Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008227.1 Hibiscus syriacus cultivar Beakdansim tig00110863_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: 654371
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 2 of 3
Found at i:261922 original size:20 final size:20
Alignment explanation
Indices: 261899--261968 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
261889 GAACTCTAAT
261899 TTCGCAACACAGTTTCCAAA
1 TTCGCAACACAGTTTCCAAA
* * *
261919 TTCGCAACGCAAATTTCCCAGA
1 TTCGCAACAC-AGTTT-CCAAA
* **
261941 TTCGCAACTCAGTTTTGAAA
1 TTCGCAACACAGTTTCCAAA
261961 TTCGCAAC
1 TTCGCAAC
261969 TCAAATTTCT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
20 19 0.47
21 8 0.20
22 13 0.32
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (20 bp):
TTCGCAACACAGTTTCCAAA
Found at i:262042 original size:20 final size:20
Alignment explanation
Indices: 262019--262067 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
262009 GCGAATTTGT
262019 AATTCGCAACACAGAAGTCA
1 AATTCGCAACACAGAAGTCA
* *
262039 AATTCGTAACACATAAGTCA
1 AATTCGCAACACAGAAGTCA
262059 AATTCGCAA
1 AATTCGCAA
262068 AGCGCGTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.45, C:0.22, G:0.12, T:0.20
Consensus pattern (20 bp):
AATTCGCAACACAGAAGTCA
Found at i:262244 original size:22 final size:22
Alignment explanation
Indices: 262219--262265 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
262209 TCTCTACGGT
*
262219 GACATCCGTCCCCATCTCCGGC
1 GACATCCGTCCCCATATCCGGC
262241 GACATCCGTCCCCATATCCGGC
1 GACATCCGTCCCCATATCCGGC
262263 GAC
1 GAC
262266 CCCCCTCTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.47, G:0.19, T:0.17
Consensus pattern (22 bp):
GACATCCGTCCCCATATCCGGC
Found at i:264211 original size:42 final size:42
Alignment explanation
Indices: 264142--264239 Score: 115
Period size: 42 Copynumber: 2.3 Consensus size: 42
264132 CCCCCCACTT
* * * * * *
264142 CGAGAACCATCACCTGATTGAGTCGATTCTACAGCTCGACAC
1 CGAGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAC
* *
264184 TGAGAGCCATCACCTGATCGAGCCGATTATATACCTCCACAC
1 CGAGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAC
*
264226 CAAGAGCCATCACC
1 CGAGAGCCATCACC
264240 AATTCCATCA
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.30, C:0.34, G:0.17, T:0.19
Consensus pattern (42 bp):
CGAGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAC
Found at i:264382 original size:21 final size:21
Alignment explanation
Indices: 264355--264404 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
264345 GTTAAGAGAG
*
264355 TTACGTGATGAGGTCAGTGCT
1 TTACGTGATGAGGTCAGTACT
* *
264376 TTGCGTGATGAGGTCGGTACT
1 TTACGTGATGAGGTCAGTACT
264397 TTACGTGA
1 TTACGTGA
264405 CGACAATGGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.18, C:0.14, G:0.34, T:0.34
Consensus pattern (21 bp):
TTACGTGATGAGGTCAGTACT
Found at i:264839 original size:21 final size:21
Alignment explanation
Indices: 264811--264908 Score: 146
Period size: 21 Copynumber: 4.7 Consensus size: 21
264801 GATTCACTTG
264811 TCATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
264832 -CTATCGTTCAAGAGGCCCCTC
1 TC-ATCGTTCAAGAGGCCCCTC
264853 TCATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
*
264874 TCATCGTTCAAGAGTCCCCTAC
1 TCATCGTTCAAGAGGCCCCT-C
*
264896 -CACCGTTCAAGAG
1 TCATCGTTCAAGAG
264909 CCTGATTCAC
Statistics
Matches: 72, Mismatches: 2, Indels: 6
0.90 0.03 0.08
Matches are distributed among these distances:
20 1 0.01
21 69 0.96
22 2 0.03
ACGTcount: A:0.21, C:0.37, G:0.18, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:265751 original size:18 final size:18
Alignment explanation
Indices: 265728--265764 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
265718 ATCATTTGGC
265728 TAAATACTTGGATGTGAT
1 TAAATACTTGGATGTGAT
265746 TAAATACTTGGATGTGAT
1 TAAATACTTGGATGTGAT
265764 T
1 T
265765 GATTATTAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.22, T:0.41
Consensus pattern (18 bp):
TAAATACTTGGATGTGAT
Found at i:266353 original size:16 final size:16
Alignment explanation
Indices: 266324--266359 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
266314 TGTAAATAAG
* *
266324 AATTGTTTTTTTGTTT
1 AATTGATTTGTTGTTT
266340 AATTGATTTGTTGTTT
1 AATTGATTTGTTGTTT
266356 AATT
1 AATT
266360 CAATTTGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.14, T:0.67
Consensus pattern (16 bp):
AATTGATTTGTTGTTT
Found at i:266367 original size:17 final size:16
Alignment explanation
Indices: 266334--266367 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
266324 AATTGTTTTT
*
266334 TTGTTTAATTGATTTG
1 TTGTTTAATTAATTTG
266350 TTGTTTAATTCAATTTG
1 TTGTTTAATT-AATTTG
266367 T
1 T
266368 ATTATGTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.21, C:0.03, G:0.15, T:0.62
Consensus pattern (16 bp):
TTGTTTAATTAATTTG
Found at i:266758 original size:18 final size:18
Alignment explanation
Indices: 266735--266770 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
266725 AAGCCGGTTG
*
266735 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
266753 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
266771 CCTTATGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:266899 original size:17 final size:17
Alignment explanation
Indices: 266879--266912 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
266869 ACCTTATATG
266879 ACCACTTTCCTTGCACC
1 ACCACTTTCCTTGCACC
266896 ACCACTTTCCTTGCACC
1 ACCACTTTCCTTGCACC
266913 GACTGCATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.47, G:0.06, T:0.29
Consensus pattern (17 bp):
ACCACTTTCCTTGCACC
Found at i:267819 original size:23 final size:23
Alignment explanation
Indices: 267793--267861 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
267783 CACCACAGCT
*
267793 CGTATAAATGCACCGAAGTGCCA
1 CGTATAATTGCACCGAAGTGCCA
* *
267816 CGTAGAATTGCACCGAAGTGCCG
1 CGTATAATTGCACCGAAGTGCCA
*
267839 CGTATAATTGCATCGAAGTGCCA
1 CGTATAATTGCACCGAAGTGCCA
267862 TATAAAATGT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.20
Consensus pattern (23 bp):
CGTATAATTGCACCGAAGTGCCA
Found at i:269551 original size:21 final size:21
Alignment explanation
Indices: 269525--269574 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
269515 TTATTTGAGA
*
269525 GTGCATTGGTACACAATGAAT
1 GTGCATCGGTACACAATGAAT
269546 GTGCATCGGTACACAATGAAT
1 GTGCATCGGTACACAATGAAT
269567 GTGCATCG
1 GTGCATCG
269575 ATGCACACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (21 bp):
GTGCATCGGTACACAATGAAT
Found at i:269581 original size:21 final size:21
Alignment explanation
Indices: 269525--269581 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
269515 TTATTTGAGA
* *
269525 GTGCATTGGTACACAATGAAT
1 GTGCATCGATACACAATGAAT
*
269546 GTGCATCGGTACACAATGAAT
1 GTGCATCGATACACAATGAAT
*
269567 GTGCATCGATGCACA
1 GTGCATCGATACACA
269582 CAACCCAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.25
Consensus pattern (21 bp):
GTGCATCGATACACAATGAAT
Found at i:273193 original size:43 final size:46
Alignment explanation
Indices: 273073--273197 Score: 141
Period size: 47 Copynumber: 2.8 Consensus size: 46
273063 TATAAAATCT
** *
273073 CTTACCATTT-ATCCCATAAGCTCGTAACCTTATTTTACCAAAATA
1 CTTACCATTTAATTTCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
273118 CTTACCATTTAAATTTCATAAGCTCGTAAGCTTATTTTATCAATATA
1 CTTACCATTT-AATTTCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
273165 TTTGCCA-TT-A-TTCATAAGCTCATAAGCTTATTT
1 CTTACCATTTAATTTCATAAGCTCGTAAGCTTATTT
273198 GCATACTTAT
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
43 22 0.31
44 1 0.01
45 10 0.14
46 2 0.03
47 35 0.50
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.41
Consensus pattern (46 bp):
CTTACCATTTAATTTCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:275579 original size:24 final size:24
Alignment explanation
Indices: 275545--275622 Score: 120
Period size: 24 Copynumber: 3.2 Consensus size: 24
275535 CTGAAACATC
* *
275545 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGGGTATTGACCAAG
275569 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGGGTATTGACCAAG
**
275593 ATCAAAGTTTGGGTATTGACCAAG
1 ATCAAAGTCCGGGTATTGACCAAG
275617 ATCAAA
1 ATCAAA
275623 TTTCGAATAC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (24 bp):
ATCAAAGTCCGGGTATTGACCAAG
Found at i:276611 original size:40 final size:42
Alignment explanation
Indices: 276567--276663 Score: 121
Period size: 40 Copynumber: 2.4 Consensus size: 42
