Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009579.1 Hibiscus syriacus cultivar Beakdansim tig00116951_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: 6215474
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 29
Found at i:1631798 original size:19 final size:19
Alignment explanation
Indices: 1631693--1631790 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
1631683 GATTCTCTCG
1631693 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
*
1631713 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1631732 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1631746 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1631765 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1631784 TTGCGAT
1 TTGCGAT
1631791 AGTCATTTTT
Statistics
Matches: 69, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
14 6 0.09
16 7 0.10
17 6 0.09
19 36 0.52
20 14 0.20
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1631916 original size:14 final size:14
Alignment explanation
Indices: 1631897--1631933 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1631887 CATCAATTAC
1631897 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1631911 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1631925 ACAAATCAA
1 ACAAATCAA
1631934 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:1633889 original size:19 final size:19
Alignment explanation
Indices: 1633847--1634005 Score: 166
Period size: 19 Copynumber: 8.6 Consensus size: 19
1633837 TAGTTTACTT
* *
1633847 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-GAAAA
* *
1633867 TCGCAACGCGAAATGATAA
1 TCGCAACGCGAAACGAAAA
* *
1633886 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAACGAAAA
*
1633905 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACGAAAA
*
1633924 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACGAAAA
* *
1633943 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAACGAAAA
1633962 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAACGAAAA
*
1633976 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACGAAAA
*
1633995 TCGCAATGCGA
1 TCGCAACGCGA
1634006 TTTTGGTTTC
Statistics
Matches: 121, Mismatches: 13, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
14 8 0.07
16 6 0.05
17 6 0.05
19 89 0.74
20 12 0.10
ACGTcount: A:0.47, C:0.25, G:0.18, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAACGAAAA
Found at i:1633912 original size:38 final size:37
Alignment explanation
Indices: 1633863--1634000 Score: 185
Period size: 38 Copynumber: 3.8 Consensus size: 37
1633853 CACGAAACTT
*
1633863 AAAATCGCAACGCGAAATGATAATCGCAACGAGAAACC
1 AAAATCGCAACGCGAAATGAAAATCGCAACG-GAAACC
**
1633901 AAAATCGCAACGCGAAACCAAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATGAAAATCGCAACG-GAAACC
*
1633939 AAAATCGCAATGCGAAATGAAAATCGCAAC-G-AA--
1 AAAATCGCAACGCGAAATGAAAATCGCAACGGAAACC
*
1633972 AGAATCGCAACGCGAAATGAAAATCGCAA
1 AAAATCGCAACGCGAAATGAAAATCGCAA
1634001 TGCGATTTTG
Statistics
Matches: 91, Mismatches: 9, Indels: 5
0.87 0.09 0.05
Matches are distributed among these distances:
33 27 0.30
35 2 0.02
36 1 0.01
38 61 0.67
ACGTcount: A:0.49, C:0.24, G:0.18, T:0.09
Consensus pattern (37 bp):
AAAATCGCAACGCGAAATGAAAATCGCAACGGAAACC
Found at i:1634036 original size:14 final size:14
Alignment explanation
Indices: 1634017--1634043 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1634007 TTTGGTTTCG
1634017 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
1634031 CGTTGCGATTTTG
1 CGTTGCGATTTTG
1634044 GTTTCGCGTT
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:0.07, C:0.15, G:0.30, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1634043 original size:33 final size:33
Alignment explanation
Indices: 1634001--1634095 Score: 147
Period size: 33 Copynumber: 2.9 Consensus size: 33
1633991 AAAATCGCAA
1634001 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
*
1634034 TGCGATTTTGGTTTCGCGTTGCGATTCTT-TTGT
1 TGCGATTTTGGTTTCGCGTTGCGATT-TTGTCGT
**
1634067 TGCGATTTTCATTTCGCGTTGCGATTTTG
1 TGCGATTTTGGTTTCGCGTTGCGATTTTG
1634096 GTTTCGCGTT
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
32 2 0.04
33 53 0.93
34 2 0.04
ACGTcount: A:0.07, C:0.16, G:0.27, T:0.49
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
Found at i:1634055 original size:19 final size:19
Alignment explanation
Indices: 1634001--1634129 Score: 134
Period size: 19 Copynumber: 7.3 Consensus size: 19
1633991 AAAATCGCAA
1634001 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1634020 TGCGATTTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
1634034 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1634053 TGCGATTCT--TTT---GT
1 TGCGATTTTGGTTTCGCGT
**
1634067 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1634086 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1634105 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
1634125 TGCGA
1 TGCGA
1634130 AAGTAAACTA
Statistics
Matches: 93, Mismatches: 6, Indels: 21
0.77 0.05 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 4 0.04
17 4 0.04
18 1 0.01
19 48 0.52
20 13 0.14
ACGTcount: A:0.09, C:0.16, G:0.28, T:0.48
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:1634310 original size:93 final size:93
Alignment explanation
Indices: 1634174--1634456 Score: 541
Period size: 93 Copynumber: 3.1 Consensus size: 93
1634164 ATGGATTGCA
1634174 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1634238 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1634266 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1634331 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
*
1634359 TTACTTTCAACCAAAAGATAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
1634424 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1634452 TTACT
1 TTACT
1634457 AAGCAATCTA
Statistics
Matches: 188, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
92 4 0.02
93 184 0.98
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.23
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:1636186 original size:20 final size:20
Alignment explanation
Indices: 1636155--1636218 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
1636145 TTTTGGTTGA
1636155 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*** *
1636175 AATGACTGTCGCAACGAGATA
1 AATGAAAATCGCAACGAGA-G
1636196 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
1636216 AAT
1 AAT
1636219 CGCAACGCGA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 19 0.54
21 16 0.46
ACGTcount: A:0.47, C:0.16, G:0.23, T:0.14
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:1636221 original size:14 final size:14
Alignment explanation
Indices: 1636202--1636257 Score: 67
Period size: 14 Copynumber: 3.7 Consensus size: 14
1636192 GATAAATGAA
1636202 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1636216 AATCGCAACGCGAAATG
1 AATCGCAA--CGAGA-G
1636233 AAATCGCAACGAGAG
1 -AATCGCAACGAGAG
1636248 AATCGCAACG
1 AATCGCAACG
1636258 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
14 18 0.50
15 1 0.03
16 8 0.22
17 1 0.03
18 8 0.22
ACGTcount: A:0.43, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1636240 original size:32 final size:33
Alignment explanation
Indices: 1636153--1636274 Score: 156
Period size: 32 Copynumber: 3.5 Consensus size: 33
1636143 TCTTTTGGTT
*
1636153 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGA
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAACGC
1636192 GATAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 G--AAATGAAAATCGCAACGAGAGAATCGCAACGC
1636227 GAAATG-AAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1636259 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1636275 TGCGATTTTG
Statistics
Matches: 79, Mismatches: 1, Indels: 12
0.86 0.01 0.13
Matches are distributed among these distances:
32 32 0.41
33 14 0.18
35 9 0.11
38 1 0.01
39 1 0.01
40 1 0.01
41 21 0.27
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1636310 original size:14 final size:14
Alignment explanation
Indices: 1636291--1636347 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1636281 TTTGGTTTCG
1636291 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1636305 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1636324 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1636338 CGTTGCGATT
1 CGTTGCGATT
1636348 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1636323 original size:33 final size:33
Alignment explanation
Indices: 1636275--1636355 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
1636265 AAAATCGCAA
**
1636275 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1636308 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1636341 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
1636356 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:1636358 original size:21 final size:21
Alignment explanation
Indices: 1636332--1636407 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
1636322 CGCGTTGCGA
1636332 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
1636353 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
1636373 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
1636394 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
1636408 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:1636388 original size:41 final size:41
Alignment explanation
Indices: 1636331--1636408 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
1636321 TCGCGTTGCG
*
1636331 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
1636372 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1636409 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:1636529 original size:33 final size:33
Alignment explanation
Indices: 1636487--1636557 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1636477 AATACTAACT
1636487 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
