Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 5 of 356
Found at i:1588774 original size:24 final size:24
Alignment explanation
Indices: 1588672--1588775 Score: 102
Period size: 24 Copynumber: 4.3 Consensus size: 24
1588662 ACTTGAAGAT
*
1588672 GCTCCAAAAGCAGGAGTGCTCGAA
1 GCTCCAAAAGCAGGAGTGCTTGAA
* * *
1588696 CCCCCAAATGCAGGAGTGCTTGAA
1 GCTCCAAAAGCAGGAGTGCTTGAA
* * * *
1588720 CCCCCAAATGCAGGAGTGCTGGAA
1 GCTCCAAAAGCAGGAGTGCTTGAA
* *
1588744 G-TGCCAAAAGCAGGTGTGCTTGAT
1 GCT-CCAAAAGCAGGAGTGCTTGAA
1588768 GCTCCAAA
1 GCTCCAAA
1588776 TGTGCCACCT
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
24 66 0.99
25 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.28, T:0.16
Consensus pattern (24 bp):
GCTCCAAAAGCAGGAGTGCTTGAA
Found at i:1588775 original size:48 final size:48
Alignment explanation
Indices: 1588669--1588777 Score: 128
Period size: 48 Copynumber: 2.3 Consensus size: 48
1588659 TGGACTTGAA
* *
1588669 GATGCTCCAAAAGCAGGAGTGCTCGAACCCCCAAATGCAGGAGTGCTT
1 GATGCTCCAAATGCAGGAGTGCTCGAACCCCCAAAAGCAGGAGTGCTT
** * * *** *
1588717 GAACCCCCAAATGCAGGAGTGCTGGAAGTGCCAAAAGCAGGTGTGCTT
1 GATGCTCCAAATGCAGGAGTGCTCGAACCCCCAAAAGCAGGAGTGCTT
1588765 GATGCTCCAAATG
1 GATGCTCCAAATG
1588778 TGCCACCTGT
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.29, C:0.25, G:0.28, T:0.17
Consensus pattern (48 bp):
GATGCTCCAAATGCAGGAGTGCTCGAACCCCCAAAAGCAGGAGTGCTT
Found at i:1588884 original size:24 final size:24
Alignment explanation
Indices: 1588857--1589018 Score: 189
Period size: 24 Copynumber: 6.8 Consensus size: 24
1588847 TTCCAGTTGA
* *
1588857 ACCAAAGGCAGGGGTGCTTGTGGC
1 ACCAAAGGCAGGGGTACTCGTGGC
* * * *
1588881 ACCAAAGGCTGGAGTACTCATGGA
1 ACCAAAGGCAGGGGTACTCGTGGC
* *
1588905 ACCAAAGGCAGGGGTACTTGTGCC
1 ACCAAAGGCAGGGGTACTCGTGGC
* *
1588929 ACCAAAAGCAGGGGCACTCGTGGC
1 ACCAAAGGCAGGGGTACTCGTGGC
*
1588953 ACCAAAGGCAGGGGTACTTGTGGC
1 ACCAAAGGCAGGGGTACTCGTGGC
* *
1588977 ACCAAAAGCAGGGGTGCTCGTGGC
1 ACCAAAGGCAGGGGTACTCGTGGC
* *
1589001 ACCGAAGGCAGGAGTACT
1 ACCAAAGGCAGGGGTACT
1589019 GGAACCAAAA
Statistics
Matches: 112, Mismatches: 26, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 112 1.00
ACGTcount: A:0.27, C:0.23, G:0.35, T:0.14
Consensus pattern (24 bp):
ACCAAAGGCAGGGGTACTCGTGGC
Found at i:1588892 original size:48 final size:48
Alignment explanation
Indices: 1588834--1588985 Score: 159
Period size: 48 Copynumber: 3.2 Consensus size: 48
1588824 TCCAGTGCTC
* * *
1588834 CCAAATGCTGGACTTCCAGTTGAACCAAAGGCAGGGGTGCTTGTGGCA
1 CCAAAAGCTGGACTTCCAGTGGAACCAAAGGCAGGGGTACTTGTGGCA
* * * *
1588882 CCAAAGGCTGGAGTACTCA-TGGAACCAAAGGCAGGGGTACTTGTGCCA
1 CCAAAAGCTGGACTTC-CAGTGGAACCAAAGGCAGGGGTACTTGTGGCA
* *
1588930 CCAAAAGCAGGGGCAC-T-C-GTGGCACCAAAGGCAGGGGTACTTGTGGCA
1 CCAAAAGC--TGG-ACTTCCAGTGGAACCAAAGGCAGGGGTACTTGTGGCA
1588978 CCAAAAGC
1 CCAAAAGC
1588986 AGGGGTGCTC
Statistics
Matches: 87, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
48 82 0.94
49 2 0.02
50 2 0.02
51 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.32, T:0.16
Consensus pattern (48 bp):
CCAAAAGCTGGACTTCCAGTGGAACCAAAGGCAGGGGTACTTGTGGCA
Found at i:1588986 original size:48 final size:48
Alignment explanation
Indices: 1588857--1589018 Score: 225
Period size: 48 Copynumber: 3.4 Consensus size: 48
1588847 TTCCAGTTGA
* * * * * *
1588857 ACCAAAGGCAGGGGTGCTTGTGGCACCAAAGGCTGGAGTACTCATGGA
1 ACCAAAGGCAGGGGTACTTGTGGCACCAAAAGCAGGGGTACTCGTGGC
* *
1588905 ACCAAAGGCAGGGGTACTTGTGCCACCAAAAGCAGGGGCACTCGTGGC
1 ACCAAAGGCAGGGGTACTTGTGGCACCAAAAGCAGGGGTACTCGTGGC
*
1588953 ACCAAAGGCAGGGGTACTTGTGGCACCAAAAGCAGGGGTGCTCGTGGC
1 ACCAAAGGCAGGGGTACTTGTGGCACCAAAAGCAGGGGTACTCGTGGC
* *
1589001 ACCGAAGGCAGGAGTACT
1 ACCAAAGGCAGGGGTACT
1589019 GGAACCAAAA
Statistics
Matches: 101, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 101 1.00
ACGTcount: A:0.27, C:0.23, G:0.35, T:0.14
Consensus pattern (48 bp):
ACCAAAGGCAGGGGTACTTGTGGCACCAAAAGCAGGGGTACTCGTGGC
Found at i:1592153 original size:25 final size:25
Alignment explanation
Indices: 1592124--1592173 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1592114 CAAAATGAAC
1592124 TTAGTTGATATAATAATGGTACTTT
1 TTAGTTGATATAATAATGGTACTTT
1592149 TTAGTTGATATAATAATGGTACTTT
1 TTAGTTGATATAATAATGGTACTTT
1592174 ATTACCTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.04, G:0.16, T:0.48
Consensus pattern (25 bp):
TTAGTTGATATAATAATGGTACTTT
Found at i:1598663 original size:22 final size:21
Alignment explanation
Indices: 1598621--1598668 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
1598611 TAATTAAATT
1598621 TAAA-AAATATAAAAGATTTA
1 TAAATAAATATAAAAGATTTA
1598641 TAAATAAATATTAATAA-ATTTA
1 TAAATAAATA-TAA-AAGATTTA
1598663 TAAATA
1 TAAATA
1598669 TAATTATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.16
21 5 0.20
22 14 0.56
23 2 0.08
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (21 bp):
TAAATAAATATAAAAGATTTA
Found at i:1627563 original size:19 final size:19
Alignment explanation
Indices: 1627541--1627611 Score: 63
Period size: 18 Copynumber: 3.7 Consensus size: 19
1627531 AAATTACAAA
*
1627541 AAAAATAAAAATAATTTTT
1 AAAAATTAAAATAATTTTT
* * *
1627560 AAAATTTAACAT-ATTTAT
1 AAAAATTAAAATAATTTTT
* *
1627578 AAAAATTTATATATATTTTT
1 AAAAATTAAAATA-ATTTTT
1627598 AAAAATTATAAATA
1 AAAAATTA-AAATA
1627612 TTCTAAAAAT
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
18 14 0.36
19 9 0.23
20 12 0.31
21 4 0.10
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAAATTAAAATAATTTTT
Found at i:1627595 original size:20 final size:20
Alignment explanation
Indices: 1627560--1627622 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 20
1627550 AATAATTTTT
*
1627560 AAAATTTA-ACATATTTATA
1 AAAATTTATAAATATTTATA
* *
1627579 AAAATTTATATATATTTTTA
1 AAAATTTATAAATATTTATA
*
1627599 AAAA-TTATAAATA-TTCTA
1 AAAATTTATAAATATTTATA
1627617 AAAATT
1 AAAATT
1627623 CTAAAAAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
18 8 0.21
19 17 0.45
20 13 0.34
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (20 bp):
AAAATTTATAAATATTTATA
Found at i:1627612 original size:19 final size:19
Alignment explanation
Indices: 1627549--1627627 Score: 74
Period size: 18 Copynumber: 4.2 Consensus size: 19
1627539 AAAAAAATAA
1627549 AAATAATTTTT-AAAATT-T
1 AAAT-ATTTTTAAAAATTAT
*
1627567 AACATATTTATAAAAATTTAT
1 AA-ATATTTTTAAAAA-TTAT
*
1627588 ATATATTTTTAAAAATTAT
1 AAATATTTTTAAAAATTAT
* *
1627607 AAATA-TTCTAAAAATTCT
1 AAATATTTTTAAAAATTAT
1627625 AAA
1 AAA
1627628 AAATACATAA
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
18 21 0.41
19 14 0.27
20 14 0.27
21 2 0.04
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (19 bp):
AAATATTTTTAAAAATTAT
Found at i:1632986 original size:3 final size:3
Alignment explanation
Indices: 1632980--1633022 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
1632970 AATGATGATT
* *
1632980 ATC ATC ATC ATC ATC ATC ATC ATC -TCC ATC ACC ATC ACC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC AT-C ATC ATC ATC ATC ATC A
1633023 CCTTCTCTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
2 1 0.03
3 32 0.94
4 1 0.03
ACGTcount: A:0.33, C:0.40, G:0.00, T:0.28
Consensus pattern (3 bp):
ATC
Found at i:1637423 original size:16 final size:17
Alignment explanation
Indices: 1637390--1637425 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1637380 AAAAGGATTG
*
1637390 ATTATTCAAATTTTAGA
1 ATTATTCAAATGTTAGA
1637407 ATTATTC-AATGTTAGA
1 ATTATTCAAATGTTAGA
1637423 ATT
1 ATT
1637426 TGGACCGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.47
Consensus pattern (17 bp):
ATTATTCAAATGTTAGA
Found at i:1640098 original size:12 final size:12
Alignment explanation
Indices: 1640081--1640148 Score: 54
Period size: 12 Copynumber: 5.8 Consensus size: 12
1640071 TTAAATTTAT
1640081 TATTTATTATTA
1 TATTTATTATTA
*
1640093 TATTTAATATATA
1 TATTTATTAT-TA
* *
1640106 AATTTATTA-AA
1 TATTTATTATTA
1640117 TATTT-TTATTGA
1 TATTTATTATT-A
1640129 TATTTA-TATGTA
1 TATTTATTAT-TA
1640141 -ATTTATTA
1 TATTTATTA
1640149 GTTTGTATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
10 3 0.07
11 10 0.23
12 21 0.48
13 10 0.23
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (12 bp):
TATTTATTATTA
Found at i:1642792 original size:36 final size:36
Alignment explanation
Indices: 1642752--1642828 Score: 154
Period size: 36 Copynumber: 2.1 Consensus size: 36
1642742 AAATAGAGAA
1642752 ATATCTTCGTTTTGATTTGTCATCCTTGCTTTGTTC
1 ATATCTTCGTTTTGATTTGTCATCCTTGCTTTGTTC
1642788 ATATCTTCGTTTTGATTTGTCATCCTTGCTTTGTTC
1 ATATCTTCGTTTTGATTTGTCATCCTTGCTTTGTTC