276557 TTGCAAAATT
276567 AAAATTCGTGTTGCGAATTCA-AAAATCGAGTTGCGAAAA-C
1 AAAATTCGTGTTGCGAATTCAGAAAATCGAGTTGCGAAAAGC
* ** *
276607 AAAATTCGTGTTGCG-ATTTAGAAAATCTTGTTGCGAAAAGG
1 AAAATTCGTGTTGCGAATTCAGAAAATCGAGTTGCGAAAAGC
*
276648 AAACTT-GTGTTGCGAA
1 AAAATTCGTGTTGCGAA
276664 AAAGAAATTC
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
39 4 0.08
40 39 0.80
41 6 0.12
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (42 bp):
AAAATTCGTGTTGCGAATTCAGAAAATCGAGTTGCGAAAAGC
Found at i:276621 original size:20 final size:20
Alignment explanation
Indices: 276536--276674 Score: 83
Period size: 20 Copynumber: 7.0 Consensus size: 20
276526 CAAAACATTT
* *
276536 GTGTTGCGAAAATAAAA-GC
1 GTGTTGCGAAAACAAAATTC
*
276555 -TGTTGC-AAAATTAAAATTC
1 GTGTTGCGAAAA-CAAAATTC
** *
276574 GTGTTGCGAATTCAAAAATC
1 GTGTTGCGAAAACAAAATTC
*
276594 GAGTTGCGAAAACAAAATTC
1 GTGTTGCGAAAACAAAATTC
** *
276614 GTGTTGCGATTTAGAAAA-TC
1 GTGTTGCGA-AAACAAAATTC
* * *
276634 TTGTTGCGAAAAGGAAACTT-
1 GTGTTGCGAAAA-CAAAATTC
276654 GTGTTGCGAAAA-AGAAATTC
1 GTGTTGCGAAAACA-AAATTC
276674 G
1 G
276675 CATTGTGAAT
Statistics
Matches: 92, Mismatches: 19, Indels: 17
0.72 0.15 0.13
Matches are distributed among these distances:
17 4 0.04
18 12 0.13
19 6 0.07
20 62 0.67
21 8 0.09
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (20 bp):
GTGTTGCGAAAACAAAATTC
Found at i:276742 original size:21 final size:20
Alignment explanation
Indices: 276667--276744 Score: 52
Period size: 21 Copynumber: 3.8 Consensus size: 20
276657 TTGCGAAAAA
* *
276667 GAAATTCGCATTGTGAA-TT
1 GAAAATCGCATTGCGAATTT
*
276686 CAGAAATCG-AGTTGCGAATTT
1 GA-AAATCGCA-TTGCGAATTT
* **
276707 GAAATTCCGTGTTGCGAATTT
1 GAAAAT-CGCATTGCGAATTT
276728 GGAAAATCGCATTGCGA
1 -GAAAATCGCATTGCGA
276745 GAAAGAAATT
Statistics
Matches: 44, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
19 2 0.05
20 14 0.32
21 23 0.52
22 5 0.11
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (20 bp):
GAAAATCGCATTGCGAATTT
Found at i:276750 original size:82 final size:81
Alignment explanation
Indices: 276657--276811 Score: 206
Period size: 82 Copynumber: 1.9 Consensus size: 81
276647 GAAACTTGTG
*
276657 TTGCGAAAAAGAAATTCGCATTGTGAATT-CAGAAATCGAGTTGCGAATTT-GAAATTCCGTGTT
1 TTGCGAAAAAGAAATTCGCATTGCG-ATTGCAGAAATCGAGTTGCGAATTTGGAAA--CCGTGTT
*
276720 GCGAATTTGGAAAATCGCA
63 GCGAAATTGGAAAATCGCA
* ** * *
276739 TTGCGAGAAAGAAATTCGTGTTGCGATTGCAGAAATTGAGTTGCGAATTTGGAAACTGTGTTGCG
1 TTGCGAAAAAGAAATTCGCATTGCGATTGCAGAAATCGAGTTGCGAATTTGGAAACCGTGTTGCG
276804 AAATTGGA
66 AAATTGGA
276812 GTTCGCGTTG
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
81 19 0.30
82 41 0.64
83 4 0.06
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (81 bp):
TTGCGAAAAAGAAATTCGCATTGCGATTGCAGAAATCGAGTTGCGAATTTGGAAACCGTGTTGCG
AAATTGGAAAATCGCA
Found at i:276793 original size:20 final size:20
Alignment explanation
Indices: 276770--276829 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
276760 TGCGATTGCA
276770 GAAATTGAGTTGCGAATTTG
1 GAAATTGAGTTGCGAATTTG
* * *
276790 GAAACTGTGTTGCGAAATTG
1 GAAATTGAGTTGCGAATTTG
* *
276810 G-AGTTCGCGTTGCGAATTTG
1 GAAATT-GAGTTGCGAATTTG
276830 TTGGTCATTT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
19 2 0.06
20 30 0.94
ACGTcount: A:0.25, C:0.10, G:0.32, T:0.33
Consensus pattern (20 bp):
GAAATTGAGTTGCGAATTTG
Found at i:277082 original size:13 final size:13
Alignment explanation
Indices: 277064--277090 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
277054 CCAGGTAAGG
277064 TTTTATTTTCTAT
1 TTTTATTTTCTAT
277077 TTTTATTTTCTAT
1 TTTTATTTTCTAT
277090 T
1 T
277091 AAACCCAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTATTTTCTAT
Found at i:277259 original size:29 final size:29
Alignment explanation
Indices: 277215--277271 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
277205 CTAATGCAAT
* *
277215 AAGAAGAAATGGGTTTATGGAAGAATAAG
1 AAGAAGAAATGAGTTTATGGAAAAATAAG
*
277244 AAGAAGCAATGAGTTTATGGAAAAATAA
1 AAGAAGAAATGAGTTTATGGAAAAATAA
277272 TAAAATGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.51, C:0.02, G:0.26, T:0.21
Consensus pattern (29 bp):
AAGAAGAAATGAGTTTATGGAAAAATAAG
Found at i:283810 original size:22 final size:22
Alignment explanation
Indices: 283782--283824 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
283772 TTAATAAAAT
*
283782 ATTTT-AAATGATATATTTTTAA
1 ATTTTAAAAT-ATATATATTTAA
283804 ATTTTAAAATATATATATTTA
1 ATTTTAAAATATATATATTTA
283825 GTTGGATGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
ATTTTAAAATATATATATTTAA
Found at i:284381 original size:2 final size:2
Alignment explanation
Indices: 284374--284403 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
284364 ACCTAAAATC
284374 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
284404 GATTCCACAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:284580 original size:29 final size:29
Alignment explanation
Indices: 284538--284603 Score: 114
Period size: 29 Copynumber: 2.3 Consensus size: 29
284528 AAAGTGGGTT
*
284538 TGGAAAAAGAGAAAATATAACACTATTGA
1 TGGAAAAAGAGAAAATATAACAATATTGA
*
284567 TGGAAAAAGAGAAAATATAATAATATTGA
1 TGGAAAAAGAGAAAATATAACAATATTGA
284596 TGGAAAAA
1 TGGAAAAA
284604 AAGCGTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.58, C:0.03, G:0.18, T:0.21
Consensus pattern (29 bp):
TGGAAAAAGAGAAAATATAACAATATTGA
Found at i:284679 original size:29 final size:29
Alignment explanation
Indices: 284637--284715 Score: 122
Period size: 29 Copynumber: 2.7 Consensus size: 29
284627 CGGTGACCAG
** * *
284637 TATATTTATCGATCTAACATCTGTCAGAT
1 TATATTTCCCGATCTAACATCGGTCAGAC
284666 TATATTTCCCGATCTAACATCGGTCAGAC
1 TATATTTCCCGATCTAACATCGGTCAGAC
284695 TATATTTCCCGATCTAACATC
1 TATATTTCCCGATCTAACATC
284716 ATTTGCAGTA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (29 bp):
TATATTTCCCGATCTAACATCGGTCAGAC
Found at i:285094 original size:17 final size:17
Alignment explanation
Indices: 285072--285109 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
285062 ATATTCTGTA
285072 TTTAATTTA-TTAAGTAT
1 TTTAATTTATTTAA-TAT
285089 TTTAATTTATTTAATAT
1 TTTAATTTATTTAATAT
285106 TTTA
1 TTTA
285110 CTTATATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (17 bp):
TTTAATTTATTTAATAT
Found at i:290039 original size:23 final size:24
Alignment explanation
Indices: 290000--290044 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
289990 ATTATAAATA
*
290000 TAGGGACTTATTTGTAAATATTTT
1 TAGGGACTTATTGGTAAATATTTT
*
290024 TAGGGA-TTATTGGTAATTATT
1 TAGGGACTTATTGGTAAATATT
290045 AAATGAAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.29, C:0.02, G:0.20, T:0.49
Consensus pattern (24 bp):
TAGGGACTTATTGGTAAATATTTT
Found at i:290810 original size:20 final size:23
Alignment explanation
Indices: 290760--290817 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 23
290750 GCATGGGTAG
290760 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTTAAAGAA
290784 TGCATCGATGCACTG-T-AA-AA
1 TGCATCGATGCACTGTTAAAGAA
*
290804 TGTATCGATGCACT
1 TGCATCGATGCACT
290818 TCAAGGGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 15 0.45
21 2 0.06
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (23 bp):
TGCATCGATGCACTGTTAAAGAA
Found at i:292307 original size:23 final size:23
Alignment explanation
Indices: 292258--292322 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
292248 GTCTACGCGG
*
292258 TCATTCGGGATA--T-ACAGTGA
1 TCATTCGGGATATTTCATAGTGA
*
292278 TCCTTCGGGATATTTCATAGTGA
1 TCATTCGGGATATTTCATAGTGA
292301 TCATTCGGGATAAATTTCATAG
1 TCATTCGGGAT--ATTTCATAG
292323 CCCCTAGTGG
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
20 11 0.30
22 1 0.03
23 16 0.43
25 9 0.24
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (23 bp):
TCATTCGGGATATTTCATAGTGA
Found at i:295494 original size:21 final size:20
Alignment explanation
Indices: 295470--295511 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
295460 TTATGATGAG
295470 ATATGGAAGATAAGATGGTTT
1 ATATGG-AGATAAGATGGTTT
* *
295491 ATATGGATATAAGTTGGTTT
1 ATATGGAGATAAGATGGTTT
295511 A
1 A
295512 AGTATGGTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.36, C:0.00, G:0.26, T:0.38
Consensus pattern (20 bp):
ATATGGAGATAAGATGGTTT
Found at i:295700 original size:62 final size:61
Alignment explanation
Indices: 295630--295763 Score: 146
Period size: 61 Copynumber: 2.2 Consensus size: 61
295620 TTCAATGTGT
* *
295630 ATCGATGCACTCTTTAAAGAAGAAACATCGAATGCAATTAGTGCATCGAT-CATAAGG-AGTGC
