Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 155 of 235
Found at i:52215042 original size:75 final size:75
Alignment explanation
Indices: 52214894--52215042 Score: 162
Period size: 75 Copynumber: 2.0 Consensus size: 75
52214884 ATATTAAAAA
* **
52214894 ATATATAAAAATATATAAAATCATAAAAATATATATAAAATTGTAAAATTTTATAAAAATCATAA
1 ATATATAAAAATATAAAAAATCATAAAAATATATATAAAATTGTAAAAAATTATAAAAATCATAA
*
52214959 AAAGTATAAG
66 AAAATATAAG
* * * *
52214969 ATATATAGAAATATAAAAAA-C-TATAAAAT-TTTATAAAGTTGTAAGAAAATTATATTAAAT-A
1 ATATATAAAAATATAAAAAATCATA-AAAATATATATAAAATTGTAA-AAAATTATA-AAAATCA
52215030 TAAAGAAATATAA
63 TAAA-AAATATAA
52215043 ATTTGGTAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
73 15 0.24
74 18 0.29
75 29 0.47
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.32
Consensus pattern (75 bp):
ATATATAAAAATATAAAAAATCATAAAAATATATATAAAATTGTAAAAAATTATAAAAATCATAA
AAAATATAAG
Found at i:52215217 original size:9 final size:9
Alignment explanation
Indices: 52215203--52215309 Score: 69
Period size: 9 Copynumber: 11.7 Consensus size: 9
52215193 GGCGTTAATT
*
52215203 TTTTTATGA
1 TTTTTATAA
52215212 TTTTTATAAAA
1 TTTTTAT--AA
*
52215223 ATTTTATAA
1 TTTTTATAA
*
52215232 TTTTTAT-T
1 TTTTTATAA
**
52215240 TTTTTACGA
1 TTTTTATAA
52215249 TTTTTATAA
1 TTTTTATAA
*
52215258 TTTTTTTCTAA
1 --TTTTTATAA
52215269 -TTTT-TAA
1 TTTTTATAA
52215276 TTTTT-TAA
1 TTTTTATAA
52215284 TTTTTTTATAA
1 --TTTTTATAA
*
52215295 TTTTTTTAA
1 TTTTTATAA
52215304 TTTTTA
1 TTTTTA
52215310 ATAAGAGTAG
Statistics
Matches: 78, Mismatches: 11, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
7 3 0.04
8 17 0.22
9 35 0.45
10 5 0.06
11 18 0.23
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (9 bp):
TTTTTATAA
Found at i:52215251 original size:37 final size:36
Alignment explanation
Indices: 52215200--52215309 Score: 123
Period size: 37 Copynumber: 3.0 Consensus size: 36
52215190 ATGGGCGTTA
*
52215200 ATTTTTTTATGATTTTTATAAAAATTTTATAATTTTT
1 ATTTTTTTA-GATTTTTATAAAATTTTTATAATTTTT
** *
52215237 ATTTTTTTACGATTTTTATAATTTTTTTCTAATTTTT
1 ATTTTTTTA-GATTTTTATAAAATTTTTATAATTTTT
* * * *
52215274 AATTTTTTA-ATTTTTTTATAATTTTTTTAATTTTT
1 ATTTTTTTAGATTTTTATAAAATTTTTATAATTTTT
52215309 A
1 A
52215310 ATAAGAGTAG
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
35 22 0.35
37 40 0.65
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (36 bp):
ATTTTTTTAGATTTTTATAAAATTTTTATAATTTTT
Found at i:52215263 original size:11 final size:11
Alignment explanation
Indices: 52215249--52215302 Score: 54
Period size: 11 Copynumber: 4.5 Consensus size: 11
52215239 TTTTTTACGA
52215249 TTTTTATAATT
1 TTTTTATAATT
*
52215260 TTTTTCTAATTTT
1 TTTTTATAA--TT
*
52215273 TAATTTTTTAATT
1 T--TTTTATAATT
52215286 TTTTTATAATT
1 TTTTTATAATT
52215297 TTTTTA
1 TTTTTA
52215303 ATTTTTAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
11 23 0.64
13 6 0.17
15 7 0.19
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTTATAATT
Found at i:52215279 original size:26 final size:26
Alignment explanation
Indices: 52215250--52215299 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
52215240 TTTTTACGAT
*
52215250 TTTTATAATTTTTTTCTAATTTTTAA
1 TTTTATAATTTTTTTATAATTTTTAA
*
52215276 TTTTTTAATTTTTTTATAATTTTT
1 TTTTATAATTTTTTTATAATTTTT
52215300 TTAATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (26 bp):
TTTTATAATTTTTTTATAATTTTTAA
Found at i:52215307 original size:26 final size:25
Alignment explanation
Indices: 52215250--52215311 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 25
52215240 TTTTTACGAT
*
52215250 TTTTATAATTTTTTTCTAATTTTTAA
1 TTTT-TAATTTTTTTATAATTTTTAA
52215276 TTTTTTAATTTTTTTATAATTTTTTTAA
1 -TTTTTAATTTTTTTATAA--TTTTTAA
52215304 TTTTTAAT
1 TTTTTAAT
52215312 AAGAGTAGGG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 13 0.41
27 12 0.38
28 7 0.22
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.73
Consensus pattern (25 bp):
TTTTTAATTTTTTTATAATTTTTAA
Found at i:52218727 original size:52 final size:52
Alignment explanation
Indices: 52218647--52218798 Score: 162
Period size: 52 Copynumber: 2.9 Consensus size: 52
52218637 TGAAAAAGAT
** * *
52218647 GTGATATGTGAGCCCGTATAAGAACATAGCTGGGCTATGGCATTGGTGCAAC
1 GTGATATGTGTTCCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGCAAC
* * * ** *
52218699 GTGATATGTGTTCCCGTATAGGACCATAGTTGGGCTATGGCGTCGGTGTGAT
1 GTGATATGTGTTCCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGCAAC
* * *
52218751 GTGATAATGTGATT-TCGTATAAGACCATATCTGGGATATGGCATCGGT
1 GTGAT-ATGTG-TTCCCGTATAAGACCATAGCTGGGCTATGGCATCGGT
52218799 ATTATATGTG
Statistics
Matches: 82, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
52 47 0.57
53 33 0.40
54 2 0.02
ACGTcount: A:0.24, C:0.15, G:0.31, T:0.30
Consensus pattern (52 bp):
GTGATATGTGTTCCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGCAAC
Found at i:52231855 original size:12 final size:12
Alignment explanation
Indices: 52231838--52231870 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
52231828 CGGCCCGCCC
52231838 ATATTAATTTTT
1 ATATTAATTTTT
52231850 ATATT-ATTTTT
1 ATATTAATTTTT
52231861 ATA-TAATTTT
1 ATATTAATTTT
52231871 AAAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:52232029 original size:30 final size:30
Alignment explanation
Indices: 52231993--52232052 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
52231983 ACTTAACAAG
*
52231993 CAAATGT-TTCTAAAATAATAACAAAATTAA
1 CAAATGTCTT-TAAAATAATAAAAAAATTAA
52232023 CAAATGTCTTTAAAATAATAAAAAAATTAA
1 CAAATGTCTTTAAAATAATAAAAAAATTAA
52232053 TAATAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 26 0.93
31 2 0.07
ACGTcount: A:0.58, C:0.08, G:0.03, T:0.30
Consensus pattern (30 bp):
CAAATGTCTTTAAAATAATAAAAAAATTAA
Found at i:52232993 original size:20 final size:20
Alignment explanation
Indices: 52232968--52233006 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
52232958 ATAAAAACTA
52232968 AAAATATTAAAAAAATTATG
1 AAAATATTAAAAAAATTATG
* *
52232988 AAAATATTAGAAATATTAT
1 AAAATATTAAAAAAATTAT
52233007 TTGAAACTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (20 bp):
AAAATATTAAAAAAATTATG
Found at i:52233228 original size:25 final size:24
Alignment explanation
Indices: 52233172--52233252 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 24
52233162 ATAAAATTTG
*
52233172 ATATTTTATAAAATATAATTTTAT
1 ATATTTTATAAAATTTAATTTTAT
* * *
52233196 ACATTTTTATACATTTTAGATTTTAT
1 ATA-TTTTATAAAATTTA-ATTTTAT
*
52233222 ATATTTTGTATAAA-TTATATTTTAT
1 ATATTTTATA-AAATTTA-ATTTTAT
52233247 ATATTT
1 ATATTT
52233253 GGACAAATAT
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
24 2 0.04
25 33 0.73
26 10 0.22
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (24 bp):
ATATTTTATAAAATTTAATTTTAT
Found at i:52233263 original size:23 final size:25
Alignment explanation
Indices: 52233215--52233270 Score: 80
Period size: 23 Copynumber: 2.3 Consensus size: 25
52233205 TACATTTTAG
* *
52233215 ATTTTATATATTTTGTATAAATTAT
1 ATTTTATATATTTTGGACAAATTAT
52233240 ATTTTATATA-TTTGGACAAA-TAT
1 ATTTTATATATTTTGGACAAATTAT
52233263 ATTTTATA
1 ATTTTATA
52233271 AAATCTTGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 11 0.38
24 8 0.28
25 10 0.34
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (25 bp):
ATTTTATATATTTTGGACAAATTAT
Found at i:52233305 original size:23 final size:23
Alignment explanation
Indices: 52233279--52233339 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
52233269 TAAAATCTTG
52233279 ATATAAAATAATATAT-TTTATAA
1 ATATAAAATAATATATATTT-TAA
*
52233302 ATATAAGAAT-TTATATATTTTAA
1 ATATAA-AATAATATATATTTTAA
* *
52233325 ATTTATAATAATATA
1 ATATAAAATAATATA
52233340 AAAATATAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
22 3 0.10
23 22 0.71
24 6 0.19
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
ATATAAAATAATATATATTTTAA
Found at i:52237414 original size:20 final size:20
Alignment explanation
Indices: 52237389--52237427 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
52237379 ACAAATTCAA
52237389 TTATTTCAC-ACATTTACAAC
1 TTATTTCACAAC-TTTACAAC
*
52237409 TTATTTTACAACTTTACAA
1 TTATTTCACAACTTTACAA
52237428 AATGGCCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.44
Consensus pattern (20 bp):
TTATTTCACAACTTTACAAC
Found at i:52244208 original size:40 final size:40
Alignment explanation
Indices: 52244138--52245294 Score: 2091
Period size: 40 Copynumber: 28.9 Consensus size: 40
52244128 CGAATACACG
* * * * * *
52244138 TCACCAGCATGATTGCTCTTCGGGATTTAGCACGGATATA
1 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACA
* * *
52244178 TCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACA
* *
52244218 TCGCTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACA
*
52244258 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACA
* * * * **
52244298 TTACTAGCACGAACGCTCTTCGAAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACA
*
52244338 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACA
*
52244378 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACA
52244418 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACA
52244458 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACA
52244498 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACA
52244538 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACA
52244578 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACA
52244618 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACA
52244658 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACA
52244698 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACA
52244738 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACA
52244778 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACA
52244818 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACA
52244858 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACA
52244898 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACA
52244938 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACA
52244978 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACA
52245018 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACA
52245058 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACA
52245098 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACA
*
52245138 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACA
52245178 TCACTAGCATGAATGCT-TTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTT-GGGACTTAGCCCGGATACA
*
52245218 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACA
*
52245258 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGAT
1 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGAT
52245295 TTAGTAATTC
Statistics
Matches: 1090, Mismatches: 25, Indels: 4
0.97 0.02 0.00
Matches are distributed among these distances:
39 2 0.00
40 1086 1.00
41 2 0.00
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (40 bp):
TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATACA
Found at i:52245718 original size:29 final size:29
Alignment explanation
Indices: 52245679--52245757 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
52245669 CTTAATAATC
*
52245679 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
52245709 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
52245738 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
52245758 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:52248962 original size:28 final size:29
Alignment explanation
Indices: 52248907--52248962 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
52248897 ACAGAGGTTT
*
52248907 TCACACGGCCAAGCACACACCCGTGTCCC
1 TCACACGGCCAAGCACACACCCATGTCCC
* *
52248936 TCACACGGCCTAG-ACACGCCCATGTCC
1 TCACACGGCCAAGCACACACCCATGTCC
52248963 AAAAACCCGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 12 0.50
29 12 0.50
ACGTcount: A:0.23, C:0.46, G:0.18, T:0.12
Consensus pattern (29 bp):
TCACACGGCCAAGCACACACCCATGTCCC
Found at i:52271452 original size:17 final size:16
Alignment explanation
Indices: 52271393--52271452 Score: 50
Period size: 17 Copynumber: 3.6 Consensus size: 16
52271383 GAGACAACCA
* *
52271393 CCATACATGCATTTAAG
1 CCATTCATGCATTT-AT
52271410 CCATTCATGCATTCTAT
1 CCATTCATGCATT-TAT
*
52271427 -CATCCCATGCATTTGAT
1 CCAT-TCATGCATTT-AT
52271444 CCATTCATG
1 CCATTCATG
52271453 GACTAGCCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
16 4 0.11
17 27 0.77
18 4 0.11
ACGTcount: A:0.27, C:0.28, G:0.10, T:0.35
Consensus pattern (16 bp):
CCATTCATGCATTTAT
Found at i:52274050 original size:12 final size:12
Alignment explanation
Indices: 52274033--52274062 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
52274023 TTTAATCTCC
*
52274033 TTTTCAATTTCT
1 TTTTCAACTTCT
52274045 TTTTCAACTTCT
1 TTTTCAACTTCT
52274057 TTTTCA
1 TTTTCA
52274063 CTCTCAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.20, G:0.00, T:0.63
Consensus pattern (12 bp):
TTTTCAACTTCT
Found at i:52274197 original size:5 final size:5
Alignment explanation
Indices: 52274187--52274243 Score: 53
Period size: 5 Copynumber: 11.0 Consensus size: 5
52274177 CTCTTGCCTC
* * *
52274187 TCTTT TCTTTT TATTT TGTTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TC-TTT TCTTT TCTTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
52274234 TCTTT TCTTT
1 TCTTT TCTTT
52274244 ATTTTCTCTT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
4 3 0.07
5 30 0.70
6 6 0.14
7 4 0.09
ACGTcount: A:0.02, C:0.16, G:0.04, T:0.79
Consensus pattern (5 bp):
TCTTT
Found at i:52274219 original size:25 final size:25
Alignment explanation
Indices: 52274191--52274239 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
52274181 TGCCTCTCTT
*
52274191 TTCTTTT-TATTTTGTTTTCTTTTTC
1 TTCTTTTCT-TTTTCTTTTCTTTTTC
52274216 TTCTTTTGCTTTTTCTTTTCTTTT
1 TTCTTTT-CTTTTTCTTTTCTTTT
52274240 CTTTATTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 13 0.62
27 1 0.05
ACGTcount: A:0.02, C:0.14, G:0.04, T:0.80
Consensus pattern (25 bp):
TTCTTTTCTTTTTCTTTTCTTTTTC
Found at i:52274253 original size:21 final size:20
Alignment explanation
Indices: 52274185--52274254 Score: 54
Period size: 20 Copynumber: 3.4 Consensus size: 20
52274175 GCCTCTTGCC
52274185 TCTCTTTTCTTTTTATT-TTGT
1 TCTCTTTTCTTTTT-TTATT-T
* **
52274206 TTTCTTTTTCTTCTTTTGCTTT
1 TCTC-TTTTCTT-TTTTTATTT
52274228 T-TCTTTTCTTTTCTTTATTT
1 TCTCTTTTCTTTT-TTTATTT
52274248 TCTCTTT
1 TCTCTTT
52274255 ACAAGAATGT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
19 2 0.05
20 13 0.32
21 10 0.25
22 10 0.25
23 5 0.12
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.77
Consensus pattern (20 bp):
TCTCTTTTCTTTTTTTATTT
Found at i:52276589 original size:14 final size:14
Alignment explanation
Indices: 52276570--52276600 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
52276560 TTATCTACAA
*
52276570 AAAAAAATAATATC
1 AAAAAAACAATATC
52276584 AAAAAAACAATATC
1 AAAAAAACAATATC
52276598 AAA
1 AAA
52276601 TTATGAGACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.74, C:0.10, G:0.00, T:0.16
Consensus pattern (14 bp):
AAAAAAACAATATC
Found at i:52278726 original size:27 final size:27
Alignment explanation
Indices: 52278696--52278845 Score: 205
Period size: 27 Copynumber: 5.6 Consensus size: 27
52278686 CCTTAATTGA
*
52278696 TAAAATGACTGTTTTGCCCTTATAAGG
1 TAAAATGACTGTTTTGCCCTTATGAGG
* *
52278723 TAAAATTACTGTTTTACCCTTATGAGG
1 TAAAATGACTGTTTTGCCCTTATGAGG
* *
52278750 TAAAATGATTGTTTTACCCTTATG-GAG
1 TAAAATGACTGTTTTGCCCTTATGAG-G
52278777 TAAAATGACTGTTTTGCCCTTATGAGG
1 TAAAATGACTGTTTTGCCCTTATGAGG
*
52278804 TAAAATGAGC-GTTTTGCCCTTATGGGG
1 TAAAATGA-CTGTTTTGCCCTTATGAGG
*
52278831 TAAAAAGACTGTTTT
1 TAAAATGACTGTTTT
52278846 ACCCCTGTGT
Statistics
Matches: 110, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
26 2 0.02
27 106 0.96
28 2 0.02
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.38
Consensus pattern (27 bp):
TAAAATGACTGTTTTGCCCTTATGAGG
Found at i:52278790 original size:81 final size:81
Alignment explanation
Indices: 52278696--52278849 Score: 238
Period size: 81 Copynumber: 1.9 Consensus size: 81
52278686 CCTTAATTGA
* * *
52278696 TAAAATGACTGTTTTGCCCTTATAAGGTAAAATTA-CTGTTTTACCCTTATGAGGTAAAATGATT
1 TAAAATGACTGTTTTGCCCTTATAAGGTAAAATGAGC-GTTTTACCCTTATGAGGTAAAAAGACT
52278760 GTTTTACCCTTATGGAG
65 GTTTTACCCTTATGGAG
* * *
52278777 TAAAATGACTGTTTTGCCCTTATGAGGTAAAATGAGCGTTTTGCCCTTATGGGGTAAAAAGACTG
1 TAAAATGACTGTTTTGCCCTTATAAGGTAAAATGAGCGTTTTACCCTTATGAGGTAAAAAGACTG
52278842 TTTTACCC
66 TTTTACCC
52278850 CTGTGTGATG
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
81 65 0.98
82 1 0.02
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (81 bp):
TAAAATGACTGTTTTGCCCTTATAAGGTAAAATGAGCGTTTTACCCTTATGAGGTAAAAAGACTG
TTTTACCCTTATGGAG
Found at i:52282652 original size:24 final size:24
Alignment explanation
Indices: 52282620--52282670 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
52282610 AAGGAAGAAT
52282620 TGGTGGCTTTGTCCACAACCTACA
1 TGGTGGCTTTGTCCACAACCTACA
*
52282644 TGGTGGCTTTGTCTACAACCTACA
1 TGGTGGCTTTGTCCACAACCTACA
52282668 TGG
1 TGG
52282671 CAGCTTGTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.20, C:0.25, G:0.24, T:0.31
Consensus pattern (24 bp):
TGGTGGCTTTGTCCACAACCTACA
Found at i:52282682 original size:23 final size:24
Alignment explanation
Indices: 52282625--52282682 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
52282615 AGAATTGGTG
* **
52282625 GCTTTGTCCACAACCTACATGGTG
1 GCTTTGTCTACAACCTACATGGCA
52282649 GCTTTGTCTACAACCTACATGGCA
1 GCTTTGTCTACAACCTACATGGCA
52282673 GC-TTGTCTAC
1 GCTTTGTCTAC
52282683 GAATATTTGT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
23 8 0.26
24 23 0.74
ACGTcount: A:0.21, C:0.29, G:0.19, T:0.31
Consensus pattern (24 bp):
GCTTTGTCTACAACCTACATGGCA
Found at i:52282697 original size:45 final size:44
Alignment explanation
Indices: 52282658--52282750 Score: 141
Period size: 45 Copynumber: 2.1 Consensus size: 44
52282648 GGCTTTGTCT
* *
52282658 ACAACCTACATGGCAGCTTGTCTACGAATATTTGTGGCTTCATCC
1 ACAACCTACATGGAAACTTGTCTACGAATA-TTGTGGCTTCATCC
*
52282703 ATAACCTACATGGAAACTTGTCTACGAATATTGATGGCTTCATCC
1 ACAACCTACATGGAAACTTGTCTACGAATATTG-TGGCTTCATCC
52282748 ACA
1 ACA
52282751 TTGGAGTGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 3 0.07
45 40 0.93
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (44 bp):
ACAACCTACATGGAAACTTGTCTACGAATATTGTGGCTTCATCC
Found at i:52282927 original size:15 final size:15
Alignment explanation
Indices: 52282907--52282938 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
52282897 AAGTATCTGT
52282907 TTATTGTTATATAAC
1 TTATTGTTATATAAC
*
52282922 TTATTGTTATTTAAC
1 TTATTGTTATATAAC
52282937 TT
1 TT
52282939 GTTATAAGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.59
Consensus pattern (15 bp):
TTATTGTTATATAAC
Found at i:52285281 original size:29 final size:29
Alignment explanation
Indices: 52285224--52285342 Score: 129
Period size: 29 Copynumber: 4.2 Consensus size: 29
52285214 TACATCCATG
*
52285224 CATATGGCCCACTAGGCCCAA-TCTTATT
1 CATATGGCCCACTAGGCCCAATTCATATT
* *
52285252 CAAATGACCCATCTA-GCCCAATTCATATT
1 CATATGGCCCA-CTAGGCCCAATTCATATT
*
52285281 CTTATGGCCCACTAGGCCCAATTC-TCATT
1 CATATGGCCCACTAGGCCCAATTCAT-ATT
* * *
52285310 CATATGGCCAATTAGGCCCAAATCATATT
1 CATATGGCCCACTAGGCCCAATTCATATT
52285339 -ATAT
1 CATAT
52285343 TCATGCTCAC
Statistics
Matches: 76, Mismatches: 10, Indels: 10
0.79 0.10 0.10
Matches are distributed among these distances:
28 23 0.30
29 52 0.68
30 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.29
Consensus pattern (29 bp):
CATATGGCCCACTAGGCCCAATTCATATT
Found at i:52285433 original size:18 final size:19
Alignment explanation
Indices: 52285410--52285445 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
52285400 ATGGGCCCAA
52285410 TAGCCCA-TCCGGCCCATC
1 TAGCCCATTCCGGCCCATC
52285428 TAGCCCATTCCGGCCCAT
1 TAGCCCATTCCGGCCCAT
52285446 TTGGCCAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.17, C:0.47, G:0.17, T:0.19
Consensus pattern (19 bp):
TAGCCCATTCCGGCCCATC
Found at i:52285456 original size:19 final size:19
Alignment explanation
Indices: 52285417--52285456 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
52285407 CAATAGCCCA
*
52285417 TCCGGCCCATCTAGCCCAT
1 TCCGGCCCATCTAGCCAAT
* *
52285436 TCCGGCCCATTTGGCCAAT
1 TCCGGCCCATCTAGCCAAT
52285455 TC
1 TC
52285457 TCAACCCAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.15, C:0.42, G:0.17, T:0.25
Consensus pattern (19 bp):
TCCGGCCCATCTAGCCAAT
Found at i:52289677 original size:29 final size:29
Alignment explanation
Indices: 52289610--52289716 Score: 110
Period size: 29 Copynumber: 3.7 Consensus size: 29
52289600 TACATCCATA
* *
52289610 CATATGGCCCACTAGGCCCAA-TCTTATT
1 CATATGGCCCATTAGGCCCAATTCTCATT
* * * *
52289638 CAAATGACCCATTTGGCCCAGTTC-CTATT
1 CATATGGCCCATTAGGCCCAATTCTC-ATT
* *
52289667 CTTATGGCCCACTAGGCCCAATTCTCATT
1 CATATGGCCCATTAGGCCCAATTCTCATT
*
52289696 CATATGGCCAATTAGGCCCAA
1 CATATGGCCCATTAGGCCCAA
52289717 ATCATATTAT
Statistics
Matches: 61, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
28 16 0.26
29 44 0.72
30 1 0.02
ACGTcount: A:0.25, C:0.32, G:0.15, T:0.28
Consensus pattern (29 bp):
CATATGGCCCATTAGGCCCAATTCTCATT
