Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold10
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: 3842500
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.31
Warning! 348197 characters in sequence are not A, C, G, or T
File 12 of 25
Found at i:1652006 original size:32 final size:32
Alignment explanation
Indices: 1651965--1652027 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1651955 TAGCTAATTA
*
1651965 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
1651997 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
1652028 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:1652109 original size:21 final size:21
Alignment explanation
Indices: 1652085--1652141 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
1652075 CATTTGTAGG
1652085 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
1652106 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
1652127 ATGTATCGATACATT
1 ATGTATCGATACATT
1652142 TGGATAAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:1656374 original size:15 final size:15
Alignment explanation
Indices: 1656354--1656384 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1656344 TAAAAATGTC
*
1656354 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1656369 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1656384 C
1 C
1656385 CAAACGAAAT
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:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1658483 original size:13 final size:13
Alignment explanation
Indices: 1658465--1658490 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1658455 ACATTTTTCT
1658465 TTGTATCGATACA
1 TTGTATCGATACA
1658478 TTGTATCGATACA
1 TTGTATCGATACA
1658491 GGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1661066 original size:20 final size:19
Alignment explanation
Indices: 1661021--1661071 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
1661011 TAGCCAAACT
* **
1661021 TGTATCGATACACCAAGTA
1 TGTATCGATACACAAAAAA
1661040 TGTATCGATACACAAAAAA
1 TGTATCGATACACAAAAAA
1661059 TGGTATCGATACA
1 T-GTATCGATACA
1661072 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.25
Consensus pattern (19 bp):
TGTATCGATACACAAAAAA
Found at i:1663591 original size:20 final size:21
Alignment explanation
Indices: 1663552--1663592 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1663542 ACAACCCATG
1663552 TTCATGCATTTTGAGCTATGT
1 TTCATGCATTTTGAGCTATGT
*
1663573 TTCATGCATTTTTAG-TATGT
1 TTCATGCATTTTGAGCTATGT
1663593 CCAACACCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.20, C:0.12, G:0.17, T:0.51
Consensus pattern (21 bp):
TTCATGCATTTTGAGCTATGT
Found at i:1667155 original size:31 final size:31
Alignment explanation
Indices: 1667120--1667178 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
1667110 CTTAAGTCTA
*
1667120 AGTCAAAGCTCACACAAGCTAGTGGCACCCG
1 AGTCAAAGCCCACACAAGCTAGTGGCACCCG
* *
1667151 AGTCAAAGCCCACATAAGCTGGTGGCAC
1 AGTCAAAGCCCACACAAGCTAGTGGCAC
1667179 TTAAGTCGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.32, C:0.31, G:0.24, T:0.14
Consensus pattern (31 bp):
AGTCAAAGCCCACACAAGCTAGTGGCACCCG
Found at i:1667318 original size:87 final size:87
Alignment explanation
Indices: 1667161--1667325 Score: 240
Period size: 87 Copynumber: 1.9 Consensus size: 87
1667151 AGTCAAAGCC
* * * * * *
1667161 CACATAAGCTGGTGGCACTTAAGTCGAAGTTAAGTCCACATTAGTTGGTACCTGTTTGAGGAGAT
1 CACAAAAGCTGGTGGCACTTAAGTCCAAGTTAAGTCCACATTAGTTGGCACCTGTCTAAAGAGAT
*
1667226 GAAGCCTTAGAATGTGAAAACT
66 CAAGCCTTAGAATGTGAAAACT
* *
1667248 CACAAAAGTTGGTGGCACTTAAGTCCAAGTTAAGTCCACATTAGTTGGCACCTGTCTAAAGAGGT
1 CACAAAAGCTGGTGGCACTTAAGTCCAAGTTAAGTCCACATTAGTTGGCACCTGTCTAAAGAGAT
*
1667313 CAAGCCTTTGAAT
66 CAAGCCTTAGAAT
1667326 ACCAAAACCC
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
87 68 1.00
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (87 bp):
CACAAAAGCTGGTGGCACTTAAGTCCAAGTTAAGTCCACATTAGTTGGCACCTGTCTAAAGAGAT
CAAGCCTTAGAATGTGAAAACT
Found at i:1669978 original size:13 final size:13
Alignment explanation
Indices: 1669960--1669985 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1669950 AATTTTTTGG
1669960 TGTATCGATACAT
1 TGTATCGATACAT
1669973 TGTATCGATACAT
1 TGTATCGATACAT
1669986 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1672097 original size:20 final size:21
Alignment explanation
Indices: 1672060--1672102 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
1672050 GGCTAGTGTG
*
1672060 GGGAGTGCCCGGTTGCGACCT
1 GGGAGTGCCCGGTCGCGACCT
1672081 GGGAGTG-CCGGTCGCGACCT
1 GGGAGTGCCCGGTCGCGACCT
1672101 GG
1 GG
1672103 TGGGTGCTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.09, C:0.28, G:0.47, T:0.16
Consensus pattern (21 bp):
GGGAGTGCCCGGTCGCGACCT
Found at i:1676483 original size:21 final size:21
Alignment explanation
Indices: 1676454--1676498 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
1676444 AAGTTTTTAT
*
1676454 TTTTCTTAGCTAA-TTCATTA
1 TTTTCTTAGCCAAGTTCATTA
*
1676474 TTTTCATTAGCCAAGTTCTTTA
1 TTTTC-TTAGCCAAGTTCATTA
1676496 TTT
1 TTT
1676499 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 7 0.33
22 9 0.43
ACGTcount: A:0.22, C:0.16, G:0.07, T:0.56
Consensus pattern (21 bp):
TTTTCTTAGCCAAGTTCATTA
Found at i:1676498 original size:22 final size:21
Alignment explanation
Indices: 1676443--1676498 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
1676433 ATGAATCATG
1676443 CAAGTT-TTTATTTTTCTTAGC
1 CAAGTTCTTTA-TTTTCTTAGC
* *
1676464 TAA-TTCATTATTTTCATTAGC
1 CAAGTTCTTTATTTTC-TTAGC
1676485 CAAGTTCTTTATTT
1 CAAGTTCTTTATTT
1676499 CAACTTGCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
20 7 0.25
21 12 0.43
22 9 0.32
ACGTcount: A:0.23, C:0.14, G:0.07, T:0.55
Consensus pattern (21 bp):
CAAGTTCTTTATTTTCTTAGC
Found at i:1678732 original size:13 final size:13
Alignment explanation
Indices: 1678714--1678739 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1678704 AATTTTTTGG