1 ATCGATGCACCCTTT-AA-AAGAAACATCGAAGGCAATTAGTGCATCGATGCAT-AGGTAGTGC
* ** * * *
295692 ATCGATGCACCCCTTTAAATGAAACATCGAAGGTGATTGGTGTATCGATGCATGGGTAGTGC
1 ATCGATGCA-CCCTTTAAAAGAAACATCGAAGGCAATTAGTGCATCGATGCATAGGTAGTGC
295754 ATCGATGCAC
1 ATCGATGCAC
295764 ATGTTAAAGA
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
61 28 0.46
62 28 0.46
63 5 0.08
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (61 bp):
ATCGATGCACCCTTTAAAAGAAACATCGAAGGCAATTAGTGCATCGATGCATAGGTAGTGC
Found at i:295796 original size:20 final size:22
Alignment explanation
Indices: 295751--295808 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
295741 GCATGGGTAG
295751 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
295775 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
*
295795 TGTATCGATGCACT
1 TGCATCGATGCACT
295809 TCAAGGGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:303647 original size:50 final size:50
Alignment explanation
Indices: 303584--303688 Score: 147
Period size: 50 Copynumber: 2.1 Consensus size: 50
303574 GGAAAACGTT
* * * * *
303584 CCCCCTGCACCGCGTTATATGTTGATTTGGCGCCACGTGGGTATATCGCG
1 CCCCCTGCACCGCGATATACGGTGATCTGGCGCCACGTGGGTATAGCGCG
* *
303634 CCCCCTGCCCCGCGATATACGGTGATCTGGCGCCACGTGGGTATAGCGTG
1 CCCCCTGCACCGCGATATACGGTGATCTGGCGCCACGTGGGTATAGCGCG
303684 CCCCC
1 CCCCC
303689 CTGATCCGCG
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.13, C:0.35, G:0.29, T:0.23
Consensus pattern (50 bp):
CCCCCTGCACCGCGATATACGGTGATCTGGCGCCACGTGGGTATAGCGCG
Found at i:304103 original size:110 final size:111
Alignment explanation
Indices: 303968--304188 Score: 381
Period size: 110 Copynumber: 2.0 Consensus size: 111
303958 TGGAAATCAT
* *
303968 ATATCTCTACACTTTGCTGATACGGTAACATTTGAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTAATACGGTAACATTTGAACGTTTTAATTTAATTTAAATTATTAGTAA
* * *
304033 TATTTAGTTGATTTATTTAATGCATGATTATTA-TTTAAGAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
*
304078 ATATCTCGACACTTTGCTAATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTAATACGGTAACATTTGAACGTTTTAATTTAATTTAAATTATTAGTAA
304143 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
304189 TTTTTGTAAT
Statistics
Matches: 104, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
110 93 0.89
111 11 0.11
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTAATACGGTAACATTTGAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:306070 original size:6 final size:6
Alignment explanation
Indices: 306059--306123 Score: 61
Period size: 6 Copynumber: 11.8 Consensus size: 6
306049 GCTCAGGACA
*
306059 ATGACG ATGACG ATGATG ATGAC- --GACG ATGACG ATG--G -TGACG
1 ATGACG ATGACG ATGACG ATGACG ATGACG ATGACG ATGACG ATGACG
* *
306101 ACGACG ATGACG ATGATG ATGAC
1 ATGACG ATGACG ATGACG ATGAC
306124 AACGAGGAGT
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
3 5 0.11
4 1 0.02
5 1 0.02
6 40 0.85
ACGTcount: A:0.32, C:0.15, G:0.34, T:0.18
Consensus pattern (6 bp):
ATGACG
Found at i:306087 original size:21 final size:21
Alignment explanation
Indices: 306061--306128 Score: 109
Period size: 21 Copynumber: 3.2 Consensus size: 21
306051 TCAGGACAAT
306061 GACGATGACGATGATGATGAC
1 GACGATGACGATGATGATGAC
* *
306082 GACGATGACGATGGTGACGAC
1 GACGATGACGATGATGATGAC
306103 GACGATGACGATGATGATGAC
1 GACGATGACGATGATGATGAC
*
306124 AACGA
1 GACGA
306129 GGAGTCAGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.34, C:0.16, G:0.34, T:0.16
Consensus pattern (21 bp):
GACGATGACGATGATGATGAC
Found at i:306119 original size:9 final size:9
Alignment explanation
Indices: 306059--306101 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
306049 GCTCAGGACA
306059 ATGACGATG
1 ATGACGATG
* *
306068 ACGATGATG
1 ATGACGATG
*
306077 ATGACGACG
1 ATGACGATG
306086 ATGACGATG
1 ATGACGATG
*
306095 GTGACGA
1 ATGACGA
306102 CGACGATGAC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.33, C:0.14, G:0.35, T:0.19
Consensus pattern (9 bp):
ATGACGATG
Found at i:310116 original size:50 final size:50
Alignment explanation
Indices: 310021--310121 Score: 112
Period size: 50 Copynumber: 2.0 Consensus size: 50
310011 AGCGCGGATC
* * * * * *
310021 GGGGGCGCATTATACCCACGTGATGTCAGATCACCGTATATCGCGGGGCA
1 GGGGGCGCATTATACCCACGTGACGCCAAATCAACATATAACGCGGGGCA
* ** *
310071 GGGGGCGCGTTATACTTACGTGACGCCAAATCAACATATAACGCGGTGCA
1 GGGGGCGCATTATACCCACGTGACGCCAAATCAACATATAACGCGGGGCA
310121 G
1 G
310122 AGGCACGCTT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
50 41 1.00
ACGTcount: A:0.25, C:0.25, G:0.31, T:0.20
Consensus pattern (50 bp):
GGGGGCGCATTATACCCACGTGACGCCAAATCAACATATAACGCGGGGCA
Found at i:316287 original size:3 final size:3
Alignment explanation
Indices: 316272--316306 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
316262 TAAAAATATC
*
316272 TTA TTA GTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
316307 TTTAAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:316569 original size:20 final size:19
Alignment explanation
Indices: 316535--316573 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
316525 AACGCCTTCC
316535 TTTTCTTTCGCGTTGCGAT
1 TTTTCTTTCGCGTTGCGAT
*
316554 TTTTCATTTCGTGTTGCGAT
1 TTTTC-TTTCGCGTTGCGAT
316574 AGTCTACAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.08, C:0.18, G:0.21, T:0.54
Consensus pattern (19 bp):
TTTTCTTTCGCGTTGCGAT
Found at i:317373 original size:41 final size:41
Alignment explanation
Indices: 317316--317407 Score: 132
Period size: 41 Copynumber: 2.2 Consensus size: 41
317306 TTTTTTAATT
* * *
317316 ATCGCAACAACAACTGTAGACTATCGCAA-CGAATTTGAAAA
1 ATCGCAACGACAACTGTAGACTAGCGCAACCGAA-ATGAAAA
317357 ATCGCAACGACAACTGTAGACTAGCGCAACGCGAAATGAAAA
1 ATCGCAACGACAACTGTAGACTAGCGCAAC-CGAAATGAAAA
317399 ATCGCAACG
1 ATCGCAACG
317408 CGATTTTCAA
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
41 27 0.59
42 15 0.33
43 4 0.09
ACGTcount: A:0.42, C:0.24, G:0.18, T:0.15
Consensus pattern (41 bp):
ATCGCAACGACAACTGTAGACTAGCGCAACCGAAATGAAAA
Found at i:320515 original size:15 final size:15
Alignment explanation
Indices: 320480--320516 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
320470 ATATTTAGTT
*
320480 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGCG
320495 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
*
320510 GTGCGGG
1 GGGCGGG
320517 TAATGTCTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.05, C:0.16, G:0.68, T:0.11
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:325895 original size:23 final size:23
Alignment explanation
Indices: 325827--325885 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
325817 ACATTTTATA
325827 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
325850 CGTCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
325873 TGGCACTTCGGTG
1 TGGCACTTCGGTG
325886 TATTTATACG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.15, C:0.27, G:0.27, T:0.31
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:330947 original size:23 final size:23
Alignment explanation
Indices: 330883--330937 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
330873 TTTATATGGT
330883 ACTTCGGTGCAATTCTACGCGGC
1 ACTTCGGTGCAATTCTACGCGGC
*
330906 ACTTCGGTGCAATTCTACGTGGC
1 ACTTCGGTGCAATTCTACGCGGC
330929 ACTTCGGTG
1 ACTTCGGTG
330938 TATTTATACG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.29
Consensus pattern (23 bp):
ACTTCGGTGCAATTCTACGCGGC
Found at i:332186 original size:16 final size:17
Alignment explanation
Indices: 332146--332186 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
332136 TGTTTAAATT
*
332146 ATTTCATTTTCTTGCTC
1 ATTTCTTTTTCTTGCTC
*
332163 ATCT-TTTTTCTTGC-C
1 ATTTCTTTTTCTTGCTC
332178 ATTTCTTTT
1 ATTTCTTTT
332187 AGGGTAAGCT
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
15 4 0.20
16 13 0.65
17 3 0.15
ACGTcount: A:0.10, C:0.22, G:0.05, T:0.63
Consensus pattern (17 bp):
ATTTCTTTTTCTTGCTC
Found at i:333617 original size:31 final size:30
Alignment explanation
Indices: 333571--333657 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 30
333561 TTCGATAATA
*
333571 TAATAATTATTTTATAGTA-TTTAGATAAATT
1 TAATAA-TATTTTATAATATTTTA-ATAAATT
*
333602 TATTAATAATTTTATAATATTTTAATAAATT
1 TAATAAT-ATTTTATAATATTTTAATAAATT
*
333633 TAATAAGTATTTTATAATTTTTTAA
1 TAATAA-TATTTTATAATATTTTAA
333658 ACTTTATTGA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
30 1 0.02
31 43 0.88
32 5 0.10
