATATTATATATATA
1 GTTTTGGAAAACATATTATATATATA
353433 TATATAGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 14 0.61
25 4 0.17
26 5 0.22
ACGTcount: A:0.44, C:0.04, G:0.10, T:0.42
Consensus pattern (26 bp):
GTTTTGGAAAACATATTATATATATA
Found at i:353497 original size:69 final size:69
Alignment explanation
Indices: 353362--353513 Score: 186
Period size: 69 Copynumber: 2.2 Consensus size: 69
353352 AAAACATGTA
* * * *
353362 ATATAGATAG-TTTTAAAAACGGTTTTTGAAAACATATATAATATAGTTTTGGAAAACATATTAT
1 ATATATATAGTTTTTAAAAACGATTTTTGAAAACATATATAATATAATTTTGGAAAACATATAAT
353426 ATAT
66 ATAT
* * *
353430 ATATATATAGTTTTTTAAAACGATTTTTGGAAACATATATAATATATAATTTTTG-AAA-ATATA
1 ATATATATAGTTTTTAAAAACGATTTTTGAAAACATATAT-A-ATATAATTTTGGAAAACATATA
353493 ATATAT
64 ATATAT
*
353499 GT-TATATAGTTTTTA
1 ATATATATAGTTTTTA
353514 TTATATATTA
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
68 21 0.29
69 37 0.51
70 4 0.06
71 10 0.14
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (69 bp):
ATATATATAGTTTTTAAAAACGATTTTTGAAAACATATATAATATAATTTTGGAAAACATATAAT
ATAT
Found at i:353517 original size:14 final size:14
Alignment explanation
Indices: 353500--353547 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 14
353490 ATAATATATG
*
353500 TTATATAGTTTTTA
1 TTATATATTTTTTA
353514 TTATATATTATTTATA
1 TTATATATT-TTT-TA
353530 TTAT-TATTTTTTA
1 TTATATATTTTTTA
353543 CTTAT
1 -TTAT
353548 TTTTATTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
13 2 0.07
14 15 0.50
15 7 0.23
16 6 0.20
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (14 bp):
TTATATATTTTTTA
Found at i:353558 original size:33 final size:33
Alignment explanation
Indices: 353521--353592 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
353511 TTATTATATA
* *
353521 TTATTTATA-TTATTATTTTTTACTTATTTTTAT
1 TTATTTATATTTA-TATTATTTACTTAGTTTTAT
* *
353554 TTATTTTTATTTATATTATTTATTTAGTTTTAT
1 TTATTTATATTTATATTATTTACTTAGTTTTAT
353587 TT-TTTA
1 TTATTTA
353593 AAAAGGTCTA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
32 3 0.09
33 27 0.82
34 3 0.09
ACGTcount: A:0.24, C:0.01, G:0.01, T:0.74
Consensus pattern (33 bp):
TTATTTATATTTATATTATTTACTTAGTTTTAT
Found at i:353587 original size:39 final size:38
Alignment explanation
Indices: 353498--353590 Score: 100
Period size: 39 Copynumber: 2.3 Consensus size: 38
353488 ATATAATATA
353498 TGTTATATAGTTTTTATTATATATTATTTATATTATTATT
1 TGTTAT-TA-TTTTTATTATATATTATTTATATTATTATT
* *
353538 TTTTACTTATTTTTATT-TATTTTTATTTATATTATTTATT
1 TGTTA-TTATTTTTATTATA-TATTATTTATATTA-TTATT
353578 TAGTT-TTATTTTT
1 T-GTTATTATTTTT
353591 TAAAAAGGTC
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
38 2 0.04
39 29 0.63
40 12 0.26
41 3 0.07
ACGTcount: A:0.25, C:0.01, G:0.03, T:0.71
Consensus pattern (38 bp):
TGTTATTATTTTTATTATATATTATTTATATTATTATT
Found at i:353588 original size:10 final size:10
Alignment explanation
Indices: 353508--353578 Score: 60
Period size: 10 Copynumber: 7.3 Consensus size: 10
353498 TGTTATATAG
353508 TTTTTA-TTA
1 TTTTTATTTA
*
353517 TATATTATTTA
1 T-TTTTATTTA
*
353528 -TATTA-TTA
1 TTTTTATTTA
*
353536 TTTTTTACTTA
1 -TTTTTATTTA
353547 TTTTTATTTA
1 TTTTTATTTA
353557 TTTTTATTTA
