Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008668.1 Hibiscus syriacus cultivar Beakdansim tig00111671_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: 2122653
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 9
Found at i:604888 original size:71 final size:71
Alignment explanation
Indices: 604800--605039 Score: 355
Period size: 71 Copynumber: 3.4 Consensus size: 71
604790 GCAACGAGAG
*
604800 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
604865 AATGAA
66 AATGAA
* * *
604871 AATCGCAATGCGAAATGAAAATCG-AA-CCGACAT---AATCGCAATGCGAAATTAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG-AA--AGAATCGCAA
*
604931 TACGAAATGAA
61 TGCGAAATGAA
604942 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
605007 AATGAA
66 AATGAA
605013 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
605040 CGAGATAATC
Statistics
Matches: 150, Mismatches: 9, Indels: 20
0.84 0.05 0.11
Matches are distributed among these distances:
66 8 0.05
68 2 0.01
69 6 0.04
70 2 0.01
71 113 0.75
72 2 0.01
73 7 0.05
74 2 0.01
76 8 0.05
ACGTcount: A:0.47, C:0.17, G:0.20, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
AATGAA
Found at i:604972 original size:142 final size:138
Alignment explanation
Indices: 604734--605071 Score: 499
Period size: 142 Copynumber: 2.4 Consensus size: 138
604724 CGGAAAATAC
* * *
604734 AATCGCAACGCGAAATGAAAATC---CCAACATGAAATCGCAATGCGGAAATGAAAATCGC-AAC
1 AATCGCAATGCGAAATGAAAATCGAACCGACAT--AATCGCAATGC-GAAATTAAAATCGCAAAC
* *
604795 GAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAA
63 GAGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAA
604860 TGCGAAATGAA
128 TGCGAAATGAA
604871 AATCGCAATGCGAAATGAAAATCGAACCGACATAATCGCAATGCGAAATTAAAATCGCAATACGA
1 AATCGCAATGCGAAATGAAAATCGAACCGACATAATCGCAATGCGAAATTAAAATCGCAA-ACG-
604936 AATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCA
64 -A-GAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCA
605001 ATGCGAAATGAA
127 ATGCGAAATGAA
*
605013 AATCGCAATGCGAAATGAAAATCGCAA-CGAGATAATCGCAATGCGAAATTATAAA-CGCA
1 AATCGCAATGCGAAATGAAAATCG-AACCGACATAATCGCAATGCGAAATTA-AAATCGCA
605072 TTGCGATTTT
Statistics
Matches: 185, Mismatches: 6, Indels: 15
0.90 0.03 0.07
Matches are distributed among these distances:
137 35 0.19
138 12 0.06
139 3 0.02
140 6 0.03
141 1 0.01
142 123 0.66
143 5 0.03
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (138 bp):
AATCGCAATGCGAAATGAAAATCGAACCGACATAATCGCAATGCGAAATTAAAATCGCAAACGAG
AAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGC
GAAATGAA
Found at i:605176 original size:19 final size:19
Alignment explanation
Indices: 605068--605168 Score: 142
Period size: 19 Copynumber: 5.6 Consensus size: 19
605058 AAATTATAAA
605068 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
605087 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
605107 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
605123 CG--TTGCGA-TTTCATTT
1 CGCATTGCGATTTTCATTT
605139 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
605158 CGCATTGCGAT
1 CGCATTGCGAT
605169 AGTCATTTTG
Statistics
Matches: 74, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
15 3 0.04
16 8 0.11
17 3 0.04
18 6 0.08
19 29 0.39
20 19 0.26
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:605292 original size:14 final size:14
Alignment explanation
Indices: 605273--605309 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
605263 CATCAATTAC
605273 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
605287 ACAAATCATCTTTT
1 ACAAATCAACTTTT
605301 ACAAATCAA
1 ACAAATCAA
605310 TTAAACAATC
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:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:605321 original size:12 final size:12
Alignment explanation
Indices: 605304--605376 Score: 53
Period size: 12 Copynumber: 6.0 Consensus size: 12
605294 ATCTTTTACA
605304 AATCAATTAAAC
1 AATCAATTAAAC
*
605316 AATCAA--AAATTG
1 AATCAATTAAA--C
**
605328 AATCAACTTTTAC
1 AATCAA-TTAAAC
605341 AAATCAATTAAAC
1 A-ATCAATTAAAC
*
605354 AATCAA-AAAAC
1 AATCAATTAAAC
605365 AATCAATTAAAC
1 AATCAATTAAAC
605377 TATTGAATCA
Statistics
Matches: 46, Mismatches: 8, Indels: 14
0.68 0.12 0.21
Matches are distributed among these distances:
10 3 0.07
11 10 0.22
12 21 0.46
13 6 0.13
14 5 0.11
15 1 0.02
ACGTcount: A:0.58, C:0.16, G:0.01, T:0.25
Consensus pattern (12 bp):
AATCAATTAAAC
Found at i:605338 original size:38 final size:38
Alignment explanation
Indices: 605290--605362 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
605280 AACTTTTACA
*
605290 AATCATCTTTTACAAATCAATTAAACAATCAAAAATTG
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
605328 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
605363 ACAATCAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.53, C:0.16, G:0.01, T:0.29
Consensus pattern (38 bp):
AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
Found at i:607248 original size:14 final size:14
Alignment explanation
Indices: 607229--607285 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
607219 GCGAAATGAA
*
607229 AATCGCAACGACAG
1 AATCGCAACGAAAG
607243 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
607260 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
607276 AATCGCAACG
1 AATCGCAACG
607286 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:607256 original size:33 final size:33
Alignment explanation
Indices: 607210--607302 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
607200 GCGAAACCAA
*
607210 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
607243 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
607276 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
607303 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:607267 original size:19 final size:19
Alignment explanation
Indices: 607173--607307 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
607163 TAGTTTACTT
* *
607173 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
607193 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
607212 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
607231 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
607245 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
607264 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
607278 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
607297 TCGCAATGCGA
1 TCGCAACGCGA
607308 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:607325 original size:19 final size:19
Alignment explanation
Indices: 607303--607431 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
607293 AAAATCGCAA
607303 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
607322 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
607336 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
607355 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
607369 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
607388 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
607407 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
607427 TGCGA
1 TGCGA
607432 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:607345 original size:33 final size:33
Alignment explanation
Indices: 607303--607394 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
607293 AAAATCGCAA
607303 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
607336 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
607369 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
607395 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:607765 original size:92 final size:93
Alignment explanation
Indices: 607475--607853 Score: 744
Period size: 92 Copynumber: 4.1 Consensus size: 93
607465 TTGAATGGAT
607475 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
607540 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
607568 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
607633 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
607661 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
607725 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
607753 AAATTTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
607817 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
607845 AAATTTACT
1 AAATTTACT
607854 AAGCAATCTA
Statistics
Matches: 285, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
91 15 0.05
92 138 0.48
93 132 0.46
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:609576 original size:14 final size:14
Alignment explanation
Indices: 609557--609646 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
609547 TTGAAATGAA
609557 AATCGCAACGAGAG
1 AATCGCAACGAGAG
609571 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
*
609588 ACAATCGCAACGATAG
1 --AATCGCAACGAGAG
*
609604 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
609623 AATCGCAACGAGAG
1 AATCGCAACGAGAG
609637 AATCGCAACG
1 AATCGCAACG
609647 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 28 0.45
15 1 0.02
16 8 0.13
17 7 0.11
18 1 0.02
19 17 0.27
ACGTcount: A:0.42, C:0.23, G:0.24, T:0.10