1636520 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1636553 TGAAA
1 TGAAA
1636558 TCTAAGTGAA
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:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:1636963 original size:20 final size:20
Alignment explanation
Indices: 1636938--1637111 Score: 235
Period size: 20 Copynumber: 8.7 Consensus size: 20
1636928 CTTTAAATAT
1636938 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1636958 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1636980 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1636999 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
1637019 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
1637039 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1637059 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1637079 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
1637099 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1637112 TCATATTCGC
Statistics
Matches: 136, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
19 2 0.01
20 117 0.86
21 15 0.11
22 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.28, T:0.34
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1637120 original size:20 final size:20
Alignment explanation
Indices: 1636937--1637130 Score: 66
Period size: 20 Copynumber: 9.7 Consensus size: 20
1636927 GCTTTAAATA
***
1636937 TCGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTATATAT
* *
1636957 ACGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGA-TTTATATAT
** ***
1636978 TATCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTATATAT
* * ***
1636998 ACGCGTTGCGATATACGGAT
1 TCGCGTTGCGATTTATATAT
* * ***
1637018 ACGCATTGCGATTTACGGAT
1 TCGCGTTGCGATTTATATAT
* ***
1637038 ACGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTATATAT
* * ***
1637058 ACACGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTATATAT
* * *
1637078 ACGCGTTGCGATTTATGTGT
1 TCGCGTTGCGATTTATATAT
1637098 TCGCGTTGCGATTT-TCATAT
1 TCGCGTTGCGATTTAT-ATAT
*
1637118 TCGCGTTGTGATT
1 TCGCGTTGCGATT
1637131 CTGGAAAATC
Statistics
Matches: 148, Mismatches: 24, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
19 1 0.01
20 132 0.89
21 15 0.10
ACGTcount: A:0.19, C:0.18, G:0.27, T:0.36
Consensus pattern (20 bp):
TCGCGTTGCGATTTATATAT
Found at i:1639448 original size:2 final size:2
Alignment explanation
Indices: 1639437--1639472 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1639427 TTCTTAACTT
1639437 TA TA -A 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 T
1639473 CACATATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1639507 original size:8 final size:8
Alignment explanation
Indices: 1639437--1639525 Score: 54
Period size: 8 Copynumber: 10.8 Consensus size: 8
1639427 TTCTTAACTT
1639437 TATAATATA
1 TATAA-ATA
*
1639446 TATATATA
1 TATAAATA
*
1639454 TATATATA
1 TATAAATA
*
1639462 TATATATA
1 TATAAATA
*
1639470 TATCACATA
1 TAT-AAATA
* *
1639479 TAAAAAAA
1 TATAAATA
1639487 TATGAAA-A
1 TAT-AAATA
*
1639495 AATAAATA
1 TATAAATA
1639503 TATAATATA
1 TATAA-ATA
* *
1639512 TATGATTA
1 TATAAATA
1639520 TATAAA
1 TATAAA
1639526 ACTATTTAAA
Statistics
Matches: 64, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
7 3 0.05
8 41 0.64
9 20 0.31
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (8 bp):
TATAAATA
Found at i:1653201 original size:32 final size:32
Alignment explanation
Indices: 1653159--1653240 Score: 128
Period size: 32 Copynumber: 2.6 Consensus size: 32
1653149 CCAAAAATGT
*
1653159 ATCAGCCCTGCTTTCTCCTTGGAGTCTGATGC
1 ATCAACCCTGCTTTCTCCTTGGAGTCTGATGC
*
1653191 ATCAATCCTGCTTTCTCCTTGGAGTCTGATGC
1 ATCAACCCTGCTTTCTCCTTGGAGTCTGATGC
* *
1653223 ATCAGCCCTCCTTTCTCC
1 ATCAACCCTGCTTTCTCC
1653241 ATTGATGCAC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.13, C:0.34, G:0.17, T:0.35
Consensus pattern (32 bp):
ATCAACCCTGCTTTCTCCTTGGAGTCTGATGC
Found at i:1653366 original size:24 final size:24
Alignment explanation
Indices: 1653312--1653369 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
1653302 CACCATAGTG
1653312 CCACGTAGAATTTGTCCCAAAAGA
1 CCACGTAGAATTTGTCCCAAAAGA
** * *
1653336 CTGCGTAGAATTTGTCTC-GAAGAA
1 CCACGTAGAATTTGTCCCAAAAG-A
1653360 CCACGTAGAA
1 CCACGTAGAA
1653370 ATATCCCGAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
23 3 0.11
24 24 0.89
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.22
Consensus pattern (24 bp):
CCACGTAGAATTTGTCCCAAAAGA
Found at i:1658884 original size:21 final size:20
Alignment explanation
Indices: 1658855--1658912 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
1658845 TAATGAGTCC
1658855 TAAATCCTAAATCATAAACAA
1 TAAA-CCTAAATCATAAACAA
* *
1658876 TAAAGCCTAAATCCTAAACCA
1 TAAA-CCTAAATCATAAACAA
1658897 TAAACCTTAAATCATA
1 TAAACC-TAAATCATA
1658913 CTTACCTCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 2 0.06
21 30 0.94
ACGTcount: A:0.52, C:0.22, G:0.02, T:0.24
Consensus pattern (20 bp):
TAAACCTAAATCATAAACAA
Found at i:1658965 original size:7 final size:7
Alignment explanation
Indices: 1658953--1659019 Score: 53
Period size: 7 Copynumber: 9.6 Consensus size: 7
1658943 AATTAATATC
*
1658953 TAAACCT
1 TAAACCA
*
1658960 TAAACCC
1 TAAACCA
*
1658967 TAAATCA
1 TAAACCA
*
1658974 TAAACCC
1 TAAACCA
* *
1658981 TAAAACT
1 TAAACCA
*
1658988 TAAACCC
1 TAAACCA
*
1658995 TAAAACA
1 TAAACCA
1659002 TAAACCA
1 TAAACCA
*
1659009 TAAACCT
1 TAAACCA
1659016 TAAA
1 TAAA
1659020 TCCGATTATG
Statistics
Matches: 47, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 47 1.00
ACGTcount: A:0.52, C:0.27, G:0.00, T:0.21
Consensus pattern (7 bp):
TAAACCA
Found at i:1658969 original size:14 final size:14
Alignment explanation
Indices: 1658952--1659019 Score: 82
Period size: 14 Copynumber: 4.9 Consensus size: 14
1658942 TAATTAATAT
*
1658952 CTAAACCTTAAACC
1 CTAAAACTTAAACC
* *
1658966 CTAAATCATAAACC
1 CTAAAACTTAAACC
1658980 CTAAAACTTAAACC
1 CTAAAACTTAAACC
*
1658994 CTAAAACATAAACC
1 CTAAAACTTAAACC
* *
1659008 ATAAACCTTAAA
1 CTAAAACTTAAA
1659020 TCCGATTATG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 46 1.00
ACGTcount: A:0.51, C:0.28, G:0.00, T:0.21
Consensus pattern (14 bp):
CTAAAACTTAAACC
Found at i:1658992 original size:28 final size:28
Alignment explanation
Indices: 1658952--1659019 Score: 109
Period size: 28 Copynumber: 2.4 Consensus size: 28
1658942 TAATTAATAT
*
1658952 CTAAACCTTAAACCCTAAATCATAAACC
1 CTAAACCTTAAACCCTAAAACATAAACC
*
1658980 CTAAAACTTAAACCCTAAAACATAAACC
1 CTAAACCTTAAACCCTAAAACATAAACC
*
1659008 ATAAACCTTAAA
1 CTAAACCTTAAA
1659020 TCCGATTATG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.51, C:0.28, G:0.00, T:0.21
Consensus pattern (28 bp):
CTAAACCTTAAACCCTAAAACATAAACC
Found at i:1661863 original size:24 final size:24
Alignment explanation
Indices: 1661836--1661946 Score: 72
Period size: 24 Copynumber: 4.8 Consensus size: 24
1661826 ATAAATTGCA
*
1661836 TCGAAGTG-CCGCGTAGAATTTGTC
1 TCGAAG-GACCGCATAGAATTTGTC
1661860 TCGAAGGACCGCATAGAATTTGTC
1 TCGAAGGACCGCATAGAATTTGTC
* * * *
1661884 -CTGAAGAACCACGTAGAA-ATGTC
1 TC-GAAGGACCGCATAGAATTTGTC
* *
1661907 -CTGAATGACCACATAG-A-TTGTC
1 TC-GAAGGACCGCATAGAATTTGTC
* *
1661929 CCGAAGGACCGCCTAGAA
1 TCGAAGGACCGCATAGAA
1661947 CCCTCGACTC
Statistics
Matches: 71, Mismatches: 12, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
22 16 0.23
23 21 0.30
24 34 0.48
ACGTcount: A:0.31, C:0.23, G:0.24, T:0.22
Consensus pattern (24 bp):
TCGAAGGACCGCATAGAATTTGTC
Found at i:1661917 original size:23 final size:23
Alignment explanation
Indices: 1661862--1661923 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
1661852 AATTTGTCTC
* * *
1661862 GAAGGACCGCATAGAATTTGTCCT
1 GAAGAACCACATAGAA-ATGTCCT
*
1661886 GAAGAACCACGTAGAAATGTCCT
1 GAAGAACCACATAGAAATGTCCT
1661909 GAATG-ACCACATAGA
1 GAA-GAACCACATAGA
1661924 TTGTCCCGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
23 18 0.56
24 14 0.44
ACGTcount: A:0.37, C:0.21, G:0.23, T:0.19
Consensus pattern (23 bp):
GAAGAACCACATAGAAATGTCCT
Found at i:1670033 original size:21 final size:21
Alignment explanation
Indices: 1670005--1670049 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
1669995 ATATATTAAC
1670005 TATTTTTTATATTAAATAA-A
1 TATTTTTTATATTAAATAATA
*
1670025 TATTCTTTTATATTATATAATA
1 TATT-TTTTATATTAAATAATA
1670047 TAT
1 TAT
1670050 AATCATCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.18
21 14 0.64
22 4 0.18
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
TATTTTTTATATTAAATAATA
Found at i:1672653 original size:2 final size:2
Alignment explanation
Indices: 1672646--1672678 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1672636 TGTACGGATA
1672646 AT AT AT AT 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 AT AT AT AT A
1672679 AAATTAAGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1676065 original size:42 final size:40
Alignment explanation
Indices: 1676001--1676318 Score: 132
Period size: 41 Copynumber: 7.8 Consensus size: 40
1675991 ATTGATACTT
*
1676001 TAGCGGCGTTTGTTGTAA-AAACGCTGCAATAGAGTTGACATA
1 TAGCGGCG-TT-TT-TAACAAACGCCGCAATAGAGTTGACATA
* ***
1676043 TAGCGGCGTTTTTACAACAAACGCCGCAATAG-GGTGGTTTA
1 TAGCGGCGTTTTT--AACAAACGCCGCAATAGAGTTGACATA
* * * *
1676084 TTGCGGCGTTTTTAACAAACGCCACAATAGAG-TGATAAA
1 TAGCGGCGTTTTTAACAAACGCCGCAATAGAGTTGACATA
* * ** * * *
1676123 TTAGCGGTGTTTATACCACAAACATCGTATTAGA-TTAACATA
1 -TAGCGGCGTTTTTA--ACAAACGCCGCAATAGAGTTGACATA
* * * * * *
1676165 TAGTGGCG-TTTTAGCCAAAACGCCTCAATAGA-TCGGCAAA
1 TAGCGGCGTTTTTA-AC-AAACGCCGCAATAGAGTTGACATA
* * *
1676205 TTAGCGGCG-TTTTACCACAAACACCGTAATAGA-TTACACATA
1 -TAGCGGCGTTTTTA--ACAAACGCCGCAATAGAGTT-GACATA
* * * *
1676247 TAGTGGCGTTTTTAGACAAACGACGCAATAGTGTTAATCA-A
1 TAGCGGCGTTTTTA-ACAAACGCCGCAATAGAGTTGA-CATA
* * *
1676288 TAGTGGCTTTTTTAGAAAAACGCCGCAATAG
1 TAGCGGCGTTTTTA-ACAAACGCCGCAATAG
1676319 TTTTAATAAA
Statistics
