Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000846.1 Hibiscus syriacus cultivar Beakdansim tig00001630_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: 988667
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 5
Found at i:8812 original size:17 final size:17
Alignment explanation
Indices: 8790--8826 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
8780 TCATTTATCT
8790 TTCACATTAATCTATAC
1 TTCACATTAATCTATAC
8807 TTCACATTAATCTATAC
1 TTCACATTAATCTATAC
8824 TTC
1 TTC
8827 TGTTGGTGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.43
Consensus pattern (17 bp):
TTCACATTAATCTATAC
Found at i:11841 original size:13 final size:13
Alignment explanation
Indices: 11820--11874 Score: 74
Period size: 13 Copynumber: 4.2 Consensus size: 13
11810 AATGATGCGC
*
11820 AATGAGCGTCATA
1 AATGTGCGTCATA
*
11833 AATGCGCGTCATA
1 AATGTGCGTCATA
*
11846 AATGTGTGTCATA
1 AATGTGCGTCATA
*
11859 AATGTGCATCATA
1 AATGTGCGTCATA
11872 AAT
1 AAT
11875 TTATGACGCA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (13 bp):
AATGTGCGTCATA
Found at i:12196 original size:45 final size:45
Alignment explanation
Indices: 12003--12198 Score: 207
Period size: 45 Copynumber: 4.3 Consensus size: 45
11993 ATAGTAGTGG
* * *
12003 CACTTACTTTAGAAGTGACACAATATTTGTATGATATTTTTGTAGCA
1 CACTTACTTTGGAAGTGTCA-AATAGTTGTATGATA-TTTTGTAGCA
* *
12050 CACTTACTTTGAAAGTGGCAAATAGTTGTATGATATTTTGT-GACA
1 CACTTACTTTGGAAGTGTCAAATAGTTGTATGATATTTTGTAG-CA
* * * *
12095 CACTTACTTTTGATGTGGT-GAATAGTTATATGATATTTTGTAGCA
1 CACTTACTTTGGAAGT-GTCAAATAGTTGTATGATATTTTGTAGCA
*** * * *
12140 CACTCGTTTTGGAAGTGTCAAACAATTGTATGATGTTTTGTAGCA
1 CACTTACTTTGGAAGTGTCAAATAGTTGTATGATATTTTGTAGCA
12185 CACTTACTTTGGAA
1 CACTTACTTTGGAA
12199 ATTTTCTTTA
Statistics
Matches: 122, Mismatches: 23, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
44 3 0.02
45 86 0.70
46 16 0.13
47 17 0.14
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (45 bp):
CACTTACTTTGGAAGTGTCAAATAGTTGTATGATATTTTGTAGCA
Found at i:13071 original size:23 final size:20
Alignment explanation
Indices: 13006--13058 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
12996 AATAAAATAA
* * *
13006 TATTAT-ATATTTTTAATAT
1 TATTATAATATATTCAATTT
*
13025 TATTATAATATATTCAATTA
1 TATTATAATATATTCAATTT
13045 TATTATAATCATAT
1 TATTATAAT-ATAT
13059 ATGATATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 6 0.21
20 18 0.64
21 4 0.14
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (20 bp):
TATTATAATATATTCAATTT
Found at i:13111 original size:21 final size:22
Alignment explanation
Indices: 13082--13122 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
13072 CTTTTTTATA
13082 ATATATAATA-AATTTATTAAC
1 ATATATAATATAATTTATTAAC
* *
13103 ATATTTAATATTATTTATTA
1 ATATATAATATAATTTATTA
13123 TTTTAATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
ATATATAATATAATTTATTAAC
Found at i:13232 original size:15 final size:15
Alignment explanation
Indices: 13212--13245 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
13202 ACTTAAAATA
* *
13212 TAATATTTTTATTTT
1 TAATATTATTAATTT
13227 TAATATTATTAATTT
1 TAATATTATTAATTT
13242 TAAT
1 TAAT
13246 TTCATAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TAATATTATTAATTT
Found at i:16041 original size:13 final size:13
Alignment explanation
Indices: 16023--16048 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16013 TTAAAGTTAG
16023 TATATATATATTT
1 TATATATATATTT
16036 TATATATATATTT
1 TATATATATATTT
16049 AATTTTAATT
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TATATATATATTT
Found at i:18631 original size:31 final size:31
Alignment explanation
Indices: 18593--18661 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
18583 GAGTCGATGG
*
18593 TTACCTATGCTCTTCGGGACATATGGACTGA
1 TTACCTATGCTCTTCAGGACATATGGACTGA
*
18624 TTACCTATGTTCTTCAGGACATATGGACTGA
1 TTACCTATGCTCTTCAGGACATATGGACTGA
*
18655 TCACCTA
1 TTACCTA
18662 GGTTCTTATA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (31 bp):
TTACCTATGCTCTTCAGGACATATGGACTGA
Found at i:18667 original size:31 final size:31
Alignment explanation
Indices: 18603--18668 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
18593 TTACCTATGC
* * *
18603 TCTTCGGGACATATGGACTGATTACCTATGT
1 TCTTCAGGACATATGGACTGATCACCTAGGT
18634 TCTTCAGGACATATGGACTGATCACCTAGGT
1 TCTTCAGGACATATGGACTGATCACCTAGGT
18665 TCTT
1 TCTT
18669 ATAGACCTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (31 bp):
TCTTCAGGACATATGGACTGATCACCTAGGT
Found at i:18680 original size:31 final size:31
Alignment explanation
Indices: 18610--18684 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 31
18600 TGCTCTTCGG
* * *
18610 GACATATGGACTGATTACCTATGTTCTTCAG
1 GACATATGGACTGATCACCTAGGTTCTTCAA
18641 GACATATGGACTGATCACCTAGGTTCTT-ATA
1 GACATATGGACTGATCACCTAGGTTCTTCA-A
*
18672 GACCTATGGACTG
1 GACATATGGACTG
18685 GTCCTTCGGG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 1 0.03
31 38 0.97
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (31 bp):
GACATATGGACTGATCACCTAGGTTCTTCAA
Found at i:22052 original size:29 final size:31
Alignment explanation
Indices: 22018--22075 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
22008 CAAGCCTAAG
* *
22018 AAAATTT-GGGGAC-CATTCTATAATTTTTT
1 AAAATTTGGGGGACTAATTCAATAATTTTTT
22047 AAAATTTGGGGGACTAATTCAATAATTTT
1 AAAATTTGGGGGACTAATTCAATAATTTT
22076 AGAAAAGTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 7 0.28
30 6 0.24
31 12 0.48
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.41
Consensus pattern (31 bp):
AAAATTTGGGGGACTAATTCAATAATTTTTT
Found at i:22076 original size:29 final size:28
Alignment explanation
Indices: 22018--22075 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 28
22008 CAAGCCTAAG
* *
22018 AAAATTTGGGGACCATTCTATAATTTTTT
1 AAAATTTGGGGACAATTCAATAA-TTTTT
22047 AAAATTTGGGGGACTAATTCAATAATTTT
1 AAAATTT-GGGGAC-AATTCAATAATTTT
22076 AGAAAAGTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 7 0.28
30 10 0.40
31 8 0.32
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.41
Consensus pattern (28 bp):
AAAATTTGGGGACAATTCAATAATTTTT
Found at i:23039 original size:31 final size:31
Alignment explanation
Indices: 23001--23069 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
22991 GAGTCGAGGG
*
23001 TTACCTATGTTCTTCGGGACATATGAACTGA
1 TTACCTATGTTCTTCGAGACATATGAACTGA
* *
23032 TTACCTATGTTCTTTGAGACATATGGACTGA
1 TTACCTATGTTCTTCGAGACATATGAACTGA
23063 TTACCTA
1 TTACCTA
23070 GGTTTTTATA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGAGACATATGAACTGA
Found at i:23088 original size:31 final size:31
Alignment explanation
Indices: 23001--23092 Score: 105
Period size: 31 Copynumber: 3.0 Consensus size: 31
22991 GAGTCGAGGG
* * * *
23001 TTACCTATGTTCTTCGGGACATATGAACTGA
1 TTACCTAGGTTCTTTGAGACATATGGACTGA
*
23032 TTACCTATGTTCTTTGAGACATATGGACTGA
1 TTACCTAGGTTCTTTGAGACATATGGACTGA
* *
23063 TTACCTAGGTT-TTTATAGACCTATGGACTG
1 TTACCTAGGTTCTTT-GAGACATATGGACTG
23093 GTCCTTCGGG
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
30 3 0.06
31 51 0.94
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (31 bp):
TTACCTAGGTTCTTTGAGACATATGGACTGA
Found at i:23309 original size:18 final size:18
Alignment explanation
Indices: 23286--23328 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
23276 TGCATTAATA
23286 ATAATGATAG-AGATGTTG
1 ATAATGAT-GTAGATGTTG
*
23304 ATAATGATGTTGATGTTG
1 ATAATGATGTAGATGTTG
23322 ATAATGA
1 ATAATGA
23329 GAGTATATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 1 0.04
18 22 0.96
ACGTcount: A:0.37, C:0.00, G:0.26, T:0.37
Consensus pattern (18 bp):
ATAATGATGTAGATGTTG
Found at i:25395 original size:277 final size:277
Alignment explanation
Indices: 24901--25454 Score: 1099
Period size: 277 Copynumber: 2.0 Consensus size: 277
24891 AAAATGAACC
24901 AAAGGAGAATGACTCAATCATTTGCTACGAATGCAAAAAGCCCAGGCATGTCAAATACGATTTCC
1 AAAGGAGAATGACTCAATCATTTGCTACGAATGCAAAAAGCCCAGGCATGTCAAATACGATTTCC
24966 CGTAATTAAAAAAAATGGTCAATCCAAGAAGAAACACAAGGCACACGTGGCTACTTGGAGTGATG
66 CGTAATTAAAAAAAATGGTCAATCCAAGAAGAAACACAAGGCACACGTGGCTACTTGGAGTGATG
25031 ATGATGAGTCATCAAATGAAGAGGAACAAGAAGTAGTGAATCTGTGCTTGATGGCCACCGAGGAA
131 ATGATGAGTCATCAAATGAAGAGGAACAAGAAGTAGTGAATCTGTGCTTGATGGCCACCGAGGAA
25096 GATTCTCAGGTAATATCTAATTCATTAGATTTCGAAGATTATTCATTTGATGAGTTCGTAGAGGA
196 GATTCTCAGGTAATATCTAATTCATTAGATTTCGAAGATTATTCATTTGATGAGTTCGTAGAGGA
25161 ATTTACTAGGTTGGCTT
261 ATTTACTAGGTTGGCTT
25178 AAAGGAGAATGACTCAATCATTTGCTACGAATGCAAAAAGCCCAGGCATGTCAAATACGATTTCC
1 AAAGGAGAATGACTCAATCATTTGCTACGAATGCAAAAAGCCCAGGCATGTCAAATACGATTTCC
25243 CGTAATTAAAAAAAATGGTCAATCCAAGAAGAAACACAAGGCACACGTGGCTACTTGGAGTGATG
66 CGTAATTAAAAAAAATGGTCAATCCAAGAAGAAACACAAGGCACACGTGGCTACTTGGAGTGATG
25308 ATGATGAGTCATCAAATGAAGAGGAACAAGAAGTAGTGAATCTGTGCTTGATGGCCACCGAGGAA
131 ATGATGAGTCATCAAATGAAGAGGAACAAGAAGTAGTGAATCTGTGCTTGATGGCCACCGAGGAA
*
25373 GATTCTCAGGTAATATCTAATTCATTAGATTTCGAAGATTATTCTTTTGATGAGTTCGTAGAGGA
196 GATTCTCAGGTAATATCTAATTCATTAGATTTCGAAGATTATTCATTTGATGAGTTCGTAGAGGA
25438 ATTTACTAGGTTGGCTT
261 ATTTACTAGGTTGGCTT
25455 CGGATTATGA
Statistics
Matches: 276, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
277 276 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.26
Consensus pattern (277 bp):
AAAGGAGAATGACTCAATCATTTGCTACGAATGCAAAAAGCCCAGGCATGTCAAATACGATTTCC
CGTAATTAAAAAAAATGGTCAATCCAAGAAGAAACACAAGGCACACGTGGCTACTTGGAGTGATG
ATGATGAGTCATCAAATGAAGAGGAACAAGAAGTAGTGAATCTGTGCTTGATGGCCACCGAGGAA
GATTCTCAGGTAATATCTAATTCATTAGATTTCGAAGATTATTCATTTGATGAGTTCGTAGAGGA
ATTTACTAGGTTGGCTT
Found at i:29393 original size:23 final size:23
Alignment explanation
Indices: 29325--29393 Score: 70
Period size: 23 Copynumber: 3.1 Consensus size: 23
29315 AAGTGTACCG
**
29325 ATGCATTCCTTGAATATGCATTG