1678714 TGTATCGATACAT
1 TGTATCGATACAT
1678727 TGTATCGATACAT
1 TGTATCGATACAT
1678740 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1681977 original size:61 final size:61
Alignment explanation
Indices: 1681865--1681988 Score: 162
Period size: 61 Copynumber: 2.0 Consensus size: 61
1681855 AAAGATGATG
* * * * *
1681865 AAGATGAGAAAAGTGATAAAGATGCCAATATGCTGATTCAGGGCTAGCGATATTGGGCTTA
1 AAGATGAGAAAAGTAATAAAGATGCCAATATGCCGATTCAAGGCCAACGATATTGGGCTTA
*
1681926 AAGATGAG-AAAGATAATAAA-AGTGCCAATATGCCGATTTAAGGCCAACGATATTGGGCTTA
1 AAGATGAGAAAAG-TAATAAAGA-TGCCAATATGCCGATTCAAGGCCAACGATATTGGGCTTA
1681987 AA
1 AA
1681989 ATGCGAAGAA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
60 5 0.09
61 50 0.91
ACGTcount: A:0.40, C:0.12, G:0.25, T:0.23
Consensus pattern (61 bp):
AAGATGAGAAAAGTAATAAAGATGCCAATATGCCGATTCAAGGCCAACGATATTGGGCTTA
Found at i:1682170 original size:49 final size:49
Alignment explanation
Indices: 1681947--1682250 Score: 216
Period size: 52 Copynumber: 6.0 Consensus size: 49
1681937 GATAATAAAA
* * * *
1681947 GTGCCAATATGCCGATTTAAGGCCAACGATATTGGGCTTAAA-ATGCGAAG
1 GTGCCAATGTGCTGATTCAAGGCCAACGATATTGGACTTAAAGAT--GAAG
* * * * ** * * *
1681997 AATGTCAATGTGTTGATTCACGGCCAGTGACATTAGACTTGAAGATAAGAAG
1 -GTGCCAATGTGCTGATTCAAGGCCAACGATATTGGACTTAAAGAT--GAAG
* * * * * * *
1682049 AATGTCAATGTGCTGATTTAAGGCCAGCGACATT-GAGCTTAGGAATGTTAAAG
1 -GTGCCAATGTGCTGATTCAAGGCCAACGATATTGGA-CTTA--AA-GATGAAG
* * * * * *
1682102 ATGCTAATATGCTGATTCAAGGCTAGCGATATCGGACTTAAAGATGAAG
1 GTGCCAATGTGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAG
*
1682151 GTGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGGTAAAG
1 GTGCCAATGTGCTGATTCAAGGCCAACGATATTGGACTTAAAGAT-G--AAG
* *
1682203 GTGCCAATGTGCTAATTCACGGCCAACGATATTGGACTTAAAGATGAA
1 GTGCCAATGTGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAA
1682251 AATGATGATA
Statistics
Matches: 203, Mismatches: 41, Indels: 20
0.77 0.16 0.08
Matches are distributed among these distances:
49 45 0.22
50 3 0.01
51 32 0.16
52 114 0.56
53 5 0.02
54 2 0.01
55 2 0.01
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (49 bp):
GTGCCAATGTGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAG
Found at i:1682173 original size:101 final size:101
Alignment explanation
Indices: 1682054--1682250 Score: 254
Period size: 101 Copynumber: 2.0 Consensus size: 101
1682044 AGAAGAATGT
* * * * * *
1682054 CAATGTGCTGATTTAAGGCCAGCGACATT-GAGCTT-AGGAATGTTAAAGATGCTAATATGCTGA
1 CAATGTGCTGATTCAAGGCCAACGACATTGGA-CTTAAAG-ATGGTAAAGATGCCAATATGCTAA
* *
1682117 TTCAAGGCTAGCGATATCGGACTTAAAGATGAAGGTGC
64 TTCAAGGCCAACGATATCGGACTTAAAGATGAAGGTGC
* *
1682155 CAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGGTAAAGGTGCCAATGTGCTAATT
1 CAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGGTAAAGATGCCAATATGCTAATT
* *
1682220 CACGGCCAACGATATTGGACTTAAAGATGAA
66 CAAGGCCAACGATATCGGACTTAAAGATGAA
1682251 AATGATGATA
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
101 78 0.95
102 4 0.05
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.25
Consensus pattern (101 bp):
CAATGTGCTGATTCAAGGCCAACGACATTGGACTTAAAGATGGTAAAGATGCCAATATGCTAATT
CAAGGCCAACGATATCGGACTTAAAGATGAAGGTGC
Found at i:1682384 original size:43 final size:43
Alignment explanation
Indices: 1682259--1682390 Score: 167
Period size: 43 Copynumber: 3.1 Consensus size: 43
1682249 AAAATGATGA
*
1682259 TAAAGGTGCCAATATGCTAATTCAAGGCC-GACGATATTAGACT
1 TAAAGGTGCCAATATGCTAATTCAAGGCCAG-CGATATTGGACT
* * ** *
1682302 TAAAGGTGCCAATGTGCTAATTTAAGGTTAGTGATATTGGACT
1 TAAAGGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGACT
* * *
1682345 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGGCT
1 TAAAGGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGACT
1682388 TAA
1 TAA
1682391 GAGGAGATGC
Statistics
Matches: 74, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
43 73 0.99
44 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (43 bp):
TAAAGGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGACT
Found at i:1682475 original size:32 final size:31
Alignment explanation
Indices: 1682402--1682551 Score: 167
Period size: 32 Copynumber: 4.8 Consensus size: 31
1682392 AGGAGATGCA
* * *
1682402 ACCAACTTTTATGGGCTTTTGAAAGGGTTGCC
1 ACCAACTTGTGTGGGCTTTAG-AAGGGTTGCC
* * * *
1682434 ACCGACTTGTGTGGCCTTTAAGAAGGGTTACT
1 ACCAACTTGTGTGGGCTTT-AGAAGGGTTGCC
* * *
1682466 ACCAGCTTGTGTAGGCTTTAGAGGGGTTGCC
1 ACCAACTTGTGTGGGCTTTAGAAGGGTTGCC
*
1682497 ACCAACTTGTGTGGGCTTTTGAAGAGGTTGCC
1 ACCAACTTGTGTGGGCTTTAGAAG-GGTTGCC
1682529 ACCAACTTGTGTGGGCTTT-GAAG
1 ACCAACTTGTGTGGGCTTTAGAAG
1682552 ATGGTTTCTC
Statistics
Matches: 98, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
31 33 0.34
32 64 0.65
33 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.30, T:0.31
Consensus pattern (31 bp):
ACCAACTTGTGTGGGCTTTAGAAGGGTTGCC
Found at i:1682505 original size:63 final size:63
Alignment explanation
Indices: 1682426--1682547 Score: 165
Period size: 63 Copynumber: 1.9 Consensus size: 63
1682416 GCTTTTGAAA
* * *
1682426 GGGTTGCCACCGACTTGTGTGGCCTTTAAGAAG-GGTTACTACCAGCTTGTGTAGGCTTTAGAG
1 GGGTTGCCACCAACTTGTGTGGCCTTT-AGAAGAGGTTACCACCAACTTGTGTAGGCTTTAGAG
* * * *
1682489 GGGTTGCCACCAACTTGTGTGGGCTTTTGAAGAGGTTGCCACCAACTTGTGTGGGCTTT
1 GGGTTGCCACCAACTTGTGTGGCCTTTAGAAGAGGTTACCACCAACTTGTGTAGGCTTT
1682548 GAAGATGGTT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
62 4 0.08
63 47 0.92
ACGTcount: A:0.17, C:0.20, G:0.32, T:0.31
Consensus pattern (63 bp):
GGGTTGCCACCAACTTGTGTGGCCTTTAGAAGAGGTTACCACCAACTTGTGTAGGCTTTAGAG
Found at i:1682506 original size:31 final size:31
Alignment explanation
Indices: 1682382--1682547 Score: 152
Period size: 32 Copynumber: 5.3 Consensus size: 31
1682372 CCAGCGACAT
* * * * * *
1682382 TGGGCTTAAGAGGAGATGCAACCAACTTTTA
1 TGGGCTTTAGAGGGGTTGCCACCAACTTGTG
* * *