1642824 ATATC
1 ATATC
1642829 GGCCGGCCGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.13, C:0.19, G:0.13, T:0.55
Consensus pattern (36 bp):
ATATCTTCGTTTTGATTTGTCATCCTTGCTTTGTTC
Found at i:1643086 original size:27 final size:27
Alignment explanation
Indices: 1643054--1643123 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
1643044 GTCTTTGCAA
1643054 TTTGGTCACCAAACTTGATGCTTTCAT
1 TTTGGTCACCAAACTTGATGCTTTCAT
*
1643081 TTTGGTCAACAAACTTGATGCTTTCAT
1 TTTGGTCACCAAACTTGATGCTTTCAT
* *
1643108 TTTAGTCACCCAACTT
1 TTTGGTCACCAAACTT
1643124 TTAGGTCGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.24, C:0.23, G:0.13, T:0.40
Consensus pattern (27 bp):
TTTGGTCACCAAACTTGATGCTTTCAT
Found at i:1647201 original size:24 final size:24
Alignment explanation
Indices: 1647168--1647228 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
1647158 ATTTTCTTGA
* * * *
1647168 AAAATATTCAATCATTATTACTTC
1 AAAATTTTCAATCATAATCACATC
*
1647192 AAAATTTTCAATTATAATCACATC
1 AAAATTTTCAATCATAATCACATC
*
1647216 CAAATTTTCAATC
1 AAAATTTTCAATC
1647229 GCAATCATGG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.43, C:0.18, G:0.00, T:0.39
Consensus pattern (24 bp):
AAAATTTTCAATCATAATCACATC
Found at i:1652171 original size:16 final size:16
Alignment explanation
Indices: 1652143--1652208 Score: 56
Period size: 16 Copynumber: 4.5 Consensus size: 16
1652133 GGGATCAGTT
1652143 ATATT-AATGTTATTTA
1 ATATTAAAT-TTATTTA
*
1652159 ATTTTAAATTTATTTA
1 ATATTAAATTTATTTA
1652175 ATATTAAA---A--TA
1 ATATTAAATTTATTTA
*
1652186 ATATTAAA-ATATTTA
1 ATATTAAATTTATTTA
1652201 ATATTAAA
1 ATATTAAA
1652209 ATAATACAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
11 10 0.23
13 2 0.05
15 10 0.23
16 18 0.42
17 3 0.07
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (16 bp):
ATATTAAATTTATTTA
Found at i:1662358 original size:9 final size:10
Alignment explanation
Indices: 1662341--1662365 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1662331 GAGTGGAACG
1662341 AATTTTTTTT
1 AATTTTTTTT
1662351 AATTTTTTTT
1 AATTTTTTTT
1662361 AATTT
1 AATTT
1662366 CGGCAGCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (10 bp):
AATTTTTTTT
Found at i:1664178 original size:7 final size:7
Alignment explanation
Indices: 1664168--1664263 Score: 69
Period size: 7 Copynumber: 14.3 Consensus size: 7
1664158 TACTTATGTT
1664168 TTATATA
1 TTATATA
1664175 -T-TATA
1 TTATATA
1664180 TTATATA
1 TTATATA
*
1664187 TAATATA
1 TTATATA
*
1664194 ATA-ATA
1 TTATATA
*
1664200 TGATATA
1 TTATATA
1664207 TTATATA
1 TTATATA
1664214 TTA-ATA
1 TTATATA
*
1664220 CTTAAATA
1 -TTATATA
1664228 TTA-A-A
1 TTATATA
1664233 TTAATATA
1 TT-ATATA
*
1664241 ATATATA
1 TTATATA
*
1664248 ATATATA
1 TTATATA
*
1664255 ATATATA
1 TTATATA
1664262 TT
1 TT
1664264 TTTATATTAA
Statistics
Matches: 73, Mismatches: 8, Indels: 16
0.75 0.08 0.16
Matches are distributed among these distances:
5 7 0.10
6 11 0.15
7 50 0.68
8 5 0.07
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (7 bp):
TTATATA
Found at i:1664263 original size:34 final size:34
Alignment explanation
Indices: 1664169--1664263 Score: 84
Period size: 39 Copynumber: 2.6 Consensus size: 34
1664159 ACTTATGTTT
* * * *
1664169 TATATATTATATTATATATAATATAATAATATGA
1 TATATAATATATAATATATATTATAATAATATAA
*
1664203 TATATTATATATTAATACTTAAATATTA-AATTAATATAA
1 TATATAATATA-TAATA--T--ATATTATAA-TAATATAA
1664242 TATATAATATATAATATATATT
1 TATATAATATATAATATATATT
1664264 TTTATATTAA
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
34 14 0.29
35 4 0.08
36 1 0.02
37 1 0.02
38 7 0.14
39 22 0.45
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (34 bp):
TATATAATATATAATATATATTATAATAATATAA
Found at i:1667707 original size:10 final size:10
Alignment explanation
Indices: 1667667--1667708 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
1667657 TAAATATAAT
1667667 TAATTATTAA
1 TAATTATTAA
*
1667677 TTATTA-TAA
1 TAATTATTAA
*
1667686 TAATTATAAA
1 TAATTATTAA
*
1667696 TAAATATTAA
1 TAATTATTAA
1667706 TAA
1 TAA
1667709 CTCTCGAGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
9 8 0.31
10 18 0.69
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (10 bp):
TAATTATTAA
Found at i:1668587 original size:16 final size:16
Alignment explanation
Indices: 1668566--1668598 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1668556 ATATATTTTA
1668566 TATATAATTTA-AATTT
1 TATAT-ATTTATAATTT
1668582 TATATATTTATAATTT
1 TATATATTTATAATTT
1668598 T
1 T
1668599 TAAAAGATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TATATATTTATAATTT
Found at i:1669418 original size:28 final size:28
Alignment explanation
Indices: 1669387--1669442 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
1669377 AAAATTACAC
*
1669387 TTTAATCTAAAAAATAATATTAAT-TTAA
1 TTTAATCTAAAAAA-AATATAAATATTAA
* *
1669415 TTTAATTTTAAAAAAATATAAATATTAA
1 TTTAATCTAAAAAAAATATAAATATTAA
1669443 AATAGTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (28 bp):
TTTAATCTAAAAAAAATATAAATATTAA
Found at i:1683299 original size:20 final size:20
Alignment explanation
Indices: 1683267--1683306 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
1683257 ATTTTGAATG
1683267 GTTTAACAG-AAAAATAAAA
1 GTTTAACAGAAAAAATAAAA
*
1683286 GTTTAAACATAAAAAATAAAA
1 GTTT-AACAGAAAAAATAAAA
1683307 AATAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 4 0.22
21 10 0.56
ACGTcount: A:0.65, C:0.05, G:0.07, T:0.23
Consensus pattern (20 bp):
GTTTAACAGAAAAAATAAAA
Found at i:1684372 original size:18 final size:18
Alignment explanation
Indices: 1684321--1684372 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
1684311 GTATCAAAAT
1684321 AAATATCGAAACTAAATTA
1 AAATATC-AAACTAAATTA
* * *
1684340 AAATATTAAATTAAATATC
1 AAATATCAAACTAAAT-TA
1684359 AAA-ATCAAACTAAA
1 AAATATCAAACTAAA
1684373 ATATTTAACG
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
18 17 0.63
19 10 0.37
ACGTcount: A:0.62, C:0.10, G:0.02, T:0.27
Consensus pattern (18 bp):
AAATATCAAACTAAATTA
Found at i:1686514 original size:3 final size:3
Alignment explanation
Indices: 1686506--1686533 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1686496 GCGGAAGCTA
1686506 GCG GCG GCG GCG GCG GCG GCG GCG GCG G
1 GCG GCG GCG GCG GCG GCG GCG GCG GCG G
1686534 TGGCTTCTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.68, T:0.00
Consensus pattern (3 bp):
GCG
Found at i:1688976 original size:150 final size:150
Alignment explanation
Indices: 1688705--1689157 Score: 843
Period size: 150 Copynumber: 3.0 Consensus size: 150
1688695 TTAAACGTAT
* *
1688705 TGAGAATAGCTCTACGGTTAAGGAAACTGCTGGAAACGACTGCAATGAAGACAGTGAGGATTTAA
1 TGAGAATAGCTCTAAGGTTAAGGAAACTGCTGGAAACAACTGCAATGAAGACAGTGAGGATTTAA
* *
1688770 GTCAAGTTGTTGATTCTTCAGGCTTAGAGGATGTGGTTAGTGGTCGAACGTCAACTGAGGGAGAA
66 GTCAAGTTGTTGATTCTTCAGGCTTAGAGGATGTGGTTAGTGGTAGAAGGTCAACTGAGGGAGAA
1688835 AGTCCCATGGTTGATGATTC
131 AGTCCCATGGTTGATGATTC
1688855 TGAGAATAGCTCTAAGGTTAAGGAAACTGCTGGAAACAACTGCAATGAAGACAGTGAGGATTTAA
1 TGAGAATAGCTCTAAGGTTAAGGAAACTGCTGGAAACAACTGCAATGAAGACAGTGAGGATTTAA
*
1688920 GTCAAGTTGTTGATTCTTCAGGCTTAGAGGATGTGGTTAGTGGTAGAAGGTCAACTGTGGGAGAA
66 GTCAAGTTGTTGATTCTTCAGGCTTAGAGGATGTGGTTAGTGGTAGAAGGTCAACTGAGGGAGAA
1688985 AGTCCCATGGTTGATGATTC
131 AGTCCCATGGTTGATGATTC
1689005 TGAGAATAGCTCTAAGGTTAAGGAAACTGCTGGAAACAACTGCAATGAAGACAGTGAGGATTTAA
1 TGAGAATAGCTCTAAGGTTAAGGAAACTGCTGGAAACAACTGCAATGAAGACAGTGAGGATTTAA
*
1689070 GTCAAGTTGTTGATTCTTCAGGCTTAGAGGATGTGGTTAGTGATAGAAGGTCAACTGAGGGAGAA
66 GTCAAGTTGTTGATTCTTCAGGCTTAGAGGATGTGGTTAGTGGTAGAAGGTCAACTGAGGGAGAA
*
1689135 AGTCCCATGGTTGATTATTC
131 AGTCCCATGGTTGATGATTC
1689155 TGA
1 TGA
1689158 TCGCCCTCCG
Statistics
Matches: 295, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
150 295 1.00
ACGTcount: A:0.31, C:0.13, G:0.30, T:0.27
Consensus pattern (150 bp):
TGAGAATAGCTCTAAGGTTAAGGAAACTGCTGGAAACAACTGCAATGAAGACAGTGAGGATTTAA
GTCAAGTTGTTGATTCTTCAGGCTTAGAGGATGTGGTTAGTGGTAGAAGGTCAACTGAGGGAGAA
AGTCCCATGGTTGATGATTC
Found at i:1691339 original size:89 final size:89
Alignment explanation
Indices: 1691195--1691358 Score: 285
Period size: 89 Copynumber: 1.8 Consensus size: 89
1691185 AATGTCTTAT
*
1691195 TTACCTGTTTTTCAGTTTTTGTTCCTCGCTTTGCCATGCATTGATGGATAATTAGATATTAAGGT
1 TTACCTGTTTTTCAGTTTTTGTTCCTCGCTTTGCCATGCATGGATGGATAATTAGATATTAAGGT
1691260 GGGATTTAGAGCGTATGTGTCTTGG
66 -GGATTTAGAGCGTATGTGTCTTGG
* *
1691285 TTACCTGTTTTTCGGTTTTT-TTCCTCGCTTTGCCATGCATGGATGGATAATTAGATATTAATGT
1 TTACCTGTTTTTCAGTTTTTGTTCCTCGCTTTGCCATGCATGGATGGATAATTAGATATTAAGGT