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (30 bp):
TAATAATATTTTATAATATTTTAATAAATT
Found at i:334404 original size:31 final size:31
Alignment explanation
Indices: 334369--334455 Score: 97
Period size: 31 Copynumber: 2.8 Consensus size: 31
334359 TCAATAAAGG
334369 TTAAAAAATTATAAAATATTTATTAAATTTA
1 TTAAAAAATTATAAAATATTTATTAAATTTA
* *
334400 TTAAAAAATTATTAAAT-TATTAATAAATTTA
1 TTAAAAAATTATAAAATAT-TTATTAAATTTA
* * *
334431 TCT-AAATACTATAAAATAATTATTA
1 T-TAAAAAATTATAAAATATTTATTA
334456 TATTATCAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
30 1 0.02
31 44 0.96
32 1 0.02
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (31 bp):
TTAAAAAATTATAAAATATTTATTAAATTTA
Found at i:334411 original size:20 final size:20
Alignment explanation
Indices: 334388--334455 Score: 68
Period size: 20 Copynumber: 3.3 Consensus size: 20
334378 TATAAAATAT
334388 TTATTAAATTTATTAAAAAA
1 TTATTAAATTTATTAAAAAA
*
334408 TTATTAAA-TTATTAATAAAT
1 TTATTAAATTTATTAA-AAAA
*
334428 TTATCTAAATACTA-TAAAATAA
1 TTAT-TAAAT-TTATTAAAA-AA
334450 TTATTA
1 TTATTA
334456 TATTATCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
19 7 0.17
20 15 0.38
21 8 0.20
22 8 0.20
23 2 0.05
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (20 bp):
TTATTAAATTTATTAAAAAA
Found at i:334842 original size:6 final size:6
Alignment explanation
Indices: 334831--334855 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
334821 TTGGGAGTAC
334831 AAATAA AAATAA AAATAA AAATAA A
1 AAATAA AAATAA AAATAA AAATAA A
334856 GAACTACCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:345187 original size:15 final size:15
Alignment explanation
Indices: 345149--345187 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
345139 TTTTCCATTT
345149 AATTCGATTCAAGAA
1 AATTCGATTCAAGAA
* *
345164 ATTTAGATTCAAGAA
1 AATTCGATTCAAGAA
345179 AATTCGATT
1 AATTCGATT
345188 AGAATTGATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (15 bp):
AATTCGATTCAAGAA
Found at i:347469 original size:18 final size:18
Alignment explanation
Indices: 347446--347526 Score: 117
Period size: 18 Copynumber: 4.4 Consensus size: 18
347436 GATATACAGC
347446 GGTCCTTCGGGACATAGT
1 GGTCCTTCGGGACATAGT
347464 GGTCCTTCGGGACATAGT
1 GGTCCTTCGGGACATAGT
* *
347482 GGTTCTTCGGAACAATCAGT
1 GGTCCTTCGGGAC-AT-AGT
*
347502 GGTCTTTCGGGACATAGT
1 GGTCCTTCGGGACATAGT
347520 GGTCCTT
1 GGTCCTT
347527 TGGAACAAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
18 38 0.69
19 4 0.07
20 13 0.24
ACGTcount: A:0.17, C:0.21, G:0.31, T:0.31
Consensus pattern (18 bp):
GGTCCTTCGGGACATAGT
Found at i:347504 original size:38 final size:38
Alignment explanation
Indices: 347446--347534 Score: 128
Period size: 38 Copynumber: 2.4 Consensus size: 38
347436 GATATACAGC
*
347446 GGTCCTTCGGGAC-AT-AGTGGTCCTTCGGGACATAGT
1 GGTCCTTCGGAACAATCAGTGGTCCTTCGGGACATAGT
* *
347482 GGTTCTTCGGAACAATCAGTGGTCTTTCGGGACATAGT
1 GGTCCTTCGGAACAATCAGTGGTCCTTCGGGACATAGT
*
347520 GGTCCTTTGGAACAA
1 GGTCCTTCGGAACAA
347535 ATACTGAACG
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
36 11 0.24
37 2 0.04
38 33 0.72
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.29
Consensus pattern (38 bp):
GGTCCTTCGGAACAATCAGTGGTCCTTCGGGACATAGT
Found at i:353762 original size:64 final size:63
Alignment explanation
Indices: 353680--353837 Score: 183
Period size: 63 Copynumber: 2.5 Consensus size: 63
353670 TTCAAGGTGT
* * **
353680 ATCGATGCACATGAAGTGCATCGATGCACTCTGATAAAATAAAAACATCGAATGCCATT-AGTGC
1 ATCGATGCATAAGAAGTGCATCGATGCAC-CCCATAAAATAAAAACATCGAATGCCATTCA-TGC
* ** * **
353744 ATCGATGCATAAGGAGTGCATCGATGCACCCCATTGAATACAAACATCGAATGTGATTCATGC
1 ATCGATGCATAAGAAGTGCATCGATGCACCCCATAAAATAAAAACATCGAATGCCATTCATGC
* *
353807 ACCGATGCATAAGTAGTGCATCGATGCACCC
1 ATCGATGCATAAGAAGTGCATCGATGCACCC
353838 GTTAAGGAAT
Statistics
Matches: 81, Mismatches: 12, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
63 54 0.67
64 27 0.33
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (63 bp):
ATCGATGCATAAGAAGTGCATCGATGCACCCCATAAAATAAAAACATCGAATGCCATTCATGC
Found at i:353850 original size:24 final size:24
Alignment explanation
Indices: 353823--353902 Score: 98
Period size: 24 Copynumber: 3.5 Consensus size: 24
353813 GCATAAGTAG
353823 TGCATCGATGCACCCGTTAAGGAA
1 TGCATCGATGCACCCGTTAAGGAA
* *
353847 TGCATCGAT-C-CAC-TATAA--AG
1 TGCATCGATGCACCCGT-TAAGGAA
353867 TGCATCGATGCACCCGTTAAGGAA
1 TGCATCGATGCACCCGTTAAGGAA
353891 TGCATCGATGCA
1 TGCATCGATGCA
353903 TTGTAGAGTG
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
20 10 0.22
21 2 0.04
22 10 0.22
23 2 0.04
24 22 0.48
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (24 bp):
TGCATCGATGCACCCGTTAAGGAA
Found at i:353871 original size:44 final size:44
Alignment explanation
Indices: 353821--353920 Score: 164
Period size: 44 Copynumber: 2.3 Consensus size: 44
353811 ATGCATAAGT
353821 AGTGCATCGATGCACCCGTTAAGGAATGCATCGATCCACTATAA
1 AGTGCATCGATGCACCCGTTAAGGAATGCATCGATCCACTATAA
* * * *
353865 AGTGCATCGATGCACCCGTTAAGGAATGCATCGATGCATTGTAG
1 AGTGCATCGATGCACCCGTTAAGGAATGCATCGATCCACTATAA
353909 AGTGCATCGATG
1 AGTGCATCGATG
353921 TATACCCTCA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 52 1.00
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.24
Consensus pattern (44 bp):
AGTGCATCGATGCACCCGTTAAGGAATGCATCGATCCACTATAA
Found at i:354331 original size:20 final size:20
Alignment explanation
Indices: 354286--354340 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
354276 TTGATACAGG
*
354286 TATGTGAATATTGAAAAGAAT
1 TATGTGTATA-TGAAAAGAAT
*
354307 CATGTGTATATGAAATA-AAT
1 TATGTGTATATGAAA-AGAAT
354327 TATGTGCTATATGA
1 TATGTG-TATATGA
354341 GAAGTTATAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.42, C:0.04, G:0.18, T:0.36
Consensus pattern (20 bp):
TATGTGTATATGAAAAGAAT
Found at i:354467 original size:18 final size:18
Alignment explanation
Indices: 354444--354502 Score: 82
Period size: 18 Copynumber: 3.2 Consensus size: 18
354434 AGGGATATAC
354444 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
354462 AGTGGTTCTTCGGAACAAT
1 AGTGGTCCTTCGGGAC-AT
354481 CAGTGGTCCTTCGGGACAT
1 -AGTGGTCCTTCGGGACAT
354500 AGT
1 AGT
354503 TGTAACACCC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
18 17 0.49
19 4 0.11
20 14 0.40
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:355154 original size:18 final size:18
Alignment explanation
Indices: 355131--355219 Score: 133
Period size: 18 Copynumber: 4.8 Consensus size: 18
355121 GTTCAATATT
355131 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
355149 TGTCCCGAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
* *
355168 TTGTTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
355187 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
355205 TGTCTCGAAGGACCA
1 TGTCCCGAAGGACCA
355220 TTGTATATCC
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
18 47 0.73
19 2 0.03
20 15 0.23
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:355177 original size:38 final size:37
Alignment explanation
Indices: 355130--355219 Score: 130
Period size: 38 Copynumber: 2.4 Consensus size: 37
355120 CGTTCAATAT
*
355130 TTGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGA
1 TTGTTCCGAAGGACCACTATGTCCCGAAGGACCACT-A
*
355168 TTGTTCCGAAGAACCACTATGTCCCGAAGGACCACTA
1 TTGTTCCGAAGGACCACTATGTCCCGAAGGACCACTA
355205 -TG-TCTCGAAGGACCA
1 TTGTTC-CGAAGGACCA
355220 TTGTATATCC
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
35 2 0.04
36 11 0.23
37 1 0.02
38 34 0.71
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (37 bp):
TTGTTCCGAAGGACCACTATGTCCCGAAGGACCACTA
Found at i:355372 original size:21 final size:20
Alignment explanation
Indices: 355325--355379 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
355315 CTATCTCTTC
355325 TCATATAGCACATAATTTATT
1 TCATATA-CACATAATTTATT
*
355346 TCATATACACATGATTCT-TT
1 TCATATACACATAATT-TATT
*
355366 TCAATATTCACATA
1 TC-ATATACACATA
355380 CTTGTATCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 12 0.41
21 17 0.59
ACGTcount: A:0.36, C:0.18, G:0.04, T:0.42
Consensus pattern (20 bp):
TCATATACACATAATTTATT
Found at i:355759 original size:21 final size:21
Alignment explanation
Indices: 355735--355788 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
355725 CTCGGAGGGA
355735 ACCGATTCCCCCATAGGGGGT
1 ACCGATTCCCCCATAGGGGGT
355756 ACCGATTCCCCCATAGGGGGT
1 ACCGATTCCCCCATAGGGGGT
355777 ACCGATTCCCCC
1 ACCGATTCCCCC
