Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009603.1 Hibiscus syriacus cultivar Beakdansim tig00116983_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: 1462390
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 7
Found at i:187091 original size:8 final size:8
Alignment explanation
Indices: 187078--187149 Score: 92
Period size: 8 Copynumber: 8.8 Consensus size: 8
187068 CATCCATCAG
187078 AGAAAAAA
1 AGAAAAAA
*
187086 AGAAAAAG
1 AGAAAAAA
187094 AGAAAAAA
1 AGAAAAAA
187102 GAGAAAAAA
1 -AGAAAAAA
187111 AGAAAAAAA
1 AG-AAAAAA
187120 AGAAAAAAA
1 AG-AAAAAA
187129 AGAAAAAA
1 AGAAAAAA
*
187137 A-AAGAAA
1 AGAAAAAA
187144 AGAAAA
1 AGAAAA
187150 GAAAAGAAAT
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
7 6 0.11
8 26 0.46
9 25 0.44
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (8 bp):
AGAAAAAA
Found at i:187106 original size:17 final size:16
Alignment explanation
Indices: 187078--187149 Score: 92
Period size: 17 Copynumber: 4.4 Consensus size: 16
187068 CATCCATCAG
*
187078 AGAAAAAAAGAAAAAG
1 AGAAAAAAAGAAAAAA
187094 AGAAAAAAGAGAAAAAA
1 AGAAAAAA-AGAAAAAA
187111 AGAAAAAAAAGAAAAAAA
1 AG-AAAAAAAG-AAAAAA
*
187129 AGAAAAAAA-AAGAAA
1 AGAAAAAAAGAAAAAA
187144 AGAAAA
1 AGAAAA
187150 GAAAAGAAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
15 11 0.22
16 8 0.16
17 18 0.35
18 14 0.27
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (16 bp):
AGAAAAAAAGAAAAAA
Found at i:187110 original size:25 final size:25
Alignment explanation
Indices: 187076--187156 Score: 99
Period size: 26 Copynumber: 3.1 Consensus size: 25
187066 TTCATCCATC
187076 AGAGAAAAAAAGAAAAAGAGAAAAA
1 AGAGAAAAAAAGAAAAAGAGAAAAA
*
187101 AGAGAAAAAAAGAAAAAAAAGAAAAA
1 AGAGAAAAAAAG-AAAAAGAGAAAAA
* * *
187127 AAAGAAAAAAAAAGAAAAGAAAAGAAA
1 AGAGAAAAAAAGA-AAAAGAGAA-AAA
187154 AGA
1 AGA
187157 AATTGAATCA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
25 13 0.28
26 29 0.62
27 5 0.11
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (25 bp):
AGAGAAAAAAAGAAAAAGAGAAAAA
Found at i:187120 original size:28 final size:28
Alignment explanation
Indices: 187076--187154 Score: 110
Period size: 28 Copynumber: 2.9 Consensus size: 28
187066 TTCATCCATC
*
187076 AGAGAAAAAAAG---AAAAAGAGAAAAA
1 AGAGAAAAAAAGAAAAAAAAGAAAAAAA
187101 AGAGAAAAAAAGAAAAAAAAGAAAAAAA
1 AGAGAAAAAAAGAAAAAAAAGAAAAAAA
*
187129 AGAAAAAAAAAGAAAAGAAAAGAAAA
1 AGAGAAAAAAAGAAAA-AAAAGAAAA
187155 GAAATTGAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
25 12 0.25
28 27 0.56
29 9 0.19
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (28 bp):
AGAGAAAAAAAGAAAAAAAAGAAAAAAA
Found at i:187158 original size:10 final size:9
Alignment explanation
Indices: 187080--187154 Score: 100
Period size: 9 Copynumber: 8.3 Consensus size: 9
187070 TCCATCAGAG
187080 AAAAAAAG-
1 AAAAAAAGA
*
187088 AAAAAGAGA
1 AAAAAAAGA
*
187097 AAAAAGAG-
1 AAAAAAAGA
187105 AAAAAAAGA
1 AAAAAAAGA
187114 AAAAAAAGA
1 AAAAAAAGA
187123 AAAAAAAGAA
1 AAAAAAAG-A
187133 AAAAAAAGA
1 AAAAAAAGA
187142 AAAGAAAAGA
1 AAA-AAAAGA
187152 AAA
1 AAA
187155 GAAATTGAAT
Statistics
Matches: 61, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
8 14 0.23
9 29 0.48
10 18 0.30
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:188586 original size:50 final size:50
Alignment explanation
Indices: 188531--188775 Score: 274
Period size: 50 Copynumber: 4.8 Consensus size: 50
188521 GGTCCATATT
* * * *
188531 ATCCATGTGGGTATCTTGAAGACTCACATCAGCATGAAAAGATAGAAGTT
1 ATCCATGTGGGTATCTTGAAGGCTCACATCAACATGAAAAGACAGAAGTA
* * * *
188581 ATCCATGTGGATATCTTGAAGGCTCACATCAGCATGAAAAGATATAAGTA
1 ATCCATGTGGGTATCTTGAAGGCTCACATCAACATGAAAAGACAGAAGTA
* * *
188631 ATCTATGTAGTTATCTTGAAGGCTCACATCAACATGAAAAAGACAGAAGTA
1 ATCCATGTGGGTATCTTGAAGGCTCACATCAACATG-AAAAGACAGAAGTA
* * * * * *
188682 ATCCACGTAGGTCATTTTAAAGACTCACATCATCATGAAAAAGACAGAAGTA
1 ATCCATGTGGGT-ATCTTGAAGGCTCACATCAACATG-AAAAGACAGAAGTA
* * *
188734 ATCTATGTGGGGCATCTTGAAGGCTCACACCAACATGAAAAG
1 ATCCATGT-GGGTATCTTGAAGGCTCACATCAACATGAAAAG
188776 GTTGGGATAT
Statistics
Matches: 166, Mismatches: 26, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
50 78 0.47
51 26 0.16
52 60 0.36
53 2 0.01
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (50 bp):
ATCCATGTGGGTATCTTGAAGGCTCACATCAACATGAAAAGACAGAAGTA
Found at i:190421 original size:42 final size:42
Alignment explanation
Indices: 190362--190443 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 42
190352 CACAAATTTG
* *
190362 TAAATCCTTCGGGTCATCTGTTAGTCTTTCGAGCATGATGCT
1 TAAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGCT
*
190404 TAAATCCTTCGGGTCATCTGTCAGTCTTTTGAGCAAGATG
1 TAAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATG
190444 ATAAGTCCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (42 bp):
TAAATCCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGCT
Found at i:190682 original size:42 final size:44
Alignment explanation
Indices: 190607--190692 Score: 122
Period size: 42 Copynumber: 2.0 Consensus size: 44
190597 TTCTCACAAA
* * *
190607 TTTATAAATCATTCGGGTCATCTATTAGTCTTTCGAGCATGATG
1 TTTATAAATCATTCGGGTCATCTATCAGCCTTTCGAGCAAGATG
*
190651 TTTA-AAATC-TTCGGGTCATCTGTCAGCCTTTCGAGCAAGATG
1 TTTATAAATCATTCGGGTCATCTATCAGCCTTTCGAGCAAGATG
190693 ATAAGTCCTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 29 0.76
43 5 0.13
44 4 0.11
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (44 bp):
TTTATAAATCATTCGGGTCATCTATCAGCCTTTCGAGCAAGATG
Found at i:190902 original size:249 final size:249
Alignment explanation
Indices: 190277--190880 Score: 962
Period size: 249 Copynumber: 2.4 Consensus size: 249
190267 CCCAACCAAC
* * * *
190277 AAGTTTCTCATTTAATTTTTTTAGAAAAT-GAAATTCTTGAAAAGTAAGAAGTTTCTTACCCAGT
1 AAGTTTCTCATTTAA-TGTTCTAGAAAATCAAAATT-TTGAAAAGTAAGAAGTTTCTTACCTAGT
*
190341 AAAGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTGTTAGTCTTTCGAGCATGATGCTTA
64 AAAGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTGTTAGTCTTTCGAGCATGATGTTTA
* * *
190406 AATCCTTCGGGTCATCTGTCAGTCTTTTGAGCAAGATGATAAGTCCTTAGGGCCATCCGTAAAGA
129 AATCCTTCGGGTCATCTGTCAGCCTTTCGAGCAAGATGATAAGTCCTTAAGGCCATCCGTAAAGA
* * *
190471 CTTTGGGTAGGATGTTCACATATGATTTTCGCAAGAAAATGAGATAGCGATTTTCA
194 CTTTGGGTAGGATGATCACATATGATTTTCACAAGAAAATGAGATAACGATTTTCA
*
190527 AAATTTCTCATTTAATGTTCTAGAAAATCAAAATTTTGAAAAGTAAGAAGTTTCTTACCTAGTAA
1 AAGTTTCTCATTTAATGTTCTAGAAAATCAAAATTTTGAAAAGTAAGAAGTTTCTTACCTAGTAA
* * * *
190592 AGTATTTCTCACAAATTTATAAATCATTCGGGTCATCTATTAGTCTTTCGAGCATGATGTTTAAA
66 AGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTGTTAGTCTTTCGAGCATGATGTTT-AA
*
190657 AT-CTTCGGGTCATCTGTCAGCCTTTCGAGCAAGATGATAAGTCCTTAAGGCCATCCGTAAAGCC
130 ATCCTTCGGGTCATCTGTCAGCCTTTCGAGCAAGATGATAAGTCCTTAAGGCCATCCGTAAAGAC
* *
190721 TTTGGGTAGGATGATCACATATGATTTTCACATGAAAATGAGATAATGATTTTCA
195 TTTGGGTAGGATGATCACATATGATTTTCACAAGAAAATGAGATAACGATTTTCA
190776 AAGTTTCTCATTTAATGTTCTAGAAAATCAAAATTTTGAAAAGTAAGAAGTTTCTTACCTAGTAA
1 AAGTTTCTCATTTAATGTTCTAGAAAATCAAAATTTTGAAAAGTAAGAAGTTTCTTACCTAGTAA
* *
190841 AGTATTTCCCACAAATTTGTGAAA-CCTCCGGTTCATCTGT
66 AGTATTTCCCACAAATTTGT-AAATCCTTCGGGTCATCTGT
190881 AAGACCTCAA
Statistics
Matches: 325, Mismatches: 26, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
249 299 0.92
250 26 0.08
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (249 bp):
AAGTTTCTCATTTAATGTTCTAGAAAATCAAAATTTTGAAAAGTAAGAAGTTTCTTACCTAGTAA
AGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTGTTAGTCTTTCGAGCATGATGTTTAAA
TCCTTCGGGTCATCTGTCAGCCTTTCGAGCAAGATGATAAGTCCTTAAGGCCATCCGTAAAGACT
TTGGGTAGGATGATCACATATGATTTTCACAAGAAAATGAGATAACGATTTTCA
Found at i:191140 original size:3 final size:3
Alignment explanation
Indices: 191132--191193 Score: 69
Period size: 3 Copynumber: 21.7 Consensus size: 3
191122 AGTTTGCATA
* *
191132 TAT TAT TAT TAT TAC TA- TAT TAT TA- TAT TAT TAC TAT TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
191177 TAT ATAT T-T TAT TAT TA
1 TAT -TAT TAT TAT TAT TA
191194 CAAATAATAC
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
2 8 0.16
3 40 0.78
4 3 0.06
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:191152 original size:17 final size:17
Alignment explanation
Indices: 191130--191194 Score: 84
Period size: 17 Copynumber: 4.0 Consensus size: 17
191120 CTAGTTTGCA
191130 TATATTATTATTATTAC
1 TATATTATTATTATTAC
*
191147 TATATTATTA-TATTAT
1 TATATTATTATTATTAC
191163 TACTATTATTATTA-TA-
1 TA-TATTATTATTATTAC
191179 TATATT-TTATTATTAC
1 TATATTATTATTATTAC
191195 AAATAATACA
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
14 6 0.14
15 6 0.14
16 9 0.21
17 20 0.47
18 2 0.05
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (17 bp):
TATATTATTATTATTAC
Found at i:193437 original size:20 final size:20
Alignment explanation
Indices: 193414--193460 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
193404 TAGCTTAATA
*
193414 ATAAAAAAATAGTGTAAATT
1 ATAAAAAAATAGTGAAAATT
* *
193434 ATAAAAGAATATTGAAAATT
1 ATAAAAAAATAGTGAAAATT
193454 ATAAAAA
1 ATAAAAA
193461 TATTTAGATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.28
Consensus pattern (20 bp):
ATAAAAAAATAGTGAAAATT
Found at i:202127 original size:17 final size:17
Alignment explanation
Indices: 202105--202142 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
202095 CTAGAGATGA
202105 AACAGTAATTCATCTCC
1 AACAGTAATTCATCTCC
202122 AACAGTAATTCATCTCC
1 AACAGTAATTCATCTCC
202139 AACA
1 AACA
202143 TTATTTTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.39, C:0.29, G:0.05, T:0.26
Consensus pattern (17 bp):
AACAGTAATTCATCTCC
Found at i:202281 original size:18 final size:18
Alignment explanation
Indices: 202258--202316 Score: 77
Period size: 18 Copynumber: 3.3 Consensus size: 18
202248 TTTGAATTTT
202258 AAAAAATCAGAAAAATAC
1 AAAAAATCAGAAAAATAC
202276 AAAAAATCAGAAAAAATA-
1 AAAAAATCAG-AAAAATAC
*
202294 AAAAAA-AAGAAAAATTAC
1 AAAAAATCAGAAAAA-TAC
202312 AAAAA
1 AAAAA
202317 TAATTAGTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
16 5 0.14
17 4 0.11
18 21 0.57
19 7 0.19
ACGTcount: A:0.78, C:0.07, G:0.05, T:0.10
Consensus pattern (18 bp):
AAAAAATCAGAAAAATAC
Found at i:210658 original size:21 final size:21
Alignment explanation
Indices: 210634--210697 Score: 58
Period size: 24 Copynumber: 2.9 Consensus size: 21
210624 TCAGTGCATC
210634 TTCATGATGTATCGATGCACA
1 TTCATGATGTATCGATGCACA
* * *
210655 TTCAAAGGGATGCATCGATGCACT
1 TTC--A-TGATGTATCGATGCACA
210679 TTCAT-AGTGTATCGATGCA
1 TTCATGA-TGTATCGATGCA
210698 TTATGCACAA
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
20 1 0.03
21 14 0.41
22 1 0.03
23 1 0.03
24 17 0.50
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (21 bp):
TTCATGATGTATCGATGCACA
Found at i:210690 original size:45 final size:44
Alignment explanation
Indices: 210595--210697 Score: 124
Period size: 45 Copynumber: 2.3 Consensus size: 44
210585 AAACCCGACG
*
210595 GATGCATCGATGCACATTCAAGGCGTGCATCAGTGCATCTTCAT
1 GATGTATCGATGCACATTCAAGGCGTGCATCAGTGCATCTTCAT