1691349 GGATTTAGAG
66 GGATTTAGAG
1691359 TGTGTTTAGT
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
88 10 0.14
89 42 0.59
90 19 0.27
ACGTcount: A:0.20, C:0.13, G:0.23, T:0.44
Consensus pattern (89 bp):
TTACCTGTTTTTCAGTTTTTGTTCCTCGCTTTGCCATGCATGGATGGATAATTAGATATTAAGGT
GGATTTAGAGCGTATGTGTCTTGG
Found at i:1691499 original size:22 final size:22
Alignment explanation
Indices: 1691474--1691516 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1691464 TAAAATAAAC
1691474 ACTA-AAAAAAAAGAAGCAAATT
1 ACTATAAAAAAAAGAA-CAAATT
* *
1691496 ACTATAAGAAAAGGAACAAAT
1 ACTATAAAAAAAAGAACAAAT
1691517 ATATGATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.65, C:0.09, G:0.12, T:0.14
Consensus pattern (22 bp):
ACTATAAAAAAAAGAACAAATT
Found at i:1695400 original size:18 final size:18
Alignment explanation
Indices: 1695379--1695413 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1695369 TCTTTCTTTC
*
1695379 TTTTTCATTTTTTTTTAT
1 TTTTTCATTTTATTTTAT
*
1695397 TTTTTTATTTTATTTTA
1 TTTTTCATTTTATTTTA
1695414 AATTTCCATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.83
Consensus pattern (18 bp):
TTTTTCATTTTATTTTAT
Found at i:1701506 original size:23 final size:22
Alignment explanation
Indices: 1701479--1701524 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
1701469 CTTAATATTC
1701479 AATAAA-ATAAATTTTGAGTTAAT
1 AATAAATATAAA-TTTGA-TTAAT
1701502 AATAAATTATAAATTTGATTAAT
1 AATAAA-TATAAATTTGATTAAT
1701525 CCGATTCGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 11 0.52
24 5 0.24
25 5 0.24
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (22 bp):
AATAAATATAAATTTGATTAAT
Found at i:1708032 original size:16 final size:16
Alignment explanation
Indices: 1708011--1708041 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1708001 ATAAAAATAT
*
1708011 AATTTTATTATTTTAA
1 AATTTTATCATTTTAA
1708027 AATTTTATCATTTTA
1 AATTTTATCATTTTA
1708042 TTAATTTATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
AATTTTATCATTTTAA
Found at i:1708040 original size:24 final size:24
Alignment explanation
Indices: 1708008--1708064 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
1707998 ATAATAAAAA
*
1708008 TATAATTTTATTATTTTAAAATTT
1 TATAATTTTATTAATTTAAAATTT
* * *
1708032 TATCATTTTATTAATTTATATTTT
1 TATAATTTTATTAATTTAAAATTT
1708056 TATAATTTT
1 TATAATTTT
1708065 TAAAGGACAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (24 bp):
TATAATTTTATTAATTTAAAATTT
Found at i:1708087 original size:30 final size:32
Alignment explanation
Indices: 1708051--1708116 Score: 100
Period size: 30 Copynumber: 2.1 Consensus size: 32
1708041 ATTAATTTAT
1708051 ATTTTTATAATTTTTAAAGGAC-AAAAT-TAA
1 ATTTTTATAATTTTTAAAGGACTAAAATATAA
**
1708081 ATTTTTATTGTTTTTAAAGGACTAAAATATAA
1 ATTTTTATAATTTTTAAAGGACTAAAATATAA
1708113 ATTT
1 ATTT
1708117 ATTAATATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 20 0.62
31 5 0.16
32 7 0.22
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (32 bp):
ATTTTTATAATTTTTAAAGGACTAAAATATAA
Found at i:1709201 original size:10 final size:11
Alignment explanation
Indices: 1709181--1709223 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
1709171 GTGATTTGTG
1709181 AAAATTAAATA
1 AAAATTAAATA
1709192 AAAATTAATATA
1 AAAATTAA-ATA
*
1709204 TAAAATTATA-A
1 -AAAATTAAATA
1709215 AAAATTAAA
1 AAAATTAAA
1709224 ATTTATGTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
10 8 0.29
11 9 0.32
12 4 0.14
13 7 0.25
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
AAAATTAAATA
Found at i:1712480 original size:21 final size:21
Alignment explanation
Indices: 1712454--1712494 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1712444 GCTAAGAATC
1712454 GGGATATTTTGAACCTATATT
1 GGGATATTTTGAACCTATATT
1712475 GGGATATTTTGAACCTATAT
1 GGGATATTTTGAACCTATAT
1712495 AACGAAGGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.41
Consensus pattern (21 bp):
GGGATATTTTGAACCTATATT
Found at i:1713649 original size:11 final size:11
Alignment explanation
Indices: 1713635--1713659 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1713625 GCAGATGTTA
1713635 TGCGCTTTAAC
1 TGCGCTTTAAC
1713646 TGCGCTTTAAC
1 TGCGCTTTAAC
1713657 TGC
1 TGC
1713660 TAAGCCAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.28, G:0.20, T:0.36
Consensus pattern (11 bp):
TGCGCTTTAAC
Found at i:1719249 original size:23 final size:22
Alignment explanation
Indices: 1719189--1719253 Score: 71
Period size: 23 Copynumber: 3.0 Consensus size: 22
1719179 CCTGATCAGT
*
1719189 ATACGACAGATAAGTGCCTG-A
1 ATACGACACATAAGTGCCTGAA
* *
1719210 A-ACGACACACGAGGTGCCTGAA
1 ATACGACACA-TAAGTGCCTGAA
1719232 ATACGACACATAAAGTGCCTGA
1 ATACGACACAT-AAGTGCCTGA
1719254 TTAGTATAGC
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
20 7 0.20
21 9 0.26
22 2 0.06
23 17 0.49
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.15
Consensus pattern (22 bp):
ATACGACACATAAGTGCCTGAA
Found at i:1725425 original size:17 final size:17
Alignment explanation
Indices: 1725403--1725436 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1725393 ATCCACTAAT
*
1725403 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
1725420 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
1725437 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:1730062 original size:17 final size:17
Alignment explanation
Indices: 1730040--1730073 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1730030 ATCCACTAAT
*
1730040 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
1730057 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
1730074 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:1732867 original size:15 final size:16
Alignment explanation
Indices: 1732831--1732864 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1732821 ATAAATTTAG
1732831 TTTT-TATTATTATTT
1 TTTTGTATTATTATTT
*
1732846 TTTTGTATTTTTATTT
1 TTTTGTATTATTATTT
1732862 TTT
1 TTT
1732865 GTAACTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (16 bp):
TTTTGTATTATTATTT
Found at i:1733014 original size:26 final size:27
Alignment explanation
Indices: 1732963--1733024 Score: 67
Period size: 26 Copynumber: 2.3 Consensus size: 27
1732953 ATTTCATATT
*
1732963 AATT-TTTCAAATTGTTTATATATTTTG
1 AATTATTT-AAATTGTTTATATATTTTA
*
1732990 AA-TATTTAAATTTTTTATA-ATTTTTA
1 AATTATTTAAATTGTTTATATA-TTTTA
1733016 AATTATTTA
1 AATTATTTA
1733025 TTGATATGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
25 1 0.03
26 18 0.60
27 11 0.37
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (27 bp):
AATTATTTAAATTGTTTATATATTTTA
Found at i:1733557 original size:22 final size:21
Alignment explanation
Indices: 1733515--1733558 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
1733505 ATTAAAAATT
* *
1733515 ATATTTAAATTTATTTATAAA
1 ATATATAAATTTAATTATAAA
1733536 ATATATAAATATTAATTATAAA
1 ATATATAAAT-TTAATTATAAA
1733558 A
1 A
1733559 CTAATTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
ATATATAAATTTAATTATAAA
Found at i:1733991 original size:22 final size:20
Alignment explanation
Indices: 1733957--1734018 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 20
1733947 AATTATACTA
*
1733957 AATATATCAAAATGAACATAT
1 AATATATCAAAAT-AAAATAT
1733978 ATATATAT-ATAAATAAAATAT
1 A-ATATATCA-AAATAAAATAT
* *
1733999 AATATCTAAAATATAAAATA
1 AATATATCAAA-ATAAAATA
1734019 AGAGTACGTG
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
20 7 0.20
21 18 0.51
22 10 0.29
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (20 bp):
AATATATCAAAATAAAATAT
Found at i:1734495 original size:66 final size:70
Alignment explanation
Indices: 1734387--1734517 Score: 216
Period size: 66 Copynumber: 1.9 Consensus size: 70
1734377 TTATTGTATA
1734387 TTTTTTTTCAATTATAAAAAGAAGTTAAAAAAGCCATAATTTGAGTAAATTGCATAGTGACTCCA
1 TTTTTTTTCAATTATAAAAAGAAGTTAAAAAAGCCATAATTTGAGTAAATTGCATAGTGACTCCA
1734452 TTGTT
66 TTGTT
* *
1734457 TTTTTTTTCAA-T-TAAAAA-AAGTT-ATAAAGCCATAATTTGAGTAAATTGCATAGTGATTCCA
1 TTTTTTTTCAATTATAAAAAGAAGTTAAAAAAGCCATAATTTGAGTAAATTGCATAGTGACTCCA
1734518 ATCTATCTTA
Statistics
Matches: 59, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
66 36 0.61
67 5 0.08
68 6 0.10
69 1 0.02
70 11 0.19
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (70 bp):
TTTTTTTTCAATTATAAAAAGAAGTTAAAAAAGCCATAATTTGAGTAAATTGCATAGTGACTCCA
TTGTT
Found at i:1736040 original size:11 final size:11
Alignment explanation
Indices: 1736020--1736049 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1736010 TCTAGTTTTG
*
1736020 TTCTTGATTTA
1 TTCTTAATTTA
1736031 TTCTTAATTTA
