Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007804.1 Hibiscus syriacus cultivar Beakdansim tig00110122_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: 1697051
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 9
Found at i:269615 original size:202 final size:204
Alignment explanation
Indices: 269257--269658 Score: 774
Period size: 202 Copynumber: 2.0 Consensus size: 204
269247 CGGCATCGTT
269257 GGTACATTATACCCAAGAGTTTGCTATATTTACTTAAACAAAATTCGTTGCCTAGGCAACAAAAA
1 GGTACATTATACCCAAGAGTTTGCTATATTTACTTAAACAAAATTCGTTGCCTAGGCAACAAAAA
269322 TTTAAATTATGTACATAAATAAATTAAGTTATTTTCTACTTTCATTATCCGTTTTATTTTATTTT
66 TTTAAATTATGTACATAAATAAATTAAGTTATTTTCTACTTTCATTATCCGTTTTATTTTATTTT
269387 CTTTATTTATTGTAGGCAAGAAAGAACACGTGGCAGCAT-GGG-GTTAGAGTATGCATGAAAAGA
131 CTTTATTTATTGTAGGCAAGAAAGAACACGTGGCAGCATGGGGAGTTAGAGTATGCATGAAAAGA
269450 AAAACTAGG
196 AAAACTAGG
269459 GGTACATTATACCCAAGAGTTTGCTATATTTACTTAAACAAAATTCGTTGCCTAGGCAACAAAAA
1 GGTACATTATACCCAAGAGTTTGCTATATTTACTTAAACAAAATTCGTTGCCTAGGCAACAAAAA
269524 TTTAAATTATGTACATAAATAAATTAAGTTATTTTCTAC-TTCATTATCCGTTTTATTTTATTTT
66 TTTAAATTATGTACATAAATAAATTAAGTTATTTTCTACTTTCATTATCCGTTTTATTTTATTTT
269588 CTTTATTTATTGTAGGCAAGAAAAGAACACGTGGCAGCATGGGGAGTTAGAGTATGCATGAAAAG
131 CTTTATTTATTGTAGGCAAG-AAAGAACACGTGGCAGCATGGGGAGTTAGAGTATGCATGAAAAG
269653 AAAAAC
195 AAAAAC
269659 CAAGGGTGCA
Statistics
Matches: 197, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
201 45 0.23
202 123 0.62
203 3 0.02
204 26 0.13
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (204 bp):
GGTACATTATACCCAAGAGTTTGCTATATTTACTTAAACAAAATTCGTTGCCTAGGCAACAAAAA
TTTAAATTATGTACATAAATAAATTAAGTTATTTTCTACTTTCATTATCCGTTTTATTTTATTTT
CTTTATTTATTGTAGGCAAGAAAGAACACGTGGCAGCATGGGGAGTTAGAGTATGCATGAAAAGA
AAAACTAGG
Found at i:272911 original size:121 final size:121
Alignment explanation
Indices: 272697--272939 Score: 486
Period size: 121 Copynumber: 2.0 Consensus size: 121
272687 CTGGATGACT
272697 TACTTCACGTGCAAGCAATCCTTCATTATTCTGACAGCCACCTTTTCTTTTAAGTTTGGTCATTT
1 TACTTCACGTGCAAGCAATCCTTCATTATTCTGACAGCCACCTTTTCTTTTAAGTTTGGTCATTT
272762 AATAATGGTTATTTAAGGAAACTCCAAAAGCATGCAAAGCCCTAGGAGATCTTTCC
66 AATAATGGTTATTTAAGGAAACTCCAAAAGCATGCAAAGCCCTAGGAGATCTTTCC
272818 TACTTCACGTGCAAGCAATCCTTCATTATTCTGACAGCCACCTTTTCTTTTAAGTTTGGTCATTT
1 TACTTCACGTGCAAGCAATCCTTCATTATTCTGACAGCCACCTTTTCTTTTAAGTTTGGTCATTT
272883 AATAATGGTTATTTAAGGAAACTCCAAAAGCATGCAAAGCCCTAGGAGATCTTTCC
66 AATAATGGTTATTTAAGGAAACTCCAAAAGCATGCAAAGCCCTAGGAGATCTTTCC
272939 T
1 T
272940 TATAAATAAC
Statistics
Matches: 122, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
121 122 1.00
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (121 bp):
TACTTCACGTGCAAGCAATCCTTCATTATTCTGACAGCCACCTTTTCTTTTAAGTTTGGTCATTT
AATAATGGTTATTTAAGGAAACTCCAAAAGCATGCAAAGCCCTAGGAGATCTTTCC
Found at i:276550 original size:19 final size:18
Alignment explanation
Indices: 276498--276552 Score: 83
Period size: 19 Copynumber: 2.9 Consensus size: 18
276488 CTAAAAAAAA
*
276498 GTCAACGGTCAATGACTG
1 GTCAACGGTCAATGGCTG
276516 GCTCAACGGTCAATGGCTAG
1 G-TCAACGGTCAATGGCT-G
276536 GTCAACGGTCAATGGCT
1 GTCAACGGTCAATGGCT
276553 CCCCCATATG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 1 0.03
19 31 0.91
20 2 0.06
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (18 bp):
GTCAACGGTCAATGGCTG
Found at i:281397 original size:17 final size:18
Alignment explanation
Indices: 281375--281421 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
281365 AGTCAACAGT
*
281375 CGGTCAATGCCA-ATCAA
1 CGGTCAATGACAGATCAA
*
281392 CGGTCAATGACAGGGTCAA
1 CGGTCAATGACA-GATCAA
281411 CGGTCAATGAC
1 CGGTCAATGAC
281422 TGGGTGAGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 11 0.42
19 15 0.58
ACGTcount: A:0.32, C:0.26, G:0.26, T:0.17
Consensus pattern (18 bp):
CGGTCAATGACAGATCAA
Found at i:281412 original size:19 final size:19
Alignment explanation
Indices: 281388--281426 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
281378 TCAATGCCAA
281388 TCAACGGTCAATGACAGGG
1 TCAACGGTCAATGACAGGG
*
281407 TCAACGGTCAATGACTGGG
1 TCAACGGTCAATGACAGGG
281426 T
1 T
281427 GAGACAATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.21, G:0.31, T:0.21
Consensus pattern (19 bp):
TCAACGGTCAATGACAGGG
Found at i:283102 original size:17 final size:17
Alignment explanation
Indices: 283080--283116 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
283070 AATGATTATT
283080 GGTGGAGGCGTGTTCGG
1 GGTGGAGGCGTGTTCGG
*
283097 GGTGGATGCGTGTTCGG
1 GGTGGAGGCGTGTTCGG
283114 GGT
1 GGT
283117 AGACTCGATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.05, C:0.11, G:0.57, T:0.27
Consensus pattern (17 bp):
GGTGGAGGCGTGTTCGG
Found at i:288885 original size:21 final size:21
Alignment explanation
Indices: 288843--288885 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
288833 GTCCAAGTTA
*
288843 GACATGCAGAAGGATGCAGCT
1 GACATGCAGAAGGAAGCAGCT
* * *
288864 GACATGCTGAATGAAGCTGCT
1 GACATGCAGAAGGAAGCAGCT
288885 G
1 G
288886 CACTTGAAGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.19, G:0.33, T:0.19
Consensus pattern (21 bp):
GACATGCAGAAGGAAGCAGCT
Found at i:291024 original size:34 final size:32
Alignment explanation
Indices: 290976--291128 Score: 177
Period size: 34 Copynumber: 4.7 Consensus size: 32
290966 AATGTTCACG
* * *
290976 AACATGTTC-TTTAGCATTCATTCGACGTTCGT
1 AACATGTTCGTTTAGCGTTCGTT-AACGTTCGT
* *
291008 GAATATGTTCGTTTAGCGTTCGTTTAAAGTTCGT
1 -AACATGTTCGTTTAGCGTTCG-TTAACGTTCGT
291042 AAACATGTTCGTTTAGCGTTCGTATAACGTTCGT
1 -AACATGTTCGTTTAGCGTTCGT-TAACGTTCGT
291076 AACATGTTCGTTTAGCGTTCGTATAAC--TCGT
1 AACATGTTCGTTTAGCGTTCGT-TAACGTTCGT
291107 AAACATGTTCGTTTAGCGTTCG
1 -AACATGTTCGTTTAGCGTTCG
291129 CGAACATGTT
Statistics
Matches: 108, Mismatches: 8, Indels: 9
0.86 0.06 0.07
Matches are distributed among these distances:
31 4 0.04
32 21 0.19
33 36 0.33
34 45 0.42
35 2 0.02
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (32 bp):
AACATGTTCGTTTAGCGTTCGTTAACGTTCGT
Found at i:291030 original size:11 final size:11
Alignment explanation
Indices: 291014--291102 Score: 58
Period size: 11 Copynumber: 8.0 Consensus size: 11
291004 TCGTGAATAT
*
291014 GTTCGTTTAGC
1 GTTCGTTTAAC
*
291025 GTTCGTTTAAA
1 GTTCGTTTAAC
*
291036 GTTCG-TAAAC
1 GTTCGTTTAAC
*
291046 ATGTTCGTTTAGC
1 --GTTCGTTTAAC
*
291059 GTTCGTATAAC
1 GTTCGTTTAAC
291070 GTTCG--TAAC
1 GTTCGTTTAAC
*
291079 ATGTTCGTTTAGC
1 --GTTCGTTTAAC
*
291092 GTTCGTATAAC
1 GTTCGTTTAAC
291103 TCGTAAACAT
Statistics
Matches: 60, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
9 4 0.07
10 3 0.05
11 42 0.70
12 5 0.08
13 6 0.10
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.40
Consensus pattern (11 bp):
GTTCGTTTAAC
Found at i:291085 original size:33 final size:34
Alignment explanation
Indices: 291000--291128 Score: 201
Period size: 34 Copynumber: 3.9 Consensus size: 34
290990 CATTCATTCG
* * *
291000 ACGTTCGTGAATATGTTCGTTTAGCGTTCGTTTA
1 ACGTTCGTAAACATGTTCGTTTAGCGTTCGTATA
*
291034 AAGTTCGTAAACATGTTCGTTTAGCGTTCGTATA
1 ACGTTCGTAAACATGTTCGTTTAGCGTTCGTATA
291068 ACGTTCGT-AACATGTTCGTTTAGCGTTCGTATA
1 ACGTTCGTAAACATGTTCGTTTAGCGTTCGTATA
291101 AC--TCGTAAACATGTTCGTTTAGCGTTCG
1 ACGTTCGTAAACATGTTCGTTTAGCGTTCG
291129 CGAACATGTT
Statistics
Matches: 89, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
31 4 0.04
32 21 0.24
33 27 0.30
34 37 0.42
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.40
Consensus pattern (34 bp):
ACGTTCGTAAACATGTTCGTTTAGCGTTCGTATA
Found at i:291148 original size:65 final size:67
Alignment explanation
Indices: 291000--291128 Score: 190
Period size: 65 Copynumber: 1.9 Consensus size: 67
290990 CATTCATTCG
* * * *
291000 ACGTTCGTGAATATGTTCGTTTAGCGTTCGTTTAAAGTTCGTAAACATGTTCGTTTAGCGTTCGT
1 ACGTTCGT-AAAATGTTCGTTTAGCGTTCGTATAAAGCTCGTAAACATGTTCGTTTAGCGTTCGG
291065 ATA
65 ATA
*
291068 ACGTTCGTAACATGTTCGTTTAGCGTTCGTAT-AA-CTCGTAAACATGTTCGTTTAGCGTTCG
1 ACGTTCGTAAAATGTTCGTTTAGCGTTCGTATAAAGCTCGTAAACATGTTCGTTTAGCGTTCG
291129 CGAACATGTT
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
65 26 0.45
66 2 0.03
67 22 0.38
68 8 0.14
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.40
Consensus pattern (67 bp):
ACGTTCGTAAAATGTTCGTTTAGCGTTCGTATAAAGCTCGTAAACATGTTCGTTTAGCGTTCGGA
TA
Found at i:291823 original size:14 final size:15
Alignment explanation
Indices: 291804--291845 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
291794 AAGATTAGTG
291804 ACGTTCATACAAA-A
1 ACGTTCATACAAACA
*
291818 ACGTTCTTACAAACA
1 ACGTTCATACAAACA
*
291833 TCGTTCATACAAA
1 ACGTTCATACAAA
291846 GATAAAACAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.43, C:0.24, G:0.07, T:0.26
Consensus pattern (15 bp):
ACGTTCATACAAACA
Found at i:293372 original size:26 final size:26
Alignment explanation
Indices: 293331--293405 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 26
293321 ATTTTCGGTT
* *
293331 TTATATTTTCACTTTTA-AAAGATAAC
1 TTATATTTTTATTTTTAGAAA-ATAAC
*
293357 TTCTATTTTTATTTTTTAGAAAATAAC
1 TTATATTTTTA-TTTTTAGAAAATAAC
*
293384 TTATTTTTTTATTTTGTAGAAA
1 TTATATTTTTATTTT-TAGAAA
293406 CTGAAAAATA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
26 13 0.32
27 25 0.61
28 3 0.07
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (26 bp):
TTATATTTTTATTTTTAGAAAATAAC
Found at i:293374 original size:27 final size:27
Alignment explanation
Indices: 293343--293405 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
293333 ATATTTTCAC
*
293343 TTTTA-AAAGATAACTTCTATTTTTATT
1 TTTTAGAAA-ATAACTTATATTTTTATT
*
293370 TTTTAGAAAATAACTTATTTTTTTATT
1 TTTTAGAAAATAACTTATATTTTTATT
*
293397 TTGTAGAAA
1 TTTTAGAAA
293406 CTGAAAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
27 29 0.91
