Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008488.1 Hibiscus syriacus cultivar Beakdansim tig00111330_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: 12876159
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 26 of 54
Found at i:6370410 original size:23 final size:23
Alignment explanation
Indices: 6370362--6370412 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
6370352 CCAGTAATTA
** *
6370362 ACCTATTTTATTATATAAGCTCT
1 ACCTATTACATTATATAAGCGCT
*
6370385 ACCTATTACATTATATAAGCGGT
1 ACCTATTACATTATATAAGCGCT
6370408 ACCTA
1 ACCTA
6370413 ATATGTTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGCT
Found at i:6371242 original size:15 final size:15
Alignment explanation
Indices: 6371222--6371250 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
6371212 GCCTGAGTGA
6371222 TGACGAACACAATGG
1 TGACGAACACAATGG
6371237 TGACGAACACAATG
1 TGACGAACACAATG
6371251 TTTCTGATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.21, G:0.24, T:0.14
Consensus pattern (15 bp):
TGACGAACACAATGG
Found at i:6374126 original size:29 final size:29
Alignment explanation
Indices: 6374094--6374169 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
6374084 TCAGAACGTA
* *
6374094 GATATAATCCCATGCAGAGTTGGGACAAT
1 GATATAATCCCATGCAGAGTTAGGACAAG
** * *
6374123 GATATAATGTCATGTAGAGTTAGGACTAG
1 GATATAATCCCATGCAGAGTTAGGACAAG
*
6374152 GATATAATCCAATGCAGA
1 GATATAATCCCATGCAGA
6374170 ATCAGGACGG
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.26
Consensus pattern (29 bp):
GATATAATCCCATGCAGAGTTAGGACAAG
Found at i:6375864 original size:15 final size:13
Alignment explanation
Indices: 6375828--6375866 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
6375818 TAATATTTAA
6375828 ATTTTAATAATTTT
1 ATTTT-ATAATTTT
6375842 ATTTTATAATTTT
1 ATTTTATAATTTT
6375855 ATAGTTTATAAT
1 AT--TTTATAAT
6375867 ATTTTAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 10 0.43
14 5 0.22
15 8 0.35
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (13 bp):
ATTTTATAATTTT
Found at i:6387658 original size:21 final size:20
Alignment explanation
Indices: 6387633--6387671 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
6387623 TATCAGGGTC
*
6387633 TTTGTTGAAGCCATGAAATCT
1 TTTGTCGAAGCCAT-AAATCT
*
6387654 TTTGTCGAGGCCATAAAT
1 TTTGTCGAAGCCATAAAT
6387672 TCCTGCAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (20 bp):
TTTGTCGAAGCCATAAATCT
Found at i:6391382 original size:117 final size:117
Alignment explanation
Indices: 6391173--6391464 Score: 444
Period size: 117 Copynumber: 2.5 Consensus size: 117
6391163 TTTTCCCGAA
* **
6391173 CATACACCCACCTGCACACAAGTAAGGACTTACCCTAAGCACGA-AGCTGAGGAGCCTGCAGTAA
1 CATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGCAC-ACAGCAAAGGAGCCTGCAGTAA
* * * *
6391237 TAACGTCTCTATCCAATCGCTTCCATCACTACAATGTGTAGGTTCCCCAGAAC
65 TAACGTCCCCATCCAATCACTTCAATCACTACAATGTGTAGGTTCCCCAGAAC
*
6391290 CATACACCCACCTGCACACCAGTAAGGACTTTCCCTAAGCACACAGCAAAGGAGCCTGCAGTAAT
1 CATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGCACACAGCAAAGGAGCCTGCAGTAAT
* *
6391355 AACTTCCCCATCCAGTCAC-TCTAATCACTACAATGTGTAGGTTCCCCAGAAC
66 AACGTCCCCATCCAATCACTTC-AATCACTACAATGTGTAGGTTCCCCAGAAC
* *
6391407 CATACACCCACCTGCACACCAGTAAGGACTTACCCTGAGCACACAACAAAGGAGCCTG
1 CATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGCACACAGCAAAGGAGCCTG
6391465 AAATAGTTCC
Statistics
Matches: 160, Mismatches: 13, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
116 3 0.02
117 157 0.98
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (117 bp):
CATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGCACACAGCAAAGGAGCCTGCAGTAAT
AACGTCCCCATCCAATCACTTCAATCACTACAATGTGTAGGTTCCCCAGAAC
Found at i:6392560 original size:29 final size:29
Alignment explanation
Indices: 6392398--6392559 Score: 202
Period size: 29 Copynumber: 5.6 Consensus size: 29
6392388 TTTTTAAAAT
* * * *
6392398 AATTACCAAAATAGCACATTTTCAAATTA
1 AATTCCCAAAATATCACCTTTTCGAATTA
* * *
6392427 AATTCCCAATATAGCACTTTTTCGAATTA
1 AATTCCCAAAATATCACCTTTTCGAATTA
* *
6392456 AATTCTCAAAATATCACTTTTTCGAATTA
1 AATTCCCAAAATATCACCTTTTCGAATTA
6392485 AATTCCCAAAATATCACCTTTTCGAATT-
1 AATTCCCAAAATATCACCTTTTCGAATTA
* *
6392513 AATTCCCAAAATAGCACCCATTTCGAATT-
1 AATTCCCAAAATATCA-CCTTTTCGAATTA
6392542 AATTCCCAAAATATCACC
1 AATTCCCAAAATATCACC
6392560 CGGTCAACGG
Statistics
Matches: 120, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
28 17 0.14
29 103 0.86
ACGTcount: A:0.40, C:0.23, G:0.04, T:0.33
Consensus pattern (29 bp):
AATTCCCAAAATATCACCTTTTCGAATTA
Found at i:6392597 original size:17 final size:18
Alignment explanation
Indices: 6392575--6392649 Score: 62
Period size: 18 Copynumber: 3.9 Consensus size: 18
6392565 AACGGTCAAC
* *
6392575 GGTCAAC-GTTCGGGTTG
1 GGTCAACGGGTCGGGTCG
6392592 GGTCAACGGGTCGGGTCGGGTCG
1 GGTCAACGGGTC--G--G-GTCG
* *
6392615 GGTCAACAGATCGGGTCG
1 GGTCAACGGGTCGGGTCG
6392633 GGTCAACGGGTCGGGTC
1 GGTCAACGGGTCGGGTC
6392650 AAAACCGGTC
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
17 7 0.15
18 22 0.48
19 1 0.02
20 1 0.02
21 1 0.02
22 1 0.02
23 13 0.28
ACGTcount: A:0.13, C:0.21, G:0.45, T:0.20
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:6392607 original size:13 final size:13
Alignment explanation
Indices: 6392585--6392651 Score: 59
Period size: 13 Copynumber: 5.0 Consensus size: 13
6392575 GGTCAACGTT
*
6392585 CGGGTTGGGTCAA
1 CGGGTCGGGTCAA
6392598 CGGGTCGGGT---
1 CGGGTCGGGTCAA
6392608 CGGGTCGGGTCAACAGA
1 CGGGTCGGGT---CA-A
6392625 TCGGGTCGGGTCAA
1 -CGGGTCGGGTCAA
6392639 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
6392652 AACCGGTCAA
Statistics
Matches: 45, Mismatches: 1, Indels: 16
0.73 0.02 0.26
Matches are distributed among these distances:
10 10 0.22
13 22 0.49
14 1 0.02
15 2 0.04
18 10 0.22
ACGTcount: A:0.15, C:0.21, G:0.46, T:0.18
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:6392617 original size:23 final size:23
Alignment explanation
Indices: 6392584--6392636 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
6392574 CGGTCAACGT
* * *
6392584 TCGGGTTGGGTCAACGGGTCGGG
1 TCGGGTCGGGTCAACAGATCGGG
6392607 TCGGGTCGGGTCAACAGATCGGG
1 TCGGGTCGGGTCAACAGATCGGG
6392630 TCGGGTC
1 TCGGGTC
6392637 AACGGGTCGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.11, C:0.21, G:0.47, T:0.21
Consensus pattern (23 bp):
TCGGGTCGGGTCAACAGATCGGG
Found at i:6392649 original size:18 final size:18
Alignment explanation
Indices: 6392603--6392649 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
6392593 GTCAACGGGT
6392603 CGGGTCGGGTCGGGTCAA
1 CGGGTCGGGTCGGGTCAA
* *
6392621 CAGATCGGGTCGGGTCAA
1 CGGGTCGGGTCGGGTCAA
6392639 CGGGTCGGGTC
1 CGGGTCGGGTC
6392650 AAAACCGGTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCGGGTCAA
Found at i:6392660 original size:41 final size:40
Alignment explanation
Indices: 6392574--6392661 Score: 104
Period size: 41 Copynumber: 2.2 Consensus size: 40
6392564 CAACGGTCAA
* * ****
6392574 CGGTCAACGTTCGGGTTGGGTCAACGGGTCGGGTCGGGTC
1 CGGTCAACGATCGGGTCGGGTCAACGGGTCGGGTCAAAAC
*
6392614 GGGTCAACAGATCGGGTCGGGTCAACGGGTCGGGTCAAAAC
1 CGGTCAAC-GATCGGGTCGGGTCAACGGGTCGGGTCAAAAC
6392655 CGGTCAA
1 CGGTCAA
6392662 ACCGGTTATT
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
40 7 0.18
41 32 0.82
ACGTcount: A:0.18, C:0.23, G:0.41, T:0.18
Consensus pattern (40 bp):
CGGTCAACGATCGGGTCGGGTCAACGGGTCGGGTCAAAAC
Found at i:6400010 original size:60 final size:58
Alignment explanation
Indices: 6399941--6400053 Score: 163
Period size: 60 Copynumber: 1.9 Consensus size: 58
6399931 TGGGTGACCA
* * **
6399941 TTTGTAACTTTTAATAGTCGAGGGACTCAACAAAGTAACACCCTATAGTCGAGGGAACAT
1 TTTGTAACTTTTAATAGTCGAGAGACT-AAAAAAACAACACCCTATAGTC-AGGGAACAT
*
6400001 TTTGTAACTTTTAATAGTCGAGAGACTAAAAAAACAACGCCCTATAGTCAGGG
1 TTTGTAACTTTTAATAGTCGAGAGACTAAAAAAACAACACCCTATAGTCAGGG
6400054 GACCATTTCT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
58 4 0.08
59 18 0.38
60 26 0.54
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (58 bp):
TTTGTAACTTTTAATAGTCGAGAGACTAAAAAAACAACACCCTATAGTCAGGGAACAT
Found at i:6400558 original size:20 final size:20
Alignment explanation
Indices: 6400533--6400576 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
6400523 ATTTTATGTT
6400533 CGTTTGTTTATGTTCATTTA
1 CGTTTGTTTATGTTCATTTA
* *
6400553 CGTTTGTTTGTGTTCGTTTA
1 CGTTTGTTTATGTTCATTTA
6400573 CGTT
1 CGTT
6400577 CGTTCATTTG
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:0.09, C:0.11, G:0.20, T:0.59
Consensus pattern (20 bp):
CGTTTGTTTATGTTCATTTA
Found at i:6400580 original size:24 final size:23
Alignment explanation
Indices: 6400525--6400593 Score: 63
Period size: 24 Copynumber: 3.0 Consensus size: 23
6400515 CACAATTAAT
* *
6400525 TTTATGTTCGTTTGTTTATGTTCA
1 TTTA-GTTCGTTTGTTTGTGTTCG
6400549 TTTA---CGTTTGTTTGTGTTCG
1 TTTAGTTCGTTTGTTTGTGTTCG
**
6400569 TTTACGTTCGTTCATTTGTGTTCG
1 TTTA-GTTCGTTTGTTTGTGTTCG
6400593 T
1 T
6400594 ATATTATTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 18 0.49
24 19 0.51
ACGTcount: A:0.09, C:0.12, G:0.20, T:0.59
Consensus pattern (23 bp):
TTTAGTTCGTTTGTTTGTGTTCG
Found at i:6400946 original size:13 final size:13
Alignment explanation
Indices: 6400928--6400952 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6400918 CAACACTTTT
6400928 AATAATTGAATAC
1 AATAATTGAATAC
6400941 AATAATTGAATA
1 AATAATTGAATA
6400953 TTTATAGTAA
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:0.56, C:0.04, G:0.08, T:0.32
Consensus pattern (13 bp):
AATAATTGAATAC
Found at i:6401254 original size:20 final size:20
Alignment explanation
Indices: 6401229--6401269 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
6401219 ATATTATTTA
6401229 TATATTATCTCAATTTAGTC