1 TTTTTATTTA
*
353567 -TATTATTTA
1 TTTTTATTTA
353576 TTT
1 TTT
353579 AGTTTTATTT
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
8 3 0.06
9 14 0.27
10 28 0.55
11 6 0.12
ACGTcount: A:0.25, C:0.01, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTTTATTTA
Found at i:357101 original size:98 final size:98
Alignment explanation
Indices: 356932--357128 Score: 394
Period size: 98 Copynumber: 2.0 Consensus size: 98
356922 TTTGAATTGG
356932 CATCCAGAAAAAGGAAACATGTCGACATTCGATTACCCCGTACTCTCACGTGCTGACATTATCTC
1 CATCCAGAAAAAGGAAACATGTCGACATTCGATTACCCCGTACTCTCACGTGCTGACATTATCTC
356997 AATCCTGGCGGAGTCACAGATCGCCGCCGTTAC
66 AATCCTGGCGGAGTCACAGATCGCCGCCGTTAC
357030 CATCCAGAAAAAGGAAACATGTCGACATTCGATTACCCCGTACTCTCACGTGCTGACATTATCTC
1 CATCCAGAAAAAGGAAACATGTCGACATTCGATTACCCCGTACTCTCACGTGCTGACATTATCTC
357095 AATCCTGGCGGAGTCACAGATCGCCGCCGTTAC
66 AATCCTGGCGGAGTCACAGATCGCCGCCGTTAC
357128 C
1 C
357129 GACAACGATT
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 99 1.00
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.22
Consensus pattern (98 bp):
CATCCAGAAAAAGGAAACATGTCGACATTCGATTACCCCGTACTCTCACGTGCTGACATTATCTC
AATCCTGGCGGAGTCACAGATCGCCGCCGTTAC
Found at i:361130 original size:31 final size:31
Alignment explanation
Indices: 361027--361131 Score: 97
Period size: 31 Copynumber: 3.4 Consensus size: 31
361017 ATTCAGTTTG
* *
361027 GTTCGGGTCAAAATCGTAG-TGGTTGGTTTTCA
1 GTTCGGGTCAATATCG-GGTTGGTTGG-TTTCA
* * * *
361059 GTTCGGGTTAATATCGGGTCGGTTAGCTTCAA
1 GTTCGGGTCAATATCGGGTTGGTTGGTTTC-A
*
361091 GTT-GGGTCAATATCGGGTTGGTTGGTTTCG
1 GTTCGGGTCAATATCGGGTTGGTTGGTTTCA
*
361121 GTTCAGGTCAA
1 GTTCGGGTCAA
361132 CCATTAGATT
Statistics
Matches: 58, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
30 3 0.05
31 32 0.55
32 23 0.40
ACGTcount: A:0.17, C:0.13, G:0.33, T:0.36
Consensus pattern (31 bp):
GTTCGGGTCAATATCGGGTTGGTTGGTTTCA
Found at i:361439 original size:16 final size:16
Alignment explanation
Indices: 361418--361448 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
361408 AGAGATGATC
361418 TTTTAACCGAGGAAAG
1 TTTTAACCGAGGAAAG
361434 TTTTAACCGAGGAAA
1 TTTTAACCGAGGAAA
361449 TCTTATTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.13, G:0.23, T:0.26
Consensus pattern (16 bp):
TTTTAACCGAGGAAAG
Found at i:361657 original size:16 final size:16
Alignment explanation
Indices: 361638--361682 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
361628 TCGGATCGGA
*
361638 TTCGGGTTGCTTTTGG
1 TTCGGGTTACTTTTGG
*
361654 TTCGGGTTAATTTTGG
1 TTCGGGTTACTTTTGG
* *
361670 TTCAGGTTTCTTT
1 TTCGGGTTACTTT
361683 CGTTTCAACT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.07, C:0.11, G:0.29, T:0.53
Consensus pattern (16 bp):
TTCGGGTTACTTTTGG
Found at i:366875 original size:20 final size:20
Alignment explanation
Indices: 366826--366880 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
366816 AACTGATCAA
* *
366826 AGTCAACTCAGACCGAACTG
1 AGTCAACTCGGACCAAACTG
366846 AGTCAACTCGGACCAAA-TCG
1 AGTCAACTCGGACCAAACT-G
*
366866 AGTCAACTCGAACCA
1 AGTCAACTCGGACCA
366881 GTCTGACCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.36, C:0.31, G:0.18, T:0.15