28 3 0.09
ACGTcount: A:0.35, C:0.05, G:0.06, T:0.54
Consensus pattern (27 bp):
TTTTAGAAAATAACTTATATTTTTATT
Found at i:294751 original size:79 final size:79
Alignment explanation
Indices: 294620--294777 Score: 262
Period size: 79 Copynumber: 2.0 Consensus size: 79
294610 ATAGTGGGCT
** *
294620 CACCAATCTCAAACCCCTTTGAACGCCTCTGTATAAAACTTAAAAGGTTTGAACAAGTCTTCTGG
1 CACCAATCTCAAACCCCTTTGAACGCCTCTCCATAAAACTTAAAAGGTTTGAACAAGTCTTCTGA
294685 GTCACACCGCTTAG
66 GTCACACCGCTTAG
* *
294699 CACCAATCTCAAATCGCTTTGAACGCCTCTCCATAAAACTTAAAAGGTTTGAACAAGTCTTCTGA
1 CACCAATCTCAAACCCCTTTGAACGCCTCTCCATAAAACTTAAAAGGTTTGAACAAGTCTTCTGA
*
294764 GTTACACCGCTTAG
66 GTCACACCGCTTAG
294778 AGTAAAATGA
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
79 73 1.00
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (79 bp):
CACCAATCTCAAACCCCTTTGAACGCCTCTCCATAAAACTTAAAAGGTTTGAACAAGTCTTCTGA
GTCACACCGCTTAG
Found at i:295055 original size:5 final size:5
Alignment explanation
Indices: 295045--295075 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
295035 AGTATTAACT
295045 AATAA AATAA AATAA AATAA AATAA AATAA A
1 AATAA AATAA AATAA AATAA AATAA AATAA A
295076 TATGGATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:301975 original size:34 final size:34
Alignment explanation
Indices: 301920--301984 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
301910 AGACTTCATG
301920 GGATTTAGAATTGAAATTATTATTAAAATTAGAT
1 GGATTTAGAATTGAAATTATTATTAAAATTAGAT
* *
301954 GGATTTATAGTTGAGAA-TATTATTAAAATTA
1 GGATTTAGAATTGA-AATTATTATTAAAATTA
301985 TTATCATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 26 0.93
35 2 0.07
ACGTcount: A:0.43, C:0.00, G:0.15, T:0.42
Consensus pattern (34 bp):
GGATTTAGAATTGAAATTATTATTAAAATTAGAT
Found at i:304912 original size:25 final size:25
Alignment explanation
Indices: 304883--305038 Score: 190
Period size: 25 Copynumber: 6.2 Consensus size: 25
304873 AAGGGACAAT
304883 ATTTTTCAAAATTCTTTCAT-AAATC
1 ATTTTTCAAAATTCTTTCATCAAA-C
* * * *
304908 ATTTTCCAAAATTATTCCATCAAAT
1 ATTTTTCAAAATTCTTTCATCAAAC
* *
304933 ATTCTTCAAAATTCTTTCATTAAAC
1 ATTTTTCAAAATTCTTTCATCAAAC
* *
304958 ATTTCTCAAAATTCTTTTATCAAAC
1 ATTTTTCAAAATTCTTTCATCAAAC
*
304983 ATTTCTCAAAATTC-TTCTATCAAAC
1 ATTTTTCAAAATTCTTTC-ATCAAAC
*
305008 ATTTTTCAAAATTCTTTCATAAAAC
1 ATTTTTCAAAATTCTTTCATCAAAC
305033 ATTTTT
1 ATTTTT
305039 AGAACTTCTT
Statistics
Matches: 111, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
24 2 0.02
25 103 0.93
26 6 0.05
ACGTcount: A:0.37, C:0.19, G:0.00, T:0.45
Consensus pattern (25 bp):
ATTTTTCAAAATTCTTTCATCAAAC
Found at i:305016 original size:75 final size:75
Alignment explanation
Indices: 304883--305036 Score: 213
Period size: 75 Copynumber: 2.1 Consensus size: 75
304873 AAGGGACAAT
* *
304883 ATTTTTCAAAATTCTTTCATAAATCATTTTCCAAAATTATTCCATCAAATATTCTTCAAAATTCT
1 ATTTCTCAAAATTCTTTCATAAATCATTTTCCAAAATTATTCCATCAAACATTCTTCAAAATTCT
*
304948 TTCATTAAAC
66 TTCATAAAAC
* * * *
304958 ATTTCTCAAAATTCTTTTATCAAA-CA-TTTCTCAAAATTCTTCTATCAAACATTTTTCAAAATT
1 ATTTCTCAAAATTCTTTCAT-AAATCATTTTC-CAAAATTATTCCATCAAACATTCTTCAAAATT
305021 CTTTCATAAAAC
64 CTTTCATAAAAC
305033 ATTT
1 ATTT
305037 TTAGAACTTC
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
74 4 0.06
75 63 0.90
76 3 0.04
ACGTcount: A:0.37, C:0.19, G:0.00, T:0.44
Consensus pattern (75 bp):
ATTTCTCAAAATTCTTTCATAAATCATTTTCCAAAATTATTCCATCAAACATTCTTCAAAATTCT
TTCATAAAAC
Found at i:305054 original size:25 final size:24
Alignment explanation
Indices: 304883--305063 Score: 152
Period size: 25 Copynumber: 7.3 Consensus size: 24
304873 AAGGGACAAT
*
304883 ATTTTTCAAAATTCTTTCATAAATC
1 ATTTTTCAAAATTC-TTCATAAAAC
* * * *
304908 ATTTTCCAAAATTATTCCATCAAAT
1 ATTTTTCAAAATTCTT-CATAAAAC
* *
304933 ATTCTTCAAAATTCTTTCATTAAAC
1 ATTTTTCAAAATTC-TTCATAAAAC
* * *
304958 ATTTCTCAAAATTCTTTTATCAAAC
1 ATTTTTCAAAATTC-TTCATAAAAC
* *
304983 ATTTCTCAAAATTCTTCTATCAAAC
1 ATTTTTCAAAATTCTTC-ATAAAAC
305008 ATTTTTCAAAATTCTTTCATAAAAC
1 ATTTTTCAAAATTC-TTCATAAAAC
*
305033 ATTTTT-AGAACTTCTTCA-ATAAAC
1 ATTTTTCA-AAATTCTTCATA-AAAC
305057 -TTTTTCA
1 ATTTTTCA
305064 CCTATTGAAA
Statistics
Matches: 131, Mismatches: 18, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
23 6 0.05
24 14 0.11
25 106 0.81
26 5 0.04
ACGTcount: A:0.36, C:0.19, G:0.01, T:0.44
Consensus pattern (24 bp):
ATTTTTCAAAATTCTTCATAAAAC
Found at i:307264 original size:64 final size:63
Alignment explanation
Indices: 307131--307273 Score: 157
Period size: 64 Copynumber: 2.2 Consensus size: 63
307121 AAAAAGCCTA
* * * *
307131 GGTGCATCGATGCATGGCTTGTGCATCAGTGCATAAAATCAATTCGATGTTTTAATATATATG
1 GGTGCATCGATGCATGGCTTGTGCATCAGTACACAAAATCAATTCGATGTTTTAATATACAAG
* * *
307194 GAGTGCATCGATGCATGG-TATGTGCATCGGTACACAAAATCCATTTGATGTTCAATTAA-A-AC
1 G-GTGCATCGATGCATGGCT-TGTGCATCAGTACACAAAATCAATTCGATGTT---TTAATATAC
307256 AAG
61 AAG
307259 GGTGCATCGATGCAT
1 GGTGCATCGATGCAT
307274 TGATTTATAC
Statistics
Matches: 68, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
63 2 0.03
64 57 0.84
65 4 0.06
66 1 0.01
67 4 0.06
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (63 bp):
GGTGCATCGATGCATGGCTTGTGCATCAGTACACAAAATCAATTCGATGTTTTAATATACAAG
Found at i:309826 original size:23 final size:23
Alignment explanation
Indices: 309796--309926 Score: 105
Period size: 23 Copynumber: 5.8 Consensus size: 23
309786 GCATGGCCTT
309796 GTGCATCGATGCACATTCAAGGA
1 GTGCATCGATGCACATTCAAGGA
* *
309819 GTGCATCGGTGCATC-TTC-ATGA
1 GTGCATCGATGCA-CATTCAAGGA
*
309841 -TGTATCGATGCACATTCAAGGA
1 GTGCATCGATGCACATTCAAGGA
* *
309863 GTGCATCGGTGCATC-TTC-ATGA
1 GTGCATCGATGCA-CATTCAAGGA
* *
309885 -TGTATCGATGCATATTCAAAGG-
1 GTGCATCGATGCACATTC-AAGGA
*
309907 GATGCATCGATGCACTTTCA
1 G-TGCATCGATGCACATTCA
309927 TAGTATATCG
Statistics
Matches: 83, Mismatches: 15, Indels: 20
0.70 0.13 0.17
Matches are distributed among these distances:
20 1 0.01
21 26 0.31
22 9 0.11
23 31 0.37
24 16 0.19
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (23 bp):
GTGCATCGATGCACATTCAAGGA
Found at i:309852 original size:21 final size:21
Alignment explanation
Indices: 309823--309902 Score: 81
Period size: 21 Copynumber: 3.7 Consensus size: 21
309813 CAAGGAGTGC
*
309823 ATCGGTGCATCTTCATGATGT
1 ATCGATGCATCTTCATGATGT
* *
309844 ATCGATGCA-CATTCAAGGAGTGC
1 ATCGATGCATC-TTC-ATGA-TGT
*
309867 ATCGGTGCATCTTCATGATGT
1 ATCGATGCATCTTCATGATGT
*
309888 ATCGATGCATATTCA
1 ATCGATGCATCTTCA
309903 AAGGGATGCA
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
20 1 0.02
21 26 0.55
22 6 0.13
23 13 0.28
24 1 0.02
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.33
Consensus pattern (21 bp):
ATCGATGCATCTTCATGATGT
Found at i:309853 original size:44 final size:44
Alignment explanation
Indices: 309800--309941 Score: 200
Period size: 44 Copynumber: 3.2 Consensus size: 44
309790 GGCCTTGTGC
309800 ATCGATGCACATTCAAGGAGTGCATCGGTGCATCTTCATGATGT
1 ATCGATGCACATTCAAGGAGTGCATCGGTGCATCTTCATGATGT
309844 ATCGATGCACATTCAAGGAGTGCATCGGTGCATCTTCATGATGT
1 ATCGATGCACATTCAAGGAGTGCATCGGTGCATCTTCATGATGT
* * *
309888 ATCGATGCATATTCAAAGG-GATGCATCGATGCA-CTTTCAT-AGTAT
1 ATCGATGCACATTC-AAGGAG-TGCATCGGTGCATC-TTCATGA-TGT
309933 ATCGATGCA
1 ATCGATGCA
309942 TTATGCACAA
Statistics
Matches: 91, Mismatches: 3, Indels: 7
0.90 0.03 0.07
Matches are distributed among these distances:
44 60 0.66
45 31 0.34
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (44 bp):
ATCGATGCACATTCAAGGAGTGCATCGGTGCATCTTCATGATGT
Found at i:319695 original size:17 final size:17
Alignment explanation
Indices: 319662--319695 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
319652 TTGAATATTT
* *
319662 TGGATTGTTTGATTTTG
1 TGGATTGTTAGACTTTG
319679 TGGATTGTTAGACTTTG
1 TGGATTGTTAGACTTTG
319696 GATTTGTTTG
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:0.15, C:0.03, G:0.29, T:0.53
Consensus pattern (17 bp):
TGGATTGTTAGACTTTG
Found at i:325651 original size:29 final size:29
Alignment explanation
Indices: 325619--325771 Score: 195
Period size: 29 Copynumber: 5.3 Consensus size: 29
325609 AAATTCCTAA
325619 AATGTCACCTTTTTCAAAATAATTCACAG
1 AATGTCACCTTTTTCAAAATAATTCACAG
*
325648 AATGTCACCTTTCTCAAAATAATTC-CTAG
1 AATGTCACCTTTTTCAAAATAATTCAC-AG
*
325677 AATGTCACCTTTTTCAAAATAATTCCCAG
1 AATGTCACCTTTTTCAAAATAATTCACAG
*
325706 AATGTCACCTTTTTC-AAATAATT-ATCAA
1 AATGTCACCTTTTTCAAAATAATTCA-CAG
* * * *
325734 AATGTCACATTTTTTAAAAATAATTCCCAA
1 AATGTCAC-CTTTTTCAAAATAATTCACAG
325764 AATGTCAC
1 AATGTCAC
325772 TGGGTCGGGT
Statistics
Matches: 111, Mismatches: 7, Indels: 11
0.86 0.05 0.09
Matches are distributed among these distances:
28 19 0.17
29 72 0.65
30 20 0.18
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.35
Consensus pattern (29 bp):
AATGTCACCTTTTTCAAAATAATTCACAG
Found at i:325700 original size:58 final size:57
Alignment explanation
Indices: 325610--325771 Score: 227
Period size: 58 Copynumber: 2.8 Consensus size: 57
325600 CACATTCGAA
*
325610 AATTCCTAAAATGTCACCTTTTTCAAAATAATTCACAGAATGTCACCTTTCTCAAAAT
1 AATTCCTAAAATGTCACCTTTTTCAAAATAATTCCCAGAATGTCACCTTTCTC-AAAT
* *
325668 AATTCCTAGAATGTCACCTTTTTCAAAATAATTCCCAGAATGTCACCTTTTTCAAAT
1 AATTCCTAAAATGTCACCTTTTTCAAAATAATTCCCAGAATGTCACCTTTCTCAAAT
* * * *
325725 AATT-ATCAAAATGTCACATTTTTTAAAAATAATTCCCAAAATGTCAC
1 AATTCCT-AAAATGTCAC-CTTTTTCAAAATAATTCCCAGAATGTCAC
325772 TGGGTCGGGT
Statistics
Matches: 94, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
56 1 0.01
57 17 0.18
58 76 0.81
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.35
Consensus pattern (57 bp):
AATTCCTAAAATGTCACCTTTTTCAAAATAATTCCCAGAATGTCACCTTTCTCAAAT
Found at i:325756 original size:87 final size:87
Alignment explanation
Indices: 325610--325771 Score: 220