1 TTCTTAATTTA
1736042 TTCTTAAT
1 TTCTTAAT
1736050 GATTTGACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.23, C:0.10, G:0.03, T:0.63
Consensus pattern (11 bp):
TTCTTAATTTA
Found at i:1736772 original size:29 final size:30
Alignment explanation
Indices: 1736712--1736778 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
1736702 AAAGTTAGAC
*
1736712 CTAAATTTTAAAATCTACAAAGTAAAGTGA
1 CTAAATTTTAAAATATACAAAGTAAAGTGA
1736742 CTAAATTCTTAAAA-ATA-AAAGTACAAG-GA
1 CTAAATT-TTAAAATATACAAAGTA-AAGTGA
1736771 CTAAATTT
1 CTAAATTT
1736779 CAAATTTATC
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
28 1 0.03
29 15 0.44
30 12 0.35
31 6 0.18
ACGTcount: A:0.51, C:0.10, G:0.09, T:0.30
Consensus pattern (30 bp):
CTAAATTTTAAAATATACAAAGTAAAGTGA
Found at i:1742935 original size:33 final size:33
Alignment explanation
Indices: 1742898--1742963 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
1742888 AGCAGCCATT
1742898 GGAGGTCTCTCTGATAGTAGTGAAAGTAGGTGA
1 GGAGGTCTCTCTGATAGTAGTGAAAGTAGGTGA
1742931 GGAGGTCTCTCTGATAGTAGTGAAAGTAGGTGA
1 GGAGGTCTCTCTGATAGTAGTGAAAGTAGGTGA
1742964 TAGATGACTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.27, C:0.09, G:0.36, T:0.27
Consensus pattern (33 bp):
GGAGGTCTCTCTGATAGTAGTGAAAGTAGGTGA
Found at i:1743549 original size:30 final size:31
Alignment explanation
Indices: 1743515--1743577 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
1743505 ACTTATTTTA
1743515 TTGTT-AATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAAATTTTGTTATTATTTTAAAGGCAT
* * *
1743545 TTGTTAAATTTTTTTATTATTTTAGAGGTAT
1 TTGTTAAATTTTGTTATTATTTTAAAGGCAT
1743576 TT
1 TT
1743578 ACTTGTTAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 5 0.17
31 24 0.83
ACGTcount: A:0.25, C:0.02, G:0.13, T:0.60
Consensus pattern (31 bp):
TTGTTAAATTTTGTTATTATTTTAAAGGCAT
Found at i:1744095 original size:29 final size:30
Alignment explanation
Indices: 1744052--1744115 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 30
1744042 TAACTTAACA
1744052 AACAAATGCCGTTAAAATAA-AAAAAAATT
1 AACAAATGCCGTTAAAATAATAAAAAAATT
* * *
1744081 AACAAATGCCTTTAAAATAATAACAAACTT
1 AACAAATGCCGTTAAAATAATAAAAAAATT
1744111 AACAA
1 AACAA
1744116 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
29 19 0.61
30 12 0.39
ACGTcount: A:0.59, C:0.14, G:0.05, T:0.22
Consensus pattern (30 bp):
AACAAATGCCGTTAAAATAATAAAAAAATT
Found at i:1750226 original size:24 final size:21
Alignment explanation
Indices: 1750194--1750243 Score: 57
Period size: 24 Copynumber: 2.3 Consensus size: 21
1750184 GTAATTGTCA
*
1750194 AATTATTTAATCAAAAGATAAATT
1 AATTTTTTAAT-AAAA-A-AAATT
1750218 AATTTTTTAATAAAAAAAATT
1 AATTTTTTAATAAAAAAAATT
1750239 -ATTTT
1 AATTTT
1750244 ACTCTTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 5 0.20
21 5 0.20
22 1 0.04
23 4 0.16
24 10 0.40
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (21 bp):
AATTTTTTAATAAAAAAAATT
Found at i:1757091 original size:17 final size:18
Alignment explanation
Indices: 1757060--1757094 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1757050 ATTTATATTT
1757060 AAAAAAATACAAAAAATA
1 AAAAAAATACAAAAAATA
*
1757078 AAAAAAAT-CTAAAAATA
1 AAAAAAATACAAAAAATA
1757095 TATACAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.80, C:0.06, G:0.00, T:0.14
Consensus pattern (18 bp):
AAAAAAATACAAAAAATA
Found at i:1767965 original size:43 final size:43
Alignment explanation
Indices: 1767912--1767998 Score: 129
Period size: 43 Copynumber: 2.0 Consensus size: 43
1767902 TAAAATGCCT
* * * * *
1767912 AAAATTATTGATAGGTTTTCTCAAACCCTTAAATAAGAGGATA
1 AAAACTATTGATAAGTTCTCTCAAACCCCTAAATAAAAGGATA
1767955 AAAACTATTGATAAGTTCTCTCAAACCCCTAAATAAAAGGATA
1 AAAACTATTGATAAGTTCTCTCAAACCCCTAAATAAAAGGATA
1767998 A
1 A
1767999 TGCACTTCAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.29
Consensus pattern (43 bp):
AAAACTATTGATAAGTTCTCTCAAACCCCTAAATAAAAGGATA
Found at i:1768662 original size:29 final size:29
Alignment explanation
Indices: 1768629--1768688 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
1768619 TAGTTTTGTC
1768629 ATTATATTTTTAGAGATTACGAATTCGAA
1 ATTATATTTTTAGAGATTACGAATTCGAA
*
1768658 ATTATATTTTTAGAGATTACGAATTTGAA
1 ATTATATTTTTAGAGATTACGAATTCGAA
1768687 AT
1 AT
1768689 AAATTTAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.38, C:0.05, G:0.13, T:0.43
Consensus pattern (29 bp):
ATTATATTTTTAGAGATTACGAATTCGAA
Found at i:1770580 original size:3 final size:3
Alignment explanation
Indices: 1770572--1770600 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1770562 AAAGCTGTGG
1770572 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1770601 TTTTTTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:1771860 original size:6 final size:6
Alignment explanation
Indices: 1771849--1771878 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
1771839 TTAAGAAAAC
1771849 AATTTT AATTTT AATTTT AATTTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT
1771879 TTAATATAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
AATTTT
Found at i:1774439 original size:53 final size:53
Alignment explanation
Indices: 1774283--1774448 Score: 221
Period size: 53 Copynumber: 3.1 Consensus size: 53
1774273 GACGAAAAAT
* **
1774283 ATGTGATAAGTGTG-C-CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCA
1 ATGTGATAA-TGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
1774335 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
1 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
* * *
1774388 ATGTGATAATGTGATTCCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGA
1 ATGTGATAATGTGACTCCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A
1774442 TATGTGA
1 -ATGTGA
1774449 ACCGTGTAAG
Statistics
Matches: 103, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
51 4 0.04
52 11 0.11
53 81 0.79
54 1 0.01
55 6 0.06
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (53 bp):
ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
Found at i:1775695 original size:51 final size:51
Alignment explanation
Indices: 1775624--1775834 Score: 343
Period size: 51 Copynumber: 4.2 Consensus size: 51
1775614 CTGATCACAT
1775624 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
*
1775675 TTATCACTTGTCACTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCAT
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
*
1775725 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATTAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
* * * * *
1775776 TTGTCACTTATCACTGATCAAATAAGTGTAGCTGAGGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
*
1775827 TTGTCACT
1 TTATCACT
1775835 GATTAGAAGT
Statistics
Matches: 150, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
50 49 0.33
51 101 0.67
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (51 bp):
TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
Found at i:1775792 original size:101 final size:102
Alignment explanation
Indices: 1775621--1775834 Score: 358
Period size: 101 Copynumber: 2.1 Consensus size: 102
1775611 ACACTGATCA
*
1775621 CATTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTATCACTTGT
1 CATTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTATCACTTAT
*
1775686 CACTGATCAGATAAGTGTAGCT-AAGCTACCACTTAT
66 CACTGATCAAATAAGTGTAGCTGAAGCTACCACTTAT
* *
1775722 CATTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATTACTTGTCACTTAT
1 CATTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTATCACTTAT
*
1775787 CACTGATCAAATAAGTGTAGCTGAGGCTACCACTTAT
66 CACTGATCAAATAAGTGTAGCTGAAGCTACCACTTAT
* *
1775824 CACTTGTCACT
1 CATTTATCACT
1775835 GATTAGAAGT
Statistics
Matches: 105, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
101 83 0.79
102 22 0.21
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (102 bp):
CATTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTATCACTTAT
CACTGATCAAATAAGTGTAGCTGAAGCTACCACTTAT
Found at i:1783356 original size:51 final size:51
Alignment explanation
Indices: 1783297--1783507 Score: 352
Period size: 51 Copynumber: 4.2 Consensus size: 51
1783287 CTGATCACAT
1783297 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
*
1783348 TTATCACTTGTCACTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCAT
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
*
1783398 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATTAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
* * * *
1783449 TTGTCACTTATCACTGATCAGATAAGTGTAGCTGAGGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
*
1783500 TTGTCACT