Matches: 206, Mismatches: 55, Indels: 31
0.71 0.19 0.11
Matches are distributed among these distances:
39 22 0.11
40 32 0.16
41 102 0.50
42 50 0.24
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (40 bp):
TAGCGGCGTTTTTAACAAACGCCGCAATAGAGTTGACATA
Found at i:1676268 original size:82 final size:82
Alignment explanation
Indices: 1676088--1676277 Score: 244
Period size: 82 Copynumber: 2.3 Consensus size: 82
1676078 GGTTTATTGC
* * *
1676088 GGCGTTTTTA-ACAAACGCCACAATAGAGTGATAAATTAGCGGTGTTTATACCACAAACATCGTA
1 GGCGTTTTTAGACAAACGCCACAATAGAGTGACAAATTAGCGGCGTTTATACCACAAACACCGTA
*
1676152 TTAGATTAACATATAGT
66 ATAGATTAACATATAGT
* * *
1676169 GGCG-TTTTAGCCAAAACGCCTCAATAGA-TCGGCAAATTAGCGGCGTTT-TACCACAAACACCG
1 GGCGTTTTTAGAC-AAACGCCACAATAGAGT-GACAAATTAGCGGCGTTTATACCACAAACACCG
1676231 TAATAGATTACACATATAGT
64 TAATAGATTA-ACATATAGT
* *
1676251 GGCGTTTTTAGACAAACGACGCAATAG
1 GGCGTTTTTAGACAAACGCCACAATAG
1676278 TGTTAATCAA
Statistics
Matches: 94, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
80 5 0.05
81 28 0.30
82 54 0.57
83 7 0.07
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.26
Consensus pattern (82 bp):
GGCGTTTTTAGACAAACGCCACAATAGAGTGACAAATTAGCGGCGTTTATACCACAAACACCGTA
ATAGATTAACATATAGT
Found at i:1676318 original size:82 final size:82
Alignment explanation
Indices: 1676223--1676383 Score: 186
Period size: 82 Copynumber: 2.0 Consensus size: 82
1676213 GTTTTACCAC
* * *
1676223 AAACACCGTAATAG-ATTACACATATAGTGGC-GTTTTTAGACAAACGA-CGCAATAGTGTTAAT
1 AAACACCGCAATAGTATTA-ACAAATAGTGGCAGTTTTTA-ACAAAC-ACCACAATAGTG-TAAT
1676285 CAATAGTGGC-TTTTTTAGAA
62 CAATAGTGGCATTTTTTAGAA
* * * *
1676305 AAACGCCGCAATAGTTTTAATAAATAGTGGCATTTTTTTAACAAACACCACAATAGTGTAATCAA
1 AAACACCGCAATAGTATTAACAAATAGTGGCA-GTTTTTAACAAACACCACAATAGTGTAATCAA
1676370 TAGTGGCATTTTTT
65 TAGTGGCATTTTTT
1676384 TGTATAAACG
Statistics
Matches: 67, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
82 37 0.55
83 24 0.36
84 6 0.09
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (82 bp):
AAACACCGCAATAGTATTAACAAATAGTGGCAGTTTTTAACAAACACCACAATAGTGTAATCAAT
AGTGGCATTTTTTAGAA
Found at i:1676319 original size:41 final size:42
Alignment explanation
Indices: 1676246--1676383 Score: 176
Period size: 41 Copynumber: 3.4 Consensus size: 42
1676236 GATTACACAT
* *
1676246 ATAGTGGC-GTTTTTAGACAAACGACGCAATAGTGTTAATCA
1 ATAGTGGCATTTTTTAGACAAACGCCGCAATAGTGTTAATCA
* * *
1676287 ATAGTGGC-TTTTTTAGAAAAACGCCGCAATAGTTTTAATAA
1 ATAGTGGCATTTTTTAGACAAACGCCGCAATAGTGTTAATCA
* *
1676328 ATAGTGGCATTTTTTTA-ACAAACACCACAATAGTG-TAATCA
1 ATAGTGGCA-TTTTTTAGACAAACGCCGCAATAGTGTTAATCA
1676369 ATAGTGGCATTTTTT
1 ATAGTGGCATTTTTT
1676384 TGTATAAACG
Statistics
Matches: 85, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
40 6 0.07
41 58 0.68
42 14 0.16
43 7 0.08
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (42 bp):
ATAGTGGCATTTTTTAGACAAACGCCGCAATAGTGTTAATCA
Found at i:1676425 original size:84 final size:84
Alignment explanation
Indices: 1676255--1676416 Score: 188
Period size: 84 Copynumber: 1.9 Consensus size: 84
1676245 TATAGTGGCG
* *
1676255 TTTTTAGACAAACGACGCAATAGTGTTAATCAATAGTGGCTTTTTTAGAAAAACGCCGCAATAGT
1 TTTTTAGACAAACGACACAATAGTGTTAATCAATAGTGGCTTTTTTAGAAAAACGCCGCAAAAGT
* *
1676320 TTTAATAAATAGTGGCATT
66 TTAAATAAATAGTGCCATT
* * *
1676339 TTTTTA-ACAAAC-ACCACAATAGTG-TAATCAATAGTGGCATTTTTTTGTATAAACGCCGTAAA
1 TTTTTAGACAAACGA-CACAATAGTGTTAATCAATAGTGGC-TTTTTTAG-AAAAACGCCGCAAA
*
1676401 A-TGTTAAATATATAGT
63 AGT-TTAAATAAATAGT
1676417 CCTCTTTTTC
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
82 15 0.22
83 23 0.34
84 29 0.43
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (84 bp):
TTTTTAGACAAACGACACAATAGTGTTAATCAATAGTGGCTTTTTTAGAAAAACGCCGCAAAAGT
TTAAATAAATAGTGCCATT
Found at i:1682115 original size:18 final size:18
Alignment explanation
Indices: 1682092--1682160 Score: 75
Period size: 18 Copynumber: 3.7 Consensus size: 18
1682082 AGGGATTATC
* *
1682092 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCAGAACAT
*
1682110 AGTGGTTCTTCAGAACAATT
1 AGTGGTCCTTCAGAAC-A-T
*
1682130 AGTGGTCCTTCAGAATAT
1 AGTGGTCCTTCAGAACAT
*
1682148 AGTGGTTCTTCAG
1 AGTGGTCCTTCAG
1682161 GACAAATATT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
18 26 0.60
19 2 0.05
20 15 0.35
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.33
Consensus pattern (18 bp):
AGTGGTCCTTCAGAACAT
Found at i:1682134 original size:20 final size:19
Alignment explanation
Indices: 1682108--1682165 Score: 73
Period size: 20 Copynumber: 3.1 Consensus size: 19
1682098 CCTTCGGGAC
1682108 ATAGTGGTTCTTCAGAACA
1 ATAGTGGTTCTTCAGAACA
* *
1682127 ATTAGTGGTCCTTCAGAA-T
1 A-TAGTGGTTCTTCAGAACA
*
1682146 ATAGTGGTTCTTCAGGACA
1 ATAGTGGTTCTTCAGAACA
1682165 A
1 A
1682166 ATATTCAGTT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
18 14 0.44
19 3 0.09
20 15 0.47
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (19 bp):
ATAGTGGTTCTTCAGAACA
Found at i:1682150 original size:38 final size:38
Alignment explanation
Indices: 1682092--1682165 Score: 112
Period size: 38 Copynumber: 1.9 Consensus size: 38
1682082 AGGGATTATC
* *
1682092 AGTGGTCCTTCGGGACATAGTGGTTCTTCAGAACAATT
1 AGTGGTCCTTCAGAACATAGTGGTTCTTCAGAACAATT
* *
1682130 AGTGGTCCTTCAGAATATAGTGGTTCTTCAGGACAA
1 AGTGGTCCTTCAGAACATAGTGGTTCTTCAGAACAA
1682166 ATATTCAGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.31
Consensus pattern (38 bp):
AGTGGTCCTTCAGAACATAGTGGTTCTTCAGAACAATT
Found at i:1684060 original size:12 final size:12
Alignment explanation
Indices: 1684039--1684071 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
1684029 AGCTACACAG
1684039 AGAGGAAGAGGT
1 AGAGGAAGAGGT
*
1684051 AGAGGTAGAGGT
1 AGAGGAAGAGGT
1684063 AGAGGAAGA
1 AGAGGAAGA
1684072 AGTCAGTCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.48, T:0.09
Consensus pattern (12 bp):
AGAGGAAGAGGT
Found at i:1688878 original size:18 final size:18
Alignment explanation
Indices: 1688855--1688925 Score: 61
Period size: 18 Copynumber: 3.8 Consensus size: 18
1688845 AGGGATTATC
1688855 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
** * *
1688873 AGTGGTTATTTGGAACAATT
1 AGTGGTCCTTCGGGAC-A-T
* *
1688893 AGTGGTTCTTCGAGACAT
1 AGTGGTCCTTCGGGACAT
*
1688911 AGTGGTCTTTCGGGA
1 AGTGGTCCTTCGGGA
1688926 TAAATATTTA
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
18 25 0.62
19 2 0.05
20 13 0.32
ACGTcount: A:0.21, C:0.14, G:0.31, T:0.34
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:1696167 original size:43 final size:43
Alignment explanation
Indices: 1696054--1696258 Score: 171
Period size: 43 Copynumber: 4.7 Consensus size: 43
1696044 CGTTTTTAGC
* * * * * **
1696054 AAAAGCGCCGCAAAACATCAACACCTACTGCGACG-TTTTAGA
1 AAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTCTA
* * *
1696096 GGAAAAACACCGCTAAACATCATA-ACCTATTGCGGCGTTTGTCTA
1 --AAAAACGCCGCTAAATATCA-ACACCTATTGCGGCGTTTTTCTA
* *
1696141 AAAAACGCCGCTAAATATCAACACCTATTGCGGCATTTTTCTG
1 AAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTCTA
* * * * * *
1696184 ACAAATGCCGCTAAATATCAACATCTATTGCGGTGTTTTTTTG
1 AAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTCTA
* * * *
1696227 ACAAACTCCGTTAAATATCAATACCTATTGCG
1 AAAAACGCCGCTAAATATCAACACCTATTGCG
1696259 ACGCTATTTT
Statistics
Matches: 134, Mismatches: 24, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
42 1 0.01
43 100 0.75
44 28 0.21
45 5 0.04
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (43 bp):
AAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTCTA
Found at i:1698069 original size:6 final size:6
Alignment explanation
Indices: 1698051--1698090 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
1698041 TTAAACTATA
*
1698051 TCTTCC TCCTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTT
1 TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTT
1698091 AGCTGTGAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (6 bp):
TCTTCC
Found at i:1699173 original size:152 final size:153
Alignment explanation
Indices: 1698897--1699204 Score: 609
Period size: 152 Copynumber: 2.0 Consensus size: 153
1698887 ATTTCAAAGC
1698897 TTTCCAGCATTTCATTGTTATGCTAGTTGATAAATTGGATCAATGTGCCTTTTTTTTTCTTGAAG
1 TTTCCAGCATTTCATTGTTATGCTAGTTGATAAATTGGATCAATGTGCCTTTTTTTTTCTTGAAG
1698962 GAGCTCAAGAACTTAAGGCCTCAGCTTTATGCTGCTGCAAAATACTCCCAAAAGTCATTTCATCA
66 GAGCTCAAGAACTTAAGGCCTCAGCTTTATGCTGCTGCAAAATACTCCCAAAAGTCATTTCATCA
1699027 CAGTGAAATGAAGCATATGT-AG
131 CAGTGAAATGAAGCATATGTAAG
1699049 TTTCCAGCATTTCATTGTTATGCTAGTTGATAAATTGGATCAATGTGCCTTTTTTTTTCTTGAAG
1 TTTCCAGCATTTCATTGTTATGCTAGTTGATAAATTGGATCAATGTGCCTTTTTTTTTCTTGAAG
1699114 GAGCTCAAGAACTTAAGGCCTCAGCTTTATGCTGCTGCAAAATACTCCCAAAAGTCATTTCATCA
66 GAGCTCAAGAACTTAAGGCCTCAGCTTTATGCTGCTGCAAAATACTCCCAAAAGTCATTTCATCA
1699179 CAGTGAAATGAAGCATATGTAAG
131 CAGTGAAATGAAGCATATGTAAG
1699202 TTT
1 TTT
1699205 ACACTTTAAA
Statistics
Matches: 155, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
152 150 0.97
153 5 0.03
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (153 bp):
TTTCCAGCATTTCATTGTTATGCTAGTTGATAAATTGGATCAATGTGCCTTTTTTTTTCTTGAAG
GAGCTCAAGAACTTAAGGCCTCAGCTTTATGCTGCTGCAAAATACTCCCAAAAGTCATTTCATCA
CAGTGAAATGAAGCATATGTAAG
Found at i:1706409 original size:52 final size:52
Alignment explanation
Indices: 1706338--1706436 Score: 135
Period size: 52 Copynumber: 1.9 Consensus size: 52
1706328 TTATGTTATG
* *
1706338 AATATATTATTGTAATATTTTATAATTATGTTTTAATTAATATATTTCTATT
1 AATATATTATTATAATATTTTATAATTATGTTATAATTAATATATTTCTATT
* * * * *
1706390 AATATATTCTTATATTATTTTTTATTTATGTTATAATTATTATATTT
1 AATATATTATTATAATATTTTATAATTATGTTATAATTAATATATTT
1706437 TCATAAAATA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 40 1.00
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (52 bp):
AATATATTATTATAATATTTTATAATTATGTTATAATTAATATATTTCTATT
Found at i:1707757 original size:22 final size:23
Alignment explanation