Period size: 87 Copynumber: 1.9 Consensus size: 87
325600 CACATTCGAA
* * * *
325610 AATTCCTAAAATGTCACCTTTTTCAAAATAATTCACAGAATGTCACCTTTCTCAAAATAATTCCT
1 AATTCCCAAAATGTCACCTTTTTCAAAATAATTCACAAAATGTCACCTTTCTAAAAATAATTCCC
*
325675 AGAATGTCACCTTTTTCAAAAT
66 AAAATGTCACCTTTTTCAAAAT
* * *
325697 AATTCCCAGAATGTCACCTTTTTC-AAATAATT-ATCAAAATGTCACATTTTTTAAAAATAATTC
1 AATTCCCAAAATGTCACCTTTTTCAAAATAATTCA-CAAAATGTCAC-CTTTCTAAAAATAATTC
325760 CCAAAATGTCAC
64 CCAAAATGTCAC
325772 TGGGTCGGGT
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
85 1 0.02
86 18 0.28
87 46 0.71
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.35
Consensus pattern (87 bp):
AATTCCCAAAATGTCACCTTTTTCAAAATAATTCACAAAATGTCACCTTTCTAAAAATAATTCCC
AAAATGTCACCTTTTTCAAAAT
Found at i:332900 original size:29 final size:29
Alignment explanation
Indices: 332865--333026 Score: 270
Period size: 29 Copynumber: 5.6 Consensus size: 29
332855 CACATTCAAA
* *
332865 AATTCCCAAAATGTCTCATTTTTCAAAAT
1 AATTCCCAGAATGTCACATTTTTCAAAAT
* * *
332894 AATTCCCAGAATGTCGCCTTTTTAAAAAT
1 AATTCCCAGAATGTCACATTTTTCAAAAT
332923 AATTCCCAGAATGTCACATTTTTCAAAAT
1 AATTCCCAGAATGTCACATTTTTCAAAAT
332952 AATTCCCAGAATGTCACATTTTTCAAAAT
1 AATTCCCAGAATGTCACATTTTTCAAAAT
*
332981 AATTCCCAGAATGTCACCTTTTTCAAAAT
1 AATTCCCAGAATGTCACATTTTTCAAAAT
333010 AATTCCCAGAATGTCAC
1 AATTCCCAGAATGTCAC
333027 TGGGTCGAGT
Statistics
Matches: 125, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 125 1.00
ACGTcount: A:0.36, C:0.22, G:0.07, T:0.34
Consensus pattern (29 bp):
AATTCCCAGAATGTCACATTTTTCAAAAT
Found at i:339016 original size:103 final size:103
Alignment explanation
Indices: 338837--339054 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
338827 GTAGAGGGTC
** *
338837 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGTTGTGAGGTCTGTTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGCGTGAGGTCTATTGAGACACATAC
338902 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
*
338940 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACAGGCGTGAGGTCTATTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGCGTGAGGTCTATTGAGACACATAC
339005 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
339043 TATGTGGTCCTT
1 TATGTGGTCCTT
339055 ATGGACATTA
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGGCGTGAGGTCTATTGAGACACATAC
TTGATCTTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:339352 original size:21 final size:20
Alignment explanation
Indices: 339328--339371 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
339318 CCATCTCATT
339328 TTGATAATTACT-TTATATTTA
1 TTGAT-ATTACTATTATA-TTA
*
339349 TTGATATTATTATTATATTA
1 TTGATATTACTATTATATTA
339369 TTG
1 TTG
339372 CCTTACTAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.32, C:0.02, G:0.07, T:0.59
Consensus pattern (20 bp):
TTGATATTACTATTATATTA
Found at i:345890 original size:103 final size:98
Alignment explanation
Indices: 345681--345893 Score: 365
Period size: 103 Copynumber: 2.1 Consensus size: 98
345671 GTAGAGGGTC
345681 TATGTGGTCCTTCGGGAATATATGATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACCATACTTG
1 TATGTGGTCCTTCGGGAATATATGATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACCATACTTG
345746 ATCTTTGGCATATGTATGATTCTTAAGGAATGA
66 ATCTTTGGCATATGTATGATTCTTAAGGAATGA
345779 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACAGGTGTGAGGTCTGTTTGAGACACATA
1 TATGTGGTCCTTCGGGA-ATATATG-ATTCTTTGGAACAGGTGTGAGGTCTG-TTGAGAC-CATA
345844 CTTGATC-TTGGCATATGTATATGATTCTTAAGGAATGA
62 CTTGATCTTTGGCATATG--TATGATTCTTAAGGAATGA
345882 TATGTGGTCCTT
1 TATGTGGTCCTT
345894 ATGGACATTA
Statistics
Matches: 109, Mismatches: 0, Indels: 7
0.94 0.00 0.06
Matches are distributed among these distances:
98 17 0.16
99 7 0.06
100 26 0.24
101 17 0.16
102 11 0.10
103 31 0.28
ACGTcount: A:0.24, C:0.12, G:0.26, T:0.38
Consensus pattern (98 bp):
TATGTGGTCCTTCGGGAATATATGATTCTTTGGAACAGGTGTGAGGTCTGTTGAGACCATACTTG
ATCTTTGGCATATGTATGATTCTTAAGGAATGA
Found at i:345943 original size:23 final size:23
Alignment explanation
Indices: 345910--345972 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 23
345900 ATTATTATAT
345910 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
345933 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
345956 GGCACTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
345973 ATATGAGCTG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 35 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:346338 original size:107 final size:107
Alignment explanation
Indices: 346132--346347 Score: 384
Period size: 107 Copynumber: 2.0 Consensus size: 107
346122 TATTGCATTG
346132 TTTACATATCTTATTACTGCAACCCATCTCATTTTGGCAATTACTTTATATTTATTTATATTATT
1 TTTACATATCTTATTACTGCAACCCATCTCATTTTGGCAATTACTTTATATTTATTTATATTATT
346197 ATATTATTGCCTCACTAAGTCGATGACTTAGCGTGTGAGTGT
66 ATATTATTGCCTCACTAAGTCGATGACTTAGCGTGTGAGTGT
346239 TTTACATACTCTTATTACTGCAACCCATCTCATTTTGGCAATTACTTTATATTTGA--T-TATTA
1 TTTACATA-TCTTATTACTGCAACCCATCTCATTTTGGCAATTACTTTATATTT-ATTTATATTA
346301 TTATTATTATTGCCTCACTAAGTCGATGACTTAGCGTGTGAGTGT
64 TTA-TATTATTGCCTCACTAAGTCGATGACTTAGCGTGTGAGTGT
346346 TT
1 TT
346348 CACACGTAGG
Statistics
Matches: 106, Mismatches: 0, Indels: 6
0.95 0.00 0.05
Matches are distributed among these distances:
106 8 0.08
107 52 0.49
108 45 0.42
109 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.12, T:0.45
Consensus pattern (107 bp):
TTTACATATCTTATTACTGCAACCCATCTCATTTTGGCAATTACTTTATATTTATTTATATTATT
ATATTATTGCCTCACTAAGTCGATGACTTAGCGTGTGAGTGT
Found at i:348008 original size:21 final size:20
Alignment explanation
Indices: 347984--348022 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
347974 CCTTTCTATT
347984 ATTATTTTATTATTTATTAAC
1 ATTATTTTATT-TTTATTAAC
348005 ATTATTTTATTTTTATTA
1 ATTATTTTATTTTTATTA
348023 TTTTATTTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (20 bp):
ATTATTTTATTTTTATTAAC
Found at i:348139 original size:17 final size:16
Alignment explanation
Indices: 348128--348163 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
348118 ACCTATACTA
348128 AACCCTAACCTAATCT
1 AACCCTAACCTAATCT
*
348144 AACCCTAACCCTAAGCT
1 AACCCTAA-CCTAATCT
348161 AAC
1 AAC
348164 TTCCCACGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.39, C:0.39, G:0.03, T:0.19
Consensus pattern (16 bp):
AACCCTAACCTAATCT
Found at i:350592 original size:2 final size:2
Alignment explanation
Indices: 350585--350680 Score: 178
Period size: 2 Copynumber: 49.0 Consensus size: 2
350575 TTTCAATTAA
350585 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
350627 AT AT -T AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
350667 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
350681 GAGATTAGAT
Statistics
Matches: 92, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
1 2 0.02
2 90 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:355252 original size:64 final size:65
Alignment explanation
Indices: 355151--355282 Score: 187
Period size: 64 Copynumber: 2.0 Consensus size: 65
355141 ATACTATCTC
* * *
355151 TTTTATTATGTTGTTAGGACTTGATACTCTTGTGTGATA-TTTTATTTTGAACATCTTTTGTTGA
1 TTTTATTATGTTGTTAGGACTTGATAATCTTGTGTGATATTTTTAATTTGAACATCTTGTGTTGA
* * *
355215 TTTTATTGTGTTGTT-GAGATTTGATAATCTTGTGTGATATTTTTAATTTGAATATCTTGTGTTG
1 TTTTATTATGTTGTTAG-GACTTGATAATCTTGTGTGATATTTTTAATTTGAACATCTTGTGTTG
355279 A
65 A
355280 TTT
1 TTT
355283 GAGACTTGAT
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
63 1 0.02
64 34 0.57
65 25 0.42
ACGTcount: A:0.20, C:0.05, G:0.18, T:0.56
Consensus pattern (65 bp):
TTTTATTATGTTGTTAGGACTTGATAATCTTGTGTGATATTTTTAATTTGAACATCTTGTGTTGA
Found at i:355308 original size:53 final size:51
Alignment explanation
Indices: 355220--355319 Score: 128
Period size: 53 Copynumber: 1.9 Consensus size: 51
355210 GTTGATTTTA
* ** *
355220 TTGTGTTGTTGAGATTTGATAATCTTGTGTGATATTTTTAATTTGAATATC
1 TTGTGTTGTTGAGACTTGATAATCTTACGTAATATTTTTAATTTGAATATC
* *
355271 TTGTGTTGATTTGAGACTTGATACTCTTACGTAATATTTTTATTTTGAA
1 TTGTGTTG--TTGAGACTTGATAATCTTACGTAATATTTTTAATTTGAA
355320 CATATCGTGT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
51 8 0.20
53 33 0.80
ACGTcount: A:0.24, C:0.06, G:0.18, T:0.52
Consensus pattern (51 bp):
TTGTGTTGTTGAGACTTGATAATCTTACGTAATATTTTTAATTTGAATATC
Found at i:355330 original size:53 final size:53
Alignment explanation
Indices: 355228--355331 Score: 127
Period size: 53 Copynumber: 2.0 Consensus size: 53
355218 TATTGTGTTG
* ** * * * *
355228 TTGAGATTTGATAATCTTGTGTGATATTTTTAATTTGAATATCTTGTGTTGAT
1 TTGAGACTTGATAATCTTACGTAATATTTTTAATTTGAACATATCGTGTTGAT
* *
355281 TTGAGACTTGATACTCTTACGTAATATTTTTATTTTGAACATATCGTGTTG
1 TTGAGACTTGATAATCTTACGTAATATTTTTAATTTGAACATATCGTGTTG
355332 GTATTTTACT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
53 42 1.00
ACGTcount: A:0.25, C:0.08, G:0.17, T:0.50
Consensus pattern (53 bp):
TTGAGACTTGATAATCTTACGTAATATTTTTAATTTGAACATATCGTGTTGAT
Found at i:355699 original size:64 final size:65
Alignment explanation
Indices: 355598--355729 Score: 187
Period size: 64 Copynumber: 2.0 Consensus size: 65
355588 ATACTATCTC
* * *
355598 TTTTATTATGTTGTTAGGACTTGATACTCTTGTGTGATA-TTTTATTTTGAACATCTTTTGTTGA
1 TTTTATTATGTTGTTAGGACTTGATAATCTTGTGTGATATTTTTAATTTGAACATCTTGTGTTGA
* * *
355662 TTTTATTGTGTTGTT-GAGATTTGATAATCTTGTGTGATATTTTTAATTTGAATATCTTGTGTTG
1 TTTTATTATGTTGTTAG-GACTTGATAATCTTGTGTGATATTTTTAATTTGAACATCTTGTGTTG
355726 A
65 A
355727 TTT
1 TTT
355730 GAGACTTGAT
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
63 1 0.02
64 34 0.57
65 25 0.42
ACGTcount: A:0.20, C:0.05, G:0.18, T:0.56
Consensus pattern (65 bp):
TTTTATTATGTTGTTAGGACTTGATAATCTTGTGTGATATTTTTAATTTGAACATCTTGTGTTGA
Found at i:355755 original size:53 final size:51