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:609594 original size:33 final size:33
Alignment explanation
Indices: 609549--609663 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
609539 TCTTTTGGTT
609549 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* * *
609582 GAGATGACAATCGCAACGATAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
609615 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
609648 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
609664 TGCGATTTTG
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 76 1.00
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:609595 original size:19 final size:19
Alignment explanation
Indices: 609552--609668 Score: 84
Period size: 19 Copynumber: 6.9 Consensus size: 19
609542 TTTGGTTGAA
609552 ATGAAAATCGCAA--CGAG
1 ATGAAAATCGCAACGCGAG
609569 A-G--AATCGCAACGCGAG
1 ATGAAAATCGCAACGCGAG
*
609585 ATGACAATCGCAA--C--G
1 ATGAAAATCGCAACGCGAG
* *
609600 AT-AGAATCGCAACGCGAA
1 ATGAAAATCGCAACGCGAG
609618 ATGAAAATCGCAA--CGAG
1 ATGAAAATCGCAACGCGAG
*
609635 A-G--AATCGCAACGCGAA
1 ATGAAAATCGCAACGCGAG
*
609651 ATGAAAATCGCAATGCGA
1 ATGAAAATCGCAACGCGA
609669 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 6, Indels: 28
0.70 0.05 0.25
Matches are distributed among these distances:
14 25 0.32
15 3 0.04
16 12 0.15
17 8 0.10
18 2 0.03
19 29 0.37
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.11
Consensus pattern (19 bp):
ATGAAAATCGCAACGCGAG
Found at i:609699 original size:14 final size:14
Alignment explanation
Indices: 609680--609734 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
609670 TTTGGTTTCG
609680 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
609694 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
609713 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
609727 CGTTGCGA
1 CGTTGCGA
609735 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:609897 original size:33 final size:33
Alignment explanation
Indices: 609855--609925 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
609845 AATACTAACT
*
609855 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
609888 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
609921 TGAAA
1 TGAAA
609926 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:610159 original size:22 final size:22
Alignment explanation
Indices: 610107--610161 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
610097 TGGTTGTGAG
**
610107 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
610129 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
610151 GGATTTCTTCG
1 GGATTTCTTCG
610162 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:610332 original size:20 final size:20
Alignment explanation
Indices: 610307--610500 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
610297 CTTTAAATAT
610307 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
610327 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
610349 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
610368 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
610388 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
610408 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
610428 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
610448 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
610468 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
610488 CGCGTTGCGATTT
1 CGCGTTGCGATTT
610501 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:610494 original size:60 final size:60
Alignment explanation
Indices: 610307--610500 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
610297 CTTTAAATAT
**
610307 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
610368 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
610428 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
610488 CGCGTTGCGATTT
1 CGCGTTGCGATTT
610501 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:610517 original size:21 final size:20
Alignment explanation
Indices: 610493--610569 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
610483 ATATTCGCGT
610493 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
610514 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
610534 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
610556 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
610570 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:610580 original size:20 final size:20
Alignment explanation
Indices: 610555--610606 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
610545 AAGAATCGCG
*
610555 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
610575 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
610595 TTGCGATTCTGG
1 TTGCGATTCTGG
610607 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:624600 original size:23 final size:23
Alignment explanation
Indices: 624574--624652 Score: 88
Period size: 23 Copynumber: 3.4 Consensus size: 23
624564 TTTGGTTCTC
*
624574 GAACATTAAATAAATATGTTCAT
1 GAACATTAAATGAATATGTTCAT
* *
624597 GAACATTATATGAATATGGTT-GT
1 GAACATTAAATGAATAT-GTTCAT
* *
624620 GACCATTAAATGAATATATTCAT
1 GAACATTAAATGAATATGTTCAT
*
624643 AAACATTAAA
1 GAACATTAAA
624653 CAAACATTCA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
22 2 0.04
23 40 0.89
24 3 0.07
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.34
Consensus pattern (23 bp):
GAACATTAAATGAATATGTTCAT
Found at i:625363 original size:20 final size:20
Alignment explanation
Indices: 625338--625407 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
625328 GCGAAGTTCG
625338 CGTTGCGATTCATTCCAAAT
1 CGTTGCGATTCATTCCAAAT
* * *
625358 CGTTGCGA-T-AGTCGAAGTT
1 CGTTGCGATTCATTCCAA-AT
625377 CGCGTTGCGATTCATTCCAAAT
1 --CGTTGCGATTCATTCCAAAT
625399 CGTTGCGAT
1 CGTTGCGAT
625408 AGGCGAAGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
18 5 0.13
19 2 0.05
20 17 0.44
21 8 0.21
22 2 0.05
23 5 0.13
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (20 bp):
CGTTGCGATTCATTCCAAAT
Found at i:625374 original size:41 final size:42
Alignment explanation
Indices: 625279--625636 Score: 625
Period size: 41 Copynumber: 8.6 Consensus size: 42
625269 GATTCGCAAC
* * * *
625279 GCGATAGTCGAAGTTTGCATTGCGATTTATTCCAAATTCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
625321 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAA-TCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
*
625362 GCGATAGTCGAAGTTCGCGTTGCGATTCATTCCAAA-TCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
625403 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCC-AATTCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
625444 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCC-AATTCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
625485 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
*
625527 GCGATAGGTGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
625569 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
*
625611 GCGATAGGCGAAGTTCGCATTGCGAT
1 GCGATAGGCGAAGTTCGCGTTGCGAT
625637 AGTCCAAATA
Statistics
Matches: 305, Mismatches: 9, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
40 2 0.01
41 156 0.51
42 147 0.48
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.32
Consensus pattern (42 bp):
GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
Found at i:625727 original size:6 final size:6
Alignment explanation
Indices: 625716--625748 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
625706 AACACGTATT
625716 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
625749 CGAGACGGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:629926 original size:2 final size:2
Alignment explanation
Indices: 629919--629943 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
629909 TGCTTGTTAT
629919 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
629944 GGACAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:630680 original size:18 final size:19
Alignment explanation
Indices: 630645--630681 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
630635 CACGAAATGT
630645 AAGATTACCAGTGAGAATAA
1 AAGATTACCAG-GAGAATAA
630665 AAGATTACCA-GAGAATA
1 AAGATTACCAGGAGAATA
630682 GGATTACTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.51, C:0.11, G:0.19, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGAGAATAA
Found at i:636733 original size:15 final size:16
Alignment explanation
Indices: 636713--636742 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
636703 ATAAATTTGT
636713 ATAAAAA-TAAAAAAA
1 ATAAAAACTAAAAAAA
636728 ATAAAAACTAAAAAA
1 ATAAAAACTAAAAAA
636743 TGTTACATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.13
Consensus pattern (16 bp):
ATAAAAACTAAAAAAA
Found at i:636913 original size:2 final size:2
Alignment explanation
Indices: 636906--636931 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
636896 TACGTTCGAC
636906 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
636932 ACTTGACCGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:637516 original size:30 final size:29
Alignment explanation
