Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008685.1 Hibiscus syriacus cultivar Beakdansim tig00111708_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: 3669133
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 19
Found at i:810814 original size:22 final size:22
Alignment explanation
Indices: 810789--810830 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
810779 AGTCAGTATT
810789 CGAAATTTGATCTTGGTCAACC
1 CGAAATTTGATCTTGGTCAACC
*
810811 CGAACTTTGATCTTGGTCAA
1 CGAAATTTGATCTTGGTCAA
810831 TACTCGGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.33
Consensus pattern (22 bp):
CGAAATTTGATCTTGGTCAACC
Found at i:811045 original size:14 final size:14
Alignment explanation
Indices: 811026--811052 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
811016 GAAGAAGAAA
811026 TCCCCAAAGAAAAG
1 TCCCCAAAGAAAAG
811040 TCCCCAAAGAAAA
1 TCCCCAAAGAAAA
811053 TGCCACGGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.30, G:0.11, T:0.07
Consensus pattern (14 bp):
TCCCCAAAGAAAAG
Found at i:812297 original size:152 final size:150
Alignment explanation
Indices: 812023--812327 Score: 592
Period size: 152 Copynumber: 2.0 Consensus size: 150
812013 GTTTCCCAGA
812023 TGCTTTTCATGGACTTTGTGGTGTCATTTGTATAGAAATCTAAAATCAAGGTCTGCTGGTATAAA
1 TGCTTTTCATGGACTTTGTGGTGTCATTTGTATAGAAATCTAAAATCAAGGTCTGCTGGTATAAA
812088 AAATCACAATGGACATACTGGAATGCTGTAAAAGCTTATCGAAAAGTGGATTTTAATAAGCATAT
66 AAATCACAATGGACATACTGGAATGCTGTAAAAGCTTATCGAAAAGTGGATTTTAATAAGCATAT
812153 AAACTGTTTAAGACGTGTTT
131 AAACTGTTTAAGACGTGTTT
812173 TGCTTTTCATGGACTTTGTGGTGTTCATTTGTATAGAAATCTAAAATCAAGGTCTGCTGGTATAA
1 TGCTTTTCATGGACTTTGTGGTG-TCATTTGTATAGAAATCTAAAATCAAGGTCTGCTGGTATAA
812238 AAAATCACAAATGGACATACTGGAATGCTGTAAAAGCTTATCGAAAAGTGGATTTTAATAAGCAT
65 AAAATCAC-AATGGACATACTGGAATGCTGTAAAAGCTTATCGAAAAGTGGATTTTAATAAGCAT
812303 ATAAACTGTTTAAGACGTGTTT
129 ATAAACTGTTTAAGACGTGTTT
812325 TGC
1 TGC
812328 CTCAGTGTGC
Statistics
Matches: 153, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
150 23 0.15
151 49 0.32
152 81 0.53
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.34
Consensus pattern (150 bp):
TGCTTTTCATGGACTTTGTGGTGTCATTTGTATAGAAATCTAAAATCAAGGTCTGCTGGTATAAA
AAATCACAATGGACATACTGGAATGCTGTAAAAGCTTATCGAAAAGTGGATTTTAATAAGCATAT
AAACTGTTTAAGACGTGTTT
Found at i:813246 original size:14 final size:14
Alignment explanation
Indices: 813227--813264 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
813217 TTTCATTTCG
813227 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
813241 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
813255 CGTTGCGATT
1 CGTTGCGATT
813265 TTCATTTCGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.08, C:0.26, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:815165 original size:19 final size:19
Alignment explanation
Indices: 815149--815270 Score: 137
Period size: 19 Copynumber: 6.6 Consensus size: 19
815139 AAAAATGACT
815149 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
* *
815168 ATCGCAACGAGAGAATAAAA
1 ATCGCAACGCGA-AATGAAA
* *
815188 ATCGCAATGCGAAACGAAA
1 ATCGCAACGCGAAATGAAA
*
815207 ATCGCAACGCGAAATAAAA
1 ATCGCAACGCGAAATGAAA
*
815226 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
*
815240 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
815259 ATCGCAACGCGA
1 ATCGCAACGCGA
815271 TTATAGTTTC
Statistics
Matches: 84, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
14 9 0.11
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 53 0.63
20 16 0.19
ACGTcount: A:0.48, C:0.20, G:0.21, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:815194 original size:39 final size:38
Alignment explanation
Indices: 815149--815270 Score: 137
Period size: 39 Copynumber: 3.3 Consensus size: 38
815139 AAAAATGACT
*
815149 ATCGCAACGCGAAATGAAAATCGCAACGAGAGAATAAAA
1 ATCGCAACGCGAAACGAAAATCGCAACGAGA-AATAAAA
* *
815188 ATCGCAATGCGAAACGAAAATCGCAACGCGAAATAAAA
1 ATCGCAACGCGAAACGAAAATCGCAACGAGAAATAAAA
* * * *
815226 ATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAACGAAAATCGCAACGAGAAATAAAA
815259 ATCGCAACGCGA
1 ATCGCAACGCGA
815271 TTATAGTTTC
Statistics
Matches: 74, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
33 27 0.36
34 1 0.01
35 2 0.03
36 2 0.03
38 14 0.19
39 28 0.38
ACGTcount: A:0.48, C:0.20, G:0.21, T:0.11
Consensus pattern (38 bp):
ATCGCAACGCGAAACGAAAATCGCAACGAGAAATAAAA
Found at i:815243 original size:33 final size:35
Alignment explanation
Indices: 815164--815267 Score: 122
Period size: 33 Copynumber: 2.9 Consensus size: 35
815154 AACGCGAAAT
*
815164 GAAAATCGCAACGAGAGAATAAAAATCGCAATGCGAAAC
1 GAAAATCGCAACGCGA-AATAAAAATCGCAA--CG-AAC
815203 GAAAATCGCAACGCGAAATAAAAATCGCAACG-A-
1 GAAAATCGCAACGCGAAATAAAAATCGCAACGAAC
* * *
815236 GAGAATCGCAATGCGAAATGAAAATCGCAACG
1 GAAAATCGCAACGCGAAATAAAAATCGCAACG
815268 CGATTATAGT
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
33 29 0.48
34 1 0.02
36 2 0.03
38 14 0.23
39 15 0.25
ACGTcount: A:0.49, C:0.19, G:0.21, T:0.11
Consensus pattern (35 bp):
GAAAATCGCAACGCGAAATAAAAATCGCAACGAAC
Found at i:815265 original size:52 final size:53
Alignment explanation
Indices: 815149--815270 Score: 174
Period size: 52 Copynumber: 2.2 Consensus size: 53
815139 AAAAATGACT
*
815149 ATCGCAACGCGAAATGAAAATCGCAACGAGAGAATAAAAATCGCAATGCGAAACGAAA
1 ATCGCAACGCGAAATAAAAATCGCAACGAGAG-----AAATCGCAATGCGAAACGAAA
*
815207 ATCGCAACGCGAAATAAAAATCGCAACGAGAG-AATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATAAAAATCGCAACGAGAGAAATCGCAATGCGAAACGAAA
815259 ATCGCAACGCGA
1 ATCGCAACGCGA
815271 TTATAGTTTC
Statistics
Matches: 62, Mismatches: 2, Indels: 6
0.89 0.03 0.09
Matches are distributed among these distances:
52 31 0.50
58 31 0.50
ACGTcount: A:0.48, C:0.20, G:0.21, T:0.11
Consensus pattern (53 bp):
ATCGCAACGCGAAATAAAAATCGCAACGAGAGAAATCGCAATGCGAAACGAAA
Found at i:815305 original size:20 final size:20
Alignment explanation
Indices: 815276--815391 Score: 121
Period size: 20 Copynumber: 5.9 Consensus size: 20
815266 CGCGATTATA
*
815276 GTTTCGCGTTGCGATTTTTG
1 GTTTCGCGTTGCGATTTTTC
* *
815296 GTTTCACGTTGCGATTTTTG
1 GTTTCGCGTTGCGATTTTTC
*
815316 GTTTCGCGTTGGGA-TTTTC
1 GTTTCGCGTTGCGATTTTTC
* **
815335 ATTTCTTGTTGCGA-TTTTC
1 GTTTCGCGTTGCGATTTTTC
815354 GTTTCGCGTTGCGA-TTTTC
1 GTTTCGCGTTGCGATTTTTC
* *
815373 ATTCTCTCGTTGCGATTTT
1 GTT-TCGCGTTGCGATTTT
815392 CATTTCAACC
Statistics
Matches: 81, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
19 37 0.46
20 41 0.51
21 3 0.04
ACGTcount: A:0.08, C:0.17, G:0.24, T:0.51
Consensus pattern (20 bp):
GTTTCGCGTTGCGATTTTTC
Found at i:815364 original size:58 final size:59
Alignment explanation
Indices: 815283--815397 Score: 153
Period size: 58 Copynumber: 2.0 Consensus size: 59
815273 ATAGTTTCGC
* ** *
815283 GTTGCGATTTTTGGTTTCACGTTGCGATTTTTGGTT-TCGCGTTGGGATTTTCATTTCTT
1 GTTGCGATTTTTCGTTTCACGTTGCGA-TTTTCATTCTCGCGTTGCGATTTTCATTTCTT
* *
815342 GTTGCGA-TTTTCGTTTCGCGTTGCGATTTTCATTCTCTCGTTGCGATTTTCATTTC
1 GTTGCGATTTTTCGTTTCACGTTGCGATTTTCATTCTCGCGTTGCGATTTTCATTTC
815398 AACCAAAAGA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
57 6 0.12
58 36 0.73
59 7 0.14
ACGTcount: A:0.09, C:0.17, G:0.23, T:0.51
Consensus pattern (59 bp):
GTTGCGATTTTTCGTTTCACGTTGCGATTTTCATTCTCGCGTTGCGATTTTCATTTCTT
Found at i:815385 original size:39 final size:38
Alignment explanation
Indices: 815267--815397 Score: 154
Period size: 39 Copynumber: 3.4 Consensus size: 38
815257 AAATCGCAAC
* * ** *
815267 GCGATTATAGTTTCGCGTTGCGATTTTTGGTTTCACGTT
1 GCGATTTTCGTTTCGCGTTGCGA-TTTTCATTTCTCGTT
* * *
815306 GCGATTTTTGGTTTCGCGTTGGGATTTTCATTTCTTGTT
1 GCGA-TTTTCGTTTCGCGTTGCGATTTTCATTTCTCGTT
815345 GCGATTTTCGTTTCGCGTTGCGATTTTCATTCTCTCGTT
1 GCGATTTTCGTTTCGCGTTGCGATTTTCATT-TCTCGTT
*
815384 GCGATTTTCATTTC
1 GCGATTTTCGTTTC
815398 AACCAAAAGA
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
38 25 0.32
39 38 0.48
40 16 0.20
ACGTcount: A:0.10, C:0.18, G:0.23, T:0.50
Consensus pattern (38 bp):
GCGATTTTCGTTTCGCGTTGCGATTTTCATTTCTCGTT
Found at i:815589 original size:93 final size:93
Alignment explanation
Indices: 815485--815691 Score: 353
Period size: 93 Copynumber: 2.2 Consensus size: 93
815475 ATGGATTGTA
* *
815485 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATT-AAGAATACACAGTT
1 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAATATTAAAGAATACACAGTT
815549 TAGCAGAATTGGCAGCAAACGAACAAAT
66 TAGCAGAATTGGCAGCAAACGAACAAAT
*
815577 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAATGTTAAAGAATACACAGT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAATATTAAAGAATACACAGT
* *
815642 TTAGCAGAATTGGCAGCAACCGAATAAAT
65 TTAGCAGAATTGGCAGCAAACGAACAAAT
815671 TTACTTCAACCAAAAGACAAA
1 TTACTTCAACCAAAAGACAAA
815692 TACTAACTTC
Statistics
Matches: 108, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
92 4 0.04
93 60 0.56
94 44 0.41
ACGTcount: A:0.49, C:0.19, G:0.12, T:0.20
Consensus pattern (93 bp):
TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAATATTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAAACGAACAAAT
Found at i:815743 original size:78 final size:79
Alignment explanation
Indices: 815601--815753 Score: 245
Period size: 78 Copynumber: 1.9 Consensus size: 79
815591 AAGACAAAAC
*
815601 AAAGACAAATACTAACTTCACAATGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAA
1 AAAGACAAATACTAACTTCACAATGTT--A-AATAAACAGTTTAGCAGAATTGGCAGCAACCGAA
815666 TAAATTTACTTCAACCA
63 TAAATTTACTTCAACCA
* *
815683 AAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCAGTATTGGCAGCAACCGAATAA
1 AAAGACAAATACTAACTTCACAATGTTAAATAAACAGTTTAGCAGAATTGGCAGCAACCGAATAA
815747 ATTTACT
66 ATTTACT
815754 AAGCAATCTA
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
78 42 0.62
82 26 0.38
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.25
Consensus pattern (79 bp):
AAAGACAAATACTAACTTCACAATGTTAAATAAACAGTTTAGCAGAATTGGCAGCAACCGAATAA
ATTTACTTCAACCA
Found at i:817453 original size:20 final size:20
Alignment explanation
Indices: 817428--817491 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
817418 TTTTGGTTGA
817428 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
* *
817448 AATGAAAATCGCAACGCGGG