Found at i:52289829 original size:10 final size:9
Alignment explanation
Indices: 52289798--52289837 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
52289788 GGGCCCAATA
*
52289798 GCCCATTAG
1 GCCCATTTG
*
52289807 GCCCATTTA
1 GCCCATTTG
52289816 GCCCATTTCG
1 GCCCATTT-G
52289826 GCCCATTTG
1 GCCCATTTG
52289835 GCC
1 GCC
52289838 AATTCTCAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.15, C:0.38, G:0.20, T:0.28
Consensus pattern (9 bp):
GCCCATTTG
Found at i:52289830 original size:19 final size:18
Alignment explanation
Indices: 52289796--52289833 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
52289786 ATGGGCCCAA
52289796 TAGCCCATTAGGCCCATT
1 TAGCCCATTAGGCCCATT
*
52289814 TAGCCCATTTCGGCCCATT
1 TAGCCCA-TTAGGCCCATT
52289833 T
1 T
52289834 GGCCAATTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.18, C:0.34, G:0.16, T:0.32
Consensus pattern (18 bp):
TAGCCCATTAGGCCCATT
Found at i:52289973 original size:24 final size:24
Alignment explanation
Indices: 52289946--52289998 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
52289936 CAACTTTTAG
*
52289946 CTTTTCGGCATTTTAGG-TTTTCGA
1 CTTTTCAGCATTTT-GGCTTTTCGA
*
52289970 CTTTTCAGCATTTTGGCTTTTTGA
1 CTTTTCAGCATTTTGGCTTTTCGA
52289994 CTTTT
1 CTTTT
52289999 GCCGAGTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 2 0.08
24 24 0.92
ACGTcount: A:0.11, C:0.17, G:0.17, T:0.55
Consensus pattern (24 bp):
CTTTTCAGCATTTTGGCTTTTCGA
Found at i:52303380 original size:14 final size:13
Alignment explanation
Indices: 52303360--52303391 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
52303350 ATATTTAAAC
52303360 TTGTTCTTAATTA
1 TTGTTCTTAATTA
52303373 TGTGTTCTTAATTA
1 T-TGTTCTTAATTA
52303387 TTGTT
1 TTGTT
52303392 TTGATTTCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.19, C:0.06, G:0.12, T:0.62
Consensus pattern (13 bp):
TTGTTCTTAATTA
Found at i:52315859 original size:48 final size:48
Alignment explanation
Indices: 52315803--52315898 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
52315793 TTTCACCCTA
52315803 AACCGGCAAAATCTTGTCACCCTATCTTTAGGCGCGCAATCAACTCTG
1 AACCGGCAAAATCTTGTCACCCTATCTTTAGGCGCGCAATCAACTCTG
52315851 AACCGGCAAAATCTTGTCACCCTATCTTTAGGCGCGCAATCAACTCTG
1 AACCGGCAAAATCTTGTCACCCTATCTTTAGGCGCGCAATCAACTCTG
52315899 CTTAATTATG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25
Consensus pattern (48 bp):
AACCGGCAAAATCTTGTCACCCTATCTTTAGGCGCGCAATCAACTCTG
Found at i:52326897 original size:28 final size:29
Alignment explanation
Indices: 52326849--52326917 Score: 95
Period size: 28 Copynumber: 2.4 Consensus size: 29
52326839 GAAAATGTGA
*
52326849 CAGAGTCACCAGATACAGATAATTTGTAG
1 CAGAGCCACCAGATACAGATAATTTGTAG
* *
52326878 CAGGGCCACCAGA-ACAGATAATTTGTGG
1 CAGAGCCACCAGATACAGATAATTTGTAG
*
52326906 CATAGCCACCAG
1 CAGAGCCACCAG
52326918 GACGCTTCCT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
28 24 0.69
29 11 0.31
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.19
Consensus pattern (29 bp):
CAGAGCCACCAGATACAGATAATTTGTAG
Found at i:52327070 original size:28 final size:28
Alignment explanation
Indices: 52327023--52327087 Score: 105
Period size: 28 Copynumber: 2.3 Consensus size: 28
52327013 AAATTAACCC
*
52327023 TAGGGGTATAGAGGTCATTTTGCATACA
1 TAGGGGTATAGAGGTAATTTTGCATACA
52327051 TAGGGGTATA-ATGGTAATTTTGCATACA
1 TAGGGGTATAGA-GGTAATTTTGCATACA
52327079 TAGGGGTAT
1 TAGGGGTAT
52327088 TCTAGTACAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
27 1 0.03
28 34 0.97
ACGTcount: A:0.29, C:0.08, G:0.29, T:0.34
Consensus pattern (28 bp):
TAGGGGTATAGAGGTAATTTTGCATACA
Found at i:52334752 original size:28 final size:28
Alignment explanation
Indices: 52334693--52334794 Score: 132
Period size: 28 Copynumber: 3.6 Consensus size: 28
52334683 ATACAGAAAA
* * *
52334693 TGTGACAGAGTCACCAGATACAGATATTT
1 TGTGGCAGAGCCACCAGA-ACAGATAATT
*
52334722 TGTGGCAGCGCCACCAGAACAGATAATT
1 TGTGGCAGAGCCACCAGAACAGATAATT
* *
52334750 TGTGGTAGGGCCACCAGAACAGATAATT
1 TGTGGCAGAGCCACCAGAACAGATAATT
*
52334778 TGTGGCATAGCCACCAG
1 TGTGGCAGAGCCACCAG
52334795 GACGCTTCCT
Statistics
Matches: 64, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
28 49 0.77
29 15 0.23
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.22
Consensus pattern (28 bp):
TGTGGCAGAGCCACCAGAACAGATAATT
Found at i:52334947 original size:28 final size:28
Alignment explanation
Indices: 52334900--52334964 Score: 105
Period size: 28 Copynumber: 2.3 Consensus size: 28
52334890 AAATTAACCC
*
52334900 TAGGGGTATAGAGGTCATTTTGCATACA
1 TAGGGGTATAGAGGTAATTTTGCATACA
52334928 TAGGGGTATA-ATGGTAATTTTGCATACA
1 TAGGGGTATAGA-GGTAATTTTGCATACA
52334956 TAGGGGTAT
1 TAGGGGTAT
52334965 TCTAGTACAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
27 1 0.03
28 34 0.97
ACGTcount: A:0.29, C:0.08, G:0.29, T:0.34
Consensus pattern (28 bp):
TAGGGGTATAGAGGTAATTTTGCATACA
Found at i:52338376 original size:49 final size:49
Alignment explanation
Indices: 52338323--52338488 Score: 199
Period size: 49 Copynumber: 3.4 Consensus size: 49
52338313 TACGCATAGG
* * *
52338323 AGCCTGCACTTAATAGTACACATGCAACCAATTATTCGGTACACGTAGT
1 AGCCTGCACTTAGTACTACACATGCGACCAATTATTCGGTACACGTAGT
* * ** *
52338372 AGCCTGCACTTAGTACTACACACGTGACCTAACCA-TCTGATACACGTAGT
1 AGCCTGCACTTAGTACTACACATGCGACC-AATTATTC-GGTACACGTAGT
* * * *
52338422 AGCTTGCACTTAGTACTACACATGCGACCAATTATCCAGTACACATAGT
1 AGCCTGCACTTAGTACTACACATGCGACCAATTATTCGGTACACGTAGT
52338471 AGCCTGCACTTAGTACTA
1 AGCCTGCACTTAGTACTA
52338489 GACACGTGAC
Statistics
Matches: 96, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
49 55 0.57
50 41 0.43
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (49 bp):
AGCCTGCACTTAGTACTACACATGCGACCAATTATTCGGTACACGTAGT
Found at i:52341352 original size:27 final size:27
Alignment explanation
Indices: 52341322--52341478 Score: 242
Period size: 27 Copynumber: 5.8 Consensus size: 27
52341312 ATTACCAACG
* *
52341322 TACCCTCGATTTACAAAATTACCGTTT
1 TACCCTCAATTTACAGAATTACCGTTT
*
52341349 TACCCTCGATTTACAGAATTACCGTTT
1 TACCCTCAATTTACAGAATTACCGTTT
* * *
52341376 TACCCTCGATTTATAGAATTACCATTT
1 TACCCTCAATTTACAGAATTACCGTTT
52341403 TACCCTCAATTTACAGAATTACCGTTT
1 TACCCTCAATTTACAGAATTACCGTTT
*
52341430 TACCCTCAATTTACAGAATTACCATTT
1 TACCCTCAATTTACAGAATTACCGTTT
*
52341457 TACCCTCAATTTACAAAATTAC
1 TACCCTCAATTTACAGAATTAC
52341479 TAAAATACCC
Statistics
Matches: 122, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 122 1.00
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.37
Consensus pattern (27 bp):
TACCCTCAATTTACAGAATTACCGTTT
Found at i:52341369 original size:54 final size:54
Alignment explanation
Indices: 52341311--52341507 Score: 232
Period size: 54 Copynumber: 3.6 Consensus size: 54
52341301 CAATTTGTAA
** * *
52341311 AATTACCAACGTACCCTCGATTTACAAAATTACCGTTTTACCCTCGATTTACAG
1 AATTACCAATTTACCCTCGATTTACAAAATTACCATTTTACCCTCAATTTACAG
** * *
52341365 AATTACCGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTCAATTTACAG
1 AATTACCAATTTACCCTCGATTTACAAAATTACCATTTTACCCTCAATTTACAG
** * * *
52341419 AATTACCGTTTTACCCTCAATTTACAGAATTACCATTTTACCCTCAATTTACAA
1 AATTACCAATTTACCCTCGATTTACAAAATTACCATTTTACCCTCAATTTACAG
* ** * *
52341473 AATTACTAAAATACCCTTGGTTTACAAAATTACCA
1 AATTACCAATTTACCCTCGATTTACAAAATTACCA
52341508 AAATACCCCT
Statistics
Matches: 123, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 123 1.00
ACGTcount: A:0.34, C:0.25, G:0.07, T:0.35
Consensus pattern (54 bp):
AATTACCAATTTACCCTCGATTTACAAAATTACCATTTTACCCTCAATTTACAG
Found at i:52341487 original size:27 final size:27
Alignment explanation
Indices: 52341277--52341624 Score: 182
Period size: 27 Copynumber: 12.9 Consensus size: 27
52341267 AATACTTTAG
* * **
52341277 TTTACCAAATTACTAAAATGTCCTCAA
1 TTTACAAAATTACCAAAATACCCTCAA
** ** *
52341304 TTTGTAAAATTACCAACGTACCCTCGA
1 TTTACAAAATTACCAAAATACCCTCAA
**** *
52341331 TTTACAAAATTACCGTTTTACCCTCGA
1 TTTACAAAATTACCAAAATACCCTCAA
* **** *
52341358 TTTACAGAATTACCGTTTTACCCTCGA
1 TTTACAAAATTACCAAAATACCCTCAA
* * ***
52341385 TTTATAGAATTACCATTTTACCCTCAA
1 TTTACAAAATTACCAAAATACCCTCAA
* ****
52341412 TTTACAGAATTACCGTTTTACCCTCAA
1 TTTACAAAATTACCAAAATACCCTCAA
* ***
52341439 TTTACAGAATTACCATTTTACCCTCAA
1 TTTACAAAATTACCAAAATACCCTCAA
* ***
52341466 TTTACAAAATTACTAAAATACCCTTGG
1 TTTACAAAATTACCAAAATACCCTCAA
*
52341493 TTTACAAAATTACCAAAATACCC-CTAG
1 TTTACAAAATTACCAAAATACCCTC-AA
** *
52341520 TTTGTAAAATTACCAAAATACCACT-AG
1 TTTACAAAATTACCAAAATACC-CTCAA
*** *
52341547 TTTGTGAAATTACCGAAATACCCTCAA
1 TTTACAAAATTACCAAAATACCCTCAA
*** *
52341574 TTCGTAAAATTACCAAAATACCC-CTGA
1 TTTACAAAATTACCAAAATACCCTC-AA
52341601 TTTACAAAATTA-CAGAAATACCCT
1 TTTACAAAATTACCA-AAATACCCT
52341625 TGACTTTTTA
Statistics
Matches: 269, Mismatches: 45, Indels: 13
0.82 0.14 0.04
Matches are distributed among these distances:
26 5 0.02
27 263 0.98
28 1 0.00
ACGTcount: A:0.37, C:0.24, G:0.07, T:0.33
Consensus pattern (27 bp):
TTTACAAAATTACCAAAATACCCTCAA
Found at i:52341515 original size:54 final size:54
Alignment explanation
Indices: 52341276--52341674 Score: 183
Period size: 54 Copynumber: 7.4 Consensus size: 54
52341266 GAATACTTTA
* * ** * ** *
52341276 GTTTACCAAATTACTAAAATGTCCTCAATTTGTAAAATTACCAACGTACCCTCG
1 GTTTACAAAATTACCAAAATACCCTCAATTTATAAAATTACCAAAATACCCTTG
* **** * * * **** *
52341330 ATTTACAAAATTACCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCG
1 GTTTACAAAATTACCAAAATACCCTCAATTTATAAAATTACCAAAATACCCTTG
* * * *** * * **** **
52341384 ATTTATAGAATTACCATTTTACCCTCAATTTACAGAATTACCGTTTTACCCTCA
1 GTTTACAAAATTACCAAAATACCCTCAATTTATAAAATTACCAAAATACCCTTG
* * *** * *
52341438 ATTTACAGAATTACCATTTTACCCTCAATTTACAAAATTACTAAAATACCCTTG
1 GTTTACAAAATTACCAAAATACCCTCAATTTATAAAATTACCAAAATACCCTTG
* * *
52341492 GTTTACAAAATTACCAAAATACCC-CTAGTTTGTAAAATTACCAAAATACCAC-TA
1 GTTTACAAAATTACCAAAATACCCTC-AATTTATAAAATTACCAAAATACC-CTTG
*** * ** *
52341546 GTTTGTGAAATTACCGAAATACCCTCAATTCGTAAAATTACCAAAATACCCCTG
1 GTTTACAAAATTACCAAAATACCCTCAATTTATAAAATTACCAAAATACCCTTG
* * * * **
52341600 ATTTACAAAATTA-CAGAAATACCCTTGACTTTTTAAAAATTATAAAAATACCCTTG
1 GTTTACAAAATTACCA-AAATACCC-TCAATTTAT-AAAATTACCAAAATACCCTTG
** *
52341656 GTTTGTAAATTTACCAAAA
1 GTTTACAAAATTACCAAAA
52341675 CACCATTGTA
Statistics
Matches: 273, Mismatches: 64, Indels: 14
0.78 0.18 0.04
Matches are distributed among these distances:
53 3 0.01
54 231 0.85
55 7 0.03
56 30 0.11
57 2 0.01
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.33
Consensus pattern (54 bp):
GTTTACAAAATTACCAAAATACCCTCAATTTATAAAATTACCAAAATACCCTTG
Found at i:52341515 original size:81 final size:81