1 TTATCACT
1783508 GATCAGATGT
Statistics
Matches: 151, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
50 49 0.32
51 102 0.68
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (51 bp):
TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
Found at i:1783415 original size:101 final size:102
Alignment explanation
Indices: 1783294--1783507 Score: 367
Period size: 101 Copynumber: 2.1 Consensus size: 102
1783284 ACACTGATCA
*
1783294 CATTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTATCACTTGT
1 CATTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTATCACTTAT
1783359 CACTGATCAGATAAGTGTAGCT-AAGCTACCACTTAT
66 CACTGATCAGATAAGTGTAGCTGAAGCTACCACTTAT
* *
1783395 CATTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATTACTTGTCACTTAT
1 CATTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTATCACTTAT
*
1783460 CACTGATCAGATAAGTGTAGCTGAGGCTACCACTTAT
66 CACTGATCAGATAAGTGTAGCTGAAGCTACCACTTAT
* *
1783497 CACTTGTCACT
1 CATTTATCACT
1783508 GATCAGATGT
Statistics
Matches: 106, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
101 84 0.79
102 22 0.21
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.33
Consensus pattern (102 bp):
CATTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTATCACTTAT
CACTGATCAGATAAGTGTAGCTGAAGCTACCACTTAT
Found at i:1790215 original size:20 final size:20
Alignment explanation
Indices: 1790192--1790232 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1790182 AGTATACAAC
1790192 ATGCAATAAAAATATATTGT
1 ATGCAATAAAAATATATTGT
*
1790212 ATGCAATAACAATATATTGT
1 ATGCAATAAAAATATATTGT
1790232 A
1 A
1790233 ATATGTTGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.07, G:0.10, T:0.34
Consensus pattern (20 bp):
ATGCAATAAAAATATATTGT
Found at i:1791946 original size:62 final size:61
Alignment explanation
Indices: 1791858--1791974 Score: 155
Period size: 62 Copynumber: 1.9 Consensus size: 61
1791848 GGGGTTTGAA
* * * *
1791858 TTTTTTTTGTATAAGTTAGTCCCTGAACTTGGTAATTGTTCCCAGATTAGGGCTTGAGCCT
1 TTTTTTTTGTATAAGTAAGTCCCTGAACTTGGTAACTATTCCCACATTAGGGCTTGAGCCT
* *
1791919 TTTTTTTCTGT-TCAAGTAAGTCTCTGAACTTGGTAACTATTCTCACATTAGGGCTT
1 TTTTTTT-TGTAT-AAGTAAGTCCCTGAACTTGGTAACTATTCCCACATTAGGGCTT
1791975 TAACTTAAAG
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
61 8 0.17
62 40 0.83
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.44
Consensus pattern (61 bp):
TTTTTTTTGTATAAGTAAGTCCCTGAACTTGGTAACTATTCCCACATTAGGGCTTGAGCCT
Found at i:1793344 original size:31 final size:31
Alignment explanation
Indices: 1793309--1793371 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
1793299 TCCCTAAACC
*
1793309 TGGCAATTG-TCCTCACATTGGAGCTTGAGCT
1 TGGCAATTGTTCCT-ACATTGGAGCATGAGCT
*
1793340 TGGCAATTGTTCCTACATTGGGGCATGAGCT
1 TGGCAATTGTTCCTACATTGGAGCATGAGCT
1793371 T
1 T
1793372 TAGGATTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 25 0.86
32 4 0.14
ACGTcount: A:0.19, C:0.21, G:0.27, T:0.33
Consensus pattern (31 bp):
TGGCAATTGTTCCTACATTGGAGCATGAGCT
Found at i:1798213 original size:20 final size:20
Alignment explanation
Indices: 1798174--1798213 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1798164 TGATAACGTT
*
1798174 TTGTATATATAATATTTAGA
1 TTGTATATATAACATTTAGA
1798194 TTGTATA-ATAACATTATAGA
1 TTGTATATATAACATT-TAGA
1798214 ATGGCACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (20 bp):
TTGTATATATAACATTTAGA
Found at i:1798544 original size:38 final size:39
Alignment explanation
Indices: 1798486--1798561 Score: 111
Period size: 38 Copynumber: 2.0 Consensus size: 39
1798476 TGCTATATAT
*
1798486 TTTTATTAATTCATATTTTAATAATAATTATATTAAAAA
1 TTTTATTAATTCATATTTTAATAATAATCATATTAAAAA
*
1798525 TTTTATTAAATT-ATA-TTTAATAATAATCCTATTAAAA
1 TTTTATT-AATTCATATTTTAATAATAATCATATTAAAA
1798562 TTTAATAACA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
38 20 0.59
39 10 0.29
40 4 0.12
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (39 bp):
TTTTATTAATTCATATTTTAATAATAATCATATTAAAAA
Found at i:1802013 original size:19 final size:21
Alignment explanation
Indices: 1801972--1802013 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1801962 CAATTTAAAC
*
1801972 TTTTTTTATCATTTATATATA
1 TTTTTATATCATTTATATATA
*
1801993 TTTTTATAT-ATTT-TATTTA
1 TTTTTATATCATTTATATATA
1802012 TT
1 TT
1802014 ATAAAATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 7 0.37
20 4 0.21
21 8 0.42
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTTTATATCATTTATATATA
Found at i:1804289 original size:46 final size:46
Alignment explanation
Indices: 1804271--1804427 Score: 140
Period size: 46 Copynumber: 3.3 Consensus size: 46
1804261 TGACAAGTGG
* * *
1804271 AAAGTGATAAGTAATAGCT-TCGGCTATACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTAT-AGCTACACTTATCTGATCAAGTGAC
*
1804317 AAAGTGATAAGTGATAGCT-TCGGCTACACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTAT-AGCTACACTTATCTGATCAAGTGAC
* * **
1804363 AAGTGAAAAGTGATAAGTGATAGCT-TCGGCTATACTTATCTGATCAAGAAAC
1 ------AAAGTGATAAGTGATAGCTAT-AGCTACACTTATCTGATCAAGTGAC
1804415 AAAGTGATAAGTG
1 AAAGTGATAAGTG
1804428 GCTACACTTA
Statistics
Matches: 100, Mismatches: 5, Indels: 12
0.85 0.04 0.10
Matches are distributed among these distances:
46 57 0.57
52 43 0.43
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (46 bp):
AAAGTGATAAGTGATAGCTATAGCTACACTTATCTGATCAAGTGAC
Found at i:1804290 original size:52 final size:51
Alignment explanation
Indices: 1804219--1804410 Score: 277
Period size: 52 Copynumber: 3.8 Consensus size: 51
1804209 ATCAAGTGAC
* **
1804219 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGT-G
* *
1804271 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC-----
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1804317 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
*
1804368 AAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAG
1 -AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAG
1804411 AAACAAAGTG
Statistics
Matches: 126, Mismatches: 8, Indels: 12
0.86 0.05 0.08
Matches are distributed among these distances:
46 44 0.35
52 82 0.65
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (51 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
Found at i:1804325 original size:98 final size:98
Alignment explanation
Indices: 1804205--1804428 Score: 385
Period size: 98 Copynumber: 2.3 Consensus size: 98
1804195 TTTGAGTACT
*
1804205 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
*
1804270 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* *
1804303 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
*
1804368 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
**
1804401 TCTGATCAAGAAACAAAGTGATAAGTGG
1 TCTGATCAAGTGACAAAGTGATAAGTGG
1804429 CTACACTTAT
Statistics
Matches: 118, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 118 1.00
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:1804437 original size:37 final size:37
Alignment explanation
Indices: 1804390--1804482 Score: 168
Period size: 37 Copynumber: 2.5 Consensus size: 37
1804380 TGATAGCTTC
*
1804390 GGCTATACTTATCTGATCAAGAAACAAAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
*
1804427 GGCTACACTTATCTGATCAAGAAACAAAGTGATAGGT
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
1804464 GGCTACACTTATCTGATCA
1 GGCTACACTTATCTGATCA
1804483 GGGACAAGTG
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 54 1.00
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (37 bp):
GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
Found at i:1806491 original size:20 final size:21
Alignment explanation
Indices: 1806463--1806501 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1806453 TTTATCATCC
*
1806463 TAATAATTTTTCTATAATAAT
1 TAATAATTTTTCTAAAATAAT
1806484 TAAT-ATTTTTCTAAAATA
1 TAATAATTTTTCTAAAATA
1806502 TAAATGATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (21 bp):
TAATAATTTTTCTAAAATAAT
Found at i:1806657 original size:33 final size:33
Alignment explanation
Indices: 1806608--1806687 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
1806598 TAATAACAGA
* *
1806608 ATTTAACCCCTCTTTTTTCCTCTTCAATTTGAG
1 ATTTAACCCTTTTTTTTTCCTCTTCAATTTGAG
1806641 ATTTAACCCTTTTTTTTTCCTCTTCAATTTGAG
1 ATTTAACCCTTTTTTTTTCCTCTTCAATTTGAG
*
1806674 ATTTAACTCTTTTT
1 ATTTAACCCTTTTT
1806688 AACTGATTCA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.19, C:0.23, G:0.05, T:0.54
Consensus pattern (33 bp):
ATTTAACCCTTTTTTTTTCCTCTTCAATTTGAG
Found at i:1811821 original size:43 final size:43
Alignment explanation