Indices: 637457--637516 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 29
637447 ACAAGGGAAA
* *
637457 TATTAAAATTTTGTAAAAAATATAGAAAT
1 TATTAAAATTTTATAAAAAATATAAAAAT
637486 TATTAAAATTTTCCATAAAAAA-ATAAAAAT
1 TATTAAAATTTT--ATAAAAAATATAAAAAT
637516 T
1 T
637517 CAAGATTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 12 0.44
30 8 0.30
31 7 0.26
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (29 bp):
TATTAAAATTTTATAAAAAATATAAAAAT
Found at i:638320 original size:65 final size:65
Alignment explanation
Indices: 638239--638457 Score: 323
Period size: 65 Copynumber: 3.4 Consensus size: 65
638229 TAAGTATAAT
* * *
638239 AAAAATAAATAAATATTTTAAAAATTAAATAATATTATTTCAGATAAATAAATAATACGATTTTG
1 AAAATTAAATAAATATTTTAAAAATTAAATAATATTATTTCAAATAAATAAATAATATGATTTTG
* *
638304 AAAATTAAATAAATA-TTTAAAAATTAAATAATATAATTTCAAATAAATAAATATTATGATTTTG
1 AAAATTAAATAAATATTTTAAAAATTAAATAATATTATTTCAAATAAATAAATAATATGATTTTG
* * * *
638368 AAAATTAAATAAATATTTTAAAAATTAAATAATATTATTTCAAATAAATAAATGATTTGGTTTTA
1 AAAATTAAATAAATATTTTAAAAATTAAATAATATTATTTCAAATAAATAAATAATATGATTTTG
* * *
638433 AAAATTAGATAAACATTTTTAAAAT
1 AAAATTAAATAAATATTTTAAAAAT
638458 ATTATAAATA
Statistics
Matches: 139, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
64 60 0.43
65 79 0.57
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (65 bp):
AAAATTAAATAAATATTTTAAAAATTAAATAATATTATTTCAAATAAATAAATAATATGATTTTG
Found at i:638390 original size:129 final size:131
Alignment explanation
Indices: 638239--638473 Score: 350
Period size: 129 Copynumber: 1.8 Consensus size: 131
638229 TAAGTATAAT
* *
638239 AAAAATAAATAAATATTTTAAAAATTAAATAATATTATTTCAGATAAATAAATAATACGATTTTG
1 AAAAATAAATAAATATTTTAAAAATTAAATAATATTATTTCAAATAAATAAATAATACGATTTTA
638304 AAAATTAAAT-AA-ATATTTAAAA-ATTAAATAATATAATTTCAAATAAATAAATATTATGATTT
66 AAAATTAAATAAACATATTTAAAATATTAAA-AATATAATTTCAAATAAATAAATATTATGATTT
638366 TG
130 TG
* * ** *
638368 AAAATTAAATAAATATTTTAAAAATTAAATAATATTATTTCAAATAAATAAATGATTTGGTTTTA
1 AAAAATAAATAAATATTTTAAAAATTAAATAATATTATTTCAAATAAATAAATAATACGATTTTA
* * *
638433 AAAATTAGATAAACATTTTTAAAATATTATAAATATAATTT
66 AAAATTAAATAAACATATTTAAAATATTAAAAATATAATTT
638474 TTAGATTGAA
Statistics
Matches: 93, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
129 67 0.72
130 2 0.02
131 19 0.20
132 5 0.05
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (131 bp):
AAAAATAAATAAATATTTTAAAAATTAAATAATATTATTTCAAATAAATAAATAATACGATTTTA
AAAATTAAATAAACATATTTAAAATATTAAAAATATAATTTCAAATAAATAAATATTATGATTTT
G
Found at i:639863 original size:17 final size:16
Alignment explanation
Indices: 639836--639869 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
639826 CTAGCTATTT
639836 TTATAAAAAATAAATA
1 TTATAAAAAATAAATA
639852 TTATATAAAAATAAATA
1 TTATA-AAAAATAAATA
639869 T
1 T
639870 ATTAATTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TTATAAAAAATAAATA
Found at i:645086 original size:24 final size:24
Alignment explanation
Indices: 645054--645099 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
645044 TATGGTTGGA
645054 GAAGAAGAGAGAAGAGGAAGCATC
1 GAAGAAGAGAGAAGAGGAAGCATC
*
645078 GAAGAAGAGAGATGAGGAAGCA
1 GAAGAAGAGAGAAGAGGAAGCA
645100 GGAGCAATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.50, C:0.07, G:0.39, T:0.04
Consensus pattern (24 bp):
GAAGAAGAGAGAAGAGGAAGCATC
Found at i:651547 original size:2 final size:2
Alignment explanation
Indices: 651540--651564 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
651530 TTGCATTTCA
651540 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
651565 CACGAGGACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:651811 original size:13 final size:13
Alignment explanation
Indices: 651793--651818 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
651783 GAATCCTAAC
651793 TCATATATATATA
1 TCATATATATATA
651806 TCATATATATATA
1 TCATATATATATA
651819 GATATAGATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
TCATATATATATA
Found at i:653987 original size:2 final size:2
Alignment explanation
Indices: 653980--654005 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
653970 TGGTGGATGG
653980 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
654006 TATTCGGGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:661102 original size:2 final size:2
Alignment explanation
Indices: 661095--661132 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
661085 TGTTTCGTCA
661095 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
661133 GAATAATGGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:662880 original size:23 final size:22
Alignment explanation
Indices: 662829--662880 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
662819 TTAACCATTT
*
662829 ATTAATGATTTTATATTATTAA
1 ATTAATAATTTTATATTATTAA
** *
662851 ACAAATAATATTTATATTTTTAA
1 ATTAATAAT-TTTATATTATTAA
662874 ATTAATA
1 ATTAATA
662881 TATAATATAA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (22 bp):
ATTAATAATTTTATATTATTAA
Found at i:663035 original size:23 final size:22
Alignment explanation
Indices: 662984--663035 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
662974 CTACCATTTT
*
662984 ATTAATGATTTTATATTATTAA
1 ATTAATAATTTTATATTATTAA
** *
663006 ACAAATAATATTTATATTTTTAA
1 ATTAATAAT-TTTATATTATTAA
663029 ATTAATA
1 ATTAATA
663036 TATAATTAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (22 bp):
ATTAATAATTTTATATTATTAA
Found at i:663139 original size:155 final size:155
Alignment explanation
Indices: 662826--663127 Score: 574
Period size: 155 Copynumber: 2.0 Consensus size: 155
662816 TTTTTAACCA
662826 TTTATTAATGATTTTATATTATTAAACAAATAATATTTATATTTTTAAATTAATATATAATATAA
1 TTTATTAATGATTTTATATTATTAAACAAATAATATTTATATTTTTAAATTAATATATAATATAA
662891 ATAAAATTATTTGAATTTGAGTTTTTAAAAATAATATGTTTTAGGTACAACCAATTTGTTTAGTA
66 ATAAAATTATTTGAATTTGAGTTTTTAAAAATAATATGTTTTAGGTACAACCAATTTGTTTAGTA
*
662956 AGATAAGATATTAGATTCCTACCAT
131 AGATAAGATATTAGATTCCTACAAT
662981 TTTATTAATGATTTTATATTATTAAACAAATAATATTTATATTTTTAAATTAATATATAAT-TAA
1 TTTATTAATGATTTTATATTATTAAACAAATAATATTTATATTTTTAAATTAATATATAATATAA
663045 ATAAAATTATTTGAATTTGAGTTTTT-AAAA-AATATGTTTTAGGTACAACCAATTTGTTTAGTA
66 ATAAAATTATTTGAATTTGAGTTTTTAAAAATAATATGTTTTAGGTACAACCAATTTGTTTAGTA
663108 AGATAAGATATTAGATTCCT
131 AGATAAGATATTAGATTCCT
663128 TAAATAATTT
Statistics
Matches: 147, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
152 53 0.36
153 4 0.03
154 29 0.20
155 61 0.41
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.46
Consensus pattern (155 bp):
TTTATTAATGATTTTATATTATTAAACAAATAATATTTATATTTTTAAATTAATATATAATATAA
ATAAAATTATTTGAATTTGAGTTTTTAAAAATAATATGTTTTAGGTACAACCAATTTGTTTAGTA
AGATAAGATATTAGATTCCTACAAT
Found at i:665788 original size:24 final size:21
Alignment explanation
Indices: 665754--665803 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
665744 TTTTGGGGTT
*
665754 TTTTTTTAAATTTGATTTTTTTA
1 TTTTTTTAAAATT-A-TTTTTTA
665777 TTTTTTTAAAATTATTTTTTA
1 TTTTTTTAAAATTATTTTTTA
665798 TTTTTT
1 TTTTTT
665804 ATTTTAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 13 0.50
22 1 0.04
23 12 0.46
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (21 bp):
TTTTTTTAAAATTATTTTTTA
Found at i:665812 original size:24 final size:23
Alignment explanation
Indices: 665752--665812 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 23
665742 AGTTTTGGGG
665752 TTTTTTTTTAAATTTGATTTTTTT
1 TTTTTTTTTAAA-TTGATTTTTTT
* *
665776 ATTTTTTTAAAATT-ATTTTTTAT
1 TTTTTTTTTAAATTGATTTTTT-T
665799 TTTTTATTTTAAAT
1 TTTTT-TTTTAAAT
665813 AAATTTCTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
22 7 0.23
23 7 0.23
24 17 0.55
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.74
Consensus pattern (23 bp):
TTTTTTTTTAAATTGATTTTTTT
Found at i:673733 original size:35 final size:35
Alignment explanation
Indices: 673694--673763 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 35
673684 CTATGAAAGA
*
673694 TCATATAAA-TTATAT-TTTCTTTATAAAATTTAAAT
1 TCATA-AAATTTATATATTT-TTTACAAAATTTAAAT
673729 TCATAAAATTTATATAATTTTTTACAAAATTTAAA
1 TCATAAAATTTATAT-ATTTTTTACAAAATTTAAA
673764 AGATAAATAG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
34 3 0.10
35 11 0.35
36 14 0.45
37 3 0.10
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (35 bp):
TCATAAAATTTATATATTTTTTACAAAATTTAAAT
Found at i:675599 original size:26 final size:26
Alignment explanation
Indices: 675543--675611 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 26
675533 TTTTTATCTT
*
675543 CTAAAATTTTATAAGTTTATCTTATC
1 CTAAAATTTTATAAATTTATCTTATC
675569 CTAAAATTTTATAAATTCT-T-TTCATC
1 CTAAAATTTTATAAATT-TATCTT-ATC
* *
675595 TTAAAATTTTAAAAATT
1 CTAAAATTTTATAAATT
675612 AATTCTTTAG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
25 2 0.05
26 35 0.92
27 1 0.03
ACGTcount: A:0.39, C:0.10, G:0.01, T:0.49
Consensus pattern (26 bp):
CTAAAATTTTATAAATTTATCTTATC
Found at i:675951 original size:23 final size:23
Alignment explanation
Indices: 675909--675969 Score: 95
Period size: 23 Copynumber: 2.6 Consensus size: 23
675899 AATTCGTGAG
*
675909 GTTTAATTTAATTTTTTTATCAGT
1 GTTTAATTTAA-TTTTTTATCAGA
*
675933 GTTTAATTTTATTTTTTATCAGA
1 GTTTAATTTAATTTTTTATCAGA