Alignment explanation
Indices: 52341298--52341506 Score: 274
Period size: 81 Copynumber: 2.6 Consensus size: 81
52341288 ACTAAAATGT
* ** *
52341298 CCTCAATTTGTAAAATTACCAACGTACCCTCGATTTACAAAATTACCGTTTTACCCTCGATTTAC
1 CCTCAATTTATAAAATTACCAAAATACCCTCGATTTACAAAATTACCGTTTTACCCTCAATTTAC
*
52341363 AGAATTACCGTTTTAC
66 AGAATTACCATTTTAC
* * *** * *
52341379 CCTCGATTTATAGAATTACCATTTTACCCTCAATTTACAGAATTACCGTTTTACCCTCAATTTAC
1 CCTCAATTTATAAAATTACCAAAATACCCTCGATTTACAAAATTACCGTTTTACCCTCAATTTAC
52341444 AGAATTACCATTTTAC
66 AGAATTACCATTTTAC
* * * *
52341460 CCTCAATTTACAAAATTACTAAAATACCCTTGGTTTACAAAATTACC
1 CCTCAATTTATAAAATTACCAAAATACCCTCGATTTACAAAATTACC
52341507 AAAATACCCC
Statistics
Matches: 107, Mismatches: 21, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
81 107 1.00
ACGTcount: A:0.33, C:0.25, G:0.07, T:0.35
Consensus pattern (81 bp):
CCTCAATTTATAAAATTACCAAAATACCCTCGATTTACAAAATTACCGTTTTACCCTCAATTTAC
AGAATTACCATTTTAC
Found at i:52341792 original size:25 final size:27
Alignment explanation
Indices: 52341713--52341792 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 27
52341703 ACCCCTAATA
* * *
52341713 GGTAAAAAGACCGTAA-AGCCCCTGTAA
1 GGTAAAATGACCGTAATA-TCCCTGTAT
*
52341740 GGTAAAGTGACCGTAATATCCCTGTAT
1 GGTAAAATGACCGTAATATCCCTGTAT
52341767 GGTAAAATGA-CG-AATATGCCCT-TAT
1 GGTAAAATGACCGTAATAT-CCCTGTAT
52341792 G
1 G
52341793 TTCCGTATGA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
25 9 0.20
26 6 0.13
27 30 0.65
28 1 0.02
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.24
Consensus pattern (27 bp):
GGTAAAATGACCGTAATATCCCTGTAT
Found at i:52342625 original size:25 final size:25
Alignment explanation
Indices: 52342587--52342656 Score: 113
Period size: 25 Copynumber: 2.8 Consensus size: 25
52342577 AGGAAGTGCT
* *
52342587 AAAAGGGCTATGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCA
*
52342612 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCA
52342637 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
52342657 ATTAAAAGAG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.27, C:0.26, G:0.23, T:0.24
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCA
Found at i:52342669 original size:24 final size:24
Alignment explanation
Indices: 52342586--52342681 Score: 95
Period size: 25 Copynumber: 3.9 Consensus size: 24
52342576 GAGGAAGTGC
*
52342586 TAAAAGGGCTATGCCCCAGTTTACC
1 TAAAAGGGCTATGCCCCAGTTTA-T
* *
52342611 GAAAAGGGCTTTGCCCCAGTTTAT
1 TAAAAGGGCTATGCCCCAGTTTAT
* *
52342635 CAAAAAGGGCTTTGCCCCAG-TTAT
1 -TAAAAGGGCTATGCCCCAGTTTAT
*
52342659 TAAAAGAGGCTAGGCCTCCAGTT
1 TAAAAG-GGCTATGCC-CCAGTT
52342682 ATATGTATAG
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
23 5 0.08
24 11 0.18
25 43 0.72
26 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.25
Consensus pattern (24 bp):
TAAAAGGGCTATGCCCCAGTTTAT
Found at i:52342680 original size:50 final size:50
Alignment explanation
Indices: 52342587--52342681 Score: 113
Period size: 50 Copynumber: 1.9 Consensus size: 50
52342577 AGGAAGTGCT
**
52342587 AAAAGGGCTATGCCCCAGTTTACCGAAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTATGCCCCAGTTTACCGAAAAGGGCTAGGCCCCAGTTTATCA
* **
52342637 AAAAGGGCTTTGCCCCAG-TTA-TTAAAAGAGGCTAGGCCTCCAGTT
1 AAAAGGGCTATGCCCCAGTTTACCGAAAAG-GGCTAGGCC-CCAGTT
52342682 ATATGTATAG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
48 5 0.13
49 10 0.26
50 23 0.61
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.24
Consensus pattern (50 bp):
AAAAGGGCTATGCCCCAGTTTACCGAAAAGGGCTAGGCCCCAGTTTATCA
Found at i:52342931 original size:31 final size:31
Alignment explanation
Indices: 52342875--52342948 Score: 114
Period size: 31 Copynumber: 2.4 Consensus size: 31
52342865 CGCTTACAGT
* *
52342875 AAAGGCTTCAG-CCACTGGTATGATTTATGA
1 AAAGGCTTCGGCCCACTGATATGATTTATGA
*
52342905 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCACTGATATGATTTATGA
52342936 AAAGGCTTCGGCC
1 AAAGGCTTCGGCC
52342949 TAATATATGT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 10 0.25
31 30 0.75
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCGGCCCACTGATATGATTTATGA
Found at i:52347214 original size:13 final size:13
Alignment explanation
Indices: 52347196--52347221 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
52347186 AATCACACAT
52347196 GGGCGTGTTACAC
1 GGGCGTGTTACAC
52347209 GGGCGTGTTACAC
1 GGGCGTGTTACAC
52347222 AAGCGTGTCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.38, T:0.23
Consensus pattern (13 bp):
GGGCGTGTTACAC
Found at i:52379412 original size:29 final size:29
Alignment explanation
Indices: 52379355--52379469 Score: 144
Period size: 29 Copynumber: 4.0 Consensus size: 29
52379345 TACCTATATC
* * * *
52379355 TGGCCCATTAAGCCC-AATCATATTCATA
1 TGGCCCTTTAGGCCCAAATCACATTTATA
* *
52379383 TGGCCCTTTAGACCCAAATCACATGTATA
1 TGGCCCTTTAGGCCCAAATCACATTTATA
*
52379412 TGGCCCATTAGGCCCAAATCACATTTATA
1 TGGCCCTTTAGGCCCAAATCACATTTATA
*
52379441 TGGCCCTTTAGGCCC-AGTCACATTTATA
1 TGGCCCTTTAGGCCCAAATCACATTTATA
52379469 T
1 T
52379470 TCATGTTCAC
Statistics
Matches: 75, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
28 25 0.33
29 50 0.67
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.30
Consensus pattern (29 bp):
TGGCCCTTTAGGCCCAAATCACATTTATA
Found at i:52379416 original size:57 final size:57
Alignment explanation
Indices: 52379355--52379469 Score: 160
Period size: 57 Copynumber: 2.0 Consensus size: 57
52379345 TACCTATATC
*
52379355 TGGCCCATTAAGCCC-AATCATATTCATATGGCCCTTTAGACCCAAATCACATGTATA
1 TGGCCCATTAAGCCCAAATCACATTCATATGGCCCTTTAGACCC-AATCACATGTATA
* * * * *
52379412 TGGCCCATTAGGCCCAAATCACATTTATATGGCCCTTTAGGCCCAGTCACATTTATA
1 TGGCCCATTAAGCCCAAATCACATTCATATGGCCCTTTAGACCCAATCACATGTATA
52379469 T
1 T
52379470 TCATGTTCAC
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
57 26 0.51
58 25 0.49
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.30
Consensus pattern (57 bp):
TGGCCCATTAAGCCCAAATCACATTCATATGGCCCTTTAGACCCAATCACATGTATA
Found at i:52381589 original size:30 final size:31
Alignment explanation
Indices: 52381530--52381589 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
52381520 TACGAGCCTT
* *
52381530 GGGGCAAAAGTGTCAAATATGTGAAAGTTTA
1 GGGGCAAAAATGTCAAATATGTCAAAGTTTA
* *
52381561 GGGGCAAAAATGT-AATTTTGTCAAAGTTT
1 GGGGCAAAAATGTCAAATATGTCAAAGTTT
52381590 GGGTCAAGGG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 13 0.52
31 12 0.48
ACGTcount: A:0.37, C:0.07, G:0.27, T:0.30
Consensus pattern (31 bp):
GGGGCAAAAATGTCAAATATGTCAAAGTTTA
Found at i:52381997 original size:46 final size:47
Alignment explanation
Indices: 52381925--52382047 Score: 142
Period size: 46 Copynumber: 2.6 Consensus size: 47
52381915 GACAGGACAG
* *
52381925 GACAGAAATGAGCCATGTAAGTCCATATCAGT-TATAT-GGCTTTGGA
1 GACAGGAATGAGCCATGTAAGTCCATATCA-TATATATAGGCATTGGA
* *
52381971 GACAGGAATGAGCCATGTAAGCCCATATTATATATATACGGCATTGGA
1 GACAGGAATGAGCCATGTAAGTCCATATCATATATATA-GGCATTGGA
* * **
52382019 GATAGGAATAATTCATGTAAGTCCATATC
1 GACAGGAATGAGCCATGTAAGTCCATATC
52382048 GAAGACATGG
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
45 1 0.02
46 32 0.50
48 31 0.48
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (47 bp):
GACAGGAATGAGCCATGTAAGTCCATATCATATATATAGGCATTGGA
Found at i:52390219 original size:58 final size:57
Alignment explanation
Indices: 52390146--52390256 Score: 161
Period size: 58 Copynumber: 1.9 Consensus size: 57
52390136 TGAATGTGAC
*
52390146 TGGGCCTAATGGGCCATATAAATGTGATTTGGGCCTAATGGGCCAT-ATACAGGTGATT
1 TGGGCCTAATGGGCCATATAAATATGA-TTGGGCCTAATGGGCC-TGATACAGGTGATT
* * *
52390204 TGGGTCTAATGGGCCATATGAATATGATTGGGCTTAATGGGCCTGATACAGGT
1 TGGGCCTAATGGGCCATATAAATATGATTGGGCCTAATGGGCCTGATACAGGT
52390257 ATGTGAAATT
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
56 1 0.02
57 23 0.48
58 24 0.50
ACGTcount: A:0.25, C:0.14, G:0.31, T:0.30
Consensus pattern (57 bp):
TGGGCCTAATGGGCCATATAAATATGATTGGGCCTAATGGGCCTGATACAGGTGATT
Found at i:52390243 original size:28 final size:29
Alignment explanation
Indices: 52390133--52390246 Score: 144
Period size: 29 Copynumber: 4.0 Consensus size: 29
52390123 TTGAACATGA
*
52390133 ATATGAATGTGA-CTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
*
52390161 ATATAAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
* *
52390190 ATAT-ACAGGTGATTTGGGTCTAATGGGCC
1 ATATGA-ATGTGATTTGGGCCTAATGGGCC
* *
52390219 ATATGAATATGA-TTGGGCTTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
52390247 TGATACAGGT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
28 26 0.35
29 48 0.64
30 1 0.01
ACGTcount: A:0.26, C:0.14, G:0.30, T:0.30
Consensus pattern (29 bp):
ATATGAATGTGATTTGGGCCTAATGGGCC
Found at i:52395579 original size:49 final size:49
Alignment explanation
Indices: 52395521--52395636 Score: 130
Period size: 49 Copynumber: 2.4 Consensus size: 49
52395511 GCATGTTCTA
* *
52395521 GACAGGTCTTACACTGACTTTTATATATCGATG-CTAATGCCATGTCC-C
1 GACAGGTCTTACACTGACTCTCATATATCGATGTC-AATGCCATGTCCAC
* * * *
52395569 AGATAGGTCTTACACT-AGCTCTCATCTATCGGTGTCGATGCCATGTCCAC
1 -GACAGGTCTTACACTGA-CTCTCATATATCGATGTCAATGCCATGTCCAC
52395619 GACAGGTCTTACACTGAC
1 GACAGGTCTTACACTGAC
52395637 ATAGAACAAG
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
48 1 0.02
49 52 0.93
50 3 0.05
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (49 bp):
GACAGGTCTTACACTGACTCTCATATATCGATGTCAATGCCATGTCCAC
Found at i:52403568 original size:111 final size:111
Alignment explanation
Indices: 52403447--52403780 Score: 623
Period size: 111 Copynumber: 3.0 Consensus size: 111
52403437 ATATATGTGG
*
52403447 AATACATGGAAACTATGGTATATGAAATATTAATATAATGAAATAAATGATATGTGTTTATAAGA
1 AATACATGGAAACTATGGTATATGAAATATTGATATAATGAAATAAATGATATGTGTTTATAAGA
* *
52403512 AAACAAAAAGAGAATGTTATGTATTAGGACATGTATATATATATAT
66 AAACAAAAAGAGAATGTTATGTATCATGACATGTATATATATATAT
52403558 AATACATGGAAACTATGGTATATGAAATATTGATATAATGAAATAAATGATATGTGTTTATAAGA
1 AATACATGGAAACTATGGTATATGAAATATTGATATAATGAAATAAATGATATGTGTTTATAAGA
* *
52403623 AGACAAAAAGAGAATGTTATGTGTCATGACATGTATATATATATAT
66 AAACAAAAAGAGAATGTTATGTATCATGACATGTATATATATATAT
52403669 AATACATGGAAACTATGGTATATGAAATATTGATATAATGAAATAAATGATATGTGTTTATAAGA
1 AATACATGGAAACTATGGTATATGAAATATTGATATAATGAAATAAATGATATGTGTTTATAAGA
52403734 AAACAAAAAGAGAATGTTATGTATCATGACATGTATATATATATAT
66 AAACAAAAAGAGAATGTTATGTATCATGACATGTATATATATATAT
52403780 A
1 A
52403781 TATGACTAGT
Statistics
Matches: 216, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 216 1.00
ACGTcount: A:0.47, C:0.04, G:0.16, T:0.33
Consensus pattern (111 bp):
AATACATGGAAACTATGGTATATGAAATATTGATATAATGAAATAAATGATATGTGTTTATAAGA