1 AATGAAAATCGCAACGAGAG
**
817468 AAATGACTATCGCAACGAGAG
1 -AATGAAAATCGCAACGAGAG
817489 AAT
1 AAT
817492 CGCAAAGCGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 21 0.57
21 16 0.43
ACGTcount: A:0.45, C:0.17, G:0.25, T:0.12
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:817495 original size:14 final size:14
Alignment explanation
Indices: 817476--817531 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
817466 GGAAATGACT
817476 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
817490 ATCGCAAAGCGAAATGAAA
1 ATCGC-AA-CG--A-GAGA
817509 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
817523 ATCGCAACG
1 ATCGCAACG
817532 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 17 0.49
15 3 0.09
16 2 0.06
17 2 0.06
18 3 0.09
19 8 0.23
ACGTcount: A:0.45, C:0.21, G:0.25, T:0.09
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:817513 original size:33 final size:33
Alignment explanation
Indices: 817426--817548 Score: 147
Period size: 33 Copynumber: 3.5 Consensus size: 33
817416 TCTTTTGGTT
817426 GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAAC--GAG-A-G--AATCGCAACGC
** *
817465 GGGAAATGACTATCGCAACGAGAGAATCGCAAAGC
1 --GAAATGAAAATCGCAACGAGAGAATCGCAACGC
817500 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
817533 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
817549 TGCGATTTTG
Statistics
Matches: 76, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
33 46 0.61
35 10 0.13
37 1 0.01
38 1 0.01
39 3 0.04
41 15 0.20
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:817611 original size:20 final size:20
Alignment explanation
Indices: 817573--817611 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
817563 CGTTGTGATT
**
817573 CTCTCGTTGCGATTTTCATC
1 CTCTCGTTGCGATAGTCATC
817593 CTCTCGTTGCGATAGTCAT
1 CTCTCGTTGCGATAGTCAT
817612 TTTTGTGTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.28, G:0.18, T:0.41
Consensus pattern (20 bp):
CTCTCGTTGCGATAGTCATC
Found at i:817632 original size:19 final size:19
Alignment explanation
Indices: 817598--817646 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
817588 TCATCCTCTC
* **
817598 GTTGCGATAGTCATTTTTGT
1 GTTGCGAT-TTCATTTTCAT
817618 GTTGCGATTTCATTTTCAT
1 GTTGCGATTTCATTTTCAT
817637 GTTGCGATTT
1 GTTGCGATTT
817647 TAAGTTTAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 18 0.69
20 8 0.31
ACGTcount: A:0.14, C:0.12, G:0.22, T:0.51
Consensus pattern (19 bp):
GTTGCGATTTCATTTTCAT
Found at i:818134 original size:20 final size:20
Alignment explanation
Indices: 818099--818146 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
818089 ATTCGCTATG
818099 CGCATTGCGA--TACGTAAT
1 CGCATTGCGATTTACGTAAT
* *
818117 CGCGTTGCGATTTACGTATT
1 CGCATTGCGATTTACGTAAT
818137 CGCATTGCGA
1 CGCATTGCGA
818147 ATTAGGAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 9 0.36
20 16 0.64
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.31
Consensus pattern (20 bp):
CGCATTGCGATTTACGTAAT
Found at i:818792 original size:12 final size:12
Alignment explanation
Indices: 818775--818799 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
818765 ATATTTTCGA
818775 TAAAAAATTATT
1 TAAAAAATTATT
818787 TAAAAAATTATT
1 TAAAAAATTATT
818799 T
1 T
818800 TTTTACCTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAAAAAATTATT
Found at i:818816 original size:20 final size:22
Alignment explanation
Indices: 818787--818826 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
818777 AAAAATTATT
818787 TAAAAAATT-AT-TTTTTTACC
1 TAAAAAATTAATATTTTTTACC
*
818807 TAAAATATTAATATTTTTTA
1 TAAAAAATTAATATTTTTTA
818827 TTCGGAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 2 0.12
22 7 0.41
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (22 bp):
TAAAAAATTAATATTTTTTACC
Found at i:818825 original size:23 final size:24
Alignment explanation
Indices: 818795--818850 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
818785 TTTAAAAAAT
*
818795 TATTTTTTTA-CCTAAAATATTAA
1 TATTTTTTTATCCGAAAATATTAA
* *
818818 TA-TTTTTTATTCGGAAATATTAA
1 TATTTTTTTATCCGAAAATATTAA
818841 TATTTTTTTA
1 TATTTTTTTA
818851 ATATTTACGG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.25
23 14 0.50
24 7 0.25
ACGTcount: A:0.34, C:0.05, G:0.04, T:0.57
Consensus pattern (24 bp):
TATTTTTTTATCCGAAAATATTAA
Found at i:818962 original size:21 final size:21
Alignment explanation
Indices: 818922--818962 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
818912 AGTAACGCCC
* **
818922 AATATTAATATTTTCGATAAA
1 AATAATAATATTTTAAATAAA
818943 AATAATAATATTTTAAATAA
1 AATAATAATATTTTAAATAA
818963 CATTTTATTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (21 bp):
AATAATAATATTTTAAATAAA
Found at i:819020 original size:16 final size:15
Alignment explanation
Indices: 818995--819026 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
818985 AATAATAACA
818995 TTTCTAATAATATAT
1 TTTCTAATAATATAT
819010 TTTCTTAATAATATAT
1 TTTC-TAATAATATAT
819026 T
1 T
819027 AAGAATAGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTCTAATAATATAT
Found at i:821108 original size:19 final size:19
Alignment explanation
Indices: 821086--821129 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
821076 TTATTTTTTA
821086 AAATAAAA-AAATAAGAATT
1 AAATAAAAGAAA-AAGAATT
*
821105 AAATAAAAGAAAAATAATT
1 AAATAAAAGAAAAAGAATT
821124 AAATAA
1 AAATAA
821130 TAAATTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 20 0.87
20 3 0.13
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (19 bp):
AAATAAAAGAAAAAGAATT
Found at i:824036 original size:16 final size:15
Alignment explanation
Indices: 824011--824041 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
824001 AAAGGAAAAA
824011 TAATATAATAAATAT
1 TAATATAATAAATAT
824026 TAATAATAATAAATAT
1 TAAT-ATAATAAATAT
824042 AAAAGGGGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TAATATAATAAATAT
Found at i:824107 original size:18 final size:19
Alignment explanation
Indices: 824069--824117 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
824059 AAGTTTTTTA
824069 AAATAAAAAAATAAGAATT
1 AAATAAAAAAATAAGAATT
* *
824088 AAATAAAGAAA-AATAATT
1 AAATAAAAAAATAAGAATT
*
824106 AAATAAACAAAT
1 AAATAAAAAAAT
824118 TAAAGAGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 16 0.62
19 10 0.38
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.20
Consensus pattern (19 bp):
AAATAAAAAAATAAGAATT
Found at i:832903 original size:21 final size:21
Alignment explanation
Indices: 832879--832928 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
832869 AGATAAAAAC
* *
832879 AAAATAAAAAT-TTAATATTAT
1 AAAATAAAAATATAAAGATT-T
*
832900 AAAATTAAAATATAAAGATTT
1 AAAATAAAAATATAAAGATTT
832921 AAAATAAA
1 AAAATAAA
832929 TTTGTAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
AAAATAAAAATATAAAGATTT
Found at i:832905 original size:15 final size:14
Alignment explanation
Indices: 832879--832926 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
832869 AGATAAAAAC
832879 AAAATA-AAAATTT
1 AAAATATAAAATTT
*
832892 AATATTATAAAA-TT
1 AA-AATATAAAATTT
832906 AAAATATAAAGATTT
1 AAAATATAAA-ATTT
832921 AAAATA
1 AAAATA
832927 AATTTGTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
13 9 0.31
14 8 0.28
15 12 0.41
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (14 bp):
AAAATATAAAATTT
Found at i:834880 original size:43 final size:43
Alignment explanation
Indices: 834801--834903 Score: 152
Period size: 43 Copynumber: 2.4 Consensus size: 43
834791 CGTTTGTTGA
* * * *
834801 CCGCAAAAGGTATTGATATTTAGCGGCGTTTTGCAGAAAAACG
1 CCGCAATAGGTGTTGATATTTAGCGGCATTTGGCAGAAAAACG
* *
834844 CCGTAATAGGTGTTGATATTTAGCGGCATTTGGCAGACAAACG
1 CCGCAATAGGTGTTGATATTTAGCGGCATTTGGCAGAAAAACG
834887 CCGCAATAGGTGTTGAT
1 CCGCAATAGGTGTTGAT
834904 TTTTGCTGCT
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 53 1.00
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (43 bp):
CCGCAATAGGTGTTGATATTTAGCGGCATTTGGCAGAAAAACG
Found at i:838035 original size:23 final size:23
Alignment explanation
Indices: 838009--838061 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
837999 GCGAAATGTG
838009 ACGACGCCGGAGACGAAGAAGGC
1 ACGACGCCGGAGACGAAGAAGGC
*
838032 ACGATGCCGGAGACGAAGAAGGC
1 ACGACGCCGGAGACGAAGAAGGC
838055 ACGACGC
1 ACGACGC
838062 AGTGAAGGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.34, C:0.26, G:0.38, T:0.02
Consensus pattern (23 bp):
ACGACGCCGGAGACGAAGAAGGC
Found at i:838300 original size:41 final size:41
Alignment explanation
Indices: 838255--838342 Score: 115
Period size: 41 Copynumber: 2.1 Consensus size: 41
838245 TTAAAATCAA
* *
838255 TTGCGGCGTTTAC-AGAAAAATGCCACTAATGTACGACCCAT
1 TTGCGGCGTTT-CTAGAAAAACGCCACTAAAGTACGACCCAT
* * *
838296 TTGCGGCGTTTCTTGTAAAACGCCACTAAAGTCCGACCCAT
1 TTGCGGCGTTTCTAGAAAAACGCCACTAAAGTACGACCCAT
838337 TTGCGG
1 TTGCGG
838343 TTTTTACCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
40 1 0.02
41 40 0.98
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (41 bp):
TTGCGGCGTTTCTAGAAAAACGCCACTAAAGTACGACCCAT
Found at i:838469 original size:42 final size:42
Alignment explanation
Indices: 838418--838786 Score: 533
Period size: 42 Copynumber: 8.8 Consensus size: 42
838408 ATGTTAACCA
* *
838418 TATTGCGGCGTTTGAGCTATAAAAGCCGCTATATTACAACTC
1 TATTGCGGCGTTTGAGCTATAAACGCCGCTATATTACTACTC
* * *
838460 TATTACGGCGCTTGAGCTATAAACGCCGCTATATTACAACTC
1 TATTGCGGCGTTTGAGCTATAAACGCCGCTATATTACTACTC
*
838502 TATTGCGGCGTTTGATCTATAAACGCCGCTATATTACTACTC
1 TATTGCGGCGTTTGAGCTATAAACGCCGCTATATTACTACTC
* * *
838544 TATTGCAG-TTTTGAGCTATAAACGCCGCTATATTACAACTC
1 TATTGCGGCGTTTGAGCTATAAACGCCGCTATATTACTACTC
** * *
838585 TATTATGGCATTTGATCTATAAACGCCGCTATATTACTACTC
1 TATTGCGGCGTTTGAGCTATAAACGCCGCTATATTACTACTC
* *
838627 TATTGCGGCGTTTAAGCTACAAACGCCGCTATATTACTACTC
1 TATTGCGGCGTTTGAGCTATAAACGCCGCTATATTACTACTC
* * *
838669 TATTACGGCGTTTTAGCTATAAACGCCACTATATTACTACTC
1 TATTGCGGCGTTTGAGCTATAAACGCCGCTATATTACTACTC
* *
838711 TATTGCGGCGTTTTAGCTACAAACGCCGCTATATTACTACTC
1 TATTGCGGCGTTTGAGCTATAAACGCCGCTATATTACTACTC
* *
838753 TATTGTGGCGTTTGAGCTACAAACGCCGCTATAT
1 TATTGCGGCGTTTGAGCTATAAACGCCGCTATAT
838787 GCTTAAAGTT
Statistics