Indices: 1707723--1707772 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
1707713 TTTATCTATT
* *
1707723 AATTTTATCAATAA-AATCATTA
1 AATTATATAAATAATAATCATTA
*
1707745 AATTATATAAATAATATTCATTA
1 AATTATATAAATAATAATCATTA
1707768 AATTA
1 AATTA
1707773 AGTGGCGAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 12 0.50
23 12 0.50
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (23 bp):
AATTATATAAATAATAATCATTA
Found at i:1707861 original size:23 final size:24
Alignment explanation
Indices: 1707810--1707861 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 24
1707800 TAGGTGAGTT
* **
1707810 TATAAAATTTTAAGGGGTGTGAACT
1 TATAAAATTTTAA-GGGTGCGAAAA
1707835 TATAAAATTTTAA-GGTGCGAAAA
1 TATAAAATTTTAAGGGTGCGAAAA
1707858 TATA
1 TATA
1707862 TTTTCAATAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 11 0.46
25 13 0.54
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.35
Consensus pattern (24 bp):
TATAAAATTTTAAGGGTGCGAAAA
Found at i:1708178 original size:22 final size:22
Alignment explanation
Indices: 1708130--1708178 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
1708120 CTTATTGGAT
*
1708130 AAATTTGATAATAATATTTATG
1 AAATTTAATAATAATATTTATG
* *
1708152 GAATTTAATAA-AATTATTTGTG
1 AAATTTAATAATAA-TATTTATG
1708174 AAATT
1 AAATT
1708179 AAACTTAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (22 bp):
AAATTTAATAATAATATTTATG
Found at i:1709900 original size:73 final size:73
Alignment explanation
Indices: 1709813--1709958 Score: 292
Period size: 73 Copynumber: 2.0 Consensus size: 73
1709803 TTTTGTACTT
1709813 GCAATTATAGTATCTTTAAAAATAAATTAATTTTTTTTACAATATAACGAGTTCGATTTTCAGAA
1 GCAATTATAGTATCTTTAAAAATAAATTAATTTTTTTTACAATATAACGAGTTCGATTTTCAGAA
1709878 TTTATAAA
66 TTTATAAA
1709886 GCAATTATAGTATCTTTAAAAATAAATTAATTTTTTTTACAATATAACGAGTTCGATTTTCAGAA
1 GCAATTATAGTATCTTTAAAAATAAATTAATTTTTTTTACAATATAACGAGTTCGATTTTCAGAA
1709951 TTTATAAA
66 TTTATAAA
1709959 AAAAAATTAA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.42
Consensus pattern (73 bp):
GCAATTATAGTATCTTTAAAAATAAATTAATTTTTTTTACAATATAACGAGTTCGATTTTCAGAA
TTTATAAA
Found at i:1714806 original size:18 final size:18
Alignment explanation
Indices: 1714783--1714827 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
1714773 ATGGTCGGAG
1714783 GAGAAGAAGAACGGCGAA
1 GAGAAGAAGAACGGCGAA
*
1714801 GAGAAGAAGAACGGCGAG
1 GAGAAGAAGAACGGCGAA
1714819 GAG-AGAAGA
1 GAGAAGAAGA
1714828 GATTGGGAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 6 0.23
18 20 0.77
ACGTcount: A:0.49, C:0.09, G:0.42, T:0.00
Consensus pattern (18 bp):
GAGAAGAAGAACGGCGAA
Found at i:1719982 original size:200 final size:199
Alignment explanation
Indices: 1719590--1719986 Score: 753
Period size: 200 Copynumber: 2.0 Consensus size: 199
1719580 TATTTCACTC
1719590 TCTTGATTCTTGGTACCTACGTGTAAATCACTACACGCTAAGTCATAGACTTAGTGAGGCAATAA
1 TCTTGATTCTTGGTACCTACGTGTAAATCACTACACGCTAAGTCATAGACTTAGTGAGGCAATAA
1719655 ATGAATATGCAACGAAACTTATGAATGTTCATACTTACCATTGGATCATGACATTTCAATGTGCA
66 ATGAATATGCAACGAAACTTATGAATGTTCATACTTACCATTGGATCATGACATTTCAATGTGCA
1719720 TTTATTTATCACATGATAACATATATAATCATATAATGCATATACGAAACTTACCTTCTTGTATC
131 TTTATTTATCACATGATAACATATATAATCATATAATGCATATACGAAACTTACCTTCTTGTATC
1719785 ACCT
196 ACCT
1719789 TCTTGATTCTTGGTACCTACGTGTAAATCACTTACACGCTAAGTCATAGACTTAGTGAGGCAATA
1 TCTTGATTCTTGGTACCTACGTGTAAATCAC-TACACGCTAAGTCATAGACTTAGTGAGGCAATA
1719854 AATGAATATGCAACGATAAACTTATGAATGTTCATACTTACCATTGGATCATGACATTTCAATGT
65 AATGAATATGCAACG--AAACTTATGAATGTTCATACTTACCATTGGATCATGACATTTCAATGT
1719919 GCA-TTATTTATCACATGATAACATATATAATCATATAATGCATATACGAAACTTACC-TCTTGT
128 GCATTTATTTATCACATGATAACATATATAATCATATAATGCATATACGAAACTTACCTTCTTGT
1719982 ATCAC
193 ATCAC
1719987 TTTCACTGTA
Statistics
Matches: 195, Mismatches: 0, Indels: 5
0.98 0.00 0.03
Matches are distributed among these distances:
199 31 0.16
200 59 0.30
201 54 0.28
202 51 0.26
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (199 bp):
TCTTGATTCTTGGTACCTACGTGTAAATCACTACACGCTAAGTCATAGACTTAGTGAGGCAATAA
ATGAATATGCAACGAAACTTATGAATGTTCATACTTACCATTGGATCATGACATTTCAATGTGCA
TTTATTTATCACATGATAACATATATAATCATATAATGCATATACGAAACTTACCTTCTTGTATC
ACCT
Found at i:1720194 original size:14 final size:15
Alignment explanation
Indices: 1720169--1720228 Score: 97
Period size: 14 Copynumber: 4.1 Consensus size: 15
1720159 GTAGGACCAT
1720169 TACATCCCGAAGGAC
1 TACATCCCGAAGGAC
1720184 TACAT-CCGAAGGAC
1 TACATCCCGAAGGAC
1720198 TACAT-CCGAAGGAC
1 TACATCCCGAAGGAC
*
1720212 TACATCCCGAAAGAC
1 TACATCCCGAAGGAC
1720227 TA
1 TA
1720229 TTATACCCTC
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
14 28 0.65
15 15 0.35
ACGTcount: A:0.37, C:0.30, G:0.18, T:0.15
Consensus pattern (15 bp):
TACATCCCGAAGGAC
Found at i:1720210 original size:28 final size:30
Alignment explanation
Indices: 1720169--1720228 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 30
1720159 GTAGGACCAT
*
1720169 TACATCCCGAAGGACTACAT-CCGAAGGAC
1 TACATCCCGAAGGACTACATCCCGAAAGAC
1720198 TACAT-CCGAAGGACTACATCCCGAAAGAC
1 TACATCCCGAAGGACTACATCCCGAAAGAC
1720227 TA
1 TA
1720229 TTATACCCTC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 14 0.48
29 15 0.52
ACGTcount: A:0.37, C:0.30, G:0.18, T:0.15
Consensus pattern (30 bp):
TACATCCCGAAGGACTACATCCCGAAAGAC
Found at i:1720382 original size:12 final size:12
Alignment explanation
Indices: 1720365--1720411 Score: 76
Period size: 12 Copynumber: 3.9 Consensus size: 12
1720355 AATCATGTTC
* *
1720365 TCATATTACATG
1 TCATATCACATA
1720377 TCATATCACATA
1 TCATATCACATA
1720389 TCATATCACATA
1 TCATATCACATA
1720401 TCATATCACAT
1 TCATATCACAT
1720412 GAACATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.36
Consensus pattern (12 bp):
TCATATCACATA
Found at i:1720821 original size:18 final size:18
Alignment explanation
Indices: 1720777--1720823 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
1720767 TATTGTTGGG
*
1720777 ATGCATCGATGCACCCTT
1 ATGCATCGATGCACCCAT
*
1720795 ATGCATCGATGCACCGAT
1 ATGCATCGATGCACCCAT
1720813 -TGCATTCGATG
1 ATGCA-TCGATG
1720824 TTTCACTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 4 0.15
18 22 0.85
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (18 bp):
ATGCATCGATGCACCCAT
Found at i:1720884 original size:64 final size:65
Alignment explanation
Indices: 1720713--1720888 Score: 209
Period size: 63 Copynumber: 2.8 Consensus size: 65
1720703 TAATGAAGGT
* * * ** * * **
1720713 ATGCATCGATGCACTACTGATGCATCGGTGCATC-AAAGGTATTCGATGTAGTATTATTGTTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCGAATTGCATTCGATGTAGTACTATTAATGGG
* *
1720777 ATGCATCGATGCAC-CCTTATGCATCGATGCACCG-ATTGCATTCGATGT-TTCACTATTAATGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCGAATTGCATTCGATGTAGT-ACTATTAATGG
1720839 G
65 G
1720840 ATGCATCGATGCACTACTTATGCATCGATGCA-CGAATTGCATTCGATGT
1 ATGCATCGATGCACTACTTATGCATCGATGCACCGAATTGCATTCGATGT
1720889 CTTTATTTTA
Statistics
Matches: 96, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
62 1 0.01
63 51 0.53
64 44 0.46
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (65 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACCGAATTGCATTCGATGTAGTACTATTAATGGG
Found at i:1720909 original size:64 final size:63
Alignment explanation
Indices: 1720713--1720936 Score: 188
Period size: 64 Copynumber: 3.5 Consensus size: 63
1720703 TAATGAAGGT
* * * ** * * * ** *
1720713 ATGCATCGATGCACTACTGATGCATCGGTGCATCAAAGGTATTCGATGTAGT-ATTATTGTTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCA-CGATTGCATTCGATGT-TTCACTATTAATGAG
* *
1720777 ATGCATCGATGCAC-CCTTATGCATCGATGCACCGATTGCATTCGATGTTTCACTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCA-CGATTGCATTCGATGTTTCACTATTAATGAG
* *
1720840 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTCTTTA-TTTTAAAAT-
1 ATGCATCGATGCACTACTTATGCATCGATGCACG-ATTGCATTCGATGT-TTCACTATT--AATG
1720903 AG
62 AG
** *
1720905 -TGCATCGATGCACTACCAAGGCATCGATGCAC
1 ATGCATCGATGCACTACTTATGCATCGATGCAC
1720937 ATTCATATAA
Statistics
Matches: 135, Mismatches: 19, Indels: 12
0.81 0.11 0.07
Matches are distributed among these distances:
62 1 0.01
63 51 0.38
64 76 0.56
65 4 0.03
66 3 0.02
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.31
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACGATTGCATTCGATGTTTCACTATTAATGAG
Found at i:1727274 original size:15 final size:15
Alignment explanation
Indices: 1727254--1727300 Score: 94
Period size: 15 Copynumber: 3.1 Consensus size: 15
1727244 GTAGGACCAT
1727254 TACATCCCGAAGGAC
1 TACATCCCGAAGGAC
1727269 TACATCCCGAAGGAC
1 TACATCCCGAAGGAC
1727284 TACATCCCGAAGGAC
1 TACATCCCGAAGGAC
1727299 TA
1 TA
1727301 TTATACCCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.34, C:0.32, G:0.19, T:0.15
Consensus pattern (15 bp):
TACATCCCGAAGGAC
Found at i:1727462 original size:12 final size:12
Alignment explanation
Indices: 1727445--1727480 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
1727435 TATCATGTTC
*
1727445 TCATATTACATG
1 TCATATCACATG
*
1727457 TCATATCACATA
1 TCATATCACATG
1727469 TCATATCACATG
1 TCATATCACATG
1727481 AACATATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.36, C:0.22, G:0.06, T:0.36
Consensus pattern (12 bp):
TCATATCACATG
Found at i:1727958 original size:64 final size:64
Alignment explanation
Indices: 1727786--1728010 Score: 219
Period size: 64 Copynumber: 3.5 Consensus size: 64
1727776 TAATGAAGGT
* * * ** * *
1727786 ATGCATCGATGCACTACTGATGCATCGGTGCATC-AAAGGTATTCGATGTAGTATTATTATTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCGAATTGTATTCGATGTATTA-TATTAATGGG
* *
1727850 ATGCATCGATGCACTCCTTATGCATCGATGCACCG-ATTATATTCGATGT-TTCACTATTAATGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCGAATTGTATTCGATGTATT-A-TATTAATGG
1727913 G
64 G
* * *
1727914 ATGCATCGATGCACTACTTATGCATCGATGCA-CGAATTGCATTCGATGTCTTTATTTTAAAAT-
1 ATGCATCGATGCACTACTTATGCATCGATGCACCGAATTGTATTCGATGT-ATTATATT--AATG
*
1727977 AG
63 GG