AAACAAAAAGAGAATGTTATGTATCATGACATGTATATATATATAT
Found at i:52409915 original size:27 final size:26
Alignment explanation
Indices: 52409871--52409922 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
52409861 GTCGCTGCAA
52409871 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGGCCTCGCCACA-ATATCTGT
* *
52409898 TCTGGTGGCTTCGTCACAATATCTG
1 TCTGGTGGCCTCGCCACAATATCTG
52409923 GCAGCCTCGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.15, C:0.27, G:0.23, T:0.35
Consensus pattern (26 bp):
TCTGGTGGCCTCGCCACAATATCTGT
Found at i:52409999 original size:27 final size:26
Alignment explanation
Indices: 52409961--52410020 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
52409951 CCACATATAT
* *
52409961 ATATTTGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
52409987 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
52410014 ATATCTG
1 ATATCTG
52410021 ATAGCTTCGC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.37
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:52411784 original size:10 final size:11
Alignment explanation
Indices: 52411754--52411783 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
52411744 TTTCTTACCG
52411754 AATACAAAAGAA
1 AATA-AAAAGAA
52411766 AATAAAAAGAA
1 AATAAAAAGAA
52411777 AATAAAA
1 AATAAAA
52411784 GGGTTTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.78
12 4 0.22
ACGTcount: A:0.80, C:0.03, G:0.07, T:0.10
Consensus pattern (11 bp):
AATAAAAAGAA
Found at i:52416132 original size:49 final size:49
Alignment explanation
Indices: 52416072--52416291 Score: 188
Period size: 49 Copynumber: 4.6 Consensus size: 49
52416062 ACATCAAAGT
52416072 TGATGCCATGTCCCAGACAGGTCTTACACTGACTTTTATATATCGAGGC
1 TGATGCCATGTCCCAGACAGGTCTTACACTGACTTTTATATATCGAGGC
* * * * * *
52416121 TGATGACATGTCCTAGACAGGTCTTACACTGGCTCTCATCTATCG-GTG-
1 TGATGCCATGTCCCAGACAGGTCTTACACTGACTTTTATATATCGAG-GC
* * * * * *
52416169 TCGATGCCGTGTCCCAGACAGGTCTTACACTAAC----ACACAAC-AAGC
1 T-GATGCCATGTCCCAGACAGGTCTTACACTGACTTTTATATATCGAGGC
* * *
52416214 TGACGCCATGTCCCAGACAGGTCTTACACT-AGCTTGTATATCTCGAGGC
1 TGATGCCATGTCCCAGACAGGTCTTACACTGA-CTTTTATATATCGAGGC
* * *
52416263 CGATG-CATGTCCCAAACATGTCTTACACT
1 TGATGCCATGTCCCAGACAGGTCTTACACT
52416292 AGCTCCCATC
Statistics
Matches: 134, Mismatches: 27, Indels: 21
0.74 0.15 0.12
Matches are distributed among these distances:
43 1 0.01
44 29 0.22
45 4 0.03
48 27 0.20
49 73 0.54
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (49 bp):
TGATGCCATGTCCCAGACAGGTCTTACACTGACTTTTATATATCGAGGC
Found at i:52416320 original size:46 final size:44
Alignment explanation
Indices: 52416263--52416386 Score: 142
Period size: 46 Copynumber: 2.7 Consensus size: 44
52416253 ATCTCGAGGC
* *
52416263 CGATGCATGTCCCAAACATGTCTTACACTAGCTCCCATCTCAATGT-
1 CGATGCATGTCCCAGACATGTCTTACACTAGCT--C-TCACAATGTA
* * * *
52416309 CGATGCATGTCCTAGACATGTCTTGCACTGGCTCTCAGAATGTGA
1 CGATGCATGTCCCAGACATGTCTTACACTAGCTCTCACAATGT-A
52416354 CCGATGCATGTCCCAGACATGTCTTACACTAGC
1 -CGATGCATGTCCCAGACATGTCTTACACTAGC
52416387 ACACATATCA
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
43 7 0.11
44 1 0.02
46 58 0.88
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (44 bp):
CGATGCATGTCCCAGACATGTCTTACACTAGCTCTCACAATGTA
Found at i:52419765 original size:80 final size:80
Alignment explanation
Indices: 52419632--52419839 Score: 287
Period size: 80 Copynumber: 2.6 Consensus size: 80
52419622 TATTCGGATG
* * * * *
52419632 ATAACCGGGCTAAGTCCCGAAGGCATTTGT-TCTAGTGACTA-ATTTCGGGCTAAGCCCCAAAGG
1 ATAACCGGGCTATGTCCCGAAGGCATTCGTGT-GAGTTACTATA-TCCGGGCTAAGCCCCAAAGG
*
52419695 CATTTGTGCGAGTCACT
64 CATTTGTGCGAGTCACC
52419712 ATAACCGGGCTATGTCCCGAAGGCATTCGTGTGAGTTACTATATCCGGGCTAAGCCCCAAAGGCA
1 ATAACCGGGCTATGTCCCGAAGGCATTCGTGTGAGTTACTATATCCGGGCTAAGCCCCAAAGGCA
*
52419777 TTTGTGCGAGTTACC
66 TTTGTGCGAGTCACC
* *
52419792 ATAACCGGGCTATGTCCCGAAGGCATTCGAGCGAG-TAGCTATATCCGG
1 ATAACCGGGCTATGTCCCGAAGGCATTCGTGTGAGTTA-CTATATCCGG
52419840 TTAAATTCCG
Statistics
Matches: 116, Mismatches: 9, Indels: 6
0.89 0.07 0.05
Matches are distributed among these distances:
79 2 0.02
80 112 0.97
81 2 0.02
ACGTcount: A:0.25, C:0.25, G:0.26, T:0.25
Consensus pattern (80 bp):
ATAACCGGGCTATGTCCCGAAGGCATTCGTGTGAGTTACTATATCCGGGCTAAGCCCCAAAGGCA
TTTGTGCGAGTCACC
Found at i:52419826 original size:40 final size:40
Alignment explanation
Indices: 52419632--52419827 Score: 187
Period size: 40 Copynumber: 4.9 Consensus size: 40
52419622 TATTCGGATG
* * * * * *
52419632 ATAACCGGGCTAAGTCCCGAAGGCATTTGTTCTAGTGACT
1 ATAACCGGGCTAAGCCCCAAAGGCATTCGTGCGAGTTACT
** * *
52419672 A-ATTTCGGGCTAAGCCCCAAAGGCATTTGTGCGAGTCACT
1 ATA-ACCGGGCTAAGCCCCAAAGGCATTCGTGCGAGTTACT
* * * *
52419712 ATAACCGGGCTATGTCCCGAAGGCATTCGTGTGAGTTACT
1 ATAACCGGGCTAAGCCCCAAAGGCATTCGTGCGAGTTACT
* * *
52419752 ATATCCGGGCTAAGCCCCAAAGGCATTTGTGCGAGTTACC
1 ATAACCGGGCTAAGCCCCAAAGGCATTCGTGCGAGTTACT
* * * *
52419792 ATAACCGGGCTATGTCCCGAAGGCATTCGAGCGAGT
1 ATAACCGGGCTAAGCCCCAAAGGCATTCGTGCGAGT
52419828 AGCTATATCC
Statistics
Matches: 126, Mismatches: 28, Indels: 4
0.80 0.18 0.03
Matches are distributed among these distances:
39 1 0.01
40 124 0.98
41 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (40 bp):
ATAACCGGGCTAAGCCCCAAAGGCATTCGTGCGAGTTACT
Found at i:52428580 original size:80 final size:79
Alignment explanation
Indices: 52428496--52428667 Score: 211
Period size: 79 Copynumber: 2.2 Consensus size: 79
52428486 GGACTAAGAT
*
52428496 CCGAAGGCATTTGTGCGAGAT-ACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACT
1 CCGAAGGCATTTGTGCGAGATGACAAA-TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACT
* *
52428560 AAATCCGGGTTAAGTC
64 AAAACCGGGCTAAGTC
* * ** * * * *
52428576 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATGACAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
*
52428641 AACCGGGCTATGTC
66 AACCGGGCTAAGTC
52428655 CCGAAGGCATTTG
1 CCGAAGGCATTTG
52428668 AACGAGGAGC
Statistics
Matches: 78, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
79 38 0.49
80 37 0.47
81 3 0.04
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATGACAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
AACCGGGCTAAGTC
Found at i:52428647 original size:39 final size:39
Alignment explanation
Indices: 52428443--52428665 Score: 200
Period size: 40 Copynumber: 5.6 Consensus size: 39
52428433 TTGAATGCTG
* * * * *
52428443 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGA-T-ACTAAA
**
52428483 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAA
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGATACTAAA
* *
52428522 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 -TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGATACTAAA
* **
52428563 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGATACTAAA
* * *
52428603 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
* * *
52428642 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
52428666 TGAACGAGGA
Statistics
Matches: 155, Mismatches: 20, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
39 39 0.25
40 102 0.66
41 13 0.08
42 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:52428685 original size:79 final size:80
Alignment explanation
Indices: 52428523--52428700 Score: 198
Period size: 79 Copynumber: 2.2 Consensus size: 80
52428513 AGATACAAAT
* * * *
52428523 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** ** *
52428588 GTGCGAGTTGTTAAA
66 GAACGAGGAGCTAAA
* * * * *
52428603 TCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
52428667 GAACGAGGAGCTATA
66 GAACGAGGAGCTAAA
*
52428682 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
52428701 TACGTGATTT
Statistics
Matches: 81, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
78 14 0.17
79 49 0.60
80 18 0.22
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGGAGCTAAA
Found at i:52436450 original size:40 final size:39
Alignment explanation
Indices: 52436406--52436801 Score: 458
Period size: 40 Copynumber: 10.2 Consensus size: 39
52436396 ACTAAGATCT
* * * *
52436406 GAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCC
1 GAAGGCATTCGTGCGAG-TATTAAAGCCGGGTTAAGTCCC
*
52436446 GAAGGCATTCATGCGAGTAATTAAAGCCGGGTTAAGTCCC
1 GAAGGCATTCGTGCGAGT-ATTAAAGCCGGGTTAAGTCCC
52436486 GAAGGCATTCGTGCGAG--TT--A------TTAAAG--CC
1 GAAGGCATTCGTGCGAGTATTAAAGCCGGGTT-AAGTCCC
* * * *
52436514 GAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCC
1 GAAGGCATTCGTGCGAG-TATTAAAGCCGGGTTAAGTCCC
52436554 GAAGGCATTCGTGCGAGTAATTAAAGCCGGGTTAAGTCCC
1 GAAGGCATTCGTGCGAGT-ATTAAAGCCGGGTTAAGTCCC
52436594 GAAGGCATTCGTGCGAGTTATTAAAGCCGGGTTAAGTCCC
1 GAAGGCATTCGTGCGAG-TATTAAAGCCGGGTTAAGTCCC
52436634 GAAGGCATTCGTGCGAGTAATTAAAGCCGGGTTAAGTCCC
1 GAAGGCATTCGTGCGAGT-ATTAAAGCCGGGTTAAGTCCC
52436674 GAAGGCATTCGTGCGAGTTATTAAAGCCGGGTTAAGTCCC
1 GAAGGCATTCGTGCGAG-TATTAAAGCCGGGTTAAGTCCC
* * *
52436714 GAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTACGTCCC
1 GAAGGCATTCGTGCGAG-TATTAAAGCCGGGTTAAGTCCC
* * * * *
52436754 GAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCC
1 GAAGGCATTCGTGCGAG-TATTAAAGCCGGGTTAAGTCCC
52436793 GAAGGCATT
1 GAAGGCATT
52436802 TGAACGAGGA
Statistics
Matches: 315, Mismatches: 22, Indels: 39
0.84 0.06 0.10
Matches are distributed among these distances:
28 17 0.05
29 2 0.01
30 3 0.01
31 1 0.00
33 1 0.00
35 1 0.00
37 2 0.01
38 3 0.01
39 38 0.12
40 245 0.78
41 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.24
Consensus pattern (39 bp):
GAAGGCATTCGTGCGAGTATTAAAGCCGGGTTAAGTCCC
Found at i:52436538 original size:28 final size:28
Alignment explanation
Indices: 52436484--52436538 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
52436474 GGGTTAAGTC
* *
52436484 CCGAAGGCATTCGTGCGAGTTATTAAAG
1 CCGAAGGCATTCGTGCGAGATACTAAAG
* *
52436512 CCGAAGGCCTTTGTGCGAGATACTAAA
1 CCGAAGGCATTCGTGCGAGATACTAAA
52436539 TCCGGGTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (28 bp):
CCGAAGGCATTCGTGCGAGATACTAAAG
Found at i:52436595 original size:108 final size:109
Alignment explanation
Indices: 52436406--52436738 Score: 481
Period size: 108 Copynumber: 3.0 Consensus size: 109
52436396 ACTAAGATCT
*
52436406 GAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCATGCGAGTAATTAAA
1 GAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTAATTAAA
52436471 GCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAAG-CC
66 GCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAAGCCC
52436514 GAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTAATTAAA
1 GAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTAATTAAA
52436579 GCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAAGCCGGGTTAAGTCCC
66 GCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATT--A--------AAG-CCC
* * * * *
52436634 GAAGGCATTCGTGCGAG-TAATTAAAGCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAA
1 GAAGGCCTTTGTGCGAGAT-ACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTAATTAA
*
52436698 AGCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
65 AGCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
52436739 TCCGGGTTAC
Statistics
Matches: 205, Mismatches: 7, Indels: 24
0.87 0.03 0.10
Matches are distributed among these distances:
108 101 0.49
110 3 0.01
118 4 0.02
119 1 0.00
120 96 0.47
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (109 bp):
GAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTAATTAAA
GCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAAGCCC
Found at i:52441394 original size:31 final size:31
Alignment explanation
Indices: 52441356--52441434 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
52441346 TTTAACGGTT
*
52441356 ACTGGGCCGAAGCCTTTTCATAAATTATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
*
52441387 ACTGGGCCGAAGCCTTTTTATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
*
52441418 ATTGGGCCGAAGCCTTT
1 ACTGGGCCGAAGCCTTT
52441435 ACTGTAAACG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.32
Consensus pattern (31 bp):
ACTGGGCCGAAGCCTTTTCATAAATCATATC
Found at i:52441505 original size:42 final size:42
Alignment explanation
Indices: 52441458--52441549 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
52441448 TGGCCCTTAG
* ** *
52441458 GCCCATTTCAATATCACATGTAATGTCAATGGATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
52441500 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
52441542 GCCCATTT
1 GCCCATTT
52441550 GGGGAGACTA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
Found at i:52441765 original size:26 final size:26
Alignment explanation
Indices: 52441695--52441816 Score: 167
Period size: 26 Copynumber: 4.8 Consensus size: 26
52441685 CTCTTTAATG
**
52441695 ACTGGGGCA-AAGCCCTTTTCGGTAA
1 ACTGGGGCATAAGCCCTTTTCAATAA
52441720 ACTGGGGCA-AAGCCCTTTTCAATAA
1 ACTGGGGCATAAGCCCTTTTCAATAA
* * **
52441745 ACTAGGGCATAAGCCCCTTTCGGTAA
1 ACTGGGGCATAAGCCCTTTTCAATAA
*
52441771 ACTGGGGCATAAGCCATTTTCAATAA
1 ACTGGGGCATAAGCCCTTTTCAATAA
52441797 ACTGGGGCATAAGCCCTTTT
1 ACTGGGGCATAAGCCCTTTT
52441817 GCGCTTCCTC
Statistics
Matches: 84, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
25 31 0.37
26 53 0.63
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.25
Consensus pattern (26 bp):
ACTGGGGCATAAGCCCTTTTCAATAA
Found at i:52441791 original size:52 final size:51
Alignment explanation
Indices: 52441699--52441812 Score: 185
Period size: 52 Copynumber: 2.2 Consensus size: 51
52441689 TTAATGACTG
* *
52441699 GGGCA-AAGCCCTTTTCGGTAAACTGGGGCAAAGCCCTTTTCAATAAACTA
1 GGGCATAAGCCCCTTTCGGTAAACTGGGGCAAAGCCATTTTCAATAAACTA
*
52441749 GGGCATAAGCCCCTTTCGGTAAACTGGGGCATAAGCCATTTTCAATAAACTG
1 GGGCATAAGCCCCTTTCGGTAAACTGGGGCA-AAGCCATTTTCAATAAACTA
52441801 GGGCATAAGCCC
1 GGGCATAAGCCC
52441813 TTTTGCGCTT
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
50 5 0.08
51 24 0.41
52 30 0.51
ACGTcount: A:0.29, C:0.25, G:0.24, T:0.23
Consensus pattern (51 bp):
GGGCATAAGCCCCTTTCGGTAAACTGGGGCAAAGCCATTTTCAATAAACTA
Found at i:52442634 original size:27 final size:26
Alignment explanation
Indices: 52442599--52442681 Score: 103
Period size: 27 Copynumber: 3.1 Consensus size: 26
52442589 GGGCATATTC
* * *
52442599 GTCATTTTACCATACAGGGGTATTACG
1 GTCACTTTACCCTAAAGGGGT-TTACG
*
52442626 GTCACTTTACCCTATAGGGGCTTTACG
1 GTCACTTTACCCTAAAGGGG-TTTACG
*
52442653 GTCACTTTACCCTAAAGGGCTTTACG
1 GTCACTTTACCCTAAAGGGGTTTACG
52442679 GTC
1 GTC
52442682 TTTTTACCTA
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
26 9 0.18
27 40 0.80
28 1 0.02
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.33
Consensus pattern (26 bp):
GTCACTTTACCCTAAAGGGGTTTACG
Found at i:52442679 original size:26 final size:27
Alignment explanation
Indices: 52442621--52442681 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
52442611 TACAGGGGTA
*
52442621 TTACGGTCACTTTACCCTATAGGGGCT
1 TTACGGTCACTTTACCCTATAAGGGCT
52442648 TTACGGTCACTTTACCCTA-AAGGGCT
1 TTACGGTCACTTTACCCTATAAGGGCT
52442674 TTACGGTC
1 TTACGGTC
52442682 TTTTTACCTA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 14 0.42
27 19 0.58
ACGTcount: A:0.20, C:0.26, G:0.21, T:0.33
Consensus pattern (27 bp):
TTACGGTCACTTTACCCTATAAGGGCT
Found at i:52442697 original size:26 final size:27
Alignment explanation
Indices: 52442621--52442697 Score: 106
Period size: 26 Copynumber: 2.9 Consensus size: 27
52442611 TACAGGGGTA
52442621 TTACGGTCACTTTACCCT-ATAGGGGCT
1 TTACGGTCACTTTACCCTAATA-GGGCT
52442648 TTACGGTCACTTTACCCTAA-AGGGCT
1 TTACGGTCACTTTACCCTAATAGGGCT
**
52442674 TTACGGTCTTTTTA-CCTAATAGGG
1 TTACGGTCACTTTACCCTAATAGGG
52442698 TATTTTAGTC
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
25 5 0.11
26 21 0.46
27 19 0.41
28 1 0.02
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (27 bp):
TTACGGTCACTTTACCCTAATAGGGCT
Found at i:52442772 original size:27 final size:27
Alignment explanation
Indices: 52442746--52443051 Score: 142
Period size: 27 Copynumber: 11.3 Consensus size: 27
52442736 ATCTACAAAC
*
52442746 CAAGGGTATTTCAGTAATTTTGTAAA-
1 CAAGGGTATTTTAGTAATTTTGTAAAT
* *
52442772 CTAATGGTATTTCCA-TAATTTT-TAGAAAGT
1 C-AAGGGTATTT-TAGTAATTTTGT--AAA-T
*
52442802 CAAGGGTATTTCT-GTAACTTTGTAAAT
1 CAAGGGTATTT-TAGTAATTTTGTAAAT
* * **
52442829 CAGGGGTATTTTGGTAATTTTACAAAT
1 CAAGGGTATTTTAGTAATTTTGTAAAT
* ** ***
52442856 TAAGGGTATTTCGGTAATTTCACAAA-
1 CAAGGGTATTTTAGTAATTTTGTAAAT
* * **
52442882 CCAGTGGTATTTTGGTAATTTTACAAA-
1 CAAG-GGTATTTTAGTAATTTTGTAAAT
* * ** *
52442909 CCAGTGGTATTTTAGCAATTTTACAGA-
1 CAAG-GGTATTTTAGTAATTTTGTAAAT
* * * *
52442936 CTAGGGTATTTTGGTAATTTTACT-GAT
1 CAAGGGTATTTTAGTAATTTT-GTAAAT
* * *
52442963 CGAGGGTATTTTGGTAATTTTGTAAAC
1 CAAGGGTATTTTAGTAATTTTGTAAAT
*
52442990 CAAGGGTATTTTACTAATTTTGTAAAT
1 CAAGGGTATTTTAGTAATTTTGTAAAT
* **** *
52443017 CGAGGGTAAAACAGTAATTCTGTAAAT
1 CAAGGGTATTTTAGTAATTTTGTAAAT
52443044 CAAGGGTA
1 CAAGGGTA
52443052 AAACAGTAAT
Statistics
Matches: 227, Mismatches: 40, Indels: 25
0.78 0.14 0.09
Matches are distributed among these distances:
26 23 0.10
27 178 0.78
28 8 0.04
29 16 0.07
30 2 0.01
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (27 bp):
CAAGGGTATTTTAGTAATTTTGTAAAT
Found at i:52442847 original size:56 final size:53
Alignment explanation
Indices: 52442739--52442989 Score: 172
Period size: 54 Copynumber: 4.6 Consensus size: 53
52442729 TTGGTAAATC
* * ***
52442739 TACAAACCAAGGGTATTTCAGTAATTTTGTAAACTAATGGTATTTCCATAATTTT
1 TACAAATCAAGGGTATTTCAGTAA-TTTGTAAAC-AGTGGTATTTTGGTAATTTT
* * *
52442794 TAGAAAGTCAAGGGTATTTCTGTAACTTTGTAAATCAGGGGTATTTTGGTAA-TTT
1 TACAAA-TCAAGGGTATTTCAGTAA-TTTGTAAA-CAGTGGTATTTTGGTAATTTT
* * **
52442849 TACAAATTAAGGGTATTTCGGTAATTTCACAAACCAGTGGTATTTTGGTAA-TTT
1 TACAAATCAAGGGTATTTCAGTAATTT-GTAAA-CAGTGGTATTTTGGTAATTTT
* * *
52442903 TACAAA-CCAGTGGTATTTTAGCAATTT-TACAGACTAG-GGTATTTTGGTAA-TTT
1 TACAAATCAAG-GGTATTTCAGTAATTTGTA-A-AC-AGTGGTATTTTGGTAATTTT
** * **
52442956 TACTGATCGAGGGTATTTTGGTAATTTTGTAAAC
1 TACAAATCAAGGGTATTTCAGTAA-TTTGTAAAC
52442990 CAAGGGTATT
Statistics
Matches: 159, Mismatches: 27, Indels: 22
0.76 0.13 0.11
Matches are distributed among these distances:
52 1 0.01
53 40 0.25
54 67 0.42
55 15 0.09
56 35 0.22
57 1 0.01
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (53 bp):
TACAAATCAAGGGTATTTCAGTAATTTGTAAACAGTGGTATTTTGGTAATTTT
Found at i:52442891 original size:54 final size:53
Alignment explanation
Indices: 52442832--52443024 Score: 181
Period size: 54 Copynumber: 3.6 Consensus size: 53
52442822 TGTAAATCAG
* *
52442832 GGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGGTAATTTCACAAACCA
1 GGGTATTTTGGTAATTTTACAAATCAAGGGTATTTTGGTAATTTCACAAACCA
* * * * * *
52442885 GTGGTATTTTGGTAATTTTACAAA-CCAGTGGTATTTTAGCAATTTTACAGACTA
1 G-GGTATTTTGGTAATTTTACAAATCAAG-GGTATTTTGGTAATTTCACAAACCA
** * ***
52442939 GGGTATTTTGGTAATTTTACTGATCGAGGGTATTTTGGTAATTTTGTAAACCAA
1 GGGTATTTTGGTAATTTTACAAATCAAGGGTATTTTGGTAATTTCACAAACC-A
** ** *
52442993 GGGTATTTTACTAATTTTGTAAATCGAGGGTA
1 GGGTATTTTGGTAATTTTACAAATCAAGGGTA
52443025 AAACAGTAAT
Statistics
Matches: 113, Mismatches: 23, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
53 41 0.36
54 72 0.64
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.40
Consensus pattern (53 bp):
GGGTATTTTGGTAATTTTACAAATCAAGGGTATTTTGGTAATTTCACAAACCA
Found at i:52443052 original size:27 final size:27
Alignment explanation
Indices: 52443004--52443132 Score: 195
Period size: 27 Copynumber: 4.8 Consensus size: 27
52442994 GGTATTTTAC
*
52443004 TAATTTTGTAAATCGAGGGTAAAACAG
1 TAATTCTGTAAATCGAGGGTAAAACAG
*
52443031 TAATTCTGTAAATCAAGGGTAAAACAG
1 TAATTCTGTAAATCGAGGGTAAAACAG
* *
52443058 TAATTCTATAAATCGAGGGTAAAACGG
1 TAATTCTGTAAATCGAGGGTAAAACAG
* *
52443085 TAATTCTGTAAATCAAGGGTAAAACGG
1 TAATTCTGTAAATCGAGGGTAAAACAG
*
52443112 TAATTCTATAAATCGAGGGTA
1 TAATTCTGTAAATCGAGGGTA
52443133 CTTTGGTAAT
Statistics
Matches: 93, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 93 1.00
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.28
Consensus pattern (27 bp):
TAATTCTGTAAATCGAGGGTAAAACAG
Found at i:52443143 original size:54 final size:54
Alignment explanation
Indices: 52443012--52443132 Score: 224
Period size: 54 Copynumber: 2.2 Consensus size: 54
52443002 ACTAATTTTG
*
52443012 TAAATCGAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAACAGTAATTCTA
1 TAAATCGAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAACAGTAATTCTA
*
52443066 TAAATCGAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAACGGTAATTCTA
1 TAAATCGAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAACAGTAATTCTA
52443120 TAAATCGAGGGTA
1 TAAATCGAGGGTA
52443133 CTTTGGTAAT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 65 1.00
ACGTcount: A:0.42, C:0.11, G:0.21, T:0.26
Consensus pattern (54 bp):
TAAATCGAGGGTAAAACGGTAATTCTGTAAATCAAGGGTAAAACAGTAATTCTA
Found at i:52455374 original size:64 final size:64
Alignment explanation
Indices: 52455295--52455429 Score: 184
Period size: 64 Copynumber: 2.1 Consensus size: 64
52455285 AGGGTATCGA
* * *
52455295 GGTAAGTTCATATGCGAGA-AATGTAATATGTACTC-TATTTTAAATTCTTAAATATTGCATGTA
1 GGTAAGTTCATATGCGA-ATAATGCAATATGTAC-CATACTTTAAATGCTTAAATATTGCATGTA
52455358 T
64 T