Matches: 294, Mismatches: 32, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
41 35 0.12
42 259 0.88
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (42 bp):
TATTGCGGCGTTTGAGCTATAAACGCCGCTATATTACTACTC
Found at i:838582 original size:125 final size:125
Alignment explanation
Indices: 838428--838786 Score: 542
Period size: 125 Copynumber: 2.9 Consensus size: 125
838418 TATTGCGGCG
* *
838428 TTTGAGCTATAAAAGCCGCTATATTACAACTCTATTACGGCGCTTGAGCTATAAACGCCGCTATA
1 TTTGAGCTATAAACGCCGCTATATTACAACTCTATTACGGCGTTTGAGCTATAAACGCCGCTATA
* * *
838493 TTACAACTCTATTGCGGCGTTTGATCTATAAACGCCGCTATATTACTACTCTATT-GCAGT
66 TTACTACTCTATTGCGGCGTTTGAGCTACAAACGCCGCTATATTACTACTCTATTAGC-GT
* * *
838553 TTTGAGCTATAAACGCCGCTATATTACAACTCTATTATGGCATTTGATCTATAAACGCCGCTATA
1 TTTGAGCTATAAACGCCGCTATATTACAACTCTATTACGGCGTTTGAGCTATAAACGCCGCTATA
*
838618 TTACTACTCTATTGCGGCGTTTAAGCTACAAACGCCGCTATATTACTACTCTATTACGGCGT
66 TTACTACTCTATTGCGGCGTTTGAGCTACAAACGCCGCTATATTACTACTCTATTA--GCGT
* * * * *
838680 TTT-AGCTATAAACGCCACTATATTACTACTCTATTGCGGCGTTTTAGCTACAAACGCCGCTATA
1 TTTGAGCTATAAACGCCGCTATATTACAACTCTATTACGGCGTTTGAGCTATAAACGCCGCTATA
*
838744 TTACTACTCTATTGTGGCGTTTGAGCTACAAACGCCGCTATAT
66 TTACTACTCTATTGCGGCGTTTGAGCTACAAACGCCGCTATAT
838787 GCTTAAAGTT
Statistics
Matches: 212, Mismatches: 19, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
125 111 0.52
126 94 0.44
127 5 0.02
128 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (125 bp):
TTTGAGCTATAAACGCCGCTATATTACAACTCTATTACGGCGTTTGAGCTATAAACGCCGCTATA
TTACTACTCTATTGCGGCGTTTGAGCTACAAACGCCGCTATATTACTACTCTATTAGCGT
Found at i:840331 original size:83 final size:82
Alignment explanation
Indices: 840211--840455 Score: 221
Period size: 82 Copynumber: 3.0 Consensus size: 82
840201 GTTTTTGTGG
* * * * *
840211 CGTTTTTATAAAAGAGCCACTATAGACAAAC-ATATTGCGGCGTTTTTAGGAAAATCGCCGCTAA
1 CGTTTTTAGAAAA-CGCCACTATAAAC-AACTATATTGCGGCGTTTATA-GAAAAACGCCGCTAA
* * *
840275 ATTATTACTCTTTTGC-G-G
63 ATTACTACTCTATTGCAGTA
* *
840293 CGTTTTTAGCACAAACGCCACTATAAACAACTCTATTGCGGCGTTTATATAAAAACGCCGCTAAA
1 CGTTTTTAG-A-AAACGCCACTATAAACAACTATATTGCGGCGTTTATAGAAAAACGCCGCTAAA
840358 TTACTACTCTATTGCAGTA
64 TTACTACTCTATTGCAGTA
** * * *
840377 TTTTTTTAGAAAATGCCACTATAAACAACTATATT-CTGGCGTTT-GAGCTATAAACGCCGCTAA
1 CGTTTTTAGAAAACGCCACTATAAACAACTATATTGC-GGCGTTTATAG--AAAAACGCCGCTAA
* * *
840440 CTTACCACCCTATTGC
63 ATTACTACTCTATTGC
840456 GGCATTTGTT
Statistics
Matches: 135, Mismatches: 20, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
81 2 0.01
82 68 0.50
83 55 0.41
84 10 0.07
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (82 bp):
CGTTTTTAGAAAACGCCACTATAAACAACTATATTGCGGCGTTTATAGAAAAACGCCGCTAAATT
ACTACTCTATTGCAGTA
Found at i:840367 original size:41 final size:42
Alignment explanation
Indices: 840243--840372 Score: 149
Period size: 41 Copynumber: 3.1 Consensus size: 42
840233 TAGACAAACA
* * *
840243 TATTGCGGCGTTTTTAGGAAAATCGCCGCTAAATTATTACTC
1 TATTGCGGCGTTTTTAGCAAAAACGCCGCTAAATTACTACTC
* * * *
840285 TTTTGCGGCGTTTTTAGCACAAACGCCACTATAA--ACAACTC
1 TATTGCGGCGTTTTTAGCAAAAACGCCGCTA-AATTACTACTC
* *
840326 TATTGCGGCGTTTATA-TAAAAACGCCGCTAAATTACTACTC
1 TATTGCGGCGTTTTTAGCAAAAACGCCGCTAAATTACTACTC
840367 TATTGC
1 TATTGC
840373 AGTATTTTTT
Statistics
Matches: 72, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
39 2 0.03
40 11 0.15
41 31 0.43
42 26 0.36
43 2 0.03
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.33
Consensus pattern (42 bp):
TATTGCGGCGTTTTTAGCAAAAACGCCGCTAAATTACTACTC
Found at i:843134 original size:30 final size:30
Alignment explanation
Indices: 843074--843138 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
843064 AGTTTAACCA
*
843074 AATACTAAACTAATGTAAATGGCTATATTG
1 AATACTAAACTAATGTAAATGGCTAAATTG
*
843104 AATACTAAACTAA-G-AATAGTGGTTAAATTG
1 AATACTAAACTAATGTAA-A-TGGCTAAATTG
843134 AATAC
1 AATAC
843139 AAAGCAGGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 2 0.06
29 2 0.06
30 27 0.87
ACGTcount: A:0.46, C:0.09, G:0.14, T:0.31
Consensus pattern (30 bp):
AATACTAAACTAATGTAAATGGCTAAATTG
Found at i:843701 original size:18 final size:18
Alignment explanation
Indices: 843657--843702 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
843647 TTCAAACCCT
*
843657 TGAAGATTTTGGCTTGTA
1 TGAAGATTTTGGCTCGTA
843675 TGTAAGATTTTGGCTCCG-A
1 TG-AAGATTTTGGCT-CGTA
843694 TGAAGATTT
1 TGAAGATTT
843703 GGTTCTCATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 9 0.36
19 15 0.60
20 1 0.04
ACGTcount: A:0.24, C:0.09, G:0.26, T:0.41
Consensus pattern (18 bp):
TGAAGATTTTGGCTCGTA
Found at i:865336 original size:46 final size:44
Alignment explanation
Indices: 865216--865364 Score: 181
Period size: 45 Copynumber: 3.3 Consensus size: 44
865206 TAATCCAAGT
* *
865216 CTTTTGATTATTTGGTTGTCAAAAGTAAAATCAAAAGATTAGTTA
1 CTTTTGATTA-TTGGTTGTAAAAAGTAAAATCAAAAGATTAGTTC
* *
865261 CTTTTGATTATTGTGTTGCAAAAAGTAAAATCAAATGATTAGTTC
1 CTTTTGATTATTG-GTTGTAAAAAGTAAAATCAAAAGATTAGTTC
* * * *
865306 CTTTTTGATTATTAGATTGTGAAAATTAAAATCAAAGGATTAGTTC
1 C-TTTTGATTATT-GGTTGTAAAAAGTAAAATCAAAAGATTAGTTC
*
865352 CTTGTGATTATTG
1 CTTTTGATTATTG
865365 AGTCGGTAAA
Statistics
Matches: 91, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
44 4 0.04
45 48 0.53
46 38 0.42
47 1 0.01
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.42
Consensus pattern (44 bp):
CTTTTGATTATTGGTTGTAAAAAGTAAAATCAAAAGATTAGTTC
Found at i:865728 original size:57 final size:57
Alignment explanation
Indices: 865556--865836 Score: 214
Period size: 58 Copynumber: 4.9 Consensus size: 57
865546 AAATATTAAG
* * * * *
865556 AATCTTGAATGATTTTAACCTTGTTAGAGAAATAAATT-TAAC-AATTTATTTCCTTGA
1 AATCTTAAATGATTCTAACTTTGTAAGAAAAATAAATTGT--CGAATTTATTTCCTTGA
* * *
865613 GAATATTGAATGATTCTAACTTTGTAAGAAAAATAAATTGTTGAATTTATTTCCTTGA
1 -AATCTTAAATGATTCTAACTTTGTAAGAAAAATAAATTGTCGAATTTATTTCCTTGA
* * *
865671 AATCTTAAATGATT-TAACTTTGTAAGGAAAATAAATTGTCGAATTTTTTTTTCTTGA
1 AATCTTAAATGATTCTAACTTTGTAAGAAAAATAAATTGTCGAA-TTTATTTCCTTGA
** * * * * ** * *
865728 ATATCACAGATGATTCTATCATT-TAAAAAGAAATAAATTGTTAAATTTATTTTCTTTA
1 A-ATCTTAAATGATTCTAACTTTGTAAGAA-AAATAAATTGTCGAATTTATTTCCTTGA
* * * **
865786 GAATCTTAAATTATTGT-ATTTTGTTAA-AAAAATAAATTGTTAAATTTATTT
1 -AATCTTAAATGATTCTAACTTTG-TAAGAAAAATAAATTGTCGAATTTATTT
865837 TCTCAGGAAT
Statistics
Matches: 183, Mismatches: 31, Indels: 19
0.79 0.13 0.08
Matches are distributed among these distances:
56 27 0.15
57 48 0.26
58 85 0.46
59 23 0.13
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.44
Consensus pattern (57 bp):
AATCTTAAATGATTCTAACTTTGTAAGAAAAATAAATTGTCGAATTTATTTCCTTGA
Found at i:865993 original size:39 final size:39
Alignment explanation
Indices: 865901--865977 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 39
865891 TCTATCTTTT
* * *
865901 AAAATGAAATAAATTGTCAGATTTATTTTCCTATTTTGG
1 AAAATGAAATAAATCGTCAAATTTAGTTTCCTATTTTGG
* *
865940 AAAATGAAACAAATCGTTAAATTTAGTTTCCTATTTTG
1 AAAATGAAATAAATCGTCAAATTTAGTTTCCTATTTTG
865978 TATAAGAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.42
Consensus pattern (39 bp):
AAAATGAAATAAATCGTCAAATTTAGTTTCCTATTTTGG
Found at i:866064 original size:39 final size:39
Alignment explanation
Indices: 865992--866070 Score: 106
Period size: 39 Copynumber: 2.0 Consensus size: 39
865982 AGAAAATAAA
* *
865992 TCTTTTATGAAAGGAAATAAATCATTGAGTTTATTTTCC
1 TCTTTTACGAAAGGAAATAAATCATGGAGTTTATTTTCC
* *
866031 TCTTTTACGAAAGGAAATAAGTTGATGGA-TTTATTTTCC
1 TCTTTTACGAAAGGAAATAA-ATCATGGAGTTTATTTTCC
866070 T
1 T
866071 GTGGATCTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 30 0.86
40 5 0.14
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.43
Consensus pattern (39 bp):
TCTTTTACGAAAGGAAATAAATCATGGAGTTTATTTTCC
Found at i:866170 original size:39 final size:39
Alignment explanation
Indices: 866096--866189 Score: 109
Period size: 39 Copynumber: 2.4 Consensus size: 39
866086 TTCTTATTTG
866096 TAAAAGAAATAAATCGTAGAATTTATTTTTACTATTTTA
1 TAAAAGAAATAAATCGTAGAATTTATTTTTACTATTTTA
* * * * *
866135 TAAAATGAAATAAATTGTTGGATTTA-TTTTCCTATTTTG
1 TAAAA-GAAATAAATCGTAGAATTTATTTTTACTATTTTA
*
866174 TAAAAGGGAATAAATC
1 TAAAA-GAAATAAATC
866190 ATTTGATTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
39 29 0.63
40 17 0.37
ACGTcount: A:0.41, C:0.05, G:0.12, T:0.41
Consensus pattern (39 bp):
TAAAAGAAATAAATCGTAGAATTTATTTTTACTATTTTA
Found at i:866198 original size:39 final size:39
Alignment explanation
Indices: 866096--866202 Score: 101
Period size: 39 Copynumber: 2.8 Consensus size: 39
866086 TTCTTATTTG
* * *
866096 TAAAA-GAAATAAATCGTAGAATTTATTTTTACTATTTTA
1 TAAAAGGAAATAAATCATTGGATTTA-TTTTACTATTTTA
* ** * *
866135 TAAAATGAAATAAATTGTTGGATTTATTTTCCTATTTTG
1 TAAAAGGAAATAAATCATTGGATTTATTTTACTATTTTA
* *
866174 TAAAAGGGAATAAATCATTTGATTT-TTTT
1 TAAAAGGAAATAAATCATTGGATTTATTTT
866203 GTTGAGAATT
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
38 4 0.07
39 36 0.63
40 17 0.30
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.46
Consensus pattern (39 bp):
TAAAAGGAAATAAATCATTGGATTTATTTTACTATTTTA
Found at i:873564 original size:23 final size:24
Alignment explanation
Indices: 873504--873564 Score: 81
Period size: 23 Copynumber: 2.6 Consensus size: 24
873494 TAATTTTGCA
* *
873504 TTTATGTCATG-TATTCTTCTACC
1 TTTATGACATGTTTTTCTTCTACC
*
873527 TTTATGACACGTTTTTC-TCTACC
1 TTTATGACATGTTTTTCTTCTACC
873550 TTTATGACATGTTTT
1 TTTATGACATGTTTT
873565 CGATCATTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 29 0.88
24 4 0.12
ACGTcount: A:0.18, C:0.20, G:0.10, T:0.52
Consensus pattern (24 bp):
TTTATGACATGTTTTTCTTCTACC
Found at i:874919 original size:16 final size:16
Alignment explanation
Indices: 874894--874958 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
874884 TAATAAATAA
*
874894 ACGAATATAAACGAAC
1 ACGAACATAAACGAAC
874910 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
* *
874926 ACAAACATAAATGAAC
1 ACGAACATAAACGAAC
874942 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
874958 A
1 A
874959 TAAACGCTGG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.58, C:0.22, G:0.11, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:874923 original size:10 final size:10