Consensus pattern (20 bp):
AGTCAACTCGGACCAAACTG
Found at i:368058 original size:27 final size:27
Alignment explanation
Indices: 368007--368060 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
367997 ATGTCCTTGA
*
368007 CCCTAAAATAACTAAAATACCCTCTAG
1 CCCTAAAATAACTAAAATAACCTCTAG
* * *
368034 CCCTAGAATGACTAAAATAATCTCTAG
1 CCCTAAAATAACTAAAATAACCTCTAG
368061 TATTGAAATG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.43, C:0.26, G:0.07, T:0.24
Consensus pattern (27 bp):
CCCTAAAATAACTAAAATAACCTCTAG
Found at i:369829 original size:26 final size:25
Alignment explanation
Indices: 369785--369833 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
369775 GTGACGAGTT
369785 TTATTAAAAAATATTTTTTTCAAGA
1 TTATTAAAAAATATTTTTTTCAAGA
* *
369810 TTATTAAGTAAATTTTTTTTTCAA
1 TTATTAA-AAAATATTTTTTTCAA
369834 AAATTAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (25 bp):
TTATTAAAAAATATTTTTTTCAAGA
Found at i:369839 original size:24 final size:26
Alignment explanation
Indices: 369793--369840 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
369783 TTTTATTAAA
*
369793 AAATATTTTTTTCAAGATTATTAAGT
1 AAATATTTTTTTCAAGATAATTAAGT
*
369819 AAATTTTTTTTTCAA-A-AATTAA
1 AAATATTTTTTTCAAGATAATTAA
369841 ATACGCCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 5 0.25
25 1 0.05
26 14 0.70
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (26 bp):
AAATATTTTTTTCAAGATAATTAAGT
Found at i:370089 original size:6 final size:6
Alignment explanation
Indices: 370071--370132 Score: 51
Period size: 6 Copynumber: 10.5 Consensus size: 6
370061 GAAGAGGGAG
* *
370071 GAAG-A GAAGAA GAATAA GAAGAA GAA-AGA GAATAA GAAGAA GAA-AGA
1 GAAGAA GAAGAA GAAGAA GAAGAA GAAGA-A GAAGAA GAAGAA GAAGA-A
370118 GAATG-A GAAGAA GAA
1 GAA-GAA GAAGAA GAA
370133 TAAAGAGTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 13
0.75 0.05 0.21
Matches are distributed among these distances:
5 7 0.15
6 39 0.83
7 1 0.02
ACGTcount: A:0.65, C:0.00, G:0.31, T:0.05
Consensus pattern (6 bp):
GAAGAA
Found at i:370092 original size:12 final size:12
Alignment explanation
Indices: 370075--370135 Score: 63
Period size: 12 Copynumber: 5.1 Consensus size: 12
370065 AGGGAGGAAG
370075 AGAAGAAGAATA
1 AGAAGAAGAATA
370087 AGAAGAAGAA-A
1 AGAAGAAGAATA
* *
370098 GAGAATAAGAAGA
1 -AGAAGAAGAATA
*
370111 AGAA-AGAGAATG
1 AGAAGA-AGAATA
370123 AGAAGAAGAATA
1 AGAAGAAGAATA
370135 A
1 A
370136 AGAGTTAGTA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
11 2 0.05
12 37 0.90
13 2 0.05
ACGTcount: A:0.66, C:0.00, G:0.28, T:0.07
Consensus pattern (12 bp):
AGAAGAAGAATA
Found at i:370139 original size:21 final size:18
Alignment explanation
Indices: 370071--370132 Score: 97
Period size: 18 Copynumber: 3.3 Consensus size: 18
370061 GAAGAGGGAG
370071 GAAGAGAAGAAGAATAAGAA
1 GAAGA-AAG-AGAATAAGAA
370091 GAAGAAAGAGAATAAGAA
1 GAAGAAAGAGAATAAGAA
*
370109 GAAGAAAGAGAATGAGAA
1 GAAGAAAGAGAATAAGAA
370127 GAAGAA
1 GAAGAA
370133 TAAAGAGTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
18 33 0.80
19 3 0.07
20 5 0.12
ACGTcount: A:0.65, C:0.00, G:0.31, T:0.05
Consensus pattern (18 bp):
GAAGAAAGAGAATAAGAA
Found at i:383231 original size:23 final size:24
