Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007931.1 Hibiscus syriacus cultivar Beakdansim tig00110339_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: 2341804
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 12
Found at i:1431469 original size:13 final size:13
Alignment explanation
Indices: 1431451--1431485 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1431441 TAATGGGCAA
*
1431451 TTTTGAAAACTAT
1 TTTTGAAAACAAT
1431464 TTTTGAAAACAAT
1 TTTTGAAAACAAT
*
1431477 GTTTGAAAA
1 TTTTGAAAA
1431486 ATCATAATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (13 bp):
TTTTGAAAACAAT
Found at i:1431983 original size:20 final size:22
Alignment explanation
Indices: 1431958--1432034 Score: 70
Period size: 23 Copynumber: 3.6 Consensus size: 22
1431948 AACTCGATGG
*
1431958 GTGTATCGGTACAC-TT-GTGA
1 GTGTATCGGTACACATTAATGA
*
1431978 GTGTATCGATACACATTCAATGA
1 GTGTATCGGTACACATT-AATGA
* *
1432001 ATGTATCGGTACACATTCAT-A
1 GTGTATCGGTACACATTAATGA
* *
1432022 GTTTATCGATACA
1 GTGTATCGGTACA
1432035 TAGCAAGGGG
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
20 13 0.28
21 13 0.28
22 2 0.04
23 18 0.39
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (22 bp):
GTGTATCGGTACACATTAATGA
Found at i:1444549 original size:59 final size:59
Alignment explanation
Indices: 1444457--1444941 Score: 783
Period size: 59 Copynumber: 8.2 Consensus size: 59
1444447 GTTTTCAACA
* *
1444457 TGTATGAATTTTCATATAGGGCACTTCGTGTGCTAATATGATAAGGAATTCATACTAAG
1 TGTATGAATTTCCATATAGGGCACTTCGTGTGCTAACATGATAAGGAATTCATACTAAG
* *
1444516 TGTATGAATTTCCATATTGGGCACTTCGTGTGCTAACATGATAAGGAATTCATACTAGG
1 TGTATGAATTTCCATATAGGGCACTTCGTGTGCTAACATGATAAGGAATTCATACTAAG
*
1444575 TGTATGAATTTCCATATAGGGCACTTCGTGTGCTAACATGATAAGGAATTTATACTAAG
1 TGTATGAATTTCCATATAGGGCACTTCGTGTGCTAACATGATAAGGAATTCATACTAAG
** **
1444634 TGTATTTATTTCCATATAGGGCACTTAATGTGCTAACATGATAAGGAATTCATACTAAG
1 TGTATGAATTTCCATATAGGGCACTTCGTGTGCTAACATGATAAGGAATTCATACTAAG
* * *
1444693 TGTATGAATTTCCTTATAGGGCACTTCGTGTGCTAACATGATAAAGAATTCATATTAAG
1 TGTATGAATTTCCATATAGGGCACTTCGTGTGCTAACATGATAAGGAATTCATACTAAG
*
1444752 TGTATGAATTTCCATATAGTGCACTTCGTGTGCTAACATGATAAGGAATTCATACTAAG
1 TGTATGAATTTCCATATAGGGCACTTCGTGTGCTAACATGATAAGGAATTCATACTAAG
* * *
1444811 TGTATCAATTTCCATATAGGGCACTTCGTGTGCTAAAATGATAAGAAATTCATACTAAG
1 TGTATGAATTTCCATATAGGGCACTTCGTGTGCTAACATGATAAGGAATTCATACTAAG
* *
1444870 TGTATGAATTTCCATATAGGGCACCTT-GTGTGCTAAAATGATAAGAAATTCATACTAAG
1 TGTATGAATTTCCATATAGGGCA-CTTCGTGTGCTAACATGATAAGGAATTCATACTAAG
*
1444929 TGTATTAATTTCC
1 TGTATGAATTTCC
1444942 GTATGAGAAA
Statistics
Matches: 396, Mismatches: 29, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
59 393 0.99
60 3 0.01
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.35
Consensus pattern (59 bp):
TGTATGAATTTCCATATAGGGCACTTCGTGTGCTAACATGATAAGGAATTCATACTAAG
Found at i:1454698 original size:90 final size:90
Alignment explanation
Indices: 1454577--1454752 Score: 280
Period size: 90 Copynumber: 2.0 Consensus size: 90
1454567 TAATCATGAA
* * * * * *
1454577 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTGATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATAAC
*
1454642 TAGGGTAACTTGGATATAAAAGGAT
66 TAGGGTAACTTGCATATAAAAGGAT
1454667 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATAAC
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATAAC
*
1454732 TAGGGTAACTTGCCTATAAAA
66 TAGGGTAACTTGCATATAAAA
1454753 AGGTGTGTTA
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 78 1.00
ACGTcount: A:0.45, C:0.08, G:0.10, T:0.37
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATAAC
TAGGGTAACTTGCATATAAAAGGAT
Found at i:1455779 original size:18 final size:19
Alignment explanation
Indices: 1455665--1455786 Score: 116
Period size: 18 Copynumber: 6.8 Consensus size: 19
1455655 ATTCTAAATA
*
1455665 TTTACAGTTATCAGGTGATT
1 TTTACAGTTATCAGATGA-T
1455685 TTTA-A-TTATCAGATGAT
1 TTTACAGTTATCAGATGAT
* * *
1455702 TTT-TAGTTATCATATGCT
1 TTTACAGTTATCAGATGAT
* *
1455720 TTT-TAGTTATAAGAT-A-
1 TTTACAGTTATCAGATGAT
*
1455736 TTTACAGTTATGAGATGAT
1 TTTACAGTTATCAGATGAT
1455755 TTT-CAGTTATCAGATG-T
1 TTTACAGTTATCAGATGAT
1455772 TTTACAGTTATCAGA
1 TTTACAGTTATCAGA
1455787 CGTAAATTAA
Statistics
Matches: 87, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
16 3 0.03
17 19 0.22
18 57 0.66
19 4 0.05
20 4 0.05
ACGTcount: A:0.30, C:0.08, G:0.16, T:0.47
Consensus pattern (19 bp):
TTTACAGTTATCAGATGAT
Found at i:1470579 original size:135 final size:135
Alignment explanation
Indices: 1470335--1470681 Score: 588
Period size: 135 Copynumber: 2.6 Consensus size: 135
1470325 TAAACCAATC
* * *
1470335 AACATTTCCAATGGAGAGTTCATAATGAGTAGAAATCATCTGATAGAGGGAGAAAAAGTTCATAA
1 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCTGATAGAGGGAGAAGAAGTTCATAA
*
1470400 TGAGAAGAACTTGTTCAACCTTTGCTCGATTCACGTCATCTTGAATCAATGATGCCTCATTTGAG
66 TGAGAAGAACTTGTTCAACCTTTGCTCGATTCACGTCATCTTGAATCAATGATGCCTCACTTGAG
1470465 GGATT
131 GGATT
*
1470470 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCATAA
1 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCTGATAGAGGGAGAAGAAGTTCATAA
* * *
1470535 TGAGAAGAATTTGTTCAACCTTTGCTCGATTCACGGT-ATTTTGAATCAGTGATGCCTCACTTGA
66 TGAGAAGAACTTGTTCAACCTTTGCTCGATTCAC-GTCATCTTGAATCAATGATGCCTCACTTGA
1470599 GGGATT
130 GGGATT
* *
1470605 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCTGATAAAGGGAGAAGAAGTTCGTAA
1 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCTGATAGAGGGAGAAGAAGTTCATAA
1470670 TGAGAAGAACTT
66 TGAGAAGAACTT
1470682 CGTAATAAGA
Statistics
Matches: 199, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
135 197 0.99
136 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (135 bp):
AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCTGATAGAGGGAGAAGAAGTTCATAA
TGAGAAGAACTTGTTCAACCTTTGCTCGATTCACGTCATCTTGAATCAATGATGCCTCACTTGAG
GGATT
Found at i:1470695 original size:20 final size:17
Alignment explanation
Indices: 1470654--1470697 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
1470644 CTGATAAAGG
*
1470654 GAGAAGAAGTTCGTAAT
1 GAGAAGAACTTCGTAAT
1470671 GAGAAGAACTTCGTAAT
1 GAGAAGAACTTCGTAAT
*
1470688 AAGAAGAACT
1 GAGAAGAACT
1470698 ATTTCAACCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.45, C:0.09, G:0.25, T:0.20
Consensus pattern (17 bp):
GAGAAGAACTTCGTAAT
Found at i:1470807 original size:152 final size:152
Alignment explanation
Indices: 1470519--1470833 Score: 443
Period size: 152 Copynumber: 2.1 Consensus size: 152
1470509 CCGATAGAGG
* * * * * *
1470519 GAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTGCTCGATTCACGGTATTTTGAATCAG
1 GAGAAGAACTTCATAATAAGAAGAATATGTTCAACCTTTGCTCAATTCACGGCATTTCGAATCAG
* * * * * *
1470584 TGATGCCTCACTTGAGGGATTAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCTGAT
66 AGACGCATCACTTGAGGGATTAACATTTCCAATGGAGAGTTCATAATAAGAAGAACTCATCCGAG
*
1470649 AAAGGGAGAAGAAGTTCGTAAT
131 AAAGGGAGAAGAAGTTCATAAT
*
1470671 GAGAAGAACTTCGTAATAAGAAGAACTAT-TTCAACCTTTGCTCAATTCACGGCATTTCGAATCA
1 GAGAAGAACTTCATAATAAGAAGAA-TATGTTCAACCTTTGCTCAATTCACGGCATTTCGAATCA
* * * *
1470735 GAGACGCATCACTTGAGGGATTAATATTTCTAATGGAGAGTTCATAATAAGAAGAGCTTATCCGA
65 GAGACGCATCACTTGAGGGATTAACATTTCCAATGGAGAGTTCATAATAAGAAGAACTCATCCGA
*
1470800 GAGAGGGAGAAGAAGTTCATAAT
130 GAAAGGGAGAAGAAGTTCATAAT
1470823 GAGAAGAACTT
1 GAGAAGAACTT
1470834 GTTCAACCTT
Statistics
Matches: 143, Mismatches: 19, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
152 141 0.99
153 2 0.01
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (152 bp):
GAGAAGAACTTCATAATAAGAAGAATATGTTCAACCTTTGCTCAATTCACGGCATTTCGAATCAG
AGACGCATCACTTGAGGGATTAACATTTCCAATGGAGAGTTCATAATAAGAAGAACTCATCCGAG
AAAGGGAGAAGAAGTTCATAAT
Found at i:1472362 original size:108 final size:109
Alignment explanation
Indices: 1472133--1472382 Score: 258
Period size: 108 Copynumber: 2.3 Consensus size: 109
1472123 GGTCCCATAG
* * * *
1472133 GTTTAGCGCGTTTTTGCATTTTGGTCACATGTATGGACCAAAACTGTTATTTCCCATTTTCTTTG
1 GTTTAGCGTGTTTTTACATTTTGGTCATATGTATGGACCAAAACTGTTATTTCCCATTTTATTTG
*** * *
1472198 TTTGTTATGTATTTTTTGGTAAATTTACTGTTTAGTCCCTCTGA
66 CAAGTTATATATTTTTAGGTAAATTTACTGTTTAGTCCCTCTGA
* * * *
1472242 CTTTATCATGTTTTTACATTTTGGTCATATGTGA-GGA-CTAAACTGTTATTTTCCC-TTTTATT
1 GTTTAGCGTGTTTTTACATTTTGGTCATATGT-ATGGACCAAAACTGTTA-TTTCCCATTTTATT
* * *
1472304 TGCAAGTTATATAATTTTTAGGT-TATTTATTGTTTAGTCCCT-TTA
64 TGCAAGTTATAT-ATTTTTAGGTAAATTTACTGTTTAGTCCCTCTGA
* * *
1472349 TGTTTAGCGTGTTTTTATACTTTGGTAATATGTA
1 -GTTTAGCGTGTTTTTACATTTTGGTCATATGTA
1472383 GTGACTTTTT
Statistics
Matches: 115, Mismatches: 22, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
107 3 0.03
108 67 0.58
109 44 0.38
110 1 0.01
ACGTcount: A:0.20, C:0.13, G:0.16, T:0.51
Consensus pattern (109 bp):
GTTTAGCGTGTTTTTACATTTTGGTCATATGTATGGACCAAAACTGTTATTTCCCATTTTATTTG
CAAGTTATATATTTTTAGGTAAATTTACTGTTTAGTCCCTCTGA
Found at i:1472674 original size:17 final size:18
Alignment explanation
Indices: 1472652--1472689 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1472642 GTATTCATGT
1472652 TTTTTTAT-CTTACTTTA
1 TTTTTTATGCTTACTTTA
*
1472669 TTTTTTATGCTTATTTTA
1 TTTTTTATGCTTACTTTA
1472687 TTT
1 TTT
1472690 AATTAGTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.16, C:0.08, G:0.03, T:0.74
Consensus pattern (18 bp):
TTTTTTATGCTTACTTTA
Found at i:1472674 original size:18 final size:19
Alignment explanation
Indices: 1472651--1472689 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
1472641 TGTATTCATG
1472651 TTTTTTTAT-CTTACTTTA
1 TTTTTTTATGCTTACTTTA
*
1472669 -TTTTTTATGCTTATTTTA
1 TTTTTTTATGCTTACTTTA
1472687 TTT
1 TTT
1472690 AATTAGTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
17 8 0.44
18 8 0.44
19 2 0.11
ACGTcount: A:0.15, C:0.08, G:0.03, T:0.74
Consensus pattern (19 bp):
TTTTTTTATGCTTACTTTA
Found at i:1474678 original size:21 final size:19
Alignment explanation
Indices: 1474647--1474693 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
1474637 GATTAAGAAG
*
1474647 AAAAAAAATTA--AAGTTA
1 AAAAAAAATTATTAAATTA
1474664 AAAAGAAAATTATTAAATTA
1 AAAA-AAAATTATTAAATTA
*
1474684 AACAAAAATT
1 AAAAAAAATT
1474694 CTAAGCATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 4 0.16
18 7 0.28
19 6 0.24
20 8 0.32
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (19 bp):
AAAAAAAATTATTAAATTA
Found at i:1476803 original size:20 final size:20
Alignment explanation
Indices: 1476778--1476822 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
1476768 TCAAATTATA
*
1476778 AGTTTCTGAAACATATAGTC
1 AGTTTCCGAAACATATAGTC
1476798 AGTTTCCGAAACATATAGTC
1 AGTTTCCGAAACATATAGTC
1476818 AGTTT
1 AGTTT
1476823 TAGAATGTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (20 bp):
AGTTTCCGAAACATATAGTC
Found at i:1479679 original size:24 final size:24
Alignment explanation
Indices: 1479617--1479679 Score: 83
Period size: 24 Copynumber: 2.6 Consensus size: 24
1479607 TCTAATTACC
*
1479617 GATCTGAATTTTGTTCTGATTTCT
1 GATCTGAATTTTGTTCTGATATCT
*
1479641 GACCT-ATATTTTGTTCTGATATCT
1 GATCTGA-ATTTTGTTCTGATATCT
*
1479665 GATCTGAATTATGTT
1 GATCTGAATTTTGTT
1479680 TTGTTTCCTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
23 1 0.03
24 31 0.94
25 1 0.03
ACGTcount: A:0.21, C:0.13, G:0.16, T:0.51
Consensus pattern (24 bp):
GATCTGAATTTTGTTCTGATATCT
Found at i:1481484 original size:17 final size:17
Alignment explanation
Indices: 1481462--1481496 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1481452 GGACCAAGTC
1481462 GTTGACTGTTGACCGTT
1 GTTGACTGTTGACCGTT
*
1481479 GTTGACTGTTGATCGTT
1 GTTGACTGTTGACCGTT
1481496 G
1 G
1481497 ACCGTTGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.11, C:0.14, G:0.31, T:0.43
Consensus pattern (17 bp):
GTTGACTGTTGACCGTT