Alignment explanation
Indices: 355667--355766 Score: 128
Period size: 53 Copynumber: 1.9 Consensus size: 51
355657 GTTGATTTTA
* ** *
355667 TTGTGTTGTTGAGATTTGATAATCTTGTGTGATATTTTTAATTTGAATATC
1 TTGTGTTGTTGAGACTTGATAATCTTACGTAATATTTTTAATTTGAATATC
* *
355718 TTGTGTTGATTTGAGACTTGATACTCTTACGTAATATTTTTATTTTGAA
1 TTGTGTTG--TTGAGACTTGATAATCTTACGTAATATTTTTAATTTGAA
355767 CATATCGTGT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
51 8 0.20
53 33 0.80
ACGTcount: A:0.24, C:0.06, G:0.18, T:0.52
Consensus pattern (51 bp):
TTGTGTTGTTGAGACTTGATAATCTTACGTAATATTTTTAATTTGAATATC
Found at i:355777 original size:53 final size:53
Alignment explanation
Indices: 355675--355778 Score: 127
Period size: 53 Copynumber: 2.0 Consensus size: 53
355665 TATTGTGTTG
* ** * * * *
355675 TTGAGATTTGATAATCTTGTGTGATATTTTTAATTTGAATATCTTGTGTTGAT
1 TTGAGACTTGATAATCTTACGTAATATTTTTAATTTGAACATATCGTGTTGAT
* *
355728 TTGAGACTTGATACTCTTACGTAATATTTTTATTTTGAACATATCGTGTTG
1 TTGAGACTTGATAATCTTACGTAATATTTTTAATTTGAACATATCGTGTTG
355779 GTTTATTTTA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
53 42 1.00
ACGTcount: A:0.25, C:0.08, G:0.17, T:0.50
Consensus pattern (53 bp):
TTGAGACTTGATAATCTTACGTAATATTTTTAATTTGAACATATCGTGTTGAT
Found at i:358170 original size:7 final size:7
Alignment explanation
Indices: 358158--358182 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
358148 AGAGTTTTTT
358158 CAATTTC
1 CAATTTC
358165 CAATTTC
1 CAATTTC
358172 CAATTTC
1 CAATTTC
358179 CAAT
1 CAAT
358183 GGATTAAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.28, G:0.00, T:0.40
Consensus pattern (7 bp):
CAATTTC
Found at i:360806 original size:22 final size:20
Alignment explanation
Indices: 360778--360850 Score: 73
Period size: 22 Copynumber: 3.6 Consensus size: 20
360768 ATAGTATAAC
360778 ATTATTAATTATAACTAAAATT
1 ATTATTAATTATAA-T-AAATT
360800 ATTATTAATTATAAT---TT
1 ATTATTAATTATAATAAATT
*
360817 -TTTTTAATTATAATTGAAATT
1 ATTATTAATTATAA-T-AAATT
360838 ATTATTAATTATA
1 ATTATTAATTATA
360851 TAATTTTTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
16 12 0.28
17 3 0.07
21 3 0.07
22 25 0.58
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (20 bp):
ATTATTAATTATAATAAATT
Found at i:360815 original size:16 final size:16
Alignment explanation
Indices: 360796--360831 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
360786 TTATAACTAA
360796 AATTATTATTAATTAT
1 AATTATTATTAATTAT
* *
360812 AATTTTTTTTAATTAT
1 AATTATTATTAATTAT
360828 AATT
1 AATT
360832 GAAATTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
AATTATTATTAATTAT
Found at i:360824 original size:38 final size:38
Alignment explanation
Indices: 360782--360864 Score: 123
Period size: 38 Copynumber: 2.2 Consensus size: 38
360772 TATAACATTA
*
360782 TTAATTATAACTAAAATTATTATTAATTATA-ATTTTTT
1 TTAATTATAACTAAAATTATTATTAATTATATA-ATTTT
* *
360820 TTAATTATAATTGAAATTATTATTAATTATATAATTTT
1 TTAATTATAACTAAAATTATTATTAATTATATAATTTT
360858 TTAATTA
1 TTAATTA
360865 GGTACAATAC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
38 40 0.98
39 1 0.02
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (38 bp):
TTAATTATAACTAAAATTATTATTAATTATATAATTTT
Found at i:362921 original size:47 final size:47
Alignment explanation
Indices: 362869--362962 Score: 127
Period size: 47 Copynumber: 2.0 Consensus size: 47
362859 TAAGGGGTGG
* **
362869 GGCTCTCTCTCACCGTATA-GGAAAAAATAGTGTGTAGTAAAGGGGCT
1 GGCTCTCTCTCACCGGATAGGGAAAAAA-ACAGTGTAGTAAAGGGGCT
* *
362916 GGCTCTCTCTCGCCGGCTAGGGAAAAAAACAGTGTAGTAAAGGGGCT
1 GGCTCTCTCTCACCGGATAGGGAAAAAAACAGTGTAGTAAAGGGGCT
362963 TTGGCCCGCC
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
47 33 0.80
48 8 0.20
ACGTcount: A:0.29, C:0.19, G:0.30, T:0.22
Consensus pattern (47 bp):
GGCTCTCTCTCACCGGATAGGGAAAAAAACAGTGTAGTAAAGGGGCT
Found at i:364536 original size:4 final size:4
Alignment explanation
Indices: 364527--364553 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
364517 ACTCTAACCT
364527 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
364554 TTGAGTATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:367491 original size:30 final size:30
Alignment explanation
Indices: 367434--367501 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
367424 ATGCATAAGT
* **
367434 AAATTCATCATTTATAATGCATCACCAATA
1 AAATGCATCATTTATAACACATCACCAATA
* *
367464 AAATGCATCATTTATAGCACATTACCAATA
1 AAATGCATCATTTATAACACATCACCAATA
*
367494 ATATGCAT
1 AAATGCAT
367502 TCGAATTTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.43, C:0.19, G:0.06, T:0.32
Consensus pattern (30 bp):
AAATGCATCATTTATAACACATCACCAATA
Found at i:374652 original size:16 final size:16
Alignment explanation
Indices: 374625--374669 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
374615 AAGGTGATGG
*
374625 AAAAATGAAAAAAGAA
1 AAAAAAGAAAAAAGAA
* * *
374641 GAAAGAGAAAAATGAA
1 AAAAAAGAAAAAAGAA
374657 AAAAAAGAAAAAA
1 AAAAAAGAAAAAA
374670 TAAATAAAGG
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (16 bp):
AAAAAAGAAAAAAGAA
Found at i:374654 original size:23 final size:22
Alignment explanation
Indices: 374624--374666 Score: 77
Period size: 23 Copynumber: 1.9 Consensus size: 22
374614 AAAGGTGATG
374624 GAAAAATGAAAAAAGAAGAAAGA
1 GAAAAATGAAAAAA-AAGAAAGA
374647 GAAAAATGAAAAAAAAGAAA
1 GAAAAATGAAAAAAAAGAAA
374667 AAATAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.05
Consensus pattern (22 bp):
GAAAAATGAAAAAAAAGAAAGA
Found at i:375920 original size:140 final size:135
Alignment explanation
Indices: 375669--376029 Score: 471
Period size: 135 Copynumber: 2.6 Consensus size: 135
375659 CAACATTAGG
* * * * * *
375669 ATAACCAGCCGTCCTCATCA-CGTAGGAACCGAGTTATCACCTTTCCTAAAGATGGCC-AGAACT
1 ATAACCAGCCGTCCCCAGCAGAGT-GGAACCGTGTTATCATCATTCCTAAAGATGGCCAAGAACT
*
375732 CTTCATCACGTATGAGCAGTGTCATCCCCCGACCATATTTCCCCAGCAGAGTGGAAACCGTGTCA
65 CTTCATCACGTATGAGCAGTGTCATCCCCCGACCAGATTTCCCCAGCAGAGTGGAAACCGTGTCA
375797 TCTACCCTCAA
130 ---A--CTCAA
375808 ATAACCAGCCGTCCCCAGCAGAGTGGAACCGTGTTATCATCATTCCTAAAGATGGCCAAGAACTC
1 ATAACCAGCCGTCCCCAGCAGAGTGGAACCGTGTTATCATCATTCCTAAAGATGGCCAAGAACTC
375873 TTCATCACGTATGAGCAGTGTCATCCCCCGACCAGATTTCCCCAGCAGAGTGGAAACCGTGTCAA
66 TTCATCACGTATGAGCAGTGTCATCCCCCGACCAGATTTCCCCAGCAGAGTGGAAACCGTGTCAA
*
375938 CTCAG
131 CTCAA
* * * * *
375943 ATAACCAGTCATCCCCTGCAGAGTGGAACCGTGTTATCCTCCA--CCTTAAAGATGACCAAGAAC
1 ATAACCAGCCGTCCCCAGCAGAGTGGAACCGTGTTATCAT-CATTCC-TAAAGATGGCCAAGAAC
* *
376006 T-TGTCATCGCGGATGAGCAGTGTC
64 TCT-TCATCACGTATGAGCAGTGTC
376030 GTCTTCAGCA
Statistics
Matches: 202, Mismatches: 15, Indels: 14
0.87 0.06 0.06
Matches are distributed among these distances:
134 3 0.01
135 76 0.38
136 2 0.01
137 1 0.00
139 48 0.24
140 72 0.36
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.22
Consensus pattern (135 bp):
ATAACCAGCCGTCCCCAGCAGAGTGGAACCGTGTTATCATCATTCCTAAAGATGGCCAAGAACTC
TTCATCACGTATGAGCAGTGTCATCCCCCGACCAGATTTCCCCAGCAGAGTGGAAACCGTGTCAA
CTCAA
Found at i:379467 original size:38 final size:38
Alignment explanation
Indices: 379424--379503 Score: 151
Period size: 38 Copynumber: 2.1 Consensus size: 38
379414 GAAACAATAC
379424 CTGACATGTTAACAACAGTATCAATGGATGAGGATTTA
1 CTGACATGTTAACAACAGTATCAATGGATGAGGATTTA
*
379462 CTGACATGTTAACAACAGTATCAATTGATGAGGATTTA
1 CTGACATGTTAACAACAGTATCAATGGATGAGGATTTA
379500 CTGA
1 CTGA
379504 GAAGATTCAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (38 bp):
CTGACATGTTAACAACAGTATCAATGGATGAGGATTTA
Found at i:381564 original size:24 final size:25
Alignment explanation
Indices: 381535--381581 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
381525 TTCATCTAAC
381535 AAACTAACT-GAAATATTAACAACA
1 AAACTAACTCGAAATATTAACAACA
* *
381559 AAACTAACTCTAAATATTTACAA
1 AAACTAACTCGAAATATTAACAA
381582 TATTCAACAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.55, C:0.17, G:0.02, T:0.26
Consensus pattern (25 bp):
AAACTAACTCGAAATATTAACAACA
Found at i:384883 original size:102 final size:102
Alignment explanation
Indices: 384705--384910 Score: 376
Period size: 102 Copynumber: 2.0 Consensus size: 102
384695 AGGAGCGTTT
*
384705 GGGCGAAGGTAAAAGATGATCTCGACTATTTTGGATTCAATCATGTGGAGGTGGTTGTGGACTTC
1 GGGCGAAGGTAAAAGATGATCTCGACTATTTTGGACTCAATCATGTGGAGGTGGTTGTGGACTTC
* *
384770 ATCCATCTGAGTCTACATATCCGGGCGAGGTGCCTCC
66 ATCCATATGAGTCTACATATCCGGACGAGGTGCCTCC
*
384807 GGGCGAAGGTAAAAGATGATCTCGACTATTTTGGACTCGATCATGTGGAGGTGGTTGTGGACTTC
1 GGGCGAAGGTAAAAGATGATCTCGACTATTTTGGACTCAATCATGTGGAGGTGGTTGTGGACTTC
384872 ATCCATATGAGTCTACATATCCGGACGAGGTGCCTCC
66 ATCCATATGAGTCTACATATCCGGACGAGGTGCCTCC
384909 GG
1 GG
384911 TTCTGGTTGT
Statistics
Matches: 100, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
102 100 1.00
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (102 bp):
GGGCGAAGGTAAAAGATGATCTCGACTATTTTGGACTCAATCATGTGGAGGTGGTTGTGGACTTC
ATCCATATGAGTCTACATATCCGGACGAGGTGCCTCC
Found at i:392626 original size:138 final size:138
Alignment explanation
Indices: 392373--393031 Score: 951
Period size: 138 Copynumber: 4.8 Consensus size: 138
392363 TGTCAGTACC
* * *
392373 CAAAGTGGTGAAAGAGCGTTCCTGGGGGCGCGCCTTCCATTATTTTGTCATAGAATATGTTATCA
1 CAAAGTGGTGAAAGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCA
*
392438 TTGCCCTATTATGTCATTCATGTCCCCCGGGGAACTATAGATGCCAGTACCTATTATTTCTGAGG
66 TTGCCCTATTATGTCACTCATGTCCCCCGGGGAACTATAGATGCCAGTACCTATTATTTCTGAGG
392503 GGACTTGG
131 GGACTTGG
* * * * *
392511 CAAAATGGTGAAAGCGCGCTCCCGGAGGTGCGCCTTCCATTATTTTGTGAGAGAATATGTTATCA
1 CAAAGTGGTGAAAGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCA
* * * * *
392576 TTACCTTATTATGTCATTCATGTCCCCTGGGGAACTATAGATGTCAGTACCTATTATTTCTGAGG
66 TTGCCCTATTATGTCACTCATGTCCCCCGGGGAACTATAGATGCCAGTACCTATTATTTCTGAGG
392641 GGACTTGG