1 ATGCATTCCTTGAATATGCATCA
* * * *
29348 ATGCACT-C-TGAAGATGAACCA
1 ATGCATTCCTTGAATATGCATCA
29369 ATGCATTCCTTGAATATGCATCA
1 ATGCATTCCTTGAATATGCATCA
29392 AT
1 AT
29394 ACACTCTATA
Statistics
Matches: 34, Mismatches: 10, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
21 14 0.41
22 2 0.06
23 18 0.53
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (23 bp):
ATGCATTCCTTGAATATGCATCA
Found at i:31686 original size:12 final size:13
Alignment explanation
Indices: 31660--31688 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
31650 GGGAATAGTA
31660 ATTTCAAAAATTG
1 ATTTCAAAAATTG
31673 ATTTCAAAAA-TG
1 ATTTCAAAAATTG
31685 ATTT
1 ATTT
31689 TTCAAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (13 bp):
ATTTCAAAAATTG
Found at i:32108 original size:64 final size:65
Alignment explanation
Indices: 32034--32189 Score: 199
Period size: 65 Copynumber: 2.4 Consensus size: 65
32024 ACACCCTAAT
* * * *
32034 TCGAATGCATTTTGTGTATCGATGCACAGTC-ATGCATCGATGCACTCCT-GATTTTATTAAAAC
1 TCGAATGCATTTTGTGTACCGATGCACAGACAATGCATCGATACACTCCTGGATCTT-TTAAAAC
32097 A
65 A
* * *
32098 TCGAATGCATTTTATGTACCGATGCACAGACAATGCATTGATACACTCCTGGATCTTTTGAAACA
1 TCGAATGCATTTTGTGTACCGATGCACAGACAATGCATCGATACACTCCTGGATCTTTTAAAACA
* * *
32163 TCGAATGTAATTAGTGTACCGATGCAC
1 TCGAATGCATTTTGTGTACCGATGCAC
32190 CCCAAGTGTC
Statistics
Matches: 79, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 28 0.35
65 46 0.58
66 5 0.06
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (65 bp):
TCGAATGCATTTTGTGTACCGATGCACAGACAATGCATCGATACACTCCTGGATCTTTTAAAACA
Found at i:38689 original size:22 final size:22
Alignment explanation
Indices: 38661--38732 Score: 117
Period size: 22 Copynumber: 3.3 Consensus size: 22
38651 TTATTTTTTT
38661 GGTCAAAGTCAACGGTCAGACC
1 GGTCAAAGTCAACGGTCAGACC
*
38683 GGTCAAAGTCAACGGTCAGACA
1 GGTCAAAGTCAACGGTCAGACC
* *
38705 GGTCAAAGTCAATGGTCATACC
1 GGTCAAAGTCAACGGTCAGACC
38727 GGTCAA
1 GGTCAA
38733 CAAGTCAGGT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.33, C:0.24, G:0.26, T:0.17
Consensus pattern (22 bp):
GGTCAAAGTCAACGGTCAGACC
Found at i:40360 original size:27 final size:27
Alignment explanation
Indices: 40330--40383 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
40320 TAGACTGCTT
*
40330 CCACACCTCTTGCACCATATGCTAAAC
1 CCACACCTCTTGAACCATATGCTAAAC
*
40357 CCACACCTCTTGAACCATATGTTAAAC
1 CCACACCTCTTGAACCATATGCTAAAC
40384 TTGACAGACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.31, C:0.37, G:0.07, T:0.24
Consensus pattern (27 bp):
CCACACCTCTTGAACCATATGCTAAAC
Found at i:41784 original size:18 final size:18
Alignment explanation
Indices: 41757--41802 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
41747 ACCGGTCACA
41757 ACCCGACCCGACCAGTTG
1 ACCCGACCCGACCAGTTG
* * *
41775 ACCTGACCCGACCCGTTT
1 ACCCGACCCGACCAGTTG
41793 ACCCGACCCG
1 ACCCGACCCG
41803 TTGACTCGAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.20, C:0.48, G:0.20, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCAGTTG
Found at i:41796 original size:13 final size:13
Alignment explanation
Indices: 41778--41823 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
41768 CCAGTTGACC
41778 TGACCCGACCCGT
1 TGACCCGACCCGT
*
41791 TTACCCGACCCGT
1 TGACCCGACCCGT
*
41804 TGACTCGACCCGT
1 TGACCCGACCCGT
41817 TGACCCG
1 TGACCCG
41824 TTGACCGTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.15, C:0.43, G:0.22, T:0.20
Consensus pattern (13 bp):
TGACCCGACCCGT
Found at i:41814 original size:18 final size:18
Alignment explanation
Indices: 41760--41815 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
41750 GGTCACAACC
*
41760 CGACCCGACCAGTTGAC-
1 CGACCCGACCCGTTGACT
41777 CTGACCCGACCCGTT---T
1 C-GACCCGACCCGTTGACT
41793 --ACCCGACCCGTTGACT
1 CGACCCGACCCGTTGACT
41809 CGACCCG
1 CGACCCG
41816 TTGACCCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 13
0.69 0.02 0.29
Matches are distributed among these distances:
13 12 0.39
16 1 0.03
17 1 0.03
18 17 0.55
ACGTcount: A:0.18, C:0.45, G:0.21, T:0.16
Consensus pattern (18 bp):
CGACCCGACCCGTTGACT
Found at i:41823 original size:8 final size:8
Alignment explanation
Indices: 41810--41843 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
41800 CCGTTGACTC
41810 GACCCGTT
1 GACCCGTT
41818 GACCCGTT
1 GACCCGTT
41826 GA-CCGTT
1 GACCCGTT
*
41833 GACTCGTT
1 GACCCGTT
41841 GAC
1 GAC
41844 TGGCGTTGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
7 7 0.29
8 17 0.71
ACGTcount: A:0.15, C:0.32, G:0.26, T:0.26
Consensus pattern (8 bp):
GACCCGTT
Found at i:41833 original size:15 final size:15
Alignment explanation
Indices: 41813--41843 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
41803 TTGACTCGAC
41813 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
*
41828 CCGTTGACTCGTTGA
1 CCGTTGACCCGTTGA
41843 C
1 C
41844 TGGCGTTGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.32, G:0.26, T:0.29
Consensus pattern (15 bp):
CCGTTGACCCGTTGA
Found at i:44345 original size:24 final size:23
Alignment explanation
Indices: 44318--44373 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
44308 AATTATTTTA
*
44318 TCTGATTTTCGACTTGAATTCTGT
1 TCTGATTTT-GACCTGAATTCTGT
**
44342 TCTGATACATGACCTGAATTCTGT
1 TCTGAT-TTTGACCTGAATTCTGT
*
44366 TCTAATTT
1 TCTGATTT
44374 CTTATATGGA
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.21, C:0.18, G:0.14, T:0.46
Consensus pattern (23 bp):
TCTGATTTTGACCTGAATTCTGT
Found at i:44388 original size:48 final size:48
Alignment explanation
Indices: 44335--44428 Score: 118
Period size: 48 Copynumber: 2.0 Consensus size: 48
44325 TTCGACTTGA
* *
44335 ATTCTGTTCTGATA-CATGACCTGAATTCTGTTCTAATTTCTTATATGG
1 ATTCTGTTCTAATATC-TGACCTGAATTCTGTTCTAATTTCTGATATGG
** * *
44383 ATTCTGTTCTAATATCTGTTCTGAATTCTGTTTTGATTTCTGATAT
1 ATTCTGTTCTAATATCTGACCTGAATTCTGTTCTAATTTCTGATAT
44429 CTCCGTTTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
48 38 0.97
49 1 0.03
ACGTcount: A:0.21, C:0.15, G:0.14, T:0.50
Consensus pattern (48 bp):
ATTCTGTTCTAATATCTGACCTGAATTCTGTTCTAATTTCTGATATGG
Found at i:44410 original size:24 final size:24
Alignment explanation
Indices: 44332--44414 Score: 80
Period size: 24 Copynumber: 3.5 Consensus size: 24
44322 ATTTTCGACT
* **
44332 TGAATTCTGTTCTGATA-CATGACC
1 TGAATTCTGTTCTAATATC-TGTTC
* *
44356 TGAATTCTGTTCTAATTTCT-TATA
1 TGAATTCTGTTCTAATATCTGT-TC
*
44380 TGGATTCTGTTCTAATATCTGTTC
1 TGAATTCTGTTCTAATATCTGTTC
44404 TGAATTCTGTT
1 TGAATTCTGTT
44415 TTGATTTCTG
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
24 45 0.96
25 2 0.04
ACGTcount: A:0.22, C:0.16, G:0.14, T:0.48
Consensus pattern (24 bp):
TGAATTCTGTTCTAATATCTGTTC
Found at i:44424 original size:24 final size:25
Alignment explanation
Indices: 44355--44430 Score: 84
Period size: 24 Copynumber: 3.1 Consensus size: 25
44345 GATACATGAC
44355 CTGAATTCTGTTCTAATTTCT-TAT
1 CTGAATTCTGTTCTAATTTCTGTAT
* * *
44379 ATGGATTCTGTTCTAATATCTGT-T
1 CTGAATTCTGTTCTAATTTCTGTAT
* *
44403 CTGAATTCTGTTTTGATTTCTGATAT
1 CTGAATTCTGTTCTAATTTCTG-TAT
44429 CT
1 CT
44431 CCGTTTAATG
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
24 36 0.88
25 2 0.05
26 3 0.07
ACGTcount: A:0.20, C:0.14, G:0.13, T:0.53
Consensus pattern (25 bp):
CTGAATTCTGTTCTAATTTCTGTAT
Found at i:46242 original size:41 final size:41
Alignment explanation
Indices: 46197--46307 Score: 145
Period size: 41 Copynumber: 2.7 Consensus size: 41
46187 ATTCACTTCA
* *
46197 ATAGTGACAAAAATAATTGTCTTCATAATTCACCAACTAAG
1 ATAGTGACAAAAATAATTGTCGTCACAATTCACCAACTAAG
* * *
46238 ATAGTGACAAACATAATTGTCGTCACAATTTACCATCTAAG
1 ATAGTGACAAAAATAATTGTCGTCACAATTCACCAACTAAG
*
46279 AGTAGTGAC-AAAAT-ATTTTCGTCACAATT
1 A-TAGTGACAAAAATAATTGTCGTCACAATT
46308 ATGAATAATA
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
40 14 0.23
41 41 0.66
42 7 0.11
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.31
Consensus pattern (41 bp):
ATAGTGACAAAAATAATTGTCGTCACAATTCACCAACTAAG
Found at i:60183 original size:20 final size:20
Alignment explanation
Indices: 60134--60189 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 20
60124 TACCGTAAGG
* *
60134 GGGTATCGGTACCATAGTAG
1 GGGTATCGATACCATAGTAA
*
60154 GGTAGTATCGATACCATGGTAA
1 GG--GTATCGATACCATAGTAA
60176 GGGTATCGATACCA
1 GGGTATCGATACCA
60190 AACAACATCG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 14 0.45
22 17 0.55
ACGTcount: A:0.29, C:0.16, G:0.30, T:0.25
Consensus pattern (20 bp):
GGGTATCGATACCATAGTAA
Found at i:60243 original size:95 final size:96
Alignment explanation
Indices: 60061--60246 Score: 259
Period size: 95 Copynumber: 1.9 Consensus size: 96
60051 TGATTCAATC
* * * * *
60061 AGTATCGATTCCATGGTAAGTGTATCGATACTAAACAAACATCGAATCTAATTTCGGTATTGATA
1 AGTATCGATACCATGGTAAGGGTATCGATACCAAACAAACATCGAACCTAATTTCGGTATCGATA
**
60126 CCGTAAGGGGGTATCGGTACCATAGTAGGGT
66 CCGTAAGGAAGTATCGGTACCATAGTAGGGT
*
60157 AGTATCGATACCATGGTAAGGGTATCGATACCAAAC-AACATCGAACCTAATTTTGGTATCGATA
1 AGTATCGATACCATGGTAAGGGTATCGATACCAAACAAACATCGAACCTAATTTCGGTATCGATA
* *
60221 CCCG-AAGTAAGTATTGGTACCATAGT
66 -CCGTAAGGAAGTATCGGTACCATAGT
60247 GTTGAAGTAT
Statistics
Matches: 79, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
95 43 0.54
96 36 0.46
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (96 bp):
AGTATCGATACCATGGTAAGGGTATCGATACCAAACAAACATCGAACCTAATTTCGGTATCGATA
CCGTAAGGAAGTATCGGTACCATAGTAGGGT
Found at i:61105 original size:79 final size:79
Alignment explanation
Indices: 60686--61081 Score: 614
Period size: 79 Copynumber: 5.0 Consensus size: 79
60676 AAATGAATGA
60686 AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGG
1 AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGG
* *
60751 TACATTGTTAGTAT
66 TACATTGTCAGCAT
60765 AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGG
1 AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGG
*
60830 TACATTGTCAACAT
66 TACATTGTCAGCAT
* * * *
60844 AAAAGAATAATGAATATGGGTGCATTATTGGCATGAAATGATGCCATAGCTAAAATGTATTTGGG
1 AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGG
60909 TACATTGTCAGCAT
66 TACATTGTCAGCAT
* * * * *
60923 AAAAGATTAATGCATATGGGTTCATTATTAGCATGAAAGGATGCCATAGTTAAAATGTATATGGG
1 AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGG
*
60988 CACATTGTCAGCAT
66 TACATTGTCAGCAT
* * * *
61002 CAAAGAATAATGCATATGGGTGCATTATTGGCATGAAATGATGCC-TTGCTGAAATGCATATGGG
1 AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGG
* *
61066 TGCATTTTCAGCAT
66 TACATTGTCAGCAT
61080 AA
1 AA
61082 GAGTATATTT
Statistics
Matches: 288, Mismatches: 29, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
78 27 0.09
79 261 0.91
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (79 bp):
AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGG
TACATTGTCAGCAT
Found at i:62414 original size:23 final size:23
Alignment explanation
Indices: 62373--62416 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
62363 AGAACAATTG
**
62373 TGTCTTTGTGACATTTTTTTCTC
1 TGTCTTTGTGACACATTTTTCTC
62396 TGTCTTTGTGACACATTTTTC
1 TGTCTTTGTGACACATTTTTC
62417 CTAATCTTTC
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:0.11, C:0.18, G:0.14, T:0.57
Consensus pattern (23 bp):
TGTCTTTGTGACACATTTTTCTC
Found at i:62424 original size:23 final size:23
Alignment explanation
Indices: 62375--62425 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
62365 AACAATTGTG
** *
62375 TCTTTGTGACATTTTTTTCTCTG
1 TCTTTGTGACACATTTTTCTCTA
62398 TCTTTGTGACACATTTTTC-CTAA
1 TCTTTGTGACACATTTTTCTCT-A
62421 TCTTT
1 TCTTT
62426 CTTAGTCATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 2 0.08
23 22 0.92
ACGTcount: A:0.14, C:0.20, G:0.10, T:0.57
Consensus pattern (23 bp):
TCTTTGTGACACATTTTTCTCTA
Found at i:63231 original size:2 final size:2
Alignment explanation
Indices: 63184--63223 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
63174 ACAATTTATG
* *
63184 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
63224 TGTATATAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
AT
Found at i:64240 original size:7 final size:7
Alignment explanation
Indices: 64228--64258 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
64218 TTTCTTAAAT
64228 AAATTTA
1 AAATTTA
64235 AAATTTA
1 AAATTTA
64242 AAATTTA
1 AAATTTA
64249 AAATTTA
1 AAATTTA
64256 AAA
1 AAA
64259 GAAACTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (7 bp):
AAATTTA
Found at i:67392 original size:28 final size:29
Alignment explanation
Indices: 67337--67394 Score: 84
Period size: 28 Copynumber: 2.0 Consensus size: 29
67327 GTCCAGACTC
67337 TACTAACATTTCTAACACTAACCACTAAT
1 TACTAACATTTCTAACACTAACCACTAAT
*
67366 TACTAACA-TT-TAACCACTAACCGCTAAT
1 TACTAACATTTCTAA-CACTAACCACTAAT
67394 T
1 T
67395 TTTATTTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 3 0.11
28 16 0.59
29 8 0.30
ACGTcount: A:0.40, C:0.28, G:0.02, T:0.31
Consensus pattern (29 bp):
TACTAACATTTCTAACACTAACCACTAAT
Found at i:67616 original size:14 final size:14
Alignment explanation
Indices: 67597--67632 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
67587 TTTTATTTTT
*
67597 TTTAATTTCAGTCC
1 TTTAATTTCAGTAC
*
67611 TTTAATTTCATTAC
1 TTTAATTTCAGTAC
67625 TTTAATTT
1 TTTAATTT
67633 ACTTTTTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.25, C:0.14, G:0.03, T:0.58
Consensus pattern (14 bp):
TTTAATTTCAGTAC
Found at i:69031 original size:54 final size:54
Alignment explanation
Indices: 68540--69032 Score: 718
Period size: 54 Copynumber: 9.1 Consensus size: 54
68530 TTTGCATCTA
* ** * * * *
68540 AGTGCCGATATGGAAATTCAAAAACTCATTATTAATTCTGTGGGTTGCACACAT
1 AGTGCCGATACGGTCATTCATAAACTCATTATGAACTCCGTGGGTTGCACACAT
* *
68594 AGTACTGATACGGTCATTCATAAACTCATTATGAACTCCGTGGGTTGCACACAT
1 AGTGCCGATACGGTCATTCATAAACTCATTATGAACTCCGTGGGTTGCACACAT
* * *
68648 AGTGTCGATACGGTCATTCATAAACTCATTATGAATTCTGTGGGTTGCACACAT
1 AGTGCCGATACGGTCATTCATAAACTCATTATGAACTCCGTGGGTTGCACACAT
* *
68702 AGTGCCGATATGGTCATTCATAAACTCATTATGAACTTCGTGGGTTGCACACAT
1 AGTGCCGATACGGTCATTCATAAACTCATTATGAACTCCGTGGGTTGCACACAT
* * *
68756 AGTGCTGATACGGTCATTCATAAACTCATTATGAATTCCATGGGTTGCACACAT
1 AGTGCCGATACGGTCATTCATAAACTCATTATGAACTCCGTGGGTTGCACACAT
* * *
68810 AGTGTCGATACGGTCATTCATAAACTAATTATGAACTTCGTGGGTTGCACACAT
1 AGTGCCGATACGGTCATTCATAAACTCATTATGAACTCCGTGGGTTGCACACAT
* * *
68864 AGTGCCGATACGGTCATTCATAAAC-CGATTATAAACTCTGTTGGTTGCACACAT
1 AGTGCCGATACGGTCATTCATAAACTC-ATTATGAACTCCGTGGGTTGCACACAT
* * * *
68918 AGTGGCGATACGGTCATTCATAAACTCATTATGAACTCTGTGGGTTGCATACAC
1 AGTGCCGATACGGTCATTCATAAACTCATTATGAACTCCGTGGGTTGCACACAT
*
68972 AGTGCCGATACGGTCATTCATAAACTCATTATGACCTCCGTGGGTTGCACACAT
1 AGTGCCGATACGGTCATTCATAAACTCATTATGAACTCCGTGGGTTGCACACAT
69026 AGTGCCG
1 AGTGCCG
69033 CTAGTACACA
Statistics
Matches: 391, Mismatches: 46, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
54 390 1.00
55 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (54 bp):
AGTGCCGATACGGTCATTCATAAACTCATTATGAACTCCGTGGGTTGCACACAT
Found at i:74612 original size:24 final size:24
Alignment explanation
Indices: 74583--74654 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 24
74573 ATTCAAGAAA
74583 CATGACTTTTGAAGAACCAATAGT
1 CATGACTTTTGAAGAACCAATAGT
* ** * *
74607 CGTGACTTTTGGTGATCCACA-AGA
1 CATGACTTTTGAAGAACCA-ATAGT
*
74631 CATGTCTTTTGAAGAACCAATAGT
1 CATGACTTTTGAAGAACCAATAGT
74655 TATGTCCCTT
Statistics
Matches: 35, Mismatches: 11, Indels: 4
0.70 0.22 0.08
Matches are distributed among these distances:
23 1 0.03
24 33 0.94
25 1 0.03
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (24 bp):
CATGACTTTTGAAGAACCAATAGT
Found at i:80612 original size:21 final size:19
Alignment explanation
Indices: 80574--80619 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
80564 AATTAATCCT
80574 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
80594 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
80615 A-TAAT
1 ACTAAT
80620 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:82359 original size:33 final size:33
Alignment explanation
Indices: 82317--82383 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
82307 AAACTTAAAG
82317 TAAGCACTTCTAAGTTGTCAAGGAAACAAATTA
1 TAAGCACTTCTAAGTTGTCAAGGAAACAAATTA
* *
82350 TAAGCACTTCTAGGTTGTCAAGGCAACAAATTA
1 TAAGCACTTCTAAGTTGTCAAGGAAACAAATTA
82383 T
1 T
82384 TCATCAGGCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.28
Consensus pattern (33 bp):
TAAGCACTTCTAAGTTGTCAAGGAAACAAATTA
Found at i:96234 original size:15 final size:16
Alignment explanation
Indices: 96214--96251 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
96204 GAAAAATTTG
96214 AGAAAATTTG-GAGAA
1 AGAAAATTTGAGAGAA
*
96229 AGAAAAATTGAGAGAA
1 AGAAAATTTGAGAGAA
96245 AGAAAAT
1 AGAAAAT
96252 AGGAGTTTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.61, C:0.00, G:0.24, T:0.16
Consensus pattern (16 bp):
AGAAAATTTGAGAGAA
Found at i:98775 original size:12 final size:12
Alignment explanation
Indices: 98758--98791 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
98748 GTAATGAATA
*
98758 TATATATATGTG
1 TATATATATATG
98770 TATATATATATG
1 TATATATATATG
98782 TATATATATA
1 TATATATATA
98792 AGTAGATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (12 bp):
TATATATATATG
Found at i:98775 original size:14 final size:14
Alignment explanation
Indices: 98755--98791 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
98745 TTTGTAATGA
98755 ATATATATATATGT
1 ATATATATATATGT
*
98769 GTATATATATATGT
1 ATATATATATATGT
98783 ATATATATA
1 ATATATATA
98792 AGTAGATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (14 bp):
ATATATATATATGT
Found at i:108938 original size:42 final size:39
Alignment explanation
Indices: 108891--109032 Score: 110
Period size: 42 Copynumber: 3.4 Consensus size: 39
108881 GCATTTTTTA
108891 ACAAACGTCGTAATAGAGTGGTAAATTAGCGGCGTTTATACC
1 ACAAACG-CGTAATAGA-T-GTAAATTAGCGGCGTTTATACC
* * *
108933 ACAAACGCCGCAATAGAT-TAACATATAGTGGTGTTT-TAGCC
1 ACAAACG-CGTAATAGATGTAA-AT-TAGCGGCGTTTATA-CC
* * *
108974 AAAATAC-CGTAATAGATCGATAAATTAGCGTCATTTATACC
1 ACAA-ACGCGTAATAGAT-G-TAAATTAGCGGCGTTTATACC
109015 ACAAACGCTGTAATAGAT
1 ACAAACGC-GTAATAGAT
109033 TACACATATA
Statistics
Matches: 79, Mismatches: 11, Indels: 20
0.72 0.10 0.18
Matches are distributed among these distances:
39 3 0.04
40 15 0.19
41 28 0.35
42 30 0.38
43 3 0.04
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (39 bp):
ACAAACGCGTAATAGATGTAAATTAGCGGCGTTTATACC
Found at i:109051 original size:42 final size:40
Alignment explanation
Indices: 108891--109053 Score: 104
Period size: 42 Copynumber: 3.9 Consensus size: 40
108881 GCATTTTTTA
* *
108891 ACAAACGTCGTAATAGAGTGGTAA-AT-TAGCGGCGTTTATACC
1 ACAAACG-CGTAATAGA-T--TAACATATAGTGGCATTTATACC
* **
108933 ACAAACGCCGCAATAGATTAACATATAGTGGTGTTT-TAGCC
1 ACAAACG-CGTAATAGATTAACATATAGTGGCATTTATA-CC
* * *
108974 AAAATAC-CGTAATAGATCGATAA-AT-TAGCGTCATTTATACC
1 ACAA-ACGCGTAATAGAT---TAACATATAGTGGCATTTATACC
109015 ACAAACGCTGTAATAGATTACACATATAGTGGCATTTAT
1 ACAAACGC-GTAATAGATTA-ACATATAGTGGCATTTAT
109054 TCTTAAAACA
Statistics
Matches: 95, Mismatches: 13, Indels: 26
0.71 0.10 0.19
Matches are distributed among these distances:
39 5 0.05
40 16 0.17
41 30 0.32
42 41 0.43
43 3 0.03
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (40 bp):
ACAAACGCGTAATAGATTAACATATAGTGGCATTTATACC
Found at i:109078 original size:82 final size:80
Alignment explanation
Indices: 108893--109078 Score: 194
Period size: 82 Copynumber: 2.2 Consensus size: 80
108883 ATTTTTTAAC
* * *
108893 AAACGTCGTAATAGAGTGGTAAATTAGCGGCGTTTATACCACAAACGCCGCAATAGATTAACATA
1 AAACATCGTAAT--AGTGATAAATTAGCGGCATTTATACCACAAACGCCGCAATAGATTAACATA