**
1727979 -TGCATCGATGCACTACCAATGCATCGATGCAC
1 ATGCATCGATGCACTACTTATGCATCGATGCAC
1728011 ATTCATATAA
Statistics
Matches: 136, Mismatches: 17, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
63 3 0.02
64 126 0.93
65 2 0.01
66 5 0.04
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.32
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACCGAATTGTATTCGATGTATTATATTAATGGG
Found at i:1729421 original size:18 final size:18
Alignment explanation
Indices: 1729398--1729442 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
1729388 ATGGTCGGAG
*
1729398 GAGAAGAAGAACGTCGAA
1 GAGAAGAAGAACGGCGAA
*
1729416 GAGAAGAAGAACGGCGAG
1 GAGAAGAAGAACGGCGAA
1729434 GAG-AGAAGA
1 GAGAAGAAGA
1729443 GATTGGGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 6 0.24
18 19 0.76
ACGTcount: A:0.49, C:0.09, G:0.40, T:0.02
Consensus pattern (18 bp):
GAGAAGAAGAACGGCGAA
Found at i:1731237 original size:5 final size:5
Alignment explanation
Indices: 1731219--1731290 Score: 67
Period size: 5 Copynumber: 13.8 Consensus size: 5
1731209 ATAATTCTTT
* *
1731219 TTTTA TCTTA -TTTA TTTTA -TTTA TTCATTA TTCTTC TCTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT--TTA TT-TTA T-TTTA TTTTA
1731266 TTTTA TTTTA TTTTTA TTTTA TTTT
1 TTTTA TTTTA -TTTTA TTTTA TTTT
1731291 CTTTATCTTC
Statistics
Matches: 56, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
4 7 0.12
5 32 0.57
6 11 0.20
7 6 0.11
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:1731290 original size:16 final size:16
Alignment explanation
Indices: 1731229--1731290 Score: 65
Period size: 16 Copynumber: 3.8 Consensus size: 16
1731219 TTTTATCTTA
1731229 TTTATTTTA-TTTATT
1 TTTATTTTATTTTATT
* *
1731244 CATTATTCTTCTCTTTA-T
1 -TTTATT-TTAT-TTTATT
1731262 TTTATTTTATTTTATT
1 TTTATTTTATTTTATT
1731278 TTTATTTTATTTT
1 TTTATTTTATTTT
1731291 CTTTATCTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
15 4 0.11
16 22 0.58
17 7 0.18
18 1 0.03
19 4 0.11
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTATTTTATTTTATT
Found at i:1735265 original size:94 final size:94
Alignment explanation
Indices: 1735132--1735316 Score: 275
Period size: 94 Copynumber: 2.0 Consensus size: 94
1735122 TATAATATTA
* * *
1735132 TATATATACAATAAAGCTTGAGTTGTCCCTCAAGAGCAATTAGTTAAACG-CCCTGCTTTATGGA
1 TATATATACAATAAAGCTTGAGCTGTCCCTCAAGAGCAATTAGTTAAACGCCCCGGCTTTATAGA
* *
1735196 TAATATTCAACTAGCCTGATAAAGGTAAT
66 TAAGATTCAACTAACCTGATAAAGGTAAT
*
1735225 TATACTATACAATAAAGCTTGAGCTGTCCCTCTAAG-GCAATTGGTTAAACGCCCCGGCTTTATA
1 TATA-TATACAATAAAGCTTGAGCTGTCCCTC-AAGAGCAATTAGTTAAACGCCCCGGCTTTATA
*
1735289 GATAAGATTCAGCTAACCTGATAAAGGT
64 GATAAGATTCAACTAACCTGATAAAGGT
1735317 GTTTATGTAT
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
93 4 0.05
94 40 0.49
95 38 0.46
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (94 bp):
TATATATACAATAAAGCTTGAGCTGTCCCTCAAGAGCAATTAGTTAAACGCCCCGGCTTTATAGA
TAAGATTCAACTAACCTGATAAAGGTAAT
Found at i:1736683 original size:84 final size:83
Alignment explanation
Indices: 1736401--1736964 Score: 446
Period size: 84 Copynumber: 6.8 Consensus size: 83
1736391 CAATTTTTAT
* * ** * *
1736401 ATTTGCAACATAGCTTAAGTCGAGAAGGGTTATCTGCCAATTAAAGACCTTCGAGTTTGACTAAG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-CACCTAAAGACCTTCGAGTTCGACTACG
* *
1736466 CTCAGCTCCAAGACACATC
65 CTCAACTCCAAGGCACATC
* * * * * * *
1736485 ATTTGCAGAATAACTTAAGTCGAGAAGAGCTATCTG---TTAAAGACCCTCGAGTTCGATTATGC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCACCTAAAGACCTTCGAGTTCGACTACGC
* * *
1736547 TCAGCTTCGAGGGCACATC
66 TCAAC-TCCAAGGCACATC
* * * * * * * *
1736566 ATTTACAACATAACTCAAGGCTAAAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-CACCTAAAGACCTTCGAGTTCGACTACG
* * *
1736631 TTCAACTCCAAGGCATAAC
65 CTCAACTCCAAGGCACATC
* *
1736650 AATTGTAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGACTAC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-C-ACCTAAAGACCTTCGAGTTCGACTAC
* *
1736714 GTTTAACTCCAAGGCACATC
64 GCTCAACTCCAAGGCACATC
* * * * *
1736734 ATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTG--CC-AAAGACCCTCAAGTTCGATTACAC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCACCTAAAGACCTTCGAGTTCGACTACGC
* * * *
1736796 TCAGCTTCGAGGGTACATC
66 TCAAC-TCCAAGGCACATC
* * * ** ** * *
1736815 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACAAAAAGATATTCGAGTTCGATTACA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-CACCTAAAGACCTTCGAGTTCGACTACG
** *
1736880 CTCAGTTCAAAGGCACCATC
65 CTCAACTCCAAGGCA-CATC
* * * * * *
1736900 ATTTACAGCATAGCTTAAGTCGAGAAGGGCTATCTG---CTAAAGACCTTCGAATTCGATTACAC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCACCTAAAGACCTTCGAGTTCGACTACGC
1736962 TCA
66 TCA
1736965 GCTCAGAGGC
Statistics
Matches: 386, Mismatches: 82, Indels: 27
0.78 0.17 0.05
Matches are distributed among these distances:
80 51 0.13
81 103 0.27
84 147 0.38
85 85 0.22
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.26
Consensus pattern (83 bp):
ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCACCTAAAGACCTTCGAGTTCGACTACGC
TCAACTCCAAGGCACATC
Found at i:1736870 original size:249 final size:249
Alignment explanation
Indices: 1736409--1736874 Score: 698
Period size: 249 Copynumber: 1.9 Consensus size: 249
1736399 ATATTTGCAA
* ** * *
1736409 CATAGCTTAAGTCGAGAAGGGTTATCTGCCAATTAAAGACCTTCGAGTTTGACTAAGCTCAGCTC
1 CATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAAGCTCAACTC
** *
1736474 CAAGACACATCATTTGCAGAATAACTTAAGTCGAGAAGAGCTATCTGTTAAAGACCCTCGAGTTC
66 CAAGACACATCATTTGCAGAATAACTTAAGTCGAGAAGAGCTATCTGCCAAAGACCCTCAAGTTC
** *
1736539 GATTATGCTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCTAAAAGGGTTATCTGTG
131 GATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCTAAAAGGGTTATCTGTC
* *
1736604 ACCAAAAGACCTTCGAGTTCGACTACGTTCAACTCCAAGGCATAACAATTGTAG
196 ACAAAAAGACATTCGAGTTCGACTACGTTCAACTCCAAGGCATAACAATTGTAG
* * *
1736658 CATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGTTTAACTC
1 CATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAAGCTCAACTC
* * * * *
1736723 CAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCTCAAGTTC
66 CAAGACACATCATTTGCAGAATAACTTAAGTCGAGAAGAGCTATCTGCCAAAGACCCTCAAGTTC
* * * *
1736788 GATTACACTCAGCTTCGAGGGTACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTC
131 GATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCTAAAAGGGTTATCTGTC
*
1736853 ACAAAAAGATATTCGAGTTCGA
196 ACAAAAAGACATTCGAGTTCGA
1736875 TTACACTCAG
Statistics
Matches: 191, Mismatches: 26, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
249 191 1.00
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (249 bp):
CATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAAGCTCAACTC
CAAGACACATCATTTGCAGAATAACTTAAGTCGAGAAGAGCTATCTGCCAAAGACCCTCAAGTTC
GATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCTAAAAGGGTTATCTGTC
ACAAAAAGACATTCGAGTTCGACTACGTTCAACTCCAAGGCATAACAATTGTAG
Found at i:1738519 original size:27 final size:30
Alignment explanation
Indices: 1738458--1738522 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
1738448 ACCCTTATAT
*
1738458 TATTATTTTTATTATTTTATTTATGTATACG
1 TATTATTTTTATTATTTTATTTA-GTATACC
*
1738489 TATT-TTTTTA-TATTTTATTTA-TATGCC
1 TATTATTTTTATTATTTTATTTAGTATACC
1738516 TATTATT
1 TATTATT
1738523 AATATATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 8 0.26
28 2 0.06
29 11 0.35
30 6 0.19
31 4 0.13
ACGTcount: A:0.25, C:0.05, G:0.05, T:0.66
Consensus pattern (30 bp):
TATTATTTTTATTATTTTATTTAGTATACC
Found at i:1738630 original size:16 final size:15
Alignment explanation
Indices: 1738611--1738662 Score: 68
Period size: 16 Copynumber: 3.3 Consensus size: 15
1738601 ATATTATATT
1738611 TTTTTATTATTTTTGA
1 TTTTTATTATTTTT-A
*
1738627 TTTTTATTATTATTA
1 TTTTTATTATTTTTA
*
1738642 TATTCTATTATTTTTA
1 T-TTTTATTATTTTTA
1738658 TTTTT
1 TTTTT
1738663 TACTCTTGTC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
15 5 0.16
16 26 0.84
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (15 bp):
TTTTTATTATTTTTA
Found at i:1738651 original size:45 final size:45
Alignment explanation
Indices: 1738602--1738690 Score: 110
Period size: 45 Copynumber: 2.0 Consensus size: 45
1738592 TATATATATA
* * *
1738602 TATTATATTTT-TTTATTATTTTTGATTTTTATTATTA-TTATATTC
1 TATTAT-TTTTATTTATTACTCTTG-TCTTTATTATTATTTATATTC
*
1738647 TATTATTTTTATTTTTTACTCTTGTCTTTATTATTATTTATATT
1 TATTATTTTTATTTATTACTCTTGTCTTTATTATTATTTATATT
1738691 ATTAAATGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
44 15 0.39
45 23 0.61
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.71
Consensus pattern (45 bp):
TATTATTTTTATTTATTACTCTTGTCTTTATTATTATTTATATTC
Found at i:1738652 original size:19 final size:17
Alignment explanation
Indices: 1738602--1738664 Score: 60
Period size: 16 Copynumber: 3.8 Consensus size: 17
1738592 TATATATATA
1738602 TATTATATTTTT-TTAT
1 TATTATATTTTTATTAT
*
1738618 TATTTTTGATTTTTATTAT
1 TA-TTAT-ATTTTTATTAT
*
1738637 TATTATA-TTCTATTAT
1 TATTATATTTTTATTAT
*
1738653 TTTTAT-TTTTTA
1 TATTATATTTTTA
1738665 CTCTTGTCTT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
16 19 0.50
17 4 0.11
18 9 0.24
19 6 0.16
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73
Consensus pattern (17 bp):
TATTATATTTTTATTAT
Found at i:1738828 original size:2 final size:2
Alignment explanation
Indices: 1738821--1738862 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
1738811 TTAAATATTT
1738821 TA TA TA TA TA TA TA TA TA TA TA TA TA T- 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
1738862 T
1 T
1738863 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1738964 original size:5 final size:5
Alignment explanation
Indices: 1738946--1739012 Score: 59
Period size: 5 Copynumber: 13.2 Consensus size: 5
1738936 ATAATTCTTT
* *
1738946 TTTTA TCTTA -TTTA TTTTA -TTTA TTCATTA TTCTTC TCTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT--TTA TT-TTA T-TTTA TTTTA