675956 GTTTAATTTAATTT
1 GTTTAATTTAATTT
675970 AGTTTTATGA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
23 24 0.71
24 10 0.29
ACGTcount: A:0.26, C:0.03, G:0.08, T:0.62
Consensus pattern (23 bp):
GTTTAATTTAATTTTTTATCAGA
Found at i:678864 original size:12 final size:12
Alignment explanation
Indices: 678845--678874 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
678835 ACGGGAGGCA
678845 GAGGAGGTGGCG
1 GAGGAGGTGGCG
*
678857 GCGGAGGTGGCG
1 GAGGAGGTGGCG
678869 GAGGAG
1 GAGGAG
678875 AGGCTGATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.17, C:0.10, G:0.67, T:0.07
Consensus pattern (12 bp):
GAGGAGGTGGCG
Found at i:680315 original size:6 final size:6
Alignment explanation
Indices: 680284--680313 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
680274 CATTAAAAAA
*
680284 GGGGAG GGGGAG GGGGAG GGGGAG AGGGAG
1 GGGGAG GGGGAG GGGGAG GGGGAG GGGGAG
680314 AGAGAGGGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.20, C:0.00, G:0.80, T:0.00
Consensus pattern (6 bp):
GGGGAG
Found at i:682954 original size:37 final size:37
Alignment explanation
Indices: 682850--682955 Score: 100
Period size: 37 Copynumber: 3.0 Consensus size: 37
682840 ATTAGGATTT
682850 TTTAGGGTAAACTACCTATTTGGTCACTT-T-TA-TA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTA
** ** **
682884 -TTA-TCTAATTTATGT-TTTGGTCACTTA-ATTATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATA-TATTA
682918 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTA
682955 T
1 T
682956 ATAATTTATG
Statistics
Matches: 52, Mismatches: 12, Indels: 13
0.68 0.16 0.17
Matches are distributed among these distances:
31 11 0.21
32 6 0.12
33 5 0.10
34 2 0.04
35 3 0.06
36 6 0.12
37 18 0.35
38 1 0.02
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.48
Consensus pattern (37 bp):
TTTAGGGTAAACTACCTATTTGGTCACTTATATATTA
Found at i:682961 original size:68 final size:68
Alignment explanation
Indices: 682850--683114 Score: 293
Period size: 68 Copynumber: 4.0 Consensus size: 68
682840 ATTAGGATTT
* *
682850 TTTAGGGTAAACTACCTATTTGGTCACTTTTATATTATCTAATTTATGTTTTGGTCACTTAATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCAATTA
682915 TTA
66 TTA
* * *
682918 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATATAATTTATGTTTTGGCCACTCGATTA
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCAATTA
682983 TTA
66 TTA
* ** **
682986 TTTAGGGT-AA--A-CTA-TTGGTCGCTTATATATTATCTAA--TAT-AATTCAT-A-T-ATATT
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCA-ATT
*
683040 TTTA
65 ATTA
* * * *
683044 TTTAGGGTAAACTACCTATATGGTCATTTATATATTATCTAATATATGTTTTGG-CTACTCGATT
1 TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTC-ACTCAATT
683108 ATTA
65 ATTA
683112 TTT
1 TTT
683115 TTTTTCAAAA
Statistics
Matches: 161, Mismatches: 23, Indels: 26
0.77 0.11 0.12
Matches are distributed among these distances:
58 15 0.09
59 3 0.02
60 2 0.01
61 4 0.02
62 3 0.02
63 41 0.25
64 3 0.02
65 4 0.02
66 2 0.01
67 3 0.02
68 81 0.50
ACGTcount: A:0.29, C:0.11, G:0.12, T:0.48
Consensus pattern (68 bp):
TTTAGGGTAAACTACCTATTTGGTCACTTATATATTATCTAATTTATGTTTTGGTCACTCAATTA
TTA
Found at i:683228 original size:36 final size:34
Alignment explanation
Indices: 683188--683256 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 34
683178 AACAATGATG
683188 CTAACATGACATTTTTAATTATGTTTGGATGTTGGA
1 CTAACAT--CATTTTTAATTATGTTTGGATGTTGGA
**
683224 CTAACATTTTTTTTAATTATGTTTGGATGTTGG
1 CTAACATCATTTTTAATTATGTTTGGATGTTGG
683257 GCTATGTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 24 0.77
36 7 0.23
ACGTcount: A:0.25, C:0.07, G:0.19, T:0.49
Consensus pattern (34 bp):
CTAACATCATTTTTAATTATGTTTGGATGTTGGA
Found at i:686445 original size:25 final size:24
Alignment explanation
Indices: 686417--686487 Score: 97
Period size: 24 Copynumber: 2.9 Consensus size: 24
686407 ACTCAAAAAA
* *
686417 AAAATTAGAAGTTCGATTGAAGCCT
1 AAAATTAG-AGCTCAATTGAAGCCT
*
686442 AAAATTTGAGCTCAATTGAAGCCT
1 AAAATTAGAGCTCAATTGAAGCCT
*
686466 AAAATTTGAGCTCAATTGAAGC
1 AAAATTAGAGCTCAATTGAAGC
686488 GAAAGAATAA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
24 36 0.84
25 7 0.16
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.28
Consensus pattern (24 bp):
AAAATTAGAGCTCAATTGAAGCCT
Found at i:686461 original size:24 final size:24
Alignment explanation
Indices: 686432--686487 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
686422 TAGAAGTTCG
686432 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
686456 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
686480 ATTGAAGC
1 ATTGAAGC
686488 GAAAGAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (24 bp):
ATTGAAGCCTAAAATTTGAGCTCA
Found at i:688178 original size:3 final size:3
Alignment explanation
Indices: 688170--688194 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
688160 TTTTCCCTCA
688170 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
688195 TGCAGTATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:689503 original size:24 final size:24
Alignment explanation
Indices: 689471--689543 Score: 128
Period size: 24 Copynumber: 3.0 Consensus size: 24
689461 ATATCCGTCG
689471 TATTCATCCCCTCCGTCGGAGTCA
1 TATTCATCCCCTCCGTCGGAGTCA
*
689495 TATTCATCCCCTCCGTCGGAGTCG
1 TATTCATCCCCTCCGTCGGAGTCA
*
689519 TATTCATCCCCTCCGTCGGATTCA
1 TATTCATCCCCTCCGTCGGAGTCA
689543 T
1 T
689544 TCGAGATGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.15, C:0.37, G:0.16, T:0.32
Consensus pattern (24 bp):
TATTCATCCCCTCCGTCGGAGTCA
Found at i:694368 original size:13 final size:13
Alignment explanation
Indices: 694350--694374 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
694340 GGGCGAGATG
694350 GAGTGGCCCAGTT
1 GAGTGGCCCAGTT
694363 GAGTGGCCCAGT
1 GAGTGGCCCAGT
694375 ACCTGAAATA
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:0.16, C:0.24, G:0.40, T:0.20
Consensus pattern (13 bp):
GAGTGGCCCAGTT
Found at i:698319 original size:33 final size:33
Alignment explanation
Indices: 698277--698343 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
698267 AGAGAGTCAA
698277 TCAGTGTTTAGAGCAGTATTTAAGGGGCATTTG
1 TCAGTGTTTAGAGCAGTATTTAAGGGGCATTTG
698310 TCAGTGTTTAGAGCAGTATTTAAGGGGCATTTG
1 TCAGTGTTTAGAGCAGTATTTAAGGGGCATTTG
698343 T
1 T
698344 TTTTTTCAGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.24, C:0.09, G:0.30, T:0.37
Consensus pattern (33 bp):
TCAGTGTTTAGAGCAGTATTTAAGGGGCATTTG
Found at i:699146 original size:24 final size:24
Alignment explanation
Indices: 699119--699166 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
699109 GAATTGGGAA
699119 TGGAGAAAGGAGGG-TTAGGGATTT
1 TGGAG-AAGGAGGGATTAGGGATTT
* *
699143 TGGAGGATGAGGGATTAGGGATTT
1 TGGAGAAGGAGGGATTAGGGATTT
699167 GCGAGAGAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.27, C:0.00, G:0.46, T:0.27
Consensus pattern (24 bp):
TGGAGAAGGAGGGATTAGGGATTT
Found at i:715671 original size:32 final size:32
Alignment explanation
Indices: 715635--715700 Score: 96
Period size: 32 Copynumber: 2.1 Consensus size: 32
715625 GAGCCATCTT
*
715635 GAAAATTAACCGATCTAATATTAACTTGAACC
1 GAAAATCAACCGATCTAATATTAACTTGAACC
* * *
715667 GAAAATCATCTGATCTAATATTAACTTGATCC
1 GAAAATCAACCGATCTAATATTAACTTGAACC
715699 GA
1 GA
715701 TATGTAACCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.30
Consensus pattern (32 bp):
GAAAATCAACCGATCTAATATTAACTTGAACC
Found at i:717178 original size:15 final size:15
Alignment explanation
Indices: 717158--717197 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
717148 ATGTAATATT
717158 AAATATAATTTTAAA
1 AAATATAATTTTAAA
717173 AAATATAATTTTAAA
1 AAATATAATTTTAAA
717188 AAATATAATT
1 AAATATAATT
717198 AGATGATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AAATATAATTTTAAA
Found at i:723036 original size:2 final size:2
Alignment explanation
Indices: 723029--723084 Score: 96
Period size: 2 Copynumber: 28.5 Consensus size: 2
723019 AAATAAATAA
*
723029 AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT -T 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
723070 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
723085 ATTGAAAGAT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:723755 original size:32 final size:32
Alignment explanation
Indices: 723719--723816 Score: 76
Period size: 32 Copynumber: 3.1 Consensus size: 32
723709 AAATCTATAA
*
723719 TTTAAATTTTATATAAAGAAATATATAAATAT
1 TTTAAATTTTATATAAAAAAATATATAAATAT
*** * * * * *
723751 TTTAAAGAATATATATATATATATAT-TATGAA
1 TTTAAATTTTATATAAAAAAATATATAAAT-AT
723783 TTTAAATTTT-T-TAAATAAAATATATAAATAT
1 TTTAAATTTTATATAAA-AAAATATATAAATAT
723814 TTT
1 TTT
723817 CTAGCTTGTT
Statistics
Matches: 47, Mismatches: 16, Indels: 7
0.67 0.23 0.10
Matches are distributed among these distances:
30 3 0.06
31 14 0.30
32 30 0.64
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (32 bp):
TTTAAATTTTATATAAAAAAATATATAAATAT
Found at i:723763 original size:20 final size:21
Alignment explanation
Indices: 723732--723816 Score: 70
Period size: 22 Copynumber: 4.0 Consensus size: 21
723722 AAATTTTATA
723732 TAAAGAAATATATAAATATTT
1 TAAAGAAATATATAAATATTT
*