* * *
52455359 GGTAAGTTCATATGCGAATTATGCAATATGTACCATACTTTAAATGCTTTAATATTGCTTGTAT
1 GGTAAGTTCATATGCGAATAATGCAATATGTACCATACTTTAAATGCTTAAATATTGCATGTAT
52455423 GGTAAGT
1 GGTAAGT
52455430 AAATATATAA
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
63 2 0.03
64 61 0.97
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (64 bp):
GGTAAGTTCATATGCGAATAATGCAATATGTACCATACTTTAAATGCTTAAATATTGCATGTAT
Found at i:52458609 original size:24 final size:24
Alignment explanation
Indices: 52458573--52458646 Score: 103
Period size: 24 Copynumber: 3.1 Consensus size: 24
52458563 GGGTCAACAT
*
52458573 TGGCACTAAGTGTGCGGATTTGAA
1 TGGCACTATGTGTGCGGATTTGAA
* * *
52458597 TGGCATTATGTGTGCGAAATTGAA
1 TGGCACTATGTGTGCGGATTTGAA
*
52458621 TGGCACTATGTGTGCTGATTTGAA
1 TGGCACTATGTGTGCGGATTTGAA
52458645 TG
1 TG
52458647 TCAATACATG
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.24, C:0.11, G:0.31, T:0.34
Consensus pattern (24 bp):
TGGCACTATGTGTGCGGATTTGAA
Found at i:52464693 original size:31 final size:31
Alignment explanation
Indices: 52464650--52464713 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
52464640 CCTTTTCATA
52464650 TTTCATAATTCATAACACTGGGCCGAAGCCT
1 TTTCATAATTCATAACACTGGGCCGAAGCCT
* ** *
52464681 TTTCATATTTCATATTACTGGGTCGAAGCCT
1 TTTCATAATTCATAACACTGGGCCGAAGCCT
52464712 TT
1 TT
52464714 ACTGTAAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.38
Consensus pattern (31 bp):
TTTCATAATTCATAACACTGGGCCGAAGCCT
Found at i:52464986 original size:23 final size:24
Alignment explanation
Indices: 52464906--52465049 Score: 213
Period size: 24 Copynumber: 6.0 Consensus size: 24
52464896 GCTTTATCAT
*
52464906 ATAACTGGAGGCCT-AGCCCCTTTTA
1 ATAACTGG-GGCATAAG-CCCTTTTA
52464931 ATAACTGGGGCA-AAGCCCTTTTTTA
1 ATAACTGGGGCATAAGCCC--TTTTA
52464956 ATAACTGGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTA
52464979 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
52465003 ATAATTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
52465027 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
52465050 GCACTTCCTC
Statistics
Matches: 111, Mismatches: 3, Indels: 11
0.89 0.02 0.09
Matches are distributed among these distances:
23 26 0.23
24 54 0.49
25 25 0.23
26 6 0.05
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.31
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:52465121 original size:9 final size:9
Alignment explanation
Indices: 52465107--52465163 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
52465097 ATCTCGTGTG
52465107 CATATCATA
1 CATATCATA
*
52465116 CATATCATGTG
1 CATATCA--TA
52465127 CATATCATA
1 CATATCATA
* *
52465136 CATGTCATGTG
1 CATATCA--TA
52465147 CATATCATA
1 CATATCATA
52465156 CATATCAT
1 CATATCAT
52465164 GTTTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:52465126 original size:20 final size:20
Alignment explanation
Indices: 52465103--52465165 Score: 117
Period size: 20 Copynumber: 3.1 Consensus size: 20
52465093 GAACATCTCG
52465103 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
*
52465123 TGTGCATATCATACATGTCA
1 TGTGCATATCATACATATCA
52465143 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
52465163 TGT
1 TGT
52465166 TTATCAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.37
Consensus pattern (20 bp):
TGTGCATATCATACATATCA
Found at i:52472806 original size:31 final size:31
Alignment explanation
Indices: 52472763--52472826 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
52472753 CCATTTCATA
52472763 TTTCATAATTCATAACACTGGGCCGAAGCCT
1 TTTCATAATTCATAACACTGGGCCGAAGCCT
* **
52472794 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATAATTCATAACACTGGGCCGAAGCCT
52472825 TT
1 TT
52472827 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCATAATTCATAACACTGGGCCGAAGCCT
Found at i:52473128 original size:47 final size:47
Alignment explanation
Indices: 52473019--52473844 Score: 1557
Period size: 47 Copynumber: 17.5 Consensus size: 47
52473009 CCTTTATCAT
* *
52473019 ATAACTGGAGGCCT-AGCCCCTTTTAATAACTAGGGCA-AAGCCCTTTTTTA
1 ATAACTGG-GGCATAAG-CCCTTTT-ATAACTGGGGCATAAGCCC--TTTTA
52473069 ATAACTGGGGCATAAGCCCTTTTATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTATAACTGGGGCATAAGCCCTTTTA
*
52473116 ATAACTGGGGCATAAGCCCTTTTAATAACTAGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTT-ATAACTGGGGCATAAGCCCTTTTA
52473164 ATAACTGGGGCATAAGCCCTTTTATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTATAACTGGGGCATAAGCCCTTTTA
52473211 ATAACTGGGGCATAAGCCCTTTTATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTATAACTGGGGCATAAGCCCTTTTA
52473258 ATAACTGGGGCATAAGCCCTTTTATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTATAACTGGGGCATAAGCCCTTTTA
52473305 ATAACTGGGGCATAAGCCCTTTTATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTATAACTGGGGCATAAGCCCTTTTA
52473352 ATAACTGGGGCATAAGCCCTTTTATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTATAACTGGGGCATAAGCCCTTTTA
52473399 ATAACTGGGGCATAAGCCCTTTTATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTATAACTGGGGCATAAGCCCTTTTA
52473446 ATAACTGGGGCATAAGCCCTTTTATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTATAACTGGGGCATAAGCCCTTTTA
52473493 ATAACTGGGGCATAAGCCCTTTTATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTATAACTGGGGCATAAGCCCTTTTA
52473540 ATAACTGGGGCATAAGCCCTTTTATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTATAACTGGGGCATAAGCCCTTTTA
52473587 ATAACTGGGGCATAAGCCCTTTTATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTATAACTGGGGCATAAGCCCTTTTA
52473634 ATAACTGGGGCATAAGCCCTTTTATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTATAACTGGGGCATAAGCCCTTTTA
52473681 ATAACTGGGGCATAAGCCCTTTTATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTATAACTGGGGCATAAGCCCTTTTA
52473728 ATAACTGGGGCATAAGCCCTTTTATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTATAACTGGGGCATAAGCCCTTTTA
52473775 ATAACTGGGGCATAAGCCCTTTTATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTATAACTGGGGCATAAGCCCTTTTA
52473822 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
52473845 GCACTTCCTC
Statistics
Matches: 769, Mismatches: 4, Indels: 9
0.98 0.01 0.01
Matches are distributed among these distances:
47 685 0.89
48 57 0.07
49 17 0.02
50 10 0.01
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (47 bp):
ATAACTGGGGCATAAGCCCTTTTATAACTGGGGCATAAGCCCTTTTA
Found at i:52473916 original size:9 final size:9
Alignment explanation
Indices: 52473902--52473958 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
52473892 ATCTCGTGTG
52473902 CATATCATA
1 CATATCATA
*
52473911 CATATCATGTG
1 CATATCA--TA
52473922 CATATCATA
1 CATATCATA
* *
52473931 CATGTCATGTG
1 CATATCA--TA
52473942 CATATCATA
1 CATATCATA
52473951 CATATCAT
1 CATATCAT
52473959 GTTTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:52473921 original size:20 final size:20
Alignment explanation
Indices: 52473898--52473960 Score: 117
Period size: 20 Copynumber: 3.1 Consensus size: 20
52473888 GAACATCTCG
52473898 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
*
52473918 TGTGCATATCATACATGTCA
1 TGTGCATATCATACATATCA
52473938 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
52473958 TGT
1 TGT
52473961 TTATCAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.37
Consensus pattern (20 bp):
TGTGCATATCATACATATCA
Found at i:52474025 original size:25 final size:25
Alignment explanation
Indices: 52473997--52474044 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
52473987 ATATATAAAC
* * *
52473997 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
52474022 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
52474045 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:52486344 original size:64 final size:64
Alignment explanation
Indices: 52486238--52486378 Score: 194
Period size: 64 Copynumber: 2.2 Consensus size: 64
52486228 TTGGTATCGG
* * * *
52486238 GGTAAGTTCGTATGCGAGTAATGCAATATGTACTCTATTTTAAATGCTTAAATATTACATGTAT
1 GGTAAGTTCATATGCAAATAATGCAATATGTACTCTACTTTAAATGCTTAAATATTACATGTAT
* * *
52486302 GGTAAGTTCATATGCAAATTATGCAATATGTAC-CATACTTTAAATGCTTTAATATTGCATGTAT
1 GGTAAGTTCATATGCAAATAATGCAATATGTACTC-TACTTTAAATGCTTAAATATTACATGTAT
*
52486366 GGTAAGTACATAT
1 GGTAAGTTCATAT
52486379 ATAATTAATG
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
63 1 0.01
64 67 0.99
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.38
Consensus pattern (64 bp):
GGTAAGTTCATATGCAAATAATGCAATATGTACTCTACTTTAAATGCTTAAATATTACATGTAT
Found at i:52490141 original size:24 final size:25
Alignment explanation
Indices: 52490114--52490200 Score: 117
Period size: 24 Copynumber: 3.6 Consensus size: 25
52490104 AAGGAAATTC
52490114 GCACACATAGTGCCATGCTAA-CCA
1 GCACACATAGTGCCATGCTAATCCA
*
52490138 GCACACATAGTGCCTTGCTAATCCA
1 GCACACATAGTGCCATGCTAATCCA
* * *
52490163 -CACACGTAGTGCCATTCAAATCC-
1 GCACACATAGTGCCATGCTAATCCA
52490186 GCACACATAGTGCCA
1 GCACACATAGTGCCA
52490201 ATGTCATTTC
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
24 52 0.95
25 3 0.05
ACGTcount: A:0.31, C:0.33, G:0.16, T:0.20
Consensus pattern (25 bp):
GCACACATAGTGCCATGCTAATCCA
Found at i:52491544 original size:17 final size:17
Alignment explanation
Indices: 52491518--52491551 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
52491508 CCCCACTTAA
* *
52491518 TATATTATAACTTATTT
1 TATATAATAACATATTT
52491535 TATATAATAACATATTT
1 TATATAATAACATATTT
52491552 CAAATATATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATAATAACATATTT
Found at i:52495657 original size:28 final size:28
Alignment explanation
Indices: 52495583--52495710 Score: 166
Period size: 28 Copynumber: 4.5 Consensus size: 28
52495573 CATGAGATTG
* * **
52495583 GCACTAAGTGTGCGGGTTTAAATTGCATA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
* *
52495612 GCACTAAGTATGCAAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
52495640 GCACTAAGTGTGCGAGTTTGATTATGTAA
1 GCACTAAGTGTGCGAGTTTGATTATAT-A
52495669 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
52495697 ACACTAAGTGTGCG
1 GCACTAAGTGTGCG
52495711 GACTTACTAT
Statistics
Matches: 87, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
28 44 0.51
29 43 0.49
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:52495672 original size:57 final size:57
Alignment explanation
Indices: 52495583--52495710 Score: 177
Period size: 57 Copynumber: 2.2 Consensus size: 57
52495573 CATGAGATTG
*
52495583 GCACTAAGTGTGCGGGTTTAAATTGCATAGCACTAAGTATGCAAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTAAATTGCATAGCACTAAGTATGCAAGTTTGATTATATA
* * * * *