355789 CTGTTCAATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.39, G:0.24, T:0.19
Consensus pattern (21 bp):
ACCGATTCCCCCATAGGGGGT
Found at i:361597 original size:20 final size:21
Alignment explanation
Indices: 361560--361620 Score: 61
Period size: 23 Copynumber: 2.9 Consensus size: 21
361550 TTTTGGTGCA
* * *
361560 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTTCCCCTTT
361580 GAGGGAACCGATTTCCCCTTT
1 GAGGGAACCGATTTCCCCTTT
*
361601 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATTTCCCC
361621 CACAGGGGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 10 0.29
21 8 0.24
22 1 0.03
23 15 0.44
ACGTcount: A:0.21, C:0.33, G:0.26, T:0.20
Consensus pattern (21 bp):
GAGGGAACCGATTTCCCCTTT
Found at i:361606 original size:22 final size:22
Alignment explanation
Indices: 361562--361643 Score: 71
Period size: 21 Copynumber: 3.8 Consensus size: 22
361552 TTGGTGCAGA
*
361562 GGGAATCGA-TCCCCCCTTGA-
1 GGGAACCGATTCCCCCCTTGAG
* *
361582 GGGAACCGATTTCCCCTTTGAAG
1 GGGAACCGATTCCCCCCTTG-AG
**
361605 GGGAACCGATTCCCCCC-ACAG
1 GGGAACCGATTCCCCCCTTGAG
* *
361626 GGGAATCGATACCCCCCT
1 GGGAACCGATTCCCCCCT
361644 GGGGTTCTGT
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
20 8 0.16
21 25 0.51
22 1 0.02
23 15 0.31
ACGTcount: A:0.22, C:0.35, G:0.24, T:0.18
Consensus pattern (22 bp):
GGGAACCGATTCCCCCCTTGAG
Found at i:365484 original size:63 final size:64
Alignment explanation
Indices: 365417--365578 Score: 193
Period size: 63 Copynumber: 2.5 Consensus size: 64
365407 ATTCCTTAAT
* *
365417 GGGTGCATCGATGCACTACTTATGCATCGGTGCA-TGAATCACATTCGATGTTTGTATTCAAT-G
1 GGGTGCATCGATGCACTACTTATGCATCGATGCACT-AATCACATTCGATGTTTGTATTCAATCA
* ** * **
365480 GGGTGCATCGATGCACTCCTTATGCATCGATGCACTAATGGCATTCGATGTTTTTATTTTATCA
1 GGGTGCATCGATGCACTACTTATGCATCGATGCACTAATCACATTCGATGTTTGTATTCAATCA
* * * *
365544 GAGTGCATCGATGCACTTCATGTGCATCGATGCAC
1 GGGTGCATCGATGCACTACTTATGCATCGATGCAC
365579 CTTGAACAAT
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
63 53 0.62
64 32 0.38
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (64 bp):
GGGTGCATCGATGCACTACTTATGCATCGATGCACTAATCACATTCGATGTTTGTATTCAATCA
Found at i:371840 original size:18 final size:18
Alignment explanation
Indices: 371725--371833 Score: 164
Period size: 18 Copynumber: 5.9 Consensus size: 18
371715 GTTCAGTATT
*
371725 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
*
371743 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
371761 TGTCCCGAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
* *
371780 TTGTTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
371799 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
371817 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
371834 GTATCCCTCG
Statistics
Matches: 84, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
18 67 0.80
19 2 0.02
20 15 0.18
ACGTcount: A:0.28, C:0.32, G:0.20, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:371975 original size:21 final size:20
Alignment explanation
Indices: 371928--371982 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
371918 CTATCACTTC
371928 TCATATAGCACATAATTTATT
1 TCATATA-CACATAATTTATT
*
371949 TCATATACACATGATTCT-TT
1 TCATATACACATAATT-TATT
*
371969 TCAATATTCACATA
1 TC-ATATACACATA
371983 CTTGTATCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 12 0.41
21 17 0.59
ACGTcount: A:0.36, C:0.18, G:0.04, T:0.42
Consensus pattern (20 bp):
TCATATACACATAATTTATT
Found at i:372446 original size:62 final size:64
Alignment explanation
Indices: 372378--372533 Score: 176
Period size: 62 Copynumber: 2.5 Consensus size: 64
372368 ATTTCTTAAC
*
372378 GGGTGCATCGATGCACTACTTATGCATCG-TGCA-TGAATCACATTCGATGTTTGTATTCAAT-G
1 GGGTGCATCGATGCACTACTTATGCATCGATGCACT-AATCACATTCGATGTTTGTATTCAATCA
* ** * **
372440 GGGTGCATCG-TGCACTCCTTATGCATCGATGCACTAATGGCATTCGATGTTTTTATTTTATCA
1 GGGTGCATCGATGCACTACTTATGCATCGATGCACTAATCACATTCGATGTTTGTATTCAATCA
* * * *
372503 GAGTGCATCGATGCACTTCATGTGCATCGAT
1 GGGTGCATCGATGCACTACTTATGCATCGAT
372534 ACACCTTGAA
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
61 17 0.22
62 35 0.44
63 10 0.13
64 17 0.22
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (64 bp):
GGGTGCATCGATGCACTACTTATGCATCGATGCACTAATCACATTCGATGTTTGTATTCAATCA
Found at i:373034 original size:13 final size:13
Alignment explanation
Indices: 373016--373042 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
373006 TCAGCTTAAA
373016 GAAATCTCACCTT
1 GAAATCTCACCTT
373029 GAAATCTCACCTT
1 GAAATCTCACCTT
373042 G
1 G
373043 CTTAGCTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.30, G:0.11, T:0.30
Consensus pattern (13 bp):
GAAATCTCACCTT
Found at i:373963 original size:16 final size:16
Alignment explanation
Indices: 373942--373973 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
373932 TAGGGGTGTT
373942 ACACGAACATAAACGA
1 ACACGAACATAAACGA
373958 ACACGAACATAAACGA
1 ACACGAACATAAACGA
373974 GCATAAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.25, G:0.12, T:0.06
Consensus pattern (16 bp):
ACACGAACATAAACGA
Found at i:376459 original size:9 final size:9
Alignment explanation
Indices: 376445--376471 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
376435 TCTCACTACC
376445 TACGAGAAA
1 TACGAGAAA
376454 TACGAGAAA
1 TACGAGAAA
376463 TACGAGAAA
1 TACGAGAAA
376472 GACAACAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.11, G:0.22, T:0.11
Consensus pattern (9 bp):
TACGAGAAA
Found at i:381538 original size:22 final size:22
Alignment explanation
Indices: 381510--381562 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
381500 TCATGAGTTA
*
381510 CAGGAGTTACATGATTTAATTT
1 CAGGAGTTACATGATATAATTT
381532 CAGGAGTTACATGATATAATTT
1 CAGGAGTTACATGATATAATTT
*
381554 CATGAGTTA
1 CAGGAGTTA
381563 TAACAGCTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.38
Consensus pattern (22 bp):
CAGGAGTTACATGATATAATTT
Found at i:383075 original size:13 final size:13
Alignment explanation
Indices: 383057--383084 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
383047 CTCTCAACAT
383057 TCAGAATTCACTC
1 TCAGAATTCACTC
383070 TCAGAATTCACTC
1 TCAGAATTCACTC
383083 TC
1 TC
383085 CAAGTGTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.32, G:0.07, T:0.32
Consensus pattern (13 bp):
TCAGAATTCACTC
Found at i:384024 original size:3 final size:3
Alignment explanation
Indices: 384016--384050 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
384006 ATTTGAGCCA
*
384016 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAA AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
384051 AAAAATTAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:386733 original size:15 final size:15
Alignment explanation
Indices: 386713--386742 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
386703 AAACAAACAT
386713 TAGATTTTAAATATC
1 TAGATTTTAAATATC
386728 TAGATTTTAAATATC
1 TAGATTTTAAATATC
386743 ATGAAAACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (15 bp):
TAGATTTTAAATATC
Found at i:394894 original size:127 final size:126
Alignment explanation
Indices: 394670--394910 Score: 448
Period size: 127 Copynumber: 1.9 Consensus size: 126
394660 GGTGTTTAGT
*
394670 ATAACAACTTTCTTCCCTCCTTTTTCTTTTTGTGTGGAGAATGTAATCTACTAAATTGGTTTAGG
1 ATAACAACTTTCTTCCATCCTTTTTCTTTTTGTGTGGAGAATGTAATCTACTAAATTGGTTTAGG
394735 ATTTTGATTGCCACTTTTCAGCTTAAAATTGGGATACTCGG-ATGAAAAATTGTAATAACA
66 ATTTTGATTGCCACTTTTCAGCTTAAAATTGGGATACTCGGAATGAAAAATTGTAATAACA
394795 ATAACAACTTTCTTCCATCCTTTTTCTTTTTGTGTGTGAGAATGTAAATCTACTAAATTGGTTTA
1 ATAACAACTTTCTTCCATCCTTTTTCTTTTTGTGTG-GAGAATGT-AATCTACTAAATTGGTTTA
394860 GGATTTTGATTGCCACTTTTCAGCTTAAAATTGGGATACTCGGAATGAAAA
64 GGATTTTGATTGCCACTTTTCAGCTTAAAATTGGGATACTCGGAATGAAAA
394911 GAACCAAAAG
Statistics
Matches: 112, Mismatches: 1, Indels: 3
0.97 0.01 0.03
Matches are distributed among these distances:
125 35 0.31
126 8 0.07
127 62 0.55
128 7 0.06
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (126 bp):
ATAACAACTTTCTTCCATCCTTTTTCTTTTTGTGTGGAGAATGTAATCTACTAAATTGGTTTAGG
ATTTTGATTGCCACTTTTCAGCTTAAAATTGGGATACTCGGAATGAAAAATTGTAATAACA
Found at i:397894 original size:15 final size:15
Alignment explanation
Indices: 397874--397904 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
397864 GATGAAAGAT
397874 TTTCTTTTAATCATA
1 TTTCTTTTAATCATA
397889 TTTCTTTTAATCATA
1 TTTCTTTTAATCATA
397904 T
1 T