131 GGACTTGG
* ** * *
392649 CAAAGTGGTGAAAGCGCATTGTCGGGGGCGCGCATTCCATTATTTTGTCAGAGAATATATTATCA
1 CAAAGTGGTGAAAGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCA
* * * ** * *
392714 TTGTCCTATTATGTCACTCATGTCCCCCAGAGAACTATTCATGTCAGTACCTATTATTTATGAGG
66 TTGCCCTATTATGTCACTCATGTCCCCCGGGGAACTATAGATGCCAGTACCTATTATTTCTGAGG
392779 GGACTTGG
131 GGACTTGG
* * *
392787 CAAAGTGGTAAAAGCGCGTTCTCGGGGGCGCGCATTCCATTATTTTGTCAGAGAATATGTTATCA
1 CAAAGTGGTGAAAGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCA
* * **
392852 TTGCCCTATTATGTCACTCATGTCCCCCGGAGAAATATTCATGCCAGTACCTATTATTTCTGAGG
66 TTGCCCTATTATGTCACTCATGTCCCCCGGGGAACTATAGATGCCAGTACCTATTATTTCTGAGG
392917 GGACTTGG
131 GGACTTGG
* * * * *
392925 CAAAGTGGTGAAAGCGC-TTTCCGGGGGCGCACCTTCAATTATTTTTTCAGAGAATATATTATCA
1 CAAAGTGGTGAAAGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCA
* *
392989 TTTCCCTATTATGTCAATCATGTCCCCCGGGGAACTATAGATG
66 TTGCCCTATTATGTCACTCATGTCCCCCGGGGAACTATAGATG
393032 GATGGTGAAA
Statistics
Matches: 466, Mismatches: 55, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
137 77 0.17
138 389 0.83
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (138 bp):
CAAAGTGGTGAAAGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCA
TTGCCCTATTATGTCACTCATGTCCCCCGGGGAACTATAGATGCCAGTACCTATTATTTCTGAGG
GGACTTGG
Found at i:393237 original size:63 final size:63
Alignment explanation
Indices: 393156--393283 Score: 202
Period size: 63 Copynumber: 2.0 Consensus size: 63
393146 GTTATGTGAA
* * *
393156 GTTTGAATAAATTAGATAAAATGTTATGAATAAGTTGAATAAATGTGAAGTGATCATTTGGTT
1 GTTTGAATAAATTAGATAAAATGTTATGAATAAATTGAATAAATGTGAAGTGATAAGTTGGTT
* * *
393219 GTTTGAATATATTGGATAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATAAGTTGGTT
1 GTTTGAATAAATTAGATAAAATGTTATGAATAAATTGAATAAATGTGAAGTGATAAGTTGGTT
393282 GT
1 GT
393284 GACATTTAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.38, C:0.01, G:0.23, T:0.38
Consensus pattern (63 bp):
GTTTGAATAAATTAGATAAAATGTTATGAATAAATTGAATAAATGTGAAGTGATAAGTTGGTT
Found at i:393368 original size:14 final size:14
Alignment explanation
Indices: 393349--393379 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
393339 TGATAAGTTG
393349 GTTTTAATGTATAT
1 GTTTTAATGTATAT
393363 GTTTTAATGTATAT
1 GTTTTAATGTATAT
393377 GTT
1 GTT
393380 AAGGATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.16, T:0.58
Consensus pattern (14 bp):
GTTTTAATGTATAT
Found at i:393529 original size:34 final size:34
Alignment explanation
Indices: 393487--393559 Score: 119
Period size: 34 Copynumber: 2.1 Consensus size: 34
393477 TTAAGTTGAA
393487 TTTAATTTTAAATTTCGAATACCATAATTTATAT
1 TTTAATTTTAAATTTCGAATACCATAATTTATAT
* *
393521 TTTAATTTTAAATTTCGAATACTATAATTTGTAT
1 TTTAATTTTAAATTTCGAATACCATAATTTATAT
*
393555 ATTAA
1 TTTAA
393560 AAACATTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.38, C:0.07, G:0.04, T:0.51
Consensus pattern (34 bp):
TTTAATTTTAAATTTCGAATACCATAATTTATAT
Found at i:394096 original size:21 final size:20
Alignment explanation
Indices: 394069--394138 Score: 95
Period size: 21 Copynumber: 3.4 Consensus size: 20
394059 GTCATAAAAC
*
394069 CCTGCGGGCTAGGCATGTAA
1 CCTGCGGGCTAGGAATGTAA
394089 CCTGGCGGGCTAGGAATGTAA
1 CCT-GCGGGCTAGGAATGTAA
*
394110 CCCTGAGGGCTAGGAATGTAA
1 -CCTGCGGGCTAGGAATGTAA
394131 CCCTGCGG
1 -CCTGCGG
394139 AGATGGCATA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
20 3 0.07
21 39 0.87
22 3 0.07
ACGTcount: A:0.21, C:0.24, G:0.36, T:0.19
Consensus pattern (20 bp):
CCTGCGGGCTAGGAATGTAA
Found at i:395806 original size:20 final size:19
Alignment explanation
Indices: 395758--395806 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
395748 TAAATTCATT
395758 ATAAAATTAAATTAAAATA
1 ATAAAATTAAATTAAAATA
*
395777 ATAAATATTAACATTAATTATA
1 ATAAA-ATTAA-ATTAA-AATA
395799 A-AAAATTA
1 ATAAAATTA
395807 CCATATCACT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 9 0.35
21 8 0.31
22 4 0.15
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (19 bp):
ATAAAATTAAATTAAAATA
Found at i:395933 original size:21 final size:22
Alignment explanation
Indices: 395907--395947 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
395897 TTAGCACAAA
*
395907 AAATAATTAATTA-ATAAATTT
1 AAATAAATAATTATATAAATTT
395928 AAATAAATAATTATATAAAT
1 AAATAAATAATTATATAAAT
395948 ATTATTTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
AAATAAATAATTATATAAATTT
Found at i:396320 original size:60 final size:60
Alignment explanation
Indices: 396208--396350 Score: 164
Period size: 60 Copynumber: 2.4 Consensus size: 60
396198 TTAATAGAAG
* * * * *
396208 GCGCGTCCTCGGGGATGCGCCTTACCCACATGACATTCGACTCAGCAGAACCC-TGTGAAA
1 GCGCGTCCCCGGGGATGCGCCTTACACACATGACATTCCACTCAGCAAAACCCAGGT-AAA
* * * *
396268 GCGTGTCCCCGGGGATGCGCCTTACACACGTGGCA-TCCAGTCAGCATAAACCCAGGTAAA
1 GCGCGTCCCCGGGGATGCGCCTTACACACATGACATTCCACTCAGCA-AAACCCAGGTAAA
*
396328 GCGCGTCCCCGGGGATGTGCCTT
1 GCGCGTCCCCGGGGATGCGCCTT
396351 TGTGCCACCT
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
59 9 0.13
60 59 0.84
61 2 0.03
ACGTcount: A:0.21, C:0.33, G:0.28, T:0.18
Consensus pattern (60 bp):
GCGCGTCCCCGGGGATGCGCCTTACACACATGACATTCCACTCAGCAAAACCCAGGTAAA
Found at i:401467 original size:21 final size:21
Alignment explanation
Indices: 401438--401477 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
401428 CATATAAAAT
* *
401438 TGTCCCGAATGACCTCATATA
1 TGTCCCGAAGGACCACATATA
*
401459 TGTCTCGAAGGACCACATA
1 TGTCCCGAAGGACCACATA
401478 GAACCCTCGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (21 bp):
TGTCCCGAAGGACCACATATA
Found at i:404001 original size:26 final size:27
Alignment explanation
Indices: 403958--404010 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 27
403948 TTAACCTCAA
* * *
403958 AATTCATTTACAATCTC-TATATTAAC
1 AATTCACTTAAAAACTCTTATATTAAC
403984 AATTCACTTAAAAACTCTTTATATTAA
1 AATTCACTTAAAAACTC-TTATATTAA
404011 ATCTTTCATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 14 0.64
28 8 0.36
ACGTcount: A:0.42, C:0.17, G:0.00, T:0.42
Consensus pattern (27 bp):
AATTCACTTAAAAACTCTTATATTAAC
Found at i:408685 original size:19 final size:19
Alignment explanation
Indices: 408663--408712 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
408653 TTCCTTATGT
* *
408663 GGTATCGATACCCTTCTTC
1 GGTACCGATACCCTCCTTC
408682 GGTACCGATACCCTCCTTC
1 GGTACCGATACCCTCCTTC
* *
408701 GATACTGATACC
1 GGTACCGATACC
408713 ATTTCAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.20, C:0.34, G:0.16, T:0.30
Consensus pattern (19 bp):
GGTACCGATACCCTCCTTC
Found at i:413360 original size:6 final size:6
Alignment explanation
Indices: 413349--413385 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
413339 TTTATAAATC
413349 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA A
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA A
413386 GTACATCTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:414563 original size:55 final size:54
Alignment explanation
Indices: 414470--414578 Score: 146
Period size: 55 Copynumber: 2.0 Consensus size: 54
414460 GGGAGGAAAT
* * * * *
414470 GGGGAGGGGGGAGTTGAGAGTGAAAGCATATTTTTTTTTTTCAAACAATGAAAGG
1 GGGGAGGGGAGAGTTGAGAGTAAAAACATA-TATATTTTTTCAAACAATGAAAGG
* *
414525 GGGGAGGGGAGAGTTGAGAGTAAAAATATATATATTTTTTCAGACAATGAAAGG
1 GGGGAGGGGAGAGTTGAGAGTAAAAACATATATATTTTTTCAAACAATGAAAGG
414579 TCGGGGAAAG
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
54 21 0.45
55 26 0.55
ACGTcount: A:0.35, C:0.05, G:0.33, T:0.28
Consensus pattern (54 bp):
GGGGAGGGGAGAGTTGAGAGTAAAAACATATATATTTTTTCAAACAATGAAAGG
Found at i:414646 original size:13 final size:13
Alignment explanation
Indices: 414630--414654 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
414620 TTGAAATACT
414630 TTTTAAAATATAA
1 TTTTAAAATATAA
414643 TTTTAAAATATA
1 TTTTAAAATATA
414655 TTAATTTGGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTTAAAATATAA
Found at i:418413 original size:29 final size:29
Alignment explanation
Indices: 418368--418425 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
418358 CTGTTGGCCG
*
418368 TAGGTCGCCATGCCTTCCGGGAGACCTAC
1 TAGGTCGCCATGCCTTCCCGGAGACCTAC
* *
418397 TAGGTCGCCATGTCTTCCCGGCGACCTAC
1 TAGGTCGCCATGCCTTCCCGGAGACCTAC
418426 AAGAGATTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.16, C:0.36, G:0.26, T:0.22
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCCGGAGACCTAC
Found at i:418478 original size:10 final size:10
Alignment explanation
Indices: 418465--418535 Score: 65
Period size: 10 Copynumber: 6.7 Consensus size: 10
418455 ACACGCTGGG
418465 CATCCGAGGC
1 CATCCGAGGC
418475 CATCCGACCGAGGC
1 CAT-C--C-GAGGC
*
418489 CATCCGAAAG-
1 CATCCG-AGGC
418499 CATCCGAGGC
1 CATCCGAGGC
418509 CATCCGAGAG-
1 CATCCGAG-GC
418519 CATCCGAGGC
1 CATCCGAGGC
418529 CATCCGA
1 CATCCGA
418536 ACCGAGGCCA
Statistics
Matches: 51, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
9 3 0.06
10 33 0.65
11 5 0.10
13 2 0.04
14 8 0.16
ACGTcount: A:0.25, C:0.38, G:0.27, T:0.10
Consensus pattern (10 bp):
CATCCGAGGC
Found at i:418487 original size:14 final size:14
Alignment explanation
Indices: 418468--418495 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
418458 CGCTGGGCAT
418468 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
418482 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
418496 AAGCATCCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.43, G:0.29, T:0.07
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:418507 original size:20 final size:20
Alignment explanation
Indices: 418482--418536 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
418472 GGCCATCCGA
418482 CCGAGGCCATCCGAAAGCAT
1 CCGAGGCCATCCGAAAGCAT
*
418502 CCGAGGCCATCCGAGAGCAT