52495640 GCACTAAGTGTGCGAGTTTGATTATGTA-AGCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTAAAT-TGCATAGCACTAAGTATGCAAGTTTGATTATATA
*
52495697 ACACTAAGTGTGCG
1 GCACTAAGTGTGCG
52495711 GACTTACTAT
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
57 60 0.95
58 3 0.05
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (57 bp):
GCACTAAGTGTGCGAGTTTAAATTGCATAGCACTAAGTATGCAAGTTTGATTATATA
Found at i:52501116 original size:24 final size:24
Alignment explanation
Indices: 52501085--52501217 Score: 131
Period size: 24 Copynumber: 5.5 Consensus size: 24
52501075 GGAAATTCGT
* *
52501085 ACACATAGTGCCATGCTAACCCGC
1 ACACATAGTGCCATGCAAATCCGC
* * *
52501109 ACACATAGTGCCTTGCTAATCCAC
1 ACACATAGTGCCATGCAAATCCGC
** * *
52501133 ACATGTAGTGCCATTCAAATCCGT
1 ACACATAGTGCCATGCAAATCCGC
* * * *
52501157 ACATACAGTGCCATTCAAATCTGC
1 ACACATAGTGCCATGCAAATCCGC
* *
52501181 ACACATAGTGCCATACAAATCCAC
1 ACACATAGTGCCATGCAAATCCGC
52501205 ACACATAGTGCCA
1 ACACATAGTGCCA
52501218 ATGTCATATC
Statistics
Matches: 90, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 90 1.00
ACGTcount: A:0.33, C:0.32, G:0.14, T:0.22
Consensus pattern (24 bp):
ACACATAGTGCCATGCAAATCCGC
Found at i:52502557 original size:17 final size:17
Alignment explanation
Indices: 52502535--52502568 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
52502525 CCCCACTTAA
*
52502535 TATATTATAACTTATTT
1 TATATTATAACATATTT
52502552 TATATTATAACATATTT
1 TATATTATAACATATTT
52502569 CAAATATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (17 bp):
TATATTATAACATATTT
Found at i:52508209 original size:19 final size:20
Alignment explanation
Indices: 52508185--52508222 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
52508175 GGTACCACCA
52508185 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
52508204 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
52508223 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:52508566 original size:93 final size:93
Alignment explanation
Indices: 52508451--52508621 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
52508441 GCCCCTAAGT
*
52508451 GAACTCGGACTCAACTCAACGAGCTC-GAGCGTTCGCATCCATAAATGAACACAGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTCGGA-CATTCGCATCCATAAATGAACACAGACTCAACTCA
52508515 ACGAGTTCGGATGCCTAATTACATCTCAC
65 ACGAGTTCGGATGCCTAATTACATCTCAC
* * * * *
52508544 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACACAGACTCAACTCAA
52508609 CGAGTTCGGATGC
66 CGAGTTCGGATGC
52508622 TCAACCATCC
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
93 69 0.97
94 2 0.03
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACACAGACTCAACTCAA
CGAGTTCGGATGCCTAATTACATCTCAC
Found at i:52508611 original size:46 final size:47
Alignment explanation
Indices: 52508446--52508618 Score: 194
Period size: 46 Copynumber: 3.7 Consensus size: 47
52508436 AACTCGCCCC
* * *
52508446 TAAGTGAACTCGGACTCAACTCAACGAGCTC-GAGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATTTGCATCCA
* * * * *
52508492 TAAATGAACACAGACTCAACTCAACGAGTTCGGATGCCTAATTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA-G-C-ATTTGCATCCA
* *
52508540 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA-CATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATTTGCATCCA
52508585 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
52508619 TGCTCAACCA
Statistics
Matches: 104, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 56 0.54
47 29 0.28
48 3 0.03
49 2 0.02
50 4 0.04
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21
Consensus pattern (47 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATTTGCATCCA
Found at i:52513626 original size:39 final size:39
Alignment explanation
Indices: 52513572--52513647 Score: 143
Period size: 39 Copynumber: 1.9 Consensus size: 39
52513562 CACCACACTA
*
52513572 CTGGCACTCGGGTTTAACAAATCTCGAGTTCCCTACATG
1 CTGGCACTCGGGTTTAACAAATCTCGAGCTCCCTACATG
52513611 CTGGCACTCGGGTTTAACAAATCTCGAGCTCCCTACA
1 CTGGCACTCGGGTTTAACAAATCTCGAGCTCCCTACA
52513648 CTGGCTGTAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (39 bp):
CTGGCACTCGGGTTTAACAAATCTCGAGCTCCCTACATG
Found at i:52515817 original size:19 final size:20
Alignment explanation
Indices: 52515793--52515830 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
52515783 GGTACCACCA
52515793 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
52515812 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
52515831 ACCCCCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:52516125 original size:46 final size:46
Alignment explanation
Indices: 52516058--52516179 Score: 190
Period size: 46 Copynumber: 2.7 Consensus size: 46
52516048 TGCCCCTAAG
* * * *
52516058 TGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAA
1 TGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAA
* *
52516104 TGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAG
1 TGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAA
52516150 TGAACTCGGACTCAACTCAACGAGTTCGGA
1 TGAACTCGGACTCAACTCAACGAGTTCGGA
52516180 TGCTCAACCA
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 70 1.00
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.21
Consensus pattern (46 bp):
TGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAA
Found at i:52534465 original size:47 final size:47
Alignment explanation
Indices: 52534396--52534489 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
52534386 GAATTCTCGC
52534396 CTATACAAGGAAGCAACGAAGTGCCGCCACGACGCTCGTTTAAAACA
1 CTATACAAGGAAGCAACGAAGTGCCGCCACGACGCTCGTTTAAAACA
52534443 CTATACAAGGAAGCAACGAAGTGCCGCCACGACGCTCGTTTAAAACA
1 CTATACAAGGAAGCAACGAAGTGCCGCCACGACGCTCGTTTAAAACA
52534490 ACACAAGCAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.36, C:0.28, G:0.21, T:0.15
Consensus pattern (47 bp):
CTATACAAGGAAGCAACGAAGTGCCGCCACGACGCTCGTTTAAAACA
Found at i:52538372 original size:27 final size:26
Alignment explanation
Indices: 52538324--52538375 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
52538314 GCGAGGCTGC
*
52538324 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
52538350 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
52538376 TTGCAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:52545691 original size:27 final size:26
Alignment explanation
Indices: 52545643--52545702 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
52545633 GCGAGGCTGC
*
52545643 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
52545670 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
52545696 CAGATAT
1 CAGATAT
52545703 ATATATGTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:52549395 original size:24 final size:24
Alignment explanation
Indices: 52549368--52549503 Score: 123
Period size: 24 Copynumber: 5.7 Consensus size: 24
52549358 GAAATGACTT
*
52549368 TGGCACAATGTGTGCGAATTTGAA
1 TGGCACTATGTGTGCGAATTTGAA
*
52549392 TGGCACTATGTGTGCGAATTTGTA
1 TGGCACTATGTGTGCGAATTTGAA
* * * *
52549416 CGGCACTATGTGTGCGGATATGTA
1 TGGCACTATGTGTGCGAATTTGAA
* * *
52549440 TGACACTATGTGTGCGGATTTTAA
1 TGGCACTATGTGTGCGAATTTGAA
* * * *
52549464 TGTCAATATGTATGTGAATTACT-AA
1 TGGCACTATGTGTGCGAATT--TGAA
52549489 -GGCACTATGTGTGCG
1 TGGCACTATGTGTGCG
52549504 GGTAAACATG
Statistics
Matches: 91, Mismatches: 19, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
24 88 0.97
25 2 0.02
26 1 0.01
ACGTcount: A:0.25, C:0.13, G:0.28, T:0.34
Consensus pattern (24 bp):
TGGCACTATGTGTGCGAATTTGAA
Found at i:52549653 original size:24 final size:24
Alignment explanation
Indices: 52549596--52549725 Score: 104
Period size: 24 Copynumber: 5.4 Consensus size: 24
52549586 CCATGTTTAC
* **
52549596 CCGCACACATAGTGCCTTAGTAAT
1 CCGCACACATAGTGCATTACAAAT
* * * *
52549620 TCACATACATATTGACATTA-AAAT
1 CCGCACACATAGTG-CATTACAAAT
*
52549644 CCGCACACATAGTGTCA-TACATAT
1 CCGCACACATAGTG-CATTACAAAT
**
52549668 CCGCACACATAGTGCCGTACAAAT
1 CCGCACACATAGTGCATTACAAAT
*
52549692 TCGCACACATAGTGCCATT-CAAAT
1 CCGCACACATAGTG-CATTACAAAT
*
52549716 TCGCACACAT
1 CCGCACACAT
52549726 TTTCATCGTT
Statistics
Matches: 85, Mismatches: 17, Indels: 8
0.77 0.15 0.07
Matches are distributed among these distances:
23 3 0.04
24 76 0.89
25 6 0.07
ACGTcount: A:0.35, C:0.28, G:0.12, T:0.25
Consensus pattern (24 bp):
CCGCACACATAGTGCATTACAAAT
Found at i:52549678 original size:48 final size:48
Alignment explanation
Indices: 52549596--52549725 Score: 118
Period size: 48 Copynumber: 2.7 Consensus size: 48
52549586 CCATGTTTAC
* ** * * * * *
52549596 CCGCACACATAGTGCCTTAGTAATTCACATACATATTGACATTA-AAAT
1 CCGCACACATAGTGCCATACAAATCCGCACACATAGTG-CAGTACAAAT
* * *
52549644 CCGCACACATAGTGTCATACATATCCGCACACATAGTGCCGTACAAAT
1 CCGCACACATAGTGCCATACAAATCCGCACACATAGTGCAGTACAAAT
* * *
52549692 TCGCACACATAGTGCCATTCAAATTCGCACACAT
1 CCGCACACATAGTGCCATACAAATCCGCACACAT
52549726 TTTCATCGTT
Statistics
Matches: 65, Mismatches: 16, Indels: 2
0.78 0.19 0.02
Matches are distributed among these distances:
47 3 0.05
48 62 0.95
ACGTcount: A:0.35, C:0.28, G:0.12, T:0.25
Consensus pattern (48 bp):
CCGCACACATAGTGCCATACAAATCCGCACACATAGTGCAGTACAAAT
Found at i:52553209 original size:54 final size:54
Alignment explanation
Indices: 52553103--52553210 Score: 164
Period size: 54 Copynumber: 2.0 Consensus size: 54
52553093 GCCACGCAAC
* *
52553103 CGCTCTTACTTCCATATTAGATTATTAATTTATAAGTATTTTAAATTGGGTATT
1 CGCTCTTACTTCCATATTAGATTATTAATTCATAAGTATTTTAAATTAGGTATT
* *
52553157 CGCTCTTACTTCCATATTAGATTTTTAATTCATAAGTAGTTTT-ATTTAGGTATT
1 CGCTCTTACTTCCATATTAGATTATTAATTCATAAGTA-TTTTAAATTAGGTATT
52553211 TTTATGTAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
54 45 0.92
55 4 0.08
ACGTcount: A:0.28, C:0.12, G:0.11, T:0.49
Consensus pattern (54 bp):
CGCTCTTACTTCCATATTAGATTATTAATTCATAAGTATTTTAAATTAGGTATT
Found at i:52554540 original size:10 final size:10
Alignment explanation
Indices: 52554527--52554556 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
52554517 TGTTTGACCG
52554527 AGTTTGAATA
1 AGTTTGAATA
52554537 AGTTTGAATA
1 AGTTTGAATA
52554547 AGTTTGAATA
1 AGTTTGAATA
52554557 TATTTATTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (10 bp):
AGTTTGAATA
Found at i:52555875 original size:17 final size:19
Alignment explanation
Indices: 52555853--52555889 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
52555843 TTGGGTTTAT
52555853 TGGG-CCACACGGG-CGTG
1 TGGGCCCACACGGGCCGTG
*
52555870 TGGGCCCACATGGGCCGTG
1 TGGGCCCACACGGGCCGTG
52555889 T
1 T
52555890 TATGGGCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 4 0.24
18 8 0.47
19 5 0.29
ACGTcount: A:0.11, C:0.30, G:0.43, T:0.16
Consensus pattern (19 bp):
TGGGCCCACACGGGCCGTG
Done.