397905 ATAGGCTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.13, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTCTTTTAATCATA
Found at i:401735 original size:2 final size:2
Alignment explanation
Indices: 401728--401755 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
401718 TCATATCTTC
401728 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
401756 TTTTTTATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:408978 original size:20 final size:20
Alignment explanation
Indices: 408953--408995 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
408943 TCTAAAAGCC
*
408953 CATTTAGGATCATATAGATG
1 CATTTAGGAGCATATAGATG
*
408973 CATTTAGGAGCATATAGTTG
1 CATTTAGGAGCATATAGATG
408993 CAT
1 CAT
408996 GTGGTGGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGAGCATATAGATG
Found at i:413630 original size:16 final size:17
Alignment explanation
Indices: 413611--413642 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
413601 CATTATGTTA
413611 AAAAAATAAA-AAAAAG
1 AAAAAATAAAGAAAAAG
413627 AAAAAATAAAGAAAAA
1 AAAAAATAAAGAAAAA
413643 ATAAAGTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.88, C:0.00, G:0.06, T:0.06
Consensus pattern (17 bp):
AAAAAATAAAGAAAAAG
Found at i:413632 original size:11 final size:11
Alignment explanation
Indices: 413618--413648 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
413608 TTAAAAAAAT
413618 AAAAA-AAAGA
1 AAAAATAAAGA
413628 AAAAATAAAGA
1 AAAAATAAAGA
413639 AAAAATAAAG
1 AAAAATAAAG
413649 TTGTGAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.25
11 15 0.75
ACGTcount: A:0.84, C:0.00, G:0.10, T:0.06
Consensus pattern (11 bp):
AAAAATAAAGA
Found at i:418544 original size:5 final size:5
Alignment explanation
Indices: 418534--418558 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
418524 AAGAGAGAAG
418534 TGGGT TGGGT TGGGT TGGGT TGGGT
1 TGGGT TGGGT TGGGT TGGGT TGGGT
418559 GTGAATCGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.60, T:0.40
Consensus pattern (5 bp):
TGGGT
Found at i:429787 original size:17 final size:17
Alignment explanation
Indices: 429765--429798 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
429755 TAATACTTTC
*
429765 TCAATTTCGTTTGGTTA
1 TCAATTTCGTTCGGTTA
429782 TCAATTTCGTTCGGTTA
1 TCAATTTCGTTCGGTTA
429799 ATTAACCGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.15, G:0.18, T:0.50
Consensus pattern (17 bp):
TCAATTTCGTTCGGTTA
Found at i:433893 original size:35 final size:36
Alignment explanation
Indices: 433808--433910 Score: 94
Period size: 35 Copynumber: 2.9 Consensus size: 36
433798 ATTTGGTATT
*
433808 TAAATACAACAAACTTACAATAA-GA-ATTAAATGG
1 TAAATACAACAAAATTACAATAATGATATTAAATGG
*
433842 TAAATGATAATC-AAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAA-CAAAATTACAATAA-TGATATTAAATGG
433880 -AAATA-AACAAAATTA-AATGAAAT-ATATTAAA
1 TAAATACAACAAAATTACAAT--AATGATATTAAA
433911 AAAAAGTCCA
Statistics
Matches: 59, Mismatches: 2, Indels: 16
0.77 0.03 0.21
Matches are distributed among these distances:
34 17 0.29
35 23 0.39
36 4 0.07
37 6 0.10
38 9 0.15
ACGTcount: A:0.57, C:0.08, G:0.08, T:0.27
Consensus pattern (36 bp):
TAAATACAACAAAATTACAATAATGATATTAAATGG
Found at i:434014 original size:45 final size:49
Alignment explanation
Indices: 433924--434014 Score: 127
Period size: 49 Copynumber: 1.9 Consensus size: 49
433914 AAGTCCAACA
* * *
433924 AATTTAACAAAATAAAGTAAGTATTAAATGATAAATAATAAAAAATTAC
1 AATTAAACAAAATAAAGTAAATATCAAATGATAAATAATAAAAAATTAC
433973 AATTAAACAAAATAAAGTAAATA-CAAAT-AT-AATAA-AAAAAAT
1 AATTAAACAAAATAAAGTAAATATCAAATGATAAATAATAAAAAAT
434015 ATATCGATGC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
45 7 0.18
46 5 0.13
47 2 0.05
48 4 0.10
49 21 0.54
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.25
Consensus pattern (49 bp):
AATTAAACAAAATAAAGTAAATATCAAATGATAAATAATAAAAAATTAC
Found at i:434134 original size:21 final size:21
Alignment explanation
Indices: 434110--434149 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
434100 TCATCGTTGT
434110 CATCGTCGA-CGTCGTCGTCAC
1 CATCGTC-ATCGTCGTCGTCAC
434131 CATCGTCATCGTCGTCGTC
1 CATCGTCATCGTCGTCGTC
434150 CTGAGCAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.12, C:0.38, G:0.23, T:0.28
Consensus pattern (21 bp):
CATCGTCATCGTCGTCGTCAC
Found at i:434950 original size:50 final size:49
Alignment explanation
Indices: 434896--435002 Score: 133
Period size: 49 Copynumber: 2.2 Consensus size: 49
434886 AGATACCCAG
* * * *
434896 GTATAGCGCGGATCAGGGGGCGCGCTATACCCACGTGGTGCCAGATCATC
1 GTATAGCGCGGAGCA-GGGGCGCGCTATACCCACGTGGCGCCAAATCAGC
* * * *
434946 GTATATCGCGGGGCAGGGGCGCGTTATACCCACGTGGCGTCAAATCAGC
1 GTATAGCGCGGAGCAGGGGCGCGCTATACCCACGTGGCGCCAAATCAGC
434995 GTATAGCG
1 GTATAGCG
435003 TGATTCAGGG
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
49 36 0.75
50 12 0.25
ACGTcount: A:0.21, C:0.26, G:0.35, T:0.19
Consensus pattern (49 bp):
GTATAGCGCGGAGCAGGGGCGCGCTATACCCACGTGGCGCCAAATCAGC
Found at i:435094 original size:30 final size:29
Alignment explanation
Indices: 435032--435094 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
435022 TACTACTACG
*
435032 GGTGTTAAATCAAAAAATATAATCTGACC
1 GGTGTTAAATCAAAAAATATAATCTCACC
* *
435061 GGTGTTAAATCGATAAATAT-ATCGATCACC
1 GGTGTTAAATCAAAAAATATAATC--TCACC
435091 GGTG
1 GGTG
435095 ATTTATCGAG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 3 0.10
29 18 0.62
30 8 0.28
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (29 bp):
GGTGTTAAATCAAAAAATATAATCTCACC
Found at i:435661 original size:31 final size:31
Alignment explanation
Indices: 435626--435719 Score: 95
Period size: 32 Copynumber: 3.0 Consensus size: 31
435616 CTATAGTAAG
435626 TGTAAAATTTTGATAAATTTAATGATCAATT
1 TGTAAAATTTTGATAAATTTAATGATCAATT
* * *
435657 TGTAATAA-TTCGATAAAATATAATGATCATTT
1 TGTAA-AATTTTGAT-AAATTTAATGATCAATT
**
435689 TGTATCATTTAT-ATAAATTTAATGA-CAATT
1 TGTAAAATTT-TGATAAATTTAATGATCAATT
435719 T
1 T
435720 TATAACTTTA
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
30 5 0.10
31 21 0.41
32 25 0.49
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (31 bp):
TGTAAAATTTTGATAAATTTAATGATCAATT
Found at i:435720 original size:31 final size:34
Alignment explanation
Indices: 435638--435720 Score: 97
Period size: 31 Copynumber: 2.6 Consensus size: 34
435628 TAAAATTTTG
435638 ATAAATTTAATGATCAA-TTTGTAATAATTCGAT
1 ATAAATTTAATGATCAATTTTGTAATAATTCGAT
* * *
435671 A-AAATATAATGATC-ATTTTGT-ATCATT-TAT
1 ATAAATTTAATGATCAATTTTGTAATAATTCGAT
435701 ATAAATTTAATGA-CAATTTT
1 ATAAATTTAATGATCAATTTT
435721 ATAACTTTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
30 4 0.09
31 21 0.49
32 17 0.40
33 1 0.02
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.45
Consensus pattern (34 bp):
ATAAATTTAATGATCAATTTTGTAATAATTCGAT
Found at i:446656 original size:23 final size:22
Alignment explanation
Indices: 446630--446679 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
446620 GATGGATATT
446630 TCATATCTCTTAAA-AATATCACA
1 TCATAT-T-TTAAACAATATCACA
*
446653 TCATATTTTAAACTAATATCATA
1 TCATATTTTAAAC-AATATCACA
446676 TCAT
1 TCAT
446680 TTAATTTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 5 0.21
22 1 0.04
23 18 0.75
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.40
Consensus pattern (22 bp):
TCATATTTTAAACAATATCACA
Found at i:447646 original size:7 final size:7
Alignment explanation
Indices: 447636--447670 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
447626 GTTGTAAGTT
447636 GTAGCCA
1 GTAGCCA
447643 GTAGCCA
1 GTAGCCA
447650 GTAGCCA
1 GTAGCCA
447657 GTAGCCA
1 GTAGCCA
447664 GTAGCCA
1 GTAGCCA
447671 AGCGGGAAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.29, C:0.29, G:0.29, T:0.14
Consensus pattern (7 bp):
GTAGCCA
Found at i:455178 original size:111 final size:111
Alignment explanation
Indices: 455038--455259 Score: 372
Period size: 111 Copynumber: 2.0 Consensus size: 111
455028 ATTACAAAAA
* * *
455038 TTAATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTAATAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATACATTAAATAAATCAACTAAATATTAATAATAATTTAAATTA
* *
455103 AATTAAACCGTTAAAATGTTACCGTATCAACAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
*
455149 TTAATTCTTAATCTAATAATCATACATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATACATTAAATAAATCAACTAAATATTAATAATAATTTAAATTA
**
455214 AATTAAAACGTTAAAATGTTACCGTATCAGTAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
455260 ATGATTTCCA
Statistics