723753 TAAAGAATATATATATATATATAT
1 TAAAGAA-ATATATA-A-ATATTT
* *
723777 T-ATG-AAT-T-TAAATTTTT
1 TAAAGAAATATATAAATATTT
*
723794 TAAATAAAATATATAAATATTT
1 TAAA-GAAATATATAAATATTT
723816 T
1 T
723817 CTAGCTTGTT
Statistics
Matches: 49, Mismatches: 7, Indels: 15
0.69 0.10 0.21
Matches are distributed among these distances:
17 5 0.10
18 2 0.04
19 2 0.04
20 4 0.08
21 10 0.20
22 17 0.35
23 3 0.06
24 6 0.12
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.45
Consensus pattern (21 bp):
TAAAGAAATATATAAATATTT
Found at i:723966 original size:17 final size:19
Alignment explanation
Indices: 723946--723989 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
723936 ACAAAATACA
723946 ACATTTC-C-AGTAATCTT
1 ACATTTCACTAGTAATCTT
*
723963 ACATTCCCACTAGTAATCTT
1 ACATT-TCACTAGTAATCTT
723983 ACATTTC
1 ACATTTC
723990 GTGAACCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 5 0.23
18 1 0.05
19 2 0.09
20 14 0.64
ACGTcount: A:0.30, C:0.27, G:0.05, T:0.39
Consensus pattern (19 bp):
ACATTTCACTAGTAATCTT
Found at i:725969 original size:253 final size:253
Alignment explanation
Indices: 725521--726096 Score: 790
Period size: 253 Copynumber: 2.3 Consensus size: 253
725511 CCGAGACCCT
***
725521 ACCCGACCCGAATATATGAATTAGAA--ACCCGATTTGAAATAATAAAAAAATTATTTTTATTTA
1 ACCCGACCCGAATATATGAATTAGAATCACCCGACCCGAAATAATAAAAAAATTATTTTTATTTA
*
725584 ATAAAAACAATAACTTAATTGGAAAACAAATATATAGAGACGAGTATTATTGTAATTATTCTTAA
66 ATAAAAACAATAACTTAATTGGAAAACAAATATATAGAGACGAGTATTATTGTAATTATTCCTAA
* * *
725649 TTATATAAGGTAAAATTATATATTTTTTGGGTCGGGTATGTTTCACCCTAAACCCAAACCCGACC
131 ATATATAAGGTAAAATTATATA--TTTCGGGTCGGGTATGTTTCACCATAAACCCAAACCCGACC
*
725714 CGACCCGAATATCACGCTTAAAAAAAACC-AACCCGACCCGACCAAAATAAAATTT-AACCG
194 CGACCCGAATATCACACTT-AAAAAAACCGAA-CCGACCCGACCAAAATAAAATTTCAACCG
725774 ACCCGACCCGAATATATGAATTAGAATTCCGACCCGACCCGAAATAATAAAAAAATTATTTTTAT
1 ACCCGACCCGAATATATGAATTAGAA-T-C-ACCCGACCCGAAATAATAAAAAAATTATTTTTAT
* * * * * * *
725839 TTAATAAAAATAGTGACTTAATT-GAAAA-AATTATATATAGAGGGGTATTATTGTAATTATTCC
63 TTAATAAAAACAATAACTTAATTGGAAAACAAATATATAGAGACGAGTATTATTGTAATTATTCC
* * *
725902 TAAATATATAAGGTAAAATTATATA-TTCGGGTCGGGTATTTTTCACCATAAACCCGAACTCGAC
128 TAAATATATAAGGTAAAATTATATATTTCGGGTCGGGTATGTTTCACCATAAACCCAAACCCGAC
* * *
725966 CCGACCCGAATATCACACTTAAAAAAACCGAACCGACCTGACCAAAATAAAGTTTCACCCG
193 CCGACCCGAATATCACACTTAAAAAAACCGAACCGACCCGACCAAAATAAAATTTCAACCG
* *
726027 ACCCGACCCAAATATATGAATTAGAAATCTAACCCGACCCAAAATAATAAAAAAA-TATTTTTAT
1 ACCCGACCCGAATATATGAATTAG-AATC--ACCCGACCCGAAATAATAAAAAAATTATTTTTAT
*
726091 TCAATA
63 TTAATA
726097 TAATTGAAGC
Statistics
Matches: 289, Mismatches: 25, Indels: 19
0.87 0.08 0.06
Matches are distributed among these distances:
252 45 0.16
253 132 0.46
254 2 0.01
256 54 0.19
257 5 0.02
258 51 0.18
ACGTcount: A:0.42, C:0.19, G:0.11, T:0.28
Consensus pattern (253 bp):
ACCCGACCCGAATATATGAATTAGAATCACCCGACCCGAAATAATAAAAAAATTATTTTTATTTA
ATAAAAACAATAACTTAATTGGAAAACAAATATATAGAGACGAGTATTATTGTAATTATTCCTAA
ATATATAAGGTAAAATTATATATTTCGGGTCGGGTATGTTTCACCATAAACCCAAACCCGACCCG
ACCCGAATATCACACTTAAAAAAACCGAACCGACCCGACCAAAATAAAATTTCAACCG
Found at i:726898 original size:16 final size:17
Alignment explanation
Indices: 726877--726911 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
726867 CATCATTGTG
726877 TTTAATA-TGCGTCTTT
1 TTTAATATTGCGTCTTT
*
726893 TTTAATATTGGGTCTTT
1 TTTAATATTGCGTCTTT
726910 TT
1 TT
726912 CACTTGGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.17, C:0.09, G:0.14, T:0.60
Consensus pattern (17 bp):
TTTAATATTGCGTCTTT
Found at i:730777 original size:14 final size:15
Alignment explanation
Indices: 730756--730785 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
730746 ATTTATTATT
*
730756 ATTTTTTAAAATATA
1 ATTTTTAAAAATATA
730771 ATTTTTAAAAATATA
1 ATTTTTAAAAATATA
730786 TTAATTTGAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTTTTAAAAATATA
Found at i:741316 original size:8 final size:8
Alignment explanation
Indices: 741303--741332 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
741293 TGGTGGTCAA
741303 TTTAAAAT
1 TTTAAAAT
741311 TTTAAAAT
1 TTTAAAAT
*
741319 TTTAAAAG
1 TTTAAAAT
741327 TTTAAA
1 TTTAAA
741333 TTAAATCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (8 bp):
TTTAAAAT
Found at i:741426 original size:19 final size:19
Alignment explanation
Indices: 741402--741439 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
741392 TAATTAAAGT
741402 TTTTTTAAATTTTGATAAG
1 TTTTTTAAATTTTGATAAG
741421 TTTTTTAAATTTTGATAAG
1 TTTTTTAAATTTTGATAAG
741440 CTTAATGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.58
Consensus pattern (19 bp):
TTTTTTAAATTTTGATAAG
Found at i:749628 original size:28 final size:28
Alignment explanation
Indices: 749583--749645 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
749573 GTAAGATTTT
* *
749583 ATGTTAATGTATTTTTACGTAGGAATAG
1 ATGTAAATGTATTTTTACGTAGAAATAG
*
749611 GTGTAAATGTATTTTTACGTAGAAATAG
1 ATGTAAATGTATTTTTACGTAGAAATAG
749639 ATGTAAA
1 ATGTAAA
749646 CTTTTAAAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.37, C:0.03, G:0.21, T:0.40
Consensus pattern (28 bp):
ATGTAAATGTATTTTTACGTAGAAATAG
Found at i:749726 original size:25 final size:26
Alignment explanation
Indices: 749684--749733 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
749674 TTTAGAGAAT
*
749684 TAAAATAATTTATCAATA-AAAAATA
1 TAAAATAATTTATAAATATAAAAATA
749709 TAAAAGTAATTTA-AAATATAAAAAT
1 TAAAA-TAATTTATAAATATAAAAAT
749734 TAGTTTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (26 bp):
TAAAATAATTTATAAATATAAAAATA
Found at i:755198 original size:21 final size:20
Alignment explanation
Indices: 755172--755269 Score: 63
Period size: 21 Copynumber: 4.8 Consensus size: 20
755162 ATCAGTTTCC
755172 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
* * *
755193 AAAATCGCGATGCGATAGTAT-
1 AAAATCGCAACGCGAT--TTTG
* ** *
755214 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTT-G
* * *
755235 ATAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTG
755255 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
755270 ACACATAAAT
Statistics
Matches: 58, Mismatches: 15, Indels: 9
0.71 0.18 0.11
Matches are distributed among these distances:
19 2 0.03
20 14 0.24
21 40 0.69
22 1 0.02
23 1 0.02
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.23
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTG
Found at i:755262 original size:20 final size:20
Alignment explanation
Indices: 755237--755430 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
755227 GATTTTCCAT
* *
755237 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
755257 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
755277 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
755297 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
755317 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
755337 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
755357 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
755377 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
755398 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
755418 AATCGCAACGCGA
1 AATCGCAACGCGA
755431 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:755282 original size:40 final size:39
Alignment explanation
Indices: 755233--755430 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
755223 TTGCGATTTT
* ** *
755233 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
755271 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
755312 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
755352 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
755391 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
755431 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:755321 original size:60 final size:60
Alignment explanation
Indices: 755237--755429 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
755227 GATTTTCCAT
* ** * *
755237 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
755297 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
755357 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
755418 AATCGCAACGCG
1 AATCGCAACGCG
755430 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:755850 original size:33 final size:33
Alignment explanation
Indices: 755811--755881 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
755801 TTCACTTAGA
*
755811 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
755844 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
755877 TTTCA
1 TTTCA
755882 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:756021 original size:14 final size:14
Alignment explanation
Indices: 756002--756056 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
755992 AGAATGACTG
756002 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
756016 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
756035 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
756049 TCGCAACG
1 TCGCAACG
756057 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:756039 original size:33 final size:33
Alignment explanation