1682413 TGGGCTTTTGAAAGGGTTGCCACCGACTTGTG
1 TGGGCTTTAG-AGGGGTTGCCACCAACTTGTG
* * * * *
1682445 TGGCCTTTAAGAAGGGTTACTACCAGCTTGTG
1 TGGGCTTT-AGAGGGGTTGCCACCAACTTGTG
*
1682477 TAGGCTTTAGAGGGGTTGCCACCAACTTGTG
1 TGGGCTTTAGAGGGGTTGCCACCAACTTGTG
* *
1682508 TGGGCTTTTGAAGAGGTTGCCACCAACTTGTG
1 TGGGCTTTAG-AGGGGTTGCCACCAACTTGTG
1682540 TGGGCTTT
1 TGGGCTTT
1682548 GAAGATGGTT
Statistics
Matches: 108, Mismatches: 24, Indels: 5
0.79 0.18 0.04
Matches are distributed among these distances:
31 35 0.32
32 72 0.67
33 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.31, T:0.31
Consensus pattern (31 bp):
TGGGCTTTAGAGGGGTTGCCACCAACTTGTG
Found at i:1682800 original size:28 final size:27
Alignment explanation
Indices: 1682731--1682800 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 27
1682721 TATAGCAAGT
1682731 GTCACTGA-TTGTGGACTTCGAAAAGAG
1 GTCACTGACTTGTGGACTTCG-AAAGAG
*
1682758 GTCACTAACTTGTGGACTTCG-AAGAG
1 GTCACTGACTTGTGGACTTCGAAAGAG
*
1682784 GTGCCACTGACTAGTGG
1 GT--CACTGACTTGTGG
1682801 GCTTTGAGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
26 7 0.19
27 7 0.19
28 23 0.62
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.26
Consensus pattern (27 bp):
GTCACTGACTTGTGGACTTCGAAAGAG
Found at i:1683274 original size:28 final size:28
Alignment explanation
Indices: 1683234--1683300 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
1683224 GGACCTTTTT
* *
1683234 TTCATTAGGGATTGTAGGCTAT-TCAAAC
1 TTCACTAGGGATTGCAGGCTATAT-AAAC
1683262 TTCACTAGGGATTGCAGGCTATATAAAC
1 TTCACTAGGGATTGCAGGCTATATAAAC
**
1683290 TTTTCTAGGGA
1 TTCACTAGGGA
1683301 AAGGACATAG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 33 0.97
29 1 0.03
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.34
Consensus pattern (28 bp):
TTCACTAGGGATTGCAGGCTATATAAAC
Found at i:1685768 original size:13 final size:13
Alignment explanation
Indices: 1685750--1685775 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1685740 TACACCAAGT
1685750 ATGTATCGATACA
1 ATGTATCGATACA
1685763 ATGTATCGATACA
1 ATGTATCGATACA
1685776 CCAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1685794 original size:34 final size:32
Alignment explanation
Indices: 1685732--1685796 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
1685722 TAGCCAAACT
**
1685732 TGTATCGATACACCAAGTATGTATCGATACAA
1 TGTATCGATACACCAAAAATGTATCGATACAA
1685764 TGTATCGATACACCAAAAAATTGTATCGATACA
1 TGTATCGATACACC-AAAAA-TGTATCGATACA
1685797 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 14 0.48
33 3 0.10
34 12 0.41
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACCAAAAATGTATCGATACAA
Found at i:1691950 original size:20 final size:20
Alignment explanation
Indices: 1691907--1691952 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1691897 AAATCTTTTG
1691907 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
1691928 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
1691948 CAAAA
1 CAAAA
1691953 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:1693804 original size:155 final size:155
Alignment explanation
Indices: 1693541--1693862 Score: 583
Period size: 155 Copynumber: 2.1 Consensus size: 155
1693531 TATGTGCAAA
* *
1693541 TAAATTTTTGATATGTGTGTAAATTACCTTATTAAGGGGGAGATTTTTTAATAAAAGGAGAGAAT
1 TAAAATTTTGATATGTGTGTAAATTACCTTATTAAAGGGGAGATTTTTTAATAAAAGGAGAGAAT
1693606 GCGTAAATTTGCTAAAATTACCTCATTAAAGGGGAGAATGTACGAACTTATTAAAATTATTTTGT
66 GCGTAAATTTGCTAAAATTACCTCATTAAAGGGGAGAATGTACGAACTTATTAAAATTATTTTGT
*
1693671 TTAAGGGAGAAAGAAAAGAAAAATG
131 TTAAGGGAGAAAAAAAAGAAAAATG
1693696 TAAAATTTTGATATGTGTGTAAATTACCTTATTAAAGGGGAGATTTTTTAATAAAATGG-GAGAA
1 TAAAATTTTGATATGTGTGTAAATTACCTTATTAAAGGGGAGATTTTTTAATAAAA-GGAGAGAA
* *
1693760 TGCGTAAATTTGCTAAAATTACCTCATTAAGGGGGAGAATGTACGAACTTGTTAAAATTATTTTG
65 TGCGTAAATTTGCTAAAATTACCTCATTAAAGGGGAGAATGTACGAACTTATTAAAATTATTTTG
1693825 TTTAAGGGAGAAAAAAAAGAAAAATG
130 TTTAAGGGAGAAAAAAAAGAAAAATG
1693851 TAAAATTTTGAT
1 TAAAATTTTGAT
1693863 TTTTGAAATC
Statistics
Matches: 161, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
155 159 0.99
156 2 0.01
ACGTcount: A:0.41, C:0.06, G:0.20, T:0.34
Consensus pattern (155 bp):
TAAAATTTTGATATGTGTGTAAATTACCTTATTAAAGGGGAGATTTTTTAATAAAAGGAGAGAAT
GCGTAAATTTGCTAAAATTACCTCATTAAAGGGGAGAATGTACGAACTTATTAAAATTATTTTGT
TTAAGGGAGAAAAAAAAGAAAAATG
Found at i:1703464 original size:20 final size:20
Alignment explanation
Indices: 1703422--1703476 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
1703412 AAATTCCCAG
**
1703422 ATGTATCGATACAAAGATCA
1 ATGTATCGATACATTGATCA
1703442 ATGTATCGATACATTGAGT-A
1 ATGTATCGATACATTGA-TCA
*
1703462 ATGTATTGATACATT
1 ATGTATCGATACATT
1703477 TCCTTGGTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACATTGATCA
Found at i:1706415 original size:11 final size:11
Alignment explanation
Indices: 1706399--1706424 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1706389 TTCCCCTCTC
1706399 TAACATGAAGA
1 TAACATGAAGA
1706410 TAACATGAAGA
1 TAACATGAAGA
1706421 TAAC
1 TAAC
1706425 CCGATGAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.12, G:0.15, T:0.19
Consensus pattern (11 bp):
TAACATGAAGA
Found at i:1712277 original size:12 final size:13
Alignment explanation
Indices: 1712252--1712280 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1712242 GGGAATGGAT
1712252 TTTTTGTTGAGTG
1 TTTTTGTTGAGTG
1712265 TTTTTGTTG-GTG
1 TTTTTGTTGAGTG
1712277 TTTT
1 TTTT
1712281 GGCTAAGATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.03, C:0.00, G:0.28, T:0.69
Consensus pattern (13 bp):
TTTTTGTTGAGTG
Found at i:1717639 original size:13 final size:13
Alignment explanation
Indices: 1717623--1717652 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1717613 ATACATTGTT
1717623 CATTGTATCGATA
1 CATTGTATCGATA
1717636 CATTGTATCGATA
1 CATTGTATCGATA
1717649 CATT
1 CATT
1717653 TTTTGGGTTT