210639 GATGTATCGATGCACATTCAAAGG-GATGCATC-GATGCA-CTTTCAT
1 GATGTATCGATGCACATTC-AAGGCG-TGCATCAG-TGCATC-TTCAT
210684 -AGTGTATCGATGCA
1 GA-TGTATCGATGCA
210698 TTATGCACAA
Statistics
Matches: 53, Mismatches: 1, Indels: 9
0.84 0.02 0.14
Matches are distributed among these distances:
44 22 0.42
45 31 0.58
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.28
Consensus pattern (44 bp):
GATGTATCGATGCACATTCAAGGCGTGCATCAGTGCATCTTCAT
Found at i:216577 original size:45 final size:45
Alignment explanation
Indices: 216513--216664 Score: 225
Period size: 45 Copynumber: 3.4 Consensus size: 45
216503 GGTGCACTAA
* * *
216513 GAGTGAATTGATGCATAAAATGAATTCGATGTTTTTAAAAAGCCT
1 GAGTGCATCGATGCATAAAATGCATTCGATGTTTTTAAAAAGCCT
*
216558 GAGTGCATCGATGCATAAAATGCATTCGATGTTTTTAAACAGGCCT
1 GAGTGCATCGATGCATAAAATGCATTCGATGTTTTTAAA-AAGCCT
* *
216604 GAGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAA-CAT
1 GAGTGCATCGATGCATAAAATGCATTCGATGTTTTTA-AAAAGCCT
216649 GAGTGCATCGATGCAT
1 GAGTGCATCGATGCAT
216665 GGTAGTGCAT
Statistics
Matches: 98, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
45 54 0.55
46 42 0.43
47 2 0.02
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (45 bp):
GAGTGCATCGATGCATAAAATGCATTCGATGTTTTTAAAAAGCCT
Found at i:216778 original size:64 final size:63
Alignment explanation
Indices: 216605--216824 Score: 327
Period size: 63 Copynumber: 3.5 Consensus size: 63
216595 AACAGGCCTG
* *
216605 AGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACATGAGTGCATCGATGCATGGT
1 AGTGTATCGATGCATAAAATGCATTCGATGTTTTCATAAAACCTGAGTGCATCGATGCATGGT
* * *
216668 AGTGCATCGATGCATAAAATGTATTCGATGTTTT--TAAACAGGCCTGAGTGCATCGATGAATGG
1 AGTGTATCGATGCATAAAATGCATTCGATGTTTTCATAAA-A--CCTGAGTGCATCGATGCATGG
216731 T
63 T
* *
216732 CTGTGTATCGATGCATAAAATGCATTCTATGTTTTCATAAAACCTGAGTGCATCGATGCATGGT
1 -AGTGTATCGATGCATAAAATGCATTCGATGTTTTCATAAAACCTGAGTGCATCGATGCATGGT
216796 AGTGTATCGATGCATAAAATGCATTCGAT
1 AGTGTATCGATGCATAAAATGCATTCGAT
216825 ATGGTGAGTG
Statistics
Matches: 141, Mismatches: 10, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
61 4 0.03
62 1 0.01
63 60 0.43
64 41 0.29
65 30 0.21
66 1 0.01
67 4 0.03
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.32
Consensus pattern (63 bp):
AGTGTATCGATGCATAAAATGCATTCGATGTTTTCATAAAACCTGAGTGCATCGATGCATGGT
Found at i:216864 original size:20 final size:20
Alignment explanation
Indices: 216829--216866 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
216819 TTCGATATGG
*
216829 TGAGTGCATCTATGCATCAA
1 TGAGTGCATCGATGCATCAA
*
216849 TGAGTGCATCGGTGCATC
1 TGAGTGCATCGATGCATC
216867 CCTTCTCAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (20 bp):
TGAGTGCATCGATGCATCAA
Found at i:221924 original size:22 final size:22
Alignment explanation
Indices: 221894--221935 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
221884 AACCATGATC
* *
221894 GAGTCATGCTCGAGTTGTGAAT
1 GAGTCATGCCCGAGTCGTGAAT
*
221916 GAGTTATGCCCGAGTCGTGA
1 GAGTCATGCCCGAGTCGTGA
221936 GTCAAGTAGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (22 bp):
GAGTCATGCCCGAGTCGTGAAT
Found at i:225723 original size:24 final size:24
Alignment explanation
Indices: 225690--225736 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
225680 TGTTTCTAAA
225690 AAAATATAAAGA-AAAATAAATACC
1 AAAATATAAA-ATAAAATAAATACC
*
225714 AAAATTTAAAATTAAAATAAATA
1 AAAATATAAAA-TAAAATAAATA
225737 ATAAAATGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 1 0.05
24 9 0.45
25 10 0.50
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.23
Consensus pattern (24 bp):
AAAATATAAAATAAAATAAATACC
Found at i:231621 original size:13 final size:12
Alignment explanation
Indices: 231603--231638 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 12
231593 AGCATTGTGA
231603 AAAGAAAATAAT
1 AAAGAAAATAAT
231615 GAAAGAAAATAAAT
1 -AAAGAAAAT-AAT
231629 AAAGAAAATA
1 AAAGAAAATA
231639 TGGAGATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 1 0.05
13 18 0.82
14 3 0.14
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.14
Consensus pattern (12 bp):
AAAGAAAATAAT
Found at i:235414 original size:43 final size:43
Alignment explanation
Indices: 235353--235439 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 43
235343 TACATCAAGA
*
235353 ACTTCACTGATATCTGATTGTAGATTTCGGAATTGGGCGATTC
1 ACTTCACTGATATCTGATTGCAGATTTCGGAATTGGGCGATTC
* *
235396 ACTTCACTGATATCTGATTGCAGATTTTGGACTTGGGCGATTC
1 ACTTCACTGATATCTGATTGCAGATTTCGGAATTGGGCGATTC
235439 A
1 A
235440 GAGGACTATT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (43 bp):
ACTTCACTGATATCTGATTGCAGATTTCGGAATTGGGCGATTC
Found at i:243333 original size:15 final size:15
Alignment explanation
Indices: 243283--243333 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
243273 AATGCATTCA
243283 ACAAATGATTATGCT
1 ACAAATGATTATGCT
**
243298 ACAAGTAT-AGTTATGAA
1 ACAA--ATGA-TTATGCT
243315 ACAAATGATTATGCT
1 ACAAATGATTATGCT
243330 ACAA
1 ACAA
243334 GTACCTAAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
15 15 0.54
16 2 0.07
17 11 0.39
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (15 bp):
ACAAATGATTATGCT
Found at i:245533 original size:2 final size:2
Alignment explanation
Indices: 245526--245555 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
245516 ATTCATCTTC
245526 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
245556 TTTCTTATAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:246779 original size:64 final size:63
Alignment explanation
Indices: 246666--246827 Score: 182
Period size: 64 Copynumber: 2.5 Consensus size: 63
246656 TTCCCTTGAA
* * *
246666 GTGCATCGATGCACTACCCATGCATCGATACACAAATCACCTTCGATGTTTTCA-TTTTAAGGGG
1 GTGCATCGATGCACT-CCTATGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAA-GGG
* * ** * *
246730 GTGCATCGATGCACTCCTTATGCATCGATGCACTAATTGCATTCTATGTTTCCATTTTTAATGG
1 GTGCATCGATGCACTCC-TATGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAAGGG
* *
246794 GTGCATCAATGCACTTCCTGTGCATCGATACACA
1 GTGCATCGATGCAC-TCCTATGCATCGATACACA
246828 CTGAACAATT
Statistics
Matches: 82, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
63 2 0.02
64 71 0.87
65 9 0.11
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTATGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAAGGG
Found at i:250238 original size:23 final size:23
Alignment explanation
Indices: 250212--250276 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
250202 CACCACAGCT
*
250212 CGTACAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
250235 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
250258 CGTAGAAATGCACCGAAGT
1 CGTAGAAATGCACCGAAGT
250277 TCCATATAAG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.31, C:0.26, G:0.26, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:250676 original size:2 final size:2
Alignment explanation
Indices: 250671--250706 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
250661 ATGTCTTATC
*
250671 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
250707 TCACCTGTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:250776 original size:2 final size:2
Alignment explanation
Indices: 250769--250799 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
250759 TTCATCTTCC
250769 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
250800 TATTTTTCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:251524 original size:19 final size:20
Alignment explanation
Indices: 251486--251524 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
251476 CTCTTTTATA
*
251486 TTCATATAATTTCTTATCAT
1 TTCATATAATTTCATATCAT
*
251506 TTCATATAGTTT-ATATCAT
1 TTCATATAATTTCATATCAT
251525 CATAACATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.31, C:0.13, G:0.03, T:0.54
Consensus pattern (20 bp):
TTCATATAATTTCATATCAT
Found at i:252026 original size:64 final size:63
Alignment explanation
Indices: 251917--252078 Score: 200
Period size: 64 Copynumber: 2.5 Consensus size: 63
251907 TTCCCTTGAA
* * *
251917 GTGCATCGATGCACTACCCATGCATCGATACACAAATCACCTTCGATGTTTTCA-TTTTAAGGGG
1 GTGCATCGATGCACT-CCTATGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAA-GGG
* * ** *
251981 GTGCATCGATGCACTCCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCATTTTTAATGG
1 GTGCATCGATGCACTCC-TATGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAAGGG
*
252045 GTGCATCGATGCACTTCCTGTGCATCGATACACA
1 GTGCATCGATGCAC-TCCTATGCATCGATACACA
252079 CTGAATAATT
Statistics
Matches: 84, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
63 2 0.02
64 73 0.87
65 9 0.11
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTATGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAAGGG
Found at i:256183 original size:3 final size:3
Alignment explanation
Indices: 256169--256254 Score: 100
Period size: 3 Copynumber: 27.7 Consensus size: 3
256159 TTTTTCATTC
* * * *
256169 TAT TAT TTT TAT TAT TAT TAT TAT TAT TAAA TAA AAT ATAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT -TAT TAT TAT
*
256216 TAT TAT TAT TAT TAT TCT ATAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TA
256255 AATAAAAAAT
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
3 66 0.92
4 6 0.08
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:257773 original size:21 final size:23
Alignment explanation
Indices: 257729--257771 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
257719 TATTTATATT
257729 TATATTTATATTTTATATGTTTA
1 TATATTTATATTTTATATGTTTA
257752 TATATTTA-ATTATTAT-TGTT
1 TATATTTATATT-TTATATGTT
257772 ATTCTTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (23 bp):
TATATTTATATTTTATATGTTTA
Found at i:257802 original size:2 final size:2
Alignment explanation
Indices: 257789--257833 Score: 51
Period size: 2 Copynumber: 24.0 Consensus size: 2
257779 TTATGTAGTC
* *
257789 AT AT AA AT AT AT AT A- AT AA AT A- AT AT -T 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
257828 AT AT AT
1 AT AT AT
257834 TAAATAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
1 3 0.08
2 33 0.92
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:257820 original size:19 final size:19
Alignment explanation
Indices: 257796--257835 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
257786 GTCATATAAA
257796 TATATATAATAAATA-ATAT
1 TATATAT-ATAAATATATAT
*
257815 TATATATATATATATATAT
1 TATATATATAAATATATAT
257834 TA
1 TA
257836 AATAAAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TATATATATAAATATATAT
Found at i:258036 original size:138 final size:138
Alignment explanation
Indices: 257894--258256 Score: 640
Period size: 138 Copynumber: 2.6 Consensus size: 138
257884 TAATCATATT
257894 TTAATATTTATTTATTTTTTAATATTAAGAAATGGGATGTCTTAAAGCACCTAGAAGTCCTTTTC
1 TTAATATTTATTTATTTTTTAATATTAAGAAATGGGATGTCTTAAAGCACCTAGAAGTCCTTTTC
257959 TGATATTCTTAAATAAATAAATATCCTATTTTTATAATTTATATATATTAATTATTTTTATAGAA
66 TGATATTCTTAAATAAATAAATATCCTATTTTTATAATTTATATATATTAATTATTTTTATAGAA
*
258024 ATGTTTTA
131 ATATTTTA