Matches: 103, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
111 103 1.00
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATACATTAAATAAATCAACTAAATATTAATAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
Found at i:455630 original size:51 final size:50
Alignment explanation
Indices: 455523--455649 Score: 164
Period size: 51 Copynumber: 2.5 Consensus size: 50
455513 AAATATACAG
* * * * **
455523 GTATAGCGTGGTGCAAGGGGCACGCTATACCTACGTGGCGCCAGCTCACC
1 GTATAGCGCGGTGCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCACC
* *
455573 GTATAGCGCGGTACAGGGGGCGCGCTATACCCCACGTGGCGCCAAATCATC
1 GTATAGCGCGGTGCAGGGGGCGCGCTATA-CCCACGTGGCGCCAAATCACC
*
455624 GTATAGCGCGGTGCAGTGGGCGCGCT
1 GTATAGCGCGGTGCAGGGGGCGCGCT
455650 TTACTGCTAA
Statistics
Matches: 66, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
50 25 0.38
51 41 0.62
ACGTcount: A:0.19, C:0.29, G:0.35, T:0.17
Consensus pattern (50 bp):
GTATAGCGCGGTGCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCACC
Found at i:456212 original size:21 final size:20
Alignment explanation
Indices: 456186--456235 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
456176 CTCCATGTCC
*
456186 CTTCTGAGCTGTCTTCTTCTG
1 CTTCTGAACT-TCTTCTTCTG
*
456207 TTTCTGTAACTTCTTCTTCTG
1 CTTCTG-AACTTCTTCTTCTG
456228 CTTCTGAA
1 CTTCTGAA
456236 AATGTTGATC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 2 0.08
21 20 0.80
22 3 0.12
ACGTcount: A:0.10, C:0.26, G:0.14, T:0.50
Consensus pattern (20 bp):
CTTCTGAACTTCTTCTTCTG
Found at i:468599 original size:2 final size:2
Alignment explanation
Indices: 468592--468637 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
468582 TTATTCCATG
468592 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- 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
468633 A- AT AT
1 AT AT AT
468638 CCAATTAACT
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:470967 original size:7 final size:7
Alignment explanation
Indices: 470955--470983 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
470945 GTTCTTAAAG
470955 TTGCAAC
1 TTGCAAC
470962 TTGCAAC
1 TTGCAAC
470969 TTGCAAC
1 TTGCAAC
470976 TTGCAAC
1 TTGCAAC
470983 T
1 T
470984 GCGAGAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (7 bp):
TTGCAAC
Found at i:471717 original size:28 final size:28
Alignment explanation
Indices: 471686--471739 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
471676 GTCGGGTCGG
*
471686 GTTTTTTTAAGTTTGATATTCAGGTCAA
1 GTTTTTTTAAGTGTGATATTCAGGTCAA
*
471714 GTTTTTTTAAGTGTGATATTCGGGTC
1 GTTTTTTTAAGTGTGATATTCAGGTC
471740 GGGTTCGGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.20, C:0.07, G:0.22, T:0.50
Consensus pattern (28 bp):
GTTTTTTTAAGTGTGATATTCAGGTCAA
Found at i:472330 original size:16 final size:16
Alignment explanation
Indices: 472309--472373 Score: 67
Period size: 16 Copynumber: 3.9 Consensus size: 16
472299 AGGTTTCAGA
*
472309 TTCAGATTCTAATTCC
1 TTCAGATTCCAATTCC
*
472325 TTCAGATCCCAATTCC
1 TTCAGATTCCAATTCC
* * *
472341 TCCAGAATCCAATTTC
1 TTCAGATTCCAATTCC
472357 TTCACAGATTCCAATTC
1 TT--CAGATTCCAATTC
472374 TCTCGTAAAG
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
16 27 0.71
18 11 0.29
ACGTcount: A:0.28, C:0.31, G:0.06, T:0.35
Consensus pattern (16 bp):
TTCAGATTCCAATTCC
Found at i:473653 original size:42 final size:42
Alignment explanation
Indices: 473594--473677 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
473584 AACAGGAAGA
*
473594 AAGCAAAACAGAGGAAGACGATAAGGGATCATCGCTCCGCCT
1 AAGCAAAACAGAGGAAGACGATAAGGGATCATCACTCCGCCT
*
473636 AAGCAAAACAGAGGAAGACGATAAGGGATCATCACTCTGCCT
1 AAGCAAAACAGAGGAAGACGATAAGGGATCATCACTCCGCCT
473678 CTAACAATGC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.39, C:0.23, G:0.25, T:0.13
Consensus pattern (42 bp):
AAGCAAAACAGAGGAAGACGATAAGGGATCATCACTCCGCCT
Found at i:475193 original size:68 final size:68
Alignment explanation
Indices: 475084--475358 Score: 388
Period size: 68 Copynumber: 4.0 Consensus size: 68
475074 AAAAGATTAA
* *
475084 GAGGCCTAACTGAGCATATGACAGAAATGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTC
1 GAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTC
475149 TTT
66 TTT
** * *
475152 GAGGCCTAACTGTTTATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAAACTAAATGTC
1 GAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTC
475217 TTT
66 TTT
* * * * *
475220 GAGGCTTAACTGTGCATATGATATAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCC
1 GAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTC
475285 TTT
66 TTT
* * * * * *
475288 GAGGCCTAACTGTGCATATGACAAAAAAGTGTCAATTATGTCAGTTAGATGAAAGATTAAGTATC
1 GAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTC
*
475353 GTT
66 TTT
475356 GAG
1 GAG
475359 TAAATGAAAA
Statistics
Matches: 181, Mismatches: 26, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
68 181 1.00
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.31
Consensus pattern (68 bp):
GAGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTC
TTT
Found at i:475428 original size:80 final size:78
Alignment explanation
Indices: 475290--475676 Score: 348
Period size: 80 Copynumber: 5.0 Consensus size: 78
475280 GTGCCTTTGA
* * * * * *
475290 GGCCTAACTGTGC-ATATGACAAAAAAGTGTCAATTATGTCAGTTAGATGAAAGATTAAGTATCG
1 GGCCTAGCTGTGCAAT-TGGCAGAAAGGTGTCAATTATG-CAGTTAGATGAACGGTTAAGTA-CG
*
475354 TTGAGTAAATGAAAAT
63 TTGAGTAAAAGAAAAT
*
475370 GGCCTAGCTGTGCAATTGGCAAAAAGGTGTCAATTATGCAAGTTAGATGAACGGTTAAGTACCGT
1 GGCCTAGCTGTGCAATTGGCAGAAAGGTGTCAATTATGC-AGTTAGATGAACGGTTAAGTA-CGT
*
475435 TGAGTAAAAAAAAAAT
64 TGAGT-AAAAGAAAAT
* * *
475451 GGCCTAGCTGTGTAATTGGCAGAATGATGTCAATTATGCCAGTTAGATGAA----T--G---GTT
1 GGCCTAGCTGTGCAATTGGCAGAAAGGTGTCAATTATG-CAGTTAGATGAACGGTTAAGTACGTT
*
475507 AAGTAAAAGAAAAT
65 GAGTAAAAGAAAAT
* * * *
475521 GGCCTAGTTGTGCAGTTGGTAGAAAGATGTCAATTATGCCAGTTAGATGAACGGTTAAGTACAGT
1 GGCCTAGCTGTGCAATTGGCAGAAAGGTGTCAATTATG-CAGTTAGATGAACGGTTAAGTAC-GT
475586 TGAGTAAAAGAATAAT
64 TGAGTAAAAGAA-AAT
*** * * * **
475602 TATCTAACTGTGC-ATTGGTAGAAAGGTGTCAATTATGTCAGTTAGACGAAC-GTTAAACACCGT
1 GGCCTAGCTGTGCAATTGGCAGAAAGGTGTCAATTATG-CAGTTAGATGAACGGTTAAGTA-CGT
*
475665 TGAGTAAGAGAA
64 TGAGTAAAAGAA
475677 TGGATAAATT
Statistics
Matches: 259, Mismatches: 32, Indels: 33
0.80 0.10 0.10
Matches are distributed among these distances:
70 55 0.21
71 6 0.02
74 1 0.00
75 1 0.00
76 1 0.00
77 1 0.00
79 20 0.08
80 107 0.41
81 66 0.25
82 1 0.00
ACGTcount: A:0.37, C:0.11, G:0.25, T:0.28
Consensus pattern (78 bp):
GGCCTAGCTGTGCAATTGGCAGAAAGGTGTCAATTATGCAGTTAGATGAACGGTTAAGTACGTTG
AGTAAAAGAAAAT
Found at i:475551 original size:70 final size:70
Alignment explanation
Indices: 475441--475581 Score: 219
Period size: 70 Copynumber: 2.0 Consensus size: 70
475431 CCGTTGAGTA
* * *
475441 AAAAAAAAATGGCCTAGCTGTGTAATTGGCAGAATGATGTCAATTATGCCAGTTAGATGAATGGT
1 AAAAAAAAATGGCCTAGCTGTGCAATTGGCAGAAAGATGTCAATTATGCCAGTTAGATGAACGGT
475506 TAAGT
66 TAAGT
* * * *
475511 AAAAGAAAATGGCCTAGTTGTGCAGTTGGTAGAAAGATGTCAATTATGCCAGTTAGATGAACGGT
1 AAAAAAAAATGGCCTAGCTGTGCAATTGGCAGAAAGATGTCAATTATGCCAGTTAGATGAACGGT
475576 TAAGT
66 TAAGT
475581 A
1 A
475582 CAGTTGAGTA
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
70 64 1.00
ACGTcount: A:0.37, C:0.10, G:0.26, T:0.28
Consensus pattern (70 bp):
AAAAAAAAATGGCCTAGCTGTGCAATTGGCAGAAAGATGTCAATTATGCCAGTTAGATGAACGGT
TAAGT
Found at i:475554 original size:151 final size:150
Alignment explanation
Indices: 475357--475647 Score: 402
Period size: 151 Copynumber: 1.9 Consensus size: 150
475347 AGTATCGTTG
* *
475357 AGTAAATGAAAATGGCCTAGCTGTGCAATTGGCAAAAAGGTGTCAATTATGCAAGTTAGATGAAC
1 AGTAAAAGAAAATGGCCTAGCTGTGCAATTGGCAAAAAGATGTCAATTATGCAAGTTAGATGAAC
* * * *
475422 GGTTAAGTACCGTTGAGTAAAAAAAAAATGGCCTAGCTGTGTAATTGGCAGAATGATGTCAATTA
66 GGTTAAGTACAGTTGAGTAAAAAAAAAATGACCTAACTGTG-AATTGGCAGAAAGATGTCAATTA
475487 TGCCAGTTAGATGAATGGTTA
130 TGCCAGTTAGATGAATGGTTA
* * * * *
475508 AGTAAAAGAAAATGGCCTAGTTGTGCAGTTGGTAGAAAGATGTCAATTATGCCAGTTAGATGAAC
1 AGTAAAAGAAAATGGCCTAGCTGTGCAATTGGCAAAAAGATGTCAATTATGCAAGTTAGATGAAC
* * * * * * *
475573 GGTTAAGTACAGTTGAGTAAAAGAATAATTATCTAACTGTGCATTGGTAGAAAGGTGTCAATTAT
66 GGTTAAGTACAGTTGAGTAAAAAAAAAATGACCTAACTGTGAATTGGCAGAAAGATGTCAATTAT
*
475638 GTCAGTTAGA
131 GCCAGTTAGA
475648 CGAACGTTAA
Statistics
Matches: 121, Mismatches: 19, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
150 29 0.24
151 92 0.76
ACGTcount: A:0.36, C:0.10, G:0.25, T:0.28