Alignment explanation
Indices: 874890--874964 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
874880 CATTTAATAA
*
874890 ATAAACGAAT
1 ATAAACGAAC
874900 ATAAACGAAC
1 ATAAACGAAC
874910 ----ACGAAC
1 ATAAACGAAC
874916 ATAAACGAAC
1 ATAAACGAAC
* *
874926 ACAAAC-ATAA
1 ATAAACGA-AC
874936 ATGAACACGAAC
1 AT-AA-ACGAAC
874948 ATAAACGAAC
1 ATAAACGAAC
874958 ATAAACG
1 ATAAACG
874965 CTGGAGACCC
Statistics
Matches: 52, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 35 0.67
11 4 0.08
12 5 0.10
13 1 0.02
ACGTcount: A:0.59, C:0.20, G:0.11, T:0.11
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:876086 original size:14 final size:14
Alignment explanation
Indices: 876067--876097 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
876057 AGCGAACATA
876067 AACGAACATAACCG
1 AACGAACATAACCG
876081 AACGAACATAACCG
1 AACGAACATAACCG
876095 AAC
1 AAC
876098 TTCCTGCCGC
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:0.52, C:0.29, G:0.13, T:0.06
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:876097 original size:10 final size:10
Alignment explanation
Indices: 876050--876083 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
876040 ATAAATGAAT
*
876050 GAACATAAGC
1 GAACATAAAC
876060 GAACATAAAC
1 GAACATAAAC
*
876070 GAACATAACC
1 GAACATAAAC
876080 GAAC
1 GAAC
876084 GAACATAACC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.53, C:0.24, G:0.15, T:0.09
Consensus pattern (10 bp):
GAACATAAAC
Found at i:877004 original size:27 final size:27
Alignment explanation
Indices: 876946--877027 Score: 69
Period size: 30 Copynumber: 2.9 Consensus size: 27
876936 TCATTAATTA
* *
876946 TTATTTTTAACAACAGTTAATAATGTATAT
1 TTATTTTTAATAA-AATTAAT-AT-TATAT
876976 TTATTTTTAATAAAATTTAATATT-TAT
1 TTATTTTTAATAAAA-TTAATATTATAT
*
877003 TTAATATTTT-TTAAAATTAATATTA
1 TT-AT-TTTTAATAAAATTAATATTA
877028 GAAAGAATAT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
27 13 0.29
28 8 0.18
29 7 0.16
30 17 0.38
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (27 bp):
TTATTTTTAATAAAATTAATATTATAT
Found at i:879735 original size:3 final size:3
Alignment explanation
Indices: 879685--879717 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
879675 TATATATGGT
879685 TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
879718 CACTGCACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:885412 original size:22 final size:22
Alignment explanation
Indices: 885358--885413 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 22
885348 CGATTCTGAT
885358 TATCGCATTGCGATTTTCCAAA
1 TATCGCATTGCGATTTTCCAAA
* * *
885380 T-TCGCCTTGCGATTTTCCGAC
1 TATCGCATTGCGATTTTCCAAA
*
885401 TATCGCAATGCGA
1 TATCGCATTGCGA
885414 ATATGTAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
21 18 0.64
22 10 0.36
ACGTcount: A:0.21, C:0.27, G:0.18, T:0.34
Consensus pattern (22 bp):
TATCGCATTGCGATTTTCCAAA
Found at i:885430 original size:20 final size:20
Alignment explanation
Indices: 885402--885458 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
885392 TTTTCCGACT
885402 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
* *
885422 ATCGTAATGAGAATATGTAA
1 ATCGCAATGCGAATATGTAA
* *
885442 ATCACAATGCGATTATG
1 ATCGCAATGCGAATATG
885459 ACTATCGCAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.28
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:885473 original size:20 final size:20
Alignment explanation
Indices: 885450--885569 Score: 231
Period size: 20 Copynumber: 6.0 Consensus size: 20
885440 AAATCACAAT
*
885450 GCGATTATGACTATCGCAAC
1 GCGATTCTGACTATCGCAAC
885470 GCGATTCTGACTATCGCAAC
1 GCGATTCTGACTATCGCAAC
885490 GCGATTCTGACTATCGCAAC
1 GCGATTCTGACTATCGCAAC
885510 GCGATTCTGACTATCGCAAC
1 GCGATTCTGACTATCGCAAC
885530 GCGATTCTGACTATCGCAAC
1 GCGATTCTGACTATCGCAAC
885550 GCGATTCTGACTATCGCAAC
1 GCGATTCTGACTATCGCAAC
885570 ATTGAATTTC
Statistics
Matches: 99, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
20 99 1.00
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (20 bp):
GCGATTCTGACTATCGCAAC
Found at i:890324 original size:2 final size:2
Alignment explanation
Indices: 890317--890351 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
890307 CAAGTGAATT
890317 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
890352 TATTTCAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:890427 original size:2 final size:2
Alignment explanation
Indices: 890420--890457 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
890410 AATTTAGACA
*
890420 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
890458 GAAAATATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:893625 original size:18 final size:17
Alignment explanation
Indices: 893604--893664 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 17
893594 TGAGGATGAT
893604 GATGATAGTGATTCTGAA
1 GATGA-AGTGATTCTGAA
* *
893622 GATGGAAGTGGTTCTGAT
1 GAT-GAAGTGATTCTGAA
* *
893640 GATGAAGATGACTCTGAG
1 GATGAAG-TGATTCTGAA
893658 GATGAAG
1 GATGAAG
893665 ACGAGGTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
17 4 0.11
18 30 0.83
19 2 0.06
ACGTcount: A:0.31, C:0.07, G:0.34, T:0.28
Consensus pattern (17 bp):
GATGAAGTGATTCTGAA
Found at i:903268 original size:21 final size:20
Alignment explanation
Indices: 903235--903273 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
903225 TTCCGCCGAC
903235 AAAAAACCAAAAACGCAATT
1 AAAAAACCAAAAACGCAATT
*
903255 AAAACAACCTAAAACGCAA
1 AAAA-AACCAAAAACGCAA
903274 GAGATAAGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.64, C:0.23, G:0.05, T:0.08
Consensus pattern (20 bp):
AAAAAACCAAAAACGCAATT
Found at i:911651 original size:45 final size:46
Alignment explanation
Indices: 911555--911662 Score: 123
Period size: 45 Copynumber: 2.4 Consensus size: 46
911545 ATTCATATAC
* *
911555 TATGCATCGATGAACTCAGAGTTTTATGAAAACATCGAATACATTT
1 TATGCATCGATGCACTCAGAGTTTTATGAAAACATCAAATACATTT
* **
911601 GATGCATCGATGCACTCAG-GCTATTT-TG-AAACATCAAATGTATTT
1 TATGCATCGATGCACTCAGAG-T-TTTATGAAAACATCAAATACATTT
*
911646 TATGCATCGGTGCACTC
1 TATGCATCGATGCACTC
911663 TTAGTGCACC
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
45 30 0.57
46 20 0.38
47 3 0.06
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (46 bp):
TATGCATCGATGCACTCAGAGTTTTATGAAAACATCAAATACATTT
Found at i:919658 original size:2 final size:2
Alignment explanation
Indices: 919651--919714 Score: 121
Period size: 2 Copynumber: 32.5 Consensus size: 2
919641 CAGCTTAAGC
919651 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
919693 TA TA TA TA TA TA -A TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
919715 TAATCAATTG
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 60 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:920253 original size:65 final size:63
Alignment explanation
Indices: 920183--920343 Score: 227
Period size: 65 Copynumber: 2.5 Consensus size: 63
920173 GAAATAAATT
*
920183 AAACATCGAATGCATTTCATGCATCGATGCACATACTATGCATCGATGCACTCAGAG-T-TTTAT
1 AAACATCGAATGCATTTCATGCATCGATGCACA-ACAATGCATCGATGCACTCAG-GCTATTT-T
920246 G
63 G
* *
920247 AGAACATCGAATGCATTTGATGCATCGATGCACCAGCAATGCATCGATGCACTCAGGCTATTTTG
1 A-AACATCGAATGCATTTCATGCATCGATGCA-CAACAATGCATCGATGCACTCAGGCTATTTTG
*
920312 AAACATCGAATGCATTTTATGCATCGATGCAC
1 AAACATCGAATGCATTTCATGCATCGATGCAC
920344 TCTTAGTGCA
Statistics
Matches: 89, Mismatches: 4, Indels: 9
0.87 0.04 0.09
Matches are distributed among these distances:
63 1 0.01
64 31 0.35
65 52 0.58
66 5 0.06
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (63 bp):
AAACATCGAATGCATTTCATGCATCGATGCACAACAATGCATCGATGCACTCAGGCTATTTTG
Found at i:921975 original size:3 final size:3
Alignment explanation
Indices: 921967--921997 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
921957 TTTTCAACAT
921967 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
921998 TCATTTTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:928585 original size:11 final size:11
Alignment explanation
Indices: 928565--928597 Score: 57
Period size: 12 Copynumber: 2.9 Consensus size: 11
928555 ATTAATAAGT
928565 ATATTTTTTTA
1 ATATTTTTTTA
928576 ATTATTTTTTTA
1 A-TATTTTTTTA
928588 ATATTTTTTT
1 ATATTTTTTT
928598 CAATGGATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
ATATTTTTTTA
Found at i:935363 original size:20 final size:20
Alignment explanation
Indices: 935296--935354 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
935286 AACAAATTCG
*
935296 CAACGCAAATATGTAAATCA
1 CAACGCGAATATGTAAATCA
935316 CAACGCGAATATGTAAATCA
1 CAACGCGAATATGTAAATCA
935336 CAACGCGAATATGTAAATC
1 CAACGCGAATATGTAAATC
935355 GCATTGCGAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.46, C:0.20, G:0.14, T:0.20
Consensus pattern (20 bp):
CAACGCGAATATGTAAATCA
Found at i:935392 original size:20 final size:20
Alignment explanation
Indices: 935369--935627 Score: 134
Period size: 20 Copynumber: 13.2 Consensus size: 20
935359 TGCGATTTTC
935369 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
* * *
935389 CAAATTTGCAACACGAATTTGT
1 CAAATTCGCAACGCGAA--AGT
* *
935411 -AAA-TCGCAACACAAAAGT
1 CAAATTCGCAACGCGAAAGT
*
935429 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGAAAGT
*
935449 CAAATTCACAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
****
935469 CAAATATTTTTACGC----G-
1 CAAAT-TCGCAACGCGAAAGT
935485 --AA-TCGCAACGCGAATATGT
1 CAAATTCGCAACGCGAA-A-GT
** ***
935504 -AAA-TCGCATTGCGATTTT
1 CAAATTCGCAACGCGAAAGT
935522 CCAAATTCGCAACGCGAAAGT
1 -CAAATTCGCAACGCGAAAGT
* *
935543 CAAATTCGCAACACGAATTTGT
1 CAAATTCGCAACGCGAA--AGT
*
935565 -AAA-TCGCAACAC-ATAAGT
1 CAAATTCGCAACGCGA-AAGT
* *
935583 CAAATTCGTAACGCGATAGT
1 CAAATTCGCAACGCGAAAGT
*
935603 CAAATTCGCAACGCGAAAAT
1 CAAATTCGCAACGCGAAAGT
935623 CAAAT
1 CAAAT
935628 GTTTTTACGC
Statistics
Matches: 179, Mismatches: 38, Indels: 44
0.69 0.15 0.17
Matches are distributed among these distances:
12 5 0.03
14 2 0.01
17 1 0.01
18 6 0.03
19 7 0.04
20 132 0.74
21 22 0.12
22 4 0.02
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:935468 original size:40 final size:40
Alignment explanation
Indices: 935288--935627 Score: 173
Period size: 40 Copynumber: 8.6 Consensus size: 40