Alignment explanation
Indices: 383189--383242 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 24
383179 CAATGATTAA
*
383189 ATGTAAATTAATATAGTTTAATTT
1 ATGTAAATTAATATAATTTAATTT
*
383213 ATGTAAATT-ATATAATTTAGTTT
1 ATGTAAATTAATATAATTTAATTT
383236 ATGTAAA
1 ATGTAAA
383243 GAAAAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
23 19 0.68
24 9 0.32
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (24 bp):
ATGTAAATTAATATAATTTAATTT
Found at i:383827 original size:17 final size:17
Alignment explanation
Indices: 383795--383829 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
383785 ATAAATTACA
*
383795 AGGCAACAATAAGCAGT
1 AGGCAACAAGAAGCAGT
*
383812 AGGCAACAAGATGCAGT
1 AGGCAACAAGAAGCAGT
383829 A
1 A
383830 TTTATGCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (17 bp):
AGGCAACAAGAAGCAGT
Found at i:384222 original size:34 final size:32
Alignment explanation
Indices: 384154--384224 Score: 79
Period size: 34 Copynumber: 2.2 Consensus size: 32
384144 TTAAACACCC
**
384154 TAAAAAATTAAAATTAAAATTAAAATAATTAA
1 TAAAAAATTAAAATTAAAATTAAAATAAAAAA
* * *
384186 TAAAAAATTGAAATATTGAGATTAACATAAAAAA
1 TAAAAAATT-AAA-ATTAAAATTAAAATAAAAAA
384220 TAAAA
1 TAAAA
384225 CAGTTCTATC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 9 0.28
33 3 0.09
34 20 0.62
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.28
Consensus pattern (32 bp):
TAAAAAATTAAAATTAAAATTAAAATAAAAAA
Found at i:386862 original size:12 final size:12
Alignment explanation
Indices: 386837--386885 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
386827 ATAATTGGAT
386837 TTTGG-TTCGGG
1 TTTGGATTCGGG
*
386848 TTTGGATTCGTG
1 TTTGGATTCGGG
386860 TTT-GAGTTCGGG
1 TTTGGA-TTCGGG
*
386872 TTTAGATTCGGG
1 TTTGGATTCGGG
386884 TT
1 TT
386886 CGAGTTTAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
11 7 0.21
12 24 0.73
13 2 0.06
ACGTcount: A:0.08, C:0.08, G:0.37, T:0.47
Consensus pattern (12 bp):
TTTGGATTCGGG
Found at i:386872 original size:24 final size:24
Alignment explanation
Indices: 386837--386911 Score: 80
Period size: 24 Copynumber: 3.2 Consensus size: 24
386827 ATAATTGGAT
* *
386837 TTTG-GTTCGGGTTTGGATTCGTG
1 TTTGAGTTCGGGTTTAGATTCGGG
386860 TTTGAGTTCGGGTTTAGATTCGGG
1 TTTGAGTTCGGGTTTAGATTCGGG
* ** * *
386884 TTCGAGTTTAGGTTCAGGTTCGGG
1 TTTGAGTTCGGGTTTAGATTCGGG
386908 TTTG
1 TTTG
386912 GGTTTGAGTT
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 4 0.09
24 39 0.91
ACGTcount: A:0.09, C:0.09, G:0.37, T:0.44
Consensus pattern (24 bp):
TTTGAGTTCGGGTTTAGATTCGGG
Found at i:386915 original size:12 final size:12
Alignment explanation
Indices: 386840--386915 Score: 53
Period size: 12 Copynumber: 6.3 Consensus size: 12
386830 ATTGGATTTT
386840 GGTTCGGGTTTG
1 GGTTCGGGTTTG
* *
386852 GATTCGTGTTTG
1 GGTTCGGGTTTG
* *
386864 AGTTCGGGTTTA
1 GGTTCGGGTTTG
* *
386876 GATTCGGGTTCG
1 GGTTCGGGTTTG
* ** **
386888 AGTTTAGGTTCA
1 GGTTCGGGTTTG
386900 GGTTCGGGTTTG
1 GGTTCGGGTTTG
386912 GGTT
1 GGTT
386916 TGAGTTCAGG
Statistics
Matches: 44, Mismatches: 20, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
12 44 1.00
ACGTcount: A:0.09, C:0.09, G:0.39, T:0.42