1738993 TTTTA TTTTA TTTT- TTTTA T
1 TTTTA TTTTA TTTTA TTTTA T
1739013 CTTCGTTTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
4 11 0.22
5 28 0.55
6 6 0.12
7 6 0.12
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:1738965 original size:9 final size:9
Alignment explanation
Indices: 1738943--1739028 Score: 59
Period size: 9 Copynumber: 9.2 Consensus size: 9
1738933 ACTATAATTC
1738943 TTTT-TTTA
1 TTTTATTTA
*
1738951 TCTTATTTA
1 TTTTATTTA
1738960 TTTTATTTA
1 TTTTATTTA
*
1738969 TTCATTA-TTC
1 TT--TTATTTA
* *
1738979 TTCTCTTTA
1 TTTTATTTA
1738988 TTTTATTTTA
1 TTTTA-TTTA
*
1738998 TTTTATTTT
1 TTTTATTTA
*
1739007 TTTTATCTTCG
1 TTTTAT-TT-A
1739018 TTTTATTTA
1 TTTTATTTA
1739027 TT
1 TT
1739029 CACGTTTATT
Statistics
Matches: 60, Mismatches: 11, Indels: 13
0.71 0.13 0.15
Matches are distributed among these distances:
8 4 0.07
9 30 0.50
10 17 0.28
11 9 0.15
ACGTcount: A:0.16, C:0.08, G:0.01, T:0.74
Consensus pattern (9 bp):
TTTTATTTA
Found at i:1739048 original size:62 final size:57
Alignment explanation
Indices: 1738960--1739075 Score: 144
Period size: 62 Copynumber: 1.9 Consensus size: 57
1738950 ATCTTATTTA
* * *
1738960 TTTTATTTATTCATTATTCTTCTCTTTATTTTATTT-TATTTTATTTTTTTTATCTTCG
1 TTTTATTTATTCATTATTATTCTCTTTATCTTATTTGT-TTTCA-TTTTTTTATCTTCG
1739018 TTTTATTTATTCACGTTTATTTATTCTCTTTATCTTATTTGTTTTCATTTTTTTATCT
1 TTTTATTTATTCA---TTA-TTATTCTCTTTATCTTATTTGTTTTCATTTTTTTATCT
1739076 AACACATTTC
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
58 13 0.26
61 14 0.28
62 22 0.44
63 1 0.02
ACGTcount: A:0.16, C:0.11, G:0.03, T:0.71
Consensus pattern (57 bp):
TTTTATTTATTCATTATTATTCTCTTTATCTTATTTGTTTTCATTTTTTTATCTTCG
Found at i:1739169 original size:52 final size:52
Alignment explanation
Indices: 1739091--1739195 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
1739081 ATTTCTTAAC
1739091 TCTCTTAAGGGTAAGCTTTTAAAACTAGCTAAGGTAAGTAATTGTGATCGTA
1 TCTCTTAAGGGTAAGCTTTTAAAACTAGCTAAGGTAAGTAATTGTGATCGTA
1739143 TCTCTTAAGGGTAAGCTTTTAAAACTAGCTAAGGTAAGTAATTGTGATCGTA
1 TCTCTTAAGGGTAAGCTTTTAAAACTAGCTAAGGTAAGTAATTGTGATCGTA
1739195 T
1 T
1739196 TTTTACCTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.35
Consensus pattern (52 bp):
TCTCTTAAGGGTAAGCTTTTAAAACTAGCTAAGGTAAGTAATTGTGATCGTA
Found at i:1739838 original size:24 final size:24
Alignment explanation
Indices: 1739806--1739854 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1739796 TCTTTCATGC
1739806 ATGTATGGGTAGGGATAGACAGAA
1 ATGTATGGGTAGGGATAGACAGAA
1739830 ATGTATGGGTAGGGATAGACAGAA
1 ATGTATGGGTAGGGATAGACAGAA
1739854 A
1 A
1739855 GGGTAGACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.39, C:0.04, G:0.37, T:0.20
Consensus pattern (24 bp):
ATGTATGGGTAGGGATAGACAGAA
Found at i:1743412 original size:2 final size:2
Alignment explanation
Indices: 1743407--1743431 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1743397 TGTGTTGTTA
1743407 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
1743432 ATCATACTAA
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:1747080 original size:41 final size:42
Alignment explanation
Indices: 1747035--1747270 Score: 184
Period size: 41 Copynumber: 5.7 Consensus size: 42
1747025 TACATATAAA
* *
1747035 TACTTTAGTGGCATTTTTAAAAAAACGCCGCCACAA-AATCC
1 TACTTTAGTGGCATTTTTAAACAAACGCCGCCAAAAGAATCC
* *
1747076 TACTTTAGTGTC-TTTTCTAAACAAACGCCG-CAAAAGAATCG
1 TACTTTAGTGGCATTTT-TAAACAAACGCCGCCAAAAGAATCC
* * ** *
1747117 TTCTTTAGTGGCATTTTTAAACAAACGCCG-CAATAGGGTACA
1 TACTTTAGTGGCATTTTTAAACAAACGCCGCCAAAAGAAT-CC
* * * * ** **
1747159 TA-TATT-GTGG-TTTTTTTAATAAACGCCGCTAAAA-CCTAG
1 TACT-TTAGTGGCATTTTTAAACAAACGCCGCCAAAAGAATCC
* *
1747198 TACTTTAGTGGCGTTTCTAAACAAACGCCG-CAAAAGAATCC
1 TACTTTAGTGGCATTTTTAAACAAACGCCGCCAAAAGAATCC
* *
1747239 TTCTTTAATGGCATTTTTAAAACAAACGCCGC
1 TACTTTAGTGGCATTTTT-AAACAAACGCCGC
1747271 AATATGTTGA
Statistics
Matches: 150, Mismatches: 33, Indels: 22
0.73 0.16 0.11
Matches are distributed among these distances:
39 4 0.03
40 33 0.22
41 93 0.62
42 20 0.13
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (42 bp):
TACTTTAGTGGCATTTTTAAACAAACGCCGCCAAAAGAATCC
Found at i:1747174 original size:122 final size:123
Alignment explanation
Indices: 1747048--1747274 Score: 341
Period size: 122 Copynumber: 1.9 Consensus size: 123
1747038 TTTAGTGGCA
* * *
1747048 TTTTTAAAAAAACGCCGCCACAAA-ATCCTACTTTAGTGTCTTTTCTAAACAAACGCCGCAAAAG
1 TTTTTAAAAAAACGCCGCCA-AAACATACTACTTTAGTGGCGTTTCTAAACAAACGCCGCAAAAG
* *
1747112 AATCGTTCTTTAGTGGCATTTTT-AAACAAACGCCGCAATAGGGTACATATATTGTGGT
65 AATCCTTCTTTAATGGCATTTTTAAAACAAACGCCGCAATAGGGTACATATATTGTGGT
* * * * *
1747170 TTTTTTAATAAACGCCGCTAAAACCTAGTACTTTAGTGGCGTTTCTAAACAAACGCCGCAAAAGA
1 TTTTTAAAAAAACGCCGCCAAAACATACTACTTTAGTGGCGTTTCTAAACAAACGCCGCAAAAGA
1747235 ATCCTTCTTTAATGGCATTTTTAAAACAAACGCCGCAATA
66 ATCCTTCTTTAATGGCATTTTTAAAACAAACGCCGCAATA
1747275 TGTTGAACCG
Statistics
Matches: 93, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
121 3 0.03
122 73 0.78
123 17 0.18
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (123 bp):
TTTTTAAAAAAACGCCGCCAAAACATACTACTTTAGTGGCGTTTCTAAACAAACGCCGCAAAAGA
ATCCTTCTTTAATGGCATTTTTAAAACAAACGCCGCAATAGGGTACATATATTGTGGT
Found at i:1748183 original size:160 final size:160
Alignment explanation
Indices: 1747919--1748239 Score: 642
Period size: 160 Copynumber: 2.0 Consensus size: 160
1747909 TTGTACATTT
1747919 TCTCCTTCACTTTTATCCCCTGTTTTGTGTATTTCTGATGCTTTTTAAATTGCTCGTTGTATCTT
1 TCTCCTTCACTTTTATCCCCTGTTTTGTGTATTTCTGATGCTTTTTAAATTGCTCGTTGTATCTT
1747984 TTTATTCCAAAATATTTTAGGTTGTATTCTGATTTTATGCTCACTAGTAAACTTGGATTATGGAA
66 TTTATTCCAAAATATTTTAGGTTGTATTCTGATTTTATGCTCACTAGTAAACTTGGATTATGGAA
1748049 TGTGCTTAATTGGAGCCTTGTTTACTTGCA
131 TGTGCTTAATTGGAGCCTTGTTTACTTGCA
1748079 TCTCCTTCACTTTTATCCCCTGTTTTGTGTATTTCTGATGCTTTTTAAATTGCTCGTTGTATCTT
1 TCTCCTTCACTTTTATCCCCTGTTTTGTGTATTTCTGATGCTTTTTAAATTGCTCGTTGTATCTT
1748144 TTTATTCCAAAATATTTTAGGTTGTATTCTGATTTTATGCTCACTAGTAAACTTGGATTATGGAA
66 TTTATTCCAAAATATTTTAGGTTGTATTCTGATTTTATGCTCACTAGTAAACTTGGATTATGGAA
1748209 TGTGCTTAATTGGAGCCTTGTTTACTTGCA
131 TGTGCTTAATTGGAGCCTTGTTTACTTGCA
1748239 T
1 T
1748240 TTATGTCGTT
Statistics
Matches: 161, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
160 161 1.00
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.48
Consensus pattern (160 bp):
TCTCCTTCACTTTTATCCCCTGTTTTGTGTATTTCTGATGCTTTTTAAATTGCTCGTTGTATCTT
TTTATTCCAAAATATTTTAGGTTGTATTCTGATTTTATGCTCACTAGTAAACTTGGATTATGGAA
TGTGCTTAATTGGAGCCTTGTTTACTTGCA
Found at i:1749121 original size:35 final size:35
Alignment explanation
Indices: 1749075--1749144 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
1749065 TTGGCTTCAA
1749075 TATATTCCAGATAAATGGATCTATTCAAGACCTGG
1 TATATTCCAGATAAATGGATCTATTCAAGACCTGG
1749110 TATATTCCAGATAAATGGATCTATTCAAGACCTGG
1 TATATTCCAGATAAATGGATCTATTCAAGACCTGG
1749145 CAGGATCCAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (35 bp):
TATATTCCAGATAAATGGATCTATTCAAGACCTGG
Found at i:1754421 original size:17 final size:17
Alignment explanation
Indices: 1754401--1754454 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
1754391 TCTTAATCTT
1754401 TTCTGTTTTTTCGATAA
1 TTCTGTTTTTTCGATAA
*
1754418 TTCTG--TTTGCG-TAA
1 TTCTGTTTTTTCGATAA
1754432 GCTTCTGTTTTTTCGATAA
1 --TTCTGTTTTTTCGATAA
1754451 TTCT
1 TTCT
1754455 TTCCTCATAG
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
14 3 0.10
15 5 0.17
16 5 0.17
17 9 0.30
18 5 0.17
19 3 0.10
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.56
Consensus pattern (17 bp):
TTCTGTTTTTTCGATAA
Found at i:1758491 original size:20 final size:20
Alignment explanation
Indices: 1758449--1758506 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
1758439 TGGTCGGTTC
* *
1758449 AGTTAACTCAGACCGGTTTG
1 AGTTAACTCAGACCGATTCG
* *
1758469 AGTTGACTCAGATCGATTCG
1 AGTTAACTCAGACCGATTCG
*
1758489 AGTTTACTC-GAACCGATT
1 AGTTAACTCAG-ACCGATT
1758507 ATAGGATATT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (20 bp):
AGTTAACTCAGACCGATTCG
Found at i:1758843 original size:93 final size:93
Alignment explanation
Indices: 1758731--1758921 Score: 382
Period size: 93 Copynumber: 2.1 Consensus size: 93
1758721 GGGATGGGTT
1758731 TTGAGCGCACGGAGGAGGGGAGTGCAGTGGTGGAGGACGTGAGGCAAGGGGACGTTAGTGGCGGA
1 TTGAGCGCACGGAGGAGGGGAGTGCAGTGGTGGAGGACGTGAGGCAAGGGGACGTTAGTGGCGGA
1758796 TGAAAAATGTAAGAAAACGAGGAAAGCC
66 TGAAAAATGTAAGAAAACGAGGAAAGCC
1758824 TTGAGCGCACGGAGGAGGGGAGTGCAGTGGTGGAGGACGTGAGGCAAGGGGACGTTAGTGGCGGA
1 TTGAGCGCACGGAGGAGGGGAGTGCAGTGGTGGAGGACGTGAGGCAAGGGGACGTTAGTGGCGGA
1758889 TGAAAAATGTAAGAAAACGAGGAAAGCC
66 TGAAAAATGTAAGAAAACGAGGAAAGCC
1758917 TTGAG
1 TTGAG
1758922 TTATCCCGGT
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 98 1.00
ACGTcount: A:0.31, C:0.12, G:0.44, T:0.14
Consensus pattern (93 bp):
TTGAGCGCACGGAGGAGGGGAGTGCAGTGGTGGAGGACGTGAGGCAAGGGGACGTTAGTGGCGGA
TGAAAAATGTAAGAAAACGAGGAAAGCC
Found at i:1760208 original size:18 final size:18
Alignment explanation
Indices: 1760161--1760201 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
1760151 AAGCTCCGAA
1760161 ACGGGGTCCGGCGGCGGC
1 ACGGGGTCCGGCGGCGGC
1760179 ACGGGGTCCGGCGGCGGC
1 ACGGGGTCCGGCGGCGGC
1760197 ACGGG
1 ACGGG
1760202 CGCCGGCTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.07, C:0.32, G:0.56, T:0.05
Consensus pattern (18 bp):
ACGGGGTCCGGCGGCGGC
Found at i:1760242 original size:15 final size:15
Alignment explanation
Indices: 1760224--1760350 Score: 89
Period size: 15 Copynumber: 8.3 Consensus size: 15
1760214 CTCCTCTTCC
*
1760224 TCTTTCTTGGGTTCT
1 TCTTTCTTTGGTTCT
*
1760239 TCTTTCTTTGGCTCT
1 TCTTTCTTTGGTTCT
* * *
1760254 TCCTTCTTAGGCTCT
1 TCTTTCTTTGGTTCT
1760269 TCTTTCTTTGGTTCCTCT
1 TCTTTCTTTGG-T--TCT
*
1760287 TCCTTCTTTGG---T
1 TCTTTCTTTGGTTCT
1760299 TCTTTCTTTGGTTCCT
1 TCTTTCTTTGGTT-CT
* *
1760315 CCACTTTCTTGGGTTCT
1 --TCTTTCTTTGGTTCT
* *
1760332 TCCTTCTTTGGTTCC