258032 TTAATATTTATTTATTTTTTAATATTAAGAAATGGGATGTCTTAAAGCACCTAGAAGTCCTTTTC
1 TTAATATTTATTTATTTTTTAATATTAAGAAATGGGATGTCTTAAAGCACCTAGAAGTCCTTTTC
*
258097 CGATATTCTTAAATAAATAAATATCCTATTTTTATAATTTATATATATTAATTATTTTTATAGAA
66 TGATATTCTTAAATAAATAAATATCCTATTTTTATAATTTATATATATTAATTATTTTTATAGAA
258162 ATATTTTA
131 ATATTTTA
* *
258170 TTAATATTTATTTATTTTTTAAGATTAAGAAAT-GGACTGTCTTAAAGCACCTAGAAGTCATTTT
1 TTAATATTTATTTATTTTTTAATATTAAGAAATGGGA-TGTCTTAAAGCACCTAGAAGTCCTTTT
* *
258234 CTAATATT-TCTAAGTAAATAAAT
65 CTGATATTCT-TAAATAAATAAAT
258257 GTCTTATATA
Statistics
Matches: 216, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
137 4 0.02
138 212 0.98
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (138 bp):
TTAATATTTATTTATTTTTTAATATTAAGAAATGGGATGTCTTAAAGCACCTAGAAGTCCTTTTC
TGATATTCTTAAATAAATAAATATCCTATTTTTATAATTTATATATATTAATTATTTTTATAGAA
ATATTTTA
Found at i:263790 original size:8 final size:8
Alignment explanation
Indices: 263779--263814 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
263769 ACAAAAACAA
263779 AAAAAAGG
1 AAAAAAGG
263787 -AAAAAGG
1 AAAAAAGG
263794 AAAAAAGG
1 AAAAAAGG
*
263802 AAAAAGGG
1 AAAAAAGG
263810 AAAAA
1 AAAAA
263815 TTGAATCAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
7 7 0.27
8 19 0.73
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (8 bp):
AAAAAAGG
Found at i:263808 original size:15 final size:16
Alignment explanation
Indices: 263779--263814 Score: 65
Period size: 15 Copynumber: 2.3 Consensus size: 16
263769 ACAAAAACAA
263779 AAAAAAGGAAAAA-GG
1 AAAAAAGGAAAAAGGG
263794 AAAAAAGGAAAAAGGG
1 AAAAAAGGAAAAAGGG
263810 AAAAA
1 AAAAA
263815 TTGAATCAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (16 bp):
AAAAAAGGAAAAAGGG
Found at i:268735 original size:45 final size:45
Alignment explanation
Indices: 268684--268790 Score: 133
Period size: 45 Copynumber: 2.3 Consensus size: 45
268674 TTTTTGATAT
* * * *
268684 TTTCAAAGCCTTCGGCTCATCTGTAATCCCTTCAGTGCATGATGC
1 TTTCAAAGCCTTCGGCTCATCCGTAAACCCTGCAGTGCAGGATGC
* * *
268729 TTTCAAAACCTTCGGGTCATCCGTAAACCCTGCAGTGCAGGATGT
1 TTTCAAAGCCTTCGGCTCATCCGTAAACCCTGCAGTGCAGGATGC
268774 TTTCAAAAAGCCTTCGG
1 TTTC--AAAGCCTTCGG
268791 GAGCTTTTTG
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
45 42 0.81
47 10 0.19
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (45 bp):
TTTCAAAGCCTTCGGCTCATCCGTAAACCCTGCAGTGCAGGATGC
Found at i:268868 original size:44 final size:45
Alignment explanation
Indices: 268805--268911 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 45
268795 TTTTTGATAA
* * * *
268805 TTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGC
1 TTTCAAAACCTTCGGGTCATCCGTAAGCCCTGCAGTGCAGGATGC
*
268850 TTTCAAAACCTT-GGGTCATCCGTAAGCCCTGCAGTGCAGGATGT
1 TTTCAAAACCTTCGGGTCATCCGTAAGCCCTGCAGTGCAGGATGC
268894 TTTCAAAAAGCCTTCGGG
1 TTTC-AAAA-CCTTCGGG
268912 AGCTTTTTGA
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
44 32 0.59
45 15 0.28
46 4 0.07
47 3 0.06
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.29
Consensus pattern (45 bp):
TTTCAAAACCTTCGGGTCATCCGTAAGCCCTGCAGTGCAGGATGC
Found at i:268929 original size:120 final size:121
Alignment explanation
Indices: 268625--269457 Score: 1420
Period size: 121 Copynumber: 6.9 Consensus size: 121
268615 CTATTTCCCA
* *
268625 CATCTGTAAGCCCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGATATTTTCAA
1 CATCCGTAAGCCCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
* *
268690 AGCCTTCGGCTCATCTGTAATCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGT
66 AGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGT
* *
268746 CATCCGTAAACCCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATAATTTCAA
1 CATCCGTAAGCCCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
268811 AGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTT-GGGT
66 AGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGT
268866 CATCCGTAAGCCCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
1 CATCCGTAAGCCCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
*
268931 AGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGAGT
66 AGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGT
* *
268987 CAT-CGTAAGCCCTGTAGTGTAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
1 CATCCGTAAGCCCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
*
269051 ATCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGT
66 AGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGT
* * **
269107 CATCTGTAAACCCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCAAGAGCTTTTTGATATTTTCAA
1 CATCCGTAAGCCCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
*
269172 AGCCTTTGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGT
66 AGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGT
* * *
269228 CATCCGTAAGCCCTGTAGTGCAAGATGTTTTCAAAAACCCTTCGGGAGCTTTTTGATATTTTCAA
1 CATCCGTAAGCCCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
* * *
269293 AACCTTCGGGTCATTTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTTGGGT
66 AGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGT
*
269349 CATCCGTAAGCCCTGTAGTGCAGGATGTTTT-AAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
1 CATCCGTAAGCCCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
* * *
269413 AACCTTCGGGTCATCTATAAGCCCTTCAGTGCATGATGTTTTCAA
66 AGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAA
269458 CATTTCAAGA
Statistics
Matches: 673, Mismatches: 37, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
120 308 0.46
121 365 0.54
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.33
Consensus pattern (121 bp):
CATCCGTAAGCCCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
AGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGT
Found at i:269018 original size:44 final size:45
Alignment explanation
Indices: 268924--269021 Score: 128
Period size: 44 Copynumber: 2.2 Consensus size: 45
268914 CTTTTTGATA
* * *
268924 TTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATG
1 TTTTCAAAACCTTCGAGTCATCTGTAAGCCCTTCAGTGCAGGATG
* *
268969 CTTTCAAAACCTTCGAGTCATC-GTAAGCCCTGT-AGTGTAGGATG
1 TTTTCAAAACCTTCGAGTCATCTGTAAGCCCT-TCAGTGCAGGATG
269013 TTTTCAAAA
1 TTTTCAAAA
269022 AGCCTTCGGG
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
44 26 0.57
45 20 0.43
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.33
Consensus pattern (45 bp):
TTTTCAAAACCTTCGAGTCATCTGTAAGCCCTTCAGTGCAGGATG
Found at i:269094 original size:45 final size:45
Alignment explanation
Indices: 269045--269142 Score: 151
Period size: 45 Copynumber: 2.2 Consensus size: 45
269035 TTTTTGATAT
* * * *
269045 TTTCAAATCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGC
1 TTTCAAAACCTTCGGGTCATCTGTAAACCCTGCAGTGCAGGATGC
*
269090 TTTCAAAACCTTCGGGTCATCTGTAAACCCTGCAGTGCAGGATGT
1 TTTCAAAACCTTCGGGTCATCTGTAAACCCTGCAGTGCAGGATGC
269135 TTTCAAAA
1 TTTCAAAA
269143 AGCCTTCAAG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.32
Consensus pattern (45 bp):
TTTCAAAACCTTCGGGTCATCTGTAAACCCTGCAGTGCAGGATGC
Found at i:269109 original size:241 final size:241
Alignment explanation
Indices: 268625--269457 Score: 1427
Period size: 241 Copynumber: 3.5 Consensus size: 241
268615 CTATTTCCCA
*
268625 CATCTGTAAGCCCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGATATTTTCAA
1 CATCCGTAAGCCCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGATATTTTCAA
* *
268690 AGCCTTCGGCTCATCTGTAATCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGTCATCCGTAA
66 AGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGTCATCCGTAA
* * * *
268755 ACCCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATAATTTCAAAGCCTTCGG
131 GCCCTGTAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAACCTTCGG
268820 GTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTGGGT
196 GTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTGGGT
*
268866 CATCCGTAAGCCCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
1 CATCCGTAAGCCCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGATATTTTCAA
*
268931 AGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGAGTCAT-CGTAA
66 AGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGTCATCCGTAA
* *
268995 GCCCTGTAGTGTAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAATCCTTCGG
131 GCCCTGTAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAACCTTCGG
269060 GTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGT
196 GTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTT-GGGT
* * *
269107 CATCTGTAAACCCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCAAGAGCTTTTTGATATTTTCAA
1 CATCCGTAAGCCCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGATATTTTCAA
*
269172 AGCCTTTGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGTCATCCGTAA
66 AGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGTCATCCGTAA
* *
269237 GCCCTGTAGTGCAAGATGTTTTCAAAAACCCTTCGGGAGCTTTTTGATATTTTCAAAACCTTCGG
131 GCCCTGTAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAACCTTCGG
*
269302 GTCATTTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTTGGGT
196 GTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACC-TTGGGT
* *
269349 CATCCGTAAGCCCTGTAGTGCAGGATGTTTT-AAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
1 CATCCGTAAGCCCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGATATTTTCAA
* * *
269413 AACCTTCGGGTCATCTATAAGCCCTTCAGTGCATGATGTTTTCAA
66 AGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAA
269458 CATTTCAAGA
Statistics
Matches: 559, Mismatches: 30, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
240 107 0.19
241 313 0.56
242 137 0.25
243 2 0.00
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.33
Consensus pattern (241 bp):
CATCCGTAAGCCCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGATATTTTCAA
AGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGTCATCCGTAA
GCCCTGTAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAAAACCTTCGG
GTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTGGGT
Found at i:269216 original size:45 final size:45
Alignment explanation
Indices: 269166--269273 Score: 137
Period size: 45 Copynumber: 2.4 Consensus size: 45
269156 TTTTTGATAT
* * * *
269166 TTTCAAAGCCTTTGGGTCATCTGTAAGCCCT-TCAGTGCATGATGC
1 TTTCAAAACCTTCGGGTCATCCGTAAGCCCTGT-AGTGCAAGATGC
*
269211 TTTCAAAACCTTCGGGTCATCCGTAAGCCCTGTAGTGCAAGATGT
1 TTTCAAAACCTTCGGGTCATCCGTAAGCCCTGTAGTGCAAGATGC
269256 TTTCAAAAACCCTTCGGG
1 TTTC-AAAA-CCTTCGGG
269274 AGCTTTTTGA
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
45 42 0.76
46 5 0.09
47 8 0.15
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.31
Consensus pattern (45 bp):
TTTCAAAACCTTCGGGTCATCCGTAAGCCCTGTAGTGCAAGATGC
Found at i:269337 original size:45 final size:45
Alignment explanation
Indices: 269287--269393 Score: 135
Period size: 45 Copynumber: 2.4 Consensus size: 45
269277 TTTTTGATAT
** *
269287 TTTCAAAACCTTCGGGTCATTTGTAAGCCCT-TCAGTGCATGATGC
1 TTTCAAAACCTTCGGGTCATCCGTAAGCCCTGT-AGTGCAGGATGC
* *