Indices: 1811755--1811840 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
1811745 AATTTATCTT
* *
1811755 GATGTAATTCTTTTTTGTTTTAAAAAAAATAAAAGAAAAAGAA
1 GATGTAATTCTTTTTCGTCTTAAAAAAAATAAAAGAAAAAGAA
*
1811798 GATGTAATTCTTTTTCGTCTTAAAAAAAATAAGAGAAAAAGAA
1 GATGTAATTCTTTTTCGTCTTAAAAAAAATAAAAGAAAAAGAA
1811841 CATTCTCTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.50, C:0.05, G:0.13, T:0.33
Consensus pattern (43 bp):
GATGTAATTCTTTTTCGTCTTAAAAAAAATAAAAGAAAAAGAA
Found at i:1814062 original size:30 final size:32
Alignment explanation
Indices: 1814028--1814105 Score: 92
Period size: 31 Copynumber: 2.5 Consensus size: 32
1814018 AATAGTTTAT
*
1814028 ATTTTTA-TATTTTTTAAAAGA-TTAAATTA-A
1 ATTTTTATTA-TTTTTAAAAGACTTAAAGTATA
*
1814058 ATTTTTATTATTTTTAAGAGACTTAAAGTATA
1 ATTTTTATTATTTTTAAAAGACTTAAAGTATA
*
1814090 A-TTTTATTATTATTAA
1 ATTTTTATTATTTTTAA
1814106 TTTAATATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
30 17 0.40
31 23 0.55
32 2 0.05
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.54
Consensus pattern (32 bp):
ATTTTTATTATTTTTAAAAGACTTAAAGTATA
Found at i:1814070 original size:31 final size:33
Alignment explanation
Indices: 1814028--1814100 Score: 93
Period size: 30 Copynumber: 2.4 Consensus size: 33
1814018 AATAGTTTAT
*
1814028 ATTTTTA-TATTTTTTAAAAGA-TTAAATTA-A
1 ATTTTTATTATTTTTTAAAAGACTTAAAGTATA
*
1814058 ATTTTTATTA-TTTTTAAGAGACTTAAAGTATA
1 ATTTTTATTATTTTTTAAAAGACTTAAAGTATA
1814090 A-TTTTATTATT
1 ATTTTTATTATT
1814101 ATTAATTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
30 17 0.46
31 17 0.46
32 3 0.08
ACGTcount: A:0.38, C:0.01, G:0.05, T:0.55
Consensus pattern (33 bp):
ATTTTTATTATTTTTTAAAAGACTTAAAGTATA
Found at i:1818754 original size:17 final size:16
Alignment explanation
Indices: 1818734--1818793 Score: 56
Period size: 17 Copynumber: 3.8 Consensus size: 16
1818724 TTTTTAAGCA
1818734 ATAAATATTAATTATTT
1 ATAAA-ATTAATTATTT
1818751 ATAAAATTTAATTA---
1 ATAAAA-TTAATTATTT
*
1818765 A-AATATTAATTATTT
1 ATAAAATTAATTATTT
1818780 ATAAAATTTAATTA
1 ATAAAA-TTAATTA
1818794 AAATATATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
12 7 0.20
13 3 0.09
14 1 0.03
15 1 0.03
16 4 0.11
17 19 0.54
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATAAAATTAATTATTT
Found at i:1818770 original size:29 final size:29
Alignment explanation
Indices: 1818736--1818799 Score: 128
Period size: 29 Copynumber: 2.2 Consensus size: 29
1818726 TTTAAGCAAT
1818736 AAATATTAATTATTTATAAAATTTAATTA
1 AAATATTAATTATTTATAAAATTTAATTA
1818765 AAATATTAATTATTTATAAAATTTAATTA
1 AAATATTAATTATTTATAAAATTTAATTA
1818794 AAATAT
1 AAATAT
1818800 ATAAACTATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
AAATATTAATTATTTATAAAATTTAATTA
Found at i:1819769 original size:6 final size:6
Alignment explanation
Indices: 1819760--1819788 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1819750 TATAAATATA
1819760 AATTTT AATTTT AATTTT AATTTT AATTT
1 AATTTT AATTTT AATTTT AATTTT AATTT
1819789 GAGTTAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
AATTTT
Found at i:1819797 original size:16 final size:15
Alignment explanation
Indices: 1819764--1819810 Score: 55
Period size: 16 Copynumber: 3.3 Consensus size: 15
1819754 AATATAAATT
1819764 TTAATTTTAA-TT--
1 TTAATTTTAATTTGA
1819776 TTAATTTTAATTTGA
1 TTAATTTTAATTTGA
*
1819791 GTTAATTTTATTTTGA
1 -TTAATTTTAATTTGA
1819807 TTAA
1 TTAA
1819811 ACTTTGCTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 10 0.33
13 2 0.07
15 4 0.13
16 14 0.47
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (15 bp):
TTAATTTTAATTTGA
Found at i:1822154 original size:22 final size:25
Alignment explanation
Indices: 1822128--1822197 Score: 101
Period size: 22 Copynumber: 2.8 Consensus size: 25
1822118 TGGACATCAA
1822128 CTCAGAGAAAGGCTCGATTA-G-G-
1 CTCAGAGAAAGGCTCGATTACGTGC
1822150 CTCAGAGAAAGGCTCGATTAGTCGTGC
1 CTCAGAGAAAGGCTCGATTA--CGTGC
1822177 CTCAGAGAAAGGCTCGATTAC
1 CTCAGAGAAAGGCTCGATTAC
1822198 TGTTCTGAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
22 20 0.47
25 2 0.05
26 1 0.02
27 20 0.47
ACGTcount: A:0.30, C:0.21, G:0.29, T:0.20
Consensus pattern (25 bp):
CTCAGAGAAAGGCTCGATTACGTGC
Found at i:1824013 original size:38 final size:38
Alignment explanation
Indices: 1823962--1824037 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
1823952 AAACTTGGTG
1823962 CATGTGATACTCCACTACTAACCTGAGCTTTTAAATCA
1 CATGTGATACTCCACTACTAACCTGAGCTTTTAAATCA
1824000 CATGTGATACTCCACTACTAACCTGAGCTTTTAAATCA
1 CATGTGATACTCCACTACTAACCTGAGCTTTTAAATCA
1824038 TGCTTTGACC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.32, C:0.26, G:0.11, T:0.32
Consensus pattern (38 bp):
CATGTGATACTCCACTACTAACCTGAGCTTTTAAATCA
Found at i:1826420 original size:25 final size:26
Alignment explanation
Indices: 1826379--1826427 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
1826369 CAACCATGCT
1826379 AATTTTTAATAATAAAAA-TAAATAA
1 AATTTTTAATAATAAAAATTAAATAA
*
1826404 AATTTTTAACTGA-AAAAATTAAAT
1 AATTTTTAA-TAATAAAAATTAAAT
1826428 TACTTTTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (26 bp):
AATTTTTAATAATAAAAATTAAATAA
Found at i:1832005 original size:52 final size:52
Alignment explanation
Indices: 1831948--1832051 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
1831938 TTTCAGGGTA
1831948 TAATTCACTGTTACTTTTTGTTTAATGCAGTTATAACAAGTAGAAAGGAATT
1 TAATTCACTGTTACTTTTTGTTTAATGCAGTTATAACAAGTAGAAAGGAATT
*
1832000 TAATTCGCTGTTACTTTTTGTTTAATGCAGTTATAACAAGTAGAAAGGAATT
1 TAATTCACTGTTACTTTTTGTTTAATGCAGTTATAACAAGTAGAAAGGAATT
1832052 CATTCTTTTT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (52 bp):
TAATTCACTGTTACTTTTTGTTTAATGCAGTTATAACAAGTAGAAAGGAATT
Found at i:1843537 original size:8 final size:8
Alignment explanation
Indices: 1843524--1843548 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1843514 ATTTCTACAA
1843524 TTTAAAAT
1 TTTAAAAT
1843532 TTTAAAAT
1 TTTAAAAT
1843540 TTTAAAAT
1 TTTAAAAT
1843548 T
1 T
1843549 GGTATGGCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TTTAAAAT
Found at i:1848049 original size:39 final size:38
Alignment explanation
Indices: 1847982--1848116 Score: 103
Period size: 39 Copynumber: 3.4 Consensus size: 38
1847972 ACCAATATGG
* *
1847982 CACCCAGTGCCTCATCGGATAGTTCGAAGTAATAGTTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAGTAATAGTTGA
* *
1848021 CACCCAGTGTCTCATCGGCCTAGCCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGTAATAGTTGA
* * * * * *
1848059 TACCCGGTACCTCATCGAATCTATCCGAAGAAATA-TAGTGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAGTAATAGT--TGA
*
1848100 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
1848117 ACTCGAGGTC
Statistics
Matches: 74, Mismatches: 16, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
38 18 0.24
39 37 0.50
40 4 0.05
41 15 0.20
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGTAATAGTTGA
Found at i:1852300 original size:30 final size:30
Alignment explanation
Indices: 1852254--1852347 Score: 152
Period size: 30 Copynumber: 3.1 Consensus size: 30
1852244 TTTTATTATG
*
1852254 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
1852285 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* *
1852315 CCATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
1852345 CCA
1 CCA
1852348 TAAATATGGA
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
30 53 0.88
31 7 0.12
ACGTcount: A:0.26, C:0.26, G:0.06, T:0.43
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:1852309 original size:15 final size:15
Alignment explanation
Indices: 1852264--1852341 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 15
1852254 CCAATATCTC
1852264 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
1852279 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
1852294 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
1852309 GACTTTCCAT-TATTT
1 GA-TACCCATATCTTT
1852324 GATACCCATATCTTT
1 GATACCCATATCTTT
1852339 GAT
1 GAT
1852342 TTTCCATAAA
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
14 9 0.19
15 29 0.62
16 9 0.19
ACGTcount: A:0.26, C:0.23, G:0.08, T:0.44
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:1856972 original size:15 final size:15
Alignment explanation
Indices: 1856927--1857034 Score: 87
Period size: 15 Copynumber: 7.2 Consensus size: 15
1856917 CCAATATCTC
*
1856927 GATACCCATATCTTT
1 GATACCCATATATTT
**
1856942 GACTTTCCA-ATATTT
1 GA-TACCCATATATTT
*
1856957 GATACCCATATCTTT
1 GATACCCATATATTT
**
1856972 GACTTTCCA-ATATTT
1 GA-TACCCATATATTT
*
1856987 GATACCCATATCTTT
1 GATACCCATATATTT