Indices: 756002--756072 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
755992 AGAATGACTG
**
756002 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
756035 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
756068 TCGCA
1 TCGCA
756073 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:756090 original size:19 final size:19
Alignment explanation
Indices: 756068--756165 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
756058 GAAACCAAAA
*
756068 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
756087 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
756101 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
756120 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
756134 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
756153 TCGCGTTGCGATT
1 TCGCGTTGCGATT
756166 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:756109 original size:14 final size:14
Alignment explanation
Indices: 756090--756179 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
756080 TTTCATTTCG
756090 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
756104 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
756123 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
756137 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
756156 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
756170 CGTTGCGATT
1 CGTTGCGATT
756180 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 1 0.02
16 5 0.08
17 5 0.08
18 1 0.02
19 20 0.32
ACGTcount: A:0.09, C:0.24, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:756115 original size:33 final size:33
Alignment explanation
Indices: 756073--756187 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
756063 CAAAATCGCA
756073 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
756106 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
756139 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
756172 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
756188 AACCAAAAGA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:758106 original size:185 final size:186
Alignment explanation
Indices: 757876--758439 Score: 1098
Period size: 185 Copynumber: 3.0 Consensus size: 186
757866 TAGATTGCTT
*
757876 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
757941 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
758006 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
758061 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAAT-GTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
758125 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
758190 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
758246 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
758311 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
758376 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTG-TTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
758431 AGTAAATTT
1 AGTAAATTT
758440 ATCCATTCAA
Statistics
Matches: 376, Mismatches: 1, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
184 93 0.25
185 177 0.47
186 106 0.28
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:758458 original size:93 final size:93
Alignment explanation
Indices: 757876--758439 Score: 1098
Period size: 93 Copynumber: 6.1 Consensus size: 93
757866 TAGATTGCTT
*
757876 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
757941 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
757969 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
758033 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
758061 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAAT-GTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
758125 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
758153 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
758218 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
758246 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
758311 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
758339 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
758404 TTTGTCTTTG-TTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
758431 AGTAAATTT
1 AGTAAATTT
758440 ATCCATTCAA
Statistics
Matches: 468, Mismatches: 1, Indels: 5
0.99 0.00 0.01
Matches are distributed among these distances:
92 208 0.44
93 260 0.56
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:758523 original size:19 final size:19
Alignment explanation
Indices: 758483--758610 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
758473 TAGTTTACTT
* *
758483 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
758503 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
758522 TCGCAACGCGAAA-TGAAA
1 TCGCAACGCGAAACCAAAA
*
758540 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
758554 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
758573 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
758587 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
758606 TCGCA
1 TCGCA
758611 TTGCGATTTT
Statistics
Matches: 88, Mismatches: 10, Indels: 21
0.74 0.08 0.18
Matches are distributed among these distances:
14 19 0.22
15 1 0.01
16 6 0.07
17 2 0.02
18 11 0.12
19 36 0.41
20 13 0.15
ACGTcount: A:0.45, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:758579 original size:33 final size:32
Alignment explanation
Indices: 758519--758610 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 32
758509 CGCGAAACCA
**
758519 AAATCGCAACGCGAAA-TGAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
758550 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
758583 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
758611 TTGCGATTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
31 1 0.02
32 16 0.29
33 39 0.70
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:758628 original size:19 final size:19
Alignment explanation
Indices: 758606--758739 Score: 83
Period size: 19 Copynumber: 7.6 Consensus size: 19
758596 GAAACCAAAA
*
758606 TCGCATTGCGATTTTTATT
1 TCGCGTTGCGATTTTTATT
*
758625 TCGCGTTGCGA---TTCTT
1 TCGCGTTGCGATTTTTATT
*
758641 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTTATT
* * *
758658 TCGCATTGCGA---TTCTG
1 TCGCGTTGCGATTTTTATT
*
758674 T--CGTTGCGA-TTTCATT
1 TCGCGTTGCGATTTTTATT
**
758690 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTTATT
*
758709 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTTA-TT
*
758729 TCGTGTTGCGA
1 TCGCGTTGCGA
758740 AAGTAAACTA
Statistics
Matches: 87, Mismatches: 17, Indels: 21
0.70 0.14 0.17
Matches are distributed among these distances:
14 15 0.17
16 11 0.13
17 4 0.05
18 8 0.09
19 37 0.43
20 12 0.14
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTTATT
Found at i:758647 original size:14 final size:14
Alignment explanation
Indices: 758628--758684 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
758618 TTTTATTTCG
758628 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
758642 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
758659 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
758675 CGTTGCGATT
1 CGTTGCGATT
758685 TCATTTCGCG
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:758692 original size:32 final size:33
Alignment explanation
Indices: 758611--758702 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
758601 CAAAATCGCA
* *
758611 TTGCGATTTTTATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
758644 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
758677 TTGCGA-TTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
758703 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
32 19 0.35
33 36 0.65
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:758711 original size:51 final size:47
Alignment explanation
Indices: 758628--758721 Score: 125
Period size: 51 Copynumber: 1.9 Consensus size: 47
758618 TTTTATTTCG
758628 CGTTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTCTGT
1 CGTTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTCTGT
** *
758675 CGTTGCGATTTCATTTCGCGTTGCGATTTTGGTTTCGCGTTGCGATT
1 CGTTGCGA-TTC-TTT--CGTTGCGATTTTCATTTCGCATTGCGATT
758722 TTAAGTTTCG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
47 8 0.20
48 3 0.08
49 3 0.08
51 26 0.65
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.46
Consensus pattern (47 bp):
CGTTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTCTGT
Found at i:758731 original size:20 final size:19
Alignment explanation
Indices: 758675--758739 Score: 87
Period size: 19 Copynumber: 3.4 Consensus size: 19
758665 GCGATTCTGT
*
758675 CGTTGCGATTTCA-TTTCG
1 CGTTGCGATTTTAGTTTCG
*
758693 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTAGTTTCG
758712 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTT-AGTTTCG
*
758732 TGTTGCGA
1 CGTTGCGA
758740 AAGTAAACTA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
18 11 0.27
19 17 0.41
20 13 0.32
ACGTcount: A:0.11, C:0.17, G:0.28, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTAGTTTCG
Found at i:759251 original size:21 final size:20
Alignment explanation