269332 TTTCAAAACCTTTGGGTCATCCGTAAGCCCTGTAGTGCAGGATGT
1 TTTCAAAACCTTCGGGTCATCCGTAAGCCCTGTAGTGCAGGATGC
*
269377 TTTAAAAAGCCTTCGGG
1 TTTCAAAA-CCTTCGGG
269394 AGCTTTTTGA
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
45 45 0.85
46 8 0.15
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.32
Consensus pattern (45 bp):
TTTCAAAACCTTCGGGTCATCCGTAAGCCCTGTAGTGCAGGATGC
Found at i:269579 original size:3 final size:3
Alignment explanation
Indices: 269565--269641 Score: 73
Period size: 3 Copynumber: 24.7 Consensus size: 3
269555 TTTTTCATTC
* * * * *
269565 TAT TAT TTT TAT TAT TAT TAT TAT AAT TAAA TAA AAT ATAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT -TAT TAT TAT
*
269612 TAT TAT TAT TAT TCT ATAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT TA
269642 AATAAAAAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
3 55 0.90
4 6 0.10
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:271162 original size:21 final size:22
Alignment explanation
Indices: 271116--271160 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
271106 TTTATTTATA
271116 TTTATAT-TTTAATTTTATATG
1 TTTATATATTTAATTTTATATG
271137 TTTATATATTTAATTATTAT-TG
1 TTTATATATTTAATT-TTATATG
271159 TT
1 TT
271161 ATTATTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.32
22 11 0.50
23 4 0.18
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (22 bp):
TTTATATATTTAATTTTATATG
Found at i:271551 original size:23 final size:23
Alignment explanation
Indices: 271525--271568 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
271515 TATATAAAAA
*
271525 TAAAAATATATTAATATATTTTT
1 TAAAAATATATTAATAAATTTTT
*
271548 TAAAATTATATTAATAAATTT
1 TAAAAATATATTAATAAATTT
271569 GAAATAACAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TAAAAATATATTAATAAATTTTT
Found at i:272238 original size:22 final size:23
Alignment explanation
Indices: 272212--272260 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
272202 GTAAAATAGC
272212 TAAAACCA-AAGAAAATGTGTCA
1 TAAAACCATAAGAAAATGTGTCA
*
272234 TAAAACCATAAGAAAATGTGTGA
1 TAAAACCATAAGAAAATGTGTCA
272257 TAAA
1 TAAA
272261 TGTAGAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 8 0.32
23 17 0.68
ACGTcount: A:0.55, C:0.10, G:0.14, T:0.20
Consensus pattern (23 bp):
TAAAACCATAAGAAAATGTGTCA
Found at i:273243 original size:23 final size:24
Alignment explanation
Indices: 273207--273254 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 24
273197 ATACCAAATT
273207 TAAAATTTATTTATA-AAAGTAATA
1 TAAAATTTATTTATAGAAA-TAATA
273231 TAAAA-TTATTTATAGAAATAATA
1 TAAAATTTATTTATAGAAATAATA
273254 T
1 T
273255 TTACTTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (24 bp):
TAAAATTTATTTATAGAAATAATA
Found at i:274779 original size:2 final size:2
Alignment explanation
Indices: 274774--274803 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
274764 TTGTGTGTAC
274774 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
274804 AGTTTCGATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:280103 original size:18 final size:19
Alignment explanation
Indices: 280080--280159 Score: 110
Period size: 18 Copynumber: 4.2 Consensus size: 19
280070 TAAATATTTG
*
280080 TCCCGAAAGACCACT-ATA
1 TCCCGAAGGACCACTGATA
280098 TCCCGAAGGACCACTGATA
1 TCCCGAAGGACCACTGATA
*
280117 TGTCCCGAAGGACCACT-ATG
1 --TCCCGAAGGACCACTGATA
280137 TCCCGAAGGACCACTGATA
1 TCCCGAAGGACCACTGATA
280156 TCCC
1 TCCC
280160 TCGACTCTTG
Statistics
Matches: 55, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
18 29 0.53
19 9 0.16
20 2 0.04
21 15 0.27
ACGTcount: A:0.30, C:0.34, G:0.19, T:0.17
Consensus pattern (19 bp):
TCCCGAAGGACCACTGATA
Found at i:280121 original size:39 final size:39
Alignment explanation
Indices: 280078--280156 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
280068 ACTAAATATT
280078 TGTCCCGAAAGACCACTATATCCCGAAGGACCACTGATA
1 TGTCCCGAAAGACCACTATATCCCGAAGGACCACTGATA
* *
280117 TGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGATA
1 TGTCCCGAAAGACCACTATATCCCGAAGGACCACTGATA
280156 T
1 T
280157 CCCTCGACTC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.19
Consensus pattern (39 bp):
TGTCCCGAAAGACCACTATATCCCGAAGGACCACTGATA
Found at i:288645 original size:44 final size:44
Alignment explanation
Indices: 288502--288806 Score: 312
Period size: 44 Copynumber: 6.9 Consensus size: 44
288492 TCTTATTCTG
* * *
288502 TGCACA-ATGCAGAGGAGCTTGCGGTAAATGGTAAGGACTTACCCT
1 TGCACATA-GCAGAGAAGCCTGCGGT-AACGGTAAGGACTTACCCT
* * * ** * *
288547 TACACATAGCAGAGGA-TCTAG-GAAAACTGTAAGGATTTACCCT
1 TGCACATAGCAGAGAAGCCT-GCGGTAACGGTAAGGACTTACCCT
* *
288590 TGCACATAGCAGAGAAGCCTGCGGTAACGGTAATGACTTGCCCT
1 TGCACATAGCAGAGAAGCCTGCGGTAACGGTAAGGACTTACCCT
* * * *
288634 TTCATATAGCAGAGGAGCTTGCGGTAACGGTAAGGACTTACCCT
1 TGCACATAGCAGAGAAGCCTGCGGTAACGGTAAGGACTTACCCT
* *
288678 TGCACATAGCAGAGGAGCCTACGGTAACGGTAAGGACTTACCCT
1 TGCACATAGCAGAGAAGCCTGCGGTAACGGTAAGGACTTACCCT
* * * *
288722 TGCACATAGCAGAGGAA-CCTACGGTAACGATAAAGAGTTACCCT
1 TGCACATAGCAGA-GAAGCCTGCGGTAACGGTAAGGACTTACCCT
* * * *
288766 TGCACATAGCAGAGAAGCGTGCGATAACAGTAAGGATTTAC
1 TGCACATAGCAGAGAAGCCTGCGGTAACGGTAAGGACTTAC
288807 AAGTCATAGA
Statistics
Matches: 216, Mismatches: 38, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
43 34 0.16
44 165 0.76
45 16 0.07
46 1 0.00
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.21
Consensus pattern (44 bp):
TGCACATAGCAGAGAAGCCTGCGGTAACGGTAAGGACTTACCCT
Found at i:288719 original size:132 final size:131
Alignment explanation
Indices: 288502--288806 Score: 382
Period size: 132 Copynumber: 2.3 Consensus size: 131
288492 TCTTATTCTG
* *
288502 TGCACA-ATGCAGAGGAGCTTGCGGTAAATGGTAAGGACTTACCCTTACACATAGCAGAGGATCT
1 TGCACATA-GCAGAGGAGCTTGCGGT-AACGGTAAGGACTTACCCTTACACATAGCAGAGGACCT
* * * * * *
288566 AGGAAAACTGTAAGGATTTACCCTTGCACATAGCAGA-GAAGCCTGCGGTAACGGTAATGACTTG
64 AGGAAAACGGTAAGGACTTACCCTTGCACATAGCAGAGGAA-CCTACGGTAACGATAAAGACTTA
288630 CCCT
128 CCCT
* * *
288634 TTCATATAGCAGAGGAGCTTGCGGTAACGGTAAGGACTTACCCTTGCACATAGCAGAGGAGCCTA
1 TGCACATAGCAGAGGAGCTTGCGGTAACGGTAAGGACTTACCCTTACACATAGCAGAGGA-CCTA
* *
288699 CGG-TAACGGTAAGGACTTACCCTTGCACATAGCAGAGGAACCTACGGTAACGATAAAGAGTTAC
65 -GGAAAACGGTAAGGACTTACCCTTGCACATAGCAGAGGAACCTACGGTAACGATAAAGACTTAC
288763 CCT
129 CCT
* * * * *
288766 TGCACATAGCAGAGAAGCGTGCGATAACAGTAAGGATTTAC
1 TGCACATAGCAGAGGAGCTTGCGGTAACGGTAAGGACTTAC
288807 AAGTCATAGA
Statistics
Matches: 149, Mismatches: 20, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
131 33 0.22
132 110 0.74
133 6 0.04
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.21
Consensus pattern (131 bp):
TGCACATAGCAGAGGAGCTTGCGGTAACGGTAAGGACTTACCCTTACACATAGCAGAGGACCTAG
GAAAACGGTAAGGACTTACCCTTGCACATAGCAGAGGAACCTACGGTAACGATAAAGACTTACCC
T
Found at i:292159 original size:19 final size:20
Alignment explanation
Indices: 292120--292173 Score: 74
Period size: 19 Copynumber: 2.7 Consensus size: 20
292110 CTCAGAGGAA
292120 ACCGATTCCCCCCAAGGGGGT
1 ACCGATTCCCCCCAA-GGGGT
*
292141 ACCGATTCCCCCTAA-GGGT
1 ACCGATTCCCCCCAAGGGGT
*
292160 ATCGATTCCCCCCA
1 ACCGATTCCCCCCA
292174 CTGTTTAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 16 0.53
21 14 0.47
ACGTcount: A:0.20, C:0.41, G:0.20, T:0.19
Consensus pattern (20 bp):
ACCGATTCCCCCCAAGGGGT
Found at i:292385 original size:19 final size:20
Alignment explanation
Indices: 292346--292399 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 20
292336 CTCAGAGGAA
292346 ACCGATTCCCCCCAAGGGGGT
1 ACCGATTCCCCCCAA-GGGGT
*
292367 ACCGATTCCCCCTAA-GGGT
1 ACCGATTCCCCCCAAGGGGT
* *
292386 ATCAATTCCCCCCA
1 ACCGATTCCCCCCA
292400 CTGTTCAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 15 0.52
21 14 0.48
ACGTcount: A:0.22, C:0.41, G:0.19, T:0.19
Consensus pattern (20 bp):
ACCGATTCCCCCCAAGGGGT
Found at i:292478 original size:226 final size:226
Alignment explanation
Indices: 292084--292535 Score: 841
Period size: 226 Copynumber: 2.0 Consensus size: 226
292074 ATTTCGAACC
292084 ATTTCAAAGCCAAAAATTCCAGATTGCTCAGAGGAAACCGATTCCCCCCAAGGGGGTACCGATTC
1 ATTTCAAAGCCAAAAATTCCAGATTGCTCAGAGGAAACCGATTCCCCCCAAGGGGGTACCGATTC
* * *
292149 CCCCTAAGGGTATCGATTCCCCCCACTGTTTAATGGTCGAAATATTTGAATTTTATACTTAGGGA
66 CCCCTAAGGGTATCAATTCCCCCCACTGTTCAATGGTAGAAATATTTGAATTTTATACTTAGGGA
* *
292214 ACTGATTCCCCTTGAGGGGTACCGATTCCCCCACGCTCCAAGCTGTTGTATTAATTATTTTCACA
131 ACTGATTCCCCATGAGGGGTACCAATTCCCCCACGCTCCAAGCTGTTGTATTAATTATTTTCACA
292279 CTTAAACGGCTCCAATAACTTCATTAATGAT
196 CTTAAACGGCTCCAATAACTTCATTAATGAT
292310 ATTTCAAAGCCAAAAATTCCAGATTGCTCAGAGGAAACCGATTCCCCCCAAGGGGGTACCGATTC
1 ATTTCAAAGCCAAAAATTCCAGATTGCTCAGAGGAAACCGATTCCCCCCAAGGGGGTACCGATTC
292375 CCCCTAAGGGTATCAATTCCCCCCACTGTTCAATGGTAGAAATATTTGAATTTTATACTTAGGGA
66 CCCCTAAGGGTATCAATTCCCCCCACTGTTCAATGGTAGAAATATTTGAATTTTATACTTAGGGA
* *
292440 ACTGATTCCCCATGAGGGGTACTAATTCCCCCACGCTCCAAGCTGTTGTATTAATTGTTTTCACA
131 ACTGATTCCCCATGAGGGGTACCAATTCCCCCACGCTCCAAGCTGTTGTATTAATTATTTTCACA
292505 CTTAAACGGCTCCAATAACTTCATTAATGAT
196 CTTAAACGGCTCCAATAACTTCATTAATGAT
292536 CCCCAATGTT
Statistics
Matches: 219, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
226 219 1.00
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (226 bp):
ATTTCAAAGCCAAAAATTCCAGATTGCTCAGAGGAAACCGATTCCCCCCAAGGGGGTACCGATTC
CCCCTAAGGGTATCAATTCCCCCCACTGTTCAATGGTAGAAATATTTGAATTTTATACTTAGGGA
ACTGATTCCCCATGAGGGGTACCAATTCCCCCACGCTCCAAGCTGTTGTATTAATTATTTTCACA
CTTAAACGGCTCCAATAACTTCATTAATGAT
Found at i:293894 original size:23 final size:23
Alignment explanation
Indices: 293866--293918 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
293856 ATGTAAGCTC
*
293866 ATAAAATGATTTATGAATGTAAA
1 ATAAAATGATTTATGAATGCAAA
293889 ATAAAATGATTTATGAATGCAAA
1 ATAAAATGATTTATGAATGCAAA
293912 ATAAAAT
1 ATAAAAT
293919 TTATTAGTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.55, C:0.02, G:0.11, T:0.32
Consensus pattern (23 bp):
ATAAAATGATTTATGAATGCAAA
Found at i:294584 original size:44 final size:44
Alignment explanation
Indices: 294530--294716 Score: 180
Period size: 44 Copynumber: 4.3 Consensus size: 44
294520 GCAGTAAAAA
* * * * * *
294530 GTAAAGACTTACCCTTTCACATAGCAAAGGAGTCTG-GGAAAATG
1 GTAAGGACTTACCCTTGCACATAGCAGAGGAGCCAGCGG-AAACG
* * *
294574 GTAAGGACTTACCATTGCACATAGTAGAGGAGCCAGCGGTAACG
1 GTAAGGACTTACCCTTGCACATAGCAGAGGAGCCAGCGGAAACG
* * *
294618 GTAAGGACTTACCCTTGCACATAGCAGAGGACCCTGCGGTAACG
1 GTAAGGACTTACCCTTGCACATAGCAGAGGAGCCAGCGGAAACG
* * * * * *
294662 ATAAAGACTTACACTTGCACATAGCAGAGGACCCTGCGGTAAC-
1 GTAAGGACTTACCCTTGCACATAGCAGAGGAGCCAGCGGAAACG
*
294705 GTAAAGACTTAC
1 GTAAGGACTTAC
294717 AAGTCATATA
Statistics
Matches: 125, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
43 11 0.09
44 112 0.90
45 2 0.02
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.20
Consensus pattern (44 bp):
GTAAGGACTTACCCTTGCACATAGCAGAGGAGCCAGCGGAAACG
Found at i:294684 original size:88 final size:87
Alignment explanation
Indices: 294530--294716 Score: 225
Period size: 88 Copynumber: 2.1 Consensus size: 87