Found at i:1484197 original size:21 final size:21
Alignment explanation
Indices: 1484159--1484199 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1484149 GTCCTTCGGG
* *
1484159 ACATATATGTAATCCTTTGGA
1 ACATATATGCAATACTTTGGA
*
1484180 ACATATATGCAGTACTTTGG
1 ACATATATGCAATACTTTGG
1484200 TACACCTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.37
Consensus pattern (21 bp):
ACATATATGCAATACTTTGGA
Found at i:1484607 original size:4 final size:4
Alignment explanation
Indices: 1484590--1484698 Score: 60
Period size: 4 Copynumber: 27.8 Consensus size: 4
1484580 TAAATGATGA
* * * * * * *
1484590 TATG TATT TATG TATG TATG TATG TACG TATA TACG TACG TACG TATA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* ** * * * *
1484638 TATG TATA TACA TACG TACG TATG TATG TATG TACG TA-- TATG TACG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* *
1484684 TACG TATG TACG TAT
1 TATG TATG TATG TAT
1484699 TGTAAATCCC
Statistics
Matches: 84, Mismatches: 19, Indels: 4
0.79 0.18 0.04
Matches are distributed among these distances:
2 2 0.02
4 82 0.98
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.41
Consensus pattern (4 bp):
TATG
Found at i:1485159 original size:8 final size:8
Alignment explanation
Indices: 1485005--1485158 Score: 272
Period size: 8 Copynumber: 19.2 Consensus size: 8
1484995 CATACGTACA
1485005 TACGTATG
1 TACGTATG
*
1485013 TGCGTATG
1 TACGTATG
*
1485021 TATGTATG
1 TACGTATG
*
1485029 TACGTATA
1 TACGTATG
1485037 TACGTATG
1 TACGTATG
1485045 TACGTATG
1 TACGTATG
1485053 TACGTATG
1 TACGTATG
1485061 TACGTATG
1 TACGTATG
1485069 TACGTATG
1 TACGTATG
1485077 TACGTATG
1 TACGTATG
1485085 TACGTATG
1 TACGTATG
1485093 TACGTATG
1 TACGTATG
1485101 TACGTATG
1 TACGTATG
1485109 TACGTATG
1 TACGTATG
1485117 TACGTATG
1 TACGTATG
1485125 TACGTATG
1 TACGTATG
1485133 TACGTATG
1 TACGTATG
1485141 TACGTATG
1 TACGTATG
*
1485149 TATGTATG
1 TACGTATG
1485157 TA
1 TA
1485159 TTTGTTACAT
Statistics
Matches: 139, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 139 1.00
ACGTcount: A:0.25, C:0.11, G:0.25, T:0.39
Consensus pattern (8 bp):
TACGTATG
Found at i:1485561 original size:16 final size:17
Alignment explanation
Indices: 1485534--1485567 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1485524 TTCTTCATTC
1485534 TTTTGTAAAAGTAAATG
1 TTTTGTAAAAGTAAATG
*
1485551 TTTTG-AAAAGTCAATG
1 TTTTGTAAAAGTAAATG
1485567 T
1 T
1485568 GACACCTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.41
Consensus pattern (17 bp):
TTTTGTAAAAGTAAATG
Found at i:1486068 original size:3 final size:3
Alignment explanation
Indices: 1486060--1486116 Score: 73
Period size: 3 Copynumber: 19.7 Consensus size: 3
1486050 ATTTTAGTTA
* * *
1486060 TAT TAT TAT TA- TAC TAT TAT TAT TAA TAA TAT TAT TAT TAT TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1486106 TAT TAT TAT TA
1 TAT TAT TAT TA
1486117 AATAATTACA
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
2 4 0.08
3 45 0.92
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:1486101 original size:32 final size:33
Alignment explanation
Indices: 1486060--1486122 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
1486050 ATTTTAGTTA
1486060 TATTATTATTATACTATTATTATT-AATAATAT
1 TATTATTATTATACTATTATTATTAAATAATAT
**
1486092 TATTATTATTATTTTATTATTATTAAATAAT
1 TATTATTATTATACTATTATTATTAAATAAT
1486123 TACATATTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 22 0.79
33 6 0.21
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (33 bp):
TATTATTATTATACTATTATTATTAAATAATAT
Found at i:1486124 original size:14 final size:14
Alignment explanation
Indices: 1486061--1486124 Score: 58
Period size: 14 Copynumber: 4.5 Consensus size: 14
1486051 TTTTAGTTAT
*
1486061 ATTATTATTA-TACT
1 ATTATTATTATTA-A
*
1486075 ATTATTATTAATAA
1 ATTATTATTATTAA
*
1486089 TATTATTATTATTAT
1 -ATTATTATTATTAA
*
1486104 TTTATTATTATTAA
1 ATTATTATTATTAA
*
1486118 ATAATTA
1 ATTATTA
1486125 CATATTACAA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
14 27 0.66
15 14 0.34
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (14 bp):
ATTATTATTATTAA
Found at i:1486130 original size:29 final size:29
Alignment explanation
Indices: 1486076--1486131 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
1486066 TATTATACTA
* *
1486076 TTATTATTAATAATATTATTATTATTATT
1 TTATTATTAATAATATAATTAATATTATT
*
1486105 TTATTATTATTAA-ATAATTACATATTA
1 TTATTATTAATAATATAATTA-ATATTA
1486132 CAAGCCCAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 6 0.26
29 17 0.74
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (29 bp):
TTATTATTAATAATATAATTAATATTATT
Found at i:1489145 original size:19 final size:19
Alignment explanation
Indices: 1489110--1489149 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1489100 CGAAAGAGTG
*
1489110 TTCATCAAATTGAAAAGTT
1 TTCATCAAATGGAAAAGTT
1489129 TTCAT-AAATGGACAAAGTT
1 TTCATCAAATGGA-AAAGTT
1489148 TT
1 TT
1489150 ATGATCAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (19 bp):
TTCATCAAATGGAAAAGTT
Found at i:1489275 original size:36 final size:36
Alignment explanation
Indices: 1489225--1489326 Score: 177
Period size: 36 Copynumber: 2.8 Consensus size: 36
1489215 AGCTATGCAT
* *
1489225 ACAAAGATCATGTTATATTGATACCAAAAGTATTCC
1 ACAAAGATCCTGTTAGATTGATACCAAAAGTATTCC
1489261 ACAAAGATCCTGTTAGATTGATACCAAAAGTATTCC
1 ACAAAGATCCTGTTAGATTGATACCAAAAGTATTCC
*
1489297 ACAAAGATCCTGTTAGATTGGTACCAAAAG
1 ACAAAGATCCTGTTAGATTGATACCAAAAG
1489327 CAATTTATGG
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 63 1.00
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (36 bp):
ACAAAGATCCTGTTAGATTGATACCAAAAGTATTCC
Found at i:1489877 original size:42 final size:43
Alignment explanation
Indices: 1489796--1489880 Score: 145
Period size: 42 Copynumber: 2.0 Consensus size: 43
1489786 TGTCTTTGGA
* *
1489796 GAAGTTAGGAGTGAAAGTTATCCCCTATATGTAAAGTTTTGTT
1 GAAGTTAGGAGTGAAAGCTATCCCCTATATATAAAGTTTTGTT
1489839 GAAGTTAGGAGTGAAAGCTAT-CCCTATATATAAAGTTTTGTT
1 GAAGTTAGGAGTGAAAGCTATCCCCTATATATAAAGTTTTGTT
1489881 TGATGTACCA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
42 20 0.50
43 20 0.50
ACGTcount: A:0.32, C:0.09, G:0.22, T:0.36
Consensus pattern (43 bp):
GAAGTTAGGAGTGAAAGCTATCCCCTATATATAAAGTTTTGTT
Found at i:1489969 original size:6 final size:7
Alignment explanation
Indices: 1489956--1489995 Score: 57
Period size: 6 Copynumber: 5.9 Consensus size: 7
1489946 TTTTCATACA
1489956 TGCATTT
1 TGCATTT
1489963 T-CATTT
1 TGCATTT
1489969 TGCATCTT
1 TGCAT-TT
1489977 TGCATTT
1 TGCATTT
1489984 T-CATTT
1 TGCATTT
1489990 TGCATT
1 TGCATT
1489996 CGTACTTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
6 12 0.40
7 11 0.37
8 7 0.23
ACGTcount: A:0.15, C:0.17, G:0.10, T:0.57
Consensus pattern (7 bp):
TGCATTT
Found at i:1489991 original size:13 final size:14
Alignment explanation
Indices: 1489956--1489995 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
1489946 TTTTCATACA
1489956 TGCATTTT-CATTT
1 TGCATTTTGCATTT
1489969 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
1489984 T-CATTTTGCATT
1 TGCATTTTGCATT
1489996 CGTACTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 13 0.52
14 6 0.24
15 6 0.24
ACGTcount: A:0.15, C:0.17, G:0.10, T:0.57
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:1490129 original size:14 final size:13
Alignment explanation
Indices: 1490112--1490155 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
1490102 TATTCGCATC
1490112 TTTGCATTTTTACA
1 TTTG-ATTTTTACA
*
1490126 TTTG-TATTTACA
1 TTTGATTTTTACA
1490138 TTTTGATTTTTACA
1 -TTTGATTTTTACA
1490152 TTTG
1 TTTG
1490156 CATATTTGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 7 0.27
13 8 0.31
14 11 0.42
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.61
Consensus pattern (13 bp):
TTTGATTTTTACA
Found at i:1490137 original size:12 final size:13
Alignment explanation
Indices: 1490120--1490162 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
1490110 TCTTTGCATT
1490120 TTTACATTTG-TA
1 TTTACATTTGATA
*
1490132 TTTACATTTTGATT
1 TTTACA-TTTGATA
1490146 TTTACATTTGCATA
1 TTTACATTTG-ATA
1490160 TTT
1 TTT
1490163 GCATAATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 6 0.23
13 8 0.31
14 12 0.46
ACGTcount: A:0.23, C:0.09, G:0.07, T:0.60
Consensus pattern (13 bp):
TTTACATTTGATA
Found at i:1494910 original size:24 final size:24
Alignment explanation
Indices: 1494878--1494924 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
1494868 GGGCATTTTA
*
1494878 AAGGCCACTTCAGACAGATCCATG
1 AAGGCCACTTCAGACAAATCCATG
1494902 AAGGCCACTTCAGACAAATCCAT
1 AAGGCCACTTCAGACAAATCCAT
1494925 ATGGGGCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.36, C:0.30, G:0.17, T:0.17
Consensus pattern (24 bp):
AAGGCCACTTCAGACAAATCCATG
Found at i:1495121 original size:75 final size:75
Alignment explanation
Indices: 1494997--1495176 Score: 254
Period size: 75 Copynumber: 2.4 Consensus size: 75
1494987 ATCAACAAGA
* *
1494997 AGCAAATGTTAGGGCATGCTGAAAGCCCATTTCAATCAGAAATTGGAATATTGACGCATTTTGAA
1 AGCAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAAATTAGAATATTGACGCATTTTGAA
1495062 CG-CTTGTATC
66 CGTC-TGTATC
* * * *
1495072 AGCAAATGTTGGGGTATGCTGAAAGCCCATTTCAATCATAAATTAGAATATTGATGTATTTTGAA
1 AGCAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAAATTAGAATATTGACGCATTTTGAA
*
1495137 CGTCTGTATT
66 CGTCTGTATC
* * *
1495147 AGCAAATGTCGGAGCATGCTGAAGGCCCAT
1 AGCAAATGTTGGGGCATGCTGAAAGCCCAT
1495177 ATCATCTTAT
Statistics
Matches: 93, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
75 92 0.99
76 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (75 bp):
AGCAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAAATTAGAATATTGACGCATTTTGAA
CGTCTGTATC
Found at i:1496208 original size:54 final size:54
Alignment explanation
Indices: 1495999--1496274 Score: 322
Period size: 54 Copynumber: 5.1 Consensus size: 54
1495989 CAATGATTGA
* * *
1495999 GAACATCTGAGCAGAAGCCACATGAAAGAATAAATGTGTTGTCAAATATTTTAC
1 GAACATCTTAGCAGAAGCCACAGGAAAGAATAAATGTGTTGTCAAATGTTTTAC
* * * *
1496053 GGAACATCCGT-GCAGTAGCCAC-GGTAAAGGATAAATGTGTTATCAAATGTTTTAC
1 -GAACAT-CTTAGCAGAAGCCACAGG-AAAGAATAAATGTGTTGTCAAATGTTTTAC
* * * * *
1496108 AGAACATCTTTGCATAAGCCACAGAAAAGAATAAATGAGTTTTCAAATGTTTTAC
1 -GAACATCTTAGCAGAAGCCACAGGAAAGAATAAATGTGTTGTCAAATGTTTTAC
* * *
1496163 GAACATCTTAGCAGAAGCCACATGAAAGTATGAATGTGTTGTCAAATGTTTTAC
1 GAACATCTTAGCAGAAGCCACAGGAAAGAATAAATGTGTTGTCAAATGTTTTAC
* * * * *
1496217 GAACATCTGAGCATAAGCCACAGGAAAGGATGAATGTGTTGTCAAATATTTTAC
1 GAACATCTTAGCAGAAGCCACAGGAAAGAATAAATGTGTTGTCAAATGTTTTAC
1496271 GAAC
1 GAAC
1496275 CAGTGATTAT
Statistics
Matches: 189, Mismatches: 28, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
54 102 0.54
55 85 0.45
56 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (54 bp):
GAACATCTTAGCAGAAGCCACAGGAAAGAATAAATGTGTTGTCAAATGTTTTAC
Found at i:1497398 original size:45 final size:45
Alignment explanation
Indices: 1497330--1497732 Score: 572
Period size: 45 Copynumber: 8.9 Consensus size: 45
1497320 TTATTTCCCA
1497330 CATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGT
*
1497375 CATATGTAAGACCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGT
* * *
1497420 CATCTGTAAGACCTTCAATGCATGATGTTTTCAAAACCTTTGGGT
1 CATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGT
* * * *
1497465 CATCTCTAAGACCTTCAATGCATGATGCTTTCAAAACCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGT
** *
1497510 CATCTGTAAGAAATTCAGTGCAGGATGTTCTCAAAACCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGT
* * *
1497555 CATCTGTAAGATCTTCATTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGT
* * * *
1497600 CGTCTGTAAGAACTTCATTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGT
* *
1497645 CATCTGTAAGACCTTCAGTGCAGGATATTTTCAAAACCATCGGGT
1 CATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGT
** * *
1497690 CATCCATAAGACCTACAGTGCAGTATGTTTTCGAAAAGCCTTC
1 CATCTGTAAGACCTTCAGTGCAGGATGTTTTC-AAAA-CCTTC
1497733 AGTAGTATTT
Statistics
Matches: 322, Mismatches: 34, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
45 314 0.98
46 4 0.01
47 4 0.01
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (45 bp):
CATCTGTAAGACCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGT
Found at i:1497843 original size:116 final size:117
Alignment explanation
Indices: 1497636--1497873 Score: 311
Period size: 116 Copynumber: 2.0 Consensus size: 117
1497626 GTTTTCAAAA
* * * *
1497636 CCTTCGGGTCATCTGTAAGACCTTCAGTGCAGGATATTTTCAAAACCATCGGGTCATCCATAAGA
1 CCTTCGGGTCATCTGTAAGACCTACAGTGCAAGATA--TTCAAAACCATAGGGCCATCCATAAGA
* * * *
1497701 CCTACAGTGCAGTATGTTTTCGAAAAGCCTTCAGTAG-TATTTTTATATTTAAAG
64 CCTACAGTGCAGGATGTTTTCAAAAAGCCTTCAGGAGCT-TTTTGATATTTAAAG
* *
1497755 CCTTCGGGTCATCTGTAAGACCTACAGTGCAAGATGA-T-AAGACCTTAGGGCCATCCATAAGAC
1 CCTTCGGGTCATCTGTAAGACCTACAGTGCAAGAT-ATTCAAAACCATAGGGCCATCCATAAGAC
* *
1497818 CTATAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAG
65 CTACAGTGCAGGATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGATATTTAAAG
1497871 CCT
1 CCT
1497874 CCGTGATACA
Statistics
Matches: 105, Mismatches: 12, Indels: 7
0.85 0.10 0.06
Matches are distributed among these distances:
116 69 0.66
117 2 0.02
119 33 0.31
120 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.31
Consensus pattern (117 bp):
CCTTCGGGTCATCTGTAAGACCTACAGTGCAAGATATTCAAAACCATAGGGCCATCCATAAGACC
TACAGTGCAGGATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGATATTTAAAG
Found at i:1499335 original size:15 final size:14
Alignment explanation
Indices: 1499288--1499336 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
1499278 ATTTTTTTTC
1499288 AAAAACAAAACAAA
1 AAAAACAAAACAAA
*
1499302 AAAAGGCAAAAACAAA
1 AAAA-AC-AAAACAAA
*
1499318 AAATACAAAACAAA
1 AAAAACAAAACAAA
1499332 AAAAA
1 AAAAA
1499337 GTCAAAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 16 0.55
15 2 0.07
16 11 0.38
ACGTcount: A:0.82, C:0.12, G:0.04, T:0.02
Consensus pattern (14 bp):
AAAAACAAAACAAA
Found at i:1499342 original size:16 final size:16
Alignment explanation
Indices: 1499293--1499343 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 16
1499283 TTTTCAAAAA
*
1499293 CAAAAC-AAAAAAAGG
1 CAAAACAAAAAAAAGT
*
1499308 CAAAA-ACAAAAAA-T
1 CAAAACAAAAAAAAGT
1499322 ACAAAACAAAAAAAAGT
1 -CAAAACAAAAAAAAGT
1499339 CAAAA
1 CAAAA
1499344 TTTCAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
15 16 0.55
16 12 0.41
17 1 0.03
ACGTcount: A:0.76, C:0.14, G:0.06, T:0.04
Consensus pattern (16 bp):
CAAAACAAAAAAAAGT
Found at i:1504147 original size:3 final size:3
Alignment explanation
Indices: 1504133--1504214 Score: 105
Period size: 3 Copynumber: 28.0 Consensus size: 3
1504123 CATTTTACTT
* * *
1504133 TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA ATA -TA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
1504180 CTA TTA ATA TTA TTA TTA TTA TT- TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1504215 AATTATAAAT
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
2 4 0.06
3 65 0.94
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1504179 original size:29 final size:29
Alignment explanation
Indices: 1504146--1504220 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
1504136 TTTTTATTAT
*
1504146 TATTATTATTATTATTATTATTAATATAC
1 TATTATTATTAATATTATTATTAATATAC
* * **
1504175 TATTACTATTAATATTATTATTATTATTT
1 TATTATTATTAATATTATTATTAATATAC
1504204 TATTATTATTAA-ATTAT
1 TATTATTATTAATATTAT
1504221 AAATAATTAC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
28 5 0.12
29 35 0.88
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (29 bp):
TATTATTATTAATATTATTATTAATATAC
Found at i:1504734 original size:16 final size:16
Alignment explanation
Indices: 1504713--1504744 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1504703 ACCAACAGCG
*
1504713 ATCAAACCACCAAATA
1 ATCAAACCAACAAATA
1504729 ATCAAACCAACAAATA
1 ATCAAACCAACAAATA
1504745 GAGAAAGACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.28, G:0.00, T:0.12
Consensus pattern (16 bp):
ATCAAACCAACAAATA
Found at i:1507967 original size:15 final size:14
Alignment explanation
Indices: 1507920--1507968 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
1507910 TATTTTTTTC
1507920 AAAAACAAAACAAA
1 AAAAACAAAACAAA
*
1507934 AAAAGGCAAAAACAAA
1 AAAA-AC-AAAACAAA
*
1507950 AAATACAAAACAAA
1 AAAAACAAAACAAA
1507964 AAAAA
1 AAAAA
1507969 GTCAAAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 16 0.55
15 2 0.07
16 11 0.38
ACGTcount: A:0.82, C:0.12, G:0.04, T:0.02
Consensus pattern (14 bp):
AAAAACAAAACAAA
Found at i:1507974 original size:16 final size:16
Alignment explanation
Indices: 1507925--1507975 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 16
1507915 TTTTCAAAAA
*
1507925 CAAAAC-AAAAAAAGG
1 CAAAACAAAAAAAAGT
*
1507940 CAAAA-ACAAAAAA-T
1 CAAAACAAAAAAAAGT
1507954 ACAAAACAAAAAAAAGT
1 -CAAAACAAAAAAAAGT
1507971 CAAAA
1 CAAAA
1507976 TTTCAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
15 16 0.55
16 12 0.41
17 1 0.03
ACGTcount: A:0.76, C:0.14, G:0.06, T:0.04
Consensus pattern (16 bp):
CAAAACAAAAAAAAGT
Found at i:1512783 original size:3 final size:3
Alignment explanation
Indices: 1512775--1512856 Score: 114
Period size: 3 Copynumber: 28.0 Consensus size: 3
1512765 TTACTTTTAT
* *
1512775 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA ATA -TA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
1512822 CTA TTA ATA TTA TTA TTA TTA TT- TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1512857 AATTATAAAT
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
2 4 0.06
3 67 0.94
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1513376 original size:16 final size:16
Alignment explanation
Indices: 1513355--1513386 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1513345 ACCAACAGCG
*
1513355 ATCAAACCACCAAATA
1 ATCAAACCAACAAATA
1513371 ATCAAACCAACAAATA
1 ATCAAACCAACAAATA
1513387 GAGAAAGACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.28, G:0.00, T:0.12
Consensus pattern (16 bp):
ATCAAACCAACAAATA
Found at i:1518077 original size:21 final size:21
Alignment explanation
Indices: 1518039--1518102 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
1518029 TTAGAATATG
**
1518039 TATGTGGTCCTTTGGGACATC
1 TATGTGGTCCTTCAGGACATC
1518060 TATGTGGTCCTTCAGGACATTTC
1 TATGTGGTCCTTCAGGACA--TC
* **
1518083 TACGCAGTCCTTCAGGACAT
1 TATGTGGTCCTTCAGGACAT
1518103 TTCTACGCAG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 18 0.50
23 18 0.50
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.34
Consensus pattern (21 bp):
TATGTGGTCCTTCAGGACATC
Found at i:1518092 original size:23 final size:23
Alignment explanation
Indices: 1518066--1518124 Score: 118
Period size: 23 Copynumber: 2.6 Consensus size: 23
1518056 CATCTATGTG
1518066 GTCCTTCAGGACATTTCTACGCA
1 GTCCTTCAGGACATTTCTACGCA
1518089 GTCCTTCAGGACATTTCTACGCA
1 GTCCTTCAGGACATTTCTACGCA
1518112 GTCCTTCAGGACA
1 GTCCTTCAGGACA
1518125 AATTCTATGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.22, C:0.31, G:0.19, T:0.29
Consensus pattern (23 bp):
GTCCTTCAGGACATTTCTACGCA
Found at i:1522731 original size:28 final size:28
Alignment explanation
Indices: 1522689--1522754 Score: 116
Period size: 28 Copynumber: 2.4 Consensus size: 28
1522679 TTTGTTCGGG
1522689 TCGGGTCGGG-TTTTTTAAGTGTGATAT
1 TCGGGTCGGGTTTTTTTAAGTGTGATAT
*
1522716 TCGGATCGGGTTTTTTTAAGTGTGATAT
1 TCGGGTCGGGTTTTTTTAAGTGTGATAT
1522744 TCGGGTCGGGT
1 TCGGGTCGGGT
1522755 CGGGTTCGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 9 0.25
28 27 0.75
ACGTcount: A:0.14, C:0.09, G:0.35, T:0.42
Consensus pattern (28 bp):
TCGGGTCGGGTTTTTTTAAGTGTGATAT
Found at i:1528987 original size:4 final size:4
Alignment explanation
Indices: 1528980--1529004 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1528970 TATACATATA
1528980 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
1529005 GGATTCTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:1530226 original size:16 final size:16
Alignment explanation
Indices: 1530178--1530230 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
1530168 AGTATATTTA
* *
1530178 TTATTATCTATATTTAA
1 TTATTATTTATA-TTAT
1530195 TTATATATTT-TCATTAT
1 TTAT-TATTTAT-ATTAT
1530212 TTATTATTTATATTAT
1 TTATTATTTATATTAT
1530228 TTA
1 TTA
1530231 CTTTTTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
16 13 0.42
17 13 0.42
18 5 0.16
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (16 bp):
TTATTATTTATATTAT
Found at i:1530381 original size:2 final size:2
Alignment explanation
Indices: 1530376--1530411 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1530366 TATTGCATTA
1530376 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
1530412 GTTTCTTTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1541034 original size:6 final size:6
Alignment explanation
Indices: 1541023--1541092 Score: 122
Period size: 6 Copynumber: 11.3 Consensus size: 6
1541013 CAAGTCGAAT
1541023 AAAGAA AAAGAAAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
1 AAAGAA AAAG--AA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
1541073 AAAGAA AAAGAA AAAGAA AA
1 AAAGAA AAAGAA AAAGAA AA
1541093 TTAAAAAAAT
Statistics
Matches: 62, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
6 56 0.90
8 6 0.10
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:1542254 original size:106 final size:108
Alignment explanation
Indices: 1541988--1542276 Score: 345
Period size: 110 Copynumber: 2.7 Consensus size: 108
1541978 GGCTTCTCAA
* * *
1541988 TTTCATAGCCAATTTCAACTTCACAGTGAAAGATATTGGACTCAAGATAACACAAGCTCAACTTC
1 TTTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTC
* * * * *
1542053 ACAAC-GAAGAGGCGGCTGATTGTTAACAAACAACTTTTCAGTT
66 ACAACAAAAGAGGCGACTGACTGTCAACAAACAACTTTCCAG-T
* * * *
1542096 TCATTCAGAGTCAATTTCAACTTTACAGTGAAGGATATTAGACTCAAGACAACACAAGCTCGACT
1 T--TTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGGACTCAAGACAACACAAGCTCAACT
* *
1542161 TCACAGCAAAAGA-GCGACT-AGCTGTCAGCAAACAA-TTTCCCAG-
64 TCACAACAAAAGAGGCGACTGA-CTGTCAACAAACAACTTT-CCAGT
* * *
1542204 TTTCAGAGCCAATTTCAACTTCACAGCGGAGGATATTGGACTCAAGACAACACAAGCTCAACATC
1 TTTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTC
1542269 ACAACAAA
66 ACAACAAA
1542277 GGGGCCACAT
Statistics
Matches: 154, Mismatches: 22, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
106 64 0.42
108 2 0.01
109 4 0.03
110 80 0.52
111 4 0.03
ACGTcount: A:0.37, C:0.24, G:0.16, T:0.23
Consensus pattern (108 bp):
TTTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTC
ACAACAAAAGAGGCGACTGACTGTCAACAAACAACTTTCCAGT
Found at i:1542952 original size:12 final size:11
Alignment explanation
Indices: 1542935--1542998 Score: 64
Period size: 12 Copynumber: 6.0 Consensus size: 11
1542925 CGTCCATTGC
1542935 TATATATATAT
1 TATATATATAT
1542946 ATATATATATAT
1 -TATATATATAT
1542958 TAT-TAT-TAT
1 TATATATATAT
1542967 TAT-TAT-TAT
1 TATATATATAT
* *
1542976 TACAAACTATAT
1 TATATA-TATAT
1542988 TATATATATAT
1 TATATATATAT
1542999 ACACGCATAA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
9 14 0.31
10 4 0.09
11 9 0.20
12 18 0.40
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (11 bp):
TATATATATAT
Found at i:1544229 original size:13 final size:13
Alignment explanation
Indices: 1544187--1544270 Score: 64
Period size: 13 Copynumber: 6.0 Consensus size: 13
1544177 AAATAGTATA
1544187 TTTATTATTATATGT
1 TTTATTATT-TAT-T
*
1544202 ATTTAATTATATATT