1 TATATTATCTCAATTTAGTC
6401249 TATATTATCTCAATTTAGTC
1 TATATTATCTCAATTTAGTC
6401269 T
1 T
6401270 TACTTTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.15, G:0.05, T:0.51
Consensus pattern (20 bp):
TATATTATCTCAATTTAGTC
Found at i:6401669 original size:31 final size:31
Alignment explanation
Indices: 6401626--6401687 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
6401616 CCAACTTATG
6401626 GTGATCACATCTTAATTAAATAAAAATGAAA
1 GTGATCACATCTTAATTAAATAAAAATGAAA
* *
6401657 GTGATCATATCTTAATTAAATATAAATGAAA
1 GTGATCACATCTTAATTAAATAAAAATGAAA
6401688 ATAACCATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.50, C:0.08, G:0.10, T:0.32
Consensus pattern (31 bp):
GTGATCACATCTTAATTAAATAAAAATGAAA
Found at i:6401697 original size:31 final size:31
Alignment explanation
Indices: 6401634--6401697 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
6401624 TGGTGATCAC
* * *
6401634 ATCTTAATTAAATAAAAATGAAAGTGATCAT
1 ATCTTAATTAAATAAAAATGAAAATAACCAT
*
6401665 ATCTTAATTAAATATAAATGAAAATAACCAT
1 ATCTTAATTAAATAAAAATGAAAATAACCAT
6401696 AT
1 AT
6401698 ATTATATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.53, C:0.08, G:0.06, T:0.33
Consensus pattern (31 bp):
ATCTTAATTAAATAAAAATGAAAATAACCAT
Found at i:6402793 original size:13 final size:13
Alignment explanation
Indices: 6402775--6402807 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
6402765 TAAAAAACCT
6402775 TTTAAAAGTG-ATG
1 TTTAAAAGTGTA-G
6402788 TTTAAAAGTGTAG
1 TTTAAAAGTGTAG
6402801 TTTAAAA
1 TTTAAAA
6402808 TTTAACTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 18 0.95
14 1 0.05
ACGTcount: A:0.42, C:0.00, G:0.18, T:0.39
Consensus pattern (13 bp):
TTTAAAAGTGTAG
Found at i:6409811 original size:22 final size:22
Alignment explanation
Indices: 6409786--6409845 Score: 102
Period size: 22 Copynumber: 2.7 Consensus size: 22
6409776 TTCAGTATTC
6409786 GTCCCGTAGGACCACTGTATAT
1 GTCCCGTAGGACCACTGTATAT
*
6409808 GTCCCGTAGGACCATTGTATAT
1 GTCCCGTAGGACCACTGTATAT
*
6409830 GTCCCATAGGACCACT
1 GTCCCGTAGGACCACT
6409846 ATGTCCCGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.27
Consensus pattern (22 bp):
GTCCCGTAGGACCACTGTATAT
Found at i:6441062 original size:320 final size:315
Alignment explanation
Indices: 6440485--6441119 Score: 1225
Period size: 320 Copynumber: 2.0 Consensus size: 315
6440475 CTATCCCACA
6440485 CTCGTCCTGACATTGCTTTCAGTGTGAGTGTTATCAGTCAATATATACTAACCCAAGGAGAACAT
1 CTCGTCCTGACATTGCTTTCAGTGTGAGTGTTATCAGTCAATATATACTAACCCAAGGAGAACAT
6440550 CTAGAGCTGTCCATAGGTGTTGAGATACTTGAAGGGAACCCCGGGTAAGGGCCTATACTTCAAGA
66 CTAGAGCTGTCCATAGGTGTTGAGATACTTGAAGGGAACCCCGGGTAAGGGCCTATACTTCAAGA
6440615 AAACAAATAACTGATATGTAGACATCTACACAGATGCTGATTGGGCAGGTTCGGTGAATGATAGA
131 AAACAAATAACTGATATGTAGACATCTACACAGATGCTGATTGGGCAGGTTCGGTGAATGATAGA
6440680 AGGTCTACAAGCGGTTACTGCAGTTACGTGTGGGGTAACCTTGTGACATGGAGAAGTAAAAAACA
196 AGGTCTACAAGCGGTTACTGCAGTTACGTGTGGGGTAACCTTGTGACATGGAGAAGTAAAAAACA
6440745 ATCTGTTGTAGCCTGCAGTAGTGCTGAAGCTGAATATCGAGCTGTGTCACATGTT
261 ATCTGTTGTAGCCTGCAGTAGTGCTGAAGCTGAATATCGAGCTGTGTCACATGTT
6440800 CTCGTCCTGACATTGCTTTCAGTGTGAGTGTTATCAGTCAATATATACATAACCCAAGGGAGAAA
1 CTCGTCCTGACATTGCTTTCAGTGTGAGTGTTATCAGTCAATATATAC-TAACCCAA-GGAG-AA
6440865 CATCTAGAGGCTGTCCATAGGGTGTTGAGATACTTGAAGGGAACCCCGGGTAAGGGCCTATACTT
63 CATCTAGA-GCTGTCCATA-GGTGTTGAGATACTTGAAGGGAACCCCGGGTAAGGGCCTATACTT
6440930 CAAGAAAACAAATAACTGATATGTAGACATCTACACAGATGCTGATTGGGCAGGTTCGGTGAATG
126 CAAGAAAACAAATAACTGATATGTAGACATCTACACAGATGCTGATTGGGCAGGTTCGGTGAATG
6440995 ATAGAAGGTCTACAAGCGGTTACTGCAGTTACGTGTGGGGTAACCTTGTGACATGGAGAAGTAAA
191 ATAGAAGGTCTACAAGCGGTTACTGCAGTTACGTGTGGGGTAACCTTGTGACATGGAGAAGTAAA
6441060 AAACAATCTGTTGTAGCCTGCAGTAGTGCTGAAGCTGAATATCGAGCTGTGTCACATGTT
256 AAACAATCTGTTGTAGCCTGCAGTAGTGCTGAAGCTGAATATCGAGCTGTGTCACATGTT
6441120 ATATGCGAGG
Statistics
Matches: 315, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
315 48 0.15
316 8 0.03
317 4 0.01
318 10 0.03
319 10 0.03
320 235 0.75
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (315 bp):
CTCGTCCTGACATTGCTTTCAGTGTGAGTGTTATCAGTCAATATATACTAACCCAAGGAGAACAT
CTAGAGCTGTCCATAGGTGTTGAGATACTTGAAGGGAACCCCGGGTAAGGGCCTATACTTCAAGA
AAACAAATAACTGATATGTAGACATCTACACAGATGCTGATTGGGCAGGTTCGGTGAATGATAGA
AGGTCTACAAGCGGTTACTGCAGTTACGTGTGGGGTAACCTTGTGACATGGAGAAGTAAAAAACA
ATCTGTTGTAGCCTGCAGTAGTGCTGAAGCTGAATATCGAGCTGTGTCACATGTT
Found at i:6446442 original size:2 final size:2
Alignment explanation
Indices: 6446437--6446536 Score: 200
Period size: 2 Copynumber: 50.0 Consensus size: 2
6446427 ATATATCACC
6446437 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
6446479 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
6446521 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
6446537 CATGAAGACC
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 98 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6447776 original size:65 final size:66
Alignment explanation
Indices: 6447667--6447815 Score: 248
Period size: 65 Copynumber: 2.3 Consensus size: 66
6447657 GACCAAGCTG
* *
6447667 TGGGAGATTCCTGCA-CCGCGACCAAGCTTTAACCCTATCCCTCATGCATGCGTTGCATCCATAG
1 TGGGAGATTCCTGCATCCGCGACCAAGCTTTAACCATATCACTCATGCATGCGTTGCATCCATAG
6447731 C
66 C
*
6447732 TGGGAGATTCCTGCATCC-CGACCAAGCTTTAACCATATCACTCATGCATGTGTTGCATCCATAG
1 TGGGAGATTCCTGCATCCGCGACCAAGCTTTAACCATATCACTCATGCATGCGTTGCATCCATAG
6447796 C
66 C
*
6447797 TGGGAGATTCATGCATCCG
1 TGGGAGATTCCTGCATCCG
6447816 TAGTTGCATG
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
65 76 0.97
66 2 0.03
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.26
Consensus pattern (66 bp):
TGGGAGATTCCTGCATCCGCGACCAAGCTTTAACCATATCACTCATGCATGCGTTGCATCCATAG
C
Found at i:6447834 original size:21 final size:20
Alignment explanation
Indices: 6447808--6447854 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 20
6447798 GGGAGATTCA
* *
6447808 TGCATCCGTAGTTGCATGCAT
1 TGCATCCATAGCTGCATG-AT
6447829 TGCATCCATAGCTGCATGAT
1 TGCATCCATAGCTGCATGAT
6447849 TGCATC
1 TGCATC
6447855 GTTAATTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (20 bp):
TGCATCCATAGCTGCATGAT
Found at i:6448232 original size:21 final size:21
Alignment explanation
Indices: 6448207--6448250 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
6448197 AATCTAGTTA
6448207 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
6448228 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
6448249 AT
1 AT
6448251 ATATTATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:6448758 original size:17 final size:17
Alignment explanation
Indices: 6448736--6448797 Score: 61
Period size: 17 Copynumber: 3.4 Consensus size: 17
6448726 AGATAATTTA
6448736 TGTTTAAAAAAATATTG
1 TGTTTAAAAAAATATTG
* *
6448753 TGTTTAAAAATATTTAGTG
1 TGTTTAAAAA-A-ATATTG
*
6448772 TTGTTTTAAAAAAATATTT
1 -TG-TTTAAAAAAATATTG
6448791 TGTTTAA
1 TGTTTAA
6448798 TTTATATTGT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
17 15 0.42
18 3 0.08
19 7 0.19
20 3 0.08
21 8 0.22
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.48
Consensus pattern (17 bp):
TGTTTAAAAAAATATTG
Found at i:6448801 original size:22 final size:23
Alignment explanation
Indices: 6448758--6448801 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
6448748 TATTGTGTTT
**
6448758 AAAAATATTTAGTGTTGTTTTAA
1 AAAAATATTTAGTGTTAATTTAA
*
6448781 AAAAATATTTTGT-TTAATTTA
1 AAAAATATTTAGTGTTAATTTA
6448802 TATTGTATGT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (23 bp):
AAAAATATTTAGTGTTAATTTAA
Found at i:6449084 original size:14 final size:13
Alignment explanation
Indices: 6449026--6449093 Score: 52
Period size: 13 Copynumber: 5.3 Consensus size: 13
6449016 AAAAAATCAT
6449026 ATTATTATTAATC
1 ATTATTATTAATC
* *
6449039 ATTAATATCAAATC
1 ATTATTAT-TAATC
*
6449053 ATTA-GATTAAT-
1 ATTATTATTAATC
*
6449064 ATAATTATTAAATC
1 ATTATTATT-AATC
*
6449078 ATTATTAGTAAT-
1 ATTATTATTAATC
6449090 ATTA
1 ATTA
6449094 GTAATCAATC
Statistics
Matches: 43, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
11 3 0.07
12 10 0.23
13 15 0.35
14 15 0.35
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.46
Consensus pattern (13 bp):
ATTATTATTAATC
Found at i:6451289 original size:49 final size:49
Alignment explanation
Indices: 6451215--6451555 Score: 610
Period size: 49 Copynumber: 7.0 Consensus size: 49
6451205 GGCACCCATC
*
6451215 TATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
1 TATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
*
6451264 TATTATTAATTTTTAATGATCTGATAGTAATGATTAGTAATAATGAAAT
1 TATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
6451313 TATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
1 TATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
*
6451362 TATTATTAATTTTTAATGATTTGATATTAATGATTAGTAATAATGAAAT
1 TATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
*
6451411 TATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAATAAAAT
1 TATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
* *
6451460 TATCATTAATATTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
1 TATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
* *
6451509 TATTATTAATTTTTAATGATTTGATACTAATGATTTGTAATAATGAA
1 TATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAATGAA
6451556 TGGAGGGACC
Statistics
Matches: 279, Mismatches: 13, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 279 1.00
ACGTcount: A:0.41, C:0.01, G:0.11, T:0.46
Consensus pattern (49 bp):
TATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAATGAAAT
Found at i:6451554 original size:13 final size:14
Alignment explanation
Indices: 6451522--6451554 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
6451512 TATTAATTTT
*
6451522 TAATGATTTGATAC