294520 GCAGTAAAAA
* ** * * *
294530 GTAAAGACTTACCCTTTCACATAGCAAAGGAGTCTGGGAAAATGGTAAGGACTTACCATTGCACA
1 GTAAAGACTTACCCTTGCACATAGCAAAGGACCCTGGGAAAACGATAAAGACTTACCATTGCACA
* *
294595 TAGTAGAGGAGCCAGCGGTAAC
66 TAGCAGAGGACCCAGCGGTAAC
* * *
294617 GGTAAGGACTTACCCTTGCACATAGCAGAGGACCCTGCGG-TAACGATAAAGACTTA-CACTTGC
1 -GTAAAGACTTACCCTTGCACATAGCAAAGGACCCTG-GGAAAACGATAAAGACTTACCA-TTGC
*
294680 ACATAGCAGAGGACCCTGCGGTAAC
63 ACATAGCAGAGGACCCAGCGGTAAC
294705 GTAAAGACTTAC
1 GTAAAGACTTAC
294717 AAGTCATATA
Statistics
Matches: 84, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
87 13 0.15
88 69 0.82
89 2 0.02
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.20
Consensus pattern (87 bp):
GTAAAGACTTACCCTTGCACATAGCAAAGGACCCTGGGAAAACGATAAAGACTTACCATTGCACA
TAGCAGAGGACCCAGCGGTAAC
Found at i:295771 original size:27 final size:26
Alignment explanation
Indices: 295720--295771 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
295710 GATATTCTCG
*
295720 GGTTATTTCCATTTCAGGGGTATTTT
1 GGTTATTTACATTTCAGGGGTATTTT
295746 GGTTATTTTACATATTCA-GGGTATTT
1 GGTTA-TTTACAT-TTCAGGGGTATTT
295772 AATTCATCCC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 5 0.22
27 14 0.61
28 4 0.17
ACGTcount: A:0.19, C:0.10, G:0.21, T:0.50
Consensus pattern (26 bp):
GGTTATTTACATTTCAGGGGTATTTT
Found at i:300804 original size:14 final size:13
Alignment explanation
Indices: 300785--300831 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 13
300775 ACTGTCAATA
300785 ATCTTATCATTTAT
1 ATCTTAT-ATTTAT
300799 ATCTTATAATTATAT
1 ATCTTAT-ATT-TAT
300814 CATCTTATATTTAT
1 -ATCTTATATTTAT
300828 -TCTT
1 ATCTT
300832 TTAATCAACA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 4 0.13
14 13 0.43
15 6 0.20
16 7 0.23
ACGTcount: A:0.30, C:0.13, G:0.00, T:0.57
Consensus pattern (13 bp):
ATCTTATATTTAT
Found at i:300820 original size:16 final size:15
Alignment explanation
Indices: 300785--300827 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
300775 ACTGTCAATA
*
300785 ATCTTATCATT-TAT
1 ATCTTATAATTATAT
300799 ATCTTATAATTATAT
1 ATCTTATAATTATAT
*
300814 CATCTTATATTTAT
1 -ATCTTATAATTAT
300828 TCTTTTAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 10 0.40
15 3 0.12
16 12 0.48
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.56
Consensus pattern (15 bp):
ATCTTATAATTATAT
Found at i:300917 original size:4 final size:4
Alignment explanation
Indices: 300908--300938 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
300898 TTAATGAGAA
300908 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
300939 TAAATCATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:301193 original size:23 final size:23
Alignment explanation
Indices: 301160--301242 Score: 87
Period size: 23 Copynumber: 3.7 Consensus size: 23
301150 CTCATATAAA
*
301160 TGCACCTAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
301183 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* * * *
301206 T-AATCGAAGTACCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
301228 TACATCGAAGTGCCA
1 TGCACCGAAGTGCCA
301243 TATAAAATGT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
22 19 0.37
23 32 0.63
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:301220 original size:22 final size:23
Alignment explanation
Indices: 301175--301238 Score: 94
Period size: 22 Copynumber: 2.8 Consensus size: 23
301165 CTAAGTGCCA
* * *
301175 CGTAGAATTGCACCGAAGTGCCG
1 CGTAGAATTACATCGAAGTACCG
301198 CGTAGAATTA-ATCGAAGTACCG
1 CGTAGAATTACATCGAAGTACCG
301220 CGTAGAATTACATCGAAGT
1 CGTAGAATTACATCGAAGT
301239 GCCATATAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
22 20 0.54
23 17 0.46
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.22
Consensus pattern (23 bp):
CGTAGAATTACATCGAAGTACCG
Found at i:305143 original size:2 final size:2
Alignment explanation
Indices: 305130--305164 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
305120 AAAATAGGAA
*
305130 AT AT AT AA 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 AT AT AT A
305165 ATAACACTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:305618 original size:37 final size:37
Alignment explanation
Indices: 305568--305672 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
305558 GTGCTTGTGG
* * * * *
305568 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
* * *
305605 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
305642 ATCCTATTTTTAGGAGTTTGAATCCTAGTAA
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAA
305673 CACAAAAATG
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
Found at i:306517 original size:105 final size:105
Alignment explanation
Indices: 306215--306845 Score: 815
Period size: 105 Copynumber: 6.0 Consensus size: 105
306205 GCATTGTTCC
* * ** *
306215 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTATTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTA-TTGTTGACA
* * * * * *
306279 ACCAGCCGTCCCTTCGTTGTGAAGGTGAAATTGTGTTGTCTC
64 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
306321 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGA-A-T--GAAATT-TTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTATTGTTGACAAC
* *
306381 CAGCGGTCCCTTCGTCGTGGAGTTGAACTTGCGTTGTTTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
306421 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTAGCTCTGTGATTGGGAAGTTATTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTATTGTTGACAAC
306486 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
306526 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTAGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTATTGTTGACAAC
*
306591 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTATCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * *
306631 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTAACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTATTGTTGACAAC
*
306696 CAGCGGTCCCTTCGTCGTGAAATTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
306736 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGCTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTT-ATTGTTGACAA
* ** * * * *
306801 CTAGCCATCCCTTCTTTGTGAAGTTGAACTTGTGTTGTCTC
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
306842 GAGT
1 GAGT
306846 GTCACGATAT
Statistics
Matches: 470, Mismatches: 48, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
100 79 0.17
101 1 0.00
102 7 0.01
104 5 0.01
105 298 0.63
106 80 0.17
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTATTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:307112 original size:35 final size:36
Alignment explanation
Indices: 307045--307119 Score: 107
Period size: 35 Copynumber: 2.1 Consensus size: 36
307035 TGTTTGGAGA
* * *
307045 GAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
*
307081 GAAACTATCTCAAGCGAGA-TAAATTCATTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
307116 GAAA
1 GAAA
307120 TGTTTTCAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
35 18 0.51
36 17 0.49
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (36 bp):
GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
Found at i:307189 original size:39 final size:39
Alignment explanation
Indices: 307135--307519 Score: 116
Period size: 39 Copynumber: 10.9 Consensus size: 39
307125 TCAATGTTTA
*
307135 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTC
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTTC
* * * * **
307174 TGTTTCGAGGGAAACTATCTCAAGAGAGAGAAAA-AATC
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTTC
* ** *
307212 -ATTTCAAGGGAAA-TGT-T-------TTC--AATGTTTA
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAAT-TTTC
*
307240 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTC
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTTC
* * ***
307279 TGTTTCGAGGGAAACTATCTCAA--GAGA-AAAAAAATC
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTTC
* ** *
307315 -ATTTCAAGGG-AA-TGT-T-------TTC--AATGTTTA
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAAT-TTTC
*
307342 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTC
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTTC
* * * * **
307381 TGTTTCGAGGGAAACTATCTCAAGAGAGAGAAAA-AATC
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTTC
* ** *
307419 -ATTTCAAGGGAAA-TGT-T-------TTC--AATGTTTA
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAAT-TTTC
*
307447 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTC
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTTC
* * * *
307486 TGTTTCGAGGGAAACTATCTCAAGAGAGAAAAAA
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAA
307520 AATCATTTCA
Statistics
Matches: 236, Mismatches: 67, Indels: 86
0.61 0.17 0.22
Matches are distributed among these distances:
26 6 0.03
27 1 0.00
28 10 0.04
29 24 0.10
30 9 0.04
31 3 0.01
32 1 0.00
33 2 0.01
34 2 0.01
35 10 0.04
36 10 0.04
37 26 0.11
38 7 0.03
39 116 0.49
40 9 0.04
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.29
Consensus pattern (39 bp):
TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTTC
Found at i:307373 original size:207 final size:208
Alignment explanation
Indices: 307020--307704 Score: 1111
Period size: 207 Copynumber: 3.4 Consensus size: 208
307010 TTCGTTAAAT
* ** *
307020 TGTTTTCAAAGTTTATGTTTGGAGAGAAACTGTCTCAAGGGAGACAAAA--TTC-GTTTCAAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
* * * *
307082 AAACTATCTCAAGCGAGATAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGA
66 AAACTATCTCAAGAGAAAAAAAATCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGA
307147 AACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCTCAAGAGAGAGAAAAAATC
131 AACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCTCAAGAGAGAGAAAAAATC
307212 ATTTCAAGGGAAA
196 ATTTCAAGGGAAA
307225 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
307290 AAACTATCTCAAGAGAAAAAAAATCATTTCAAGGG-AATGTTTTCAATGTTTATGTTTCAAGAGA
66 AAACTATCTCAAGAGAAAAAAAATCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGA
307354 AACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCTCAAGAGAGAGAAAAAATC
131 AACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCTCAAGAGAGAGAAAAAATC
307419 ATTTCAAGGGAAA
196 ATTTCAAGGGAAA
307432 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
307497 AAACTATCTCAAGAGAGAAAAAAAATCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGA
66 AAACTATCTC-A-AGAGAAAAAAAATCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGA
* *
307562 GAAACTGTCTCAAAGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCTCAGGAGAGA-AAAAAA
129 GAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCTCAAGAGAGAGAAAAAA
*
307626 TAATTTCAAGGG--A
194 TCATTTCAAGGGAAA
*
307639 -------AATG----T-TTTCAAGAGAAACTGTCTCAAGGGAGACGAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
307692 AAACTATCTCAAG
66 AAACTATCTCAAG
307705 CAAAATAAAA
Statistics
Matches: 462, Mismatches: 12, Indels: 24
0.93 0.02 0.05