1 -TTT-ATTATTTATT
*
1544217 TTCATTATTTATTAT
1 TTTATTATTTA-T-T
1544232 TTATATTATTTACTT
1 TT-TATTATTTA-TT
1544247 TTT-TTATTTATT
1 TTTATTATTTATT
1544259 TTTATT-TTTATT
1 TTTATTATTTATT
1544271 ATATATATAT
Statistics
Matches: 58, Mismatches: 5, Indels: 14
0.75 0.06 0.18
Matches are distributed among these distances:
12 11 0.19
13 16 0.28
14 4 0.07
15 7 0.12
16 15 0.26
17 5 0.09
ACGTcount: A:0.26, C:0.02, G:0.01, T:0.70
Consensus pattern (13 bp):
TTTATTATTTATT
Found at i:1544266 original size:16 final size:16
Alignment explanation
Indices: 1544185--1544270 Score: 52
Period size: 16 Copynumber: 5.2 Consensus size: 16
1544175 TTAAATAGTA
* * *
1544185 TATTTATTATTATATG
1 TATTTATTTTTATTTT
*
1544201 TATTTAATTATATATTTT
1 TATTT-ATT-TTTATTTT
* *
1544219 CA-TTATTTATTATTTA
1 TATTTATTT-TTATTTT
1544235 TA-TTATTTACTT-TTTT
1 TATTTATTT--TTATTTT
1544251 TATTTATTTTTATTTT
1 TATTTATTTTTATTTT
1544267 TATT
1 TATT
1544271 ATATATATAT
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
15 3 0.06
16 33 0.61
17 13 0.24
18 5 0.09
ACGTcount: A:0.27, C:0.02, G:0.01, T:0.70
Consensus pattern (16 bp):
TATTTATTTTTATTTT
Found at i:1545537 original size:14 final size:14
Alignment explanation
Indices: 1545518--1545547 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1545508 TTTAGCTTTT
*
1545518 TTAAAATTACATTA
1 TTAAAAATACATTA
1545532 TTAAAAATACATTA
1 TTAAAAATACATTA
1545546 TT
1 TT
1545548 GATGAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAATACATTA
Found at i:1545821 original size:7 final size:7
Alignment explanation
Indices: 1545809--1545937 Score: 63
Period size: 7 Copynumber: 18.9 Consensus size: 7
1545799 TATGTGATAA
1545809 GGTTTAG
1 GGTTTAG
1545816 GGTTTAG
1 GGTTTAG
1545823 GGTTTA-
1 GGTTTAG
* *
1545829 TGTGATAG
1 GGT-TTAG
* *
1545837 GATTTAA
1 GGTTTAG
1545844 GGTTTAG
1 GGTTTAG
*
1545851 GGTTTAA
1 GGTTTAG
* *
1545858 AGTTTAA
1 GGTTTAG
1545865 GGTTTA-
1 GGTTTAG
*
1545871 TGTATTAG
1 GGT-TTAG
1545879 GGTTTAG
1 GGTTTAG
1545886 GGTTTA-
1 GGTTTAG
* *
1545892 --TATAAA
1 GGT-TTAG
1545898 GG-TTAG
1 GGTTTAG
* *
1545904 AGTTTAA
1 GGTTTAG
1545911 GGTTTAG
1 GGTTTAG
*
1545918 AGTTTAG
1 GGTTTAG
1545925 GGTTTAG
1 GGTTTAG
*
1545932 AGTTTA
1 GGTTTA
1545938 AGTTATGCAC
Statistics
Matches: 90, Mismatches: 23, Indels: 18
0.69 0.18 0.14
Matches are distributed among these distances:
4 1 0.01
5 2 0.02
6 7 0.08
7 77 0.86
8 3 0.03
ACGTcount: A:0.26, C:0.00, G:0.31, T:0.43
Consensus pattern (7 bp):
GGTTTAG
Found at i:1545828 original size:14 final size:14
Alignment explanation
Indices: 1545809--1545939 Score: 76
Period size: 14 Copynumber: 9.6 Consensus size: 14
1545799 TATGTGATAA
*
1545809 GGTTTAGGGTTTAG
1 GGTTTAAGGTTTAG
* *
1545823 GGTTT-ATGTGATAG
1 GGTTTAAGGT-TTAG
*
1545837 GATTTAAGGTTTAG
1 GGTTTAAGGTTTAG
* *
1545851 GGTTTAAAGTTTAA
1 GGTTTAAGGTTTAG
*
1545865 GGTTT-ATGTATTAG
1 GGTTTAAGGT-TTAG
*
1545879 GGTTTAGGGTTTA-
1 GGTTTAAGGTTTAG
*
1545892 --TATAAAGG-TTAG
1 GGT-TTAAGGTTTAG
*
1545904 AGTTTAAGGTTTAG
1 GGTTTAAGGTTTAG
* *
1545918 AGTTTAGGGTTTAG
1 GGTTTAAGGTTTAG
*
1545932 AGTTTAAG
1 GGTTTAAG
1545940 TTATGCACAT
Statistics
Matches: 90, Mismatches: 18, Indels: 18
0.71 0.14 0.14
Matches are distributed among these distances:
11 4 0.04
12 4 0.04
13 10 0.11
14 67 0.74
15 5 0.06
ACGTcount: A:0.26, C:0.00, G:0.31, T:0.43
Consensus pattern (14 bp):
GGTTTAAGGTTTAG
Found at i:1545842 original size:28 final size:28
Alignment explanation
Indices: 1545798--1545856 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
1545788 TCATAACTAA
*
1545798 TTATGTGATAAGGTTTAGGGTTTAGGGT
1 TTATGTGATAAGGTTTAAGGTTTAGGGT
1545826 TTATGTGAT-AGGATTTAAGGTTTAGGGT
1 TTATGTGATAAGG-TTTAAGGTTTAGGGT
1545854 TTA
1 TTA
1545857 AAGTTTAAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 3 0.10
28 26 0.90
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (28 bp):
TTATGTGATAAGGTTTAAGGTTTAGGGT
Found at i:1545883 original size:21 final size:21
Alignment explanation
Indices: 1545812--1545892 Score: 76
Period size: 21 Copynumber: 3.9 Consensus size: 21
1545802 GTGATAAGGT
*
1545812 TTAGGGTTTAGGGTTTATGTGA
1 TTAGGGTTTAAGGTTTATGT-A
* *
1545834 -TAGGATTTAAGGTTTAGGGT-
1 TTAGGGTTTAAGGTTTA-TGTA
**
1545854 TTAAAGTTTAAGGTTTATGTA
1 TTAGGGTTTAAGGTTTATGTA
*
1545875 TTAGGGTTTAGGGTTTAT
1 TTAGGGTTTAAGGTTTAT
1545893 ATAAAGGTTA
Statistics
Matches: 46, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
20 2 0.04
21 42 0.91
22 2 0.04
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (21 bp):
TTAGGGTTTAAGGTTTATGTA
Found at i:1547337 original size:23 final size:23
Alignment explanation
Indices: 1547311--1547361 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
1547301 GCTCGAAATT
1547311 GAGCTTAATTTCGAGTTTTAATC
1 GAGCTTAATTTCGAGTTTTAATC
*
1547334 GAGCTTAGTTTCGAGTTTTAATC
1 GAGCTTAATTTCGAGTTTTAATC
1547357 GAGCT
1 GAGCT
1547362 CTTAAATTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.24, C:0.14, G:0.22, T:0.41
Consensus pattern (23 bp):
GAGCTTAATTTCGAGTTTTAATC
Found at i:1557003 original size:2 final size:2
Alignment explanation
Indices: 1556998--1557042 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
1556988 ATTTTTTTAA
1556998 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1557038 AT AT A
1 AT AT A
1557043 AATCTACACA
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1558054 original size:87 final size:87
Alignment explanation
Indices: 1557908--1558070 Score: 308
Period size: 87 Copynumber: 1.9 Consensus size: 87
1557898 TATGTTATAT
1557908 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
1 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
1557973 AGCGCTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAATAGG
* *
1557995 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
1 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
1558060 AGCGCTTATAT
66 AGCGCTTATAT
1558071 TGACCTATTT
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 74 1.00
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (87 bp):
TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
AGCGCTTATATAATAAAATAGG
Found at i:1559147 original size:181 final size:182
Alignment explanation
Indices: 1558205--1559774 Score: 2605
Period size: 181 Copynumber: 8.6 Consensus size: 182
1558195 TGCGTTCACC
** ** * * * * *
1558205 TTTTGTCATTTATAGACCAATTTTATCATATTTTTATATGTTATATTATTATAGATCGATATATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
1558270 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTATT-AATTCCAAAAGTGTCG
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTT-TTAAATTCCAAAAGTGTCG
*
1558334 ATACTTATAATAAATTATCGACACTTTCAACATATCCGGTAGCGCTTTACCTG
130 ATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
* * * *
1558387 TTTTTTCATTTCGAGACCGATTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
*
1558452 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCTA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
1558517 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTTTTTACCTG
131 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGC----TTTACCTG
* * * * *
1558573 TTTTATCATTTCGAGATCGGTTTTTTCATATTATTACTTGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
* *
1558638 TTTATCAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTTCAAAAGTGTCGA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
1558703 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
131 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
1558755 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
* *
1558820 TTTATAAAGTATCGACACGTTATTGGCGCTATAACTTCATCTCTTATT-AATTCCAAAA-T-TCG
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTT-TTAAATTCCAAAAGTGTCG
1558882 ATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
130 ATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
* *
1558935 TTTTGTCATTTCGAGACCGGTTTTTTCATATTTTTACATGTTATATTGTTATGGATCGATAAATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
*
1559000 TTTATAAAGTATCGACACTTTATTGGCGCTATAAC-TCTTCTCTTTTAAATTCCAAAAGTGTTGA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
*
1559064 TACGTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
131 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
* * *
1559116 ATTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCAATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
* * * * *
1559181 TTTATAAAGTATCGAAACTTTATTGGCGCTATAAATTATTCTCTTTTAAATTTCAAAAGTGTAGA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
1559246 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
131 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
* * *
1559298 TTTTGTCATTTTGAGATCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
*
1559363 TTTATAAAATATCGACACTTTATTGGCGCTATAAC-TCTTCTCTTTTAAATTCCAAAAGTGTCGA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
1559427 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
131 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
*
1559479 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGACCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
1559544 TTTATAAAGTATCGACACTTTATTGGCGCTATAAC-TCTTCTCTTTTAAATTCCAAAAGTGTCGA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
*
1559608 TACGTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
131 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
* *
1559660 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATATATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
* * * *
1559725 TTTATAAAGTATCGACACTTTATTGACGATATAACTTATTCTGTTTTAAA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAA
1559775 AAAGGTAAAA
Statistics
Matches: 1308, Mismatches: 69, Indels: 22
0.93 0.05 0.02
Matches are distributed among these distances:
178 2 0.00
179 18 0.01
180 154 0.12
181 498 0.38
182 461 0.35
183 2 0.00
186 173 0.13
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (182 bp):
TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
Found at i:1559674 original size:544 final size:545
Alignment explanation
Indices: 1558205--1559774 Score: 2680
Period size: 544 Copynumber: 2.9 Consensus size: 545
1558195 TGCGTTCACC
** ** * * * * *
1558205 TTTTGTCATTTATAGACCAATTTTATCATATTTTTATATGTTATATTATTATAGATCGATATATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
1558270 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTATTAATTCCAAAAGTGTCGA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTATTAATTCCAAAAGTGTCGA
* *
1558335 TACTTATAATAAATTATCGACACTTTCAACATATCCGGTAGCGCTTTACCTGTTTTTTCATTTCG
131 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTCG
* *
1558400 AGACCGATTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATC
196 AGACCGGTTTTATCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATC
* *
1558465 GACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCTATACTTATAATAAA
261 GACACTTTATTGGCGCTATAAC-TCTTCTCTTTTAAATTCCAAAAGTGTCGATACGTATAATAAA
* *
1558530 TTATCGACACTTTCAACATAACCGGTAGCGCTTTTTTTACCTGTTTTATCATTTCGAGATCGGTT
325 TTATCGACACTTTCAACATAACCGGTAGCGC----TTTACCTGTTTTGTCATTTCGAGACCGGTT
* * * *
1558595 TTTTCATATTATTACTTGTTATATTGTTATGGATCGATACATTTTTATCAAGTATCGACACTTTA
386 TTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTA
* *
1558660 TTGGCGCTATAACTTCTTCTCTTTTAAATTTCAAAAGTGTCGATACTTATAATAAATTATCGACA
451 TTGGCGCTATAACTTATTCTCTTTTAAATTTCAAAAGTGTAGATACTTATAATAAATTATCGACA
1558725 CTTTCAACATAACCGGTAGCGCTTTACCTG
516 CTTTCAACATAACCGGTAGCGCTTTACCTG
1558755 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
* *
1558820 TTTATAAAGTATCGACACGTTATTGGCGCTATAACTTCATCTCTTATTAATTCCAAAA-T-TCGA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTATTAATTCCAAAAGTGTCGA
1558883 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTCG
131 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTCG
* *
1558948 AGACCGGTTTTTTCATATTTTTACATGTTATATTGTTATGGATCGATAAATTTTTATAAAGTATC
196 AGACCGGTTTTATCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATC
*
1559013 GACACTTTATTGGCGCTATAACTCTTCTCTTTTAAATTCCAAAAGTGTTGATACGTATAATAAAT
261 GACACTTTATTGGCGCTATAACTCTTCTCTTTTAAATTCCAAAAGTGTCGATACGTATAATAAAT
*
1559078 TATCGACACTTTCAACATAACCGGTAGCGCTTTACCTGATTTGTCATTTCGAGACCGGTTTTGTC
326 TATCGACACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTCGAGACCGGTTTTGTC
* *
1559143 ATATTTTTACCTGTTATATTGTTATGGATCAATACATTTTTATAAAGTATCGAAACTTTATTGGC
391 ATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATTGGC
*
1559208 GCTATAAATTATTCTCTTTTAAATTTCAAAAGTGTAGATACTTATAATAAATTATCGACACTTTC
456 GCTATAACTTATTCTCTTTTAAATTTCAAAAGTGTAGATACTTATAATAAATTATCGACACTTTC
1559273 AACATAACCGGTAGCGCTTTACCTG
521 AACATAACCGGTAGCGCTTTACCTG
* * *
1559298 TTTTGTCATTTTGAGATCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
*
1559363 TTTATAAAATATCGACACTTTATTGGCGCTATAAC-TCTTCTCTT-TTAAATTCCAAAAGTGTCG
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTATT-AATTCCAAAAGTGTCG
1559426 ATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTC
130 ATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTC
* *
1559491 GAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGACCGATACATTTTTATAAAGTAT
195 GAGACCGGTTTTATCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTAT
1559556 CGACACTTTATTGGCGCTATAACTCTTCTCTTTTAAATTCCAAAAGTGTCGATACGTATAATAAA
260 CGACACTTTATTGGCGCTATAACTCTTCTCTTTTAAATTCCAAAAGTGTCGATACGTATAATAAA
1559621 TTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTCGAGACCGGTTTTGT
325 TTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTCGAGACCGGTTTTGT
* *
1559686 CATATTTTTACCTGTTATATTGTTATGGATCGATATATTTTTATAAAGTATCGACACTTTATTGA
390 CATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATTGG
* *
1559751 CGATATAACTTATTCTGTTTTAAA
455 CGCTATAACTTATTCTCTTTTAAA
1559775 AAAGGTAAAA
Statistics
Matches: 967, Mismatches: 50, Indels: 12
0.94 0.05 0.01
Matches are distributed among these distances:
541 2 0.00
542 18 0.02
543 274 0.28
544 340 0.35
547 70 0.07
548 150 0.16
549 1 0.00
550 112 0.12
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (545 bp):
TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTATTAATTCCAAAAGTGTCGA
TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTCG
AGACCGGTTTTATCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATC
GACACTTTATTGGCGCTATAACTCTTCTCTTTTAAATTCCAAAAGTGTCGATACGTATAATAAAT
TATCGACACTTTCAACATAACCGGTAGCGCTTTACCTGTTTTGTCATTTCGAGACCGGTTTTGTC
ATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATTGGC
GCTATAACTTATTCTCTTTTAAATTTCAAAAGTGTAGATACTTATAATAAATTATCGACACTTTC
AACATAACCGGTAGCGCTTTACCTG
Found at i:1560698 original size:3 final size:3
Alignment explanation
Indices: 1560690--1560740 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
1560680 AATTGTTTGG
* * * * *
1560690 ATC ATC ATC ATC ATA ATC ATC ATC ATC GTC ATC TTC ATC GTC ATC TTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1560738 ATC
1 ATC
1560741 GTCAGGTTCA
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.27, C:0.31, G:0.04, T:0.37
Consensus pattern (3 bp):
ATC
Found at i:1560721 original size:12 final size:12
Alignment explanation
Indices: 1560694--1560744 Score: 66
Period size: 12 Copynumber: 4.2 Consensus size: 12
1560684 GTTTGGATCA
**
1560694 TCATCATCATAA
1 TCATCATCATCG
1560706 TCATCATCATCG
1 TCATCATCATCG
*
1560718 TCATCTTCATCG
1 TCATCATCATCG
*
1560730 TCATCTTCATCG
1 TCATCATCATCG
1560742 TCA
1 TCA
1560745 GGTTCATCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.25, C:0.31, G:0.06, T:0.37
Consensus pattern (12 bp):
TCATCATCATCG
Found at i:1560752 original size:12 final size:12
Alignment explanation
Indices: 1560706--1560744 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
1560696 ATCATCATAA
*
1560706 TCATCATCATCG
1 TCATCTTCATCG
1560718 TCATCTTCATCG
1 TCATCTTCATCG
1560730 TCATCTTCATCG
1 TCATCTTCATCG
1560742 TCA
1 TCA
1560745 GGTTCATCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.21, C:0.33, G:0.08, T:0.38
Consensus pattern (12 bp):
TCATCTTCATCG
Found at i:1560756 original size:6 final size:6
Alignment explanation
Indices: 1560706--1560757 Score: 50
Period size: 6 Copynumber: 8.7 Consensus size: 6
1560696 ATCATCATAA
* * * * **
1560706 TCATCA TCATCG TCATCT TCATCG TCATCT TCATCG TCAGGT TCATCT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
1560754 TCAT
1 TCAT
1560758 TGACCGCTTG
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.19, C:0.31, G:0.10, T:0.40
Consensus pattern (6 bp):
TCATCT
Found at i:1562615 original size:200 final size:200
Alignment explanation
Indices: 1562267--1563408 Score: 2194
Period size: 200 Copynumber: 5.7 Consensus size: 200
1562257 GATATTTAAA
*
1562267 AATAATATCGACACAAAATTAAAAAGTGTCGATACATATATTACACCTATTCTCTCATAAATCCG
1 AATAGTATCGACACAAAATTAAAAAGTGTCGATACATATATTACACCTATTCTCTCATAAATCCG
* *
1562332 GTATACTTATACCGGTTAGATTAAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTT
66 GTATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTC
1562397 TGGGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCT
131 TGGGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCT
1562462 GGACC
196 GGACC
1562467 AATAGTATCGACACAAAATTAAAAAGTGTCGATACATATATTACACCTATTCTCTCATAAATCCG
1 AATAGTATCGACACAAAATTAAAAAGTGTCGATACATATATTACACCTATTCTCTCATAAATCCG
1562532 GTATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTC
66 GTATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTC
*
1562597 TGGGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTACCATTCATTCT
131 TGGGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCT
1562662 GGACC
196 GGACC
*
1562667 AATAGTATCGACACAAAATTAAAAAGTGTCGATACATATATTACACCTATTCTCTCATAAATCCA
1 AATAGTATCGACACAAAATTAAAAAGTGTCGATACATATATTACACCTATTCTCTCATAAATCCG
1562732 GTATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTC
66 GTATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTC
*
1562797 TGGGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCATGTTTGCCATTCATTCT
131 TGGGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCT
1562862 GGACC
196 GGACC
1562867 AATAGTATCGACACAAAATTAAAAAGTGTCGATACATATATTACACCTATTCTCTCATAAATCCG
1 AATAGTATCGACACAAAATTAAAAAGTGTCGATACATATATTACACCTATTCTCTCATAAATCCG
*
1562932 GTATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATATTTC
66 GTATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTC
**
1562997 TGGGATCGACATATTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCT
131 TGGGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCT
1563062 GGACC
196 GGACC
1563067 AATAGTATCGACACAAAATTAAAAAGTGTCGATACATATATTACACCTATTCTCTCATAAATCCG
1 AATAGTATCGACACAAAATTAAAAAGTGTCGATACATATATTACACCTATTCTCTCATAAATCCG
1563132 GTATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTC
66 GTATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTC
*
1563197 TGGGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTTT
131 TGGGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCT
1563262 GGACC
196 GGACC
1563267 AATAGTATCGACACAAAATTAAAAAGTGTCGATACATATATTACACCTATTCTCTCATAAATCCG
1 AATAGTATCGACACAAAATTAAAAAGTGTCGATACATATATTACACCTATTCTCTCATAAATCCG
1563332 GTATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTC
66 GTATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTC
1563397 TGGGATCGACAC
131 TGGGATCGACAC
1563409 TTTATGGTTG
Statistics
Matches: 926, Mismatches: 16, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
200 926 1.00
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (200 bp):
AATAGTATCGACACAAAATTAAAAAGTGTCGATACATATATTACACCTATTCTCTCATAAATCCG
GTATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTC
TGGGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCT
GGACC
Found at i:1563692 original size:19 final size:19
Alignment explanation
Indices: 1563668--1563716 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
1563658 TTACATTCAC
1563668 ATACAAAATTATAAATCGT-
1 ATACAAAATTATAAATC-TA
1563687 ATACAAAATTATAAATCTA
1 ATACAAAATTATAAATCTA
1563706 ATACAAAATTA
1 ATACAAAATTA
1563717 ACCCTACATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
18 1 0.03
19 28 0.97
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCTA
Found at i:1565319 original size:33 final size:33
Alignment explanation
Indices: 1565267--1565354 Score: 142
Period size: 33 Copynumber: 2.7 Consensus size: 33
1565257 ATGACATCGA
*
1565267 CTTCCTTCCT-CCTCATTTCTTCCATCTCTTCTT
1 CTTCC-TCCTCCCTCTTTTCTTCCATCTCTTCTT
*
1565300 CTTCCTCCTCCCTCTTTTCTTTCATCTCTTCTT
1 CTTCCTCCTCCCTCTTTTCTTCCATCTCTTCTT
1565333 CTTCCTCCTCCCTCTTTTCTTC
1 CTTCCTCCTCCCTCTTTTCTTC
1565355 TTCATAATTT
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
32 4 0.08
33 47 0.92
ACGTcount: A:0.03, C:0.44, G:0.00, T:0.52
Consensus pattern (33 bp):
CTTCCTCCTCCCTCTTTTCTTCCATCTCTTCTT
Found at i:1565579 original size:33 final size:33
Alignment explanation
Indices: 1565542--1565607 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
1565532 CATCTTAAGA
*
1565542 TCACCCCTTAACACCTCAACTTCTTTCACCACT
1 TCACCCCTCAACACCTCAACTTCTTTCACCACT
*
1565575 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCTCAACTTCTTTCACCACT
1565608 CCATCTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.23, C:0.47, G:0.00, T:0.30
Consensus pattern (33 bp):
TCACCCCTCAACACCTCAACTTCTTTCACCACT
Found at i:1565668 original size:21 final size:21
Alignment explanation
Indices: 1565644--1565684 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1565634 CTTATGCCTC
1565644 TCAAGTGTATCTTCGACTCTA
1 TCAAGTGTATCTTCGACTCTA
* *
1565665 TCAAGTTTCTCTTCGACTCT
1 TCAAGTGTATCTTCGACTCT
1565685 TGATTGTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.27, G:0.12, T:0.41
Consensus pattern (21 bp):
TCAAGTGTATCTTCGACTCTA
Found at i:1567986 original size:20 final size:19
Alignment explanation
Indices: 1567940--1567986 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1567930 TCCGGAATCA
*
1567940 TTTTACTGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
1567959 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
1567980 TTTTACC
1 TTTTACC
1567987 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.19, C:0.15, G:0.11, T:0.55
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:1568265 original size:181 final size:181
Alignment explanation
Indices: 1567907--1568380 Score: 662
Period size: 182 Copynumber: 2.6 Consensus size: 181
1567897 CGTACTTACG
* * * * *
1567907 AAAGTATCGACACTTTTAATATATCCGGAATCATTTTACTGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTACCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
*
1567972 TATCATATTTTTACCTGTTATATCGTTGTTTGATCGATACATTTTTTTAAAGTATCGACACTTTA
66 TATCATATTTTTA-CTGTTATATCGTTG-TTGATCGATACATTTTTTGAAAGTATCGACACTTTA
*
1568037 TAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTATCGATCCTTATA-T
129 TAGGCGCTAAAACTGCTTCTCTTTTAAATTAACAAAGTATCGATCCTTATATT
* * * * * *
1568089 AAAGTTTCGACACTTTCAATATATCCGGTAGCGTTTTACCGATTTCATCATTTTGATACCAGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTACCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
*
1568154 TATCATATTTTTACATGTTATATCGTTGTTGATCGATATATTTTTTGAAAGTATCGACACTTTAT
66 TATCATATTTTTAC-TGTTATATCGTTGTTGATCGATACATTTTTTGAAAGTATCGACACTTTAT
* * *
1568219 AGGCGCTAAAACTGCTTCTCTTTTAAATTAACGAAGTGTTGATCCTTATATT
130 AGGCGCTAAAACTGCTTCTCTTTTAAATTAACAAAGTATCGATCCTTATATT
* * * * ** *
1568271 AAAGTACCGACACTTTAAATATATTCGGTACCGCTTTATCGGTTTTATCATTTCAATACTGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTACCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