1 CCGAGGCCATCCGAAAGCAT
418522 CCGAGGCCATCCGAA
1 CCGAGGCCATCCGAA
418537 CCGAGGCCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.27, C:0.36, G:0.27, T:0.09
Consensus pattern (20 bp):
CCGAGGCCATCCGAAAGCAT
Found at i:418550 original size:10 final size:10
Alignment explanation
Indices: 418482--418535 Score: 67
Period size: 10 Copynumber: 5.4 Consensus size: 10
418472 GGCCATCCGA
418482 CCGAGGCCAT
1 CCGAGGCCAT
*
418492 CCGAAAG-CAT
1 CCG-AGGCCAT
418502 CCGAGGCCAT
1 CCGAGGCCAT
418512 CCGAGAG-CAT
1 CCGAG-GCCAT
418522 CCGAGGCCAT
1 CCGAGGCCAT
418532 CCGA
1 CCGA
418536 ACCGAGGCCA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
9 3 0.08
10 32 0.84
11 3 0.08
ACGTcount: A:0.26, C:0.37, G:0.28, T:0.09
Consensus pattern (10 bp):
CCGAGGCCAT
Found at i:418706 original size:23 final size:23
Alignment explanation
Indices: 418648--418707 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
418638 CTCGGTTGCC
* **
418648 CTCGGATTCCCTCTTATAGCTCG
1 CTCGGATGCCCTCGCATAGCTCG
*
418671 CTCGGTTGCCCTCGCATAGCTCG
1 CTCGGATGCCCTCGCATAGCTCG
* *
418694 TTCGGATGGCCTCG
1 CTCGGATGCCCTCG
418708 GTCGGATGGC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.10, C:0.35, G:0.25, T:0.30
Consensus pattern (23 bp):
CTCGGATGCCCTCGCATAGCTCG
Found at i:418712 original size:14 final size:14
Alignment explanation
Indices: 418690--418722 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
418680 CCTCGCATAG
*
418690 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
418704 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
418718 CTCGG
1 CTCGG
418723 ATGCTCTCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.30, G:0.39, T:0.24
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:419040 original size:22 final size:22
Alignment explanation
Indices: 419004--419050 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
418994 AAATTTAGCG
*
419004 AAACCGAAAGCAACCCAAACCA
1 AAACCGAAAGCAACCCAAACAA
** *
419026 AAACCGAAATTAACCCGAACAA
1 AAACCGAAAGCAACCCAAACAA
419048 AAA
1 AAA
419051 ATAACCCCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.57, C:0.30, G:0.09, T:0.04
Consensus pattern (22 bp):
AAACCGAAAGCAACCCAAACAA
Found at i:419073 original size:31 final size:31
Alignment explanation
Indices: 419020--419127 Score: 114
Period size: 31 Copynumber: 3.5 Consensus size: 31
419010 AAAGCAACCC
* * *
419020 AAACCAAAACCGAAATTAACCCGAACAAAAA
1 AAACCCAAACTGAAACTAACCCGAACAAAAA
* *
419051 ATAACCCCAA-TCGAAACT-ACCCGAACAGAAAG
1 A-AACCCAAACT-GAAACTAACCCGAACA-AAAA
419083 AAACCCAAACTGAAACTAACCCGAA-AAAAA
1 AAACCCAAACTGAAACTAACCCGAACAAAAA
419113 GAAACCCAAACTGAA
1 -AAACCCAAACTGAA
419128 TTTTAACCCG
Statistics
Matches: 64, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
30 3 0.05
31 38 0.59
32 23 0.36
ACGTcount: A:0.56, C:0.28, G:0.09, T:0.07
Consensus pattern (31 bp):
AAACCCAAACTGAAACTAACCCGAACAAAAA
Found at i:419135 original size:32 final size:33
Alignment explanation
Indices: 419069--419171 Score: 122
Period size: 33 Copynumber: 3.2 Consensus size: 33
419059 AATCGAAACT
**
419069 ACCCGAACAGAAAGAAACCCAAACTGAA-ACTA
1 ACCCGAACAGAAAGAAACCCAAACTGAATTTTA
*
419101 ACCCGAA-AAAAAGAAACCCAAACTGAATTTTA
1 ACCCGAACAGAAAGAAACCCAAACTGAATTTTA
* * *
419133 ACCCGAATC-GAAATAAACCCGAACCGAATTTTA
1 ACCCGAA-CAGAAAGAAACCCAAACTGAATTTTA
419166 ACCCGA
1 ACCCGA
419172 TCCGAAAGCA
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
31 19 0.31
32 16 0.26
33 26 0.43
ACGTcount: A:0.49, C:0.27, G:0.12, T:0.13
Consensus pattern (33 bp):
ACCCGAACAGAAAGAAACCCAAACTGAATTTTA
Found at i:419170 original size:17 final size:17
Alignment explanation
Indices: 419115--419177 Score: 65
Period size: 17 Copynumber: 3.8 Consensus size: 17
419105 GAAAAAAAGA
* *
419115 AACCCAAACTGAATTTT
1 AACCCGAACCGAATTTT
* * *
419132 AACCCGAATCGAA-ATA
1 AACCCGAACCGAATTTT
419148 AACCCGAACCGAATTTT
1 AACCCGAACCGAATTTT
*
419165 AACCCGATCCGAA
1 AACCCGAACCGAA
419178 AGCAGCTTGA
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
16 13 0.36
17 23 0.64
ACGTcount: A:0.41, C:0.29, G:0.11, T:0.19
Consensus pattern (17 bp):
AACCCGAACCGAATTTT
Found at i:419833 original size:14 final size:14
Alignment explanation
Indices: 419810--419839 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
419800 TTGCATTGAG
419810 TTTCTCAATAAAAC
1 TTTCTCAATAAAAC
*
419824 TTTCTTAATAAAAC
1 TTTCTCAATAAAAC
419838 TT
1 TT
419840 AAAAGATCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.43
Consensus pattern (14 bp):
TTTCTCAATAAAAC
Found at i:420504 original size:21 final size:21
Alignment explanation
Indices: 420479--420538 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
420469 AAAAAACAGT
* *
420479 AAAAATGAAAAATATTAAATG
1 AAAAATGAAAAATATAAAATA
*
420500 AAAAATGAAAAATAAAAAATA
1 AAAAATGAAAAATATAAAATA
*
420521 AAAAAGTTAAAAATATAA
1 AAAAA-TGAAAAATATAA
420539 GAAACTTACT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
21 23 0.70
22 10 0.30
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (21 bp):
AAAAATGAAAAATATAAAATA
Found at i:420525 original size:7 final size:7
Alignment explanation
Indices: 420479--420535 Score: 51
Period size: 7 Copynumber: 8.0 Consensus size: 7
420469 AAAAAACAGT
*
420479 AAAAATG
1 AAAAATA
420486 AAAAATA
1 AAAAATA
** *
420493 TTAAATG
1 AAAAATA
*
420500 AAAAATG
1 AAAAATA
420507 AAAAATA
1 AAAAATA
420514 AAAAATA
1 AAAAATA
*
420521 AAAAAGTT
1 AAAAA-TA
420529 AAAAATA
1 AAAAATA
420536 TAAGAAACTT
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
7 34 0.85
8 6 0.15
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (7 bp):
AAAAATA
Found at i:420525 original size:14 final size:14
Alignment explanation
Indices: 420479--420535 Score: 60
Period size: 14 Copynumber: 4.0 Consensus size: 14
420469 AAAAAACAGT
420479 AAAAATGAAAAATA
1 AAAAATGAAAAATA
** *
420493 TTAAATGAAAAATG
1 AAAAATGAAAAATA
*
420507 AAAAATAAAAAATA
1 AAAAATGAAAAATA
*
420521 AAAAAGTTAAAAATA
1 AAAAA-TGAAAAATA
420536 TAAGAAACTT
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
14 26 0.76
15 8 0.24
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (14 bp):
AAAAATGAAAAATA
Found at i:425246 original size:20 final size:20
Alignment explanation
Indices: 425232--425282 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
425222 GCAAAAGTTT
425232 ATTTTGAAAAACAAAATGAA
1 ATTTTGAAAAACAAAATGAA
425252 ATTTTGAAAAACAAAATGAA
1 ATTTTGAAAAACAAAATGAA
425272 ATTTTGAAAAA
1 ATTTTGAAAAA
425283 ATGATTTAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.59, C:0.04, G:0.10, T:0.27
Consensus pattern (20 bp):
ATTTTGAAAAACAAAATGAA
Found at i:428805 original size:16 final size:16
Alignment explanation
Indices: 428780--428816 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
428770 AAATTTCTCT
428780 TCAA-CAATGTATAAG
1 TCAATCAATGTATAAG
428795 TCAATCAATGTATAAG
1 TCAATCAATGTATAAG
428811 TCAATC
1 TCAATC
428817 GGAAGGAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.43, C:0.16, G:0.11, T:0.30
Consensus pattern (16 bp):
TCAATCAATGTATAAG
Found at i:429737 original size:21 final size:21
Alignment explanation
Indices: 429678--429750 Score: 74
Period size: 21 Copynumber: 3.5 Consensus size: 21
429668 AGTAGGTTTG
* * *
429678 GGATCAATCCCTTCACCAAAA
1 GGATTAATCCCTTCCCCTAAA
429699 GGATTAATCCCTTCCCCTAAA
1 GGATTAATCCCTTCCCCTAAA
* * *
429720 GGATTGATCTCTTTCCCTAAA
1 GGATTAATCCCTTCCCCTAAA
* *
429741 TGATCAATCC
1 GGATTAATCC
429751 ATTTCTTGAA
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.30, C:0.30, G:0.11, T:0.29
Consensus pattern (21 bp):
GGATTAATCCCTTCCCCTAAA
Found at i:432129 original size:18 final size:17
Alignment explanation
Indices: 432097--432130 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
432087 ATTTCATGCA
*
432097 ATTTTATTTTTTATATG
1 ATTTTATTGTTTATATG
432114 ATTTTATATGTTTATAT
1 ATTTTAT-TGTTTATAT
432131 ATATGATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (17 bp):
ATTTTATTGTTTATATG
Found at i:438591 original size:20 final size:20
Alignment explanation
Indices: 438554--438595 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
438544 ATTCCACCAC
*
438554 ATGCAACTATATGCTCCTAA
1 ATGCAACTACATGCTCCTAA
* *
438574 ATGCATCTACATGGTCCTAA
1 ATGCAACTACATGCTCCTAA
438594 AT
1 AT
438596 TGGCTCTTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.31
Consensus pattern (20 bp):
ATGCAACTACATGCTCCTAA
Found at i:441183 original size:26 final size:26
Alignment explanation
Indices: 441149--441203 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
441139 TACTTAGTGC
*
441149 TTATGGTGGGCACAAACTTATGTGTA
1 TTATAGTGGGCACAAACTTATGTGTA
***
441175 TTATAGTGGGCACGTCCTTATGTGTA
1 TTATAGTGGGCACAAACTTATGTGTA
441201 TTA
1 TTA
441204 GCACTTCGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.24, C:0.13, G:0.25, T:0.38
Consensus pattern (26 bp):
TTATAGTGGGCACAAACTTATGTGTA
Found at i:444373 original size:22 final size:22
Alignment explanation
Indices: 444347--444388 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
444337 AGTGCAATGC
*
444347 ACTTCTGTACCAGTGCTAAGGT
1 ACTTCCGTACCAGTGCTAAGGT
*
444369 ACTTCCGTACTAGTGCTAAG
1 ACTTCCGTACCAGTGCTAAG
444389 ACACTTTAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (22 bp):
ACTTCCGTACCAGTGCTAAGGT
Found at i:444394 original size:22 final size:22
Alignment explanation
Indices: 444346--444394 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
444336 TAGTGCAATG
* *
444346 CACTTCTGTACCAGTGCTAAGG
1 CACTTCCGTACCAGTGCTAAGA
* *
444368 TACTTCCGTACTAGTGCTAAGA
1 CACTTCCGTACCAGTGCTAAGA
444390 CACTT
1 CACTT
444395 TAGCTAGGAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (22 bp):
CACTTCCGTACCAGTGCTAAGA
Found at i:451125 original size:19 final size:20
Alignment explanation
Indices: 451098--451153 Score: 71