Indices: 759198--759257 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
759188 CTCGAGAGTC
*
759198 CCCTCCCACCGTTCAAGAGG
1 CCCTCCCACCATTCAAGAGG
** * *
759218 CCCTGTCATCATTGAAGAGG
1 CCCTCCCACCATTCAAGAGG
759238 TCCCTCCCACCATTCAAGAG
1 -CCCTCCCACCATTCAAGAG
759258 CCGATTCACA
Statistics
Matches: 30, Mismatches: 9, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.23, C:0.38, G:0.18, T:0.20
Consensus pattern (20 bp):
CCCTCCCACCATTCAAGAGG
Found at i:760505 original size:11 final size:12
Alignment explanation
Indices: 760483--760519 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
760473 TGATTCAATA
760483 GTTTAATTGATT
1 GTTTAATTGATT
*
760495 GTTT-TTTGATT
1 GTTTAATTGATT
760506 GTTTAATTGATT
1 GTTTAATTGATT
760518 GT
1 GT
760520 AAAAGTTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.62
Consensus pattern (12 bp):
GTTTAATTGATT
Found at i:760602 original size:14 final size:14
Alignment explanation
Indices: 760583--760618 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
760573 ATTGTTTAAT
760583 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
760597 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
760611 TGATTTGT
1 TGATTTGT
760619 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:760739 original size:19 final size:19
Alignment explanation
Indices: 760723--760824 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
760713 AAAAATGACT
760723 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
760742 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
760761 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
760775 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
760794 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
760814 ATCGCAATGCG
1 ATCGCAATGCG
760825 TTTATATTTC
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:760876 original size:19 final size:19
Alignment explanation
Indices: 760852--761153 Score: 340
Period size: 19 Copynumber: 17.4 Consensus size: 19
760842 GATTATCTCG
760852 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
760871 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
760890 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
760904 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
760922 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
760941 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
760960 TTGCGA-TTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
760978 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
760992 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
761010 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
761029 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
761043 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
761062 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
761081 TTGCGA--TTC---TCG--
1 TTGCGATTTTCATTTCGCA
761093 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
761113 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
761127 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
761146 TTGCGATT
1 TTGCGATT
761154 GTATTTCCGT
Statistics
Matches: 247, Mismatches: 8, Indels: 56
0.79 0.03 0.18
Matches are distributed among these distances:
12 6 0.02
14 35 0.14
15 6 0.02
16 27 0.11
17 17 0.07
18 32 0.13
19 112 0.45
20 12 0.05
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:760919 original size:51 final size:55
Alignment explanation
Indices: 760830--761169 Score: 312
Period size: 51 Copynumber: 6.6 Consensus size: 55
760820 ATGCGTTTAT
*
760830 ATTTCGCATTGCGA-TT-ATCTCG-TTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTCATTTCGATTGCGATTTTCATTTCGCATTGCGATTTTC
760882 ATTTCGCATTGCGA-TTC-TTTCG-TTGCGA-TTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTCATTTCGATTGCGATTTTCATTTCGCATTGCGATTTTC
*
760933 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTTAATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTCATTTCGCATTGCGATTTTC
*
760987 -TGTCG--TTGCGATTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGATTTCATTTCG-ATTGCGATTTTCATTTCGCATTGCGATTTTC
*
761038 -TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTCATTTCGCATTGCGATTTTC
*
761090 ---TCG--TTGCGATTTTCATTTCCGCATTGCGATTTTCA--T-G--TTGGGATTTTC
1 ATTTCGCATTGCGA-TTTCATTT-CG-ATTGCGATTTTCATTTCGCATTGCGATTTTC
*
761138 ATTTCGCGTTGCGATTGT-ATTTCCG-TTGCGAT
1 ATTTCGCATTGCGATT-TCATTT-CGATTGCGAT
761170 AGTCAAATGC
Statistics
Matches: 265, Mismatches: 6, Indels: 36
0.86 0.02 0.12
Matches are distributed among these distances:
46 5 0.02
48 4 0.02
49 1 0.00
50 43 0.16
51 92 0.35
52 75 0.28
53 14 0.05
54 8 0.03
56 23 0.09
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (55 bp):
ATTTCGCATTGCGATTTCATTTCGATTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:764356 original size:20 final size:20
Alignment explanation
Indices: 764328--764696 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
764318 AAAATTCAGT
* * * *
764328 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
764348 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
764368 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
764388 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
764408 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
764428 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
764448 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
764468 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
764488 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
764508 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
764528 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
764548 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
764568 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
764588 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
764608 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
764628 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
764648 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
764668 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
764688 GTTGCGATT
1 GTTGCGATT
764697 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:767036 original size:21 final size:21
Alignment explanation
Indices: 767010--767050 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
767000 TTGTATTCTT
*
767010 TGAACAATAAA-GAGCTGTGGA
1 TGAACAAGAAAGGA-CTGTGGA
767031 TGAACAAGAAAGGACTGTGG
1 TGAACAAGAAAGGACTGTGG
767051 GGGAAAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.41, C:0.10, G:0.32, T:0.17
Consensus pattern (21 bp):
TGAACAAGAAAGGACTGTGGA
Found at i:776119 original size:21 final size:21
Alignment explanation
Indices: 776095--776134 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
776085 TCAAAAAAAT
776095 GAAAAC-AAATAACATAATATA
1 GAAAACAAAATAAC-TAATATA
776116 GAAAACAAAATAACTAATA
1 GAAAACAAAATAACTAATA
776135 GTCATTAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.68, C:0.10, G:0.05, T:0.17
Consensus pattern (21 bp):
GAAAACAAAATAACTAATATA
Found at i:782944 original size:2 final size:2
Alignment explanation
Indices: 782937--782969 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
782927 CTATTTACTA
782937 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
782970 GATAATATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:782974 original size:12 final size:12
Alignment explanation
Indices: 782935--782978 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
782925 CACTATTTAC
782935 TAATA-TATATA
1 TAATATTATATA
782946 TATATATATATATA
1 TA-ATAT-TATATA
*
782960 TAATATTATAGA
1 TAATATTATATA
782972 TAATATT
1 TAATATT
782979 TTCAGGTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
11 2 0.07
12 15 0.52
13 4 0.14
14 8 0.28
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (12 bp):
TAATATTATATA
Found at i:788853 original size:62 final size:61
Alignment explanation
Indices: 788756--788879 Score: 239
Period size: 62 Copynumber: 2.0 Consensus size: 61
788746 CAATTCCCAG
788756 TTTCTGCAATTTTACAGATAGAATTTAGGTCAAAGCTCACAAGACCATATTTTCATTCAAAA
1 TTTCTGCAATTTTACAGATAGAATTTAGGTCAAAGCTCACAAGACCATA-TTTCATTCAAAA
788818 TTTCTGCAATTTTACAGATAGAATTTAGGTCAAAGCTCACAAGACCATATTTCATTCAAAA
1 TTTCTGCAATTTTACAGATAGAATTTAGGTCAAAGCTCACAAGACCATATTTCATTCAAAA
788879 T
1 T
788880 CAAATTTCCA
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
61 13 0.21
62 49 0.79
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (61 bp):
TTTCTGCAATTTTACAGATAGAATTTAGGTCAAAGCTCACAAGACCATATTTCATTCAAAA
Found at i:789954 original size:21 final size:21
Alignment explanation
Indices: 789906--789954 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
789896 AATATTGCTT
*
789906 TAAAAAA-TTTAATTATTTAA
1 TAAAAAATTTTAAATATTTAA
*
789926 TAATAAATTTTAAATATTT-A
1 TAAAAAATTTTAAATATTTAA
789946 TACAAAAAT
1 TA-AAAAAT
789955 AGTACTCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
TAAAAAATTTTAAATATTTAA
Found at i:792438 original size:23 final size:23
Alignment explanation
Indices: 792408--792451 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
792398 CTCTAGTGCA
792408 AGTATCAAATCCGGGTATGTGTG