1568336 TGTCATAGTTTTATCTGTTATATCGTTGTGGATCGATACATTTTT
66 TATCATATTTTTA-CTGTTATATCGTTGTTGATCGATACATTTTT
1568381 AATTTGGATC
Statistics
Matches: 257, Mismatches: 32, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
181 82 0.32
182 174 0.68
183 1 0.00
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (181 bp):
AAAGTATCGACACTTTAAATATATCCGGTACCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACTGTTATATCGTTGTTGATCGATACATTTTTTGAAAGTATCGACACTTTATA
GGCGCTAAAACTGCTTCTCTTTTAAATTAACAAAGTATCGATCCTTATATT
Found at i:1578428 original size:3 final size:3
Alignment explanation
Indices: 1578420--1578463 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
1578410 TTTTCAACCG
1578420 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1578464 TCAAACCCGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1583507 original size:22 final size:20
Alignment explanation
Indices: 1583461--1583549 Score: 63
Period size: 22 Copynumber: 4.2 Consensus size: 20
1583451 TATTTAGCTA
* *
1583461 ATATATATTTACCTTTATGTGT
1 ATATATATTTA-TTTTAT-TTT
1583483 ATATATATTATCATTTTATTTT
1 ATATATATT-T-ATTTTATTTT
*
1583505 ATAT-TTTTTAATTGTTATTTAT
1 ATATATATTT-ATT-TTATTT-T
* *
1583527 CTATATATTTATTTTAATTT
1 ATATATATTTATTTTATTTT
1583547 ATA
1 ATA
1583550 AAATATTTTC
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
20 7 0.13
21 14 0.26
22 22 0.41
23 10 0.19
24 1 0.02
ACGTcount: A:0.30, C:0.04, G:0.03, T:0.62
Consensus pattern (20 bp):
ATATATATTTATTTTATTTT
Found at i:1586821 original size:102 final size:102
Alignment explanation
Indices: 1586640--1586842 Score: 316
Period size: 102 Copynumber: 2.0 Consensus size: 102
1586630 CAAGGGATGG
* *
1586640 CTCTACCTGACTAGCTCAGGGGTGGAAGGTATGCTCCTTTTCACTTAGAGTGTGGGATGGTAGTG
1 CTCTACCTGACTAGCTCAGGGGTGGAAGGTAGGCTCCCTTTCACTTAGAGTGTGGGATGGTAGTG
* * * *
1586705 TGATGAGCTGACTCCCCTTAAAGTATGCTTAAAAAAA
66 TGATAAGATAACTCCCCTTAAAGTATGCATAAAAAAA
* * *
1586742 CTCTACTTGACTGGCTCGGGGGTGGAAGGTAGGCTCCCTTTCACTTAGAGTGTGGGATGGTAGTG
1 CTCTACCTGACTAGCTCAGGGGTGGAAGGTAGGCTCCCTTTCACTTAGAGTGTGGGATGGTAGTG
*
1586807 TGCTAAGATAACTCCCCTTAAAGTATGCATAAAAAA
66 TGATAAGATAACTCCCCTTAAAGTATGCATAAAAAA
1586843 TAGTTGAAGT
Statistics
Matches: 91, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
102 91 1.00
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.29
Consensus pattern (102 bp):
CTCTACCTGACTAGCTCAGGGGTGGAAGGTAGGCTCCCTTTCACTTAGAGTGTGGGATGGTAGTG
TGATAAGATAACTCCCCTTAAAGTATGCATAAAAAAA
Found at i:1597287 original size:16 final size:16
Alignment explanation
Indices: 1597266--1597305 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
1597256 AGACTAACAT
1597266 AACCCAATTTCAAACG
1 AACCCAATTTCAAACG
1597282 AACCCAATTTCAAACG
1 AACCCAATTTCAAACG
1597298 AACCCAAT
1 AACCCAAT
1597306 CACTTCAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.45, C:0.33, G:0.05, T:0.17
Consensus pattern (16 bp):
AACCCAATTTCAAACG
Found at i:1599547 original size:10 final size:10
Alignment explanation
Indices: 1599532--1599561 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1599522 CCACCACATA
1599532 CAACTATATG
1 CAACTATATG
1599542 CAACTATATG
1 CAACTATATG
*
1599552 CATCTATATG
1 CAACTATATG
1599562 ATCCTATATG
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:0.37, C:0.20, G:0.10, T:0.33
Consensus pattern (10 bp):
CAACTATATG
Found at i:1599908 original size:161 final size:160
Alignment explanation
Indices: 1599679--1599992 Score: 443
Period size: 161 Copynumber: 2.0 Consensus size: 160
1599669 ATACTTCATT
* ** * *
1599679 CTATCACGTAAGGAGTTGGATCAGCATCACCTTAGGTCATCCATCACAGAAGGAGTTGGATCGAT
1 CTATCACATAAGGAGTTGGATCAGCATCACCTTAAATCATCCATCACAAAAGGAGTTAGATCGAT
* * * *
1599744 ATTCCTGATAAGAGAAGTTTGTAAT-AAGAAGAACTTGCTCAATAATTGCTTGATTTCATCAC-A
66 ATTCCCGATAAGAGAAGTTCGTAATGAA-AA-AAATTGCTCAACAATTGCTTGATTTCATC-CTA
*
1599807 TAAGGAGTTGGAACAACACCCACCTTGGCTCAC
128 TAAAGAGTTGGAACAACACCCACCTTGGCTCAC
* * *
1599840 CTATCACATCAGGAGTTGGATCAGCGTCACCTTAAATCATCCATCACAAAAGGAGTTAGATTGAT
1 CTATCACATAAGGAGTTGGATCAGCATCACCTTAAATCATCCATCACAAAAGGAGTTAGATCGAT
* *
1599905 ATTCCCGATAGGAGAAGTTCGTAATGAAAAAAATTGCTCAACATTTGCTTGATTTCATCCTATAA
66 ATTCCCGATAAGAGAAGTTCGTAATGAAAAAAATTGCTCAACAATTGCTTGATTTCATCCTATAA
*
1599970 AGAGTTGGAACAACACCGACCTT
131 AGAGTTGGAACAACACCCACCTT
1599993 AGCTTATCCA
Statistics
Matches: 135, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
159 1 0.01
160 51 0.38
161 81 0.60
162 2 0.01
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.27
Consensus pattern (160 bp):
CTATCACATAAGGAGTTGGATCAGCATCACCTTAAATCATCCATCACAAAAGGAGTTAGATCGAT
ATTCCCGATAAGAGAAGTTCGTAATGAAAAAAATTGCTCAACAATTGCTTGATTTCATCCTATAA
AGAGTTGGAACAACACCCACCTTGGCTCAC
Found at i:1600056 original size:160 final size:160
Alignment explanation
Indices: 1599715--1600033 Score: 385
Period size: 160 Copynumber: 2.0 Consensus size: 160
1599705 TCACCTTAGG
* * * * *
1599715 TCATCCATCACAGAAGGAGTTGGATCGATATTCCTGATAAGAGAAGTTTGTAATAAGAAGAACTT
1 TCAT-CATCACAAAAGGAGTTAGATCGATATTCCCGATAAGAGAAGTTCGTAATAAGAAGAAATT
* * *
1599780 GCTCAATAATTGCTTGATTTCATCACATAAGGAGTTGGAACAACACCCACCTTGGCTCACCTATC
65 GCTCAACAATTGCTTGATTTCATCACATAAAGAGTTGGAACAACACCCACCTTAGCTCACCTATC
** ** * * *
1599845 ACATCAGGAGTTGGATCAGCGTCACCTTAAA
130 ACAAAAAAAGTTGGATCAACGACACCATAAA
* *
1599876 TCATCCATCACAAAAGGAGTTAGATTGATATTCCCGATAGGAGAAGTTCGTAATGAA-AA-AAAT
1 TCAT-CATCACAAAAGGAGTTAGATCGATATTCCCGATAAGAGAAGTTCGTAAT-AAGAAGAAAT
* * *
1599939 TGCTCAACATTTGCTTGATTTCATC-CTATAAAGAGTTGGAACAACACCGACCTTAGCTTATCC-
64 TGCTCAACAATTGCTTGATTTCATCAC-ATAAAGAGTTGGAACAACACCCACCTTAGCTCA-CCT
1600002 ATCACAAAAAAAGTTGGATCAACGACACCATA
127 ATCACAAAAAAAGTTGGATCAACGACACCATA
1600034 TGTTACATAT
Statistics
Matches: 135, Mismatches: 20, Indels: 7
0.83 0.12 0.04
Matches are distributed among these distances:
159 1 0.01
160 80 0.59
161 52 0.39
162 2 0.01
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (160 bp):
TCATCATCACAAAAGGAGTTAGATCGATATTCCCGATAAGAGAAGTTCGTAATAAGAAGAAATTG
CTCAACAATTGCTTGATTTCATCACATAAAGAGTTGGAACAACACCCACCTTAGCTCACCTATCA
CAAAAAAAGTTGGATCAACGACACCATAAA
Found at i:1600299 original size:3 final size:3
Alignment explanation
Indices: 1600291--1600370 Score: 124
Period size: 3 Copynumber: 26.0 Consensus size: 3
1600281 TCAACCGTTA
* *
1600291 TAT TAT TAT TAT TAT TAT TGT TAT TGTT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT
1600337 TAT TAT TAT TAT TATT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT
1600371 GCAACACCCT
Statistics
Matches: 71, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
3 66 0.93
4 5 0.07
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1601095 original size:23 final size:23
Alignment explanation
Indices: 1601053--1601155 Score: 107
Period size: 23 Copynumber: 4.4 Consensus size: 23
1601043 CACCAAAGTG
1601053 CCACGTAGAAATTGTCCCGAATGA
1 CCACGTAGAAA-TGTCCCGAATGA
* * *
1601077 CCACATAGATATGTCCCGAAGGA
1 CCACGTAGAAATGTCCCGAATGA
* *
1601100 CCGCGTAGAAAAGTCCCGAATGA
1 CCACGTAGAAATGTCCCGAATGA
* * * *
1601123 CCACGTAGAATTGTTCCAAAGGA
1 CCACGTAGAAATGTCCCGAATGA
*
1601146 CAACGTAGAA
1 CCACGTAGAA
1601156 CCCTCAACTT
Statistics
Matches: 64, Mismatches: 15, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
23 55 0.86
24 9 0.14
ACGTcount: A:0.36, C:0.24, G:0.22, T:0.17
Consensus pattern (23 bp):
CCACGTAGAAATGTCCCGAATGA
Found at i:1601145 original size:46 final size:47
Alignment explanation
Indices: 1601055--1601155 Score: 125
Period size: 46 Copynumber: 2.2 Consensus size: 47
1601045 CCAAAGTGCC
* * *
1601055 ACGTAGAAATTGTCCCGAATGACCACATAGATATGTCCCGAAGGACC
1 ACGTAGAAATAGTCCCGAATGACCACATAGATATGTCCCAAAGGACA
* * *
1601102 GCGTAGAAA-AGTCCCGAATGACCACGTAGA-ATTGTTCCAAAGGACA
1 ACGTAGAAATAGTCCCGAATGACCACATAGATA-TGTCCCAAAGGACA
1601148 ACGTAGAA
1 ACGTAGAA
1601156 CCCTCAACTT
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
45 1 0.02
46 37 0.80
47 8 0.17
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.18
Consensus pattern (47 bp):
ACGTAGAAATAGTCCCGAATGACCACATAGATATGTCCCAAAGGACA
Found at i:1604393 original size:45 final size:46
Alignment explanation
Indices: 1604320--1604423 Score: 176
Period size: 45 Copynumber: 2.3 Consensus size: 46
1604310 GACCAAATAG
*
1604320 ATGTCCCGAAGGACCACATATAATACATATGTCCCG-AAGAACCACT
1 ATGTCCCGAAGGACCACATATAACACATATGTCCCGAAAG-ACCACT
1604366 ATGTCCCGAAGG-CCACATATAACACATATGTCCCGAAAGACCACT
1 ATGTCCCGAAGGACCACATATAACACATATGTCCCGAAAGACCACT
1604411 ATGTCCCGAAGGA
1 ATGTCCCGAAGGA
1604424 TCGCGTAGAC
Statistics
Matches: 55, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
45 40 0.73
46 15 0.27
ACGTcount: A:0.36, C:0.29, G:0.17, T:0.18
Consensus pattern (46 bp):
ATGTCCCGAAGGACCACATATAACACATATGTCCCGAAAGACCACT
Found at i:1607275 original size:14 final size:14
Alignment explanation
Indices: 1607256--1607282 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1607246 CAAAAAAAAT
1607256 ATACATCTTTCCTG
1 ATACATCTTTCCTG
1607270 ATACATCTTTCCT
1 ATACATCTTTCCT
1607283 TCAAAACTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.30, G:0.04, T:0.44
Consensus pattern (14 bp):
ATACATCTTTCCTG
Found at i:1609968 original size:90 final size:89
Alignment explanation
Indices: 1609824--1609988 Score: 294
Period size: 90 Copynumber: 1.8 Consensus size: 89
1609814 TTTTATAGCC
*
1609824 AAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTAATTCATTG
1 AAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTAATTAATTG
* *
1609889 GAATTTAATAATCCTCTTATATCT
66 AAATTAAATAATCCTCTTATATCT
1609913 AAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATATTTAATTAATT
1 AAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTATATTTAATTAATT
1609978 GAAATTAAATA
65 GAAATTAAATA
1609989 TTCGGGATTA
Statistics
Matches: 72, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
89 23 0.32
90 49 0.68
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (89 bp):
AAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTAATTAATTG
AAATTAAATAATCCTCTTATATCT
Found at i:1616873 original size:90 final size:89
Alignment explanation
Indices: 1616721--1616893 Score: 319
Period size: 90 Copynumber: 1.9 Consensus size: 89
1616711 ACACACTCTT
1616721 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
1 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
*
1616786 ATTAATTGAAATTTAATAATCCTC
66 ATTAATTGAAATTAAATAATCCTC
*
1616810 TTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATATTT
1 TTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTATATTT
1616875 AATTAATTGAAATTAAATA
65 AATTAATTGAAATTAAATA
1616894 TTTGGGATTA
Statistics
Matches: 81, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
89 30 0.37
90 51 0.63
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (89 bp):
TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
ATTAATTGAAATTAAATAATCCTC
Found at i:1619138 original size:23 final size:23
Alignment explanation
Indices: 1619087--1619155 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
1619077 ACACATAAAT
*
1619087 ATGTCCCAAAGAACCACGTAGAA
1 ATGTCCCAAAGGACCACGTAGAA
* **
1619110 AAGTCCCAAAGGACCACGTATTA
1 ATGTCCCAAAGGACCACGTAGAA
* * *
1619133 TTGTCCCGAATGACCACGTAGAA
1 ATGTCCCAAAGGACCACGTAGAA
1619156 CCCTCGACTC
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.17
Consensus pattern (23 bp):
ATGTCCCAAAGGACCACGTAGAA
Found at i:1620694 original size:3 final size:3
Alignment explanation
Indices: 1620686--1620784 Score: 189
Period size: 3 Copynumber: 32.7 Consensus size: 3
1620676 GGATGTTACA
1620686 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1620734 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TATT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T
1620780 TAT TA
1 TAT TA
1620785 CAAACCTGGA
Statistics