Consensus pattern (12 bp):
GGTTCGGGTTTG
Found at i:386915 original size:18 final size:18
Alignment explanation
Indices: 386865--386915 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
386855 TCGTGTTTGA
* *
386865 GTTCGGGTTTAGATTCGG
1 GTTCGGGTTTAGGTTCAG
*
386883 GTTCGAGTTTAGGTTCAG
1 GTTCGGGTTTAGGTTCAG
*
386901 GTTCGGGTTTGGGTT
1 GTTCGGGTTTAGGTT
386916 TGAGTTCAGG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.10, C:0.10, G:0.39, T:0.41
Consensus pattern (18 bp):
GTTCGGGTTTAGGTTCAG
Found at i:386916 original size:24 final size:24
Alignment explanation
Indices: 386878--386927 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
386868 CGGGTTTAGA
386878 TTCGGGTTCGAGTTT-AGGTTCAGG
1 TTCGGGTTCGAGTTTGA-GTTCAGG
* *
386902 TTCGGGTTTGGGTTTGAGTTCAGG
1 TTCGGGTTCGAGTTTGAGTTCAGG
386926 TT
1 TT
386928 TGGGATAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 22 0.96
25 1 0.04
ACGTcount: A:0.10, C:0.10, G:0.38, T:0.42
Consensus pattern (24 bp):
TTCGGGTTCGAGTTTGAGTTCAGG
Found at i:386922 original size:18 final size:18
Alignment explanation
Indices: 386859--386928 Score: 61
Period size: 18 Copynumber: 3.9 Consensus size: 18
386849 TTGGATTCGT
386859 GTTTGAGTTCGGGTTTAG
1 GTTTGAGTTCGGGTTTAG
* * * *
386877 ATTCGGGTTCGAGTTTAG
1 GTTTGAGTTCGGGTTTAG
* *
386895 G-TTCAGGTTCGGGTTTGG
1 GTTTGA-GTTCGGGTTTAG
*
386913 GTTTGAGTTCAGGTTT
1 GTTTGAGTTCGGGTTT
386929 GGGATAGAAG
Statistics
Matches: 38, Mismatches: 12, Indels: 4
0.70 0.22 0.07
Matches are distributed among these distances:
17 1 0.03
18 34 0.89
19 3 0.08
ACGTcount: A:0.11, C:0.09, G:0.37, T:0.43
Consensus pattern (18 bp):
GTTTGAGTTCGGGTTTAG
Found at i:387679 original size:6 final size:6
Alignment explanation
Indices: 387668--387788 Score: 59
Period size: 6 Copynumber: 21.3 Consensus size: 6
387658 ACTATTTATA
387668 ATTAAT ATTAAT A-TAA- ATTATAT ATT-AT AATTAAT ATTAAT A-T-A-
1 ATTAAT ATTAAT ATTAAT ATTA-AT ATTAAT -ATTAAT ATTAAT ATTAAT
* *
387712 ATTAAT ATTAA- CTT-AT ATTAAT A-TAAT ATGT--G ATTAAT ATTAAT
1 ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT AT-TAAT ATTAAT ATTAAT
* * * *
387756 A-TAAA ATATAGT CTATAAA ATTAAT ATTAAT AT
1 ATTAAT AT-TAAT AT-TAAT ATTAAT ATTAAT AT
387789 AAATTATATT
Statistics
Matches: 87, Mismatches: 12, Indels: 32
0.66 0.09 0.24
Matches are distributed among these distances:
3 1 0.01
4 5 0.06
5 24 0.28
6 44 0.51
7 13 0.15
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (6 bp):
ATTAAT
Found at i:387731 original size:25 final size:28
Alignment explanation
Indices: 387663--387804 Score: 122
Period size: 29 Copynumber: 5.2 Consensus size: 28
387653 TAAAAACTAT
387663 TTATAATTAATATTAATATAAATTATATA
1 TTATAATTAATATTAATAT-AATTATATA
387692 TTATAATTAATATTAATATAATTA-ATA
1 TTATAATTAATATTAATATAATTATATA
* *
387719 TTA-ACTT-ATATTAATATAA-TATGTGA
1 TTATAATTAATATTAATATAATTATAT-A
* *
387745 TTA-ATATTAATA-TAAAAT-A-TAGTCTA
1 TTATA-ATTAATATTAATATAATTA-TATA
* *
387771 -TAAAATTAATATTAATATAAATTATATT
1 TTATAATTAATATTAATAT-AATTATATA
387799 TTATAA
1 TTATAA
387805 ATTATATAGT
Statistics
Matches: 93, Mismatches: 9, Indels: 22
0.75 0.07 0.18
Matches are distributed among these distances:
24 2 0.02