**
108958 TAGTGGTGTTTTAGCCA
64 TAGTGGCATTTTAGCCA
* * * * *
108975 AAATACCGTAATAGATCGATAAATTAGCGTCATTTATACCACAAACGCTGTAATAGATTACACAT
1 AAACATCGTAATAG-T-GATAAATTAGCGGCATTTATACCACAAACGCCGCAATAGATTA-ACAT
* *
109040 ATAGTGGCA-TTTATTCTTA
63 ATAGTGGCATTTTA-GC-CA
109059 AAACATCGTAATAGTGATAA
1 AAACATCGTAATAGTGATAA
109079 TAAATAGTGG
Statistics
Matches: 85, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
80 2 0.02
81 1 0.01
82 56 0.66
83 13 0.15
84 13 0.15
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (80 bp):
AAACATCGTAATAGTGATAAATTAGCGGCATTTATACCACAAACGCCGCAATAGATTAACATATA
GTGGCATTTTAGCCA
Found at i:109115 original size:41 final size:41
Alignment explanation
Indices: 109068--109209 Score: 189
Period size: 41 Copynumber: 3.5 Consensus size: 41
109058 AAAACATCGT
* * * *
109068 AATAGTGATAATAAATAGTGGTGTTTTTAGATAAACGCCAC
1 AATAGTGTTAATCAATAGTGGCGTTTTTAGAAAAACGCCAC
* *
109109 AATAGTGTTAATCAATAGGGGCGTTTTTAGAAAAACGCCGC
1 AATAGTGTTAATCAATAGTGGCGTTTTTAGAAAAACGCCAC
* *
109150 AATAGTTTTAATCAATAGTGGCGTTTTTTA-ACAAACGCCAC
1 AATAGTGTTAATCAATAGTGGCG-TTTTTAGAAAAACGCCAC
109191 AATAGTG-TAATCAATAGTG
1 AATAGTGTTAATCAATAGTG
109210 ACATTTTTTT
Statistics
Matches: 89, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
40 12 0.13
41 71 0.80
42 6 0.07
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.31
Consensus pattern (41 bp):
AATAGTGTTAATCAATAGTGGCGTTTTTAGAAAAACGCCAC
Found at i:110956 original size:82 final size:81
Alignment explanation
Indices: 110606--110968 Score: 408
Period size: 82 Copynumber: 4.4 Consensus size: 81
110596 TTTTCATTTA
* *
110606 TAGTGGTGTTTTTCCAATAAACGCCGCTATAG-GTACGTACTTTAGTGGCATTTTTATACAAACG
1 TAGTGGTGTTTTT--AATAAACGCCGCTATAGACTA-GTACTTTAGTGGCGTTTTTATACAAACG
* * *
110670 CCGCTATAGAATCGTACGT
63 CCGCTATAGACTCATACTT
* * *
110689 TAGTGGCGTTTTT-ATACAATCGCCGCTATATACTAGTACTTTAGTGGCGTTTCTATACAAACGC
1 TAGTGGTGTTTTTAATA-AA-CGCCGCTATAGACTAGTACTTTAGTGGCGTTTTTATACAAACGC
*
110753 CGCTATATACTCATACTT
64 CGCTATAGACTCATACTT
* * * * * * *
110771 TAGTGGCGTTTTGAATCTAAACGTCGCTATAAACTTGTATTTTAGTGGCGTTTTGAATGA-AAAC
1 TAGTGGTGTTTTTAA--TAAACGCCGCTATAGACTAGTACTTTAGTGGCGTTTT-TAT-ACAAAC
*
110835 GCCGCTAAAGACTCATACTT
62 GCCGCTATAGACTCATACTT
* *
110855 TAGTAGTGTTTTTATATAAACACCGCTATAGACTAGTACTTTAGTGGCGTTTTTATACAAACGCC
1 TAGTGGTGTTTTTA-ATAAACGCCGCTATAGACTAGTACTTTAGTGGCGTTTTTATACAAACGCC
*
110920 GCTATAGACTCGTACTT
65 GCTATAGACTCATACTT
* *
110937 TAGTGGTGTTTTTAGATAAATGCCGCAATAGA
1 TAGTGGTGTTTTTA-ATAAACGCCGCTATAGA
110969 TATAATATTT
Statistics
Matches: 236, Mismatches: 34, Indels: 21
0.81 0.12 0.07
Matches are distributed among these distances:
80 3 0.01
81 3 0.01
82 114 0.48
83 75 0.32
84 37 0.16
85 4 0.02
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (81 bp):
TAGTGGTGTTTTTAATAAACGCCGCTATAGACTAGTACTTTAGTGGCGTTTTTATACAAACGCCG
CTATAGACTCATACTT
Found at i:110962 original size:41 final size:40
Alignment explanation
Indices: 110606--110968 Score: 334
Period size: 41 Copynumber: 8.8 Consensus size: 40
110596 TTTTCATTTA
* *
110606 TAGTGGTGTTTTTCCAATAAACGCCGCTATAG-GTACGTACTT
1 TAGTGGCGTTTTT--AATAAACGCCGCTATAGACT-CGTACTT
* * * *
110648 TAGTGGCATTTTTATACAAACGCCGCTATAGAATCGTACGT
1 TAGTGGCGTTTTTA-ATAAACGCCGCTATAGACTCGTACTT
* *
110689 TAGTGGCGTTTTT-ATACAATCGCCGCTATATACTAGTACTT
1 TAGTGGCGTTTTTAATA-AA-CGCCGCTATAGACTCGTACTT
* * * *
110730 TAGTGGCGTTTCTATACAAACGCCGCTATATACTCATACTT
1 TAGTGGCGTTTTTA-ATAAACGCCGCTATAGACTCGTACTT
* * * * *
110771 TAGTGGCGTTTTGAATCTAAACGTCGCTATAAACTTGTATTT
1 TAGTGGCGTTTTTAA--TAAACGCCGCTATAGACTCGTACTT
* * *
110813 TAGTGGCGTTTTGAATGAAAACGCCGCTAAAGACTCATACTT
1 TAGTGGCGTTTTTAAT--AAACGCCGCTATAGACTCGTACTT
* * * *
110855 TAGTAGTGTTTTTATATAAACACCGCTATAGACTAGTACTT
1 TAGTGGCGTTTTTA-ATAAACGCCGCTATAGACTCGTACTT
*
110896 TAGTGGCGTTTTTATACAAACGCCGCTATAGACTCGTACTT
1 TAGTGGCGTTTTTA-ATAAACGCCGCTATAGACTCGTACTT
* * *
110937 TAGTGGTGTTTTTAGATAAATGCCGCAATAGA
1 TAGTGGCGTTTTTA-ATAAACGCCGCTATAGA
110969 TATAATATTT
Statistics
Matches: 264, Mismatches: 46, Indels: 23
0.79 0.14 0.07
Matches are distributed among these distances:
39 2 0.01
40 5 0.02
41 176 0.67
42 77 0.29
43 4 0.02
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (40 bp):
TAGTGGCGTTTTTAATAAACGCCGCTATAGACTCGTACTT
Found at i:111034 original size:44 final size:44
Alignment explanation
Indices: 110945--111034 Score: 135
Period size: 44 Copynumber: 2.0 Consensus size: 44
110935 TTTAGTGGTG
***
110945 TTTTTAGATAAATGCCGCAATAGATATAATATTTTGTGGCATTT
1 TTTTTAGATAAATGCCGCAATAGATATAATATTTTGCAACATTT
* *
110989 TTTTTAGATAAATGCCGCAATCGATATAATATTTTGCAACGTTT
1 TTTTTAGATAAATGCCGCAATAGATATAATATTTTGCAACATTT
111033 TT
1 TT
111035 ATAAAAATGC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.43
Consensus pattern (44 bp):
TTTTTAGATAAATGCCGCAATAGATATAATATTTTGCAACATTT
Found at i:111046 original size:41 final size:44
Alignment explanation
Indices: 110944--111052 Score: 134
Period size: 44 Copynumber: 2.5 Consensus size: 44
110934 CTTTAGTGGT
**
110944 GTTTTTAGATAAATGCCGCAATAGATATAATATTTTGTGGCATT
1 GTTTTTAGATAAATGCCGCAATAGATATAATATTTTGTGGCAAC
* *
110988 TTTTTTAGATAAATGCCGCAATCGATATAATA-TTT-T-GCAAC
1 GTTTTTAGATAAATGCCGCAATAGATATAATATTTTGTGGCAAC
* * *
111029 GTTTTTATAAAAATGCCGCTATAG
1 GTTTTTAGATAAATGCCGCAATAG
111053 GCTAGGGCAG
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
41 22 0.39
42 1 0.02
43 3 0.05
44 30 0.54
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (44 bp):
GTTTTTAGATAAATGCCGCAATAGATATAATATTTTGTGGCAAC
Found at i:120078 original size:43 final size:43
Alignment explanation
Indices: 119976--120071 Score: 115
Period size: 43 Copynumber: 2.2 Consensus size: 43
119966 AGAAACACCA
*
119976 CAAAACATCAATACCTACTACGGCGTTTGTGAAAACAACGCCG
1 CAAAACATCAACACCTACTACGGCGTTTGTGAAAACAACGCCG
* **
120019 CAAAAAATCAACACCTACTGTGGCGTTT-TAGAGAAA-AACGCCG
1 CAAAACATCAACACCTACTACGGCGTTTGT-GA-AAACAACGCCG
*
120062 CTAAACATCA
1 CAAAACATCA
120072 TAACCTATTG
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
42 1 0.02
43 41 0.91
44 3 0.07
ACGTcount: A:0.40, C:0.26, G:0.16, T:0.19
Consensus pattern (43 bp):
CAAAACATCAACACCTACTACGGCGTTTGTGAAAACAACGCCG
Found at i:120121 original size:43 final size:43
Alignment explanation
Indices: 120012--120358 Score: 270
Period size: 43 Copynumber: 7.9 Consensus size: 43
120002 TTGTGAAAAC
* * * * *
120012 AACGCCGCAAAAAATCAACACCTACTGTGGCG-TTTTAGAGAAA
1 AACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTA-TGAAA
* ** * *
120055 AACGCCGCTAAACATCATA-ACCTATTGCAACGTTTGTCTGAAA
1 AACGCCGCTAAATATCA-ACACCTATTGCGGCGTTTTTATGAAA
* * ** * *
120098 AACGCTGCTAAATATTAACACCTATTGCGGTATTTTTATTACA
1 AACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTATGAAA
*
120141 AACGCCGCTAAATATCAACAGCTATTGCGGCGTTTTTAT-AACA
1 AACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTATGAA-A
* * * *
120184 AACACCACTAAATATCAACACCTATTGCGGCGTTTCTCTGAAA
1 AACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTATGAAA
* *
120227 AACGCTGCTAAATATCAACACCTATTGCGACGTTTCGGCGTTTTTATGACA
1 AACGCCGCTAAATATCAACACCTATT-----G---CGGCGTTTTTATGAAA
* ** * * * *
120278 AACGCTGCTAAATATCAACACCTATTATGGCATTTGTCA-CACA
1 AACGCCGCTAAATATCAACACCTATTGCGGCGTTT-TTATGAAA
*
120321 AACGCCGCTAAATATCAATACCTATTGCGGCGGTTTTT
1 AACGCCGCTAAATATCAACACCTATTGCGGC-GTTTTT
120359 CACAAAAAAA
Statistics
Matches: 241, Mismatches: 48, Indels: 30
0.76 0.15 0.09
Matches are distributed among these distances:
42 2 0.01
43 188 0.78
44 11 0.05
48 1 0.00
51 39 0.16
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (43 bp):
AACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTATGAAA
Found at i:120224 original size:129 final size:129
Alignment explanation
Indices: 120012--120255 Score: 330
Period size: 129 Copynumber: 1.9 Consensus size: 129
120002 TTGTGAAAAC
* * *
120012 AACGCCGCAAAAAATCAACACCTACTGTGGCGTTTTAGAGAAAAACGCCGCTAAACATCATAACC
1 AACGCCGCAAAAAATCAACACCTACTGCGGCGTTTTAGAGAAAAACACCACTAAACATCATAACC
* *
120077 TATTGCAACGTTTGTCTGAAAAACGCTGCTAAATATTAACACCTATTGCGGTATTTTTATTACA
66 TATTGCAACGTTTCTCTGAAAAACGCTGCTAAATATCAACACCTATTGCGGTATTTTTATTACA
* * * * * * *
120141 AACGCCGCTAAATATCAACAGCTATTGCGGCGTTTTTATA-ACAAACACCACTAAATATCA-ACA
1 AACGCCGCAAAAAATCAACACCTACTGCGGCG-TTTTAGAGAAAAACACCACTAAACATCATA-A
**
120204 CCTATTGCGGCGTTTCTCTGAAAAACGCTGCTAAATATCAACACCTATTGCG
64 CCTATTGCAACGTTTCTCTGAAAAACGCTGCTAAATATCAACACCTATTGCG
120256 ACGTTTCGGC
Statistics
Matches: 99, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
128 1 0.01
129 92 0.93
130 6 0.06
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.27
Consensus pattern (129 bp):
AACGCCGCAAAAAATCAACACCTACTGCGGCGTTTTAGAGAAAAACACCACTAAACATCATAACC
TATTGCAACGTTTCTCTGAAAAACGCTGCTAAATATCAACACCTATTGCGGTATTTTTATTACA
Found at i:120331 original size:94 final size:94
Alignment explanation
Indices: 120168--120349 Score: 247
Period size: 94 Copynumber: 1.9 Consensus size: 94
120158 ACAGCTATTG
* * ** *
120168 CGGCGTTTTTATAACAAACACCACTAAATATCAACACCTATTGCGGCGTTTCTCTGAAAAACGCT
1 CGGCGTTTTTATAACAAACACCACTAAATATCAACACCTATTACGGCATTTCTCACAAAAACGCC
120233 GCTAAATATCAACACCTATTGCGACGTTT
66 GCTAAATATCAACACCTATTGCGACGTTT
* * ** * * *
120262 CGGCGTTTTTATGACAAACGCTGCTAAATATCAACACCTATTATGGCATTTGTCACACAAACGCC
1 CGGCGTTTTTATAACAAACACCACTAAATATCAACACCTATTACGGCATTTCTCACAAAAACGCC
*
120327 GCTAAATATCAATACCTATTGCG
66 GCTAAATATCAACACCTATTGCG
120350 GCGGTTTTTC
Statistics
Matches: 75, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
94 75 1.00
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.29
Consensus pattern (94 bp):
CGGCGTTTTTATAACAAACACCACTAAATATCAACACCTATTACGGCATTTCTCACAAAAACGCC
GCTAAATATCAACACCTATTGCGACGTTT
Found at i:127732 original size:24 final size:24
Alignment explanation