**
1857002 GACTTTCCAT-TATTT
1 GA-TACCCATATATTT
1857017 GATACCCATATATTT
1 GATACCCATATATTT
1857032 GAT
1 GAT
1857035 TTTCCATAAA
Statistics
Matches: 70, Mismatches: 17, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
14 13 0.19
15 44 0.63
16 13 0.19
ACGTcount: A:0.27, C:0.22, G:0.07, T:0.44
Consensus pattern (15 bp):
GATACCCATATATTT
Found at i:1857041 original size:30 final size:30
Alignment explanation
Indices: 1856917--1857040 Score: 203
Period size: 30 Copynumber: 4.1 Consensus size: 30
1856907 TTTTATTATG
*
1856917 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
1856948 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
1856978 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * *
1857008 CCATTATTTGATACCCATATATTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
1857038 CCA
1 CCA
1857041 TAAATATGGA
Statistics
Matches: 89, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
30 82 0.92
31 7 0.08
ACGTcount: A:0.27, C:0.24, G:0.06, T:0.43
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:1862988 original size:21 final size:21
Alignment explanation
Indices: 1862962--1863002 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1862952 ATCTGCTCAA
* *
1862962 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
1862983 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
1863003 TTGCTCGTCT
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:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:1877545 original size:15 final size:15
Alignment explanation
Indices: 1877527--1877557 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1877517 GAAATAATTA
*
1877527 GTAAAAGAATAAAAG
1 GTAAAAGAAAAAAAG
1877542 GTAAAAGAAAAAAAG
1 GTAAAAGAAAAAAAG
1877557 G
1 G
1877558 ATTAAGAGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.23, T:0.10
Consensus pattern (15 bp):
GTAAAAGAAAAAAAG
Found at i:1881595 original size:54 final size:54
Alignment explanation
Indices: 1881528--1881637 Score: 220
Period size: 54 Copynumber: 2.0 Consensus size: 54
1881518 AAAAATAAAC
1881528 ATATTAAATTAACAAAAATTGATTAAAAATACCGACAAAGATAATGATTAGGCT
1 ATATTAAATTAACAAAAATTGATTAAAAATACCGACAAAGATAATGATTAGGCT
1881582 ATATTAAATTAACAAAAATTGATTAAAAATACCGACAAAGATAATGATTAGGCT
1 ATATTAAATTAACAAAAATTGATTAAAAATACCGACAAAGATAATGATTAGGCT
1881636 AT
1 AT
1881638 GTATAATTTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.52, C:0.09, G:0.11, T:0.28
Consensus pattern (54 bp):
ATATTAAATTAACAAAAATTGATTAAAAATACCGACAAAGATAATGATTAGGCT
Found at i:1884501 original size:30 final size:30
Alignment explanation
Indices: 1884467--1884538 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 30
1884457 TTTTAAATTA
*
1884467 ATAAAATTATAATTTGATCCCCTAAAAATG
1 ATAAAATTATAATTTAATCCCCTAAAAATG
* ** *
1884497 ATAAAAATT-TAATTTAATTCTTTAAAAATT
1 AT-AAAATTATAATTTAATCCCCTAAAAATG
*
1884527 ATAAAAATATAA
1 ATAAAATTATAA
1884539 ATTATTAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
29 5 0.15
30 23 0.68
31 6 0.18
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.38
Consensus pattern (30 bp):
ATAAAATTATAATTTAATCCCCTAAAAATG
Found at i:1888312 original size:35 final size:35
Alignment explanation
Indices: 1888273--1888344 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
1888263 CATCTCCAGA
*
1888273 GCTTGGCAAATATGGAAAGTAATCTTCAAAGATAT
1 GCTTGGCAAATATGGAAAGGAATCTTCAAAGATAT
* *
1888308 GCTTGGCACATATGGAAGGGAATCTTCAAAGATAT
1 GCTTGGCAAATATGGAAAGGAATCTTCAAAGATAT
1888343 GC
1 GC
1888345 GATCCTAGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26
Consensus pattern (35 bp):
GCTTGGCAAATATGGAAAGGAATCTTCAAAGATAT
Found at i:1896342 original size:35 final size:35
Alignment explanation
Indices: 1896303--1896374 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
1896293 CATCTCCGGA
*
1896303 GCTTGGCAAATATGGAAAGTAATCTTCAAAGATAT
1 GCTTGGCAAATATGGAAAGGAATCTTCAAAGATAT
*
1896338 GCTTGGCAAATATGGAAGGGAATCTTCAAAGATAT
1 GCTTGGCAAATATGGAAAGGAATCTTCAAAGATAT
1896373 GC
1 GC
1896375 GATCCTAGAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.38, C:0.12, G:0.24, T:0.26
Consensus pattern (35 bp):
GCTTGGCAAATATGGAAAGGAATCTTCAAAGATAT
Found at i:1897154 original size:13 final size:14
Alignment explanation
Indices: 1897136--1897168 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1897126 TTTCCACATG
1897136 AAAATTTAAT-TTT
1 AAAATTTAATGTTT
1897149 AAAATTTAATGTTT
1 AAAATTTAATGTTT
*
1897163 ACAATT
1 AAAATT
1897169 CCATTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (14 bp):
AAAATTTAATGTTT
Found at i:1897620 original size:106 final size:106
Alignment explanation
Indices: 1897509--1897780 Score: 404
Period size: 106 Copynumber: 2.6 Consensus size: 106
1897499 TAAGTTGTAA
* * *
1897509 AAAAAGGCTTATATAATTTCTCAAGTTTTATGATATAAGTATGTGAGGTGTATAAAGGTCGCATG
1 AAAAAGGCTTATATAATTTCTCAAGTTTCATGAGATAAATATGTGAGGTGTATAAAGGTCGCATG
* *
1897574 TAGATCATGCATAACCCATATCATTCTCAATTAAGTCATTG
66 TAGATCATGCATAACCCATATCATTCTCAATTAAATCATAG
*
1897615 AAAAAGGCTTATATAATTTTTCAAGTTTCATGAGATAAATATGTGAGGTGTATAAAGGTCGCATG
1 AAAAAGGCTTATATAATTTCTCAAGTTTCATGAGATAAATATGTGAGGTGTATAAAGGTCGCATG
* **
1897680 TAGATCATGTATAGTCCATATCATTCTCAATTAAATCATAG
66 TAGATCATGCATAACCCATATCATTCTCAATTAAATCATAG
* **
1897721 AAAAAGGCTTATATAATTTCTCAA-ATTCAAT-AGGATAAATATGTGAGGAATATAAAGGTC
1 AAAAAGGCTTATATAATTTCTCAAGTTTC-ATGA-GATAAATATGTGAGGTGTATAAAGGTC
1897781 ACGAATAGAT
Statistics
Matches: 151, Mismatches: 13, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
105 4 0.03
106 147 0.97
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (106 bp):
AAAAAGGCTTATATAATTTCTCAAGTTTCATGAGATAAATATGTGAGGTGTATAAAGGTCGCATG
TAGATCATGCATAACCCATATCATTCTCAATTAAATCATAG
Found at i:1903556 original size:4 final size:4
Alignment explanation
Indices: 1903547--1903609 Score: 126
Period size: 4 Copynumber: 15.8 Consensus size: 4
1903537 ATCAATTTTA
1903547 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1903595 ACAT ACAT ACAT ACA
1 ACAT ACAT ACAT ACA
1903610 CGGACACGCA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 59 1.00
ACGTcount: A:0.51, C:0.25, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:1911119 original size:31 final size:31
Alignment explanation
Indices: 1911056--1911138 Score: 80
Period size: 31 Copynumber: 2.7 Consensus size: 31
1911046 AATTTCAAAT
* * *
1911056 TTCAAAAAGTACAA-AGATTATAATTGACCAA
1 TTCAAAAAGTACAATA-ACTAAAATCGACCAA
*
1911087 TTCAAAAAGTACAATAACTAAAATCGATCAA
1 TTCAAAAAGTACAATAACTAAAATCGACCAA
***
1911118 TT-TTGAAGTACAATAACTAAA
1 TTCAAAAAGTACAATAACTAAA
1911139 TCCATAACTT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
30 16 0.36
31 27 0.61
32 1 0.02
ACGTcount: A:0.52, C:0.13, G:0.08, T:0.27
Consensus pattern (31 bp):
TTCAAAAAGTACAATAACTAAAATCGACCAA
Found at i:1912197 original size:44 final size:44
Alignment explanation
Indices: 1912138--1912222 Score: 125
Period size: 44 Copynumber: 1.9 Consensus size: 44
1912128 ATAATATATC
* * *
1912138 AAATATACTACAAACATTAAAATAAATATTTTCTAATAAATTAA
1 AAATATACTAAAAACATTAAAATAAATATTTACTAACAAATTAA
* *
1912182 AAATATATTAAAAACATTGAAATAAATATTTACTAACAAAT
1 AAATATACTAAAAACATTAAAATAAATATTTACTAACAAAT
1912223 ATTAAAAAGA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.58, C:0.08, G:0.01, T:0.33
Consensus pattern (44 bp):
AAATATACTAAAAACATTAAAATAAATATTTACTAACAAATTAA
Found at i:1914589 original size:31 final size:31
Alignment explanation
Indices: 1914535--1914600 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
1914525 AGGTTGAATA
* *
1914535 ACTAAAATGAAAAAAAATTAATAGTTGAGTG
1 ACTAAAATGAAAAAAAATGAATAGATGAGTG
*
1914566 ACTAAAAT-AAAAAGAACTGAATAGATGAGTG
1 ACTAAAATGAAAAA-AAATGAATAGATGAGTG
1914597 ACTA
1 ACTA
1914601 TTCATGTACT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 5 0.16
31 26 0.84
ACGTcount: A:0.55, C:0.06, G:0.17, T:0.23
Consensus pattern (31 bp):
ACTAAAATGAAAAAAAATGAATAGATGAGTG
Found at i:1921172 original size:9 final size:9
Alignment explanation
Indices: 1921150--1921180 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
1921140 TAATTTATTT
1921150 ATTTTTAAA
1 ATTTTTAAA
1921159 GATTTTTAAA
1 -ATTTTTAAA
1921169 ATTTTTAAA
1 ATTTTTAAA
1921178 ATT
1 ATT
1921181 ATGTTTGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (9 bp):
ATTTTTAAA
Found at i:1926650 original size:30 final size:29
Alignment explanation
Indices: 1926616--1926686 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
1926606 TAAAATAACA
*
1926616 ATAAAATTATACTTTAATCTTTCAAAAATG
1 ATAAAATTATAATTTAAT-TTTCAAAAATG
* *
1926646 ATAAATATT-TAATTTAATTTTTAAAAATT