Consensus pattern (150 bp):
AGTAAAAGAAAATGGCCTAGCTGTGCAATTGGCAAAAAGATGTCAATTATGCAAGTTAGATGAAC
GGTTAAGTACAGTTGAGTAAAAAAAAAATGACCTAACTGTGAATTGGCAGAAAGATGTCAATTAT
GCCAGTTAGATGAATGGTTA
Found at i:477281 original size:10 final size:10
Alignment explanation
Indices: 477266--477312 Score: 66
Period size: 10 Copynumber: 5.1 Consensus size: 10
477256 CATTTAATAA
477266 ATAAACGAAC
1 ATAAACGAAC
477276 ATAAACGAAC
1 ATAAACGAAC
477286 ATAAACGAAC
1 ATAAACGAAC
477296 ----ACGAAC
1 ATAAACGAAC
477302 ATAAACGAAC
1 ATAAACGAAC
477312 A
1 A
477313 AAATGTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
6 6 0.18
10 27 0.82
ACGTcount: A:0.60, C:0.21, G:0.11, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:477301 original size:16 final size:16
Alignment explanation
Indices: 477280--477312 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
477270 ACGAACATAA
477280 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
477296 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
477312 A
1 A
477313 AAATGTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:477406 original size:16 final size:16
Alignment explanation
Indices: 477385--477453 Score: 111
Period size: 16 Copynumber: 4.3 Consensus size: 16
477375 TAAATAAACG
477385 AACATAAACGAACACA
1 AACATAAACGAACACA
*
477401 AACATAAACGAACACG
1 AACATAAACGAACACA
*
477417 AACATAAATGAACACA
1 AACATAAACGAACACA
*
477433 AACATAAACGAACATA
1 AACATAAACGAACACA
477449 AACAT
1 AACAT
477454 TGGAGACCCT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.61, C:0.22, G:0.07, T:0.10
Consensus pattern (16 bp):
AACATAAACGAACACA
Found at i:478135 original size:14 final size:14
Alignment explanation
Indices: 478079--478144 Score: 68
Period size: 14 Copynumber: 5.0 Consensus size: 14
478069 AATTGGCTTA
* *
478079 AACATAAATGAATG
1 AACATAACTGAACG
* *
478093 AACATAACCGAACA
1 AACATAACTGAACG
478107 AACAT-A---AACG
1 AACATAACTGAACG
478117 AACATAACTGAACG
1 AACATAACTGAACG
478131 AACATAACTGAACG
1 AACATAACTGAACG
478145 TTCACGAACG
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
10 8 0.19
11 1 0.02
13 1 0.02
14 33 0.77
ACGTcount: A:0.55, C:0.20, G:0.12, T:0.14
Consensus pattern (14 bp):
AACATAACTGAACG
Found at i:478143 original size:24 final size:25
Alignment explanation
Indices: 478091--478143 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 25
478081 CATAAATGAA
478091 TGAACATAACCGAACAAACATAAAC
1 TGAACATAACCGAACAAACATAAAC
* *
478116 -GAACATAACTGAACGAACAT-AAC
1 TGAACATAACCGAACAAACATAAAC
478139 TGAAC
1 TGAAC
478144 GTTCACGAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 3 0.12
24 22 0.88
ACGTcount: A:0.53, C:0.23, G:0.11, T:0.13
Consensus pattern (25 bp):
TGAACATAACCGAACAAACATAAAC
Found at i:478423 original size:64 final size:63
Alignment explanation
Indices: 478337--478495 Score: 196
Period size: 64 Copynumber: 2.5 Consensus size: 63
478327 TGCACTAAGA
* * *
478337 GTGCATCGATGCATTAAGTGCATTCGATGTTTCA-AAATAGCCAGAGTGCATCTATGCATG-GCT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAA-AGCCAGAGTGCATCGATGCATGTG-T
* * **
478400 GGTGTATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTTAGTGCATCGATGCATGTGT
1 -GTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAAGCCAGAGTGCATCGATGCATGTGT
*
478465 GTGCATCGATGCATGAAATGCATTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
478496 CAATTTATTT
Statistics
Matches: 83, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
63 2 0.02
64 53 0.64
65 24 0.29
66 4 0.05
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAAGCCAGAGTGCATCGATGCATGTGT
Found at i:479746 original size:65 final size:63
Alignment explanation
Indices: 479677--479836 Score: 196
Period size: 65 Copynumber: 2.5 Consensus size: 63
479667 AATTAAATTG
*
479677 AACATCGAATGCATTTCATGCATCGATGCACATACCATGCACCGATGCACTGAGGAT-TTTATGA
1 AACATCGAATGCATTTAATGCATCGATGCACA-ACCATGCACCGATGCACTGAGGATATTT-TG-
479741 A
63 A
* * * ** *
479742 AACATCGAATGTATTTAATGCATCGATGCACCAGCCATGCATCGATGCACTTTGGCTATTTTGA
1 AACATCGAATGCATTTAATGCATCGATGCA-CAACCATGCACCGATGCACTGAGGATATTTTGA
* *
479806 AACATCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTAATGCATCGATGCAC
479837 TCTTAGTGCA
Statistics
Matches: 83, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
63 1 0.01
64 28 0.34
65 49 0.59
66 5 0.06
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.28
Consensus pattern (63 bp):
AACATCGAATGCATTTAATGCATCGATGCACAACCATGCACCGATGCACTGAGGATATTTTGA
Found at i:479836 original size:17 final size:19
Alignment explanation
Indices: 479808--479856 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
479798 TATTTTGAAA
479808 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
479826 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
479845 CACCGATGCACT
1 CATCGATGCACT
479857 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:486428 original size:34 final size:32
Alignment explanation
Indices: 486375--486444 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
486365 CCTTACAAAC
*
486375 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
486407 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
486441 TCCC
1 TCCC
486445 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:486752 original size:21 final size:21
Alignment explanation
Indices: 486726--486767 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
486716 CCAGAATGGG
*
486726 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
486747 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
486768 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:486993 original size:30 final size:31
Alignment explanation
Indices: 486942--487032 Score: 159
Period size: 31 Copynumber: 3.0 Consensus size: 31
486932 AAATTTTGAA
486942 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
*
486971 TAAATTCAATTCAAGTCTAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
487002 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
487033 CCTTAAATTG
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
29 11 0.19
30 10 0.17
31 37 0.64
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:487882 original size:19 final size:19
Alignment explanation
Indices: 487858--487895 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
487848 TAAAATCAAA
487858 ACTCATGCATGCTTAAAAT
1 ACTCATGCATGCTTAAAAT
487877 ACTCATGCATGCTTAAAAT
1 ACTCATGCATGCTTAAAAT
487896 TAAATGAGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.32
Consensus pattern (19 bp):
ACTCATGCATGCTTAAAAT
Found at i:488150 original size:30 final size:31
Alignment explanation
Indices: 488099--488189 Score: 159
Period size: 31 Copynumber: 3.0 Consensus size: 31
488089 AAATTTTGAA
488099 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
*
488128 TAAATTCAATTCAAGTCTAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
488159 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
488190 CCTTAAATTG
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
29 11 0.19
30 10 0.17
31 37 0.64
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:490088 original size:11 final size:10
Alignment explanation
Indices: 490058--490087 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
490048 TAGTAAGGGG
*
490058 GAGTAATTTG
1 GAGTAATTTT
490068 GAGTAATTTT
1 GAGTAATTTT
490078 GAGTAATTTT
1 GAGTAATTTT
490088 TCAATTGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (10 bp):
GAGTAATTTT
Found at i:490617 original size:64 final size:64
Alignment explanation
Indices: 490410--490619 Score: 214
Period size: 65 Copynumber: 3.2 Consensus size: 64
490400 TTTTTCAAAG
* **
490410 TGATGCA-CTGATGCACCAATCCATGCATCGATGCAC-CATGAATTAAATTG-AACATCGAATGC
1 TGATGCATC-GATGCACCAA-CCATGCATCGATGCACTC-TGGA-TATTTTGAAACATCGAATGC
490472 ATT
62 ATT
* * * **
490475 TCATGCATCGATG-AACATACCATGCACCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCA
1 TGATGCATCGATGCACCA-ACCATGCATCGATGCACTCTGGATATTT-TG-AAACATCGAATGCA
490538 TT
63 TT
* * *
490540 TGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCACCAACCATGCATCGATGCACTCTGGATATTTTGAAACATCGAATGCATT
*
490604 TGATGCATTGATGCAC
1 TGATGCATCGATGCAC
490620 TCTTAGTGCA
Statistics
Matches: 120, Mismatches: 17, Indels: 17
0.78 0.11 0.11
Matches are distributed among these distances:
62 1 0.01
63 3 0.03
64 50 0.42
65 59 0.49
66 7 0.06
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (64 bp):
TGATGCATCGATGCACCAACCATGCATCGATGCACTCTGGATATTTTGAAACATCGAATGCATT
Done.