Indices: 127679--127734 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
127669 TTATAACATT
* * *
127679 TTTTTTATTTCTTTATTTTTCTAT
1 TTTTTTATCTCTTTATTTTGCTAC
127703 TGTTTTTA-CTCTTTATTTTGCATAC
1 T-TTTTTATCTCTTTATTTTGC-TAC
127728 TTTTTTA
1 TTTTTTA
127735 GGTTTTACTG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 18 0.67
25 9 0.33
ACGTcount: A:0.14, C:0.11, G:0.04, T:0.71
Consensus pattern (24 bp):
TTTTTTATCTCTTTATTTTGCTAC
Found at i:136160 original size:18 final size:18
Alignment explanation
Indices: 136131--136199 Score: 77
Period size: 18 Copynumber: 3.8 Consensus size: 18
136121 ACATTTCTTT
*
136131 ATTTTCAGATTCATAACTT
1 ATTTT-AGATTCATAACTC
136150 ATTTTAGATTCATAACTC
1 ATTTTAGATTCATAACTC
* * *
136168 ATTTTCGAATTTATATCTC
1 ATTTTAG-ATTCATAACTC
136187 A-TTTAGATTCATA
1 ATTTTAGATTCATA
136200 GCCCAATGTA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
17 6 0.14
18 22 0.51
19 15 0.35
ACGTcount: A:0.32, C:0.14, G:0.06, T:0.48
Consensus pattern (18 bp):
ATTTTAGATTCATAACTC
Found at i:136346 original size:34 final size:34
Alignment explanation
Indices: 136264--136346 Score: 87
Period size: 34 Copynumber: 2.4 Consensus size: 34
136254 TAGTAAGCAT
* *
136264 TCCAGGTGCTATCATCAGAAATAGAAATATGCAC
1 TCCAGGTGCAATCATCAGAAATAGAAATATACAC
** * *
136298 TCCTTGCGTAATCATCA-AATATAGAAATATACAC
1 TCCAGGTGCAATCATCAGAA-ATAGAAATATACAC
*
136332 TCCAGGTGCCATCAT
1 TCCAGGTGCAATCAT
136347 ATAATGTACA
Statistics
Matches: 37, Mismatches: 11, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
33 2 0.05
34 35 0.95
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (34 bp):
TCCAGGTGCAATCATCAGAAATAGAAATATACAC
Found at i:140435 original size:22 final size:22
Alignment explanation
Indices: 140410--140457 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
140400 AAGTTAACTT
140410 TTGGTCAAAGTCAAAATCAACG
1 TTGGTCAAAGTCAAAATCAACG
* * * *
140432 TTGGTCCAAGTCTAAGTCAACT
1 TTGGTCAAAGTCAAAATCAACG
140454 TTGG
1 TTGG
140458 ACAGAGACAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (22 bp):
TTGGTCAAAGTCAAAATCAACG
Found at i:140559 original size:15 final size:15
Alignment explanation
Indices: 140530--140580 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
140520 TCCTTTTGAT
*
140530 TTGACTCAGCACAAG
1 TTGACTCAGTACAAG
*
140545 TTGACTCAGTGCAAG
1 TTGACTCAGTACAAG
* * *
140560 CTGACTTAGTTCAAG
1 TTGACTCAGTACAAG
140575 TTGACT
1 TTGACT
140581 TATTTGATCC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (15 bp):
TTGACTCAGTACAAG
Found at i:141602 original size:54 final size:54
Alignment explanation
Indices: 141486--141603 Score: 137
Period size: 54 Copynumber: 2.2 Consensus size: 54
141476 ATTGCACCAA
* * *
141486 AGTGCCGAAATGGAAATTCACAAACTCATTATGAATTCCATGGATTGCACAGAT
1 AGTGTCGAAATGGAAATTCACAAACGCATTATGAATACCATGGATTGCACAGAT
* ** * * * **
141540 AGTATCGAAATGGTCATTCATAAACGCATTATGAATACTATGGGTTGCACATTT
1 AGTGTCGAAATGGAAATTCACAAACGCATTATGAATACCATGGATTGCACAGAT
141594 AGTGTCGAAA
1 AGTGTCGAAA
141604 ATGCACCGTT
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (54 bp):
AGTGTCGAAATGGAAATTCACAAACGCATTATGAATACCATGGATTGCACAGAT
Found at i:148656 original size:54 final size:54
Alignment explanation
Indices: 148589--148700 Score: 145
Period size: 54 Copynumber: 2.1 Consensus size: 54
148579 TCGAAGTGCT
*
148589 GAAATGGAAATTCAAAAACT-CATTATGAATTCCATGGATTGCACATATAGTACC
1 GAAATGGAAATTCAAAAA-TGCATTATGAATACCATGGATTGCACATATAGTACC
** * * * *
148643 GAAATGGTCATTCATAAATGCATTATGAATACCATGGGTTGCACATTTAGTGCC
1 GAAATGGAAATTCAAAAATGCATTATGAATACCATGGATTGCACATATAGTACC
148697 GAAA
1 GAAA
148701 ATGCACTGTT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
53 1 0.02
54 49 0.98
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (54 bp):
GAAATGGAAATTCAAAAATGCATTATGAATACCATGGATTGCACATATAGTACC
Found at i:150745 original size:29 final size:29
Alignment explanation
Indices: 150700--150789 Score: 85
Period size: 29 Copynumber: 3.1 Consensus size: 29
150690 GCTGCTGGAA
* *
150700 ACCGGTTTTCAACCGGTTCTGACCGGTGTG
1 ACCGG-TTTCAATCGGTTCTGACCGGTCTG
*
150730 ACCGGTTTCAATCGGTTC-GAACCGGTTTG
1 ACCGGTTTCAATCGGTTCTG-ACCGGTCTG
* * * *
150759 ACTGGTCTGAATCGGTT-TGAACGGTCTG
1 ACCGGTTTCAATCGGTTCTGACCGGTCTG
150787 ACC
1 ACC
150790 CGACCGACCG
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
28 10 0.20
29 35 0.70
30 5 0.10
ACGTcount: A:0.17, C:0.24, G:0.29, T:0.30
Consensus pattern (29 bp):
ACCGGTTTCAATCGGTTCTGACCGGTCTG
Found at i:150834 original size:22 final size:22
Alignment explanation
Indices: 150806--150848 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
150796 ACCGACCGTT
150806 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
*
150828 GACCCGACCGGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
150849 GTTGACCGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.19, C:0.47, G:0.26, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:150848 original size:17 final size:17
Alignment explanation
Indices: 150793--150837 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
150783 TCTGACCCGA
150793 CCGA-CCGACCGTTGAC
1 CCGACCCGACCGTTGAC
150809 CCGACCCGACCGTTGAC
1 CCGACCCGACCGTTGAC
150826 CCGACCCGACCG
1 CCGACCCGACCG
150838 GACCGTTGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 4 0.14
17 24 0.86
ACGTcount: A:0.18, C:0.49, G:0.24, T:0.09
Consensus pattern (17 bp):
CCGACCCGACCGTTGAC
Found at i:164193 original size:9 final size:9
Alignment explanation
Indices: 164179--164260 Score: 65
Period size: 10 Copynumber: 8.6 Consensus size: 9
164169 GGCTGCTGGA
164179 AACCGGTTT
1 AACCGGTTT
164188 AACCGGTTTT
1 AACCGG-TTT
164198 CAACCGGTTT
1 -AACCGGTTT
*
164208 GACCGGTTT
1 AACCGGTTT
*
164217 CAACCGGTTCG
1 -AACCGGTT-T
164228 AACCGGTTT
1 AACCGGTTT
* * *
164237 GATCGGTCTA
1 AACCGGT-TT
164247 AACCGGTTT
1 AACCGGTTT
*
164256 GACCG
1 AACCG
164261 ATCTGACCCG
Statistics
Matches: 57, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
9 24 0.42
10 27 0.47
11 6 0.11
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.29
Consensus pattern (9 bp):
AACCGGTTT
Found at i:164204 original size:20 final size:20
Alignment explanation
Indices: 164179--164236 Score: 82
Period size: 20 Copynumber: 2.9 Consensus size: 20
164169 GGCTGCTGGA
164179 AACCGGTTTAACCGGTTTTC
1 AACCGGTTTAACCGGTTTTC
*
164199 AACCGGTTTGACCGG-TTTC
1 AACCGGTTTAACCGGTTTTC
*
164218 AACCGGTTCGAACCGGTTT
1 AACCGGTT-TAACCGGTTT
164237 GATCGGTCTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
19 12 0.36
20 19 0.58
21 2 0.06
ACGTcount: A:0.19, C:0.26, G:0.24, T:0.31
Consensus pattern (20 bp):
AACCGGTTTAACCGGTTTTC
Found at i:164224 original size:10 final size:10
Alignment explanation
Indices: 164179--164236 Score: 68
Period size: 9 Copynumber: 5.9 Consensus size: 10
164169 GGCTGCTGGA
164179 AACCGGTTT-
1 AACCGGTTTC
164188 AACCGGTTTTC
1 AACCGG-TTTC
164199 AACCGGTTT-
1 AACCGGTTTC
*
164208 GACCGGTTTC
1 AACCGGTTTC
164218 AACCGG-TTC
1 AACCGGTTTC
164227 GAACCGGTTT
1 -AACCGGTTT
164237 GATCGGTCTA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
9 17 0.40
10 17 0.40
11 8 0.19
ACGTcount: A:0.19, C:0.26, G:0.24, T:0.31
Consensus pattern (10 bp):
AACCGGTTTC
Found at i:164231 original size:29 final size:27
Alignment explanation
Indices: 164180--164254 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 27
164170 GCTGCTGGAA
164180 ACCGGTTTAACCGGTTTTCAACCGGTTTG
1 ACCGGTTTAACCGG--TTCAACCGGTTTG
164209 ACCGGTTTCAACCGGTTCGAACCGGTTTG
1 ACCGGTTT-AACCGGTTC-AACCGGTTTG
* *
164238 ATCGGTCTAAACCGGTT
1 ACCGGT-TTAACCGGTT
164255 TGACCGATCT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
28 3 0.07
29 31 0.76
30 7 0.17
ACGTcount: A:0.19, C:0.25, G:0.25, T:0.31
Consensus pattern (27 bp):
ACCGGTTTAACCGGTTCAACCGGTTTG
Found at i:164301 original size:22 final size:22
Alignment explanation
Indices: 164276--164320 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
164266 ACCCGACCGA
164276 CCGACCCAACCCGACCGTTGAC
1 CCGACCCAACCCGACCGTTGAC
*
164298 CCGACCCGACCCGACCGTTGAC
1 CCGACCCAACCCGACCGTTGAC
164320 C
1 C
164321 GTTGACTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.20, C:0.51, G:0.20, T:0.09
Consensus pattern (22 bp):
CCGACCCAACCCGACCGTTGAC
Found at i:167210 original size:42 final size:42
Alignment explanation
Indices: 167146--167265 Score: 222
Period size: 42 Copynumber: 2.9 Consensus size: 42
167136 TTTCCCCGAA
* *
167146 TTCCAGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
167188 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
167230 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
167266 TGTAATTCAT
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.17, C:0.20, G:0.19, T:0.44
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
Found at i:167481 original size:10 final size:10
Alignment explanation
Indices: 167466--167512 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
167456 TATTTAAAAT
167466 ATATTTATTA
1 ATATTTATTA
167476 ATATTTATAATA
1 ATATTTAT--TA
167488 ATATTATATT-
1 ATATT-TATTA
*
167498 ATATTTTTTA
1 ATATTTATTA
167508 ATATT
1 ATATT
167513 ATATAAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
9 3 0.09
10 18 0.56
11 1 0.03
12 7 0.22
13 3 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
ATATTTATTA
Found at i:167497 original size:23 final size:23
Alignment explanation
Indices: 167454--167516 Score: 73
Period size: 21 Copynumber: 3.0 Consensus size: 23
167444 TAATTATTAA
*
167454 AATATTTAAAAT-ATATT-TATT
1 AATATTTATAATAATATTATATT
167475 AATATTTATAATAATATTATATT
1 AATATTTATAATAATATTATATT
*
167498 -ATATTT-T-TTAATATTATAT
1 AATATTTATAATAATATTATAT
167517 AAAATAATCA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
20 11 0.29
21 12 0.32
22 11 0.29
23 4 0.11
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
AATATTTATAATAATATTATATT