935278 AAATGACCAA
* *
935288 CAAATTCGCAACGCAAATATGT-AAA-TCACAACGCGAATATGT
1 CAAATTCGCAACGCGAA-A-GTCAAATTCGCAACGCG-AT-TGT
* ** *
935330 -AAA-TCACAACGCGAATATGT-AAA-TCGCATTGCGATTTT
1 CAAATTCGCAACGCGAA-A-GTCAAATTCGCAACGCGATTGT
* *
935368 CCAAATTCGCAACGCGAAAGTCAAATTTGCAACACGAATTTGT
1 -CAAATTCGCAACGCGAAAGTCAAATTCGCAACGCG-A-TTGT
* * *
935411 -AAA-TCGCAACACAAAAGTCAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGAAAGTCAAATTCGCAACGCGATTGT
* ****
935449 CAAATTCACAACGCGAAAGTCAAATATTTTTACGC----G-
1 CAAATTCGCAACGCGAAAGTCAAAT-TCGCAACGCGATTGT
** *
935485 --AA-TCGCAACGCGAATATGT-AAA-TCGCATTGCGATTTT
1 CAAATTCGCAACGCGAA-A-GTCAAATTCGCAACGCGATTGT
*
935522 CCAAATTCGCAACGCGAAAGTCAAATTCGCAACACGAATTTGT
1 -CAAATTCGCAACGCGAAAGTCAAATTCGCAACGCG-A-TTGT
* * *
935565 -AAA-TCGCAACAC-ATAAGTCAAATTCGTAACGCGATAGT
1 CAAATTCGCAACGCGA-AAGTCAAATTCGCAACGCGATTGT
*
935603 CAAATTCGCAACGCGAAAATCAAAT
1 CAAATTCGCAACGCGAAAGTCAAAT
935628 GTTTTTACGC
Statistics
Matches: 227, Mismatches: 42, Indels: 60
0.69 0.13 0.18
Matches are distributed among these distances:
32 3 0.01
33 11 0.05
34 6 0.03
35 2 0.01
37 1 0.00
38 8 0.04
39 15 0.07
40 122 0.54
41 51 0.22
42 2 0.01
43 6 0.03
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.23
Consensus pattern (40 bp):
CAAATTCGCAACGCGAAAGTCAAATTCGCAACGCGATTGT
Found at i:935616 original size:154 final size:154
Alignment explanation
Indices: 935331--935646 Score: 560
Period size: 154 Copynumber: 2.1 Consensus size: 154
935321 CGAATATGTA
*
935331 AATCACAACGCGAATATGTAAATCGCATTGCGATTTTCCAAATTCGCAACGCGAAAGTCAAATTT
1 AATCACAACGCGAATATGTAAATCGCATTGCGATTTTCCAAATTCGCAACGCGAAAGTCAAATTC
935396 GCAACACGAATTTGTAAATCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCACAAC
66 GCAACACGAATTTGTAAATCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCACAAC
*
935461 GCGAAAGTCAAATATTTTTACGCG
131 GCGAAAATCAAATATTTTTACGCG
*
935485 AATCGCAACGCGAATATGTAAATCGCATTGCGATTTTCCAAATTCGCAACGCGAAAGTCAAATTC
1 AATCACAACGCGAATATGTAAATCGCATTGCGATTTTCCAAATTCGCAACGCGAAAGTCAAATTC
* * *
935550 GCAACACGAATTTGTAAATCGCAACACATAAGTCAAATTCGTAACGCGATAGTCAAATTCGCAAC
66 GCAACACGAATTTGTAAATCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCACAAC
*
935615 GCGAAAATCAAATGTTTTTACGCG
131 GCGAAAATCAAATATTTTTACGCG
*
935639 AAACACAA
1 AATCACAA
935647 TATTAATTTC
Statistics
Matches: 153, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
154 153 1.00
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.23
Consensus pattern (154 bp):
AATCACAACGCGAATATGTAAATCGCATTGCGATTTTCCAAATTCGCAACGCGAAAGTCAAATTC
GCAACACGAATTTGTAAATCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCACAAC
GCGAAAATCAAATATTTTTACGCG
Found at i:935785 original size:22 final size:22
Alignment explanation
Indices: 935760--935802 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
935750 GCGACATCTC
*
935760 TCCCCATCTCCGACGAAATCCG
1 TCCCCATCTCCGACAAAATCCG
*
935782 TCCCCATTTCCGACAAAATCC
1 TCCCCATCTCCGACAAAATCC
935803 ATCTATCTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.44, G:0.09, T:0.21
Consensus pattern (22 bp):
TCCCCATCTCCGACAAAATCCG
Found at i:937060 original size:17 final size:17
Alignment explanation
Indices: 937038--937079 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
937028 GAATTTCTAT
937038 ATTATAATGTTTCCAAA
1 ATTATAATGTTTCCAAA
937055 ATTATAATGTTTCCAAA
1 ATTATAATGTTTCCAAA
937072 ATTATAAT
1 ATTATAAT
937080 TAATTATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.43, C:0.10, G:0.05, T:0.43
Consensus pattern (17 bp):
ATTATAATGTTTCCAAA
Found at i:939663 original size:14 final size:14
Alignment explanation
Indices: 939644--939683 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
939634 TTTTGATTAA
939644 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
** *
939658 TTGATTTGTTTAAT
1 TTGATTTGTAAAAG
939672 TTGATTTGTAAA
1 TTGATTTGTAAA
939684 TATTTTTTTC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:940081 original size:39 final size:39
Alignment explanation
Indices: 940027--940113 Score: 165
Period size: 39 Copynumber: 2.2 Consensus size: 39
940017 TCAAGTTGTA
940027 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
940066 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
940105 GATTTTGAT
1 GATTTTGAT
940114 GAGCATCGGA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.17, C:0.15, G:0.21, T:0.47
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:940428 original size:6 final size:6
Alignment explanation
Indices: 940417--940455 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
940407 ATTTATATTG
* * *
940417 AAATTC AAATTC AAACTC AAATTG AAATTT AAATTC AAA
1 AAATTC AAATTC AAATTC AAATTC AAATTC AAATTC AAA
940456 CTCCAATTAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.54, C:0.13, G:0.03, T:0.31
Consensus pattern (6 bp):
AAATTC
Found at i:940436 original size:12 final size:12
Alignment explanation
Indices: 940421--940463 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
940411 ATATTGAAAT
940421 TCAAATTCAAAC
1 TCAAATTCAAAC
* *
940433 TCAAATTGAAAT
1 TCAAATTCAAAC
*
940445 TTAAATTCAAAC
1 TCAAATTCAAAC
*
940457 TCCAATT
1 TCAAATT
940464 ACATATGAAA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.47, C:0.19, G:0.02, T:0.33
Consensus pattern (12 bp):
TCAAATTCAAAC
Found at i:940445 original size:24 final size:24
Alignment explanation
Indices: 940413--940463 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
940403 CGGAATTTAT
940413 ATTGAAATTCAAATTCAAACTCAA
1 ATTGAAATTCAAATTCAAACTCAA
* *
940437 ATTGAAATTTAAATTCAAACTCCA
1 ATTGAAATTCAAATTCAAACTCAA
940461 ATT
1 ATT
940464 ACATATGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.47, C:0.16, G:0.04, T:0.33
Consensus pattern (24 bp):
ATTGAAATTCAAATTCAAACTCAA
Found at i:940879 original size:25 final size:25
Alignment explanation
Indices: 940842--940891 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
940832 ATTATTTTTC
*
940842 CAAATAATATACCCATAACAATGTT
1 CAAATAATATACCCACAACAATGTT
*
940867 CAAATAATGTACCCACAACAATGTT
1 CAAATAATATACCCACAACAATGTT
940892 TAATTGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.46, C:0.22, G:0.06, T:0.26
Consensus pattern (25 bp):
CAAATAATATACCCACAACAATGTT
Found at i:941005 original size:20 final size:20
Alignment explanation
Indices: 940982--941023 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
940972 AATAAGCGTT
940982 GCGATAGTCAAATTCGCAAC
1 GCGATAGTCAAATTCGCAAC
941002 GCGATAGTCAAATTCGCAAC
1 GCGATAGTCAAATTCGCAAC
941022 GC
1 GC
941024 TTATTTCGCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.19
Consensus pattern (20 bp):
GCGATAGTCAAATTCGCAAC
Found at i:943690 original size:24 final size:24
Alignment explanation
Indices: 943639--943690 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
943629 ATCTGAGTAT
** *
943639 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
943663 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
943687 TGAC
1 TGAC
943691 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:943823 original size:12 final size:12
Alignment explanation
Indices: 943802--943835 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
943792 GGTTGTAGGT
*
943802 TTTGAGATTGTG
1 TTTGATATTGTG
943814 TTTGATATTGTG
1 TTTGATATTGTG
*
943826 TTTGGTATTG
1 TTTGATATTG
943836 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:944597 original size:19 final size:19
Alignment explanation
Indices: 944573--944636 Score: 85
Period size: 19 Copynumber: 3.4 Consensus size: 19
944563 ACTAAAACCT
* *
944573 GTTGCGAAATT-AAATTCGC
1 GTTGCGAATTTGAAATTC-A
944592 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
944611 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
*
944630 ATTGCGA
1 GTTGCGA
944637 TTTACAATTC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 35 0.85
20 6 0.15
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.34
Consensus pattern (19 bp):
GTTGCGAATTTGAAATTCA
Found at i:945224 original size:28 final size:28
Alignment explanation
Indices: 945136--945225 Score: 69
Period size: 29 Copynumber: 3.2 Consensus size: 28
945126 ACTAATCTTG
* * *
945136 AAAC-TTTGAATATTTTAATTTCATCCC
1 AAACTTTTGAACATTCTAATTTGATCCC
* * *
945163 TAAA-TTATG-ACATTCACTAAATTGATTCTC
1 -AAACTTTTGAACATT--CTAATTTGA-TCCC
945193 AAACTTTTGAACATTCTAATTTGATCCC
1 AAACTTTTGAACATTCTAATTTGATCCC
945221 AAACT
1 AAACT
945226 ATACGCATAT
Statistics
Matches: 47, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
27 4 0.09
28 14 0.30
29 17 0.36
30 7 0.15
31 5 0.11
ACGTcount: A:0.36, C:0.19, G:0.06, T:0.40
Consensus pattern (28 bp):
AAACTTTTGAACATTCTAATTTGATCCC
Found at i:945471 original size:20 final size:20
Alignment explanation
Indices: 945448--945491 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
945438 TGTGTGTGCA
945448 TGTGCGCGTGTACGTGCGTG
1 TGTGCGCGTGTACGTGCGTG
945468 TGTGCGCGTGTACGTGCGTG
1 TGTGCGCGTGTACGTGCGTG
945488 TGTG
1 TGTG
945492 TGCATGTGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.05, C:0.18, G:0.45, T:0.32
Consensus pattern (20 bp):
TGTGCGCGTGTACGTGCGTG
Found at i:948718 original size:22 final size:21
Alignment explanation
Indices: 948670--948737 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
948660 GAATAGCATC
* *
948670 TCTTGATATTAATATTAGATT
1 TCTTTATATTAATATTATATT
948691 TCTTTATATTAACTATTATATCT
1 TCTTTATATTAA-TATTATAT-T
* * *
948714 T-TTTATGTTAAAATTATATA
1 TCTTTATATTAATATTATATT
948734 TCTT
1 TCTT
948738 CATGTTAACA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
20 1 0.03
21 20 0.51
22 16 0.41
23 2 0.05
ACGTcount: A:0.32, C:0.07, G:0.04, T:0.56
Consensus pattern (21 bp):
TCTTTATATTAATATTATATT
Found at i:948815 original size:26 final size:25
Alignment explanation
Indices: 948782--948837 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
948772 AATTTAAATA
948782 ATTAATAT-TATTAAAT-ATAATTAAT
1 ATTAATATGTA-TAAATAAT-ATTAAT
*
948807 ATTATATATGTATATATAATATTAAT
1 ATTA-ATATGTATAAATAATATTAAT
948833 ATTAA
1 ATTAA
948838 GCTTAAGAGC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
25 5 0.19
26 18 0.67
27 4 0.15
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (25 bp):
ATTAATATGTATAAATAATATTAAT