1 TAATGATTTGATAA
6451536 TAATGATTTG-TAA
1 TAATGATTTGATAA
6451549 TAATGA
1 TAATGA
6451555 ATGGAGGGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (14 bp):
TAATGATTTGATAA
Found at i:6451669 original size:12 final size:12
Alignment explanation
Indices: 6451638--6451672 Score: 56
Period size: 11 Copynumber: 3.1 Consensus size: 12
6451628 TAACCATAAA
6451638 AATG-ATTTAAT
1 AATGAATTTAAT
6451649 AAT-AATTTAAT
1 AATGAATTTAAT
6451660 AATGAATTTAAT
1 AATGAATTTAAT
6451672 A
1 A
6451673 TTTGATGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 13 0.59
12 9 0.41
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (12 bp):
AATGAATTTAAT
Found at i:6451718 original size:26 final size:26
Alignment explanation
Indices: 6451689--6451891 Score: 198
Period size: 26 Copynumber: 7.9 Consensus size: 26
6451679 GATTTGATGA
* *
6451689 TTTAGTAATGATTTGATAATAATCAT
1 TTTAATAATGATTTAATAATAATCAT
* *
6451715 TTTAGTAATGATTTGATAATAATCAT
1 TTTAATAATGATTTAATAATAATCAT
* *
6451741 TATAATAATGATTTAGTAATAATCAT
1 TTTAATAATGATTTAATAATAATCAT
* *
6451767 TATAATAATGATTTAATAATAATGA-
1 TTTAATAATGATTTAATAATAATCAT
*
6451792 --TAATAATGATTTAATAATAATAAT
1 TTTAATAATGATTTAATAATAATCAT
** * *
6451816 GATAATAATGATTTAATAGTAATTA-
1 TTTAATAATGATTTAATAATAATCAT
* * *
6451841 TTTAGTAATGATTTTATAATAATGAT
1 TTTAATAATGATTTAATAATAATCAT
* *
6451867 TTAATACTAATGATTTAATAGTAAT
1 TT--TAATAATGATTTAATAATAAT
6451892 TTATTAATAA
Statistics
Matches: 153, Mismatches: 18, Indels: 10
0.85 0.10 0.06
Matches are distributed among these distances:
23 22 0.14
25 19 0.12
26 94 0.61
28 18 0.12
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.44
Consensus pattern (26 bp):
TTTAATAATGATTTAATAATAATCAT
Found at i:6451748 original size:3 final size:3
Alignment explanation
Indices: 6451730--6451824 Score: 52
Period size: 3 Copynumber: 32.7 Consensus size: 3
6451720 TAATGATTTG
* * * * * * * *
6451730 ATA ATA ATC ATT ATA ATA ATG AT- TTA GTA ATA ATC ATT ATA ATA ATG
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
6451777 AT- TTA ATA ATA ATG ATA ATA ATG AT- TTA ATA ATA ATA ATG ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
6451823 AT
1 AT
6451825 GATTTAATAG
Statistics
Matches: 69, Mismatches: 20, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
2 3 0.04
3 66 0.96
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (3 bp):
ATA
Found at i:6451796 original size:9 final size:9
Alignment explanation
Indices: 6451782--6451827 Score: 67
Period size: 9 Copynumber: 5.2 Consensus size: 9
6451772 TAATGATTTA
6451782 ATAATAATG
1 ATAATAATG
6451791 ATAATAATG
1 ATAATAATG
* *
6451800 AT-TTAATA
1 ATAATAATG
6451808 ATAATAATG
1 ATAATAATG
6451817 ATAATAATG
1 ATAATAATG
6451826 AT
1 AT
6451828 TTAATAGTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
8 6 0.19
9 26 0.81
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (9 bp):
ATAATAATG
Found at i:6451832 original size:17 final size:17
Alignment explanation
Indices: 6451786--6451818 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
6451776 GATTTAATAA
*
6451786 TAATGATAATAATGATT
1 TAATAATAATAATGATT
6451803 TAATAATAATAATGAT
1 TAATAATAATAATGAT
6451819 AATAATGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (17 bp):
TAATAATAATAATGATT
Found at i:6451964 original size:14 final size:13
Alignment explanation
Indices: 6451694--6451962 Score: 149
Period size: 14 Copynumber: 20.8 Consensus size: 13
6451684 GATGATTTAG
6451694 TAATGATTTGATAA
1 TAATGATTT-ATAA
* *
6451708 TAATCATTT-TAG
1 TAATGATTTATAA
6451720 TAATGATTTGATAA
1 TAATGATTT-ATAA
*
6451734 TAATCA-TTATAA
1 TAATGATTTATAA
6451746 TAATGATTTAGTAA
1 TAATGATTTA-TAA
*
6451760 TAATCA-TTATAA
1 TAATGATTTATAA
6451772 TAATGATTTAATAA
1 TAATGATTT-ATAA
6451786 TAATG----ATAA
1 TAATGATTTATAA
6451795 TAATGATTTAATAA
1 TAATGATTT-ATAA
* *
6451809 TAAT-AATGATAA
1 TAATGATTTATAA
*
6451821 TAATGATTTAATAG
1 TAATGATTT-ATAA
* *
6451835 TAATTA-TT-TAG
1 TAATGATTTATAA
6451846 TAATGATTTTATAA
1 TAATGA-TTTATAA
*
6451860 TAATGATTTAATAC
1 TAATGATTT-ATAA
6451874 TAATGA-TT-TAA
1 TAATGATTTATAA
* *
6451885 TAGTAATTTATTAA
1 TAATGATTTA-TAA
* *
6451899 TAAT-TTTTAAATATT
1 TAATGATTT--ATA-A
*
6451914 TAATGATTTGATAC
1 TAATGATTT-ATAA
6451928 TAATGATTTACTAA
1 TAATGATTTA-TAA
6451942 T--T-A-TTATTAA
1 TAATGATTTA-TAA
6451952 TAATGATTTAT
1 TAATGATTTAT
6451963 TATTAATATT
Statistics
Matches: 198, Mismatches: 28, Indels: 59
0.69 0.10 0.21
Matches are distributed among these distances:
9 9 0.05
10 7 0.04
11 15 0.08
12 39 0.20
13 29 0.15
14 88 0.44
15 8 0.04
16 3 0.02
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (13 bp):
TAATGATTTATAA
Found at i:6451979 original size:17 final size:17
Alignment explanation
Indices: 6451939--6451980 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
6451929 AATGATTTAC
6451939 TAATTATTATTAATAAT
1 TAATTATTATTAATAAT
* * *
6451956 GATTTATTATTAATATT
1 TAATTATTATTAATAAT
6451973 TAATTATT
1 TAATTATT
6451981 TGATACTAAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
TAATTATTATTAATAAT
Found at i:6451982 original size:59 final size:54
Alignment explanation
Indices: 6451860--6452040 Score: 171
Period size: 54 Copynumber: 3.4 Consensus size: 54
6451850 GATTTTATAA
* *
6451860 TAATGATTTAATACTAATGATTTAATAGTAATTTATTAATAATTTTTAAATATT
1 TAATGATTTGATACTAATGATTTAATAATAATTTATTAATAATTTTTAAATATT
* *
6451914 TAATGATTTGATACTAATGATTTACTAATTA-TTATTAATAATGATTTATTATTAATATT
1 TAATGATTTGATACTAATGATTTAATAATAATTTATTAAT-A--ATTT-TTA--AATATT
* * * *
6451973 TAATTATTTGATACTAATGA-TT--TAA-AA-TT-GTCA-AATTATTAAATATT
1 TAATGATTTGATACTAATGATTTAATAATAATTTATTAATAATTTTTAAATATT
*
6452020 TAATTATTTGATACTAATGAT
1 TAATGATTTGATACTAATGAT
6452041 ACTAGTAATG
Statistics
Matches: 111, Mismatches: 9, Indels: 20
0.79 0.06 0.14
Matches are distributed among these distances:
47 26 0.23
49 3 0.03
50 3 0.03
52 1 0.01
53 8 0.07
54 30 0.27
55 3 0.03
56 7 0.06
57 3 0.03
58 2 0.02
59 25 0.23
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.49
Consensus pattern (54 bp):
TAATGATTTGATACTAATGATTTAATAATAATTTATTAATAATTTTTAAATATT
Found at i:6453015 original size:23 final size:23
Alignment explanation
Indices: 6452989--6453033 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
6452979 AAAATTACAA
*
6452989 AAATAATAAAATTGATTTAAATC
1 AAATAATAAAATTAATTTAAATC
* *
6453012 AAATAATATAGTTAATTTAAAT
1 AAATAATAAAATTAATTTAAAT
6453034 AATAATTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (23 bp):
AAATAATAAAATTAATTTAAATC
Found at i:6454376 original size:22 final size:23
Alignment explanation
Indices: 6454343--6454390 Score: 80
Period size: 22 Copynumber: 2.1 Consensus size: 23
6454333 AAACAACTAA
*
6454343 TAAACTATTCTTTAATATAACTT
1 TAAACTATTCTTTAATATAACGT
6454366 TAAA-TATTCTTTAATATAACGT
1 TAAACTATTCTTTAATATAACGT
6454388 TAA
1 TAA
6454391 CTAATAAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.42, C:0.10, G:0.02, T:0.46
Consensus pattern (23 bp):
TAAACTATTCTTTAATATAACGT
Found at i:6454404 original size:30 final size:28
Alignment explanation
Indices: 6454337--6454444 Score: 113
Period size: 30 Copynumber: 3.9 Consensus size: 28
6454327 TCCCTTAAAC
6454337 AACTAATAAACTATTCTTTAATATAAC-T
1 AACTAATAAA-TATTCTTTAATATAACTT
6454365 ---T--TAAATATTCTTTAATATAACGTT
1 AACTAATAAATATTCTTTAATATAAC-TT
6454389 AACTAATAAACTATTCTTTAATATAACTT
1 AACTAATAAA-TATTCTTTAATATAACTT
6454418 AAACTAATAAATGATT-TTTAATTATAA
1 -AACTAATAAAT-ATTCTTTAA-TATAA
6454445 TTTATTACTA
Statistics
Matches: 69, Mismatches: 0, Indels: 20
0.78 0.00 0.22
Matches are distributed among these distances:
22 16 0.23
23 4 0.06
24 1 0.01
25 1 0.01
27 1 0.01
29 12 0.17
30 34 0.49
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.43
Consensus pattern (28 bp):
AACTAATAAATATTCTTTAATATAACTT
Found at i:6454421 original size:22 final size:22
Alignment explanation
Indices: 6454343--6454423 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 22
6454333 AAACAACTAA
6454343 TAAACTATTCTTTAATATAACTT
1 TAAACTATTCTTTAATATAAC-T
6454366 TAAA-TATTCTTTAATATAACGTTAACT
1 TAAACTATTCTTT-A-AT-A---TAACT
6454393 AATAAACTATTCTTTAATATAACT
1 --TAAACTATTCTTTAATATAACT
6454417 TAAACTA
1 TAAACTA
6454424 ATAAATGATT
Statistics
Matches: 49, Mismatches: 0, Indels: 19
0.72 0.00 0.28
Matches are distributed among these distances:
22 15 0.31
23 5 0.10
24 7 0.14
25 1 0.02
27 2 0.04
28 6 0.12
29 5 0.10
30 8 0.16
ACGTcount: A:0.43, C:0.12, G:0.01, T:0.43
Consensus pattern (22 bp):
TAAACTATTCTTTAATATAACT
Found at i:6454695 original size:21 final size:21
Alignment explanation
Indices: 6454642--6454681 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
6454632 TTTCTATATG
6454642 ATATAACTTAAACTAACAATA
1 ATATAACTTAAACTAACAATA
6454663 ATATAACTTAAACTAACAA
1 ATATAACTTAAACTAACAA
6454682 ACTAATTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (21 bp):
ATATAACTTAAACTAACAATA
Found at i:6454762 original size:18 final size:18
Alignment explanation
Indices: 6454709--6454763 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
6454699 TTGTTTTACC
*
6454709 CTAATTTATAATAATAAA
1 CTAATTTATAACAATAAA
6454727 CTAA--T-TAAC--T-AA
1 CTAATTTATAACAATAAA
6454739 -TAATTTATAACAATAAA
1 CTAATTTATAACAATAAA
6454756 CTAATTTA
1 CTAATTTA
6454764 AATAATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 14
0.66 0.02 0.32
Matches are distributed among these distances:
11 3 0.10
12 2 0.07
13 2 0.07
14 4 0.14
15 3 0.10
16 2 0.07
17 2 0.07
18 11 0.38
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (18 bp):
CTAATTTATAACAATAAA
Found at i:6454822 original size:35 final size:36
Alignment explanation
Indices: 6454783--6454854 Score: 103
Period size: 38 Copynumber: 2.0 Consensus size: 36
6454773 TTTTTTATAT
6454783 AACTTAAAC-TAATAAACT-ATTTTTTATTATAATAA