Found at i:167499 original size:26 final size:25
Alignment explanation
Indices: 167437--167499 Score: 71
Period size: 23 Copynumber: 2.6 Consensus size: 25
167427 CATTTTCATC
167437 AAAATATTA-ATTATTAAAATATTT
1 AAAATATTATATTATTAAAATATTT
*
167461 AAAATA-TAT-TTATTAATAT-TTAT
1 AAAATATTATATTATTAAAATATT-T
167484 AATAATATTATATTAT
1 AA-AATATTATATTAT
167500 ATTTTTTAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 14 0.42
24 10 0.30
25 3 0.09
26 4 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
AAAATATTATATTATTAAAATATTT
Found at i:167509 original size:32 final size:35
Alignment explanation
Indices: 167465--167537 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 35
167455 ATATTTAAAA
167465 TATATTTATTAATATT-TAT-AATAAT-ATTATAT
1 TATATTTATTAATATTATATAAATAATAATTATAT
*
167497 TATATTTTTTAATATTATATAAAATAATCAATTATAT
1 TATATTTATTAATATTATAT-AAATAAT-AATTATAT
167534 TATA
1 TATA
167538 ATAATATAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
32 15 0.43
33 3 0.09
35 6 0.17
37 11 0.31
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.53
Consensus pattern (35 bp):
TATATTTATTAATATTATATAAATAATAATTATAT
Found at i:167545 original size:28 final size:28
Alignment explanation
Indices: 167513--167579 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 28
167503 TTTTAATATT
167513 ATATAAAATAATCAATTATATTATAATA
1 ATATAAAATAATCAATTATATTATAATA
* * ** * *
167541 ATATAAGATATTTTATTTTATTTTAATA
1 ATATAAAATAATCAATTATATTATAATA
*
167569 ATATATAATAA
1 ATATAAAATAA
167580 ATTTTTTATA
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (28 bp):
ATATAAAATAATCAATTATATTATAATA
Found at i:167584 original size:30 final size:31
Alignment explanation
Indices: 167535--167630 Score: 94
Period size: 30 Copynumber: 3.2 Consensus size: 31
167525 CAATTATATT
* * *
167535 ATAATAATATAAGATATTTTATTTTAT-TTTA
1 ATAATAATATAATAAATTTT-TTATATATTTA
167566 ATAAT-ATATAATAAATTTTTTATATATTTA
1 ATAATAATATAATAAATTTTTTATATATTTA
* *
167596 ATAATGA-ATAAT--ATTATTTATATATTTCA
1 ATAATAATATAATAAATTTTTTATATATTT-A
167625 ATAATA
1 ATAATA
167631 TTTTAGTAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
28 14 0.25
29 11 0.19
30 26 0.46
31 6 0.11
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (31 bp):
ATAATAATATAATAAATTTTTTATATATTTA
Found at i:167855 original size:20 final size:20
Alignment explanation
Indices: 167830--167877 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
167820 TTTTCAGATG
167830 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
167850 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
167870 TTTTCCAG
1 TTTTCCAG
167878 TAATTCATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:167882 original size:15 final size:15
Alignment explanation
Indices: 167862--167933 Score: 99
Period size: 15 Copynumber: 4.8 Consensus size: 15
167852 TTCCAGAAAT
167862 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
167877 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
167892 GTAATTCAAATTCCA
1 GTAATTCATTTTCCA
***
167907 GTAATTCAAACTCCA
1 GTAATTCATTTTCCA
167922 GTAATTCATTTT
1 GTAATTCATTTT
167934 TCGGAAAACC
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 51 1.00
ACGTcount: A:0.32, C:0.19, G:0.07, T:0.42
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:169323 original size:19 final size:19
Alignment explanation
Indices: 169299--169335 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
169289 TTTCTATGTA
169299 ATCTATAACTC-TAACAGTT
1 ATCTATAAC-CATAACAGTT
169318 ATCTATAACCATAACAGT
1 ATCTATAACCATAACAGT
169336 GATTTCCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 1 0.06
19 16 0.94
ACGTcount: A:0.41, C:0.22, G:0.05, T:0.32
Consensus pattern (19 bp):
ATCTATAACCATAACAGTT
Found at i:170567 original size:39 final size:39
Alignment explanation
Indices: 170459--170665 Score: 159
Period size: 39 Copynumber: 5.3 Consensus size: 39
170449 TAAGGATCTG
* * * *
170459 CGGTAAGGACTTACCCTGTGCACAAAG-CAGAAGAGTCTG
1 CGGTAAGGACTTACCCTGAGCACAAAGTC-GAGGAGCCTA
** * * * *
170498 TTGTACGGACTTA-CCTGAGTACAAAATCGAGGAACCTA
1 CGGTAAGGACTTACCCTGAGCACAAAGTCGAGGAGCCTA
* *
170536 CGGTAAGGACTTACCCTGAGCATAAAGTCGAGGAGCCTG
1 CGGTAAGGACTTACCCTGAGCACAAAGTCGAGGAGCCTA
* ** * *
170575 TGGTAAGGACTTAATCTAAGCAGAAAGTCGAGGAGCC-A
1 CGGTAAGGACTTACCCTGAGCACAAAGTCGAGGAGCCTA
* * * * * *
170613 GCGGTAAGGACTTACTCAGACCACAAAGACGAGGAGCATG
1 -CGGTAAGGACTTACCCTGAGCACAAAGTCGAGGAGCCTA
*
170653 TGGTAAGGACTTA
1 CGGTAAGGACTTA
170666 AAAGTCGTAG
Statistics
Matches: 130, Mismatches: 34, Indels: 8
0.76 0.20 0.05
Matches are distributed among these distances:
38 26 0.20
39 104 0.80
ACGTcount: A:0.33, C:0.20, G:0.28, T:0.19
Consensus pattern (39 bp):
CGGTAAGGACTTACCCTGAGCACAAAGTCGAGGAGCCTA
Found at i:174430 original size:39 final size:39
Alignment explanation
Indices: 174379--174533 Score: 184
Period size: 39 Copynumber: 4.0 Consensus size: 39
174369 AGGATATATA
* * ** *
174379 GTAATGACTTACCCTGTGCACAAAGTAGAGGAGCCTACG
1 GTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTGCG
* *
174418 GTAAGGATTTACCCTGAGCACAAAGCCGAGGAGCATGCG
1 GTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTGCG
* * *
174457 GTAAGGACTTACCCTAAGCACAATGCCGAGGAGCCTGTG
1 GTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTGCG
* * * *
174496 GTAAGGACCTACCCTGAGCATAAAGTCGATGAGCCTGC
1 GTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTGC
174534 TATAAAGATT
Statistics
Matches: 97, Mismatches: 19, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 97 1.00
ACGTcount: A:0.30, C:0.25, G:0.28, T:0.18
Consensus pattern (39 bp):
GTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTGCG
Found at i:175598 original size:18 final size:18
Alignment explanation
Indices: 175575--175611 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
175565 AGCTACGGTC
* *
175575 GGCGACGGAATGACGATT
1 GGCGACAGAACGACGATT
175593 GGCGACAGAACGACGATT
1 GGCGACAGAACGACGATT
175611 G
1 G
175612 AAGTTTCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.19, G:0.38, T:0.14
Consensus pattern (18 bp):
GGCGACAGAACGACGATT
Found at i:177014 original size:563 final size:564
Alignment explanation
Indices: 176339--177373 Score: 1363
Period size: 563 Copynumber: 1.8 Consensus size: 564
176329 AAGGTTTGTC
*
176339 TGAAAATAATGGTTTAAAGTTGTAATTTGAACCAGGTCCATCAAATGAGACCCGTAATCTAAGCA
1 TGAAAATAATGGTTTAAAGTTGTAATTTGAACCAGGTCCATCAAATGAGACCAGTAATCTAAGCA
* * * **
176404 TGCCGAATCTTGTTTTTTCAAGAGCTGAAAAGGCACTTATAAAGAATTTACATTCGTAACTGTAA
66 TACCAAATCTTGTTTTTTCAAGAGCTGAAAAGACACTTATAAAGAATTTACATTCGTAACCATAA
* * * *
176469 ATAAATGTTGGAAAGTATAGTAAATCAAACTAAGATTGTGTAATT-AA-GAAA-AAGAACCCATT
131 ATAAATGTTGAAAAGTATAGTAAATCAAACTAAGACTGTGCAATTGAATCAAAGAAGAACCCATT
* * * * ** *
176531 T-TGTTACTTATTCTTTTAACCTTTGCATTTCAATAACTTGAATATTCATATCTAGCTTGA-CTT
196 TCTG-TACTTATTCTTCTAAACTTTGCATTTCAAGAAATTGAATATTCATATCTAGC-ACATCTC
* * **
176594 CAATCCTTGAACTTCTTCAAGAACGTGAAGTAAT-C-T-CCGACCAAGATC-GATTTCAAGATTG
259 CAATCCTTGAACTTCTTCAAGAACATGAAGTAATACATGCCGACCAAGATCAG-TTTCAACATCC
* * * *
176655 CCTTCTTTTTCCTCGAATCATCAGGAGTCAAGATAGAGATGAATAATCATGTTCTGGAGATACAG
323 CCTTC-TTTTCCTCAAACCATCAGGAGTCAAGATAGAGATGAATAATCAAGTTCTGGAAATACAG
* *
176720 AGGTAAGAAGAATAAGTGATGAAATGGGGATTTCTTCTCCTGATTCAATTGGACAATCTTAGTTA
387 AGGTAAGAAG----AGTGAGGAAATGGGGATTTCTTCTCCTGATTCAATTGCACAATCTTAGTTA
176785 GATTTACTACTACTTTCCAGTTTTTCAACTATCATCATCGATACGTAGATTTTTGGTGCTCCACA
448 GATTTACTACTACTTTCCAGTTTTTCAACTATCATCATCGATACGTAGATTTTTGGTGCTCCACA
176850 TATGCCATCAGCAGCAGCATCCCAACTTTAGACCATCTTCCAAAATTTTCTT
513 TATGCCATCAGCAGCAGCATCCCAACTTTAGACCATCTTCCAAAATTTTCTT
* * * * * *
176902 TGAAAATCATGGTTTAAAGTTTTAATTTG-ATCTGGATCCATCTAATGAGACGAGTAATCTTAA-
1 TGAAAATAATGGTTTAAAGTTGTAATTTGAACCAGG-TCCATCAAATGAGACCAGTAATC-TAAG
* * * *
176965 CATATCAAATCTTGTTTTTTTAAGAGCTGAAAAGACACTTATGAAGAATTTATATTCGTAACCAT
64 CATACCAAATCTTGTTTTTTCAAGAGCTGAAAAGACACTTATAAAGAATTTACATTCGTAACCAT
*
177030 AAATGAATGTTGAAAAGTATAGTAAATCAAACTAAGACTGTGCAATTGAATCAAAGGAAGAACCC
129 AAATAAATGTTGAAAAGTATAGTAAATCAAACTAAGACTGTGCAATTGAATCAAA-GAAGAACCC
177095 ATTTCTGTACTTATTCTTCTAAACTTTGCATTTCAAGAAATTGAATATTCATATCTAGCACATCT
193 ATTTCTGTACTTATTCTTCTAAACTTTGCATTTCAAGAAATTGAATATTCATATCTAGCACATCT
* * *
177160 CCAATTCTTGAACTTCTTCAAGAACATGACGTAATACAAAGAGATTGGCCGACCATGATCAGTTT
258 CCAATCCTTGAACTTCTTCAAGAACATGAAGTAATAC------A-T-GCCGACCAAGATCAGTTT
* * * * *
177225 CAACATCCCCTTCTTTTGCTCAAACCATCCGGAGTCGAGCTAGAGATGAATATTCAAGTTCTGGA
315 CAACATCCCCTTCTTTTCCTCAAACCATCAGGAGTCAAGATAGAGATGAATAATCAAGTTCTGGA
** * * *
177290 AATGTAGAGGTTAGAAGGGTGAGGAAATGGGGATTTCTTCTTCTGATTCAATTGCACAATCTTAG
380 AATACAGAGGTAAGAAGAGTGAGGAAATGGGGATTTCTTCTCCTGATTCAATTGCACAATCTTAG
177355 TTAGATTTACTACTACTTT
445 TTAGATTTACTACTACTTT
177374 GAAACTTTTC
Statistics
Matches: 401, Mismatches: 51, Indels: 30
0.83 0.11 0.06
Matches are distributed among these distances:
562 4 0.01
563 146 0.36
564 5 0.01
565 3 0.01
566 1 0.00
567 93 0.23
568 3 0.01
573 63 0.16
576 1 0.00
577 57 0.14
578 24 0.06
579 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (564 bp):
TGAAAATAATGGTTTAAAGTTGTAATTTGAACCAGGTCCATCAAATGAGACCAGTAATCTAAGCA
TACCAAATCTTGTTTTTTCAAGAGCTGAAAAGACACTTATAAAGAATTTACATTCGTAACCATAA
ATAAATGTTGAAAAGTATAGTAAATCAAACTAAGACTGTGCAATTGAATCAAAGAAGAACCCATT
TCTGTACTTATTCTTCTAAACTTTGCATTTCAAGAAATTGAATATTCATATCTAGCACATCTCCA
ATCCTTGAACTTCTTCAAGAACATGAAGTAATACATGCCGACCAAGATCAGTTTCAACATCCCCT
TCTTTTCCTCAAACCATCAGGAGTCAAGATAGAGATGAATAATCAAGTTCTGGAAATACAGAGGT
AAGAAGAGTGAGGAAATGGGGATTTCTTCTCCTGATTCAATTGCACAATCTTAGTTAGATTTACT
ACTACTTTCCAGTTTTTCAACTATCATCATCGATACGTAGATTTTTGGTGCTCCACATATGCCAT
CAGCAGCAGCATCCCAACTTTAGACCATCTTCCAAAATTTTCTT
Found at i:182326 original size:22 final size:22
Alignment explanation
Indices: 182295--182336 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