Found at i:949855 original size:18 final size:19
Alignment explanation
Indices: 949814--949858 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
949804 ATTGTTTAAA
*
949814 GTTTTAAGTTAGGATTTGG
1 GTTTTAAGTTAGGATTTAG
949833 GTTTTAAGTTAGG-TTTAG
1 GTTTTAAGTTAGGATTTAG
949851 GTTTTAAG
1 GTTTTAAG
949859 GTTTAGGCAG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 12 0.48
19 13 0.52
ACGTcount: A:0.22, C:0.00, G:0.29, T:0.49
Consensus pattern (19 bp):
GTTTTAAGTTAGGATTTAG
Found at i:952464 original size:14 final size:13
Alignment explanation
Indices: 952424--952472 Score: 64
Period size: 13 Copynumber: 3.6 Consensus size: 13
952414 AATTAAAATA
952424 ATTAAATACAAAC
1 ATTAAATACAAAC
952437 ATTAAATACAAAC
1 ATTAAATACAAAC
952450 ATTACAAGT-CAAAC
1 ATTA-AA-TACAAAC
952464 AATTAAATA
1 -ATTAAATA
952473 ATAACAACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
13 18 0.56
14 9 0.28
15 5 0.16
ACGTcount: A:0.59, C:0.14, G:0.02, T:0.24
Consensus pattern (13 bp):
ATTAAATACAAAC
Found at i:953038 original size:21 final size:21
Alignment explanation
Indices: 952998--953039 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
952988 AACCGACTGC
*
952998 AGTGACATCTGAAATAGTTGT
1 AGTGACATCTGAAACAGTTGT
* *
953019 AGTGCCATCTGAAACGGTTGT
1 AGTGACATCTGAAACAGTTGT
953040 GATGTACCCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (21 bp):
AGTGACATCTGAAACAGTTGT
Found at i:961240 original size:2 final size:2
Alignment explanation
Indices: 961233--961273 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
961223 AACTTTATTT
961233 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
961274 TACAATCTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:989725 original size:199 final size:195
Alignment explanation
Indices: 989379--989773 Score: 566
Period size: 199 Copynumber: 2.0 Consensus size: 195
989369 ATCCGACCTG
989379 AATATATAAATTAGAAACCCGACCCGACCCGAAATAATAAAAAAATATTTTTATTCAATAAAAAC
1 AATATATAAATTAGAAACCCGACCCGACCCGAAATAATAAAAAAATATTTTTATTCAATAAAAAC
* *
989444 AATGACTTAATTAAAAAAATTATATATATATATAGGGGTATTATTGTAATTATTCCTAAATATAT
66 AATGACTTAATTAAAAAAATTATATATATAGATAGGGGTATTACTGTAATTATTCCTAAATATAT
* * *
989509 AAGGTAAAATAATATATTTTTTGGGTCGGTTGAGTCGGGTA-TTTTCACCCTAAACCCGAACCCG
131 AAGGTAAAATAATATA-TTTTCGGGTC-G--G-GTCGAGTATTTTTCACCCTAAACCCAAACCCG
989573 ACCCA
191 ACCCA
* * *
989578 AATATATGAATTTGAAACCCGACCCGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAG
1 AATATATAAATTAGAAACCCGACCCGACCCGAAATAATAAAAAAA-TATTTTTATTCAATAAAAA
* *
989643 CAGTGACTTAATTGAAAAAAA-T-TATATATAGA-A-GGGTATTACTGTAATTATTTCTAAATAT
65 CAATGACTTAATT-AAAAAAATTATATATATAGATAGGGGTATTACTGTAATTATTCCTAAATAT
* *
989704 ATAAGGTAAAATTATATATATTTTCGGTTCGGGTCGAGTATTTTTCACCCTAAACCCAAACTCGA
129 ATAAGGTAAAA-TA-ATATATTTTCGGGTCGGGTCGAGTATTTTTCACCCTAAACCCAAACCCGA
989769 CCCA
192 CCCA
989773 A
1 A
989774 CCCGAATATC
Statistics
Matches: 179, Mismatches: 12, Indels: 14
0.87 0.06 0.07
Matches are distributed among these distances:
194 7 0.04
195 28 0.16
197 38 0.21
198 11 0.06
199 57 0.32
200 31 0.17
201 7 0.04
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (195 bp):
AATATATAAATTAGAAACCCGACCCGACCCGAAATAATAAAAAAATATTTTTATTCAATAAAAAC
AATGACTTAATTAAAAAAATTATATATATAGATAGGGGTATTACTGTAATTATTCCTAAATATAT
AAGGTAAAATAATATATTTTCGGGTCGGGTCGAGTATTTTTCACCCTAAACCCAAACCCGACCCA
Found at i:1002705 original size:31 final size:31
Alignment explanation
Indices: 1002667--1002731 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
1002657 AGAGTCAAGG
*
1002667 GTTTACCTATG-TCTTTCGAGACATATGGACA
1 GTTTACCTAGGTTC-TTCGAGACATATGGACA
*
1002698 GTTTACCTAGGTTCTTCGAGACCTATGGACA
1 GTTTACCTAGGTTCTTCGAGACATATGGACA
1002729 GTT
1 GTT
1002732 GCCGAGGTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 29 0.94
32 2 0.06
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (31 bp):
GTTTACCTAGGTTCTTCGAGACATATGGACA
Found at i:1002742 original size:30 final size:30
Alignment explanation
Indices: 1002681--1002765 Score: 98
Period size: 30 Copynumber: 2.8 Consensus size: 30
1002671 ACCTATGTCT
* *
1002681 TTCGAGACATATGGACAGTTTACCTAGGTTC
1 TTCGAGACCTATGGACAG-TTACCGAGGTTC
*
1002712 TTCGAGACCTATGGACAGTTGCCGAGGTTC
1 TTCGAGACCTATGGACAGTTACCGAGGTTC
* * * *
1002742 TTTGTGACCTCTGGATAGTTACCG
1 TTCGAGACCTATGGACAGTTACCG
1002766 GGGTCTTTGT
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
30 29 0.63
31 17 0.37
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (30 bp):
TTCGAGACCTATGGACAGTTACCGAGGTTC
Found at i:1002773 original size:29 final size:30
Alignment explanation
Indices: 1002717--1002788 Score: 101
Period size: 29 Copynumber: 2.4 Consensus size: 30
1002707 GGTTCTTCGA
* * * *
1002717 GACCTATGGACAGTTGCCGAGGTTCTTTGT
1 GACCTCTGGATAGTTACCGAGGGTCTTTGT
1002747 GACCTCTGGATAGTTACCG-GGGTCTTTGT
1 GACCTCTGGATAGTTACCGAGGGTCTTTGT
1002776 GACCTCTGGATAG
1 GACCTCTGGATAG
1002789 GTCCTTCGGG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
29 22 0.58
30 16 0.42
ACGTcount: A:0.17, C:0.21, G:0.31, T:0.32
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGGTCTTTGT
Found at i:1004550 original size:31 final size:31
Alignment explanation
Indices: 1004527--1004667 Score: 255
Period size: 31 Copynumber: 4.5 Consensus size: 31
1004517 CATAGATTCT
* *
1004527 GAAGAACCTAGGTAATCAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
*
1004558 GAAGAACATAAGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
1004589 GAAGAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
1004620 GAAGAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
1004651 GAAGAACATAGGTAAAC
1 GAAGAACATAGGTAAAC
1004668 CCTCGACCCT
Statistics
Matches: 106, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 106 1.00
ACGTcount: A:0.40, C:0.22, G:0.19, T:0.19
Consensus pattern (31 bp):
GAAGAACATAGGTAAACAGTCCATATGTCCC
Found at i:1008785 original size:31 final size:31
Alignment explanation
Indices: 1008711--1008864 Score: 235
Period size: 31 Copynumber: 5.1 Consensus size: 31
1008701 GTCCCGAAGG
* *
1008711 ACAGTCCATA-GATTCCGAAGAACCTAGGTAA
1 ACAGTCCATATG-TCCCGAAGAACATAGGTAA
* *
1008742 TCAGT-CATATGTCCCGAAGAACATAAGTAA
1 ACAGTCCATATGTCCCGAAGAACATAGGTAA
1008772 ACAGTCCATATGTCCCGAAGAACATAGGTAA
1 ACAGTCCATATGTCCCGAAGAACATAGGTAA
1008803 ACAGTCCATATGTCCCGAAGAACATAGGTAA
1 ACAGTCCATATGTCCCGAAGAACATAGGTAA
1008834 ACAGTCCATATGT-CCG-AGAACATAGGTAA
1 ACAGTCCATATGTCCCGAAGAACATAGGTAA
1008863 AC
1 AC
1008865 CCTCGACCCT
Statistics
Matches: 115, Mismatches: 6, Indels: 6
0.91 0.05 0.05
Matches are distributed among these distances:
29 15 0.13
30 27 0.23
31 73 0.63
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.20
Consensus pattern (31 bp):
ACAGTCCATATGTCCCGAAGAACATAGGTAA
Found at i:1009311 original size:20 final size:20
Alignment explanation
Indices: 1009286--1009323 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1009276 ATTTTCATTT
1009286 AGGGGAATCGATACCCCCCC
1 AGGGGAATCGATACCCCCCC
1009306 AGGGGAATCGATACCCCC
1 AGGGGAATCGATACCCCC
1009324 TGAACATACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.37, G:0.26, T:0.11
Consensus pattern (20 bp):
AGGGGAATCGATACCCCCCC
Found at i:1012811 original size:31 final size:31
Alignment explanation
Indices: 1012773--1012928 Score: 251
Period size: 31 Copynumber: 5.0 Consensus size: 31
1012763 CCCGAAGGAC
* * *
1012773 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
1012804 CAGTCCATATGTCCCGAAGAACATAAGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1012835 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1012866 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
1012897 CAGTCCATATGTCCCAAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1012928 C
1 C
1012929 CCTCGACCCT
Statistics
Matches: 118, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
31 117 0.99
32 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1017044 original size:31 final size:31
Alignment explanation
Indices: 1017006--1017161 Score: 251
Period size: 31 Copynumber: 5.0 Consensus size: 31
1016996 CCCGAAGGAC
* * *
1017006 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
1017037 CAGTCCATATGTCCCGAAGAACATAAGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1017068 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1017099 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
1017130 CAGTCCATATGTCCCAAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1017161 C
1 C
1017162 CCTCGACCCT
Statistics
Matches: 118, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
31 117 0.99
32 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1021070 original size:23 final size:23
Alignment explanation
Indices: 1021040--1021091 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
1021030 AGTGTTATAT
1021040 TATATTTTAAAAATATTAATTAA
1 TATATTTTAAAAATATTAATTAA
* *
1021063 TATATTTTAAATATATTTATTAA
1 TATATTTTAAAAATATTAATTAA
*
1021086 AATATT
1 TATATT
1021092 ATTAGATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATTAA
Found at i:1021093 original size:11 final size:11
Alignment explanation
Indices: 1021049--1021126 Score: 54
Period size: 11 Copynumber: 7.0 Consensus size: 11
1021039 TTATATTTTA
1021049 AAAATATTAATT
1 AAAATATT-ATT
*
1021061 AATATATT-TT
1 AAAATATTATT
1021071 AAATATATTTATT
1 AAA-ATA-TTATT
1021084 AAAATATTATT
1 AAAATATTATT
* * *
1021095 AGATTAATATT
1 AAAATATTATT
*
1021106 -AAAT-TTATA
1 AAAATATTATT
1021115 AATAATATTATT
1 AA-AATATTATT
1021127 CATTATTAAT
Statistics
Matches: 50, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
9 3 0.06
10 7 0.14
11 19 0.38
12 16 0.32
13 5 0.10
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (11 bp):
AAAATATTATT
Found at i:1021172 original size:27 final size:26
Alignment explanation
Indices: 1021105--1021176 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 26
1021095 AGATTAATAT
*
1021105 TAAATTTATAAATAATATTATTCATTA
1 TAAATTAATAAATAATATTATTCA-TA
* * *
1021132 TTAA-TAATTTAATAATATTATTTATA
1 TAAATTAA-TAAATAATATTATTCATA
1021158 TGAAATTAATAAATAATAT
1 T-AAATTAATAAATAATAT
1021177 AAATTTTATT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
26 5 0.14
27 28 0.78
28 3 0.08