1 AACTTAAACATAATAAACTAATTTTTTA-TATAATAA
6454818 AACTTAAACTAATAATAAACTAATTTTTTATATAATA
1 AACTTAAAC--ATAATAAACTAATTTTTTATATAATA
6454855 TAAATTCAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
35 9 0.27
38 16 0.48
39 8 0.24
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (36 bp):
AACTTAAACATAATAAACTAATTTTTTATATAATAA
Found at i:6454825 original size:27 final size:28
Alignment explanation
Indices: 6454773--6454828 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
6454763 AAATAATTAT
*
6454773 TTTTTTATATAACTTAAACTAATAAACTA
1 TTTTTTATATAACTAAAACT-ATAAACTA
6454802 TTTTTTATTATAA-TAAAACT-TAAACTA
1 TTTTTTA-TATAACTAAAACTATAAACTA
6454829 ATAATAAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 7 0.28
29 13 0.52
30 5 0.20
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.46
Consensus pattern (28 bp):
TTTTTTATATAACTAAAACTATAAACTA
Found at i:6455053 original size:9 final size:9
Alignment explanation
Indices: 6455021--6455058 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
6455011 CTAACAAACT
6455021 AATAATTTAA
1 AATAA-TTAA
6455031 AATAA-TAA
1 AATAATTAA
*
6455039 ACTAATTAA
1 AATAATTAA
6455048 AATAATTAA
1 AATAATTAA
6455057 AA
1 AA
6455059 AACTTACCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 7 0.28
9 13 0.52
10 5 0.20
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (9 bp):
AATAATTAA
Found at i:6455280 original size:12 final size:11
Alignment explanation
Indices: 6455249--6455284 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
6455239 ACGTTCACGG
6455249 GCTGCAATAAT
1 GCTGCAATAAT
*
6455260 GCAGCAATAAGT
1 GCTGCAATAA-T
6455272 GCTGCAATAAT
1 GCTGCAATAAT
6455283 GC
1 GC
6455285 ATCTGATTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.22
Consensus pattern (11 bp):
GCTGCAATAAT
Found at i:6455391 original size:29 final size:28
Alignment explanation
Indices: 6455359--6455442 Score: 114
Period size: 29 Copynumber: 2.9 Consensus size: 28
6455349 GAAGGCATAG
*
6455359 GTCGTTGGGATCCCTTGGCGACCTACAAT
1 GTCGCTGGGATCCC-TGGCGACCTACAAT
6455388 GTCGCTGGGATGCCCTGGCGACCTACAAT
1 GTCGCTGGGAT-CCCTGGCGACCTACAAT
* *
6455417 GTCACTGGGATTCCCTGGTGACCTAC
1 GTCGCTGGGA-TCCCTGGCGACCTAC
6455443 CCACGTTGCC
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.17, C:0.30, G:0.29, T:0.25
Consensus pattern (28 bp):
GTCGCTGGGATCCCTGGCGACCTACAAT
Found at i:6455563 original size:60 final size:60
Alignment explanation
Indices: 6455462--6455582 Score: 224
Period size: 60 Copynumber: 2.0 Consensus size: 60
6455452 CATGCTGCCA
* *
6455462 CCAGACCCATGCCACGTTGCCATGCCGCCATGGACAGCCATGCAGAGACTCCAAGCTCGC
1 CCAGACCCATGCCACGTTGCCATGCCGCCATGCACAACCATGCAGAGACTCCAAGCTCGC
6455522 CCAGACCCATGCCACGTTGCCATGCCGCCATGCACAACCATGCAGAGACTCCAAGCTCGC
1 CCAGACCCATGCCACGTTGCCATGCCGCCATGCACAACCATGCAGAGACTCCAAGCTCGC
6455582 C
1 C
6455583 GGGATGCCGT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.24, C:0.41, G:0.21, T:0.13
Consensus pattern (60 bp):
CCAGACCCATGCCACGTTGCCATGCCGCCATGCACAACCATGCAGAGACTCCAAGCTCGC
Found at i:6459356 original size:21 final size:21
Alignment explanation
Indices: 6459328--6459382 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 21
6459318 CTAATGTGAG
6459328 AGGAGTATCGATACATGTTCA
1 AGGAGTATCGATACATGTTCA
* ** * *
6459349 AGGGGTATTAATA-TTGTTTA
1 AGGAGTATCGATACATGTTCA
6459369 AGGAGTATCGATAC
1 AGGAGTATCGATAC
6459383 TTAGGAGCCT
Statistics
Matches: 25, Mismatches: 8, Indels: 2
0.71 0.23 0.06
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.33, C:0.09, G:0.25, T:0.33
Consensus pattern (21 bp):
AGGAGTATCGATACATGTTCA
Found at i:6462486 original size:23 final size:23
Alignment explanation
Indices: 6462451--6462494 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
6462441 AGTGTAGAGC
*
6462451 TAGACAACTCAAA-ATTCATAAAT
1 TAGACAACACAAAGATT-ATAAAT
*
6462474 TAGATAACACAAAGATTATAA
1 TAGACAACACAAAGATTATAA
6462495 TGGCAAACGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 15 0.83
24 3 0.17
ACGTcount: A:0.55, C:0.14, G:0.07, T:0.25
Consensus pattern (23 bp):
TAGACAACACAAAGATTATAAAT
Found at i:6471721 original size:23 final size:22
Alignment explanation
Indices: 6471637--6471724 Score: 65
Period size: 22 Copynumber: 4.0 Consensus size: 22
6471627 TTTGATCAAA
* *
6471637 GTCAATAGTCAACG-GTCTGACCG
1 GTCAA-AGTCAATGAGT-TGACTG
*
6471660 GTCAAAGTCAATG-GTTAAC-G
1 GTCAAAGTCAATGAGTTGACTG
* * *
6471680 GTCAACGACTAACGAGTTGACTTG
1 GTCAAAGTC-AATGAGTTGAC-TG
6471704 GTCAAAGTCAATGAGTTGACT
1 GTCAAAGTCAATGAGTTGACT
6471725 CAGTGACTGG
Statistics
Matches: 52, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
20 8 0.15
21 6 0.12
22 15 0.29
23 15 0.29
24 8 0.15
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (22 bp):
GTCAAAGTCAATGAGTTGACTG
Found at i:6474871 original size:79 final size:77
Alignment explanation
Indices: 6474704--6474855 Score: 270
Period size: 79 Copynumber: 2.0 Consensus size: 77
6474694 GTGATCCTTC
6474704 TTCCTTTTGATTTTTAATTTTTTTTTAAATAAGTCATCTTTGAGATTATATTAGTTTACATTAAA
1 TTCCTTTTGATTTTTAATTTTTTTTTAAATAAGTCATCTTTGAGATTATATTAGTTTACATTAAA
6474769 TTTGAATTTAAA
66 TTTGAATTTAAA
*
6474781 TTCCTTTTGATTTTTAATTTTTGTTTTTAAATAAGTCATCTTTGAGATTATATTAGTTTACGTTA
1 TTCCTTTTGATTTTTAA-TTTT-TTTTTAAATAAGTCATCTTTGAGATTATATTAGTTTACATTA
6474846 AATTT-AATTT
64 AATTTGAATTT
6474856 TTGTTTTTAT
Statistics
Matches: 72, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
77 17 0.24
78 9 0.12
79 46 0.64
ACGTcount: A:0.29, C:0.07, G:0.09, T:0.56
Consensus pattern (77 bp):
TTCCTTTTGATTTTTAATTTTTTTTTAAATAAGTCATCTTTGAGATTATATTAGTTTACATTAAA
TTTGAATTTAAA
Found at i:6478442 original size:18 final size:18
Alignment explanation
Indices: 6478415--6478458 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
6478405 CTAGCTTCCC
6478415 TCACCGGAGGGAAGCCGG
1 TCACCGGAGGGAAGCCGG
*
6478433 TCATCGGAGGGAAGCCGG
1 TCACCGGAGGGAAGCCGG
6478451 TCACCGGA
1 TCACCGGA
6478459 CGACAACCGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.23, C:0.27, G:0.41, T:0.09
Consensus pattern (18 bp):
TCACCGGAGGGAAGCCGG
Found at i:6478697 original size:15 final size:15
Alignment explanation
Indices: 6478673--6478704 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
6478663 CCTCGGTAAG
6478673 TTTCTCTTCTTTCTT
1 TTTCTCTTCTTTCTT
*
6478688 TTTCTTTTCTTTCTT
1 TTTCTCTTCTTTCTT
6478703 TT
1 TT
6478705 CTGCTGTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTCTCTTCTTTCTT
Found at i:6479027 original size:16 final size:16
Alignment explanation
Indices: 6479006--6479048 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
6478996 CTGGACCGTT
6479006 GGCAGAGGCGGCTGGA
1 GGCAGAGGCGGCTGGA
6479022 GGCAGAGGCGGCTGGA
1 GGCAGAGGCGGCTGGA
6479038 GGCAGAGGCGG
1 GGCAGAGGCGG
6479049 TTTGGCCATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.19, C:0.19, G:0.58, T:0.05
Consensus pattern (16 bp):
GGCAGAGGCGGCTGGA
Found at i:6479143 original size:3 final size:3
Alignment explanation
Indices: 6479135--6479202 Score: 111
Period size: 3 Copynumber: 22.7 Consensus size: 3
6479125 GGCCCGTTTG
*
6479135 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TCA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
6479182 TAA TAA TAAA TAA TAA TAA TA
1 TAA TAA T-AA TAA TAA TAA TA
6479203 GTAAATAAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
2 2 0.03
3 56 0.92
4 3 0.05
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:6479706 original size:113 final size:113
Alignment explanation
Indices: 6479512--6480191 Score: 872
Period size: 113 Copynumber: 6.0 Consensus size: 113
6479502 TAGAATTATG
** *
6479512 CAAAAAGTTGAACAAGCTCTTCTTATTATGAAC---TTCTT-CTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
6479573 TTATGAACTTTACCTGGCAATGTTAATCCATTGAATGATGGATTTAAA
66 TTATGAACTCTACCTGGCAATGTTAATCCATTGAATGATGGATTTAAA
* * *
6479621 CAAAAGGTTGAACAAATTCTTCTTATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTAA
1 CAAAAAGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
6479686 TTATGGACTCTACCTGGCAATGTTAATCCATTGAATGATGGATTTAAA
66 TTATGAACTCTACCTGGCAATGTTAATCCATTGAATGATGGATTTAAA
6479734 CAAAAAGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGACGAGTTCTTC
1 CAAAAAGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGAT---GAGTTCTTC
* * * ** *
6479799 TTATTATGAACTCTACCTGGTAATGTTGATCCATCAAATGATGAATTTAAA
63 TCATTATGAACTCTACCTGGCAATGTTAATCCATTGAATGATGGATTTAAA
6479850 CAAAAAGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGACGAGTTCTTC
1 CAAAAAGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGAT---GAGTTCTTC
* * ** * * *
6479915 TTATTATGAACTCTACCTGGCAATGTTGATCCATCAAATAATGAATTCAAA
63 TCATTATGAACTCTACCTGGCAATGTTAATCCATTGAATGATGGATTTAAA
* *
6479966 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * * * * * *
6480031 TTATGAACT-TTCTCTAGAAAAGATAATCCA-TCAAGTGATAGATTTGAGA
66 TTATGAACTCTAC-CTGGCAATGTTAATCCATTGAA-TGATGGATTT-AAA
* * *
6480080 -AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * *
6480144 TTATGAACT-TTCTCTGGAAAAGCTAATCCATTGAATGATGGATTTAAA
66 TTATGAACTCTAC-CTGGCAATGTTAATCCATTGAATGATGGATTTAAA
6480192 TCTTTGCTAA
Statistics
Matches: 518, Mismatches: 42, Indels: 19
0.89 0.07 0.03
Matches are distributed among these distances:
109 30 0.06
112 11 0.02
113 255 0.49
114 5 0.01
116 217 0.42
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (113 bp):
CAAAAAGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTCTACCTGGCAATGTTAATCCATTGAATGATGGATTTAAA
Found at i:6480025 original size:229 final size:225
Alignment explanation
Indices: 6479512--6480152 Score: 871
Period size: 229 Copynumber: 2.8 Consensus size: 225
6479502 TAGAATTATG
* *
6479512 CAAAAAGTTGAACAAGCTCTTCTTATTATGAA---CTTCTT-CTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* ** *