182285 GTTTAAAAAT
182295 ACTAACATTTATATAGCTATCA
1 ACTAACATTTATATAGCTATCA
*
182317 ACTAATATTTATATAGCTAT
1 ACTAACATTTATATAGCTAT
182337 TTAATAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.14, G:0.05, T:0.40
Consensus pattern (22 bp):
ACTAACATTTATATAGCTATCA
Found at i:191591 original size:31 final size:31
Alignment explanation
Indices: 191554--191639 Score: 127
Period size: 31 Copynumber: 2.8 Consensus size: 31
191544 GGCATAAGAT
* *
191554 CCTACCCAAGAAAGATCTCGGGGCCACAGGG
1 CCTACCCAAGAAAGATATCGGGGCCACAAGG
* * *
191585 CCTACCCAAGAAAAATATCAGCGCCACAAGG
1 CCTACCCAAGAAAGATATCGGGGCCACAAGG
191616 CCTACCCAAGAAAGATATCGGGGC
1 CCTACCCAAGAAAGATATCGGGGC
191640 TGCAGAGCCT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.35, C:0.31, G:0.23, T:0.10
Consensus pattern (31 bp):
CCTACCCAAGAAAGATATCGGGGCCACAAGG
Found at i:191650 original size:31 final size:31
Alignment explanation
Indices: 191554--191656 Score: 118
Period size: 31 Copynumber: 3.3 Consensus size: 31
191544 GGCATAAGAT
* *
191554 CCTACCCAAGAAAGATCTCGGGGCCACAGGG
1 CCTACCCAAGAAAGATATCGGGGCCACAGAG
* * *
191585 CCTACCCAAGAAAAATATCAGCGCCACA-AGG
1 CCTACCCAAGAAAGATATCGGGGCCACAGA-G
**
191616 CCTACCCAAGAAAGATATCGGGGCTGCAGAG
1 CCTACCCAAGAAAGATATCGGGGCCACAGAG
*
191647 CCTACTCAAG
1 CCTACCCAAG
191657 GGTCGCTTTA
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
31 58 0.98
32 1 0.02
ACGTcount: A:0.34, C:0.31, G:0.23, T:0.12
Consensus pattern (31 bp):
CCTACCCAAGAAAGATATCGGGGCCACAGAG
Found at i:194338 original size:40 final size:40
Alignment explanation
Indices: 194283--194404 Score: 244
Period size: 40 Copynumber: 3.0 Consensus size: 40
194273 TGCAGGTTTA
194283 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
194323 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
194363 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
194403 TA
1 TA
194405 GCACTACGGT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 82 1.00
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:196383 original size:6 final size:6
Alignment explanation
Indices: 196372--196426 Score: 101
Period size: 6 Copynumber: 9.2 Consensus size: 6
196362 AAGACCCATA
*
196372 GGTCAT GGTCAT GGTCAT GGTCAT GGTCAT GGTCAT GGTCAT GGTCAC
1 GGTCAT GGTCAT GGTCAT GGTCAT GGTCAT GGTCAT GGTCAT GGTCAT
196420 GGTCAT G
1 GGTCAT G
196427 ATACAAGTGT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.16, C:0.18, G:0.35, T:0.31
Consensus pattern (6 bp):
GGTCAT
Found at i:197557 original size:11 final size:11
Alignment explanation
Indices: 197541--197599 Score: 54
Period size: 10 Copynumber: 5.5 Consensus size: 11
197531 AAACAGAAGA
197541 AGAAAAAAAAT
1 AGAAAAAAAAT
197552 AGAAAAAAAA-
1 AGAAAAAAAAT
197562 AGAAAATGAAAAT
1 AGAAAA--AAAAT
* *
197575 -GAAAAAGAAG
1 AGAAAAAAAAT
197585 A-AAAAAAAAT
1 AGAAAAAAAAT
197595 -GAAAA
1 AGAAAA
197600 TGAGAAAGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
10 20 0.51
11 10 0.26
12 9 0.23
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.07
Consensus pattern (11 bp):
AGAAAAAAAAT
Found at i:197558 original size:28 final size:27
Alignment explanation
Indices: 197526--197619 Score: 88
Period size: 26 Copynumber: 3.4 Consensus size: 27
197516 TATAAGAAGA
197526 AAAAAAAACAGAAGAA-GAAAA-AAAATAG
1 AAAAAAAA-AGAA-AATGAAAAGAAAA-AG
197554 AAAAAAAAAGAAAATGAAAATGAAAAAG
1 AAAAAAAAAGAAAATGAAAA-GAAAAAG
* *
197582 -AAGAAAAA-AAAATGAAAATGAGAAAG
1 AAAAAAAAAGAAAATGAAAA-GAAAAAG
197608 AAAAGAAAAAGA
1 AAAA-AAAAAGA
197620 GAAAAAAAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 11
0.80 0.04 0.15
Matches are distributed among these distances:
26 19 0.33
27 18 0.32
28 15 0.26
29 5 0.09
ACGTcount: A:0.78, C:0.01, G:0.16, T:0.05
Consensus pattern (27 bp):
AAAAAAAAAGAAAATGAAAAGAAAAAG
Found at i:197559 original size:10 final size:10
Alignment explanation
Indices: 197540--197628 Score: 72
Period size: 11 Copynumber: 8.2 Consensus size: 10
197530 AAAACAGAAG
197540 AAGAAAAAAA
1 AAGAAAAAAA
197550 ATAGAAAAAAA
1 A-AGAAAAAAA
197561 AAGAAAATGAAA
1 AAGAAAA--AAA
* *
197573 ATG-AAAAAG
1 AAGAAAAAAA
197582 AAGAAAAAAA
1 AAGAAAAAAA
*
197592 AATGAAAATGAGA
1 AA-GAAAA--AAA
197605 AAGAAAAGAAA
1 AAGAAAA-AAA
197616 AAGAGAAAAAA
1 AAGA-AAAAAA
197627 AA
1 AA
197629 AACTGAGAGA
Statistics
Matches: 65, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
9 4 0.06
10 14 0.22
11 30 0.46
12 13 0.20
13 4 0.06
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.06
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:197565 original size:39 final size:39
Alignment explanation
Indices: 197522--197630 Score: 100
Period size: 42 Copynumber: 2.7 Consensus size: 39
197512 ATATTATAAG
197522 AAGAAAAAAAAACAGAAGAAG-AAAAAAAATAGAAAA-AAA
1 AAGAAAAAAAAA-AGAAGAAGAAAAAAAAAT-GAAAAGAAA
* *
197561 AAGAAAATGAAAATGAAAAAGAAGAAAAAAAAATGAAAATGAGA
1 AAGAAAA--AAAA--AAGAAGAAGAAAAAAAAATGAAAA-GAAA
*
197605 AAGAAAAGAAAAAG-AGAA-AAAAAAAA
1 AAGAAAAAAAAAAGAAGAAGAAAAAAAA
197631 CTGAGAGATG
Statistics
Matches: 59, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
38 8 0.14
39 11 0.19
40 2 0.03
41 4 0.07
42 15 0.25
43 10 0.17
44 9 0.15
ACGTcount: A:0.79, C:0.01, G:0.16, T:0.05
Consensus pattern (39 bp):
AAGAAAAAAAAAAGAAGAAGAAAAAAAAATGAAAAGAAA
Found at i:197567 original size:17 final size:16
Alignment explanation
Indices: 197525--197630 Score: 81
Period size: 17 Copynumber: 6.4 Consensus size: 16
197515 TTATAAGAAG
*
197525 AAAAAAAAACAGAAGAA
1 AAAAAAAAATAGAA-AA
*
197542 GAAAAAAAATAGAAAA
1 AAAAAAAAATAGAAAA
197558 AAAAAGAAAAT-GAAAA
1 AAAAA-AAAATAGAAAA
** *
197574 TGAAAAAGA-AGAAAA
1 AAAAAAAAATAGAAAA
197589 AAAAATGAAAATGAGAAAGA
1 AAAAA--AAAAT-AGAAA-A
* *
197609 AAAGAAAAAGAGAAAA
1 AAAAAAAAATAGAAAA
197625 AAAAAA
1 AAAAAA
197631 CTGAGAGATG
Statistics
Matches: 70, Mismatches: 12, Indels: 15
0.72 0.12 0.15
Matches are distributed among these distances:
15 11 0.16
16 20 0.29
17 25 0.36
18 4 0.06
19 5 0.07
20 5 0.07
ACGTcount: A:0.79, C:0.01, G:0.15, T:0.05
Consensus pattern (16 bp):
AAAAAAAAATAGAAAA
Found at i:197580 original size:32 final size:33
Alignment explanation
Indices: 197544--197649 Score: 121
Period size: 32 Copynumber: 3.3 Consensus size: 33
197534 CAGAAGAAGA
197544 AAAAAAATAGAAAAAAAAAGAAAATGA-AAATG
1 AAAAAAATAGAAAAAAAAAGAAAATGAGAAATG
*
197576 AAAAAGA-AGAAAAAAAAATGAAAATGAGAAA-G
1 AAAAAAATAGAAAAAAAAA-GAAAATGAGAAATG
* * * *
197608 AAAAGAAAAAGAGAAAAAAA-AAACTGAGAGATG
1 AAAA-AAATAGAAAAAAAAAGAAAATGAGAAATG
197641 AAAAAAATA
1 AAAAAAATA
197650 AATATTTCAC
Statistics
Matches: 63, Mismatches: 6, Indels: 10
0.80 0.08 0.13
Matches are distributed among these distances:
31 11 0.17
32 32 0.51
33 10 0.16
34 10 0.16
ACGTcount: A:0.75, C:0.01, G:0.16, T:0.08
Consensus pattern (33 bp):
AAAAAAATAGAAAAAAAAAGAAAATGAGAAATG
Found at i:197617 original size:6 final size:6
Alignment explanation
Indices: 197522--197629 Score: 75
Period size: 6 Copynumber: 18.3 Consensus size: 6
197512 ATATTATAAG
* *
197522 AAGAAA AA-AAA ACAGAAG AAGAAA AA-AAA TAG-AA AA-AAA AAGAAA
1 AAGAAA AAGAAA A-AGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
* * * * *
197567 ATGAAA ATGAAA AAGAAGA AAAAAA AATGAAA ATGAGA AAG-AA AAGAAA
1 AAGAAA AAGAAA AAGAA-A AAGAAA AA-GAAA AAGAAA AAGAAA AAGAAA
197616 AAGAGAA AA-AAA AA
1 AAGA-AA AAGAAA AA
197630 ACTGAGAGAT
Statistics
Matches: 81, Mismatches: 12, Indels: 19
0.72 0.11 0.17
Matches are distributed among these distances:
5 23 0.28
6 42 0.52
7 16 0.20
ACGTcount: A:0.79, C:0.01, G:0.16, T:0.05
Consensus pattern (6 bp):
AAGAAA
Found at i:200925 original size:40 final size:40
Alignment explanation
Indices: 200870--200991 Score: 235
Period size: 40 Copynumber: 3.0 Consensus size: 40
200860 TGCAGGTTTA
200870 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
200910 TAATACACTTCGGTGTATATGGTGGGTACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
200950 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
200990 TA
1 TA
200992 GCACTACGGT
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 80 1.00
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:201645 original size:22 final size:22
Alignment explanation
Indices: 201620--201671 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
201610 AAGGGGTACT
201620 GATTCCCCTGCTACAGGGAATC
1 GATTCCCCTGCTACAGGGAATC
201642 GATTCCCCTGCTACAGGGAATC
1 GATTCCCCTGCTACAGGGAATC
201664 GATTCCCC
1 GATTCCCC
201672 CACTATTCAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.21, C:0.35, G:0.21, T:0.23
Consensus pattern (22 bp):
GATTCCCCTGCTACAGGGAATC
Found at i:225395 original size:18 final size:18
Alignment explanation
Indices: 225374--225408 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
225364 AATAAAACTT
* *
225374 AAAATGAAAATGAAAACG
1 AAAACGAAAACGAAAACG
225392 AAAACGAAAACGAAAAC
1 AAAACGAAAACGAAAAC
225409 TTGAAAATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.69, C:0.11, G:0.14, T:0.06
Consensus pattern (18 bp):
AAAACGAAAACGAAAACG
Found at i:225408 original size:12 final size:12
Alignment explanation
Indices: 225374--225408 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
225364 AATAAAACTT
* *
225374 AAAATGAAAATG
1 AAAACGAAAACG
225386 AAAACGAAAACG
1 AAAACGAAAACG
225398 AAAACGAAAAC
1 AAAACGAAAAC
225409 TTGAAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.69, C:0.11, G:0.14, T:0.06
Consensus pattern (12 bp):
AAAACGAAAACG
Found at i:230980 original size:2 final size:2
Alignment explanation
Indices: 230975--231031 Score: 59
Period size: 2 Copynumber: 30.5 Consensus size: 2
230965 TATGTGTGTT
* * *
230975 TA TA TA TA TA TA TA TA TA TA TA T- TA T- TA T- TT TA TC T- TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
231013 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