25 22 0.24
26 18 0.19
27 15 0.16
28 11 0.12
29 25 0.27
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.46
Consensus pattern (28 bp):
TTATAATTAATATTAATATAATTATATA
Found at i:387754 original size:22 final size:21
Alignment explanation
Indices: 387666--387759 Score: 72
Period size: 22 Copynumber: 4.4 Consensus size: 21
387656 AAACTATTTA
387666 TAAT-TAATATTAATATAA-AT
1 TAATATAATATTAAT-TAATAT
*
387686 TATATATTATAATTAATATTAATA-
1 TA-ATATAAT-ATT-A-ATTAATAT
387710 TAAT-TAATATTAACTT-ATAT
1 TAATATAATATTAA-TTAATAT
*
387730 TAATATAATATGTGATTAATAT
1 TAATATAATAT-TAATTAATAT
387752 TAATATAA
1 TAATATAA
387760 AATATAGTCT
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
19 4 0.07
20 9 0.15
21 13 0.22
22 20 0.33
23 5 0.08
24 6 0.10
25 3 0.05
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (21 bp):
TAATATAATATTAATTAATAT
Found at i:387782 original size:31 final size:30
Alignment explanation
Indices: 387744--387854 Score: 98
Period size: 31 Copynumber: 3.5 Consensus size: 30
387734 ATAATATGTG
387744 ATTAATATTAATATAAAATATAGTCTATAAA
1 ATTAATATTAATATAAAATATAGT-TATAAA
* *
387775 ATTAATATTAATATAAATTATA-TTTTATAA
1 ATTAATATTAATATAAAATATAGTTATA-AA
* * *
387805 ATTATATAGTATAGTTTATAAACTATAGTTAATATA
1 ATTA-ATA-T-TA--ATATAAAATATAGTT-ATAAA
387841 ATTAATATTAATAT
1 ATTAATATTAATAT
387855 TAATATAAAC
Statistics
Matches: 65, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
29 3 0.05
30 7 0.11
31 27 0.42
32 1 0.02
33 4 0.06
34 1 0.02
35 13 0.20
36 7 0.11
37 2 0.03
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.45
Consensus pattern (30 bp):
ATTAATATTAATATAAAATATAGTTATAAA
Found at i:387787 original size:107 final size:103
Alignment explanation
Indices: 387667--387870 Score: 270
Period size: 107 Copynumber: 1.9 Consensus size: 103
387657 AACTATTTAT
*
387667 AATTAATATTAATATAAATTATATATTAT-AATTAATATTAATATAATTAATATTAACTTATA-T
1 AATTAATATTAATATAAATTATATATTATAAATT-ATA-TAATATAATT--TATAAAC-TATAGT
*
387730 TAATATAA-TATGTGATTAATATTAATATAAAATATAGTCTATAA
61 TAATATAATTA-AT-ATTAATATTAATATAAAATATAGTCTATAA
* * *
387774 AATTAATATTAATATAAATTATATTTTATAAATTATATAGTATAGTTTATAAACTATAGTTAATA
1 AATTAATATTAATATAAATTATATATTATAAATTATATAATATAATTTATAAACTATAGTTAATA
*
387839 TAATTAATATTAATATTAATATAAACTATAGT
66 TAATTAATATTAATATTAATATAAAATATAGT
387871 TAATATGTTA
Statistics
Matches: 88, Mismatches: 6, Indels: 10
0.85 0.06 0.10
Matches are distributed among these distances:
103 27 0.31
104 16 0.18
105 2 0.02
106 8 0.09
107 31 0.35
108 4 0.05
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (103 bp):
AATTAATATTAATATAAATTATATATTATAAATTATATAATATAATTTATAAACTATAGTTAATA
TAATTAATATTAATATTAATATAAAATATAGTCTATAA
Found at i:387923 original size:36 final size:36
Alignment explanation
Indices: 387883--387973 Score: 121
Period size: 36 Copynumber: 2.5 Consensus size: 36
387873 ATATGTTAAT
* *
387883 ATTAATGTAAACTATAGTTTATAAACTATCA-ACTAC
1 ATTAATATAAATTATAGTTTATAAACTAT-ATACTAC
* * *
387919 ATTAATACAAATTACAGTTTATAAACTATATACTAT
1 ATTAATATAAATTATAGTTTATAAACTATATACTAC
387955 ATTAATATAAATTATAGTT
1 ATTAATATAAATTATAGTT
387974 AAGATAATTA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
35 1 0.02