6479573 TTATGAACTTTACCTGGCAATGTTAATCCATTGAATGATGGATTTAAACAAAAGGTTGAACAAAT
66 TTATGAAC-TTACCTGGAAATGTTAATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAAAT
* *
6479638 TCTTCTTATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTAATTATGGACTCTACCTGG
130 TCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTAATTATGAACTCTACCTGG
** * * *
6479703 CAATGTTAATCCATTGAATGATGGATTTAAA
195 CAATGTTAATCCATCAAATAATGAATTCAAA
* *
6479734 CAAAAAGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGACGAGTTCTTC
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTC
* * * *
6479799 TTATTATGAACTCTACCTGGTAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACA
63 TCATTATGAACT-TACCTGGAAATGTTAATCCATCAAATGATGAATTTAAACAAAAGGTTGAACA
*
6479864 AATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGACGAGTTCTTCTTATTATGAACTCT
127 AATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGAT---GAGTTCTTCTAATTATGAACTCT
*
6479929 ACCTGGCAATGTTGATCCATCAAATAATGAATTCAAA
189 ACCTGGCAATGTTAATCCATCAAATAATGAATTCAAA
6479966 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * * * *
6480031 TTATGAACTTTCTCTAGAAAAGATAATCCATCAAGTGAT-AGATTTGAGA-AAAAGGTTGAACAA
66 TTATGAACTTAC-CTGGAAATGTTAATCCATCAAATGATGA-ATTT-AAACAAAAGGTTGAACAA
* * *
6480094 ATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
128 ATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTAATTATGAACT
6480153 TTCTCTGGAA
Statistics
Matches: 370, Mismatches: 35, Indels: 24
0.86 0.08 0.06
Matches are distributed among these distances:
222 29 0.08
225 5 0.01
226 31 0.08
228 4 0.01
229 196 0.53
230 2 0.01
232 103 0.28
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (225 bp):
CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTACCTGGAAATGTTAATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAAATT
CTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTAATTATGAACTCTACCTGGC
AATGTTAATCCATCAAATAATGAATTCAAA
Found at i:6481216 original size:83 final size:83
Alignment explanation
Indices: 6480977--6481577 Score: 885
Period size: 83 Copynumber: 7.3 Consensus size: 83
6480967 CTTATTTCTA
* * *
6480977 CTATGAGCAAATTCATCTTCCAAATTTAATGATTGGTTTTGTCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
*
6481042 GAACACTTCCATAAGATG
66 GAACACTTCCAGAAGATG
* * * * *
6481060 ATATTG-GCAAATTCATCTTCTAATTTCAATAATTGGTT-TACCAAACCAGATCAGATAACTCAA
1 CTA-TGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAA
6481123 AGAACACTTCCAGAAGATG
65 AGAACACTTCCAGAAGATG
* *
6481142 CTATGAGCACATTCATCTTCCCAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
6481207 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* *
6481225 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGTTC-AACCAGATCAGATAACTCAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTG-CCAAACCAGATCAGATAACTCAA
6481289 AGAACACTTCCAGAAGATG
65 AGAACACTTCCAGAAGATG
* * * *
6481308 TTATTG-GCAAATTCATCTTCTAAATTCACTGATTGGTT-TACCAAACCAGATCAGATAACTCAA
1 CTA-TGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAA
6481371 AGAACACTTCCAGAAGATG
65 AGAACACTTCCAGAAGATG
* *
6481390 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGTTC-AACCAGATCAGATAACTCAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTG-CCAAACCAGATCAGATAACTCAA
6481454 AGAACACTTCCAGAAGATG
65 AGAACACTTCCAGAAGATG
* *
6481473 CTATTG-GCAAATTCATCTTCTAAATTCAATGATTGGTTTTGTCC-AACCAGATCAGATAACTCA
1 CTA-TGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTG-CCAAACCAGATCAGATAACTCA
*
6481536 AAGAACATTTCCAGAAGATG
64 AAGAACACTTCCAGAAGATG
*
6481556 CTATGAGCACATTCATCTTCCA
1 CTATGAGCAAATTCATCTTCCA
6481578 GTTAATGTTT
Statistics
Matches: 471, Mismatches: 36, Indels: 22
0.89 0.07 0.04
Matches are distributed among these distances:
81 5 0.01
82 143 0.30
83 315 0.67
84 8 0.02
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.29
Consensus pattern (83 bp):
CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATG
Found at i:6481262 original size:165 final size:166
Alignment explanation
Indices: 6480983--6481577 Score: 941
Period size: 165 Copynumber: 3.6 Consensus size: 166
6480973 TCTACTATGA
* *
6480983 GCAAATTCATCTTCCAAATTTAATGATTGGTTTTGTCAAACCAGATCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCCAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAAGAACAC
* * * * * * **
6481048 TTCCATAAGATGATATTG-GCAAATTCATCTTCTAATTTCAATAATTGGTT-T-ACCAAACCAGA
66 TTCCAGAAGATGCTA-TGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGTTC-AACCAGA
6481110 TCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TG
129 TCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG
* * *
6481147 AGCACATTCATCTTCCCAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACA
1 -GCAAATTCATCTTCCAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAAGAACA
6481212 CTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGTTCAACCAGAT
65 CTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGTTCAACCAGAT
*
6481277 CAGATAACTCAAAGAACACTTCCAGAAGATGTTATTG
130 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG
* * *
6481314 GCAAATTCATCTTCTAAATTCACTGATTGG-TTTACCAAACCAGATCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCCAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAAGAACAC
6481378 TTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGTTCAACCAGATC
66 TTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGTTCAACCAGATC
6481443 AGATAACTCAAAGAACACTTCCAGAAGATGCTATTG
131 AGATAACTCAAAGAACACTTCCAGAAGATGCTATTG
*
6481479 GCAAATTCATCTTCTAAATTCAATGATTGGTTTTGTCC-AACCAGATCAGATAACTCAAAGAACA
1 GCAAATTCATCTTCCAAATTCAATGATTGGTTTTG-CCAAACCAGATCAGATAACTCAAAGAACA
*
6481543 TTTCCAGAAGATGCTATGAGCACATTCATCTTCCA
65 CTTCCAGAAGATGCTATGAGCACATTCATCTTCCA
6481578 GTTAATGTTT
Statistics
Matches: 400, Mismatches: 24, Indels: 11
0.92 0.06 0.03
Matches are distributed among these distances:
164 2 0.00
165 262 0.65
166 131 0.33
167 5 0.01
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.29
Consensus pattern (166 bp):
GCAAATTCATCTTCCAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAAGAACAC
TTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGTTCAACCAGATC
AGATAACTCAAAGAACACTTCCAGAAGATGCTATTG
Found at i:6481418 original size:248 final size:248
Alignment explanation
Indices: 6480977--6481575 Score: 999
Period size: 248 Copynumber: 2.4 Consensus size: 248
6480967 CTTATTTCTA
*
6480977 CTATGAGCAAATTCATCTTCCAAATTTAATGATTGGTTTTG-TCAAACCAGATCAGATAACTCAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTTTGTTC-AACCAGATCAGATAACTCAA
* *
6481041 AGAACACTTCCATAAGATGATATTGGCAAATTCATCTTCTAATTTCAATAATTGGTTTACCAAAC
65 AGAACACTTCCAGAAGATGATATTGGCAAATTCATCTTCTAAATTCAATAATTGGTTTACCAAAC
*
6481106 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCCAATTCAA
130 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATTCAA
6481171 TGATTGGTTCTG-CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
195 TGATTGGTTCTGTCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
* *
6481225 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGTTCAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTTTGTTCAACCAGATCAGATAACTCAAA
* * *
6481290 GAACACTTCCAGAAGATGTTATTGGCAAATTCATCTTCTAAATTCACTGATTGGTTTACCAAACC
66 GAACACTTCCAGAAGATGATATTGGCAAATTCATCTTCTAAATTCAATAATTGGTTTACCAAACC
6481355 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATTCAAT
131 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATTCAAT
*
6481420 GATTGGTTCTGTTCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
196 GATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
* *
6481473 CTATTG-GCAAATTCATCTTCTAAATTCAATGATTGGTTTTGTCCAACCAGATCAGATAACTCAA
1 CTA-TGAGCAAATTCATCTTCCAAATTCAATGATTGGTTTTGTTCAACCAGATCAGATAACTCAA
* * *
6481537 AGAACATTTCCAGAAGATGCTA-TGAGCACATTCATCTTC
65 AGAACACTTCCAGAAGATGATATTG-GCAAATTCATCTTC
6481576 CAGTTAATGT
Statistics
Matches: 330, Mismatches: 17, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
247 2 0.01
248 323 0.98
249 5 0.02
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.29
Consensus pattern (248 bp):
CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTTTGTTCAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATGATATTGGCAAATTCATCTTCTAAATTCAATAATTGGTTTACCAAACC
AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATTCAAT
GATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
Found at i:6482392 original size:18 final size:19
Alignment explanation
Indices: 6482337--6482386 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
6482327 TCAATAAAAG
6482337 AATAAATTGAATTTTCAAA
1 AATAAATTGAATTTTCAAA
6482356 AATAAATTGAATTTTCAAA
1 AATAAATTGAATTTTCAAA
6482375 AATAAATTGAAT
1 AATAAATTGAAT
6482387 CTCAAATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.36
Consensus pattern (19 bp):
AATAAATTGAATTTTCAAA
Found at i:6482395 original size:16 final size:18
Alignment explanation
Indices: 6482337--6482399 Score: 76
Period size: 19 Copynumber: 3.5 Consensus size: 18
6482327 TCAATAAAAG
*
6482337 AATAAATTGAATTTTCAAA
1 AATAAATTGAATTCTC-AA
*
6482356 AATAAATTGAATTTTCAAA
1 AATAAATTGAATTCTC-AA
6482375 AATAAATTGAA-TCTC-A
1 AATAAATTGAATTCTCAA
6482391 AATAAATTG
1 AATAAATTG
6482400 GACTTGAAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
16 10 0.23
18 3 0.07
19 30 0.70
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.35
Consensus pattern (18 bp):
AATAAATTGAATTCTCAA
Found at i:6482756 original size:19 final size:19
Alignment explanation
Indices: 6482732--6482810 Score: 75
Period size: 18 Copynumber: 4.5 Consensus size: 19
6482722 GACCCCCCCC
6482732 CTTTTTCTTCTTTTTTTCT
1 CTTTTTCTTCTTTTTTTCT
6482751 C-TTTT-TTC-TTTTTTCT
1 CTTTTTCTTCTTTTTTTCT
* *
6482767 -TTTAT-TTCTTTTTTTTT
1 CTTTTTCTTCTTTTTTTCT