Period size: 22 Copynumber: 2.8 Consensus size: 20
451088 AATCTAATTT
451098 GGGTATCGATACC-TAG-AG
1 GGGTATCGATACCATAGTAG
451116 GGGTTATCGATACCATAGCTTAG
1 GGG-TATCGATACCATAG--TAG
451139 GGGTATCGATACCAT
1 GGGTATCGATACCAT
451154 GATGAAGGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
18 3 0.09
19 10 0.30
20 3 0.09
22 12 0.36
23 5 0.15
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.27
Consensus pattern (20 bp):
GGGTATCGATACCATAGTAG
Found at i:451170 original size:95 final size:94
Alignment explanation
Indices: 451045--451266 Score: 229
Period size: 95 Copynumber: 2.3 Consensus size: 94
451035 CAAGCAATGA
* * * *
451045 GGTATCGATACCATGGTAAGGGTATTGATACCA-GTAAATTTTGAATCTAATTTGGGTATCGATA
1 GGTATCGATACCATGATAAGGGTATCGATACCAGGTAAA-TTCGAAGCTAATTTGGGTATCGATA
*
451109 CCTAG-AGGGGTTATCGATACCATAGCTTAGG
65 CAT-GCAGGGG-TATCGATACCATAGCTTAGG
* * * *
451140 GGTATCGATACCATGATGAA-GGTATCGATACTAGGTTAATTCGAAGCTAATTTTGGTATTGATA
1 GGTATCGATACCATGAT-AAGGGTATCGATACCAGGTAAATTCGAAGCTAATTTGGGTATCGATA
* *
451204 CATGCAGGGGTATCGATACCCTA--ATAGG
65 CATGCAGGGGTATCGATACCATAGCTTAGG
* *
451232 GTAGTATCGATACCATAAGTAGGGGTATCGATACC
1 G--GTATCGATACCATGA-TAAGGGTATCGATACC
451267 TAAGGGCTGG
Statistics
Matches: 106, Mismatches: 14, Indels: 14
0.79 0.10 0.10
Matches are distributed among these distances:
92 5 0.05
94 28 0.26
95 67 0.63
96 6 0.06
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.30
Consensus pattern (94 bp):
GGTATCGATACCATGATAAGGGTATCGATACCAGGTAAATTCGAAGCTAATTTGGGTATCGATAC
ATGCAGGGGTATCGATACCATAGCTTAGG
Found at i:451239 original size:22 final size:21
Alignment explanation
Indices: 451209--451270 Score: 83
Period size: 22 Copynumber: 3.0 Consensus size: 21
451199 TGATACATGC
*
451209 AGGGGTATCGATACCCTAA-T
1 AGGGGTATCGATACCATAAGT
451229 AGGGTAGTATCGATACCATAAGT
1 AGGG--GTATCGATACCATAAGT
451252 AGGGGTATCGATACC-TAAG
1 AGGGGTATCGATACCATAAG
451271 GGCTGGAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
20 8 0.21
21 11 0.29
22 14 0.37
23 5 0.13
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.24
Consensus pattern (21 bp):
AGGGGTATCGATACCATAAGT
Found at i:451261 original size:21 final size:20
Alignment explanation
Indices: 451209--451270 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 20
451199 TGATACATGC
451209 AGGGGTATCGATACCCTAA-T
1 AGGGGTATCGATA-CCTAAGT
451229 AGGGTAGTATCGATACCATAAGT
1 AGGG--GTATCGATACC-TAAGT
451252 AGGGGTATCGATACCTAAG
1 AGGGGTATCGATACCTAAG
451271 GGCTGGAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
20 8 0.21
21 13 0.34
22 12 0.32
23 5 0.13
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.24
Consensus pattern (20 bp):
AGGGGTATCGATACCTAAGT
Found at i:451687 original size:59 final size:59
Alignment explanation
Indices: 451614--451833 Score: 325
Period size: 59 Copynumber: 3.7 Consensus size: 59
451604 CTAAAATGGT
* * *
451614 TTTCCAAATAGGGCACTTTGTGTGATAAAATGGTAAGGAAATCATACAAAGGGTATGAA
1 TTTCCAGATAGGGCACTTTGTGTGATAAAATGGTAAGGAAATCATACTAAGTGTATGAA
*
451673 TTTCCAGATAGGGCACTTTGTGTGATAAAATGGTAAGGAAATCATACTATGTGTATGAA
1 TTTCCAGATAGGGCACTTTGTGTGATAAAATGGTAAGGAAATCATACTAAGTGTATGAA
* * *
451732 TTTCCAGATAGGGCGCTTTGTATGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAA
1 TTTCCAGATAGGGCACTTTGTGTGATAAAATGGTAAGGAAATCATACTAAGTGTATGAA
* * * *
451791 TTTCTAGATAGGGCA-TTCTATGTGCTAAAATGATAAGGAAATC
1 TTTCCAGATAGGGCACTT-TGTGTGATAAAATGGTAAGGAAATC
451834 TTATTGTTTG
Statistics
Matches: 147, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
58 2 0.01
59 145 0.99
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.30
Consensus pattern (59 bp):
TTTCCAGATAGGGCACTTTGTGTGATAAAATGGTAAGGAAATCATACTAAGTGTATGAA
Found at i:457843 original size:22 final size:23
Alignment explanation
Indices: 457815--457872 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
457805 CATGAAGGGG
*
457815 GTATCGATACCCTAA-TAGGGTA
1 GTATCGATACCATAAGTAGGGTA
457837 GTATCGATACCATAAGTAGGG--
1 GTATCGATACCATAAGTAGGGTA
*
457858 GTATCAATACC-TAAG
1 GTATCGATACCATAAG
457873 GGCTGGAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.12
21 10 0.30
22 14 0.42
23 5 0.15
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.26
Consensus pattern (23 bp):
GTATCGATACCATAAGTAGGGTA
Found at i:457867 original size:21 final size:20
Alignment explanation
Indices: 457812--457872 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 20
457802 ATACATGAAG
457812 GGGGTATCGATACCCTAA-TA
1 GGGGTATCGATA-CCTAAGTA
457832 GGGTAGTATCGATACCATAAGTA
1 GGG--GTATCGATACC-TAAGTA
*
457855 GGGGTATCAATACCTAAG
1 GGGGTATCGATACCTAAG
457873 GGCTGGAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
20 7 0.19
21 12 0.33
22 12 0.33
23 5 0.14
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.25
Consensus pattern (20 bp):
GGGGTATCGATACCTAAGTA
Found at i:458280 original size:59 final size:59
Alignment explanation
Indices: 458188--458401 Score: 304
Period size: 59 Copynumber: 3.6 Consensus size: 59
458178 GATTTACCGA
* * * * **
458188 AGGGCACTTTGTGTGCTAAAATGGTAAGAAAATCATACAAAGGGTGTGAATTTTTAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
*
458247 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTATGTGTATGAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* * * *
458306 AGGGCACTTTGTATACTAAAATGGTAAGGGAGTCATACTAAGTGTATGAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
*
458365 AGGGCACTCTT-TGTGCTAAAATGATAAGGAAATCATA
1 AGGGCACT-TTGTGTGCTAAAATGGTAAGGAAATCATA
458402 TTGTTTGTAT
Statistics
Matches: 137, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
59 135 0.99
60 2 0.01
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (59 bp):
AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
Found at i:458813 original size:32 final size:32
Alignment explanation
Indices: 458777--458858 Score: 87
Period size: 32 Copynumber: 2.6 Consensus size: 32
458767 CATATCATCC
458777 AAAGTGATGATGTGATAT-ATGTCAAATCACTA
1 AAAGTGATGATGTGATATGA-GTCAAATCACTA
* * * * *
458809 AAAGTGATTACGTGATATGAGTCATATTATTA
1 AAAGTGATGATGTGATATGAGTCAAATCACTA
*
458841 AAA-TGATGATATGATATG
1 AAAGTGATGATGTGATATG
458859 TGTTATAGTG
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
31 12 0.29
32 28 0.68
33 1 0.02
ACGTcount: A:0.40, C:0.06, G:0.20, T:0.34
Consensus pattern (32 bp):
AAAGTGATGATGTGATATGAGTCAAATCACTA
Found at i:475250 original size:17 final size:18
Alignment explanation
Indices: 475228--475266 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
475218 ATTTTGAAAA
475228 ATATGTTTT-CAAAAACT
1 ATATGTTTTCCAAAAACT
475245 ATATGTTTTCCAAAAACT
1 ATATGTTTTCCAAAAACT
475263 ATAT
1 ATAT
475267 ATTATATGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.41, C:0.13, G:0.05, T:0.41
Consensus pattern (18 bp):
ATATGTTTTCCAAAAACT
Found at i:475303 original size:36 final size:36
Alignment explanation
Indices: 475250--475337 Score: 133
Period size: 36 Copynumber: 2.4 Consensus size: 36
475240 AAACTATATG
*
475250 TTTTCCAAAAACTATATATTATATGTTTTCATAAACCA
1 TTTT-CAAAAACTATATATTATATGTTTTCA-AAAACA
*
475288 TTTT-AAAAACTATATATTATATGTTTTCAAAAATA
1 TTTTCAAAAACTATATATTATATGTTTTCAAAAACA
475323 TTTTCAAAAACTATA
1 TTTTCAAAAACTATA
475338 CTATATTATT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
35 8 0.17
36 35 0.74
38 4 0.09
ACGTcount: A:0.43, C:0.11, G:0.02, T:0.43
Consensus pattern (36 bp):
TTTTCAAAAACTATATATTATATGTTTTCAAAAACA
Found at i:475862 original size:79 final size:78
Alignment explanation
Indices: 475648--475862 Score: 214
Period size: 79 Copynumber: 2.7 Consensus size: 78
475638 TGTCGCAAAT
** * *
475648 TTGAGTCAATCTTGAGATGTCTTTAAGCATGATATCCTTCGTCATGAAGTTGAAATCGTGGTTGA
1 TTGAGTCAATCTTG-GATG--TTTGGGCATGATATCCTTCGTTATGAAGTTGAAATCGTGGGTGA
* *
475713 CCCCTTCGTTATGAAG
63 CCCCTTCGTCATAAAG
* * * * ** * ** ** *
475729 TTGAGTCAATATCGAATGCCTTGGGCACCATGTATTTCGTTATGAAGTCAAAATCGTGGGTGACT
1 TTGAGTCAATCTTGGATG-TTTGGGCATGATATCCTTCGTTATGAAGTTGAAATCGTGGGTGACC
475794 CCTTCGTCATAAAG
65 CCTTCGTCATAAAG
*
475808 TTGAGTCAATCTTGGATGTTTCGGGCATGATATCCTTCGTTGTGAAGTTGAAATC
1 TTGAGTCAATCTTGGATGTTT-GGGCATGATATCCTTCGTTATGAAGTTGAAATC
475863 TAGTTCGAAA
Statistics
Matches: 103, Mismatches: 30, Indels: 4
0.75 0.22 0.03
Matches are distributed among these distances:
78 2 0.02
79 86 0.83
80 3 0.03
81 12 0.12
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (78 bp):
TTGAGTCAATCTTGGATGTTTGGGCATGATATCCTTCGTTATGAAGTTGAAATCGTGGGTGACCC
CTTCGTCATAAAG
Found at i:476553 original size:198 final size:199
Alignment explanation
Indices: 475913--476637 Score: 913
Period size: 200 Copynumber: 3.6 Consensus size: 199
475903 AATCGTAGTC
* * * * *
475913 AACATTGGTCTTCTTCTTGGCTTAAAGACCTCGGATTTTAAATTAAACCAAAAAGTAGTTCCTCG
1 AACATAGGTCTTCTTCTTGACTTAAAGACCTC-GATTTAAAATTCAACCAGAAAGTAGTTCCTCG
* * * * * *
475978 CTGCTCCCATGCGGTTGATATGCCCTCGAGCTAAATGGAATCGAAATCAAAAGGTTTCGTTGATA
65 CTGCTACCATGCGGTTGATATGCCCTCGAGCTGAATGGAATCGAACTCAAAAGTTTTCATTGACA
* * *
476043 GACATCTTCTCTCGACTTAAGCTATGTTGTAAATTAGGTTGGGAGATAGTTCCTTGTTGCTAAAT
130 GACAACTTTTCTCGACTT-A-CTATGTTGTAAATTAGGCTGGGAGATAGTTCCTTGTTGCTAAAT
*
476108 CGCAACC
193 CGCAACT
* * * *
476115 AACCTAGGTCTTCTTCTTGAATTAAAGACCTC-AGTTTAAACTTCAACCAGAAAATAGTTCCTCG
1 AACATAGGTCTTCTTCTTGACTTAAAGACCTCGA-TTTAAAATTCAACCAGAAAGTAGTTCCTCG
* * *
476179 CTGCTACCATGCGGTTTATATGCCCTCGAGCTGAATGGAATC-AATCTCGAAAGTTTT-GTTGAC
65 CTGCTACCATGCGGTTGATATGCCCTCGAGCTGAATGGAATCGAA-CTCAAAAGTTTTCATTGAC
* ** * * * * *
476242 AGATAACCCTTCTCGCCTTGAGCTATGATGTAAATTAGGCTGTGAGATAGCTCCTTGTTACTAAA
129 AGACAACTTTTCTCGACTT-A-CTATGTTGTAAATTAGGCTGGGAGATAGTTCCTTGTTGCTAAA
*
476307 TCGCAACA
192 TCGCAACT
* * * *
476315 AACATAGGTCTTCTTCTTAACTTAAAGACCTCGGTTTAAAATTCAACCAGAATGTAGTTCCTCAC