231032 TATTAGTTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
1 4 0.08
2 44 0.92
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (2 bp):
TA
Found at i:241235 original size:19 final size:17
Alignment explanation
Indices: 241199--241237 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
241189 AATAAGATTT
241199 TAATATTAAACAAAAAA
1 TAATATTAAACAAAAAA
*
241216 TAATATTATTAACAATAAA
1 TAATATTA--AACAAAAAA
241235 TAA
1 TAA
241238 ATAAATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
19 11 0.58
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (17 bp):
TAATATTAAACAAAAAA
Found at i:241582 original size:2 final size:2
Alignment explanation
Indices: 241569--241607 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
241559 CAAAACCATA
241569 AT AT ACT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
241608 TGTACAATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:252642 original size:62 final size:62
Alignment explanation
Indices: 252559--252681 Score: 174
Period size: 62 Copynumber: 2.0 Consensus size: 62
252549 ATGCTTAATT
* *
252559 CTTGTAAGAAAAATAAGATATTTCTATAAATATTTGTCAATGTAGATATCTATGATAATAAG
1 CTTGTAAGAAAAATAAGATATTACTATAAATATTTGTCAATGTACATATCTATGATAATAAG
* * * * * *
252621 CTTGTAAGGAAGATAATATATTACTATGAATATTTGTTAATGTACATCTCTATGATAATAA
1 CTTGTAAGAAAAATAAGATATTACTATAAATATTTGTCAATGTACATATCTATGATAATAA
252682 CTTTAGGCTT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
62 53 1.00
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.38
Consensus pattern (62 bp):
CTTGTAAGAAAAATAAGATATTACTATAAATATTTGTCAATGTACATATCTATGATAATAAG
Found at i:254288 original size:2 final size:2
Alignment explanation
Indices: 254281--254314 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
254271 TACGATAATC
*
254281 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
254315 TAGAAAACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:254852 original size:85 final size:85
Alignment explanation
Indices: 254707--254863 Score: 226
Period size: 85 Copynumber: 1.8 Consensus size: 85
254697 GAGCCTGCAT
* * *
254707 TAAGGTCTTATGCTGTGCACAAAAAAGAGGAGCCTGCAGTAAGGACATACCCTGAACACAAGGCC
1 TAAGGTCTTATCCTGTGCACAAAAAAGAGGAGCCTGCAGTAAGGACATACCCTGAACACAAAGCA
254772 GAGGAGCCTACGGTTAGCGG
66 GAGGAGCCTACGGTTAGCGG
* ** * *
254792 TAAGGTCTTATCCTGTGCAGAAAGCAGAGGAGCCTGTAGTAAGGACTTACCCT-AAGCACAAAGC
1 TAAGGTCTTATCCTGTGCACAAAAAAGAGGAGCCTGCAGTAAGGACATACCCTGAA-CACAAAGC
254856 AGAGGAGC
65 AGAGGAGC
254864 ATGCGGTAAG
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
84 2 0.03
85 61 0.97
ACGTcount: A:0.32, C:0.22, G:0.29, T:0.17
Consensus pattern (85 bp):
TAAGGTCTTATCCTGTGCACAAAAAAGAGGAGCCTGCAGTAAGGACATACCCTGAACACAAAGCA
GAGGAGCCTACGGTTAGCGG
Found at i:254855 original size:39 final size:39
Alignment explanation
Indices: 254812--254912 Score: 139
Period size: 39 Copynumber: 2.6 Consensus size: 39
254802 TCCTGTGCAG
* *
254812 AAAGCAGAGGAGCCTGTAGTAAGGACTTACCCTAAGCAC
1 AAAGCAGAGGAGCCTGCAGTAAGAACTTACCCTAAGCAC
* * *
254851 AAAGCAGAGGAGCATGCGGTAAGAACTTACCCTGAGCAC
1 AAAGCAGAGGAGCCTGCAGTAAGAACTTACCCTAAGCAC
* *
254890 AAAGCAGAAGAGCCTGCAATAAG
1 AAAGCAGAGGAGCCTGCAGTAAG
254913 GTTTTACAAG
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 53 1.00
ACGTcount: A:0.39, C:0.22, G:0.27, T:0.13
Consensus pattern (39 bp):
AAAGCAGAGGAGCCTGCAGTAAGAACTTACCCTAAGCAC
Found at i:254891 original size:124 final size:124
Alignment explanation
Indices: 254667--254891 Score: 279
Period size: 124 Copynumber: 1.8 Consensus size: 124
254657 TATACACTCA
* * ** **
254667 GTAAGGGCTTACCCTATGCACAAAGCAGAAGAGCCTGCATTAAGGTCTTATGCTGTGCACAAAAA
1 GTAAGGGCTTACCCTATGCACAAAGCAGAAGAGCCTGCAGTAAGGACTTACCCTAAGCACAAAAA
* *
254732 AGAGGAGCCTGCAGTAAGGACATACCCTGAACACAAGGCCGAGGAGCCTACGGTTAGCG
66 AGAGGAGCATGCAGTAAGAACATACCCTGAACACAAGGCCGAGGAGCCTACGGTTAGCG
* * * * * * **
254791 GTAAGGTCTTATCCTGTGCAGAAAGCAGAGGAGCCTGTAGTAAGGACTTACCCTAAGCACAAAGC
1 GTAAGGGCTTACCCTATGCACAAAGCAGAAGAGCCTGCAGTAAGGACTTACCCTAAGCACAAAAA
* * *
254856 AGAGGAGCATGCGGTAAGAACTTACCCTGAGCACAA
66 AGAGGAGCATGCAGTAAGAACATACCCTGAACACAA
254892 AGCAGAAGAG
Statistics
Matches: 82, Mismatches: 19, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
124 82 1.00
ACGTcount: A:0.33, C:0.23, G:0.27, T:0.17
Consensus pattern (124 bp):
GTAAGGGCTTACCCTATGCACAAAGCAGAAGAGCCTGCAGTAAGGACTTACCCTAAGCACAAAAA
AGAGGAGCATGCAGTAAGAACATACCCTGAACACAAGGCCGAGGAGCCTACGGTTAGCG
Found at i:260286 original size:12 final size:12
Alignment explanation
Indices: 260269--260293 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
260259 CATACGATAA
260269 ACATATATATAT
1 ACATATATATAT
260281 ACATATATATAT
1 ACATATATATAT
260293 A
1 A
260294 AAAAACCGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (12 bp):
ACATATATATAT
Found at i:260755 original size:39 final size:38
Alignment explanation
Indices: 260658--260941 Score: 205
Period size: 39 Copynumber: 7.1 Consensus size: 38
260648 TACACCCAGC
* * * * * *
260658 AAGGGCTTACCTTGTGCACAAAGCAGAGAAGCCTACGGT
1 AAGGACTTACC-TGAGCACAAAGCAGAGGAGCATGCAGT
* * *
260697 ATGGTCTTATCCTGTGCACAAAGCAGAGGAGCATGCAGT
1 AAGGACTTA-CCTGAGCACAAAGCAGAGGAGCATGCAGT
*
260736 AAGGACTTACCATGAGCACAAAGTC-GAGGAGCTTGCGGCAAGTGGT
1 AAGGACTTACC-TGAGCACAAAG-CAGAGGAGCAT---GC-A---GT
* * *
260782 AAGGTCTTATCCTGTGCACAAAGCAGAGGAGCCTGCAGT
1 AAGGACTTA-CCTGAGCACAAAGCAGAGGAGCATGCAGT
* *
260821 AAGGACTTACCCTGAGCACAAAGTAGAGGAACATGC-GTT
1 AAGGACTTA-CCTGAGCACAAAGCAGAGGAGCATGCAG-T
**
260860 AAGGACTTAGCCTGAGCACAAAGCAGAGGAGCATGTGGT
1 AAGGACTTA-CCTGAGCACAAAGCAGAGGAGCATGCAGT
* * * *
260899 ATGGACTTACCCTGAGCATAAAGTAGAAGAGCATG-AGGT
1 AAGGACTTA-CCTGAGCACAAAGCAGAGGAGCATGCA-GT
260938 AAGG
1 AAGG
260942 TTTTAAAAGT
Statistics
Matches: 200, Mismatches: 30, Indels: 30
0.77 0.12 0.12
Matches are distributed among these distances:
38 3 0.01
39 156 0.78
40 4 0.02
42 3 0.01
43 3 0.01
45 1 0.00
46 28 0.14
47 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.30, T:0.19
Consensus pattern (38 bp):
AAGGACTTACCTGAGCACAAAGCAGAGGAGCATGCAGT
Found at i:260842 original size:85 final size:80
Alignment explanation
Indices: 260694--260925 Score: 288
Period size: 85 Copynumber: 2.9 Consensus size: 80
260684 AGAAGCCTAC
* *
260694 GGTATGGTCTTATCCTGTGCACAAAGCAGAGGAGCATGCAGTAAGGACTTACCATGAGCACAAAG
1 GGTAAGGTCTTATCCTGTGCACAAAGCAGAGGAGCATGCAGTAAGGACTTACCCTGAGCACAAAG
* * *
260759 TCGAGGAGCTTGCGGCAAGT
66 TAGAGGAACAT---GC--GT
*
260779 GGTAAGGTCTTATCCTGTGCACAAAGCAGAGGAGCCTGCAGTAAGGACTTACCCTGAGCACAAAG
1 GGTAAGGTCTTATCCTGTGCACAAAGCAGAGGAGCATGCAGTAAGGACTTACCCTGAGCACAAAG
260844 TAGAGGAACATGCGT
66 TAGAGGAACATGCGT
* * * ** * *
260859 --TAAGGACTTAGCCTGAGCACAAAGCAGAGGAGCATGTGGTATGGACTTACCCTGAGCATAAAG
1 GGTAAGGTCTTATCCTGTGCACAAAGCAGAGGAGCATGCAGTAAGGACTTACCCTGAGCACAAAG
260922 TAGA
66 TAGA
260926 AGAGCATGAG
Statistics
Matches: 133, Mismatches: 14, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
78 59 0.44
80 2 0.02
82 2 0.02
85 70 0.53
ACGTcount: A:0.31, C:0.20, G:0.29, T:0.19
Consensus pattern (80 bp):
GGTAAGGTCTTATCCTGTGCACAAAGCAGAGGAGCATGCAGTAAGGACTTACCCTGAGCACAAAG
TAGAGGAACATGCGT
Found at i:264519 original size:11 final size:12
Alignment explanation
Indices: 264499--264527 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
264489 ATAAAATTTT
264499 AATAATAAATAA
1 AATAATAAATAA
264511 AATAA-AAATAA
1 AATAATAAATAA
264522 AATAAT
1 AATAAT
264528 GTATATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AATAATAAATAA
Found at i:264544 original size:19 final size:20
Alignment explanation
Indices: 264517--264566 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 20
264507 ATAAAATAAA
* *
264517 AATAAAATAATGT-ATATAT
1 AATATAATAACGTAATATAT
264536 AATATAAT-ACGTAATATAT
1 AATATAATAACGTAATATAT
264555 ATATATATATAA
1 A-ATATA-ATAA
264567 GTTTTTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 3 0.12
19 14 0.56
20 5 0.20
21 2 0.08
22 1 0.04
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (20 bp):
AATATAATAACGTAATATAT
Found at i:264611 original size:19 final size:18
Alignment explanation
Indices: 264577--264627 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 18
264567 GTTTTTAAAT
264577 ATATATACTACTTATTTTGAC
1 ATATATACTA--TATTTT-AC
*
264598 ATATATACTATATTTTAT
1 ATATATACTATATTTTAC
264616 A-ATATACTATAT
1 ATATATACTATAT
264628 AAAAATATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 11 0.38
18 2 0.07
19 6 0.21
21 10 0.34
ACGTcount: A:0.39, C:0.10, G:0.02, T:0.49
Consensus pattern (18 bp):
ATATATACTATATTTTAC
Found at i:264747 original size:25 final size:24
Alignment explanation
Indices: 264718--264791 Score: 67
Period size: 25 Copynumber: 2.9 Consensus size: 24
264708 TTTCGAAACC
264718 ATATTTATAAAAACTTTATATATAT
1 ATATTT-TAAAAACTTTATATATAT
* * * *
264743 TTATTTTCAAAACTATAATATGTAT
1 ATATTTTAAAAACT-TTATATATAT
*
264768 ATATTTTTAATAAACTATATATAT
1 ATA-TTTTAA-AAACTTTATATAT
264792 TGTATATAAT
Statistics
Matches: 37, Mismatches: 9, Indels: 5
0.73 0.18 0.10
Matches are distributed among these distances:
24 7 0.19
25 15 0.41
26 10 0.27
27 5 0.14
ACGTcount: A:0.45, C:0.05, G:0.01, T:0.49
Consensus pattern (24 bp):
ATATTTTAAAAACTTTATATATAT
Found at i:274953 original size:31 final size:31
Alignment explanation
Indices: 274883--274956 Score: 82
Period size: 31 Copynumber: 2.4 Consensus size: 31
274873 GGGGCCTGAG
274883 AGCCTACCCAAGACAATTCTCGGGCCACTGAT
1 AGCCTACCCAAGACAATTCTCGGGCCAC-GAT
**
274915 A-TTTACCCAAGA-AATATCTCGGGGCCAC-AT
1 AGCCTACCCAAGACAAT-TCTC-GGGCCACGAT
274945 AGCCTACCCAAG
1 AGCCTACCCAAG
274957 GGTCACCTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
30 6 0.17
31 21 0.60
32 8 0.23
ACGTcount: A:0.31, C:0.32, G:0.18, T:0.19
Consensus pattern (31 bp):
AGCCTACCCAAGACAATTCTCGGGCCACGAT
Done.