6482784 C-TTTTCTT-TCTTTTTTCT
1 CTTTTTCTTCT-TTTTTTCT
6482802 -TTTTTCTTC
1 CTTTTTCTTC
6482811 AAGCGTAATA
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
16 14 0.29
17 14 0.29
18 20 0.41
19 1 0.02
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.81
Consensus pattern (19 bp):
CTTTTTCTTCTTTTTTTCT
Found at i:6482760 original size:7 final size:7
Alignment explanation
Indices: 6482733--6482809 Score: 79
Period size: 7 Copynumber: 11.1 Consensus size: 7
6482723 ACCCCCCCCC
6482733 TTTTTCT
1 TTTTTCT
*
6482740 TCTTT-T
1 TTTTTCT
*
6482746 TTTCTCT
1 TTTTTCT
6482753 TTTTTCT
1 TTTTTCT
6482760 TTTTTCTT
1 TTTTTC-T
6482768 TTATTTCT
1 TT-TTTCT
6482776 TTTTT-T
1 TTTTTCT
*
6482782 TTCTT-T
1 TTTTTCT
*
6482788 TCTTTCT
1 TTTTTCT
6482795 TTTTTCT
1 TTTTTCT
6482802 TTTTTCT
1 TTTTTCT
6482809 T
1 T
6482810 CAAGCGTAAT
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
6 13 0.22
7 35 0.60
8 6 0.10
9 4 0.07
ACGTcount: A:0.01, C:0.16, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTTTCT
Found at i:6482764 original size:16 final size:16
Alignment explanation
Indices: 6482743--6482804 Score: 72
Period size: 16 Copynumber: 3.7 Consensus size: 16
6482733 TTTTTCTTCT
6482743 TTTTTTCTCTTT-TTTC
1 TTTTTTCT-TTTATTTC
6482759 TTTTTTCTTTTATTTC
1 TTTTTTCTTTTATTTC
*
6482775 TTTTTTTTTCTTTTCTTTC
1 ---TTTTTTCTTTTATTTC
6482794 TTTTTTCTTTT
1 TTTTTTCTTTT
6482805 TTCTTCAAGC
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
15 3 0.07
16 23 0.56
19 15 0.37
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTTCTTTTATTTC
Found at i:6482794 original size:35 final size:36
Alignment explanation
Indices: 6482735--6482804 Score: 117
Period size: 35 Copynumber: 2.0 Consensus size: 36
6482725 CCCCCCCCTT
6482735 TTTCTTCTTTTTTTCTCTTTTTTCTTTTTTCTTTTA
1 TTTCTTCTTTTTTTCTCTTTTTTCTTTTTTCTTTTA
6482771 TTTCTT-TTTTTTTCT-TTTCTTTCTTTTTTCTTTT
1 TTTCTTCTTTTTTTCTCTTT-TTTCTTTTTTCTTTT
6482805 TTCTTCAAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
34 3 0.09
35 24 0.73
36 6 0.18
ACGTcount: A:0.01, C:0.16, G:0.00, T:0.83
Consensus pattern (36 bp):
TTTCTTCTTTTTTTCTCTTTTTTCTTTTTTCTTTTA
Found at i:6491128 original size:16 final size:16
Alignment explanation
Indices: 6491109--6491161 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
6491099 AAATTTAAAA
*
6491109 AATTCAAAATATATTT
1 AATTTAAAATATATTT
*
6491125 AATTTATAATCATA-TT
1 AATTTAAAAT-ATATTT
*
6491141 ATTTTAAAATATATTT
1 AATTTAAAATATATTT
6491157 -ATTTA
1 AATTTA
6491162 TTTAAAATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
15 7 0.23
16 20 0.67
17 3 0.10
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (16 bp):
AATTTAAAATATATTT
Found at i:6491154 original size:15 final size:16
Alignment explanation
Indices: 6491114--6491160 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
6491104 TAAAAAATTC
*
6491114 AAAATATATTTAATTT
1 AAAATATATTTATTTT
*
6491130 ATAATCATA-TTATTTT
1 AAAAT-ATATTTATTTT
6491146 AAAATATATTTATTT
1 AAAATATATTTATTT
6491161 ATTTAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 3 0.12
16 20 0.77
17 3 0.12
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (16 bp):
AAAATATATTTATTTT
Found at i:6491358 original size:28 final size:28
Alignment explanation
Indices: 6491315--6491371 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
6491305 CTTCGATATA
6491315 AAAAATAAATATTAAAATAA-AATTTATT
1 AAAAATAAATATT-AAATAATAATTTATT
*
6491343 AAAAA-AAATATATAAATAATTATTTATT
1 AAAAATAAATAT-TAAATAATAATTTATT
6491371 A
1 A
6491372 TATATATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 12 0.46
28 14 0.54
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (28 bp):
AAAAATAAATATTAAATAATAATTTATT
Found at i:6492273 original size:15 final size:15
Alignment explanation
Indices: 6492249--6492280 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
6492239 CCTCGGTAAG
6492249 TTTCTCTTCTTTCTT
1 TTTCTCTTCTTTCTT
*
6492264 TTTCTTTTCTTTCTT
1 TTTCTCTTCTTTCTT
6492279 TT
1 TT
6492281 CTGCTGTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTCTCTTCTTTCTT
Found at i:6492718 original size:3 final size:3
Alignment explanation
Indices: 6492710--6492773 Score: 121
Period size: 3 Copynumber: 21.7 Consensus size: 3
6492700 GGCCCGTTTG
6492710 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
6492757 TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA
6492774 GTAAATAAAA
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 58 0.97
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:6503017 original size:2 final size:2
Alignment explanation
Indices: 6502953--6503000 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
6502943 ATTAAAAATC
6502953 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
6502995 AT AT AT
1 AT AT AT
6503001 TAACTCTAGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6504717 original size:16 final size:17
Alignment explanation
Indices: 6504696--6504732 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
6504686 TAACCGGTGA
6504696 TGGATTTA-GTTTTGGT
1 TGGATTTACGTTTTGGT
6504712 TGGATTTACCGTTTTGGT
1 TGGATTTA-CGTTTTGGT
6504730 TGG
1 TGG
6504733 GTTCCTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.42
18 11 0.58
ACGTcount: A:0.11, C:0.05, G:0.32, T:0.51
Consensus pattern (17 bp):
TGGATTTACGTTTTGGT
Found at i:6506919 original size:25 final size:26
Alignment explanation
Indices: 6506882--6506932 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
6506872 TTTGTACTGT
6506882 GATATTTTCCAATCATTCAAA-TCAA
1 GATATTTTCCAATCATTCAAAGTCAA
6506907 GATA-TTTCACAATCATTCAAAGTCAA
1 GATATTTTC-CAATCATTCAAAGTCAA
6506933 CCATGATGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 4 0.17
25 16 0.67
26 4 0.17
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.33
Consensus pattern (26 bp):
GATATTTTCCAATCATTCAAAGTCAA
Found at i:6512190 original size:2 final size:2
Alignment explanation
Indices: 6512178--6512260 Score: 150
Period size: 2 Copynumber: 41.5 Consensus size: 2
6512168 ATTCGGGATA
6512178 AT AT CAT 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
6512221 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6512261 CGTACAACAA
Statistics
Matches: 79, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.01
2 76 0.96
3 2 0.03
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6513956 original size:16 final size:17
Alignment explanation
Indices: 6513935--6513971 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
6513925 TAACCGGTGA
6513935 TGGATTTA-GTTTTGGT
1 TGGATTTACGTTTTGGT
6513951 TGGATTTACCGTTTTGGT
1 TGGATTTA-CGTTTTGGT
6513969 TGG
1 TGG
6513972 GTTCCTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.42
18 11 0.58
ACGTcount: A:0.11, C:0.05, G:0.32, T:0.51
Consensus pattern (17 bp):
TGGATTTACGTTTTGGT
Found at i:6524505 original size:220 final size:222
Alignment explanation
Indices: 6524123--6524567 Score: 867
Period size: 220 Copynumber: 2.0 Consensus size: 222
6524113 ACTAATATTG
6524123 AAATTGTTTCTTATTAATCTTCTAGTTCCTTAAAAAGTTAATCGAGTCTTATTTAGTTTACTAAT
1 AAATTGTTTCTTATTAATCTTCTAGTTCCTTAAAAAGTTAATCGAGTCTTATTTAGTTTACTAAT
6524188 TTTATACCATATTCATTTTGATTCTAGTAATAATTAAATATATATAGTTGAAAATTTGTTTCCAT
66 TTTATACCATATTCATTTTGATTCTAGTAATAATTAAATATATATAGTTGAAAATTTGTTTCCAT
6524253 TCATGCTTTTACTAATTATCAACTAGTTCAGTAAAGCTACAAAACGTAGT-AGTATTACCTTGA-
131 TCATGCTTTTACTAATTATCAACTAGTTCAGTAAAGCTACAAAACGTAGTAAGTATTACCTTGAT
6524316 TTTTAGGCACATCGGCTAGACATTACA
196 TTTTAGGCACATCGGCTAGACATTACA
6524343 AAATTGTTTCTTATTAATCTTCTAGTTCCTTAAAAAGTTAATCGAGTCTTATTTAGTTTACTAAT
1 AAATTGTTTCTTATTAATCTTCTAGTTCCTTAAAAAGTTAATCGAGTCTTATTTAGTTTACTAAT
6524408 TTTATACCATATTCATTTTGATTCTAGTAATAATTAAATATATATAGTTGAAAATTTGTTTCCAT
66 TTTATACCATATTCATTTTGATTCTAGTAATAATTAAATATATATAGTTGAAAATTTGTTTCCAT
6524473 TCATGCTTTTACTAATTATCAACTAGTTCAGTAAAGCTACAAAACGTAGTAGAGTATTACCTTGA
131 TCATGCTTTTACTAATTATCAACTAGTTCAGTAAAGCTACAAAACGTAGTA-AGTATTACCTTGA
6524538 TTTTTAGGCACATCGGCTAGACATTACA
195 TTTTTAGGCACATCGGCTAGACATTACA
6524566 AA
1 AA
6524568 TCCATTCGAT
Statistics
Matches: 222, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
220 180 0.81
222 13 0.06
223 29 0.13
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (222 bp):
AAATTGTTTCTTATTAATCTTCTAGTTCCTTAAAAAGTTAATCGAGTCTTATTTAGTTTACTAAT
TTTATACCATATTCATTTTGATTCTAGTAATAATTAAATATATATAGTTGAAAATTTGTTTCCAT
TCATGCTTTTACTAATTATCAACTAGTTCAGTAAAGCTACAAAACGTAGTAAGTATTACCTTGAT
TTTTAGGCACATCGGCTAGACATTACA
Found at i:6527436 original size:21 final size:21
Alignment explanation
Indices: 6527404--6527526 Score: 58
Period size: 21 Copynumber: 5.8 Consensus size: 21
6527394 TTTTAATAAT
* *
6527404 ATATAAAA--AAATTTATATG
1 ATATAAAATTAAATATATATA
*
6527423 ATATAAAATTAAATATCTATA
1 ATATAAAATTAAATATATATA
* *
6527444 ATATAATATTAAA-AAAT-TA
1 ATATAAAATTAAATATATATA
** * *
6527463 ATATTTAATTTTAAA-AAAAATTA
1 ATA--TAAAATTAAATATATA-TA
* *
6527486 ATATTGAAATTAAAATCAAATATA
1 ATA-TAAAATT-AAAT-ATATATA
6527510 ATATAAAATTAAATATA
1 ATATAAAATTAAATATA
6527527 AAACCTCTTT
Statistics
Matches: 81, Mismatches: 14, Indels: 16
0.73 0.13 0.14
Matches are distributed among these distances:
19 13 0.16
20 2 0.02
21 34 0.42
22 9 0.11
23 14 0.17
24 5 0.06
25 4 0.05
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
ATATAAAATTAAATATATATA
Found at i:6527466 original size:19 final size:20
Alignment explanation
Indices: 6527442--6527500 Score: 59
Period size: 23 Copynumber: 2.9 Consensus size: 20
6527432 TAAATATCTA
6527442 TAATA-TAATATTAAAAAAT
1 TAATATTAATATTAAAAAAT
*
6527461 TAATATTTAATTTTAAAAAAAAT
1 TAATA-TTAATATT--AAAAAAT
6527484 TAATATTGAA-ATTAAAA
1 TAATATT-AATATTAAAA
6527501 TCAAATATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
19 5 0.15
20 4 0.12
21 6 0.18
22 4 0.12