36 46 0.98
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.40
Consensus pattern (36 bp):
ATTAATATAAATTATAGTTTATAAACTATATACTAC
Found at i:388115 original size:2 final size:2
Alignment explanation
Indices: 388100--388238 Score: 74
Period size: 2 Copynumber: 70.5 Consensus size: 2
388090 TATAGATTAC
* * * * *
388100 AT AT AT AGT TT AT AT AA AT -T AT AT AT AG AT -T GT AT AT AT AC
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
388141 AT A- AT AT AT AT ACT AT AG GT -T AT AT AT AT AGT TT AC AT AT AA
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
* * *
388183 AT AG AT -T GT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
*
388225 TT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT A
388239 CATAGTTTAG
Statistics
Matches: 102, Mismatches: 25, Indels: 20
0.69 0.17 0.14
Matches are distributed among these distances:
1 6 0.06
2 91 0.89
3 5 0.05
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (2 bp):
AT
Found at i:388239 original size:44 final size:44
Alignment explanation
Indices: 388097--388242 Score: 111
Period size: 44 Copynumber: 3.1 Consensus size: 44
388087 AACTATAGAT
* * *
388097 TACATATATAGTTTATATAAAT-TATATATAGATTGTATATAT-ACA
1 TACATATATA-TATATATATATATATATATAG-TT-TATATATAATA
**
388142 TA-ATATATATACTATAGGT-TATATATATAGTTTACATATAAATAGATTGTA
1 TACATATATATA-TATATATATATATATATAGTTT--ATAT--ATA-A---TA
388193 TACATATATATATATATATATATATATATAGTTTATATATAATA
1 TACATATATATATATATATATATATATATAGTTTATATATAATA
388237 TACATA
1 TACATA
388243 GTTTAGACAT
Statistics
Matches: 81, Mismatches: 7, Indels: 27
0.70 0.06 0.23
Matches are distributed among these distances:
42 1 0.01
43 4 0.05
44 32 0.40
45 2 0.02
46 2 0.02
47 1 0.01
48 4 0.05
50 4 0.05
51 8 0.10
52 23 0.28
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (44 bp):
TACATATATATATATATATATATATATATAGTTTATATATAATA
Found at i:388243 original size:20 final size:21
Alignment explanation
Indices: 388205--388247 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
388195 CATATATATA
*
388205 TATATATATATATATATAGTT
1 TATATATATATATACATAGTT
388226 TATATATA-ATATACATAGTT
1 TATATATATATATACATAGTT
388246 TA
1 TA
388248 GACATACATG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (21 bp):
TATATATATATATACATAGTT
Found at i:388500 original size:51 final size:48
Alignment explanation
Indices: 388396--388506 Score: 150
Period size: 49 Copynumber: 2.2 Consensus size: 48
388386 TATATAGTTG
* * *
388396 ATATAGTTTAGGGTTTAGGGTTTCTATAAACTATATACTTTGTTACTTT
1 ATATAGTTTA-TGCTTAGGGTTTCTATAAACTATATACTTTATTACTTT
*
388445 ATATAGTATTATGCTTAGTGTTTCTATAAACTATATATACTTTATTACTTT
1 ATATAGT-TTATGCTTAGGGTTTCTATAAAC--TATATACTTTATTACTTT
388496 ATATAGTTTAT
1 ATATAGTTTAT
388507 ATAGCTATAT
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
49 24 0.44
50 7 0.13
51 24 0.44
ACGTcount: A:0.30, C:0.08, G:0.12, T:0.50
Consensus pattern (48 bp):
ATATAGTTTATGCTTAGGGTTTCTATAAACTATATACTTTATTACTTT
Found at i:388507 original size:9 final size:9
Alignment explanation
Indices: 388478--388519 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
388468 CTATAAACTA
388478 TATATACTT
1 TATATACTT
388487 TAT-TACTT
1 TATATACTT