Matches: 95, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
3 92 0.97
4 3 0.03
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1620843 original size:17 final size:17
Alignment explanation
Indices: 1620820--1620865 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
1620810 AATTTGAAAC
1620820 CCTAACCCAATACCTAAA
1 CCTAACCCAATA-CTAAA
*
1620838 -CTAACCTAAT-CTAAA
1 CCTAACCCAATACTAAA
1620853 CCTAACCCTAATA
1 CCTAACCC-AATA
1620866 TACCTTTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
15 5 0.22
16 6 0.26
17 12 0.52
ACGTcount: A:0.43, C:0.35, G:0.00, T:0.22
Consensus pattern (17 bp):
CCTAACCCAATACTAAA
Found at i:1626585 original size:23 final size:23
Alignment explanation
Indices: 1626559--1626661 Score: 107
Period size: 23 Copynumber: 4.4 Consensus size: 23
1626549 CCGTAAATGC
*
1626559 TAAATAAACATGTTCATGAACAT
1 TAAATAAACATGTTCGTGAACAT
* *
1626582 TAAATGAATATGTTCGTGAACAT
1 TAAATAAACATGTTCGTGAACAT
* * *
1626605 ATAAATGAACATGTTCTTAAACAT
1 -TAAATAAACATGTTCGTGAACAT
* * * *
1626629 TAAATAAGCACGTTCGCGAACAA
1 TAAATAAACATGTTCGTGAACAT
1626652 TAAATAAACA
1 TAAATAAACA
1626662 AACACGAATA
Statistics
Matches: 65, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
23 45 0.69
24 20 0.31
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.28
Consensus pattern (23 bp):
TAAATAAACATGTTCGTGAACAT
Found at i:1626644 original size:47 final size:46
Alignment explanation
Indices: 1626559--1626661 Score: 127
Period size: 47 Copynumber: 2.2 Consensus size: 46
1626549 CCGTAAATGC
* * * *
1626559 TAAATAAACATGTTCATGAACATTAAATGAATATGTTCGTGAACATA
1 TAAATAAACATGTTCATAAACATTAAATGAACACGTTCGCGAACA-A
* *
1626606 TAAATGAACATGTTCTTAAACATTAAAT-AAGCACGTTCGCGAACAA
1 TAAATAAACATGTTCATAAACATTAAATGAA-CACGTTCGCGAACAA
1626652 TAAATAAACA
1 TAAATAAACA
1626662 AACACGAATA
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
46 12 0.25
47 36 0.75
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.28
Consensus pattern (46 bp):
TAAATAAACATGTTCATAAACATTAAATGAACACGTTCGCGAACAA
Found at i:1634693 original size:23 final size:23
Alignment explanation
Indices: 1634646--1634694 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
1634636 AATAACATAT
**
1634646 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATAAAA
1634669 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGCGCTTATATAATAAAA
1634692 TAG
1 TAG
1634695 ATATTTAACC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.39, C:0.08, G:0.20, T:0.33
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATAAAA
Found at i:1634756 original size:87 final size:87
Alignment explanation
Indices: 1634610--1634771 Score: 306
Period size: 87 Copynumber: 1.9 Consensus size: 87
1634600 ATGTTATATC
*
1634610 ATTTAACCGGAAATATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTA
1 ATTTAACCGGAAATATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAATGTAATAGATA
1634675 GCGCTTATATAATAAAATAGAT
66 GCGCTTATATAATAAAATAGAT
*
1634697 ATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGATA
1 ATTTAACCGGAAATATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAATGTAATAGATA
1634762 GCGCTTATAT
66 GCGCTTATAT
1634772 TGACTTATTT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 73 1.00
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (87 bp):
ATTTAACCGGAAATATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAATGTAATAGATA
GCGCTTATATAATAAAATAGAT
Found at i:1635662 original size:183 final size:182
Alignment explanation
Indices: 1635154--1636035 Score: 1308
Period size: 182 Copynumber: 4.8 Consensus size: 182
1635144 TGTTGACCTA
* * *
1635154 TTTTCTCATATTTTTAGCTGTTATATTGTTATCGATCGATACATTTTTATAAAGTGTCGACACTT
1 TTTTGTCATATTTTTAGCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCGACACTT
*
1635219 TTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGCCGATACTTATATTAAATTATCGA
66 TTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGA
* *
1635284 CACTTTTAACATATCCGGTAGCGTTTTACCAGTTTTGTCATTTTGAGACCGG
131 CACTTTCAACATATCCGGTAGCGTTTTACCTGTTTTGTCATTTTGAGACCGG
* * * *
1635336 TTTTGTCATATTTTTA-CATGTTATATTGTTATGGATCGATACATTTT-TTAAAGTATCGATACT
1 TTTTGTCATATTTTTAGC-TGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCGACACT
* * *
1635399 TTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCA-AAAGTATCGATACTTATATTAAAGTATC
65 TTTTAGGCGCTATAACTTCTTCTCTTTTAAATT-CAGAAAGTGTCGATACTTATATTAAATTATC
* * *
1635463 GACACTTTCAACATATCTGGTAG-TTATTTAACCTGTTTTGTCATTTTGAGATCGG
129 GACACTTTCAACATATCCGGTAGCGT-TTT-ACCTGTTTTGTCATTTTGAGACCGG
*
1635518 TTTTGTCATATTTTTAGCTGTTATATTGTTATAGATCGATAAATTTTCATAAAGTGTCGACACTT
1 TTTTGTCATATTTTTAGCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCGACACTT
* * *
1635583 TTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTTGATACTTATGTTAAATTAGCGA
66 TTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGA
*
1635648 CACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTCATTTTGAGACCGG
131 CACTTTCAACATATCCGGTAGCGTTTTACCTGTTTTGTCATTTTGAGACCGG
* * * * ** *
1635700 TTTTGTTATATTTTTACCTGTAATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACACTT
1 TTTTGTCATATTTTTAGCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCGACACTT
* * * * ** * *
1635765 TTTAGGTGCTATAACTTATTCTCTTTTTATTTCCA-AAAGTGTTAATACTAATATTAAAGTATCG
66 TTTAGGCGCTATAACTTCTTCTCTTTTAAATT-CAGAAAGTGTCGATACTTATATTAAATTATCG
* * *
1635829 ACACTGTCAACATATCCGGTAG-TTATTTACCTTTTTTTGTCATTTTGAGACCGG
130 ACACTTTCAACATATCCGGTAGCGT-TTTACC-TGTTTTGTCATTTTGAGACCGG
1635883 TTTTGTCATATTTTTAGCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCGACACTT
1 TTTTGTCATATTTTTAGCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCGACACTT
1635948 TTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGA
66 TTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGA
1636013 CACTTTCAACATATCCGGTAGCG
131 CACTTTCAACATATCCGGTAGCG
1636036 CTTATATAAT
Statistics
Matches: 620, Mismatches: 67, Indels: 24
0.87 0.09 0.03
Matches are distributed among these distances:
180 1 0.00
181 96 0.15
182 274 0.44
183 248 0.40
184 1 0.00
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (182 bp):
TTTTGTCATATTTTTAGCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCGACACTT
TTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGA
CACTTTCAACATATCCGGTAGCGTTTTACCTGTTTTGTCATTTTGAGACCGG
Found at i:1635949 original size:365 final size:364
Alignment explanation
Indices: 1635154--1636035 Score: 1496
Period size: 365 Copynumber: 2.4 Consensus size: 364
1635144 TGTTGACCTA
* * *
1635154 TTTTCTCATATTTTTAGCTGTTATATTGTTATCGATCGATACATTTTTATAAAGTGTCGACACTT
1 TTTTGTCATATTTTTAGCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCGACACTT
*
1635219 TTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGCCGATACTTATATTAAATTATCGA
66 TTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGA
*
1635284 CACTTTTAACATATCCGGTAGCGTTTTACCAGTTTTGTCATTTTGAGACCGGTTTTGTCATATTT
131 CACTTTCAACATATCCGGTAGCGTTTTACCAGTTTTGTCATTTTGAGACCGGTTTTGTCATATTT
* *
1635349 TTACATGTTATATTGTTATGGATCGATACATTTTTTAAAGTATCGATACTTTATAGGCGCTATAA
196 TTACATGTAATATTGTTATGGATCGATACATTTTTTAAAGTATCGACACTTTATAGGCGCTATAA
* * * *
1635414 CTTCTTCTCTTTTAAATTCCAAAAGTATCGATACTTATATTAAAGTATCGACACTTTCAACATAT
261 CTTATTCTCTTTTAAATTCCAAAAGTATCAATACTAATATTAAAGTATCGACACTGTCAACATAT
* *
1635479 CTGGTAGTTATTTAACCTGTTTTGTCATTTTGAGATCGG
326 CCGGTAGTTATTTAACCTGTTTTGTCATTTTGAGACCGG
*
1635518 TTTTGTCATATTTTTAGCTGTTATATTGTTATAGATCGATAAATTTTCATAAAGTGTCGACACTT
1 TTTTGTCATATTTTTAGCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCGACACTT
* * *
1635583 TTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTTGATACTTATGTTAAATTAGCGA
66 TTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGA
* *
1635648 CACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTCATTTTGAGACCGGTTTTGTTATATTT
131 CACTTTCAACATATCCGGTAGCGTTTTACCAGTTTTGTCATTTTGAGACCGGTTTTGTCATATTT
* * *
1635713 TTACCTGTAATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACACTTTTTAGGTGCTATA
196 TTACATGTAATATTGTTATGGATCGATACA-TTTTTTAAAGTATCGACACTTTATAGGCGCTATA
* * * *
1635778 ACTTATTCTCTTTTTATTTCCAAAAGTGTTAATACTAATATTAAAGTATCGACACTGTCAACATA
260 ACTTATTCTCTTTTAAATTCCAAAAGTATCAATACTAATATTAAAGTATCGACACTGTCAACATA
*
1635843 TCCGGTAGTTATTT-ACCTTTTTTTGTCATTTTGAGACCGG
325 TCCGGTAGTTATTTAACC-TGTTTTGTCATTTTGAGACCGG
1635883 TTTTGTCATATTTTTAGCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCGACACTT
1 TTTTGTCATATTTTTAGCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCGACACTT
1635948 TTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGA
66 TTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGA
1636013 CACTTTCAACATATCCGGTAGCG
131 CACTTTCAACATATCCGGTAGCG
1636036 CTTATATAAT
Statistics
Matches: 485, Mismatches: 31, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
364 215 0.44
365 270 0.56
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (364 bp):
TTTTGTCATATTTTTAGCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCGACACTT
TTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGA
CACTTTCAACATATCCGGTAGCGTTTTACCAGTTTTGTCATTTTGAGACCGGTTTTGTCATATTT
TTACATGTAATATTGTTATGGATCGATACATTTTTTAAAGTATCGACACTTTATAGGCGCTATAA
CTTATTCTCTTTTAAATTCCAAAAGTATCAATACTAATATTAAAGTATCGACACTGTCAACATAT
CCGGTAGTTATTTAACCTGTTTTGTCATTTTGAGACCGG
Found at i:1636074 original size:23 final size:23
Alignment explanation
Indices: 1636029--1636076 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
1636019 CAACATATCC
**
1636029 GGTAGCGCTTATATAATGTAATA
1 GGTAGCGCTTATATAATAAAATA
1636052 GGTAGCGCTTATATAATAAAATA
1 GGTAGCGCTTATATAATAAAATA
1636075 GG
1 GG
1636077 CATTTAACTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (23 bp):
GGTAGCGCTTATATAATAAAATA
Found at i:1640520 original size:201 final size:195
Alignment explanation
Indices: 1640047--1640614 Score: 611
Period size: 199 Copynumber: 2.8 Consensus size: 195
1640037 CGCGTAATTT
* * * *
1640047 TAAAAAGTGTCGACACGAATTTAAAAAGTGTCGACACATTATGTT-GACCTATTTTCT-ATTTAC
1 TAAAAAGTATCGACACAAATT-AAAAAGTGTCGATACATTAT-TTAGACCTATTTTCTCA--TAA
* * * *
1640110 ACCGGTAAATTTCAACAGGTTACATTGTAAATTGACCTATTACATTATAATTTTTTGTCTCGATG
62 AACGGTAAATTTAAAC-GGTTACATTGTAAATTAACCTATTACATTATAA-TTTTCGTCTCGATG
* * * * *
1640175 TATTTGGGGTCGATACTTTTTATAAATATATCGAAACTTTATGCGTGGACATCGGTTGGCATTAA
125 TATTTGGGGTCGATAC-TTTTATAAATGTATCGAAACTTTAAGCGTGCACATAGGTTGGAATTAA
*
1640240 TTATGGA
189 TTATGCA
* * * * *
1640247 -CATAAGTATCGACACAAATGTAAAAAGTATCGATACATTATATAGACCTATTTGCTCATAAAAT
1 TAAAAAGTATCGACACAAAT-TAAAAAGTGTCGATACATTATTTAGACCTATTTTCTCATAAAA-
* * * *
1640311 CGGTAAATTGAAATCGGTTACAGTGTAAAGTAACCTATTACATTATAATTTTCGATCTCTATGTA
64 CGGTAAATTTAAA-CGGTTACATTGTAAATTAACCTATTACATTATAATTTTCG-TCTCGATGTA
* * * * *
1640376 TTTGGGGTTGATACTTTTAATAAATGTATCTACACTTTAAGCGTGCACATAGTTTGGGAATTCAT
127 TTTGGGGTCGATACTTTT-ATAAATGTATCGAAACTTTAAGCGTGCACATAGGTT-GGAATTAAT
1640441 TATGCA
190 TATGCA
*
1640447 TAAAAAGTATCGACACAAATAAATAAAGTGTCGATACATTATTTAGACCTATTTTCTCATAAAAC
1 TAAAAAGTATCGACACAAATTAA-AAAGTGTCGATACATTATTTAGACCTATTTTCTCATAAAAC
* * * * * *
1640512 ATGTAAATTTAAACCTGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTT
65 -GGTAAATTTAAA-CGGTTACATTGTAAATTAACCTATTACATTATAATTTTC-GTCTCGATGTA
* * *
1640577 TTTGGGATCGACACTTGTTATAAATGTATCGATACTTT
127 TTTGGGGTCGATACTT-TTATAAATGTATCGAAACTTT
1640615 GTTGTGCACT
Statistics
Matches: 305, Mismatches: 50, Indels: 25
0.80 0.13 0.07
Matches are distributed among these distances:
198 13 0.04
199 136 0.45
200 18 0.06
201 135 0.44
202 3 0.01
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (195 bp):
TAAAAAGTATCGACACAAATTAAAAAGTGTCGATACATTATTTAGACCTATTTTCTCATAAAACG
GTAAATTTAAACGGTTACATTGTAAATTAACCTATTACATTATAATTTTCGTCTCGATGTATTTG