23 14 0.42
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (20 bp):
TAATATTAATATTAAAAAAT
Found at i:6527506 original size:23 final size:22
Alignment explanation
Indices: 6527454--6527522 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 22
6527444 ATATAATATT
**
6527454 AAAAAATTAATATTTAATTTTAA
1 AAAAAATTAATA-TTAAAATTAA
*
6527477 AAAAAATTAATATTGAAATTAA
1 AAAAAATTAATATTAAAATTAA
*
6527499 AATCAAATATAATA-TAAAATTAA
1 AA-AAAAT-TAATATTAAAATTAA
6527522 A
1 A
6527523 TATAAAACCT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
22 9 0.23
23 25 0.64
24 5 0.13
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (22 bp):
AAAAAATTAATATTAAAATTAA
Found at i:6531300 original size:19 final size:19
Alignment explanation
Indices: 6531259--6531300 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
6531249 CACAATTATT
*
6531259 CACTTCTTAATACTGACTA
1 CACTTCTTAATACTAACTA
*
6531278 CACTTCTTAATACTAACTG
1 CACTTCTTAATACTAACTA
6531297 CACT
1 CACT
6531301 ATTTGAACTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.05, T:0.36
Consensus pattern (19 bp):
CACTTCTTAATACTAACTA
Found at i:6536720 original size:14 final size:14
Alignment explanation
Indices: 6536688--6536731 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
6536678 TTTTGTCAAA
6536688 GTCAACAGTCAAC-G
1 GTCAA-AGTCAACGG
* *
6536702 ATCAAAGTCAATGG
1 GTCAAAGTCAACGG
6536716 GTCAAAGTCAACGG
1 GTCAAAGTCAACGG
6536730 GT
1 GT
6536732 TGACTCGGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
13 6 0.24
14 19 0.76
ACGTcount: A:0.36, C:0.20, G:0.25, T:0.18
Consensus pattern (14 bp):
GTCAAAGTCAACGG
Found at i:6540695 original size:15 final size:15
Alignment explanation
Indices: 6540667--6540728 Score: 106
Period size: 15 Copynumber: 4.1 Consensus size: 15
6540657 TAATAAAGTA
*
6540667 TATCTTTGTCAACTTG
1 TATCTTT-TCAACTTT
6540683 TATCTTTTCAACTTT
1 TATCTTTTCAACTTT
6540698 TATCTTTTCAACTTT
1 TATCTTTTCAACTTT
6540713 TATCTTTTCAACTTT
1 TATCTTTTCAACTTT
6540728 T
1 T
6540729 CTATCTATAT
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
15 38 0.84
16 7 0.16
ACGTcount: A:0.19, C:0.19, G:0.03, T:0.58
Consensus pattern (15 bp):
TATCTTTTCAACTTT
Found at i:6540697 original size:8 final size:8
Alignment explanation
Indices: 6540686--6540729 Score: 56
Period size: 8 Copynumber: 5.8 Consensus size: 8
6540676 CAACTTGTAT
6540686 CTTTTCAA
1 CTTTTCAA
*
6540694 CTTTT-AT
1 CTTTTCAA
6540701 CTTTTCAA
1 CTTTTCAA
*
6540709 CTTTT-AT
1 CTTTTCAA
6540716 CTTTTCAA
1 CTTTTCAA
6540724 CTTTTC
1 CTTTTC
6540730 TATCTATATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
7 12 0.40
8 18 0.60
ACGTcount: A:0.18, C:0.23, G:0.00, T:0.59
Consensus pattern (8 bp):
CTTTTCAA
Found at i:6541120 original size:23 final size:23
Alignment explanation
Indices: 6541086--6541136 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
6541076 AAAAACAAGA
6541086 TAAAAAAATAGTGAAAGTTCGAC
1 TAAAAAAATAGTGAAAGTTCGAC
* * * *
6541109 TAAAAAATTAGTGGAAGTTTGAT
1 TAAAAAAATAGTGAAAGTTCGAC
6541132 TAAAA
1 TAAAA
6541137 GTTAGAACTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.51, C:0.04, G:0.18, T:0.27
Consensus pattern (23 bp):
TAAAAAAATAGTGAAAGTTCGAC
Found at i:6542059 original size:2 final size:2
Alignment explanation
Indices: 6542052--6542082 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6542042 ATACACAAAC
6542052 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 A
6542083 ATACCTATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6542604 original size:37 final size:37
Alignment explanation
Indices: 6542541--6542691 Score: 126
Period size: 37 Copynumber: 4.1 Consensus size: 37
6542531 AAGTAAATTG
* * *
6542541 TCTCAA-ACGAGAAGAAATTTGCTTTTAAGGAAAAGAA
1 TCTCAAGA-GAGACGAAATTTGTTTTTAAGGAAAACAA
* * * *
6542578 TCTTAAGTGAGATGAAATTTGTTTTTATGGAAAAACAA
1 TCTCAAGAGAGACGAAATTTGTTTTTAAGG-AAAACAA
* * * * *
6542616 TCTCGAGAGAGACGAAGTTCGTTTTTAAGTAAAATAA
1 TCTCAAGAGAGACGAAATTTGTTTTTAAGGAAAACAA
* * * *
6542653 TATCAAGAGAGACGGAATTT-ATTTTAAGAAAAACAA
1 TCTCAAGAGAGACGAAATTTGTTTTTAAGGAAAACAA
6542689 TCT
1 TCT
6542692 TAAATGAGAT
Statistics
Matches: 88, Mismatches: 24, Indels: 5
0.75 0.21 0.04
Matches are distributed among these distances:
36 15 0.17
37 45 0.51
38 28 0.32
ACGTcount: A:0.42, C:0.09, G:0.19, T:0.30
Consensus pattern (37 bp):
TCTCAAGAGAGACGAAATTTGTTTTTAAGGAAAACAA
Found at i:6542935 original size:37 final size:36
Alignment explanation
Indices: 6542778--6543005 Score: 185
Period size: 36 Copynumber: 6.3 Consensus size: 36
6542768 AAAATTTCAT
*
6542778 TTTTAAGAAAAACAATCTCAAGTGAAAT-AAGATTTG
1 TTTTAAGAAAAACAATCTCAAGTGAGATGAA-ATTTG
* * **
6542814 TTTTGAGAAAAACAATCTAAAAAGA-AGTGAAATTTG
1 TTTTAAGAAAAACAATCTCAAGTGAGA-TGAAATTTG
* * * * **
6542850 TTTTGAGAAAAACAAACTCTAGTGAGA-CAAAAAT-
1 TTTTAAGAAAAACAATCTCAAGTGAGATGAAATTTG
* * * *
6542884 ATCTAAGTAAAACAATCTCAAGTGAGATGAAATTTTA
1 TTTTAAGAAAAACAATCTCAAGTGAGATGAAA-TTTG
* * *
6542921 TTTTAAGAAAAACAATCTTAAGAGAGATAAAATTTTG
1 TTTTAAGAAAAACAATCTCAAGTGAGATGAAA-TTTG
** * *
6542958 TTCCAAGAAAAACAATCTCAAATGAGAGGAAATTTG
1 TTTTAAGAAAAACAATCTCAAGTGAGATGAAATTTG
*
6542994 TCTTAAGAAAAA
1 TTTTAAGAAAAA
6543006 AATTAAGTAA
Statistics
Matches: 148, Mismatches: 38, Indels: 12
0.75 0.19 0.06
Matches are distributed among these distances:
34 21 0.14
35 8 0.05
36 61 0.41
37 58 0.39
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.28
Consensus pattern (36 bp):
TTTTAAGAAAAACAATCTCAAGTGAGATGAAATTTG
Found at i:6548932 original size:23 final size:22
Alignment explanation
Indices: 6548890--6548941 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
6548880 TCCAGAAGGA
* *
6548890 CCACATAGTTTGCACTGAAGTG
1 CCACATAGGTTGCACCGAAGTG
6548912 CCACATAGGGTTGCACCGAAGTG
1 CCACATA-GGTTGCACCGAAGTG
6548935 CCACATA
1 CCACATA
6548942 TTTGTCCCGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 7 0.26
23 20 0.74
ACGTcount: A:0.29, C:0.27, G:0.23, T:0.21
Consensus pattern (22 bp):
CCACATAGGTTGCACCGAAGTG
Found at i:6548961 original size:21 final size:21
Alignment explanation
Indices: 6548935--6548983 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
6548925 CACCGAAGTG
* * * *
6548935 CCACATATTTGTCCCGGAGGA
1 CCACATAATTATCCCGAAGAA
6548956 CCACATAATTATCCCGAAGAA
1 CCACATAATTATCCCGAAGAA
6548977 CCACATA
1 CCACATA
6548984 GAGCCTCGAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.35, C:0.31, G:0.14, T:0.20
Consensus pattern (21 bp):
CCACATAATTATCCCGAAGAA
Found at i:6549204 original size:12 final size:13
Alignment explanation
Indices: 6549177--6549207 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
6549167 TTGGAAATTG
6549177 AATAAAACATTTA
1 AATAAAACATTTA
6549190 AATAAAACA-TTA
1 AATAAAACATTTA
6549202 AATAAA
1 AATAAA
6549208 TATATAGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.50
13 9 0.50
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (13 bp):
AATAAAACATTTA
Found at i:6549596 original size:55 final size:55
Alignment explanation
Indices: 6549537--6549674 Score: 204
Period size: 55 Copynumber: 2.5 Consensus size: 55
6549527 CAAGGGTATT
*
6549537 GATACACTCCTCAATGTACCGATACACAAATAACATTTGATGTTTTGAGAGTACC
1 GATACACTCCTCAATGTACCGATACACAAATAACATTCGATGTTTTGAGAGTACC
* *** * *
6549592 GATACACTCCTCAGTGTACCGATACACAAATGGTATTCGATGTTTTGAGGGTATC
1 GATACACTCCTCAATGTACCGATACACAAATAACATTCGATGTTTTGAGAGTACC
*
6549647 GATACACTCCTCAATGTACGGATACACA
1 GATACACTCCTCAATGTACCGATACACA
6549675 CTCATACAAT
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 74 1.00
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.28
Consensus pattern (55 bp):
GATACACTCCTCAATGTACCGATACACAAATAACATTCGATGTTTTGAGAGTACC
Found at i:6555843 original size:23 final size:22
Alignment explanation
Indices: 6555770--6555851 Score: 87
Period size: 23 Copynumber: 3.7 Consensus size: 22
6555760 CGTAATTTGC
*
6555770 ACCGAAGTGCCACATA-ATTTT
1 ACCGAAGTGCCACATAGATTGT
* * *
6555791 CCCGAAG-GACCACATAGTTTGC
1 ACCGAAGTG-CCACATAGATTGT
*
6555813 ACCGAAGTGCCACATAGGGTTGT
1 ACCGAAGTGCCACATA-GATTGT
6555836 ACCGAAGTGCCACATA
1 ACCGAAGTGCCACATA
6555852 TTTATCCCGG
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
20 1 0.02
21 13 0.26
22 15 0.30
23 21 0.42
ACGTcount: A:0.30, C:0.27, G:0.22, T:0.21
Consensus pattern (22 bp):
ACCGAAGTGCCACATAGATTGT
Found at i:6555889 original size:21 final size:21
Alignment explanation
Indices: 6555771--6555884 Score: 97
Period size: 21 Copynumber: 5.3 Consensus size: 21
6555761 GTAATTTGCA
*
6555771 CCGAAGTGCCACATAATTTTC
1 CCGAAGTGCCACATAATTATC
*
6555792 CCGAAG-GACCACATAGTT-TGC
1 CCGAAGTG-CCACATAATTAT-C
* * *
6555813 ACCGAAGTGCCACATAGGGTTGTA
1 -CCGAAGTGCCACATA--ATTATC
*
6555837 CCGAAGTGCCACATATTTATC
1 CCGAAGTGCCACATAATTATC
* *
6555858 CCGGAGTACCACATAATTATC
1 CCGAAGTGCCACATAATTATC
6555879 CCGAAG
1 CCGAAG
6555885 GACCATATAG
Statistics
Matches: 77, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
20 2 0.03
21 42 0.55
22 13 0.17
23 16 0.21
24 3 0.04
25 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (21 bp):
CCGAAGTGCCACATAATTATC
Found at i:6556474 original size:55 final size:55
Alignment explanation
Indices: 6556377--6556574 Score: 190
Period size: 55 Copynumber: 3.6 Consensus size: 55
6556367 TTACACTTGG
* * * ** *
6556377 GGGTATCGATAC-CTACACA-TGTATCGATAC-CTAAATTGCATTCGAAATGGAAA
1 GGGTATCGATACACTCCTCAGTGTACCGATACAC-AAATAACATTCGAAATGTAAA
* **
6556430 GGGCATCGATACACTCCTCAGTGTACCGATACACAAATAACATTC--AATGTTTCGA
1 GGGTATCGATACACTCCTCAGTGTACCGATACACAAATAACATTCGAAATG--TAAA
** * * * *
6556485 GGGTATCGATACACTCCTCAGTGTACCGATACACAAATGGCATTCGAAGTTTTAC
1 GGGTATCGATACACTCCTCAGTGTACCGATACACAAATAACATTCGAAATGTAAA
*
6556540 GGGTATCGATACACTCCTCAGTGTATCGATACACA
1 GGGTATCGATACACTCCTCAGTGTACCGATACACA
6556575 CTCATACAGT