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:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:1717695 original size:20 final size:19
Alignment explanation
Indices: 1717670--1717743 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 19
1717660 TTTACCCAGA
*
1717670 TGTATCGATAAATTTTGCAT
1 TGTATCGATACATTTT-CAT
*
1717690 TGTATCGATACATTGCTCAT
1 TGTATCGATACATT-TTCAT
* *
1717710 TATATCGATACATTTTACAA
1 TGTATCGATACATTTT-CAT
1717730 TGTATCGATACATT
1 TGTATCGATACATT
1717744 CAAGCATTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
19 1 0.02
20 44 0.96
21 1 0.02
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (19 bp):
TGTATCGATACATTTTCAT
Found at i:1720338 original size:28 final size:26
Alignment explanation
Indices: 1720303--1720373 Score: 72
Period size: 28 Copynumber: 2.6 Consensus size: 26
1720293 TTTATAATCA
1720303 GGGG-TACTCCAACCCCGTTATGTCATC
1 GGGGATACTCCAACCCCGTTATGTC--C
* * *
1720330 GGGGATACTCTAATCCCGTTATTTCC
1 GGGGATACTCCAACCCCGTTATGTCC
1720356 GAAGGGATACTCCAACCC
1 G--GGGATACTCCAACCC
1720374 TGATTTTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
26 2 0.06
27 4 0.11
28 30 0.83
ACGTcount: A:0.23, C:0.31, G:0.21, T:0.25
Consensus pattern (26 bp):
GGGGATACTCCAACCCCGTTATGTCC
Found at i:1720419 original size:107 final size:105
Alignment explanation
Indices: 1720146--1720422 Score: 277
Period size: 107 Copynumber: 2.6 Consensus size: 105
1720136 CCACAATCGA
*
1720146 GGATACTCCAACTCCGATTTTATTT-TCAAAATACCAATTTTTTACAATTGGGGATACTCAAACC
1 GGATACTCCAAC-CCGATTTTATTTCT-AAAATACCAATTTTTTACAATT-GGGATACTCCAACC
* ** *
1720210 CCGTTATTTCATCGAAAATACTCCAACCCCATTATTTTTGAGG
63 CCGTTATGTCATCGAAAATACTCCAACCCCATTATTTCCGAAG
* * * * *** * * *
1720253 GGATACTCTAACCCCAGCTTTATATCTAAAATATTGATTTTTTATAATCAGGGGTACTCCAACCC
1 GGATACTCCAACCCGA-TTTTATTTCTAAAATACCAATTTTTTACAAT-TGGGATACTCCAACCC
*** * * *
1720318 CGTTATGTCATCGGGGATACTCTAATCCCGTTATTTCCGAAG
64 CGTTATGTCATCGAAAATACTCCAACCCCATTATTTCCGAAG
* *
1720360 GGATACTCCAACCCTGATTTTATTTCTTAAATACCAATTTTTCACAATTGGAGATACTCCAAC
1 GGATACTCCAACCC-GATTTTATTTCTAAAATACCAATTTTTTACAATTGG-GATACTCCAAC
1720423 TCCGATTTTA
Statistics
Matches: 132, Mismatches: 33, Indels: 10
0.75 0.19 0.06
Matches are distributed among these distances:
106 5 0.04
107 125 0.95
108 2 0.02
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (105 bp):
GGATACTCCAACCCGATTTTATTTCTAAAATACCAATTTTTTACAATTGGGATACTCCAACCCCG
TTATGTCATCGAAAATACTCCAACCCCATTATTTCCGAAG
Found at i:1720467 original size:51 final size:51
Alignment explanation
Indices: 1720358--1720475 Score: 127
Period size: 51 Copynumber: 2.3 Consensus size: 51
1720348 TTATTTCCGA
* *
1720358 AGGGATACTCCAAC-CCTGATTTTATTTCTTAAATACCAATTTTTCACAAT
1 AGGGATACTCCAACTCCTGATTTTATTTCTAAAACACCAATTTTTCACAAT
* *
1720408 TGGAGATACTCCAACTCC-GATTTTATTT-TCAAAACACCAA-TTTTCTATAAT
1 AGG-GATACTCCAACTCCTGATTTTATTTCT-AAAACACCAATTTTTC-ACAAT
*
1720459 CAGGGATACCCCAACTC
1 -AGGGATACTCCAACTC
1720476 TGTTATTTCC
Statistics
Matches: 57, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
50 8 0.14
51 45 0.79
52 4 0.07
ACGTcount: A:0.32, C:0.25, G:0.09, T:0.34
Consensus pattern (51 bp):
AGGGATACTCCAACTCCTGATTTTATTTCTAAAACACCAATTTTTCACAAT
Found at i:1720517 original size:79 final size:79
Alignment explanation
Indices: 1720412--1720640 Score: 280
Period size: 79 Copynumber: 2.9 Consensus size: 79
1720402 CACAATTGGA
* * * * *
1720412 GATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCAGGGATACCCCAACTCT
1 GATACTCCAACCCCGATTTTACTTTCAAAACACTAATTTTCTATAATCAGGGATACTCCAACCCT
1720477 GTTATTTCCGA-AGG
66 GTTATTTCCGAGA-G
* * * * *
1720491 GATACTCCAACCCCGATTTTAGTTTCAAAATACTTATTTTCTATAATCAGGGATATTCTAACCCT
1 GATACTCCAACCCCGATTTTACTTTCAAAACACTAATTTTCTATAATCAGGGATACTCCAACCCT
* * *
1720556 ATAATTTCTGAGAG
66 GTTATTTCCGAGAG
* * * * *
1720570 GATACTCCAACCTCGATTTTACTTCCAAAACACTAATTTTCCATAATCGGGGATACTCCAGCCCT
1 GATACTCCAACCCCGATTTTACTTTCAAAACACTAATTTTCTATAATCAGGGATACTCCAACCCT
1720635 GTTATT
66 GTTATT
1720641 ATCTCCAAAA
Statistics
Matches: 125, Mismatches: 24, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
79 124 0.99
80 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.34
Consensus pattern (79 bp):
GATACTCCAACCCCGATTTTACTTTCAAAACACTAATTTTCTATAATCAGGGATACTCCAACCCT
GTTATTTCCGAGAG
Found at i:1722704 original size:4 final size:4
Alignment explanation
Indices: 1722695--1722721 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1722685 TTTTGAGGTG
1722695 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1722722 GTTTGTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:1733047 original size:17 final size:17
Alignment explanation
Indices: 1733005--1733050 Score: 76
Period size: 16 Copynumber: 2.8 Consensus size: 17
1732995 CCACCTTTTT
*
1733005 AAAAAAAAACAAAAAAC
1 AAAAAAAAATAAAAAAC
1733022 -AAAAAAAATAAAAAAC
1 AAAAAAAAATAAAAAAC
1733038 AAAAAAAAATAAA
1 AAAAAAAAATAAA
1733051 GAAAAGAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 15 0.56
17 12 0.44
ACGTcount: A:0.89, C:0.07, G:0.00, T:0.04
Consensus pattern (17 bp):
AAAAAAAAATAAAAAAC
Found at i:1733055 original size:14 final size:13
Alignment explanation
Indices: 1733005--1733069 Score: 53
Period size: 12 Copynumber: 5.1 Consensus size: 13
1732995 CCACCTTTTT
*
1733005 AAAAAAAAACAAA
1 AAAAAAAAAGAAA
*
1733018 AAACAAAAA-AAA
1 AAAAAAAAAGAAA
* *
1733030 TAAAAAACA-AAA
1 AAAAAAAAAGAAA
*
1733042 AAAAATAAAGAAA
1 AAAAAAAAAGAAA
*
1733055 AGAAAGAAAAGAAA
1 A-AAAAAAAAGAAA
1733069 A
1 A
1733070 GAACCTACTT
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
12 18 0.44
13 12 0.29
14 11 0.27
ACGTcount: A:0.86, C:0.05, G:0.06, T:0.03
Consensus pattern (13 bp):
AAAAAAAAAGAAA
Found at i:1734203 original size:55 final size:55
Alignment explanation
Indices: 1734143--1734738 Score: 628
Period size: 55 Copynumber: 10.5 Consensus size: 55
1734133 TTCACCCTTT
* * *
1734143 AGTCCTCAAAGAGCAGAATGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTC
* *
1734198 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTTT
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA-CTTTTC
* * *
1734254 AGTCCTCAAAGAGCAGAATGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTC
* * *
1734309 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCATACAAGTTGGTGGCATTTTTTT
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA-CTTTTC
* * *
1734365 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACA-AAGGTTGGTGGCACTTTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAA-GTTGGTGGCACTTTTC
* * * * *
1734420 ACTCCTCAAAGAGCAAGACACCTTTTCCTTTTAAAGCCCATACAAGTTGGTGGC-TTTTTC
1 AGTCCTCAAAGAGCAGGACGCC-TTT-C----AAAGCCCACACAAGTTGGTGGCACTTTTC
* *
1734480 TAGTCCTCAAAGAGCAGGATGCATTTTCTTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 -AGTCCTCAAAGAGCAGGACGC-----C-TTTCAAAGCCCACACAAGTTGGTGGCACTTTT-C
*
1734542 AGTCCTCAAAGAGCAGGACGCC-TTCTAAAGCCCACATAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTC-AAAGCCCACACAAGTTGGTGGCACTTTT-C
* *
1734597 AGTCCTCAAAGAGTAGGACAG-CTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC
1 AGTCCTCAAAGAGCAGGAC-GCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTC
* * * * * *
1734652 TAGTCCTCAAAGAGCATGACACTTTTTCATTTCAAAGCCTACACGAGTTGGTGGCATTTTTT
1 -AGTCCTCAAAGAGCAGGACGC-----C-TTTCAAAGCCCACACAAGTTGGTGGCACTTTTC
*
1734714 AGCCCTCAAAGAGCAGGACGCCTTT
1 AGTCCTCAAAGAGCAGGACGCCTTT
1734739 TCCTTTTCTC
Statistics
Matches: 460, Mismatches: 51, Indels: 60
0.81 0.09 0.11
Matches are distributed among these distances:
54 2 0.00
55 194 0.42
56 125 0.27
60 4 0.01
61 99 0.22
62 31 0.07
66 5 0.01
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.27
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTC
Found at i:1734334 original size:111 final size:111
Alignment explanation
Indices: 1734140--1734739 Score: 687
Period size: 111 Copynumber: 5.3 Consensus size: 111
1734130 CCTTTCACCC
*
1734140 TTTAGTCCTCAAAGAGCAGAATGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTC
1 TTTAGTCCTCAAAGAGCAGAATGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTC
1734205 AAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTT
66 AAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTT
*
1734251 TTTAGTCCTCAAAGAGCAGAATGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTC
1 TTTAGTCCTCAAAGAGCAGAATGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTC
*
1734316 AAAGAGCAGGACGCCTTTCAAAGCCCATACAAGTTGGTGGCATTTT
66 AAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTT
* ** *
1734362 TTTAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACA-AAGGTTGGTGGCA-CTTTCCACTCC
1 TTTAGTCCTCAAAGAGCAGAATGCCTTTTAAAGCCCACACAA-GTTGGTGGCACCTTT-CAGTCC
* * *
1734425 TCAAAGAGCAAGACACCTTTTCCTTTTAAAGCCCATACAAGTTGGTGGC-TTTT
64 TCAAAGAGCAGGACGCC-TTT-C----AAAGCCCACACAAGTTGGTGGCATTTT
* * *
1734478 TCTAGTCCTCAAAGAGCAGGATGCATTTTCTTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 TTTAGTCCTCAAAGAGCAGAATGC-----C-TTTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
*
1734542 AGTCCTCAAAGAGCAGGACGCC-TTCTAAAGCCCACATAAGTTGGTGGCA-TTT
59 AGTCCTCAAAGAGCAGGACGCCTTTC-AAAGCCCACACAAGTTGGTGGCATTTT
** * *
1734594 TCCAGTCCTCAAAGAGTAGGACA-G-CTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTC
1 TTTAGTCCTCAAAGAGCA-GA-ATGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC-AGTC
* * * *
1734657 CTCAAAGAGCATGACACTTTTTCATTTCAAAGCCTACACGAGTTGGTGGCA-TTT
63 CTCAAAGAGCAGGACGC-----C-TTTCAAAGCCCACACAAGTTGGTGGCATTTT
* * *
1734711 TTTAGCCCTCAAAGAGCAGGACGCCTTTT
1 TTTAGTCCTCAAAGAGCAGAATGCCTTTT
1734740 CCTTTTCTCC
Statistics
Matches: 430, Mismatches: 30, Indels: 52
0.84 0.06 0.10
Matches are distributed among these distances:
110 34 0.08
111 199 0.46
112 3 0.01
113 1 0.00
115 1 0.00
116 68 0.16
117 66 0.15
118 4 0.01
119 1 0.00
120 2 0.00
121 1 0.00
122 48 0.11
123 2 0.00
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (111 bp):
TTTAGTCCTCAAAGAGCAGAATGCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTC
AAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTT
Found at i:1734574 original size:233 final size:229
Alignment explanation
Indices: 1734140--1734745 Score: 763
Period size: 233 Copynumber: 2.6 Consensus size: 229
1734130 CCTTTCACCC
* ** *
1734140 TTTAGTCCTCAAAGAGCAGAATGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCT
1 TTTAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTTCCAGTCCT
* *
1734204 CAAAGAGCAGGACGCC-TTT-C---AAAGCCCACACAAGTTGGTGGCATTTTTTTAGTCCTCAAA
65 CAAAGAGCAAGACACCTTTTCCTTTAAAGCCCACACAAGTTGGTGGCA-TTTTTTAGTCCTCAAA
* *
1734264 GAGCAGAATGC----CTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAG
129 GAGCAGGATGCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAG
*
1734325 GACGCCTTTCAAAGCCCATACAAGTTGGTGGCATTTT
194 GACGCCTTTCAAAGCCCACACAAGTTGGTGGCA-TTT
*
1734362 TTTAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACA-AAGGTTGGTGGCACTTTCCACTCCT
1 TTTAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAA-GTTGGTGGCACTTTCCAGTCCT
*
1734426 CAAAGAGCAAGACACCTTTTCCTTTTAAAGCCCATACAAGTTGGTGGC-TTTTTCTAGTCCTCAA
65 CAAAGAGCAAGACACCTTTTCC-TTTAAAGCCCACACAAGTTGGTGGCATTTTT-TAGTCCTCAA
*
1734490 AGAGCAGGATGCATTTTCTTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGA
128 AGAGCAGGATGC-TTTTC-TTTTAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGA
*
1734554 GCAGGACGCC-TTCTAAAGCCCACATAAGTTGGTGGCATTT
190 GCAGGACGCCTTTC-AAAGCCCACACAAGTTGGTGGCATTT
** * * *
1734594 TCCAGTCCTCAAAGAGTAGGACAGCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCT
1 TTTAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCAC-TTTCCAGTCCT
* * * * * *
1734659 CAAAGAGCATGACACTTTTTCATTTCAAAGCCTACACGAGTTGGTGGCATTTTTTAGCCCTCAAA
65 CAAAGAGCAAGACACCTTTTCCTTT-AAAGCCCACACAAGTTGGTGGCATTTTTTAGTCCTCAAA
*
1734724 GAGCAGGACGCCTTTTCCTTTT
129 GAGCAGGATG-CTTTT-CTTTT
1734746 CTCCTTTGTC