Matches are distributed among these distances:
193 2 0.00
194 1 0.00
195 57 0.12
196 1 0.00
200 4 0.01
205 46 0.10
207 186 0.40
208 41 0.09
209 41 0.09
210 83 0.18
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.30
Consensus pattern (208 bp):
TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
AAACTATCTCAAGAGAAAAAAAATCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGA
AACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCTCAAGAGAGAGAAAAAATC
ATTTCAAGGGAAA
Found at i:307582 original size:312 final size:312
Alignment explanation
Indices: 307020--307704 Score: 1127
Period size: 312 Copynumber: 2.2 Consensus size: 312
307010 TTCGTTAAAT
* ** *
307020 TGTTTTCAAAGTTTATGTTTGGAGAGAAACTGTCTCAAGGGAGACAAAA--TTC-GTTTCAAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
* * *
307082 AAACTATCTC-A-AGCGAGATAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGA
66 AAACTATCTCAAGAGAGAGAAAAAATCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGA
*
307145 GAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCTCAAGAGAGAGAAAAAA
131 GAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCTCAAGAGAGAAAAAAAA
*
307210 TCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAAT
196 TCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAAT
*
307275 TTTCTGTTTCGAGGGAAACTATCTCAAGAGA-AAAAAAATCATTTCAAGGGAA
261 TTTCTGTTTCGAGGGAAACTATCTCAAGAGAGAAAAAAATAATTTCAAGGG-A
307327 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
307392 AAACTATCTCAAGAGAGAGAAAAAATCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGA
66 AAACTATCTCAAGAGAGAGAAAAAATCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGA
307457 GAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCTCAAGAGAGAAAAAAAA
131 GAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCTCAAGAGAGAAAAAAAA
307522 TCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAAT
196 TCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAAT
*
307587 TTTCTGTTTCGAGGGAAACTATCTCAGGAGAGAAAAAAATAATTTCAAGGGA
261 TTTCTGTTTCGAGGGAAACTATCTCAAGAGAGAAAAAAATAATTTCAAGGGA
*
307639 -------AATG----T-TTTCAAGAGAAACTGTCTCAAGGGAGACGAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
307692 AAACTATCTCAAG
66 AAACTATCTCAAG
307705 CAAAATAAAA
Statistics
Matches: 360, Mismatches: 12, Indels: 19
0.92 0.03 0.05
Matches are distributed among these distances:
300 60 0.17
301 1 0.00
305 4 0.01
307 46 0.13
309 3 0.01
310 19 0.05
311 1 0.00
312 208 0.58
313 18 0.05
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.30
Consensus pattern (312 bp):
TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
AAACTATCTCAAGAGAGAGAAAAAATCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGA
GAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCTCAAGAGAGAAAAAAAA
TCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAAT
TTTCTGTTTCGAGGGAAACTATCTCAAGAGAGAAAAAAATAATTTCAAGGGA
Found at i:307665 original size:105 final size:104
Alignment explanation
Indices: 307020--307649 Score: 1101
Period size: 105 Copynumber: 6.1 Consensus size: 104
307010 TTCGTTAAAT
* ** *
307020 TGTTTTCAAAGTTTATGTTTGGAGAGAAACTGTCTCAAGGGAGACAAAA--TTC-GTTTCAAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
* * *
307082 AAACTATCTCAAGCGAG-ATAAATTCATTTCAAGGGAAA
66 AAACTATCTCAAGAGAGAAAAAAATCATTTCAAGGGAAA
307120 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
307185 AAACTATCTCAAGAGAGAGAAAAAATCATTTCAAGGGAAA
66 AAACTATCTCAAGAGAGA-AAAAAATCATTTCAAGGGAAA
307225 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
307290 AAACTATCTCAAGAGA-AAAAAAATCATTTCAAGGG-AA
66 AAACTATCTCAAGAGAGAAAAAAATCATTTCAAGGGAAA
307327 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
307392 AAACTATCTCAAGAGAGAGAAAAAATCATTTCAAGGGAAA
66 AAACTATCTCAAGAGAGA-AAAAAATCATTTCAAGGGAAA
307432 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
307497 AAACTATCTCAAGAGAGAAAAAAAATCATTTCAAGGGAAA
66 AAACTATCTCAAGAGAG-AAAAAAATCATTTCAAGGGAAA
*
307537 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
* *
307602 AAACTATCTCAGGAGAGAAAAAAATAATTTCAAGGGAAA
66 AAACTATCTCAAGAGAGAAAAAAATCATTTCAAGGGAAA
307641 TGTTTTCAA
1 TGTTTTCAA
307650 GAGAAACTGT
Statistics
Matches: 511, Mismatches: 10, Indels: 14
0.96 0.02 0.03
Matches are distributed among these distances:
100 46 0.09
102 86 0.17
103 44 0.09
104 49 0.10
105 285 0.56
106 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.30
Consensus pattern (104 bp):
TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
AAACTATCTCAAGAGAGAAAAAAATCATTTCAAGGGAAA
Found at i:307827 original size:36 final size:36
Alignment explanation
Indices: 307774--307881 Score: 101
Period size: 36 Copynumber: 3.0 Consensus size: 36
307764 GTGAAAACGG
* * *
307774 TCTCAAGCGAGACAAATCTTGTTTTAAGAAAAATAA
1 TCTCAAGTGAAACAAATCTTGTTTTAAGAAAAACAA
* * * ** *
307810 TCTTAAGTGAAATAAATCTTCTTTCGAGAAAAACAG
1 TCTCAAGTGAAACAAATCTTGTTTTAAGAAAAACAA
* *
307846 TCTCAAGTGAGACAAAGT-ATGTTTTAAGAAAAACAA
1 TCTCAAGTGAAACAAA-TCTTGTTTTAAGAAAAACAA
307882 ATTTGAGTGA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
36 53 0.98
37 1 0.02
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (36 bp):
TCTCAAGTGAAACAAATCTTGTTTTAAGAAAAACAA
Found at i:307858 original size:72 final size:75
Alignment explanation
Indices: 307739--307878 Score: 198
Period size: 72 Copynumber: 1.9 Consensus size: 75
307729 AACAGCCTTG
* * *
307739 AGTGAAATGAAATGCCTTCTTTCGAGTGAAAACGGTCTCAAGCGAGACAAA-TCTTGTTTTAAGA
1 AGTGAAATGAAAT-CCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACAAAGT-ATGTTTTAAGA
307803 AAAATAATCTTA
64 AAAATAATCTTA
*
307815 AGTGAAAT-AAAT-CTTCTTTCGAG-AAAAACAGTCTCAAGTGAGACAAAGTATGTTTTAAGAAA
1 AGTGAAATGAAATCCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACAAAGTATGTTTTAAGAAA
307877 AA
66 AA
307879 CAAATTTGAG
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
72 35 0.59
73 12 0.20
75 4 0.07
76 8 0.14
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (75 bp):
AGTGAAATGAAATCCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACAAAGTATGTTTTAAGAAA
AATAATCTTA
Found at i:307891 original size:72 final size:74
Alignment explanation
Indices: 307735--307896 Score: 197
Period size: 72 Copynumber: 2.2 Consensus size: 74
307725 AAAAAACAGC
* * *
307735 CTTGAGTGAAATGAAATGCCTTCTTTCGAGTGAAAACGGTCTCAAGCGAGACAAATCTTGTTTTA
1 CTTGAGTGAAAT-AAAT-CCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACAAATCATGTTTTA
*
307800 AGAAAAATAAT
64 AGAAAAAAAAT
* *
307811 CTTAAGTGAAATAAAT-CTTCTTTCGAG-AAAAACAGTCTCAAGTGAGACAAAGT-ATGTTTTAA
1 CTTGAGTGAAATAAATCCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACAAA-TCATGTTTTAA
307873 GAAAAACAAAT
65 GAAAAA-AAAT
*
307884 -TTGAGTGAGATAA
1 CTTGAGTGAAATAA
307897 TCATCTGCAT
Statistics
Matches: 76, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
72 46 0.61
73 15 0.20
75 4 0.05
76 11 0.14
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (74 bp):
CTTGAGTGAAATAAATCCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACAAATCATGTTTTAAG
AAAAAAAAT
Found at i:309386 original size:184 final size:183
Alignment explanation
Indices: 309026--309563 Score: 900
Period size: 184 Copynumber: 2.9 Consensus size: 183
309016 ATCAGGTTTA
* *
309026 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGACTTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
* * ** * * *
309091 GCCAAGTGTCCGAGCAATGTCAT-GATTTGAATGTAATCTATTCATAAAGCCAGAGCTTTTAAGT
66 GCCAAGTGTCTGAGCAGTGTCATAG-TTTGAACATAATCTATTCATAAAGCCAGGGCTTTCAGGT
309155 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
130 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
*
309209 ACTGAAGGGTTCGTCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
*
309274 ACCAAGTGTCTGAGCAGTGTCATAGTTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCAGGT
66 GCCAAGTGTCTGAGCAGTGTCATAG-TTTGAACATAATCTATTCATAAAGCCAGGGCTTTCAGGT
309339 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
130 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
*
309393 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGTAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
*
309458 GCCAAGTGTCTGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAATCCAGGGCTTTC-GAGT
66 GCCAAGTGTCTGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCAG-GT
* *
309522 TTTCTCTATAACCAATTTCCTTAGTGGAATAGCTCAGCTTTA
130 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
309564 CGGATTTAAT
Statistics
Matches: 335, Mismatches: 18, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
182 1 0.00
183 158 0.47
184 176 0.53
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (183 bp):
ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
GCCAAGTGTCTGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCAGGTT
TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
Found at i:313078 original size:19 final size:19
Alignment explanation
Indices: 313045--313081 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
313035 TACAGATGAT
313045 GGAAATAAAATAAAAGAGA
1 GGAAATAAAATAAAAGAGA
313064 GGAAA-AAAATGAAAAGAG
1 GGAAATAAAAT-AAAAGAG
313082 TTAGTAAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.68, C:0.00, G:0.24, T:0.08
Consensus pattern (19 bp):
GGAAATAAAATAAAAGAGA
Found at i:313766 original size:39 final size:39
Alignment explanation
Indices: 313712--313791 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
313702 TCGAAATGTT
*
313712 ACCTTAAAATTTAAACTTACCCTTTTCATTAAAAAGATA
1 ACCTTAAAATTTAAACTTACCATTTTCATTAAAAAGATA
313751 ACCTTAAAATTTAAACTTACCATTTTCATTAAAAAGATA
1 ACCTTAAAATTTAAACTTACCATTTTCATTAAAAAGATA
313790 AC
1 AC
313792 TGGAAATTAC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.45, C:0.17, G:0.03, T:0.35
Consensus pattern (39 bp):
ACCTTAAAATTTAAACTTACCATTTTCATTAAAAAGATA
Found at i:314530 original size:2 final size:2
Alignment explanation
Indices: 314517--314549 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
314507 AAAATAGAAA
*
314517 AT AT AT AA 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 AT AT A
314550 ACACTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:315036 original size:37 final size:37
Alignment explanation
Indices: 314954--315055 Score: 123
Period size: 37 Copynumber: 2.8 Consensus size: 37
314944 GTGCTTGTGG
* * * * * *
314954 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
* * *
314991 ATCATATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
315028 ATCCTATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
315056 TAGGACGAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
Found at i:316467 original size:18 final size:18
Alignment explanation
Indices: 316444--316480 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
316434 AATTTATTTT
316444 ATTATTAATAAAAATAAA
1 ATTATTAATAAAAATAAA
*
316462 ATTATTAATAAAATTAAA
1 ATTATTAATAAAAATAAA
316480 A
1 A
316481 AAGTTCAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
ATTATTAATAAAAATAAA
Found at i:317575 original size:22 final size:22
Alignment explanation