Statistics
Matches: 120, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
53 15 0.12
54 5 0.04
55 97 0.81
56 1 0.01
57 2 0.02
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (55 bp):
GGGTATCGATACACTCCTCAGTGTACCGATACACAAATAACATTCGAAATGTAAA
Found at i:6568784 original size:2 final size:2
Alignment explanation
Indices: 6568777--6568821 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
6568767 TATGATAAAC
6568777 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
6568819 AT A
1 AT A
6568822 AGAAAATCGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6573848 original size:19 final size:22
Alignment explanation
Indices: 6573794--6573848 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 22
6573784 GCAAATTTTA
6573794 AAAGAAAATTAAAGATAAGAAAT
1 AAAGAAAATTAAAGATAAG-AAT
6573817 AAAGCAAAA-TAAA-A-AAG-AT
1 AAAG-AAAATTAAAGATAAGAAT
6573836 AAAGAAAATTAAA
1 AAAGAAAATTAAA
6573849 TTCACAGGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
18 4 0.13
19 10 0.33
21 3 0.10
22 1 0.03
23 8 0.27
24 4 0.13
ACGTcount: A:0.73, C:0.02, G:0.11, T:0.15
Consensus pattern (22 bp):
AAAGAAAATTAAAGATAAGAAT
Found at i:6578309 original size:15 final size:15
Alignment explanation
Indices: 6578291--6578346 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
6578281 TAACCGGTTT
*
6578291 CGGTTTTAAAAAAAA
1 CGGTTTTAAAAAAAC
*
6578306 CGGTTTTTTTAAAAAAC
1 CGG--TTTTAAAAAAAC
*
6578323 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
6578338 CGATTTTAA
1 CGGTTTTAA
6578347 TATTTCAGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 20 0.61
17 13 0.39
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:6578319 original size:17 final size:17
Alignment explanation
Indices: 6578294--6578327 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
6578284 CCGGTTTCGG
6578294 TTTTAAAAAAAACGGTT
1 TTTTAAAAAAAACGGTT
* *
6578311 TTTTTAAAAAACCGGTT
1 TTTTAAAAAAAACGGTT
6578328 ATAAAAAAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (17 bp):
TTTTAAAAAAAACGGTT
Found at i:6578540 original size:21 final size:21
Alignment explanation
Indices: 6578516--6578568 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
6578506 ACACTTAGGG
6578516 AACCGATTCCCTATGAGAGGA
1 AACCGATTCCCTATGAGAGGA
*
6578537 AACCGATTCCCTATGAGAGGG
1 AACCGATTCCCTATGAGAGGA
*
6578558 TACCGATTCCC
1 AACCGATTCCC
6578569 CCACGCTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (21 bp):
AACCGATTCCCTATGAGAGGA
Found at i:6578785 original size:13 final size:13
Alignment explanation
Indices: 6578764--6578818 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
6578754 AAGTTCGATA
*
6578764 AATTCAAATACTT
1 AATTGAAATACTT
6578777 AATTGAAATACTT
1 AATTGAAATACTT
* *
6578790 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
6578804 AATTGAAATACTT
1 AATTGAAATACTT
6578817 AA
1 AA
6578819 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:6578900 original size:32 final size:33
Alignment explanation
Indices: 6578804--6578902 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
6578794 AACTCAACAT
* * *
6578804 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
6578837 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
6578870 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
6578902 A
1 A
6578903 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:6578921 original size:21 final size:21
Alignment explanation
Indices: 6578897--6578936 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
6578887 ACTTCAAGTT
6578897 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
6578918 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
6578937 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:6598957 original size:19 final size:19
Alignment explanation
Indices: 6598913--6598978 Score: 105
Period size: 19 Copynumber: 3.4 Consensus size: 19
6598903 AACCGCTAAA
* *
6598913 GAACCGACAAAACCAGTTGG
1 GAACCGGCAAAACCAG-TGT
6598933 GAACCGGCAAAACCAGTGT
1 GAACCGGCAAAACCAGTGT
6598952 GAACCGGCAAAACCAGTGT
1 GAACCGGCAAAACCAGTGT
6598971 GAACCGGC
1 GAACCGGC
6598979 GGTTCTTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
19 29 0.66
20 15 0.34
ACGTcount: A:0.36, C:0.27, G:0.27, T:0.09
Consensus pattern (19 bp):
GAACCGGCAAAACCAGTGT
Found at i:6599260 original size:27 final size:27
Alignment explanation
Indices: 6599222--6599277 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
6599212 ATGAAGATCT
*
6599222 TGATGCTGTGGACTTTCAAGTTCAAAG
1 TGATGCTATGGACTTTCAAGTTCAAAG
*
6599249 TGATGCTATGGAGTTTCAAGTTCAAAG
1 TGATGCTATGGACTTTCAAGTTCAAAG
6599276 TG
1 TG
6599278 GTGATGGCAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.34
Consensus pattern (27 bp):
TGATGCTATGGACTTTCAAGTTCAAAG
Found at i:6602488 original size:16 final size:16
Alignment explanation
Indices: 6602467--6602530 Score: 83
Period size: 16 Copynumber: 4.0 Consensus size: 16
6602457 TCACAACCAA
*
6602467 AGAAAGATTTAAGGAT
1 AGAAAGATTCAAGGAT
*
6602483 AGAAAGATTCTAGGAT
1 AGAAAGATTCAAGGAT
***
6602499 TTCAAGATTCAAGGAT
1 AGAAAGATTCAAGGAT
6602515 AGAAAGATTCAAGGAT
1 AGAAAGATTCAAGGAT
6602531 TTCAAGTCAT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.45, C:0.06, G:0.23, T:0.25
Consensus pattern (16 bp):
AGAAAGATTCAAGGAT
Found at i:6602506 original size:32 final size:32
Alignment explanation
Indices: 6602470--6602536 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
6602460 CAACCAAAGA
* *
6602470 AAGATTTAAGGATAGAAAGATTCTAGGATTTC
1 AAGATTCAAGGATAGAAAGATTCAAGGATTTC
6602502 AAGATTCAAGGATAGAAAGATTCAAGGATTTC
1 AAGATTCAAGGATAGAAAGATTCAAGGATTTC
6602534 AAG
1 AAG
6602537 TCATCAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.43, C:0.07, G:0.22, T:0.27
Consensus pattern (32 bp):
AAGATTCAAGGATAGAAAGATTCAAGGATTTC
Found at i:6604681 original size:16 final size:18
Alignment explanation
Indices: 6604654--6604691 Score: 62
Period size: 16 Copynumber: 2.2 Consensus size: 18
6604644 ATACTTAAAG
6604654 TAAATAAAAATTTATT-T
1 TAAATAAAAATTTATTGT
6604671 TAAAT-AAAATTTATTGT
1 TAAATAAAAATTTATTGT
6604688 TAAA
1 TAAA
6604692 AATTTAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (18 bp):
TAAATAAAAATTTATTGT
Found at i:6604823 original size:19 final size:19
Alignment explanation
Indices: 6604791--6604832 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
6604781 TTTATCAAAA
6604791 TTTA-TATAAATTAAATAC
1 TTTATTATAAATTAAATAC
*
6604809 TTTATTATAATTTAAATAC
1 TTTATTATAAATTAAATAC
*
6604828 ATTAT
1 TTTAT
6604833 GATATAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTATTATAAATTAAATAC
Found at i:6607724 original size:20 final size:21
Alignment explanation
Indices: 6607682--6607724 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
6607672 TACTCAGGTG
*
6607682 TAGTATCAATACTAAATGGAT
1 TAGTATCAATACTAAATGAAT
*
6607703 TAGTATCAATAC-CAATGAAT
1 TAGTATCAATACTAAATGAAT
6607723 TA
1 TA
6607725 ATTTGGGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.33
Consensus pattern (21 bp):
TAGTATCAATACTAAATGAAT
Found at i:6608501 original size:15 final size:16
Alignment explanation
Indices: 6608474--6608503 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
6608464 GAGGATTATG
6608474 AGAGTTGACCAAAAGT
1 AGAGTTGACCAAAAGT
6608490 AGAGTT-ACCAAAAG
1 AGAGTTGACCAAAAG
6608504 GGTAAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.47, C:0.13, G:0.23, T:0.17
Consensus pattern (16 bp):
AGAGTTGACCAAAAGT
Found at i:6609517 original size:20 final size:20
Alignment explanation
Indices: 6609492--6609529 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6609482 AAGCTAAAAA
*
6609492 TGGTATTGATACCCAGGGTT
1 TGGTATCGATACCCAGGGTT
*
6609512 TGGTATCGATACTCAGGG
1 TGGTATCGATACCCAGGG
6609530 GTCACTATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.16, G:0.32, T:0.32
Consensus pattern (20 bp):
TGGTATCGATACCCAGGGTT
Found at i:6610790 original size:15 final size:16
Alignment explanation
Indices: 6610770--6610799 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
6610760 AGATTTTGGC
6610770 TAAGTTT-GGCTTGAA
1 TAAGTTTGGGCTTGAA
6610785 TAAGTTTGGGCTTGA
1 TAAGTTTGGGCTTGA
6610800 GAACATTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.23, C:0.07, G:0.30, T:0.40
Consensus pattern (16 bp):
TAAGTTTGGGCTTGAA
Found at i:6618977 original size:27 final size:27
Alignment explanation
Indices: 6618943--6618997 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
6618933 TAATATTAGG
6618943 CCCTTATTGATCTCATCAATATTCATT
1 CCCTTATTGATCTCATCAATATTCATT
6618970 CCCTTATTGATCTCATCAATATTCATT
1 CCCTTATTGATCTCATCAATATTCATT
6618997 C
1 C
6618998 TTATTTTATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.27, G:0.04, T:0.44
Consensus pattern (27 bp):
CCCTTATTGATCTCATCAATATTCATT
Found at i:6629263 original size:17 final size:17
Alignment explanation
Indices: 6629241--6629285 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
6629231 CCGGTTCGAC
6629241 CCGACCCGACCGTTAAT
1 CCGACCCGACCGTTAAT
*
6629258 CCGACCCGACCGTTGAT
1 CCGACCCGACCGTTAAT
6629275 CCGACCCGACC
1 CCGACCCGACC
6629286 CGACTGTTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.20, C:0.47, G:0.20, T:0.13
Consensus pattern (17 bp):
CCGACCCGACCGTTAAT
Found at i:6629327 original size:22 final size:22
Alignment explanation
Indices: 6629261--6629340 Score: 106
Period size: 22 Copynumber: 3.6 Consensus size: 22
6629251 CGTTAATCCG
* *
6629261 ACCCGACCGTTGATCCGACCCG
1 ACCCGACCGTTGACCCGACCCA
*
6629283 ACCCGACTGTTGACCCGACCCA
1 ACCCGACCGTTGACCCGACCCA
*
6629305 ACCCGACCGTTGACCCGAACCA
1 ACCCGACCGTTGACCCGACCCA
* *
6629327 ATCCAACCGTTGAC
1 ACCCGACCGTTGAC
6629341 TCGGGTGTTA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.24, C:0.44, G:0.19, T:0.14
Consensus pattern (22 bp):
ACCCGACCGTTGACCCGACCCA
Done.