1 TCTTTCTTTGGTTCT
1760347 TCTT
1 TCTT
1760351 CCTTCTCTGG
Statistics
Matches: 87, Mismatches: 16, Indels: 18
0.72 0.13 0.15
Matches are distributed among these distances:
12 11 0.13
15 49 0.56
16 1 0.01
17 2 0.02
18 24 0.28
ACGTcount: A:0.02, C:0.28, G:0.14, T:0.57
Consensus pattern (15 bp):
TCTTTCTTTGGTTCT
Found at i:1760286 original size:18 final size:18
Alignment explanation
Indices: 1760265--1760365 Score: 85
Period size: 18 Copynumber: 6.1 Consensus size: 18
1760255 CCTTCTTAGG
*
1760265 CTCTTCTTTCTTTGGTTC
1 CTCTTCCTTCTTTGGTTC
1760283 CTCTTCCTTCTTTGG-T-
1 CTCTTCCTTCTTTGGTTC
1760299 -TC-T--TTCTTTGGTTC
1 CTCTTCCTTCTTTGGTTC
** * *
1760313 CTCCACTTTC-TTGGGT-
1 CTCTTCCTTCTTTGGTTC
1760329 -TCTTCCTTCTTTGGTTC
1 CTCTTCCTTCTTTGGTTC
*
1760346 CTCTTCCTTCTCTGGTTC
1 CTCTTCCTTCTTTGGTTC
1760364 CT
1 CT
1760366 TTGCTGGCCC
Statistics
Matches: 66, Mismatches: 8, Indels: 18
0.72 0.09 0.20
Matches are distributed among these distances:
12 8 0.12
13 1 0.02
14 1 0.02
15 10 0.15
16 5 0.08
17 6 0.09
18 35 0.53
ACGTcount: A:0.01, C:0.31, G:0.13, T:0.55
Consensus pattern (18 bp):
CTCTTCCTTCTTTGGTTC
Found at i:1760363 original size:33 final size:33
Alignment explanation
Indices: 1760227--1760356 Score: 155
Period size: 30 Copynumber: 4.1 Consensus size: 33
1760217 CTCTTCCTCT
1760227 TTCTTGGGTTCTTCTTTCTTTGG---CTCTTCC
1 TTCTTGGGTTCTTCTTTCTTTGGTTCCTCTTCC
* *
1760257 TTCTTAGGCTCTTCTTTCTTTGGTTCCTCTTCC
1 TTCTTGGGTTCTTCTTTCTTTGGTTCCTCTTCC
* ** *
1760290 TTCTTTGG---TTCTTTCTTTGGTTCCTCCACT
1 TTCTTGGGTTCTTCTTTCTTTGGTTCCTCTTCC
*
1760320 TTCTTGGGTTCTTCCTTCTTTGGTTCCTCTTCC
1 TTCTTGGGTTCTTCTTTCTTTGGTTCCTCTTCC
1760353 TTCT
1 TTCT
1760357 CTGGTTCCTT
Statistics
Matches: 83, Mismatches: 11, Indels: 9
0.81 0.11 0.09
Matches are distributed among these distances:
30 47 0.57
33 36 0.43
ACGTcount: A:0.02, C:0.28, G:0.14, T:0.56
Consensus pattern (33 bp):
TTCTTGGGTTCTTCTTTCTTTGGTTCCTCTTCC
Found at i:1762709 original size:11 final size:11
Alignment explanation
Indices: 1762695--1762732 Score: 67
Period size: 11 Copynumber: 3.5 Consensus size: 11
1762685 ATAAATGAAT
*
1762695 AATTATTTTTA
1 AATTATTTTAA
1762706 AATTATTTTAA
1 AATTATTTTAA
1762717 AATTATTTTAA
1 AATTATTTTAA
1762728 AATTA
1 AATTA
1762733 ATGAATCTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
AATTATTTTAA
Found at i:1764981 original size:13 final size:13
Alignment explanation
Indices: 1764963--1764987 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1764953 AAAAGTGTTC
1764963 ATATTTAAAATTT
1 ATATTTAAAATTT
1764976 ATATTTAAAATT
1 ATATTTAAAATT
1764988 AATAATATGC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATATTTAAAATTT
Found at i:1770497 original size:2 final size:2
Alignment explanation
Indices: 1770490--1770525 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1770480 AAAAATATGA
1770490 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
1770526 TACATATAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1771056 original size:20 final size:20
Alignment explanation
Indices: 1771011--1771056 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
1771001 GACCAACAAA
* *
1771011 ATCGCAATGCGATCTCTAAT
1 ATCGCAACGCGATCTCCAAT
*
1771031 -TCGCAACGCGATCTCCATT
1 ATCGCAACGCGATCTCCAAT
1771050 ATCGCAA
1 ATCGCAA
1771057 ATTCGCGTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATCTCCAAT
Found at i:1771771 original size:14 final size:14
Alignment explanation
Indices: 1771752--1771838 Score: 57
Period size: 14 Copynumber: 5.5 Consensus size: 14
1771742 CAAAATCGCA
1771752 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
1771766 TTGCGATTTTCATTTCGCG
1 TTGCGA--TTC---TCTCG
*
1771785 TTGCGATTCTCTTG
1 TTGCGATTCTCTCG
*
1771799 TTGCGATAGTCATTTCG
1 TTGCGAT--TC-TCTCG
1771816 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
1771832 TTGCGAT
1 TTGCGAT
1771839 AGTCATTTCC
Statistics
Matches: 57, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 23 0.40
16 9 0.16
17 8 0.14
19 17 0.30
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:1771794 original size:33 final size:33
Alignment explanation
Indices: 1771747--1771862 Score: 169
Period size: 33 Copynumber: 3.5 Consensus size: 33
1771737 GAAACCAAAA
**
1771747 TCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATAGTCATT
* *
1771780 TCGCGTTGCGATTCTCTTGTTGCGATAGTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATAGTCATT
1771813 TCGCATTGCGATTCTCTCGTTGCGATAGTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATAGTCATT
* *
1771846 TCCGCGTTGTGATTCTC
1 T-CGCATTGCGATTCTC
1771863 ATTATCTCGT
Statistics
Matches: 74, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
33 61 0.82
34 13 0.18
ACGTcount: A:0.12, C:0.24, G:0.22, T:0.42
Consensus pattern (33 bp):
TCGCATTGCGATTCTCTCGTTGCGATAGTCATT
Found at i:1771864 original size:20 final size:20
Alignment explanation
Indices: 1771830--1771887 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
1771820 GCGATTCTCT
**
1771830 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
* *
1771850 CGTTGTGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
1771870 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
1771888 AACCAAAAGA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
19 1 0.03
20 28 0.93
21 1 0.03
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.45
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:1773605 original size:91 final size:90
Alignment explanation
Indices: 1773440--1773622 Score: 282
Period size: 91 Copynumber: 2.0 Consensus size: 90
1773430 TAGATTGCTT
1773440 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTAACACTGTGAAGTTAGTATTT
1 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTAACACTGTGAAGTTAGTATTT
*
1773505 GTCTTTTTGTTTTGTCTTTTGGTTGA
66 GTC-TTTTGTTTTATCTTTTGGTTGA
*
1773531 AGTAAATTTATTCGGTTGCTGCCAAT-CTGCTAAACTGTGTATTCTTTAACACTGTGAAG-TAGT
1 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1773594 ATTTGTC-TTTGTTTTATCTTTTGGTTGA
62 ATTTGTCTTTTGTTTTATCTTTTGGTTGA
1773622 A
1 A
1773623 TTGAAATATA
Statistics
Matches: 86, Mismatches: 2, Indels: 8
0.90 0.02 0.08
Matches are distributed among these distances:
90 9 0.10
91 47 0.55
92 3 0.03
93 13 0.15
94 14 0.16
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (90 bp):
AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTAACACTGTGAAGTTAGTATTT
GTCTTTTGTTTTATCTTTTGGTTGA
Found at i:1773887 original size:42 final size:42
Alignment explanation
Indices: 1773811--1773899 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
1773801 GACTCGCCTG
* * *
1773811 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* * * * *
1773853 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
1773895 TCATC
1 TCATC
1773900 GTTGAAGAGG
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.21, C:0.38, G:0.17, T:0.24
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
Found at i:1775439 original size:19 final size:19
Alignment explanation
Indices: 1775415--1775492 Score: 94
Period size: 19 Copynumber: 4.4 Consensus size: 19
1775405 AAAAAGTACT
1775415 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1775434 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1775453 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
* *
1775467 ATCGCAACGCAAAATGAAA
1 ATCGCAATGCGAAATGAAA
1775486 ATCGCAA
1 ATCGCAA
1775493 CGAGAGAATC
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
14 10 0.20
15 1 0.02
16 1 0.02
17 2 0.04
18 1 0.02
19 36 0.71
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1775471 original size:14 final size:14
Alignment explanation
Indices: 1775452--1775505 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
1775442 GCGAAATGAA
1775452 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1775466 AATCGCAACGCAAAATGAA
1 AATCGCAACG----A-GAG
1775485 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1775499 AATCGCA
1 AATCGCA
1775506 CGCGAATTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 19 0.58
15 1 0.03
18 1 0.03
19 12 0.36
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1775482 original size:33 final size:33
Alignment explanation
Indices: 1775433--1775505 Score: 128
Period size: 33 Copynumber: 2.2 Consensus size: 33
1775423 GCGAAATGAA
* *
1775433 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCAAAATGAAAATCGCAACGAGAG
1775466 AATCGCAACGCAAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCAAAATGAAAATCGCAACGAGAG
1775499 AATCGCA
1 AATCGCA
1775506 CGCGAATTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.47, C:0.21, G:0.22, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCAAAATGAAAATCGCAACGAGAG
Found at i:1775571 original size:33 final size:33
Alignment explanation
Indices: 1775521--1775613 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
1775511 ATTAAATTCG
1775521 CGTTGCGA-TTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
1775553 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1775586 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1775614 AGTAATTTCG
Statistics
Matches: 59, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 8 0.14
33 51 0.86
ACGTcount: A:0.13, C:0.25, G:0.19, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:1775579 original size:19 final size:19
Alignment explanation
Indices: 1775517--1775632 Score: 83
Period size: 19 Copynumber: 6.7 Consensus size: 19
1775507 GCGAATTAAA
*
1775517 TTCGCGTTGCGA-TTTCAT
1 TTCGCATTGCGATTTTCAT
*
1775535 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
1775551 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
1775568 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
1775584 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
** *
1775601 TTCGCATTGCGATAGTAAT
1 TTCGCATTGCGATTTTCAT
*
1775620 TTCGCGTTGCGAT
1 TTCGCATTGCGAT
1775633 AGACATTAAG
Statistics
Matches: 77, Mismatches: 11, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