GGGTCGATACTTTTATAAATGTATCGAAACTTTAAGCGTGCACATAGGTTGGAATTAATTATGCA
Found at i:1640552 original size:20 final size:21
Alignment explanation
Indices: 1640513--1640555 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
1640503 TCATAAAACA
*
1640513 TGTAAATTTAAACCTGTTACAT
1 TGTAAATTT-AACCTATTACAT
1640535 TGTAAATTT-ACCTATTACAT
1 TGTAAATTTAACCTATTACAT
1640555 T
1 T
1640556 ATAATTATCG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
22 9 0.45
ACGTcount: A:0.35, C:0.14, G:0.07, T:0.44
Consensus pattern (21 bp):
TGTAAATTTAACCTATTACAT
Found at i:1640788 original size:200 final size:200
Alignment explanation
Indices: 1640474--1641413 Score: 1359
Period size: 200 Copynumber: 4.7 Consensus size: 200
1640464 AATAAATAAA
* * * * ** * * * *
1640474 GTGTCGATACATTATTTAGACCTATTTTCTCATAAAACATGTAAATTTAAACCTGTTACATTGTA
1 GTGTCGATACTTTATGTATACCTGTTTTCTCAT-AAACCGGTATATTTAGACCGGTTACATTGTT
* * *
1640539 AATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGT
65 AATTTACCTATTACATTATAACTATGGGTTTCGATGTTTTTGAGATCGACACTTGTTATAAATGT
* * *
1640604 ATCGATACTTTGTTGTGCACTTGGTTTTTAAAATACACTCTGGACAAAAAGTATCGACACTTGTT
130 ATCGACACTTTGTTGTGCACTTGGTTTTTAAAATACACGCTGGACAAAAAGTATCGACACTTATT
1640669 AG-ATTT
195 -GTATTT
* * *
1640675 GTGTCGATACTTTATGTATACATGTTTTCTCATAAACCGGTATATGTAGACCGGTTACATTCTTA
1 GTGTCGATACTTTATGTATACCTGTTTTCTCATAAACCGGTATATTTAGACCGGTTACATTGTTA
1640740 ATTTACCTATTACATTATAACTATGGGTTTCGATGTTTTTGAGATCGACACTTGTTATAAATGTA
66 ATTTACCTATTACATTATAACTATGGGTTTCGATGTTTTTGAGATCGACACTTGTTATAAATGTA
* * * *
1640805 TCGATACTTTGTTGTGCACTTGATTTTTAAAATGCACTCTGGACAAAAAGTATCGACACTTATT-
131 TCGACACTTTGTTGTGCACTTGGTTTTTAAAATACACGCTGGACAAAAAGTATCGACACTTATTG
1640869 TCATTT
196 T-ATTT
* *
1640875 GTGTCGATACTTTATGTATACTTGTTTTCTCATAAACCAGTATATTTAGACCGGTTACATTGTTA
1 GTGTCGATACTTTATGTATACCTGTTTTCTCATAAACCGGTATATTTAGACCGGTTACATTGTTA
* * * *
1640940 ATTTACCTATTACATTATAATTATGGGTTTCGATATTTTTGGGATCGACACTTATTATAAATGTA
66 ATTTACCTATTACATTATAACTATGGGTTTCGATGTTTTTGAGATCGACACTTGTTATAAATGTA
1641005 TCGACACTTTGTTGTGCACTTGGTTTTTAAAATACACGCTGGACAAAAAGTATCGACACTTATTG
131 TCGACACTTTGTTGTGCACTTGGTTTTTAAAATACACGCTGGACAAAAAGTATCGACACTTATTG
1641070 TATTT
196 TATTT
* ** *
1641075 GTGTCGATACTTTATGTATACCTGTTTTCTCAAAAACCGGTATATTTAGGTCGGTTATATTGTTA
1 GTGTCGATACTTTATGTATACCTGTTTTCTCATAAACCGGTATATTTAGACCGGTTACATTGTTA
* * * *
1641140 TTTTACCTATTACATTATATCTATGTGTTTCGATATTTTT-AGTATCGACACTTGTTATAAATGT
66 ATTTACCTATTACATTATAACTATGGGTTTCGATGTTTTTGAG-ATCGACACTTGTTATAAATGT
* * * *
1641204 ATTGACACTTT-TTAGTGCACTTGGTTTATAAAATACACGCTGAACAAAAAATATCGACACTTAT
130 ATCGACACTTTGTT-GTGCACTTGGTTTTTAAAATACACGCTGGACAAAAAGTATCGACACTTAT
1641268 TGTATTT
194 TGTATTT
* * *
1641275 GTGTCGATACTTTATGTATATCTGTTTTCTCAAAAACTGGTATATTTAGACCGGTTACATTGTTA
1 GTGTCGATACTTTATGTATACCTGTTTTCTCATAAACCGGTATATTTAGACCGGTTACATTGTTA
* * **
1641340 TTTTACCTATTACATTATATCTATGTATTTCGATGTTTTT-AGTATCGACACTTGTTATAAATGT
66 ATTTACCTATTACATTATAACTATGGGTTTCGATGTTTTTGAG-ATCGACACTTGTTATAAATGT
1641404 ATCGACACTT
130 ATCGACACTT
1641414 GTTATAAATG
Statistics
Matches: 679, Mismatches: 55, Indels: 11
0.91 0.07 0.01
Matches are distributed among these distances:
199 3 0.00
200 647 0.95
201 29 0.04
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.42
Consensus pattern (200 bp):
GTGTCGATACTTTATGTATACCTGTTTTCTCATAAACCGGTATATTTAGACCGGTTACATTGTTA
ATTTACCTATTACATTATAACTATGGGTTTCGATGTTTTTGAGATCGACACTTGTTATAAATGTA
TCGACACTTTGTTGTGCACTTGGTTTTTAAAATACACGCTGGACAAAAAGTATCGACACTTATTG
TATTT
Found at i:1641405 original size:21 final size:21
Alignment explanation
Indices: 1641381--1641431 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
1641371 GATGTTTTTA
1641381 GTATCGACACTTGTTATAAAT
1 GTATCGACACTTGTTATAAAT
1641402 GTATCGACACTTGTTATAAAT
1 GTATCGACACTTGTTATAAAT
1641423 GTATCGACA
1 GTATCGACA
1641432 TTTTTTTCGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (21 bp):
GTATCGACACTTGTTATAAAT
Found at i:1641554 original size:24 final size:24
Alignment explanation
Indices: 1641524--1641575 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
1641514 TTATCACTAG
1641524 TGTTGATATTTGAAAAAGGTAAGT
1 TGTTGATATTTGAAAAAGGTAAGT
1641548 TGTTGATATTTGAAAAAGGTAAGT
1 TGTTGATATTTGAAAAAGGTAAGT
1641572 TGTT
1 TGTT
1641576 ACCTTAGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.25, T:0.40
Consensus pattern (24 bp):
TGTTGATATTTGAAAAAGGTAAGT
Found at i:1641585 original size:23 final size:24
Alignment explanation
Indices: 1641524--1641585 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
1641514 TTATCACTAG
* *
1641524 TGTTGATATTTGAAAAAGGTAAGT
1 TGTTGACATTAGAAAAAGGTAAGT
* *
1641548 TGTTGATATTTGAAAAAGGTAAGT
1 TGTTGACATTAGAAAAAGGTAAGT
*
1641572 TGTT-ACCTTAGAAA
1 TGTTGACATTAGAAA
1641586 TGGAATTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
23 7 0.20
24 28 0.80
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (24 bp):
TGTTGACATTAGAAAAAGGTAAGT
Found at i:1641707 original size:24 final size:24
Alignment explanation
Indices: 1641680--1641738 Score: 91
Period size: 24 Copynumber: 2.4 Consensus size: 24
1641670 AGTGGAGCTT
*
1641680 AAATTTACATTTAAATTCAAACTC
1 AAATTTAAATTTAAATTCAAACTC
1641704 AAATTTAAATTTAAATTCAAACTC
1 AAATTTAAATTTAAATTCAAACTC
*
1641728 TAATTATAAAT
1 AAATT-TAAAT
1641739 AAAATGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 27 0.84
25 5 0.16
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (24 bp):
AAATTTAAATTTAAATTCAAACTC
Found at i:1641711 original size:18 final size:18
Alignment explanation
Indices: 1641688--1641724 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1641678 TTAAATTTAC
1641688 ATTTAAATTCAAACTCAA
1 ATTTAAATTCAAACTCAA
* *
1641706 ATTTAAATTTAAATTCAA
1 ATTTAAATTCAAACTCAA
1641724 A
1 A
1641725 CTCTAATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTTAAATTCAAACTCAA
Found at i:1641713 original size:6 final size:6
Alignment explanation
Indices: 1641678--1641720 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
1641668 ATAGTGGAGC
* * * *
1641678 TTAAAT TTACAT TTAAAT TCAAAC TCAAAT TTAAAT TTAAAT T
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT T
1641721 CAAACTCTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (6 bp):
TTAAAT
Found at i:1642322 original size:17 final size:18
Alignment explanation
Indices: 1642300--1642333 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1642290 AAAATAAAAG
1642300 AATATA-ATTATAATAAA
1 AATATATATTATAATAAA
*
1642317 AATATATTTTATAATAA
1 AATATATATTATAATAA
1642334 GCACAAGGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AATATATATTATAATAAA
Found at i:1642323 original size:19 final size:18
Alignment explanation
Indices: 1642292--1642333 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
1642282 AAATTAATAA
1642292 AATAAAAGAATATAATTAT
1 AATAAAAGAATAT-ATTAT
*
1642311 AATAAAA-ATATATTTTAT
1 AATAAAAGA-ATATATTAT
1642329 AATAA
1 AATAA
1642334 GCACAAGGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
AATAAAAGAATATATTAT
Found at i:1642948 original size:56 final size:55
Alignment explanation
Indices: 1642886--1642990 Score: 133
Period size: 56 Copynumber: 1.9 Consensus size: 55
1642876 AAAATATATT
*
1642886 TTTAAAGTATATT-GTTTTATCTGA-TTATTTAAAATAATTTATAGTCAAAACAATTA
1 TTTAAAGTAT-TTAGTTTTATCTAAGTT-TTTAAAATAATTTATA-TCAAAACAATTA
* * *
1642942 TTTAAAGTATTTATTTTTATCTAAGTTTTTAAAATATTTTTTATCAAAA
1 TTTAAAGTATTTAGTTTTATCTAAGTTTTTAAAATAATTTATATCAAAA
1642991 TAAATAATTA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
55 8 0.19
56 33 0.77
57 2 0.05
ACGTcount: A:0.39, C:0.05, G:0.06, T:0.50
Consensus pattern (55 bp):
TTTAAAGTATTTAGTTTTATCTAAGTTTTTAAAATAATTTATATCAAAACAATTA
Found at i:1643006 original size:2 final size:2
Alignment explanation
Indices: 1642999--1643027 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1642989 AATAAATAAT
1642999 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1643028 TTAATTTAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1657061 original size:45 final size:45
Alignment explanation
Indices: 1656978--1657179 Score: 361
Period size: 45 Copynumber: 4.5 Consensus size: 45
1656968 GGTAAGTATA
*
1656978 AAAATAAGCTTACGAGCTTATGGAAT-AATGGCAAGTATGTTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATGTTGGT
*
1657022 AAAATAAGCTTACGAGCTTATGGAATAAATGATAAGTATGTTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATGTTGGT
1657067 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATGTTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATGTTGGT
*
1657112 AAAATAAGCTTATGAGCTTATGGAATAAATGGTAAGTATGTTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATGTTGGT
*
1657157 AAAATAAGCTTACAAGCTTATGG
1 AAAATAAGCTTACGAGCTTATGG
1657180 GATTAAATTG
Statistics
Matches: 151, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
44 26 0.17
45 125 0.83
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.31
Consensus pattern (45 bp):
AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATGTTGGT
Found at i:1658441 original size:9 final size:9
Alignment explanation
Indices: 1658429--1658462 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
1658419 TTTTATTAAT
1658429 AATAATAGC
1 AATAATAGC
**
1658438 AATAATAAT
1 AATAATAGC
1658447 AATAATAGC
1 AATAATAGC
1658456 AATAATA
1 AATAATA
1658463 ATAGTATAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.26
Consensus pattern (9 bp):
AATAATAGC
Found at i:1658448 original size:18 final size:18
Alignment explanation
Indices: 1658425--1658465 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
1658415 TTAATTTTAT
1658425 TAATAATAATAGCAATAA
1 TAATAATAATAGCAATAA
1658443 TAATAATAATAGCAATAA
1 TAATAATAATAGCAATAA
1658461 TAATA
1 TAATA
1658466 GTATAAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.29
Consensus pattern (18 bp):
TAATAATAATAGCAATAA
Found at i:1659664 original size:22 final size:22
Alignment explanation
Indices: 1659636--1659681 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
1659626 CAATCAGTTC
**
1659636 AACCGTAGTTAAATTGTGATTG
1 AACCGTAGTTAAATTACGATTG
1659658 AACCGTAGTTAAATTACGATTG
1 AACCGTAGTTAAATTACGATTG
1659680 AA
1 AA
1659682 TCGATTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.33
Consensus pattern (22 bp):
AACCGTAGTTAAATTACGATTG
Found at i:1661967 original size:17 final size:17
Alignment explanation
Indices: 1661945--1661980 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1661935 ACCGTTTGTC
1661945 ACATAATTATGACATTA
1 ACATAATTATGACATTA
1661962 ACATAATTATGACATTA
1 ACATAATTATGACATTA
1661979 AC
1 AC
1661981 GATTTATCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.14, G:0.06, T:0.33
Consensus pattern (17 bp):
ACATAATTATGACATTA
Found at i:1680714 original size:2 final size:2
Alignment explanation
Indices: 1680707--1680798 Score: 184
Period size: 2 Copynumber: 46.0 Consensus size: 2
1680697 ATCTAGTTTG
1680707 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
1680749 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
1680791 AT AT AT AT
1 AT AT AT AT
1680799 TAAGTTCATT
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 90 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1682053 original size:12 final size:12
Alignment explanation
Indices: 1682038--1682103 Score: 57
Period size: 12 Copynumber: 5.5 Consensus size: 12
1682028 AAACGAATCG
1682038 ATAAATAGACAT
1 ATAAATAGACAT
1682050 ATAAAT-GA-AT
1 ATAAATAGACAT
1682060 CGATAAATAGACAT
1 --ATAAATAGACAT
* * *
1682074 ATGAATGAGTC-G
1 ATAAAT-AGACAT
1682086 ATAAATAGACAT
1 ATAAATAGACAT
1682098 ATAAAT
1 ATAAAT
1682104 GAGTCGATAA
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
10 2 0.05
11 5 0.12
12 28 0.67
13 5 0.12
14 2 0.05
ACGTcount: A:0.53, C:0.08, G:0.14, T:0.26
Consensus pattern (12 bp):
ATAAATAGACAT
Done.