Indices: 317550--317602 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
317540 GCATGATGAC
317550 AAAATTAGTCCCAACGTTTACT
1 AAAATTAGTCCCAACGTTTACT
317572 AAAATTAGTCCCAACGTTTACT
1 AAAATTAGTCCCAACGTTTACT
317594 AAAA-TAGTC
1 AAAATTAGTC
317603 ATTTTACTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 5 0.16
22 26 0.84
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (22 bp):
AAAATTAGTCCCAACGTTTACT
Found at i:319202 original size:14 final size:15
Alignment explanation
Indices: 319165--319199 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
319155 ATGAGGTTTT
319165 TGAAAAGATTTTTAA
1 TGAAAAGATTTTTAA
319180 TGAAAAGATTTTTAA
1 TGAAAAGATTTTTAA
319195 TGAAA
1 TGAAA
319200 GATGGGAGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (15 bp):
TGAAAAGATTTTTAA
Found at i:320184 original size:23 final size:23
Alignment explanation
Indices: 320162--320210 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
320152 CAAAAATATT
320162 TTATTA-TATT-ATATTTATTTA
1 TTATTATTATTAATATTTATTTA
*
320183 TTATTATTATTAATATTTTTTTA
1 TTATTATTATTAATATTTATTTA
320206 TTATT
1 TTATT
320211 TTTGTAGGCC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 6 0.24
22 4 0.16
23 15 0.60
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (23 bp):
TTATTATTATTAATATTTATTTA
Found at i:320305 original size:33 final size:33
Alignment explanation
Indices: 320260--320345 Score: 118
Period size: 33 Copynumber: 2.6 Consensus size: 33
320250 TTCAGAAAAT
* *
320260 AAATCAATGTATTTGAGTCTTATTGAAACACTA
1 AAATCAAAGTATTTGAGTCCTATTGAAACACTA
* *
320293 AAATCAACGTATTTAAGTCCTATTGAAACACTA
1 AAATCAAAGTATTTGAGTCCTATTGAAACACTA
* *
320326 AAACCAAAGCATTTGAGTCC
1 AAATCAAAGTATTTGAGTCC
320346 AAGTATGACT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.30
Consensus pattern (33 bp):
AAATCAAAGTATTTGAGTCCTATTGAAACACTA
Found at i:320829 original size:7 final size:7
Alignment explanation
Indices: 320817--320867 Score: 59
Period size: 7 Copynumber: 6.9 Consensus size: 7
320807 ATGATAATAC
320817 ATTATTT
1 ATTATTT
320824 ATTA-TT
1 ATTATTT
320830 ATTTATTTT
1 A-TTA-TTT
320839 ATTATTT
1 ATTATTT
320846 ATTTATTTT
1 A-TTA-TTT
320855 ATTATTT
1 ATTATTT
320862 ATTATT
1 ATTATT
320868 CATTTTTTCC
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
6 3 0.08
7 20 0.51
8 9 0.23
9 7 0.18
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
ATTATTT
Found at i:320849 original size:16 final size:16
Alignment explanation
Indices: 320821--320864 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
320811 TAATACATTA
320821 TTTATTA-TTATTTAT
1 TTTATTATTTATTTAT
320836 TTTATTATTTATTTAT
1 TTTATTATTTATTTAT
320852 TTTATTATTTATT
1 TTTATTATTTATT
320865 ATTCATTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
15 7 0.25
16 21 0.75
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTATTATTTATTTAT
Found at i:324743 original size:109 final size:110
Alignment explanation
Indices: 324589--324843 Score: 331
Period size: 109 Copynumber: 2.4 Consensus size: 110
324579 GCTTCCCAAT
* * *
324589 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACCCAAGACAACACAAGCTC-ACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACAAAAGATATTGGACCCAAGACAACACAAGCTCAACTTCA
* *
324653 CGATGAAGGGGCGGCTGATTGTCAACAAACAACTTTTCAATTTCA
66 CGACGAAGGGGCGGCTAATTGTCAACAAACAACTTTTCAATTTCA
* * * * *
324698 TTCAGAGTCAATTTCAACTTCATAACAAAAGATTTTGGACTCAAGATAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACAAAAGATATTGGACCCAAGACAACACAAGCTCAACTTCA
* * *
324763 CGACGAAGGGGCGGCTAATTGTCAACAAACAA-TTTCCCAGTTC-
66 CGACGAAGGGGCGGCTAATTGTCAACAAACAACTTTTCAATTTCA
** *
324806 --CAGAGCCAATTTCAACTTCACAACGGAGGATATTGGAC
1 TTCAGAGCCAATTTCAACTTCACAACAAAAGATATTGGAC
324844 TCGGAGCAAT
Statistics
Matches: 126, Mismatches: 19, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
106 32 0.25
109 58 0.46
110 36 0.29
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.24
Consensus pattern (110 bp):
TTCAGAGCCAATTTCAACTTCACAACAAAAGATATTGGACCCAAGACAACACAAGCTCAACTTCA
CGACGAAGGGGCGGCTAATTGTCAACAAACAACTTTTCAATTTCA
Found at i:325264 original size:254 final size:252
Alignment explanation
Indices: 324812--325273 Score: 606
Period size: 254 Copynumber: 1.8 Consensus size: 252
324802 GTTCCAGAGC
* * *
324812 CAATTTCAACTTCACAACGGAGGATATTGGACTCGGAGCAATACAACTTACTTGGATTTCAACTT
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCGAAACAATACAACTTACTTGGATTTCAACTT
* * * * *
324877 CACGTCGAAGGATATCCAATTTCAGGCTCAACTTCACGACGAAGGGGCCACCCGCAGTTTCAACT
66 CACGACGAAGGATATCCAATCTAAGGCTCAACTTCACGACGAAGGGACCACACGCAGTTTCAACT
* * * *
324942 TCACGACGAAGGGAATCGTGCACACAAGCAGCATCCATCTCTAGATTGGATTTTAACTTCAAGAC
131 TCACGACGAAGGGAATCATGCACACAAGCAACATCCACCTCTAGATTGGATTTCAACTTCAAGAC
325007 GAAGGATATCCAACTCAAAGAAGGAGTATCTGTCAATAAACTTTCTAGTTTCAAAGT
196 GAAGGATATCCAACTCAAAGAAGGAGTATCTGTCAATAAACTTTCTAGTTTCAAAGT
* ** * *
325064 CAATTTCATCTTCACAGTGAAGGATATTGGCCTCGAAAC-ATCATAACTTACATTGGATTTCAAC
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCGAAACAAT-ACAACTTAC-TTGGATTTCAAC
* * * *
325128 TTCACGACGAATGATATCCAACTCTAAGGTTCAACTTCACGACGAAGGGACCATA--TATGATTT
64 TTCACGACGAAGGATATCCAA-TCTAAGGCTCAACTTCACGACGAAGGGACCACACGCA-G-TTT
* ** * * *
325191 CAACTTCATGACGAAGGGAATCATGTTCACCAGCAACATTCACCTTTAGATTGGATTTCAACTTC
126 CAACTTCACGACGAAGGGAATCATGCACACAAGCAACATCCACCTCTAGATTGGATTTCAACTTC
*
325256 ACGACGAAGGATATCCAA
191 AAGACGAAGGATATCCAA
325274 TTCCAGGCTC
Statistics
Matches: 177, Mismatches: 28, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
251 2 0.01
252 41 0.23
253 32 0.18
254 102 0.58
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (252 bp):
CAATTTCAACTTCACAACGAAGGATATTGGACTCGAAACAATACAACTTACTTGGATTTCAACTT
CACGACGAAGGATATCCAATCTAAGGCTCAACTTCACGACGAAGGGACCACACGCAGTTTCAACT
TCACGACGAAGGGAATCATGCACACAAGCAACATCCACCTCTAGATTGGATTTCAACTTCAAGAC
GAAGGATATCCAACTCAAAGAAGGAGTATCTGTCAATAAACTTTCTAGTTTCAAAGT
Found at i:325286 original size:34 final size:34
Alignment explanation
Indices: 325248--325336 Score: 105
Period size: 32 Copynumber: 2.7 Consensus size: 34
325238 AGATTGGATT
325248 TCAACTTCACGACGAAGGATATCCAATTCCA-G-GC
1 TCAACTTCACGACGAAGGATATCC-A-TCCACGAGC
* **
325282 TCAACTTCACGACGAAGG--GTCCATCCACGATT
1 TCAACTTCACGACGAAGGATATCCATCCACGAGC
325314 TCAACTTCACGACGAAGGATATC
1 TCAACTTCACGACGAAGGATATC
325337 GTGTTCATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
30 4 0.09
31 2 0.04
32 21 0.45
34 20 0.43
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.21
Consensus pattern (34 bp):
TCAACTTCACGACGAAGGATATCCATCCACGAGC
Found at i:325843 original size:3 final size:3
Alignment explanation
Indices: 325819--325864 Score: 55
Period size: 3 Copynumber: 16.3 Consensus size: 3
325809 TCTACAAAAA
325819 TAT T-T TAT TA- TAT TA- TATT TAT TAT TAT TAT TAT TAT TAT T-T
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT
325861 TAT T
1 TAT T
325865 TTTGCAGGCC
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
2 8 0.21
3 28 0.74
4 2 0.05
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:325955 original size:33 final size:33
Alignment explanation
Indices: 325918--325999 Score: 112
Period size: 33 Copynumber: 2.5 Consensus size: 33
325908 GAAAATAAAT
* **
325918 CAACGTATTTGAGTCTTATTGAAATTCTAAAAC
1 CAACGTATTTGAGTCCTATTGAAACACTAAAAC
325951 CAACGTATTTGAGTCCTATTGAAACACTAAAAC
1 CAACGTATTTGAGTCCTATTGAAACACTAAAAC
*
325984 CGAA-GCATTTGAGTCC
1 C-AACGTATTTGAGTCC
326000 AAGTATGACT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
33 42 0.95
34 2 0.05
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (33 bp):
CAACGTATTTGAGTCCTATTGAAACACTAAAAC
Found at i:326483 original size:7 final size:7
Alignment explanation
Indices: 326471--326520 Score: 66
Period size: 7 Copynumber: 6.9 Consensus size: 7
326461 ATGATAATAC
326471 ATTATTT
1 ATTATTT
326478 ATTA-TT
1 ATTATTT
326484 ATTTATTT
1 A-TTATTT
326492 ATTTATTT
1 A-TTATTT
326500 ATTATTTT
1 ATTA-TTT
326508 ATTATTT
1 ATTATTT
326515 ATTATT
1 ATTATT
326521 CATTTTTTTC
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
6 3 0.08
7 19 0.47
8 18 0.45
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
ATTATTT
Found at i:326489 original size:4 final size:4
Alignment explanation
Indices: 326472--326517 Score: 55
Period size: 4 Copynumber: 12.2 Consensus size: 4
326462 TGATAATACA
326472 TTAT TTA- TTA- TTAT TTAT TTAT TTAT TTA- TTAT TT-T ATTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT -TTAT TTAT
326517 T
1 T
326518 ATTCATTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
3 10 0.26
4 27 0.71
5 1 0.03
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:326503 original size:19 final size:19
Alignment explanation
Indices: 326471--326526 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 19
326461 ATGATAATAC
326471 ATTATTTA-TTATTA-TTT
1 ATTATTTATTTATTATTTT
326488 ATTTATTTATTTATTATTTT
1 A-TTATTTATTTATTATTTT
326508 ATTATTTA-TTATTCATTTT
1 ATTATTTATTTATT-ATTTT
326527 TTTCCTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
17 1 0.03
18 12 0.34
19 18 0.51
20 4 0.11
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (19 bp):
ATTATTTATTTATTATTTT
Found at i:326504 original size:15 final size:15
Alignment explanation
Indices: 326471--326525 Score: 62
Period size: 15 Copynumber: 3.7 Consensus size: 15
326461 ATGATAATAC
326471 ATTATTTA-TTA-TT
1 ATTATTTATTTATTT
326484 ATTTATTTATTTATTT
1 A-TTATTTATTTATTT
326500 ATTATTT-TATTATTT
1 ATTATTTAT-TTATTT
*
326515 ATTATTCATTT
1 ATTATTTATTT
326526 TTTTCCTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
13 1 0.03
14 8 0.22
15 23 0.64
16 4 0.11
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (15 bp):
ATTATTTATTTATTT
Found at i:327049 original size:27 final size:26
Alignment explanation
Indices: 327019--327076 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
327009 TTATAATGAG
*
327019 TATACGAAAGTTACACATTTAGTGTCA
1 TATAC-AAAGTTACACATATAGTGTCA
* * *
327046 TATAACCAATTTACACATATAGTGTCG
1 TAT-ACAAAGTTACACATATAGTGTCA
327073 TATA
1 TATA
327077 GAATATACAG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 1 0.04
27 23 0.88
28 2 0.08
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (26 bp):
TATACAAAGTTACACATATAGTGTCA
Found at i:331398 original size:13 final size:13
Alignment explanation
Indices: 331380--331406 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
331370 TACTTAATTG
331380 AGTAAAATTTAAA
1 AGTAAAATTTAAA
331393 AGTAAAATTTAAA
1 AGTAAAATTTAAA
331406 A
1 A
331407 AATATTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (13 bp):
AGTAAAATTTAAA
Found at i:334264 original size:32 final size:32
Alignment explanation
Indices: 334226--334317 Score: 123
Period size: 32 Copynumber: 2.9 Consensus size: 32
334216 CCCACAACGC
*
334226 CAAAAATTGGTACCTAGTTAAAGACCCTATAT
1 CAAAAATTAGTACCTAGTTAAAGACCCTATAT
** *
334258 TTAAAATTAGTACCTAGTCAAAGACCCTATAT
1 CAAAAATTAGTACCTAGTTAAAGACCCTATAT
*
334290 CAAAAATTAGTA-CTCAATTAAAGACCCT
1 CAAAAATTAGTACCT-AGTTAAAGACCCT