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (26 bp):
TAAATTAATAAATAATATTATTCATA
Found at i:1021197 original size:10 final size:10
Alignment explanation
Indices: 1021182--1021207 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1021172 AATATAAATT
1021182 TTATTATATA
1 TTATTATATA
1021192 TTATTATATA
1 TTATTATATA
1021202 TTATTA
1 TTATTA
1021208 AAATAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TTATTATATA
Found at i:1021266 original size:51 final size:44
Alignment explanation
Indices: 1021165--1021283 Score: 114
Period size: 51 Copynumber: 2.5 Consensus size: 44
1021155 ATATGAAATT
*
1021165 AATAAATAATATAA-ATTTTATTATATATTATTATATATTATTAA
1 AATAAA-AATATAATATTTTATTATATATAATTATATATTATTAA
*
1021209 AATAAAAATATAATATCTTATATTATAATATAATTGATTATTTTATTATA
1 AATAAAAATATAATAT-TT-TATTAT-ATATAATT-A-TATATTATTA-A
* *
1021259 ATATAAAAGTATAATAGTATTATTA
1 A-ATAAAAATATAATA-TTTTATTA
1021284 GAAATATTAT
Statistics
Matches: 62, Mismatches: 4, Indels: 12
0.79 0.05 0.15
Matches are distributed among these distances:
43 7 0.11
44 8 0.13
45 2 0.03
46 6 0.10
47 7 0.11
48 1 0.02
49 9 0.15
50 7 0.11
51 14 0.23
52 1 0.02
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.47
Consensus pattern (44 bp):
AATAAAAATATAATATTTTATTATATATAATTATATATTATTAA
Found at i:1021363 original size:24 final size:23
Alignment explanation
Indices: 1021318--1021363 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
1021308 TATTTTAATA
1021318 ATTAATATTTTGATTAAAATTAT
1 ATTAATATTTTGATTAAAATTAT
* *
1021341 ATTAATATATTTTATTAATATTA
1 ATTAATAT-TTTGATTAAAATTA
1021364 AATTCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (23 bp):
ATTAATATTTTGATTAAAATTAT
Found at i:1026335 original size:5 final size:5
Alignment explanation
Indices: 1026325--1026350 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1026315 TGGAGATGAT
1026325 GGAGG GGAGG GGAGG GGAGG GGAGG G
1 GGAGG GGAGG GGAGG GGAGG GGAGG G
1026351 AGAAATATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.81, T:0.00
Consensus pattern (5 bp):
GGAGG
Found at i:1027350 original size:2 final size:2
Alignment explanation
Indices: 1027343--1027380 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1027333 GAAAACAACA
1027343 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
1027381 TTACATGTAA
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:1028923 original size:137 final size:142
Alignment explanation
Indices: 1028772--1029156 Score: 464
Period size: 149 Copynumber: 2.7 Consensus size: 142
1028762 TCATATTTTA
* * ** * * *
1028772 AATATATATTTATTTTTCAATATTAAGAAA-GAGCAGTCTTAAAGCAACTGGATGTCCATTTTCT
1 AATATTTATTTATTTTTTAATATTAAGAAATGAGTTGTCTTAAAGCACCTAGAAGTCCATTTTCT
1028836 GATATTTTTAAATAAATAAATATTTTACTTTTATAAATTATATATATTAA-TCTATTTT-A-A-T
66 GATATTTTTAAATAAATAAATATTTTA-TTTTATAAATTATATATATTAATTCTATTTTAATATT
1028897 -AAATGTTTTATT
130 AAAATGTTTTATT
* *
1028909 AATATTTATGTATTTTTTTATATTAAGAAATGAGTTGTCTTAAAGCACCTAGAAGTCC-TTTTCT
1 AATATTTATTTATTTTTTAATATTAAGAAATGAGTTGTCTTAAAGCACCTAGAAGTCCATTTTCT
** * *
1028973 GATATACTTAAATAAATAAATATTCTATTTTTATAAATTATATATATTAATTTTATTTTAATTAT
66 GATATTTTTAAATAAATAAATATTTTA-TTTTATAAATTATATATATTAATTCTATTTTAA-TA-
1029038 TTTTAGAGAAATGTTTTATT
128 --TT--A-AAATGTTTTATT
* *
1029058 AATATTTATTTATTTTTTAATATTAAGAAATGGGTTGTCCTAAAGCACCTAGAAGT-CATTTTCT
1 AATATTTATTTATTTTTTAATATTAAGAAATGAGTTGTCTTAAAGCACCTAGAAGTCCATTTTCT
* * *
1029122 GATATTTCTAAGTAAATAAATATCTTA-TTTATAAA
66 GATATTTTTAAATAAATAAATATTTTATTTTATAAA
1029157 AATATAAATA
Statistics
Matches: 210, Mismatches: 24, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
137 78 0.37
138 29 0.14
139 1 0.00
141 1 0.00
145 1 0.00
147 8 0.04
148 1 0.00
149 91 0.43
ACGTcount: A:0.37, C:0.07, G:0.08, T:0.47
Consensus pattern (142 bp):
AATATTTATTTATTTTTTAATATTAAGAAATGAGTTGTCTTAAAGCACCTAGAAGTCCATTTTCT
GATATTTTTAAATAAATAAATATTTTATTTTATAAATTATATATATTAATTCTATTTTAATATTA
AAATGTTTTATT
Found at i:1029198 original size:149 final size:149
Alignment explanation
Indices: 1028897--1029190 Score: 375
Period size: 149 Copynumber: 2.0 Consensus size: 149
1028887 CTATTTTAAT
* *
1028897 AAATGTTTTATTAATATTTATGTATTTTTTTATATTAAGAAATGAGTTGTCTTAAAGCACCTAGA
1 AAATGTTTTATTAATATTTATGTATTTTTTAATATTAAGAAATGAGTTGTCCTAAAGCACCTAGA
* * * *
1028962 AGTCCTTTTCTGATATACTTAAATAAATAAATATTCTATTTTTATAAATTATATATATTAATTTT
66 AGTCATTTTCTGATATACTTAAATAAATAAATATTCTATATTTATAAATAATATATAATAATTTT
** ** *
1029027 ATTTTAATTATTTTTAGAG
131 ATTAAAATTATTAATAAAG
* *
1029046 AAATGTTTTATTAATATTTATTTATTTTTTAATATTAAGAAATGGGTTGTCCTAAAGCACCTAGA
1 AAATGTTTTATTAATATTTATGTATTTTTTAATATTAAGAAATGAGTTGTCCTAAAGCACCTAGA
* *
1029111 AGTCATTTTCTGATAT-TTCTAAGTAAATAAATA-TCT-TATTTATAAA-AATATA-AAT-ATTT
66 AGTCATTTTCTGATATACT-TAAATAAATAAATATTCTATATTTATAAATAATATATAATAATTT
*
1029170 TCTTAAAATTATACTAATAAA
130 TATTAAAATTAT--TAATAAA
1029191 TTTGAAATAA
Statistics
Matches: 126, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
144 13 0.10
145 2 0.02
146 9 0.07
147 9 0.07
148 4 0.03
149 89 0.71
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.47
Consensus pattern (149 bp):
AAATGTTTTATTAATATTTATGTATTTTTTAATATTAAGAAATGAGTTGTCCTAAAGCACCTAGA
AGTCATTTTCTGATATACTTAAATAAATAAATATTCTATATTTATAAATAATATATAATAATTTT
ATTAAAATTATTAATAAAG
Found at i:1038563 original size:22 final size:22
Alignment explanation
Indices: 1038537--1038617 Score: 80
Period size: 23 Copynumber: 3.8 Consensus size: 22
1038527 ATAGGGTAGA
1038537 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATACCCCCTTGAAG
*
1038559 GGGAA-CTGATTCCCCCTTTGAAG
1 GGGAATC-GATACCCCC-TTGAAG
* *
1038582 GGGAACCGATTCCCCC-T--AG
1 GGGAATCGATACCCCCTTGAAG
*
1038601 GGGAATTGATACCCCCT
1 GGGAATCGATACCCCCT
1038618 GGGGTTCTGG
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
19 15 0.29
21 2 0.04
22 13 0.25
23 20 0.39
24 1 0.02
ACGTcount: A:0.23, C:0.30, G:0.26, T:0.21
Consensus pattern (22 bp):
GGGAATCGATACCCCCTTGAAG
Found at i:1038579 original size:23 final size:23
Alignment explanation
Indices: 1038537--1038598 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1038527 ATAGGGTAGA
* *
1038537 GGGAATCGATACCCCC-TTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
*
1038559 GGGAACTGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
1038582 GGGAACCGATTCCCCCT
1 GGGAACCGATTCCCCCT
1038599 AGGGGAATTG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
22 13 0.37
23 22 0.63
ACGTcount: A:0.23, C:0.31, G:0.26, T:0.21
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTGAAG
Found at i:1047515 original size:22 final size:20
Alignment explanation
Indices: 1047465--1047519 Score: 92
Period size: 20 Copynumber: 2.6 Consensus size: 20
1047455 ACATCTACAT
1047465 TCTTCAAAGATGATAGATTC
1 TCTTCAAAGATGATAGATTC
1047485 TCTTCAAAGATGATAGATTC
1 TCTTCAAAGATGATAGATTC
1047505 TCTTTTCAAAGATGA
1 TC--TTCAAAGATGA
1047520 AGCTTTATGG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 22 0.67
22 11 0.33
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Consensus pattern (20 bp):
TCTTCAAAGATGATAGATTC
Found at i:1048311 original size:37 final size:37
Alignment explanation
Indices: 1048269--1048391 Score: 122
Period size: 37 Copynumber: 3.4 Consensus size: 37
1048259 CTGCGTCTTG
* *
1048269 CTTGAGACAATTTCACTCGAAACAACAATTTATCTCA
1 CTTGAGATAGTTTCACTCGAAACAACAATTTATCTCA
* ** ** * *** *
1048306 CTTGAGATTGTTTTTCTTAAAACAA-ACTACGTCTCG
1 CTTGAGATAGTTTCACTCGAAACAACAATTTATCTCA
1048342 CTTGAGATAGTTTCACTCGAAACAACAATTTATCTCA
1 CTTGAGATAGTTTCACTCGAAACAACAATTTATCTCA
*
1048379 CTTGAGATTGTTT
1 CTTGAGATAGTTT
1048392 TTCTTAAAAC
Statistics
Matches: 62, Mismatches: 23, Indels: 2
0.71 0.26 0.02
Matches are distributed among these distances:
36 26 0.42
37 36 0.58
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (37 bp):
CTTGAGATAGTTTCACTCGAAACAACAATTTATCTCA
Found at i:1048349 original size:36 final size:37
Alignment explanation
Indices: 1048228--1048421 Score: 133
Period size: 36 Copynumber: 5.3 Consensus size: 37
1048218 TAGTAATTTA
* * *
1048228 TCTCACTTAAGATTGTTTTTCTTAAAACAA-ACTGCG
1 TCTCACTTGAGATTGTTTTTCTTAAAACAACAATTCG
** *** ** ** **
1048264 TCTTGCTTGAGACAATTTCACTCGAAACAACAATTTA
1 TCTCACTTGAGATTGTTTTTCTTAAAACAACAATTCG
* *
1048301 TCTCACTTGAGATTGTTTTTCTTAAAACAA-ACTACG
1 TCTCACTTGAGATTGTTTTTCTTAAAACAACAATTCG
* * ** ** **
1048337 TCTCGCTTGAGATAGTTTCACTCGAAACAACAATTTA
1 TCTCACTTGAGATTGTTTTTCTTAAAACAACAATTCG
*
1048374 TCTCACTTGAGATTGTTTTTCTTAAAACAA-GATTCG
1 TCTCACTTGAGATTGTTTTTCTTAAAACAACAATTCG
*
1048410 TCTCGCTTGAGA
1 TCTCACTTGAGA
1048422 CAGTTTCACT
Statistics
Matches: 109, Mismatches: 47, Indels: 4
0.68 0.29 0.03
Matches are distributed among these distances:
36 60 0.55
37 49 0.45
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (37 bp):
TCTCACTTGAGATTGTTTTTCTTAAAACAACAATTCG
Found at i:1048402 original size:37 final size:37
Alignment explanation
Indices: 1048288--1048403 Score: 135
Period size: 37 Copynumber: 3.2 Consensus size: 37
1048278 ATTTCACTCG
1048288 AAACAACAATTTATCTCACTTGAGATTGTTTTTCTTA
1 AAACAACAATTTATCTCACTTGAGATTGTTTTTCTTA
* *** * * ** **
1048325 AAACAA-ACTACGTCTCGCTTGAGATAGTTTCACTCG
1 AAACAACAATTTATCTCACTTGAGATTGTTTTTCTTA
1048361 AAACAACAATTTATCTCACTTGAGATTGTTTTTCTTA
1 AAACAACAATTTATCTCACTTGAGATTGTTTTTCTTA
1048398 AAACAA
1 AAACAA
1048404 GATTCGTCTC
Statistics
Matches: 58, Mismatches: 20, Indels: 2
0.73 0.25 0.03
Matches are distributed among these distances:
36 26 0.45
37 32 0.55
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.36
Consensus pattern (37 bp):
AAACAACAATTTATCTCACTTGAGATTGTTTTTCTTA
Found at i:1048453 original size:73 final size:73
Alignment explanation
Indices: 1048222--1048436 Score: 351
Period size: 73 Copynumber: 2.9 Consensus size: 73
1048212 TTTAAATAGT
* * * *
1048222 AATTTATCTCACTTAAGATTGTTTTTCTTAAAACAAACTGCGTCTTGCTTGAGACAATTTCACTC
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTACGTCTCGCTTGAGACAGTTTCACTC
1048287 GAAACAAC
66 GAAACAAC
*
1048295 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTACGTCTCGCTTGAGATAGTTTCACTC
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTACGTCTCGCTTGAGACAGTTTCACTC
1048360 GAAACAAC
66 GAAACAAC
*