Statistics
Matches: 334, Mismatches: 27, Indels: 35
0.84 0.07 0.09
Matches are distributed among these distances:
221 6 0.02
222 65 0.19
223 3 0.01
224 1 0.00
226 5 0.01
227 21 0.06
228 21 0.06
232 59 0.18
233 146 0.44
234 7 0.02
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.28
Consensus pattern (229 bp):
TTTAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTC
AAAGAGCAAGACACCTTTTCCTTTAAAGCCCACACAAGTTGGTGGCATTTTTTAGTCCTCAAAGA
GCAGGATGCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGA
CGCCTTTCAAAGCCCACACAAGTTGGTGGCATTT
Found at i:1734768 original size:38 final size:39
Alignment explanation
Indices: 1734717--1734858 Score: 128
Period size: 42 Copynumber: 3.4 Consensus size: 39
1734707 ATTTTTTAGC
1734717 CCTCAAAGAGCAGGACGC-CTTTTCCTTTTCTCCTTTGT
1 CCTCAAAGAGCAGGACGCACTTTTCCTTTTCTCCTTTGT
* *
1734755 CCTCAAAGAGCAGGACACACTTCATTCCCTTCTTTTCCCTTTGGT
1 CCTCAAAGAGCAGGACGCACTT--TT-CCTT-TTCT-CCTTT-GT
* *
1734800 CCTCAAAGAGCAAGACGCACTTTATTTTCCTCTTTCT--TTTAT
1 CCTCAAAGAGCAGGACGCAC----TTTTCCT-TTTCTCCTTTGT
1734842 CCTCAAAGAGCAGGACG
1 CCTCAAAGAGCAGGACG
1734859 TATTTCGTTT
Statistics
Matches: 85, Mismatches: 7, Indels: 20
0.76 0.06 0.18
Matches are distributed among these distances:
38 17 0.20
39 3 0.04
41 2 0.02
42 21 0.25
43 6 0.07
44 5 0.06
45 20 0.24
46 6 0.07
47 3 0.04
49 2 0.02
ACGTcount: A:0.22, C:0.30, G:0.15, T:0.33
Consensus pattern (39 bp):
CCTCAAAGAGCAGGACGCACTTTTCCTTTTCTCCTTTGT
Found at i:1734834 original size:45 final size:44
Alignment explanation
Indices: 1734741--1734858 Score: 134
Period size: 45 Copynumber: 2.7 Consensus size: 44
1734731 ACGCCTTTTC
*
1734741 CTTTTCTCCTTTGTCCTCAAAGAGCAGGACACACTTCATTCCCTT
1 CTTTTC-CCTTTGTCCTCAAAGAGCAGGACGCACTTCATTCCCTT
* * *
1734786 CTTTTCCCTTTGGTCCTCAAAGAGCAAGACGCACTTTATTTTCC-T
1 CTTTTCCCTTT-GTCCTCAAAGAGCAGGACGCACTTCA-TTCCCTT
* *
1734831 C-TTT-CTTTTATCCTCAAAGAGCAGGACG
1 CTTTTCCCTTTGTCCTCAAAGAGCAGGACG
1734859 TATTTCGTTT
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
42 17 0.27
43 4 0.06
44 8 0.12
45 31 0.48
46 4 0.06
ACGTcount: A:0.21, C:0.30, G:0.14, T:0.36
Consensus pattern (44 bp):
CTTTTCCCTTTGTCCTCAAAGAGCAGGACGCACTTCATTCCCTT
Found at i:1735154 original size:33 final size:33
Alignment explanation
Indices: 1735110--1735173 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 33
1735100 TTTCACAATT
1735110 TGTATCAATACATTGTT-CATTGTATCGATACGA
1 TGTATCAATACATT-TTGCATTGTATCGATACGA
*
1735143 TGTATCGATACATTTTGCATTGTATCGATAC
1 TGTATCAATACATTTTGCATTGTATCGATAC
1735174 ATTTACATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 2 0.07
33 27 0.93
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.41
Consensus pattern (33 bp):
TGTATCAATACATTTTGCATTGTATCGATACGA
Found at i:1735202 original size:13 final size:13
Alignment explanation
Indices: 1735127--1735212 Score: 66
Period size: 13 Copynumber: 7.1 Consensus size: 13
1735117 ATACATTGTT
1735127 CATTGTATCGATA
1 CATTGTATCGATA
1735140 CGA-TGTATCGATA
1 C-ATTGTATCGATA
1735153 CATT-T-T-G---
1 CATTGTATCGATA
1735160 CATTGTATCGATA
1 CATTGTATCGATA
1735173 CATT-TA-C-ATTA
1 CATTGTATCGA-TA
1735184 CTCATTGTATCGATA
1 --CATTGTATCGATA
1735199 CATTGTATCGATA
1 CATTGTATCGATA
1735212 C
1 C
1735213 GTTGCTTATT
Statistics
Matches: 59, Mismatches: 0, Indels: 28
0.68 0.00 0.32
Matches are distributed among these distances:
7 4 0.07
8 1 0.02
9 1 0.02
10 3 0.05
11 4 0.07
12 4 0.07
13 35 0.59
14 3 0.05
15 3 0.05
16 1 0.02
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:1737887 original size:107 final size:106
Alignment explanation
Indices: 1737687--1737923 Score: 273
Period size: 107 Copynumber: 2.2 Consensus size: 106
1737677 TCAAAACACT
* ** ** *
1737687 AATTTTTCACAATTGAAGATACTGAAACCCCGTTATTTCATCGGGATACTACAACCTCGTTATTT
1 AATTTTTCACAATCGGGGATACTCTAACCCCGTTATGTCATCGGGATACTACAACCTCGTTATTT
* * **
1737752 TCGAGGGGATACTCTAACCACGGCTTTATATCTAAAATATT
66 TCGAGGGGATACTCCAACCACGACTTTATATCTAAAATACC
* * *
1737793 AATTTTTCATAATCGGGGGTACTCTAACCCTGTTATGTCATCGGGAATACT-CTAATCCT-GTTA
1 AATTTTTCACAATCGGGGATACTCTAACCCCGTTATGTCATCGGG-ATACTAC-AA-CCTCGTTA
* *
1737856 TTTTCGAGGGGATACTCCAACC-CTGATTTTATTTCTAAAATACC
63 TTTTCGAGGGGATACTCCAACCAC-GACTTTATATCTAAAATACC
*
1737900 AATTTTTCACAATTGGGGATACTC
1 AATTTTTCACAATCGGGGATACTC
1737924 CAACTCCGAT
Statistics
Matches: 109, Mismatches: 18, Indels: 7
0.81 0.13 0.05
Matches are distributed among these distances:
106 38 0.35
107 68 0.62
108 3 0.03
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (106 bp):
AATTTTTCACAATCGGGGATACTCTAACCCCGTTATGTCATCGGGATACTACAACCTCGTTATTT
TCGAGGGGATACTCCAACCACGACTTTATATCTAAAATACC
Found at i:1737935 original size:51 final size:51
Alignment explanation
Indices: 1737863--1737982 Score: 163
Period size: 51 Copynumber: 2.4 Consensus size: 51
1737853 TTATTTTCGA
* *
1737863 GGGGATACTCCAACCCTGATTTTA-TTTCTAAAATACCAATTTTTCACAATT
1 GGGGATACTCCAACCCTGATTTTATTTTC-AAAACACCAATTTTTCACAATC
* *
1737914 GGGGATACTCCAACTCC-GATTTTATTTTCAAAACACCAATTTTTTATAATC
1 GGGGATACTCCAAC-CCTGATTTTATTTTCAAAACACCAATTTTTCACAATC
*
1737965 AGGGATACTCCAACCCTG
1 GGGGATACTCCAACCCTG
1737983 TTATTTTCGA
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
50 2 0.03
51 53 0.87
52 6 0.10
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.34
Consensus pattern (51 bp):
GGGGATACTCCAACCCTGATTTTATTTTCAAAACACCAATTTTTCACAATC
Found at i:1737986 original size:26 final size:28
Alignment explanation
Indices: 1737957--1738008 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
1737947 CACCAATTTT
1737957 TTATAATC-A-GGGATACTCCAACCCTG
1 TTATAATCGAGGGGATACTCCAACCCTG
**
1737983 TTATTTTCGAGGGGATACTCCAACCC
1 TTATAATCGAGGGGATACTCCAACCC
1738009 CGATTTTAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 6 0.27
27 1 0.05
28 15 0.68
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (28 bp):
TTATAATCGAGGGGATACTCCAACCCTG