1 ATAAA-ATTATAATTTAATTTTCAAAAATG
*
1926675 ATAAAAATATAA
1 ATAAAATTATAA
1926687 ATTATTAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 2 0.06
29 17 0.49
30 13 0.37
31 3 0.09
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.42
Consensus pattern (29 bp):
ATAAAATTATAATTTAATTTTCAAAAATG
Found at i:1926688 original size:15 final size:17
Alignment explanation
Indices: 1926669--1926709 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
1926659 TTAATTTTTA
1926669 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATAAT
*
1926685 -AAATTATTAAAATAAT
1 AAAATTATAAAAATAAT
1926701 AAAATTATA
1 AAAATTATA
1926710 TTTATATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATAAT
Found at i:1931565 original size:19 final size:19
Alignment explanation
Indices: 1931541--1931577 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1931531 ATTTTTTATC
* *
1931541 AATTTATTTTTTATTTTTA
1 AATTTAGTTTTAATTTTTA
1931560 AATTTAGTTTTAATTTTT
1 AATTTAGTTTTAATTTTT
1931578 TTTAAAAATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (19 bp):
AATTTAGTTTTAATTTTTA
Found at i:1935009 original size:22 final size:22
Alignment explanation
Indices: 1934984--1935034 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
1934974 TAATAACAAA
*
1934984 AAAATAATAGCAACATAATA-G
1 AAAATAATAGCAAAATAATACG
* *
1935005 TAAAATAGTAGTAAAATAATACG
1 -AAAATAATAGCAAAATAATACG
1935028 AAAATAA
1 AAAATAA
1935035 CAAGAAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 23 0.96
23 1 0.04
ACGTcount: A:0.63, C:0.06, G:0.10, T:0.22
Consensus pattern (22 bp):
AAAATAATAGCAAAATAATACG
Found at i:1943094 original size:18 final size:18
Alignment explanation
Indices: 1943071--1943113 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
1943061 GGAGGAAGAA
1943071 GAAGAAGAAGAACCAGAG
1 GAAGAAGAAGAACCAGAG
*
1943089 GAAGAAGAGGAACCAGAG
1 GAAGAAGAAGAACCAGAG
1943107 GAAGAAG
1 GAAGAAG
1943114 GAGTTCAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.53, C:0.09, G:0.37, T:0.00
Consensus pattern (18 bp):
GAAGAAGAAGAACCAGAG
Found at i:1947690 original size:30 final size:31
Alignment explanation
Indices: 1947650--1947707 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
1947640 AATAAAAAAG
* *
1947650 ATTTAAGTCTTAATGTGAGAATAATTACTTA
1 ATTTAAGTCTTAATATAAGAATAATTACTTA
1947681 ATTT-AGTCTTAATATAAGAATAATTAC
1 ATTTAAGTCTTAATATAAGAATAATTAC
1947708 AAAGTTATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.41
Consensus pattern (31 bp):
ATTTAAGTCTTAATATAAGAATAATTACTTA
Found at i:1950314 original size:89 final size:89
Alignment explanation
Indices: 1950158--1950335 Score: 338
Period size: 89 Copynumber: 2.0 Consensus size: 89
1950148 TCTACTTATC
*
1950158 TAAAATGTAGGATTTAGTCTATATTAATTATTTTAATAAATATATATTACAATTTTTATAAACAT
1 TAAAATGTAGGATTTAGTCTATATTAATTATTTTAATAAATATATATTACAATTTTAATAAACAT
1950223 TGAATAAATAATTATAATATAATG
66 TGAATAAATAATTATAATATAATG
*
1950247 TAAAGTGTAGGATTTAGTCTATATTAATTATTTTAATAAATATATATTACAATTTTAATAAACAT
1 TAAAATGTAGGATTTAGTCTATATTAATTATTTTAATAAATATATATTACAATTTTAATAAACAT
1950312 TGAATAAATAATTATAATATAATG
66 TGAATAAATAATTATAATATAATG
1950336 GGATAAATCT
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 87 1.00
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.43
Consensus pattern (89 bp):
TAAAATGTAGGATTTAGTCTATATTAATTATTTTAATAAATATATATTACAATTTTAATAAACAT
TGAATAAATAATTATAATATAATG
Found at i:1951260 original size:19 final size:19
Alignment explanation
Indices: 1951238--1951281 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1951228 TATTAATTTT
*
1951238 ATATAAAAATATTTTAAAA
1 ATATAAAAATATTATAAAA
* * *
1951257 ATATTAAATTATTATAATA
1 ATATAAAAATATTATAAAA
1951276 ATATAA
1 ATATAA
1951282 CTTATTTTAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
ATATAAAAATATTATAAAA
Found at i:1951294 original size:19 final size:20
Alignment explanation
Indices: 1951247--1951295 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
1951237 TATATAAAAA
1951247 TATTTTAAA-AATATTAAAT
1 TATTTTAAATAATATTAAAT
* *
1951266 TATTAT-AATAATA-TAACT
1 TATTTTAAATAATATTAAAT
1951284 TATTTTAAATAA
1 TATTTTAAATAA
1951296 AAAATAATGG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 11 0.44
19 14 0.56
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
TATTTTAAATAATATTAAAT
Found at i:1957008 original size:13 final size:13
Alignment explanation
Indices: 1956990--1957019 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1956980 CCTTTGATCG
1956990 AATTAGATCAATT
1 AATTAGATCAATT
1957003 AATTAGATCAATT
1 AATTAGATCAATT
1957016 AATT
1 AATT
1957020 CAATTTTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (13 bp):
AATTAGATCAATT
Found at i:1957238 original size:15 final size:14
Alignment explanation
Indices: 1957200--1957242 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
1957190 AATCCTTGAA
1957200 ATTATTTTTAAAAT
1 ATTATTTTTAAAAT
*
1957214 TTTAGCTTTTTAATAAT
1 ATTA--TTTTTAA-AAT
1957231 ATTATTTTTAAA
1 ATTATTTTTAAA
1957243 TTATAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
14 4 0.17
15 7 0.29
16 7 0.29
17 6 0.25
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (14 bp):
ATTATTTTTAAAAT
Found at i:1958625 original size:58 final size:57
Alignment explanation
Indices: 1958487--1958638 Score: 171
Period size: 59 Copynumber: 2.6 Consensus size: 57
1958477 CAAATTGAAC
* *
1958487 CTAAAAAAAAGCTTAGGTACCAAATTAGGAAAAAAAGTCAAGTTCAGGTACCAAATTGGG
1 CTAAAAAAAA-TTTA-GTACCAAA-TAAGAAAAAAAGTCAAGTTCAGGTACCAAATTGGG
* ** * *
1958547 CTCAAAAAAATTTATGTACCAAACTAAGAAAAAGTGTCAAGTTCAGGTATCAAATTTGG
1 CTAAAAAAAATTTA-GTACCAAA-TAAGAAAAAAAGTCAAGTTCAGGTACCAAATTGGG
*
1958606 C-AAAAAAAATTTAGATACCAAATTAGAAAAAAA
1 CTAAAAAAAATTTAG-TACCAAATAAGAAAAAAA
1958639 TGTTAAATTC
Statistics
Matches: 78, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
57 9 0.12
58 18 0.23
59 42 0.54
60 9 0.12
ACGTcount: A:0.50, C:0.12, G:0.15, T:0.22
Consensus pattern (57 bp):
CTAAAAAAAATTTAGTACCAAATAAGAAAAAAAGTCAAGTTCAGGTACCAAATTGGG
Found at i:1959501 original size:29 final size:29
Alignment explanation
Indices: 1959466--1959521 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
1959456 TAATAATTAA
*
1959466 GTGACTATTAATGCAATTTAT-CCTTAAAT
1 GTGACTATTAATACAATTT-TCCCTTAAAT
1959495 GTGACTATTAATACAATTTTCCCTTAA
1 GTGACTATTAATACAATTTTCCCTTAA
1959522 TATATTAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 1 0.04
29 24 0.96
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (29 bp):
GTGACTATTAATACAATTTTCCCTTAAAT
Found at i:1963561 original size:46 final size:46
Alignment explanation
Indices: 1963502--1963593 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 46
1963492 TAAATTTATG
1963502 TCTAATCACTTAGATTTGGTAATTGATTCATATTAAATGTATAATA
1 TCTAATCACTTAGATTTGGTAATTGATTCATATTAAATGTATAATA
* *
1963548 TCTAATCAGTTAGATTTGGTAGTTGATTCATATTAAATGTATAATA
1 TCTAATCACTTAGATTTGGTAATTGATTCATATTAAATGTATAATA
1963594 AAAAACAAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.43
Consensus pattern (46 bp):
TCTAATCACTTAGATTTGGTAATTGATTCATATTAAATGTATAATA
Found at i:1966211 original size:45 final size:46
Alignment explanation
Indices: 1966150--1966243 Score: 163
Period size: 45 Copynumber: 2.1 Consensus size: 46
1966140 ATTTAAATAA
1966150 TTTAACCATCAATCTTTACACGTTGTGTAA-TTTTTTTTGTGCAAT
1 TTTAACCATCAATCTTTACACGTTGTGTAATTTTTTTTTGTGCAAT
* *
1966195 TTTAACCCTCAATCTTTACACGTTGTGTAATTTTTTTTTTTGCAAT
1 TTTAACCATCAATCTTTACACGTTGTGTAATTTTTTTTTGTGCAAT
1966241 TTT
1 TTT
1966244 GATTTCTTTC
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
45 29 0.63
46 17 0.37
ACGTcount: A:0.22, C:0.16, G:0.10, T:0.52
Consensus pattern (46 bp):
TTTAACCATCAATCTTTACACGTTGTGTAATTTTTTTTTGTGCAAT
Found at i:1972222 original size:17 final size:17
Alignment explanation
Indices: 1972185--1972223 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1972175 ACGAAACACT
* **
1972185 AAAAACCAGAAAAAAGG
1 AAAAACCAAAAAAAAAA
1972202 AAAAACCAAAAAAAAAA
1 AAAAACCAAAAAAAAAA
1972219 AAAAA
1 AAAAA
1972224 ACAGTTGATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.82, C:0.10, G:0.08, T:0.00
Consensus pattern (17 bp):
AAAAACCAAAAAAAAAA
Found at i:1978716 original size:16 final size:15
Alignment explanation
Indices: 1978688--1978732 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
1978678 TATAATGGTA
*
1978688 AATTTAATTTTTAAT
1 AATTTATTTTTTAAT
* *
1978703 ATTTATATTTTTTATT
1 AATT-TATTTTTTAAT
1978719 AATTTATTTTTTAA
1 AATTTATTTTTTAA
1978733 ATTAAATTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
AATTTATTTTTTAAT
Done.