*
388495 TATATAGTT
1 TATATACTT
*
388504 TATATAGCTA
1 TATATA-CTT
388514 TATATA
1 TATATA
388520 TATATATCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
8 8 0.29
9 13 0.46
10 7 0.25
ACGTcount: A:0.36, C:0.07, G:0.05, T:0.52
Consensus pattern (9 bp):
TATATACTT
Found at i:388517 original size:19 final size:17
Alignment explanation
Indices: 388474--388519 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
388464 GTTTCTATAA
388474 ACTATATATACTTTATT
1 ACTATATATACTTTATT
* *
388491 ACTTTATATAGTTTATAT
1 ACTATATATACTTTAT-T
388509 AGCTATATATA
1 A-CTATATATA
388520 TATATATCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 14 0.58
18 2 0.08
19 8 0.33
ACGTcount: A:0.37, C:0.09, G:0.04, T:0.50
Consensus pattern (17 bp):
ACTATATATACTTTATT
Found at i:388591 original size:28 final size:27
Alignment explanation
Indices: 388549--388686 Score: 100
Period size: 28 Copynumber: 4.9 Consensus size: 27
388539 ATGACTTTTT
*
388549 ATAGTTTATACATATGTAGTT-TATATAC
1 ATAGTTTAT--ATATATAGTTATATATAC
*
388577 ATAGTTTATATATATAGTTCATATAAAC
1 ATAGTTTATATATATAGTT-ATATATAC
* *
388605 ATAATTTATATATATAGCTTATAATAATTAT
1 ATAGTTTATATATATAG-TTAT-AT-A-TAC
* * *
388636 ATAGTTTATA-ATATAATATAGTTTATAT
1 ATAGTTTATATATATAGT-TA-TATATAC
* *
388664 ATAGTTTATATATAAACTTATAT
1 ATAGTTTATATATATAGTTATAT
388687 TATATTAATA
Statistics
Matches: 90, Mismatches: 11, Indels: 19
0.75 0.09 0.16
Matches are distributed among these distances:
26 9 0.10
27 2 0.02
28 48 0.53
29 11 0.12
30 9 0.10
31 11 0.12
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.47
Consensus pattern (27 bp):
ATAGTTTATATATATAGTTATATATAC
Found at i:388638 original size:18 final size:17
Alignment explanation
Indices: 388615--388662 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
388605 ATAATTTATA
*
388615 TATATAGCTTATAATAAT
1 TATATAGTTTATAAT-AT
388633 TATATAGTTTATAATAT
1 TATATAGTTTATAATAT
*
388650 AATATAGTTTATA
1 TATATAGTTTATA
388663 TATAGTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
17 14 0.50
18 14 0.50
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (17 bp):
TATATAGTTTATAATAT
Found at i:388656 original size:17 final size:17
Alignment explanation
Indices: 388611--388666 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 17
388601 AAACATAATT
*
388611 TATATATATAGCTTATAA
1 TATA-ATATAGTTTATAA
*
388629 TAATTATATAGTTTATAA
1 T-ATAATATAGTTTATAA
388647 TATAATATAGTTTAT-A
1 TATAATATAGTTTATAA
388663 TATA
1 TATA
388667 GTTTATATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
16 5 0.15
17 13 0.38
18 14 0.41
19 2 0.06
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (17 bp):
TATAATATAGTTTATAA
Found at i:388667 original size:11 final size:11
Alignment explanation
Indices: 388633--388677 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
388623 TTATAATAAT
388633 TATATAGTTTA
1 TATATAGTTTA
388644 TA-ATA---TA
1 TATATAGTTTA
388651 -ATATAGTTTA
1 TATATAGTTTA
388661 TATATAGTTTA
1 TATATAGTTTA
388672 TATATA
1 TATATA
388678 AACTTATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
6 1 0.03
7 5 0.17
10 5 0.17
11 18 0.62
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (11 bp):
TATATAGTTTA
Done.