Found at i:1738145 original size:79 final size:79
Alignment explanation
Indices: 1737914--1738134 Score: 343
Period size: 79 Copynumber: 2.8 Consensus size: 79
1737904 TTTCACAATT
* * *
1737914 GGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTTTATAATCAGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTACTTTCAAAACACCAATTTTCTATAATCAGGGATACTCCAAC
1737979 CCTGTTATTTTCGA
66 CCTGTTATTTTCGA
* * *
1737993 GGGGATACTCCAACCCCGATTTTAGTTTCAAAATACCAATTTTCTATAATCAGGGATATTCCAAC
1 GGGGATACTCCAACCCCGATTTTACTTTCAAAACACCAATTTTCTATAATCAGGGATACTCCAAC
*
1738058 CCTGTTATTTTTGA
66 CCTGTTATTTTCGA
* * * *
1738072 GGGGATACTCCAACCCCGATTTTACTTCCAAAACACCGATTTTCCATAATCGGGGATACTCCA
1 GGGGATACTCCAACCCCGATTTTACTTTCAAAACACCAATTTTCTATAATCAGGGATACTCCA
1738135 GCCCCATTAT
Statistics
Matches: 129, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
79 129 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGATTTTACTTTCAAAACACCAATTTTCTATAATCAGGGATACTCCAAC
CCTGTTATTTTCGA
Found at i:1739484 original size:19 final size:20
Alignment explanation
Indices: 1739447--1739484 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1739437 TCCCATAGCT
1739447 ATGTATCGATACAATTCATA
1 ATGTATCGATACAATTCATA
1739467 ATGTATCGATAC-ATTCAT
1 ATGTATCGATACAATTCAT
1739485 TTGAAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACAATTCATA
Found at i:1746153 original size:13 final size:13
Alignment explanation
Indices: 1746135--1746159 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1746125 CATAAAATGT
1746135 TGTATCGATACAA
1 TGTATCGATACAA
1746148 TGTATCGATACA
1 TGTATCGATACA
1746160 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1746157 original size:33 final size:33
Alignment explanation
Indices: 1746115--1746179 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
1746105 TTCAACAATT
1746115 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1746148 TGTATCGATACATATTTTTTTGTATCGATACA
1 TGTATCGATACATAAAATGTTGTATCGATACA
1746180 TTTTAAGCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1746240 original size:13 final size:13
Alignment explanation
Indices: 1746222--1746249 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1746212 ATTACTCAAA
1746222 TGTATCGATACAT
1 TGTATCGATACAT
1746235 TGTATCGATACAT
1 TGTATCGATACAT
1746248 TG
1 TG
1746250 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1746300 original size:52 final size:52
Alignment explanation
Indices: 1746255--1746379 Score: 205
Period size: 52 Copynumber: 2.4 Consensus size: 52
1746245 CATTGATCTT
1746255 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGACACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGACACATTATAAAA
* * * *
1746307 TGTATCGATACATGCAGGCAAATTTGCCCAGAAGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGACACATTATAAAA
*
1746359 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
1746380 CTTTTCATAT
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 68 1.00
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGACACATTATAAAA
Found at i:1751342 original size:19 final size:19
Alignment explanation
Indices: 1751297--1751350 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
1751287 ACTGCCAGTT
1751297 TCATGTATCGATACAATTG
1 TCATGTATCGATACAATTG
*
1751316 TCCATGTATCGATATAA-TG
1 T-CATGTATCGATACAATTG
1751335 ATCATGTATCGATACA
1 -TCATGTATCGATACA
1751351 TCTGGGTATG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (19 bp):
TCATGTATCGATACAATTG
Found at i:1755329 original size:15 final size:15
Alignment explanation
Indices: 1755309--1755341 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1755299 TCATCGTGTT
1755309 TATCATGATTACAAA
1 TATCATGATTACAAA
*
1755324 TATCATGATTATAAA
1 TATCATGATTACAAA
1755339 TAT
1 TAT
1755342 AACTGATGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.39
Consensus pattern (15 bp):
TATCATGATTACAAA
Found at i:1756494 original size:13 final size:13
Alignment explanation
Indices: 1756476--1756506 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1756466 TTATTTAAAC
1756476 CAAAAAAAAAAAA
1 CAAAAAAAAAAAA
*
1756489 CAAAAAACAAAAA
1 CAAAAAAAAAAAA
1756502 CAAAA
1 CAAAA
1756507 CAAAGAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (13 bp):
CAAAAAAAAAAAA
Found at i:1757421 original size:2 final size:2
Alignment explanation
Indices: 1757348--1757401 Score: 83
Period size: 2 Copynumber: 27.0 Consensus size: 2
1757338 AATATCTATG
*
1757348 TA TA TA TA TA TA -A TCA TA TT TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
1757390 TA TA TA TA TA TA
1 TA TA TA TA TA TA
1757402 CCCCTGCATA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
1 1 0.02
2 45 0.94
3 2 0.04
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1757432 original size:22 final size:21
Alignment explanation
Indices: 1757348--1757425 Score: 79
Period size: 24 Copynumber: 3.6 Consensus size: 21
1757338 AATATCTATG
1757348 TATATATATATA-ATCATATTTA
1 TATATATATATACATCATA--TA
*
1757370 TATATATATATATAT-ATATA
1 TATATATATATACATCATATA
*
1757390 TATATATATATACCCCTGCATATA
1 TATATATATATA--CAT-CATATA
1757414 TATATATATATA
1 TATATATATATA
1757426 ATAGCATGAT
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
20 14 0.29
22 16 0.33
23 2 0.04
24 17 0.35
ACGTcount: A:0.45, C:0.08, G:0.01, T:0.46
Consensus pattern (21 bp):
TATATATATATACATCATATA
Found at i:1757840 original size:22 final size:22
Alignment explanation
Indices: 1757815--1757885 Score: 83
Period size: 22 Copynumber: 3.3 Consensus size: 22
1757805 TAATTAATTC
*
1757815 AATTTAATTTTAAATATTTATA
1 AATTAAATTTTAAATATTTATA
*
1757837 AATTAAATTTAAAATTATTTA-A
1 AATTAAATTTTAAA-TATTTATA
* *
1757859 AATTAAATATTAAATAATT-TA
1 AATTAAATTTTAAATATTTATA
1757880 AATTAA
1 AATTAA
1757886 TTAAATTTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
21 11 0.26
22 25 0.60
23 6 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
AATTAAATTTTAAATATTTATA
Found at i:1757870 original size:17 final size:16