1 AACATAGGTCTTCTTCTTGACTTAAAGACCTCGATTTAAAATTCAACCAGAAAGTAGTTCCTCGC
* * * *
476380 TGCTATCATGCGATTGATACGCCCTCGAGCTGAATGGAATCGAACTTAAAAGTTTTCATTGACAG
66 TGCTACCATGCGGTTGATATGCCCTCGAGCTGAATGGAATCGAACTCAAAAGTTTTCATTGACAG
476445 ACAACTTTTCTCGACTT-CTATGTTGTAAATTAGGCTGGGAGATAGTTCCTTGTTGCTAAATCG-
131 ACAACTTTTCTCGACTTACTATGTTGTAAATTAGGCTGGGAGATAGTTCCTTGTTGCTAAATCGC
476508 AAGCT
196 AA-CT
* * * * * *
476513 AACCTAGGTCTTCTTATGGGCTTAAAGGCCTCGATTTAAAATTCAACC-GAAAAGTAGTTCCTTG
1 AACATAGGTCTTCTTCTTGACTTAAAGACCTCGATTTAAAATTCAACCAG-AAAGTAGTTCCTCG
*
476577 CTGCTACCATGCGGTTGATATGCCCTCGAGCTGAATGGAATCGAACTCGAAAGTTTTCATT
65 CTGCTACCATGCGGTTGATATGCCCTCGAGCTGAATGGAATCGAACTCAAAAGTTTTCATT
476638 AATAGATAGA
Statistics
Matches: 448, Mismatches: 68, Indels: 18
0.84 0.13 0.03
Matches are distributed among these distances:
197 3 0.01
198 151 0.34
200 171 0.38
201 95 0.21
202 28 0.06
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (199 bp):
AACATAGGTCTTCTTCTTGACTTAAAGACCTCGATTTAAAATTCAACCAGAAAGTAGTTCCTCGC
TGCTACCATGCGGTTGATATGCCCTCGAGCTGAATGGAATCGAACTCAAAAGTTTTCATTGACAG
ACAACTTTTCTCGACTTACTATGTTGTAAATTAGGCTGGGAGATAGTTCCTTGTTGCTAAATCGC
AACT
Found at i:478439 original size:20 final size:21
Alignment explanation
Indices: 478414--478453 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
478404 CTTTACATAG
478414 TAGTATCGATACCAT-AGGCT
1 TAGTATCGATACCATCAGGCT
478434 TAGTATCGATACCATCAGGC
1 TAGTATCGATACCATCAGGC
478454 CCAATGACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.28
Consensus pattern (21 bp):
TAGTATCGATACCATCAGGCT
Found at i:482270 original size:14 final size:14
Alignment explanation
Indices: 482251--482279 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
482241 GGGTGATTCT
482251 AGTTTAGCCAAGTG
1 AGTTTAGCCAAGTG
482265 AGTTTAGCCAAGTG
1 AGTTTAGCCAAGTG
482279 A
1 A
482280 AAACTAAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.28
Consensus pattern (14 bp):
AGTTTAGCCAAGTG
Found at i:486694 original size:23 final size:23
Alignment explanation
Indices: 486667--486793 Score: 101
Period size: 23 Copynumber: 5.4 Consensus size: 23
486657 TAATTATGTC
**
486667 TTTATCTCTATCTTTATGATATG
1 TTTATCTCTATCTTTATGATACA
* * **
486690 TTTATTTCATATTTTTTATGATATG
1 TTTATCTC-TA-TCTTTATGATACA
* *
486715 TTTATCTCTGTTTTTATGATACA
1 TTTATCTCTATCTTTATGATACA
** *
486738 TTTATCTCCGTCTTTATGACACA
1 TTTATCTCTATCTTTATGATACA
* * *
486761 TTTATTTATATCTTTATGACACA
1 TTTATCTCTATCTTTATGATACA
*
486784 TTTTTCTCTA
1 TTTATCTCTA
486794 ATTTTTGATT
Statistics
Matches: 86, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
23 64 0.74
24 3 0.03
25 19 0.22
ACGTcount: A:0.23, C:0.14, G:0.07, T:0.56
Consensus pattern (23 bp):
TTTATCTCTATCTTTATGATACA
Found at i:488727 original size:37 final size:37
Alignment explanation
Indices: 488673--488858 Score: 186
Period size: 37 Copynumber: 5.0 Consensus size: 37
488663 TGAAAATACA
488673 TATATAATATATAGTTTTCTTAAAAACATTTTGAAAA-
1 TATATAATATATAGTTTT-TTAAAAACATTTTGAAAAC
* *
488710 TGTATAGTATATAGTTTTTTTAAAACACA-TTTGAAAAC
1 TATATAATATATAG-TTTTTTAAAA-ACATTTTGAAAAC
* *
488748 TATATAATATATAG-TTTTT-AAAACATTTAGAAAAA
1 TATATAATATATAGTTTTTTAAAAACATTTTGAAAAC
** *
488783 TATATAATATAT-GGGTTTTAAAATCATATTTTTTGAAAAC
1 TATATAATATATAGTTTTTTAAAA--ACA--TTTTGAAAAC
*
488823 TTATATAATATATAG-TTTTTAAAAACATTTTTAAAA
1 -TATATAATATATAGTTTTTTAAAAACATTTTGAAAA
488859 AATTATATAT
Statistics
Matches: 124, Mismatches: 13, Indels: 24
0.77 0.08 0.15
Matches are distributed among these distances:
34 4 0.03
35 26 0.21
36 8 0.06
37 34 0.27
38 21 0.17
39 2 0.02
40 8 0.06
41 20 0.16
42 1 0.01
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.44
Consensus pattern (37 bp):
TATATAATATATAGTTTTTTAAAAACATTTTGAAAAC
Found at i:488865 original size:38 final size:35
Alignment explanation
Indices: 488672--488886 Score: 162
Period size: 38 Copynumber: 5.7 Consensus size: 35
488662 TTGAAAATAC
*
488672 ATATATAATATATAGTTTTCTTAAAAACATTTTGAAA
1 ATATATAATATATAG-TTT-TTAAAAACATTTTAAAA
* * *
488709 ATGTATAGTATATAGTTTTTTTAAAACACATTTGAAAA
1 ATATATAATATATAG--TTTTTAAAA-ACATTTTAAAA
* *
488747 CTATATAATATATAGTTTTT-AAAACATTTAGAAAA
1 ATATATAATATATAGTTTTTAAAAACATTT-TAAAA
* * *
488782 ATATATAATATATGGGTTTTAAAATCATATTTTTTGAAAA
1 ATATATAATATATAGTTTTTAAAA--ACA--TTTT-AAAA
*
488822 CTTATATAATATATAGTTTTTAAAAACATTTTTAAAAAA
1 -ATATATAATATATAGTTTTTAAAAACA-TTTT--AAAA
* *
488861 TTATATATAATATATAATTTCTAAAA
1 --ATATATAATATATAGTTTTTAAAA
488887 CTCTTTTGGA
Statistics
Matches: 145, Mismatches: 21, Indels: 21
0.78 0.11 0.11
Matches are distributed among these distances:
34 6 0.04
35 25 0.17
36 8 0.06
37 19 0.13
38 32 0.22
39 6 0.04
40 28 0.19
41 21 0.14
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (35 bp):
ATATATAATATATAGTTTTTAAAAACATTTTAAAA
Found at i:488868 original size:40 final size:39
Alignment explanation
Indices: 488659--488886 Score: 174
Period size: 40 Copynumber: 5.9 Consensus size: 39
488649 TCACAAACGG
488659 TTTTT-GAAAATACATATATAATATATAGTTTTCTTAAAAACA
1 TTTTTAGAAAAT--ATATATAATATATAG-TTT-TTAAAAACA
* * *
488701 -TTTT-G-AAA-ATGTATAGTATATAGTTTTTTTAAAACA
1 TTTTTAGAAAATATATATAATATATAG-TTTTTAAAAACA
** *
488737 CATTT-GAAAA-CTATATAATATATAGTTTTT-AAAACA
1 TTTTTAGAAAATATATATAATATATAGTTTTTAAAAACA
* * *
488773 --TTTAGAAAA-ATATATAATATATGGGTTTTAAAATCATA
1 TTTTTAGAAAATATATATAATATATAGTTTTTAAAA--ACA
*
488811 TTTTTTGAAAACT-TATATAATATATAGTTTTTAAAAACA
1 TTTTTAGAAAA-TATATATAATATATAGTTTTTAAAAACA
* * *
488850 TTTTTAAAAAATTATATATAATATATAATTTCTAAAA
1 TTTTTAGAAAA-TATATATAATATATAGTTTTTAAAA
488887 CTCTTTTGGA
Statistics
Matches: 155, Mismatches: 20, Indels: 24
0.78 0.10 0.12
Matches are distributed among these distances:
34 3 0.02
35 22 0.14
36 17 0.11
37 26 0.17
38 17 0.11
39 12 0.08
40 32 0.21
41 26 0.17
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (39 bp):
TTTTTAGAAAATATATATAATATATAGTTTTTAAAAACA
Found at i:489024 original size:11 final size:11
Alignment explanation
Indices: 489008--489035 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
488998 TTTTAAAAAT
489008 TATATTATATA
1 TATATTATATA
489019 TATATTATATA
1 TATATTATATA
489030 TATATT
1 TATATT
489036 TAAATAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
TATATTATATA
Found at i:489284 original size:16 final size:15
Alignment explanation
Indices: 489263--489292 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
489253 GCCAGCGAAA
489263 ATCCCGGGACTGACCC
1 ATCCCGGGA-TGACCC
489279 ATCCCGGGATGACC
1 ATCCCGGGATGACC
489293 TCGCGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.20, C:0.40, G:0.27, T:0.13
Consensus pattern (15 bp):
ATCCCGGGATGACCC
Found at i:489866 original size:14 final size:16
Alignment explanation
Indices: 489834--489866 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
489824 TTTTATTTTG
489834 TTTTATCGTCATTATT
1 TTTTATCGTCATTATT
*
489850 TTTTCTCGT-ATTATT
1 TTTTATCGTCATTATT
489865 TT
1 TT
489867 ATTTTATTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.15, C:0.12, G:0.06, T:0.67
Consensus pattern (16 bp):
TTTTATCGTCATTATT
Found at i:490061 original size:8 final size:8
Alignment explanation
Indices: 489976--490073 Score: 58
Period size: 8 Copynumber: 12.0 Consensus size: 8
489966 CTTTTGCAAC
489976 TTTTATTT
1 TTTTATTT
489984 TTATT-TTT
1 TT-TTATTT
489992 CTTTTCATTT
1 -TTTT-ATTT
*
490002 TTTTAATT
1 TTTTATTT
*
490010 TGTTATTT
1 TTTTATTT
* *
490018 TATTCTTT
1 TTTTATTT
*
490026 TATTTA-CT
1 T-TTTATTT
* *
490034 CTTGATTT
1 TTTTATTT
*
490042 ATTTATTT
1 TTTTATTT
490050 TTTT-TTT
1 TTTTATTT
490057 ATTTTATTT
1 -TTTTATTT
490066 TTTTATTT
1 TTTTATTT
490074 ATTGTCGCTA
Statistics
Matches: 68, Mismatches: 14, Indels: 16
0.69 0.14 0.16
Matches are distributed among these distances:
7 6 0.09
8 46 0.68
9 13 0.19
10 3 0.04
ACGTcount: A:0.15, C:0.05, G:0.02, T:0.78
Consensus pattern (8 bp):
TTTTATTT
Found at i:490091 original size:43 final size:44
Alignment explanation
Indices: 490012--490102 Score: 105
Period size: 43 Copynumber: 2.1 Consensus size: 44
490002 TTTTAATTTG
* *
490012 TTATTTTATTCTTTTATTTACTCTTGATTTATTTATT-TTTTTT
1 TTATTTTATTCTTTTATTTACTCTCGATTTATTTATTATTTTTC
* * * *
490055 TTATTTTATTTTTTTATTTATTGTCGCTATTA-TTATTATTTTTC
1 TTATTTTATTCTTTTATTTACTCTCGAT-TTATTTATTATTTTTC
490099 TTAT
1 TTAT
490103 CTAACATGAT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
43 28 0.70
44 12 0.30
ACGTcount: A:0.18, C:0.07, G:0.03, T:0.73
Consensus pattern (44 bp):
TTATTTTATTCTTTTATTTACTCTCGATTTATTTATTATTTTTC
Found at i:491398 original size:13 final size:13
Alignment explanation
Indices: 491380--491404 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
491370 AGGAAAATAT
491380 TTATTTATTATTG
1 TTATTTATTATTG
491393 TTATTTATTATT
1 TTATTTATTATT
491405 ATTTGTTTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (13 bp):
TTATTTATTATTG
Found at i:491410 original size:17 final size:17
Alignment explanation
Indices: 491377--491424 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
491367 ACAAGGAAAA
491377 TATTTATTTATTA-TTGT
1 TATTTA-TTATTATTTGT
491394 TATTTATTATTATTTGT
1 TATTTATTATTATTTGT
*
491411 T-TCTATTACTTATT
1 TATTTATTA-TTATT
491425 ATTCATTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 12 0.43
17 16 0.57
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.69
Consensus pattern (17 bp):
TATTTATTATTATTTGT
Found at i:492606 original size:14 final size:16
Alignment explanation
Indices: 492574--492606 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
492564 TTTTATTTTG
492574 TTTTATCGTCATTATT
1 TTTTATCGTCATTATT
*
492590 TTTTCTCGT-ATTATT
1 TTTTATCGTCATTATT
492605 TT
1 TT
492607 ATTTTATTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.15, C:0.12, G:0.06, T:0.67
Consensus pattern (16 bp):
TTTTATCGTCATTATT
Done.