1048368 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGA-TTCGTCTCGCTTGAGACAGTTTCACT
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA-ACTACGTCTCGCTTGAGACAGTTTCACT
*
1048432 AGAAA
65 CGAAA
1048437 TATAAATTTC
Statistics
Matches: 133, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
73 132 0.99
74 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.36
Consensus pattern (73 bp):
AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTACGTCTCGCTTGAGACAGTTTCACTC
GAAACAAC
Found at i:1048717 original size:122 final size:121
Alignment explanation
Indices: 1048460--1049030 Score: 798
Period size: 122 Copynumber: 4.7 Consensus size: 121
1048450 CACTCGATGG
* **
1048460 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGA-AGTGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATA
* * *
1048525 ATGAGAATAACTTGTTCAAC-TTTTGCAT-GACTCTATCACAGAAGGAGATAGATCAGC
65 ATGAGAAGAACTTGTTCAACTTTTTGC-TCGATTCTATCACA-AAAGAGATAGATCAGC
* * *
1048582 ATCAACATTTCCAGAAGTGTTCATAATGAGAAAAACTCATCTGAAGAATAAGAAGAACTTCATAA
1 ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAA
* * *
1048647 TGGGAAGAACTTGTTCAACTTTTTGCTCGATTTTATCACAGAAAGAGATAGATCAGT
66 TGAGAAGAACTTGTTCAACTTTTTGCTCGATTCTATCACA-AAAGAGATAGATCAGC
*
1048704 ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
1 ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAA
*
1048769 TGAGAAGAACTTGTTCAACTTTTTGCTCAATTCTATCAC---AGA-ATAGATCAGC
66 TGAGAAGAACTTGTTCAACTTTTTGCTCGATTCTATCACAAAAGAGATAGATCAGC
1048821 ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAA-AAGAAAGAAGAAGTTCATA
1 ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAAG-AAGAAGAAGTTCATA
* * ** * *
1048885 ATGAGAAGAATTTATTCAACCATTTGCTCGATTCTATCACATAAGAAGATAGATCAAC
65 ATGAGAAGAACTTGTTCAACTTTTTGCTCGATTCTATCACAAAAG-AGATAGATCAGC
* * *
1048943 ATCCACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAG-AGAAAAAAGAAGTTCAT
1 ATCAACATTTCCAGAA-GTGTTCATAATGAGAAGAACTCATCTGAAGAAG-AAGAAGAAGTTCAT
*
1049007 AATGAGAAGAACTTGTTCGACTTT
64 AATGAGAAGAACTTGTTCAACTTT
1049031 AGCTTGATTC
Statistics
Matches: 404, Mismatches: 35, Indels: 19
0.88 0.08 0.04
Matches are distributed among these distances:
116 2 0.00
117 104 0.26
118 3 0.01
120 2 0.00
121 64 0.16
122 166 0.41
123 63 0.16
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (121 bp):
ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAA
TGAGAAGAACTTGTTCAACTTTTTGCTCGATTCTATCACAAAAGAGATAGATCAGC
Found at i:1048913 original size:239 final size:242
Alignment explanation
Indices: 1048460--1049030 Score: 823
Period size: 239 Copynumber: 2.4 Consensus size: 242
1048450 CACTCGATGG
* * *
1048460 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGA-AGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* *
1048525 ATGAGAATAACTTGTTCAAC-TTTTGCATGACTCTATCACAGAAGGAGATAGATCAGCATCAACA
65 ATGAGAAGAACTTGTTCAACTTTTTGCATAACTCTATCAC--AAGGAGATAGATCAGCATCAACA
* *
1048589 TTTCCAGAAGTGTTCATAATGAGAAAAACTCATCTGAAGAATAAGAAGAACTTCATAATGGGAAG
128 TTTCCAGAAGTGTTCATAATGAGAAAAACTCATCTGAAGAAAAAGAAGAACTTCATAATGAGAAG
* ** * **
1048654 AACTTGTTCAACTTTTTGCTCGATTTTATCACAGAAAG-AGATAGATCAGT
193 AACTTATTCAACCATTTGCTCGATTCTATCACA-AAAGAAGATAGATCAAC
*
1048704 ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
*
1048769 TGAGAAGAACTTGTTCAACTTTTTGC-TCAATTCTATCAC-A-GA-ATAGATCAGCATCAACATT
66 TGAGAAGAACTTGTTCAACTTTTTGCAT-AACTCTATCACAAGGAGATAGATCAGCATCAACATT
* *
1048830 TCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAA-AAGAAAGAAGAAGTTCATAATGAGAAGA
130 TCCAGAAGTGTTCATAATGAGAAAAACTCATCTGAAGAA-AAAGAAGAACTTCATAATGAGAAGA
* *
1048894 ATTTATTCAACCATTTGCTCGATTCTATCACATAAGAAGATAGATCAAC
194 ACTTATTCAACCATTTGCTCGATTCTATCACAAAAGAAGATAGATCAAC
* * *
1048943 ATCCACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAGAGAAAAAAGAAGTTCATA
1 ATCAACATTTCCAGAA-GAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
*
1049008 ATGAGAAGAACTTGTTCGACTTT
65 ATGAGAAGAACTTGTTCAACTTT
1049031 AGCTTGATTC
Statistics
Matches: 298, Mismatches: 24, Indels: 14
0.89 0.07 0.04
Matches are distributed among these distances:
238 5 0.02
239 128 0.43
240 69 0.23
241 1 0.00
243 66 0.22
244 29 0.10
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (242 bp):
ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAA
TGAGAAGAACTTGTTCAACTTTTTGCATAACTCTATCACAAGGAGATAGATCAGCATCAACATTT
CCAGAAGTGTTCATAATGAGAAAAACTCATCTGAAGAAAAAGAAGAACTTCATAATGAGAAGAAC
TTATTCAACCATTTGCTCGATTCTATCACAAAAGAAGATAGATCAAC
Found at i:1049834 original size:2 final size:2
Alignment explanation
Indices: 1049827--1049921 Score: 190
Period size: 2 Copynumber: 47.5 Consensus size: 2
1049817 GAAAACAACA
1049827 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
1049869 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
1049911 AT AT AT AT AT A
1 AT AT AT AT AT A
1049922 CATGTAAACT
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 93 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1053352 original size:8 final size:8
Alignment explanation
Indices: 1053341--1053417 Score: 59
Period size: 8 Copynumber: 9.8 Consensus size: 8
1053331 TTTTTATTCA
1053341 TTAATTAT
1 TTAATTAT
1053349 TTAATTAT
1 TTAATTAT
* *
1053357 TTAAGTAA
1 TTAATTAT
*
1053365 TTAAATAT
1 TTAATTAT
*
1053373 TTTATTA-
1 TTAATTAT
*
1053380 TTATTTTAT
1 TTA-ATTAT
* *
1053389 TTTAGTAT
1 TTAATTAT
1053397 TT-ATTAT
1 TTAATTAT
*
1053404 TTTATTAT
1 TTAATTAT
1053412 TTAATT
1 TTAATT
1053418 GTAAACTTAT
Statistics
Matches: 53, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
7 8 0.15
8 43 0.81
9 2 0.04
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.64
Consensus pattern (8 bp):
TTAATTAT
Found at i:1055604 original size:33 final size:33
Alignment explanation
Indices: 1055567--1055643 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 33
1055557 TATTGAGAGT
**
1055567 GATGATGACGATGAGGACAATGAGGAGGGGGAG
1 GATGATGACGATGAGGACAATGAGGAGAAGGAG
* *
1055600 GATGA-GAACGATGATGACGATGAGGAGAAGGAG
1 GATGATG-ACGATGAGGACAATGAGGAGAAGGAG
*
1055633 GAGGATGACGA
1 GATGATGACGA
1055644 CAAAGAGGAC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
32 1 0.03
33 35 0.95
34 1 0.03
ACGTcount: A:0.36, C:0.06, G:0.45, T:0.12
Consensus pattern (33 bp):
GATGATGACGATGAGGACAATGAGGAGAAGGAG
Found at i:1055877 original size:83 final size:83
Alignment explanation
Indices: 1055719--1056259 Score: 564
Period size: 83 Copynumber: 6.5 Consensus size: 83
1055709 GTGGAACATA
* * *
1055719 TTCCAGGGAAAGTGTTTTCCATTATTATTCAGAGAATCTCTGCCATGTCAGAGTGTTCCATCCCA
1 TTCCAGGGGAAGCGTTTTCCATTATTATTCAGAGAATCTCTGTCATGTCAGAGTGTTCCATCCCA
* * *
1055784 TCTGACATGAAAGGCGCG
66 TCCGAAATGAAAGGCACG
* * *
1055802 TTCTAGGGGAAGCGTTTTCTATTATTATTCAGAGAATCTCTGCCATGTCAGAGTGTTCCATCCCA
1 TTCCAGGGGAAGCGTTTTCCATTATTATTCAGAGAATCTCTGTCATGTCAGAGTGTTCCATCCCA
1055867 TCCGAAATGAAATGTGCA--
66 TCCGAAATGAAA-G-GCACG
* * ** * *
1055885 TTTCAAGAAAAGCGTTTTCCATTGTTATTCAGAGAATCTCTGTCATGTCAGAGTGTTCTATCCCA
1 TTCCAGGGGAAGCGTTTTCCATTATTATTCAGAGAATCTCTGTCATGTCAGAGTGTTCCATCCCA
* * *
1055950 TACAAAATGAAAGGCACA
66 TCCGAAATGAAAGGCACG
* ** * * * * * * *
1055968 TTCTAAAGGAAACATTTTCCATTGTTATTTAGAGAATCTCTGTCATGTCATAGTGTTTCATCTCA
1 TTCCAGGGGAAGCGTTTTCCATTATTATTCAGAGAATCTCTGTCATGTCAGAGTGTTCCATCCCA
* * *
1056033 TTCGAAATGAAAAGGTATG
66 TCCGAAATG-AAAGGCACG
* * * * * * *
1056052 TTCCAGGGGAAGTGTTTTCCATTATTATTTAGATAATATATGTCATGTCATAGTGTTTCATCCCA
1 TTCCAGGGGAAGCGTTTTCCATTATTATTCAGAGAATCTCTGTCATGTCAGAGTGTTCCATCCCA
* * *
1056117 TCCGAAATAAAAGGAATG
66 TCCGAAATGAAAGGCACG
* ** * * * *
1056135 TCCCAGGGGAAGATTTTTCCATTATTATTCAGAGAATCTCTATGATTTCATAGTGTTCCATCCCA
1 TTCCAGGGGAAGCGTTTTCCATTATTATTCAGAGAATCTCTGTCATGTCAGAGTGTTCCATCCCA
* * *
1056200 TCCAAAATGAAATGCGCG
66 TCCGAAATGAAAGGCACG
* *
1056218 TTCCAGGGGAAGTGTTTTCTATTATTATTCAGAGAATCTCTG
1 TTCCAGGGGAAGCGTTTTCCATTATTATTCAGAGAATCTCTG
1056260 CCATTTCACA
Statistics
Matches: 382, Mismatches: 71, Indels: 10
0.83 0.15 0.02
Matches are distributed among these distances:
81 3 0.01
82 1 0.00
83 308 0.81
84 68 0.18
85 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (83 bp):
TTCCAGGGGAAGCGTTTTCCATTATTATTCAGAGAATCTCTGTCATGTCAGAGTGTTCCATCCCA
TCCGAAATGAAAGGCACG
Found at i:1056173 original size:250 final size:249
Alignment explanation
Indices: 1055733--1056263 Score: 600
Period size: 250 Copynumber: 2.1 Consensus size: 249
1055723 AGGGAAAGTG
*
1055733 TTTTCCATTATTATTCAGAGAATCTCTGCCATGTCAGAGTGTTCCATCCCATCTGACATGAAAGG
1 TTTTCCATTATTATTCAGAGAATCTCTGCCATGTCAGAGTGTTCCATCCCATCTGAAATGAAAGG
* * * * *
1055798 CGCGTTCTAGGGGAAGCGTTTTCTATTATTATTCAGAGAATCTCTGCCATGTCAGAGTGTTCCAT
66 CACGTTCCAGGGGAAGCGTTTTCCATTATTATTCAGAGAATATATGCCATGTCAGAGTGTTCCAT
* * * * * *
1055863 CCCATCCGAAATGAAATGTGCATTTCAAGAAAAGCGTTTTCCATTGTTATTCAGAGAATCTCTGT
131 CCCATCCGAAATGAAAAGTGAATTCCAAGAAAAGAGTTTTCCATTATTATTCAGAGAATCTCTAT
*
1055928 CATGTCAGAGTGTTCTATCCCATACAAAATGAAAGGCACATTCTAAAGGAAACA
196 CATGTCAGAGTGTTCCATCCCATACAAAATGAAAGGCACATTCTAAAGGAAACA
* * * * * *
1055982 TTTTCCATTGTTATTTAGAGAATCTCTGTCATGTCATAGTGTTTCATCTCAT-TCGAAATGAAAA
1 TTTTCCATTATTATTCAGAGAATCTCTGCCATGTCAGAGTGTTCCATCCCATCT-GAAATG-AAA
* * * * * * * *
1056046 GGTATGTTCCAGGGGAAGTGTTTTCCATTATTATTTAGATAATATATGTCATGTCATAGTGTTTC
64 GGCACGTTCCAGGGGAAGCGTTTTCCATTATTATTCAGAGAATATATGCCATGTCAGAGTGTTCC
* ** *
1056111 ATCCCATCCGAAAT-AAAAG-GAATGTCCCAGGGGAAGATTTTTCCATTATTATTCAGAGAATCT
129 ATCCCATCCGAAATGAAAAGTGAAT-T-CCAAGAAAAGAGTTTTCCATTATTATTCAGAGAATCT
* * * * * * * * ** ***
1056174 CTATGATTTCATAGTGTTCCATCCCATCCAAAATGAAATGCGCGTTCCAGGGGAAGTG
192 CTATCATGTCAGAGTGTTCCATCCCATACAAAATGAAAGGCACATTCTAAAGGAAACA
*
1056232 TTTTCTATTATTATTCAGAGAATCTCTGCCAT
1 TTTTCCATTATTATTCAGAGAATCTCTGCCAT
1056264 TTCACATAAT
Statistics
Matches: 230, Mismatches: 48, Indels: 7
0.81 0.17 0.02
Matches are distributed among these distances:
248 4 0.02
249 56 0.24
250 170 0.74
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (249 bp):
TTTTCCATTATTATTCAGAGAATCTCTGCCATGTCAGAGTGTTCCATCCCATCTGAAATGAAAGG
CACGTTCCAGGGGAAGCGTTTTCCATTATTATTCAGAGAATATATGCCATGTCAGAGTGTTCCAT
CCCATCCGAAATGAAAAGTGAATTCCAAGAAAAGAGTTTTCCATTATTATTCAGAGAATCTCTAT
CATGTCAGAGTGTTCCATCCCATACAAAATGAAAGGCACATTCTAAAGGAAACA
Done.