334318 CAAAGCATAA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
31 2 0.04
32 49 0.96
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28
Consensus pattern (32 bp):
CAAAAATTAGTACCTAGTTAAAGACCCTATAT
Found at i:342158 original size:15 final size:15
Alignment explanation
Indices: 342138--342167 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
342128 TAAATAAGTT
342138 AGTAACTTATTTACC
1 AGTAACTTATTTACC
342153 AGTAACTTATTTACC
1 AGTAACTTATTTACC
342168 TTATCTTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (15 bp):
AGTAACTTATTTACC
Found at i:350794 original size:20 final size:20
Alignment explanation
Indices: 350769--350941 Score: 203
Period size: 20 Copynumber: 8.6 Consensus size: 20
350759 TTGCGATTTT
*
350769 CGTAAATCGCAATGCGAATA
1 CGTAAATCGCAATGCGATTA
350789 CGTAAATCGCAATGCGATTA
1 CGTAAATCGCAATGCGATTA
350809 CGTAAATCGCAATGCGAATTA
1 CGTAAATCGCAATGCG-ATTA
* *
350830 GGAAAATCG-AATGCGATTA
1 CGTAAATCGCAATGCGATTA
350849 CGTAAATCGCAATGCGAATTA
1 CGTAAATCGCAATGCG-ATTA
350870 CGTAAATCG-AATTGCGATTTA
1 CGTAAATCGCAA-TGCGA-TTA
*
350891 CGT-AATCGCATTGCGATTTA
1 CGTAAATCGCAATGCGA-TTA
* *
350911 TGT-AATCGCATTGCGATTTA
1 CGTAAATCGCAATGCGA-TTA
350931 -GTAAATCGCAA
1 CGTAAATCGCAA
350942 CGAGATTCTG
Statistics
Matches: 138, Mismatches: 8, Indels: 14
0.86 0.05 0.09
Matches are distributed among these distances:
19 13 0.09
20 90 0.65
21 35 0.25
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.27
Consensus pattern (20 bp):
CGTAAATCGCAATGCGATTA
Found at i:350815 original size:40 final size:41
Alignment explanation
Indices: 350760--350941 Score: 232
Period size: 40 Copynumber: 4.5 Consensus size: 41
350750 AAATTCGTGT
*
350760 TGCGATTTTCGTAAATCGCAATGCGAA-TACGTAAATCGCAA
1 TGCGATTTACGTAAATCGCAATGCGAATTACGTAAATCG-AA
* *
350801 TGCGA-TTACGTAAATCGCAATGCGAATTAGGAAAATCGAA
1 TGCGATTTACGTAAATCGCAATGCGAATTACGTAAATCGAA
350841 TGCGA-TTACGTAAATCGCAATGCGAATTACGTAAATCGAA
1 TGCGATTTACGTAAATCGCAATGCGAATTACGTAAATCGAA
* * * *
350881 TTGCGATTTACGT-AATCGCATTGCGATTTATGT-AATCGCAT
1 -TGCGATTTACGTAAATCGCAATGCGAATTACGTAAATCG-AA
350922 TGCGATTTA-GTAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
350942 CGAGATTCTG
Statistics
Matches: 126, Mismatches: 10, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
39 2 0.02
40 81 0.64
41 37 0.29
42 6 0.05
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (41 bp):
TGCGATTTACGTAAATCGCAATGCGAATTACGTAAATCGAA
Found at i:350886 original size:81 final size:81
Alignment explanation
Indices: 350760--350941 Score: 239
Period size: 81 Copynumber: 2.3 Consensus size: 81
350750 AAATTCGTGT
*
350760 TGCGATTTTCGTAAATCGCAATGCGAATACGTAAATCGCAATGCGA-TTACGTAAATCGCAATGC
1 TGCGATTTACGTAAATCGCAATGCGAATACGTAAATCGCAATGCGATTTACGT-AATCGCAATGC
350824 GAATTAGGAAAATCG-AA
65 GAATTAGG-AAATCGCAA
*
350841 TGCGA-TTACGTAAATCGCAATGCGAATTACGTAAATCG-AATTGCGATTTACGTAATCGCATTG
1 TGCGATTTACGTAAATCGCAATGCGAA-TACGTAAATCGCAA-TGCGATTTACGTAATCGCAATG
* * * *
350904 CGATTTATGTAATCGCAT
64 CGAATTAGGAAATCGCAA
350922 TGCGATTTA-GTAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
350942 CGAGATTCTG
Statistics
Matches: 90, Mismatches: 6, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
80 27 0.30
81 54 0.60
82 9 0.10
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (81 bp):
TGCGATTTACGTAAATCGCAATGCGAATACGTAAATCGCAATGCGATTTACGTAATCGCAATGCG
AATTAGGAAATCGCAA
Found at i:354397 original size:19 final size:19
Alignment explanation
Indices: 354375--354433 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
354365 GGAAATTACT
354375 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
354394 ATCGTAA--C--AA-GAGA
1 ATCGCAATGCGAAATGAAA
354408 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
354427 ATCGCAA
1 ATCGCAA
354434 CGACAAAATC
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
14 9 0.29
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 16 0.52
ACGTcount: A:0.47, C:0.17, G:0.20, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:354444 original size:33 final size:33
Alignment explanation
Indices: 354375--354468 Score: 109
Period size: 33 Copynumber: 2.8 Consensus size: 33
354365 GGAAATTACT
* * * *
354375 ATCGCAATGCGAAATGAAAATCGTAACAAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
354408 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* * *
354441 ATCGTAACGCGAAACT-AAAATCACAACG
1 ATCGCAATGCGAAA-TGAAAATCGCAACG
354469 CGAAACTAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
33 52 0.98
34 1 0.02
ACGTcount: A:0.48, C:0.20, G:0.18, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:354525 original size:33 final size:33
Alignment explanation
Indices: 354483--354609 Score: 191
Period size: 33 Copynumber: 3.8 Consensus size: 33
354473 ACTAAATTCG
* *
354483 CGTTGCGATTTTCATTTCGCTTTGCGAGTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
354516 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
* *
354549 CGTCGCGATTTTAATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
* *
354582 CGTTGTGATTTTTATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
354610 AGTCATTTTT
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 85 1.00
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:354542 original size:19 final size:19
Alignment explanation
Indices: 354518--354577 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
354508 GAGTCCCTCG
354518 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
354537 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
* *
354551 TCGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
354570 TTGCGATT
1 TTGCGATT
354578 CCCTCGTTGT
Statistics
Matches: 31, Mismatches: 5, Indels: 10
0.67 0.11 0.22
Matches are distributed among these distances:
14 5 0.16
16 6 0.19
17 7 0.23
19 13 0.42
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:354937 original size:20 final size:20
Alignment explanation
Indices: 354912--354952 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
354902 AATAATTCAG
*
354912 TCATTTTCGTGTTGCGATTT
1 TCATTTTCATGTTGCGATTT
354932 TCATTTTCATGTTGCGATTT
1 TCATTTTCATGTTGCGATTT
354952 T
1 T
354953 AAGTTTCGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.12, C:0.15, G:0.17, T:0.56
Consensus pattern (20 bp):
TCATTTTCATGTTGCGATTT
Found at i:354959 original size:20 final size:20
Alignment explanation
Indices: 354916--354959 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
354906 ATTCAGTCAT
* * *
354916 TTTCGTGTTGCGATTTTCAT
1 TTTCATGTTGCGATTTTAAG
354936 TTTCATGTTGCGATTTTAAG
1 TTTCATGTTGCGATTTTAAG
354956 TTTC
1 TTTC
354960 GAAACTATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.18, T:0.55
Consensus pattern (20 bp):
TTTCATGTTGCGATTTTAAG
Found at i:357476 original size:21 final size:21
Alignment explanation
Indices: 357450--357521 Score: 78
Period size: 21 Copynumber: 3.5 Consensus size: 21
357440 ATGAAGTTGA
357450 AAATATATAATAAAATAAAAT
1 AAATATATAATAAAATAAAAT
**
357471 AAATATTATAATTTAA-AAAAT
1 AAATA-TATAATAAAATAAAAT
357492 -AATA-ATAATAATAATAAAAT
1 AAATATATAATAA-AATAAAAT
*
357512 AAATAAATAA
1 AAATATATAA
357522 AAAGGGAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
18 5 0.12
19 2 0.05
20 9 0.21
21 14 0.33
22 12 0.29
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
AAATATATAATAAAATAAAAT
Found at i:357487 original size:24 final size:23
Alignment explanation
Indices: 357451--357521 Score: 69
Period size: 22 Copynumber: 3.1 Consensus size: 23
357441 TGAAGTTGAA
357451 AATATATAATAAAATAAAATAAAT
1 AATA-ATAATAAAATAAAATAAAT
*
357475 ATTATAAT-TTAAAA-AATAAT-AAT
1 A--ATAATAATAAAATAA-AATAAAT
357498 AATAATAATAAAAT-AAATAAAT
1 AATAATAATAAAATAAAATAAAT
357520 AA
1 AA
357522 AAAGGGAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
21 8 0.21
22 11 0.28
23 6 0.15
24 9 0.23
25 2 0.05
26 3 0.08
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (23 bp):
AATAATAATAAAATAAAATAAAT
Found at i:357516 original size:15 final size:15
Alignment explanation
Indices: 357458--357550 Score: 56
Period size: 15 Copynumber: 6.5 Consensus size: 15
357448 GAAAATATAT
357458 AATAA-AATAAAATA
1 AATAATAATAAAATA
* **
357472 AAT-ATTATAATTTA
1 AATAATAATAAAATA
*
357486 AAAAATAAT--AAT-
1 AATAATAATAAAATA
357498 AATAATAATAAAATA
1 AATAATAATAAAATA
**
357513 AATAAATAA-AAAGGGA
1 AAT-AATAATAAA-ATA
357529 AATAATAA-AATAATA
1 AATAATAATAA-AATA
357544 AATAATA
1 AATAATA
357551 GTAGTAAAGA
Statistics
Matches: 59, Mismatches: 12, Indels: 15
0.69 0.14 0.17
Matches are distributed among these distances:
12 8 0.14
13 2 0.03
14 14 0.24
15 25 0.42
16 10 0.17
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (15 bp):
AATAATAATAAAATA
Found at i:357613 original size:18 final size:18
Alignment explanation
Indices: 357590--357632 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
357580 TTATTTTTTA
*
357590 AAATAAAAGATAAGAATT
1 AAATAAAAGAAAAGAATT
* *
357608 AAATAAAGGAAAATAATT
1 AAATAAAAGAAAAGAATT
357626 AAATAAA
1 AAATAAA
357633 CAAATTAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:358335 original size:75 final size:76
Alignment explanation
Indices: 358240--358437 Score: 301
Period size: 76 Copynumber: 2.6 Consensus size: 76
358230 TTAAATCCTA
* * * * *
358240 ATTAAAA-CTATTTAAACTAAAATACCTAAAACAAAAATAATAT-TTAAAATAATATTCTAAATC
1 ATTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAATATTATAAAAC
358303 CTAATTAAAAT
66 CTAATTAAAAT
358314 ATTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAATATTATAAAAC
1 ATTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAATATTATAAAAC
*
358379 TTAATTAAAAT
66 CTAATTAAAAT
* * *
358390 ACTAAAACCTATTTAAATTAAAATAACTAAAACAAAGATAAAATATAA
1 ATTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
358438 CGTTTAAAAT
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
74 7 0.06
75 34 0.30
76 72 0.64
ACGTcount: A:0.60, C:0.10, G:0.01, T:0.29
Consensus pattern (76 bp):
ATTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAATATTATAAAAC
CTAATTAAAAT
Found at i:361712 original size:5 final size:6
Alignment explanation
Indices: 361694--361722 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
361684 TTACAAACAA
361694 CCTCCC CCTCCC CCTCCC CCTCCC CCTCC
1 CCTCCC CCTCCC CCTCCC CCTCCC CCTCC
361723 ATCATCATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.83, G:0.00, T:0.17
Consensus pattern (6 bp):
CCTCCC
Found at i:362218 original size:53 final size:53
Alignment explanation
Indices: 362150--362257 Score: 216
Period size: 53 Copynumber: 2.0 Consensus size: 53
362140 TTTTGTTCAT
362150 ATACTTTTATGATACAATTTTCTTTATCATTATGATAATTTTGTATCACATTC
1 ATACTTTTATGATACAATTTTCTTTATCATTATGATAATTTTGTATCACATTC
362203 ATACTTTTATGATACAATTTTCTTTATCATTATGATAATTTTGTATCACATTC
1 ATACTTTTATGATACAATTTTCTTTATCATTATGATAATTTTGTATCACATTC
362256 AT
1 AT
362258 CATAACGTAC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.31, C:0.13, G:0.06, T:0.51
Consensus pattern (53 bp):
ATACTTTTATGATACAATTTTCTTTATCATTATGATAATTTTGTATCACATTC
Done.