14 12 0.16
16 13 0.17
17 13 0.17
18 11 0.14
19 28 0.36
ACGTcount: A:0.14, C:0.23, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:1777886 original size:12 final size:12
Alignment explanation
Indices: 1777869--1777894 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1777859 TCTTCGGGGA
1777869 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1777881 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1777893 CT
1 CT
1777895 CTTCCGGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1777901 original size:94 final size:95
Alignment explanation
Indices: 1777800--1777989 Score: 373
Period size: 95 Copynumber: 2.0 Consensus size: 95
1777790 TACCAACTCT
1777800 TCTTCCGGTATCTGAAGTAATTCTGGCATATTCCAG-TATACTCCCGTGGCATTTTCTTTTCTTC
1 TCTTCCGGTATCTGAAGTAATTCTGGCATATTCCAGTTATACTCCCGTGGCATTTTCTTTTCTTC
1777864 GGGGACTTTTTCTTCTTCTTTTTCTTCTTC
66 GGGGACTTTTTCTTCTTCTTTTTCTTCTTC
1777894 TCTTCCGGTATCTGAAGTAATTCTGGCATATTCCAGTTATACTCCCGTGGCATTTTCTTTTCTTC
1 TCTTCCGGTATCTGAAGTAATTCTGGCATATTCCAGTTATACTCCCGTGGCATTTTCTTTTCTTC
1777959 GGGGACTTTTTCTTCTTCTTTTTCTTCTTC
66 GGGGACTTTTTCTTCTTCTTTTTCTTCTTC
1777989 T
1 T
1777990 TTTTATTCTT
Statistics
Matches: 95, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
94 36 0.38
95 59 0.62
ACGTcount: A:0.13, C:0.24, G:0.15, T:0.48
Consensus pattern (95 bp):
TCTTCCGGTATCTGAAGTAATTCTGGCATATTCCAGTTATACTCCCGTGGCATTTTCTTTTCTTC
GGGGACTTTTTCTTCTTCTTTTTCTTCTTC
Found at i:1777981 original size:12 final size:12
Alignment explanation
Indices: 1777964--1778000 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
1777954 TCTTCGGGGA
1777964 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1777976 CTTTTTCTTCTT
1 CTTTTTCTTCTT
*
1777988 CTTTTTATTCTT
1 CTTTTTCTTCTT
1778000 C
1 C
1778001 AGGATTATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.73
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1777986 original size:15 final size:15
Alignment explanation
Indices: 1777968--1778000 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1777958 CGGGGACTTT
1777968 TTCTTCTTCTTT-TTC
1 TTCTTCTT-TTTATTC
1777983 TTCTTCTTTTTATTC
1 TTCTTCTTTTTATTC
1777998 TTC
1 TTC
1778001 AGGATTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.18
15 14 0.82
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.73
Consensus pattern (15 bp):
TTCTTCTTTTTATTC
Found at i:1778213 original size:24 final size:24
Alignment explanation
Indices: 1778186--1778232 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1778176 CAAAATCTGA
* *
1778186 GTATTGATCAATATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
1778210 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
1778233 AATACTGACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:1779035 original size:20 final size:21
Alignment explanation
Indices: 1779010--1779061 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1779000 TTTTCCTAAT
*
1779010 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
1779030 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1779051 TCGCAATGCGA
1 TCGCAATGCGA
1779062 TACTAACAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1781467 original size:20 final size:20
Alignment explanation
Indices: 1781444--1781497 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
1781434 GAAACTTAAA
1781444 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
1781464 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGAAAATGACT
*
1781484 ATCGCAATGCGAAA
1 ATCGCAACGCGAAA
1781498 TGCAAATCGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1781526 original size:33 final size:31
Alignment explanation
Indices: 1781484--1781559 Score: 116
Period size: 33 Copynumber: 2.4 Consensus size: 31
1781474 GGAAATGGCT
1781484 ATCGCAATGCGAAATGCAAATCGCAACGACAAA
1 ATCGCAATGCGAAATG-AAATCGCAACGAC-AA
*
1781517 ATCGCAATGCGAAATGAAATCGCAATGACAA
1 ATCGCAATGCGAAATGAAATCGCAACGACAA
*
1781548 ATCGCATTGCGA
1 ATCGCAATGCGA
1781560 TTTTGTCGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
31 13 0.32
32 12 0.29
33 16 0.39
ACGTcount: A:0.42, C:0.22, G:0.20, T:0.16
Consensus pattern (31 bp):
ATCGCAATGCGAAATGAAATCGCAACGACAA
Found at i:1781549 original size:18 final size:18
Alignment explanation
Indices: 1781442--1781543 Score: 77
Period size: 20 Copynumber: 5.6 Consensus size: 18
1781432 ACGAAACTTA
*
1781442 AAATCGCAACGCGAAAATG
1 AAATCGCAATGCG-AAATG
* *
1781461 ACTATCGCAACGCGGAAATGG
1 A-AATCGCAATGC-GAAAT-G
**
1781482 CTATCGCAATGCGAAATG
1 AAATCGCAATGCGAAATG
*
1781500 CAAATCGCAA--CGACA--
1 -AAATCGCAATGCGAAATG
1781515 AAATCGCAATGCGAAATG
1 AAATCGCAATGCGAAATG
1781533 AAATCGCAATG
1 AAATCGCAATG
1781544 ACAAATCGCA
Statistics
Matches: 68, Mismatches: 7, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
14 9 0.13
16 4 0.06
17 4 0.06
18 12 0.18
19 13 0.19
20 24 0.35
21 2 0.03
ACGTcount: A:0.41, C:0.23, G:0.22, T:0.15
Consensus pattern (18 bp):
AAATCGCAATGCGAAATG
Found at i:1781592 original size:19 final size:18
Alignment explanation
Indices: 1781549--1781625 Score: 71
Period size: 14 Copynumber: 4.7 Consensus size: 18
1781539 CAATGACAAA
*
1781549 TCGCATTGCGATTT--TG
1 TCGCATTGCGATTTCATT
1781565 TCG--TTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
*
1781582 TCGCATTGCGATTT--TG
1 TCGCATTGCGATTTCATT
1781598 TCG--TTGCGATTTCATT
1 TCGCATTGCGATTTCATT
1781614 TCGCATTGCGAT
1 TCGCATTGCGAT
1781626 AGCCATTTTC
Statistics
Matches: 49, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
14 15 0.31
15 3 0.06
16 11 0.22
17 4 0.08
18 10 0.20
19 6 0.12
ACGTcount: A:0.13, C:0.19, G:0.22, T:0.45
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:1781616 original size:32 final size:33
Alignment explanation
Indices: 1781549--1781625 Score: 147
Period size: 33 Copynumber: 2.4 Consensus size: 33
1781539 CAATGACAAA
1781549 TCGCATTGCGATTTTGTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTGTCGTTGCGATTTTCATT
1781582 TCGCATTGCGATTTTGTCGTTGCGA-TTTCATT
1 TCGCATTGCGATTTTGTCGTTGCGATTTTCATT
1781614 TCGCATTGCGAT
1 TCGCATTGCGAT
1781626 AGCCATTTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
32 19 0.43
33 25 0.57
ACGTcount: A:0.13, C:0.19, G:0.22, T:0.45
Consensus pattern (33 bp):
TCGCATTGCGATTTTGTCGTTGCGATTTTCATT
Found at i:1781637 original size:20 final size:20
Alignment explanation
Indices: 1781612--1781655 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1781602 TGCGATTTCA
1781612 TTTCGCATTGCGATAGCCAT
1 TTTCGCATTGCGATAGCCAT
* *
1781632 TTTCGCGTTGCGATAGTCAT
1 TTTCGCATTGCGATAGCCAT
1781652 TTTC
1 TTTC
1781656 ATGTTGCGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.41
Consensus pattern (20 bp):
TTTCGCATTGCGATAGCCAT
Found at i:1781661 original size:20 final size:20
Alignment explanation
Indices: 1781619--1781664 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1781609 TCATTTCGCA
*
1781619 TTGCGATAGCCATTTTCGCG
1 TTGCGATAGCCATTTTCACG
* *
1781639 TTGCGATAGTCATTTTCATG
1 TTGCGATAGCCATTTTCACG
1781659 TTGCGA
1 TTGCGA
1781665 AAGTAAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.39
Consensus pattern (20 bp):
TTGCGATAGCCATTTTCACG
Found at i:1783476 original size:20 final size:20
Alignment explanation
Indices: 1783451--1783524 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
1783441 AATAGTTTCT
*
1783451 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACGC
**
1783471 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACGC
** **
1783491 GAATTTGACTATCGCAACGC
1 GAAAATGAAAATCGCAACGC
*
1783511 GAAACT-AAAATCGC
1 GAAAATGAAAATCGC
1783525 GTTGCGATTT
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 6 0.13
20 39 0.87
ACGTcount: A:0.43, C:0.23, G:0.18, T:0.16
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACGC
Found at i:1783783 original size:21 final size:21
Alignment explanation
Indices: 1783757--1783799 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1783747 GATGGAGATA
1783757 GACGGATTTCGCCGGAGATGG
1 GACGGATTTCGCCGGAGATGG
*
1783778 GACGGATTTCGTCGGAGATGG
1 GACGGATTTCGCCGGAGATGG
1783799 G
1 G
1783800 TGAGAGAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.16, G:0.44, T:0.21
Consensus pattern (21 bp):
GACGGATTTCGCCGGAGATGG
Found at i:1784034 original size:19 final size:20
Alignment explanation
Indices: 1783987--1784036 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
1783977 CGATTATGTT
*
1783987 ATCGC-TTGTGAAAGTCAGA
1 ATCGCGTTGCGAAAGTCAGA
*
1784006 ATCGCGTTGCGAAAGTC-GT
1 ATCGCGTTGCGAAAGTCAGA
*
1784025 ATCTCGTTGCGA
1 ATCGCGTTGCGA
1784037 TTTTGTATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTCAGA
Found at i:1784075 original size:20 final size:20
Alignment explanation
Indices: 1784045--1784097 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
1784035 GATTTTGTAT
1784045 TATCGCA-TGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
* *
1784064 TATCTCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
1784084 TATCGCATTGCGAT
1 TATCGCATTGCGAT
1784098 TTTCCCAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 6 0.20
20 24 0.80
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:1786564 original size:25 final size:24
Alignment explanation
Indices: 1786523--1786570 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
1786513 TTATTTTAGA
*
1786523 ATTAAGATTAAGTTAAATTTAAAT
1 ATTAAGATTAAGTTAAAATTAAAT
1786547 ATTAAGTATTAA-TATAAAATTAAA
1 ATTAAG-ATTAAGT-TAAAATTAAA
1786571 ATTTTTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (24 bp):
ATTAAGATTAAGTTAAAATTAAAT
Found at i:1788981 original size:20 final size:20
Alignment explanation
Indices: 1788956--1788993 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1788946 TTTGCTTCAC
1788956 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
1788976 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
1788994 GGAATAGGAT
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:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Done.