1 AGTATCAAATCCGGGTATGTGTG
792431 AGTATCAAATCCGGGTATGTG
1 AGTATCAAATCCGGGTATGTG
792452 CCAAACATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.27, C:0.14, G:0.30, T:0.30
Consensus pattern (23 bp):
AGTATCAAATCCGGGTATGTGTG
Found at i:802250 original size:30 final size:30
Alignment explanation
Indices: 802179--802250 Score: 74
Period size: 31 Copynumber: 2.4 Consensus size: 30
802169 CTAAGTTGCT
** *
802179 ATTAGACCCTCAATTTTTTTTGAAATTCTC
1 ATTAGACCCTCAATTAGTTTTGAAATTCTA
* *
802209 ATTAAACCCCTCAA-TAGTTTTGAAAATTGTA
1 ATTAGA-CCCTCAATTAGTTTTG-AAATTCTA
802240 ATTAGACCCTC
1 ATTAGACCCTC
802251 CAAATTATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
30 16 0.47
31 18 0.53
ACGTcount: A:0.32, C:0.21, G:0.08, T:0.39
Consensus pattern (30 bp):
ATTAGACCCTCAATTAGTTTTGAAATTCTA
Found at i:806729 original size:41 final size:41
Alignment explanation
Indices: 806683--806799 Score: 164
Period size: 41 Copynumber: 2.8 Consensus size: 41
806673 TTTCCCCGAA
**
806683 TTTCCGTGTTTGTTTCACGTAATTAATTTTCCGAAAA-ATAT
1 TTTCCGTGTTTGTTTCACGTAATTCGTTTTCCGAAAACAT-T
* *
806724 TTTCCGTGTTTGTTTCACGTAATTCGTTTTCTAGAAAACGTT
1 TTTCCGTGTTTGTTTCACGTAATTCGTTTTC-CGAAAACATT
806766 TTTCCGTGTTTGTTTTCACGTAATTCGTTTTCCG
1 TTTCCGTGTTTG-TTTCACGTAATTCGTTTTCCG
806800 GAATGTAATT
Statistics
Matches: 68, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
41 29 0.43
42 19 0.28
43 20 0.29
ACGTcount: A:0.19, C:0.17, G:0.15, T:0.49
Consensus pattern (41 bp):
TTTCCGTGTTTGTTTCACGTAATTCGTTTTCCGAAAACATT
Found at i:807036 original size:22 final size:22
Alignment explanation
Indices: 807011--807091 Score: 65
Period size: 22 Copynumber: 3.5 Consensus size: 22
807001 ATATATTTAT
807011 TAATATTTATAATAATATAATA
1 TAATATTTATAATAATATAATA
* *
807033 TAATATTTTTAATATTATATAAAA
1 TAATATTTATAATA--ATATAATA
* *
807057 TAATCAATTAT-ATTATAATAATA
1 TAAT-ATTTATAATAAT-ATAATA
*
807080 TAAGATATTATA
1 TAATAT-TTATA
807092 TTTTTATTTT
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
22 16 0.36
23 12 0.27
24 13 0.29
25 4 0.09
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (22 bp):
TAATATTTATAATAATATAATA
Found at i:807059 original size:34 final size:34
Alignment explanation
Indices: 806983--807060 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 34
806973 CAAAATATTA
*
806983 ATTAT-TAAAAT-ATTTAAAATATATTTATTAAT
1 ATTATATAAAATAATATAAAATATATTTATTAAT
*
807015 ATT-TAT--AATAATATAATATAATATTT-TTAAT
1 ATTATATAAAATAATATAAAAT-ATATTTATTAAT
807046 ATTATATAAAATAAT
1 ATTATATAAAATAAT
807061 CAATTATATT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
30 3 0.08
31 16 0.42
32 13 0.34
34 6 0.16
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (34 bp):
ATTATATAAAATAATATAAAATATATTTATTAAT
Found at i:807549 original size:14 final size:15
Alignment explanation
Indices: 807528--807598 Score: 72
Period size: 15 Copynumber: 4.8 Consensus size: 15
807518 TTTAAAAAAT
807528 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
807543 G-AATTCAAATTCCA
1 GTAATTCATTTTCCA
*
807557 GTAATTCATTTTTCA
1 GTAATTCATTTTCCA
* **
807572 ATAATTCAAATTCCA
1 GTAATTCATTTTCCA
*
807587 TTAATTCATTTT
1 GTAATTCATTTT
807599 ATAAAAAACT
Statistics
Matches: 43, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
14 12 0.28
15 31 0.72
ACGTcount: A:0.34, C:0.17, G:0.04, T:0.45
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:807578 original size:30 final size:30
Alignment explanation
Indices: 807528--807598 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
807518 TTTAAAAAAT
*
807528 GTAATTCA-TTTTCCAGAATTCAAATTCCA
1 GTAATTCATTTTTCAAGAATTCAAATTCCA
*
807557 GTAATTCATTTTTCAATAATTCAAATTCCA
1 GTAATTCATTTTTCAAGAATTCAAATTCCA
*
807587 TTAATTCATTTT
1 GTAATTCATTTT
807599 ATAAAAAACT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
29 8 0.21
30 30 0.79
ACGTcount: A:0.34, C:0.17, G:0.04, T:0.45
Consensus pattern (30 bp):
GTAATTCATTTTTCAAGAATTCAAATTCCA
Found at i:811754 original size:12 final size:12
Alignment explanation
Indices: 811723--811757 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
811713 AAGATGGATG
*
811723 GATGGAGATGGA
1 GATGGAGCTGGA
811735 GATGGAGCTGGA
1 GATGGAGCTGGA
*
811747 GCTGGAGCTGG
1 GATGGAGCTGG
811758 GGGAGTTCTT
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:0.23, C:0.09, G:0.51, T:0.17
Consensus pattern (12 bp):
GATGGAGCTGGA
Found at i:814563 original size:32 final size:32
Alignment explanation
Indices: 814522--814594 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
814512 GGACGATTCT
814522 CAATGGGCAATGTGCTGCTGGTTCATATGGTG
1 CAATGGGCAATGTGCTGCTGGTTCATATGGTG
*
814554 CAATGGGCAATGTGCTGCTGGTTTATATGGTG
1 CAATGGGCAATGTGCTGCTGGTTCATATGGTG
814586 CAATGGGCA
1 CAATGGGCA
814595 GTTTGTTTAC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.21, C:0.15, G:0.34, T:0.30
Consensus pattern (32 bp):
CAATGGGCAATGTGCTGCTGGTTCATATGGTG
Found at i:815831 original size:148 final size:148
Alignment explanation
Indices: 815568--815880 Score: 486
Period size: 148 Copynumber: 2.1 Consensus size: 148
815558 TATAATTGCA
815568 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATAT
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATAT
* * * * * *
815632 TCCTTAAGAATCATATACATATACTAGGGATCAAGCATGTGTCTTACAAGACTTCACACATGTTC
65 TCCTTAAAAATCATATACATATACTAAGGATCAAGCATGTGCCTCACAAGACCTCACAAATGTTC
* *
815697 CACAGAATATATATATATC
130 CAAAGAATATACATATATC
*
815716 CCGAAGGACCGCATAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATA-TAT
* *
815781 TCCTTAAAAATCATATACATATACTAAGGATCAAGTATGTGCCTCA-AAGACCTCATAAATGTTC
65 TCCTTAAAAATCATATACATATACTAAGGATCAAGCATGTGCCTCACAAGACCTCACAAATGTTC
*
815845 CAAAGAATATACATATGTC
130 CAAAGAATATACATATATC
815864 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
815881 CCCTCGATTC
Statistics
Matches: 150, Mismatches: 13, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
147 1 0.01
148 105 0.70
149 44 0.29
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (148 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATATT
CCTTAAAAATCATATACATATACTAAGGATCAAGCATGTGCCTCACAAGACCTCACAAATGTTCC
AAAGAATATACATATATC
Found at i:822932 original size:13 final size:13
Alignment explanation
Indices: 822914--822940 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
822904 TTACAATAAT
822914 TTAACTATAATTC
1 TTAACTATAATTC
822927 TTAACTATAATTC
1 TTAACTATAATTC
822940 T
1 T
822941 ATAAGAATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.00, T:0.48
Consensus pattern (13 bp):
TTAACTATAATTC
Found at i:832493 original size:21 final size:21
Alignment explanation
Indices: 832467--832509 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
832457 TTTTCGGGCT
* *
832467 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
832488 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
832509 A
1 A
832510 CGAAATGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:832610 original size:68 final size:68
Alignment explanation
Indices: 832489--832640 Score: 209
Period size: 68 Copynumber: 2.2 Consensus size: 68
832479 ACCCATTCAA
* * *
832489 GGGGAACCGATACCCCTTCAACGAAATGAATTTCCAGAATGTTAGAGGGGAATCGGTACCCCCA-
1 GGGGAACCGATACCCCCTCAACGAAATGAAATTCCAGAATGTTAGAGGGGAATCGATACCCCCAG
832553 GGG
66 GGG
* * *
832556 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCTT-GAGGGGAATCGATACCCCC
1 GGGGAACCGATACCCCCTCAACG-AAATGAAATTCCAGAATG-TTAGAGGGGAATCGATACCCCC
832620 AGGGG
64 AGGGG
*
832625 GGGGAACCGATTCCCC
1 GGGGAACCGATACCCC
832641 ATGAGAAAAG
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
67 21 0.28
68 34 0.45
69 20 0.27
ACGTcount: A:0.27, C:0.26, G:0.28, T:0.18
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGAAATGAAATTCCAGAATGTTAGAGGGGAATCGATACCCCCAG
GGG
Found at i:833039 original size:30 final size:30
Alignment explanation
Indices: 833005--833063 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
832995 GTTATATGAG
* * *
833005 CTATGTGATAAATGTATGTAAATGATATGT
1 CTATGTGATAAAGGTATGGAAATAATATGT
833035 CTATGTGATAAAGGTATGGAAATAATATG
1 CTATGTGATAAAGGTATGGAAATAATATG
833064 ACTACGCGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36
Consensus pattern (30 bp):
CTATGTGATAAAGGTATGGAAATAATATGT
Found at i:833337 original size:23 final size:22
Alignment explanation
Indices: 833277--833344 Score: 127
Period size: 22 Copynumber: 3.0 Consensus size: 22
833267 TTATGGACAT
833277 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
833299 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
833321 AATTCTACGGGGCACTTCGGTGC
1 AATTCTAC-GGGCACTTCGGTGC
833344 A
1 A
833345 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 30 0.67
23 15 0.33
ACGTcount: A:0.19, C:0.26, G:0.28, T:0.26
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:835436 original size:16 final size:16
Alignment explanation
Indices: 835415--835448 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
835405 ATTGGCTTAT
835415 GTTATAGTGGCTATTC
1 GTTATAGTGGCTATTC
835431 GTTATAGTGGCTATTC
1 GTTATAGTGGCTATTC
835447 GT
1 GT
835449 CAGGAAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.18, C:0.12, G:0.26, T:0.44
Consensus pattern (16 bp):
GTTATAGTGGCTATTC
Done.