Alignment explanation
Indices: 1757839--1757914 Score: 57
Period size: 16 Copynumber: 4.8 Consensus size: 16
1757829 TATTTATAAA
*
1757839 TTAAATTTAAAATTAT
1 TTAAAATTAAAATTAT
1757855 TTAAAATT-AAA-TAT
1 TTAAAATTAAAATTAT
* * *
1757869 TAAATAATTTAAATTAA
1 TTAA-AATTAAAATTAT
* *
1757886 TTAAATTTAAAAATAT
1 TTAAAATTAAAATTAT
* *
1757902 CTAAACTTAAAAT
1 TTAAAATTAAAAT
1757915 AAAATAATTC
Statistics
Matches: 46, Mismatches: 11, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
14 6 0.13
15 7 0.15
16 28 0.61
17 5 0.11
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
TTAAAATTAAAATTAT
Found at i:1757894 original size:37 final size:36
Alignment explanation
Indices: 1757797--1757897 Score: 89
Period size: 37 Copynumber: 2.7 Consensus size: 36
1757787 AATTTTAATT
* ** *
1757797 TAATTATATAATTAATTCAATTTAATTTTAAATATTTA
1 TAATT-TA-AATTAATTAAATTTAAAATTAAATATTAA
*
1757835 TAAATTAAATTTAA--AATTATTTAAAATTAAATATTAAA
1 TAATTTAAA-TTAATTAA--ATTTAAAATTAAATATT-AA
1757873 TAATTTAAATTAATTAAATTTAAAA
1 TAATTTAAATTAATTAAATTTAAAA
1757898 ATATCTAAAC
Statistics
Matches: 51, Mismatches: 6, Indels: 13
0.73 0.09 0.19
Matches are distributed among these distances:
35 1 0.02
36 2 0.04
37 33 0.65
38 13 0.25
39 2 0.04
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (36 bp):
TAATTTAAATTAATTAAATTTAAAATTAAATATTAA
Found at i:1757979 original size:16 final size:16
Alignment explanation
Indices: 1757927--1757979 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
1757917 AATAATTCTT
* * *
1757927 AAAATAAATCAAATTA
1 AAAATAATTTAAATTC
**
1757943 AAAATAATTTAAACCC
1 AAAATAATTTAAATTC
*
1757959 CAAATAATTTAAATTC
1 AAAATAATTTAAATTC
1757975 AAAAT
1 AAAAT
1757980 CAAACTCCTT
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.28
Consensus pattern (16 bp):
AAAATAATTTAAATTC
Found at i:1758722 original size:2 final size:2
Alignment explanation
Indices: 1758715--1758744 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1758705 ATTGAGTTGA
1758715 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
1758745 GAATTTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1759557 original size:22 final size:22
Alignment explanation
Indices: 1759511--1759556 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
1759501 AAGAGTTTTG
*
1759511 AATGAACTTTAAATAATTATAA
1 AATGAACTTTAAACAATTATAA
*
1759533 AATGAACTTTAAACGATTCATAA
1 AATGAACTTTAAACAATT-ATAA
1759556 A
1 A
1759557 TAAACATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.52, C:0.09, G:0.07, T:0.33
Consensus pattern (22 bp):
AATGAACTTTAAACAATTATAA
Found at i:1759874 original size:55 final size:55
Alignment explanation
Indices: 1759808--1759920 Score: 217
Period size: 55 Copynumber: 2.1 Consensus size: 55
1759798 CAACATGGTG
1759808 CACATCTCCATAGAATCATTTTTGTGGCACATAATCTTAGCAAGCCTATTCAAAC
1 CACATCTCCATAGAATCATTTTTGTGGCACATAATCTTAGCAAGCCTATTCAAAC
*
1759863 CACATCTCCATAGAATCATTTTTGTGGCACATAATCTTAGCAAGCCTGTTCAAAC
1 CACATCTCCATAGAATCATTTTTGTGGCACATAATCTTAGCAAGCCTATTCAAAC
1759918 CAC
1 CAC
1759921 CTTACTTATT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.32, C:0.27, G:0.12, T:0.30
Consensus pattern (55 bp):
CACATCTCCATAGAATCATTTTTGTGGCACATAATCTTAGCAAGCCTATTCAAAC
Found at i:1760636 original size:2 final size:2
Alignment explanation
Indices: 1760629--1760656 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1760619 GAATAATACA
1760629 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
1760657 CCCTTTACGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1761422 original size:72 final size:72
Alignment explanation
Indices: 1761332--1761473 Score: 266
Period size: 72 Copynumber: 2.0 Consensus size: 72
1761322 AATGTAGAAC
*
1761332 GCAGGGCAGAAAAGATTTCCCTAGTTCCAACAGAATGGCCAAAGATGGTACCTGTCTTCCATGCA
1 GCAGGGCAGAAAAGATTTCCCTAGTTCCAACAGAATGGCCAAAGATGGTACCTGGCTTCCATGCA
1761397 AAGGAAT
66 AAGGAAT
*
1761404 GCAGGGCAGAAAAGATTTCCCTAGTTCCAACAGAATGGCCAAAGATGTTACCTGGCTTCCATGCA
1 GCAGGGCAGAAAAGATTTCCCTAGTTCCAACAGAATGGCCAAAGATGGTACCTGGCTTCCATGCA
1761469 AAGGA
66 AAGGA
1761474 GATTATCATG
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 68 1.00
ACGTcount: A:0.33, C:0.23, G:0.24, T:0.20
Consensus pattern (72 bp):
GCAGGGCAGAAAAGATTTCCCTAGTTCCAACAGAATGGCCAAAGATGGTACCTGGCTTCCATGCA
AAGGAAT
Found at i:1767996 original size:2 final size:2
Alignment explanation
Indices: 1767984--1768054 Score: 85
Period size: 2 Copynumber: 36.5 Consensus size: 2
1767974 AACAACACGG
* *
1767984 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA AA CTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
*
1768026 -A CA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1768055 GTGTGTGTAA
Statistics
Matches: 61, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
1 3 0.05
2 57 0.93
3 1 0.02
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1768118 original size:2 final size:2
Alignment explanation
Indices: 1768111--1768172 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
1768101 CGTCATTTTC
1768111 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
1768153 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
1768173 CCAATATGAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1768265 original size:10 final size:8
Alignment explanation
Indices: 1768111--1768384 Score: 91
Period size: 8 Copynumber: 32.9 Consensus size: 8
1768101 CGTCATTTTC
*
1768111 ATATATAT
1 ATATATAA
*
1768119 ATATATAT
1 ATATATAA
*
1768127 ATATATAT
1 ATATATAA
*
1768135 ATATATAT
1 ATATATAA
*
1768143 ATATATAT
1 ATATATAA
*
1768151 ATATATAT
1 ATATATAA
*
1768159 ATATATAT
1 ATATATAA
*
1768167 ATATATCCA
1 ATATAT-AA
1768176 ATATGATATA
1 ATAT-ATA-A
*
1768186 AT-TAT-G
1 ATATATAA
1768192 ATATATAA
1 ATATATAA
1768200 A-A-ATAA
1 ATATATAA
* * *
1768206 TTAAATTA
1 ATATATAA
* *
1768214 TTTTATAA
1 ATATATAA
* *
1768222 AAAAATAA
1 ATATATAA
1768230 A-ATA-AA
1 ATATATAA
1768236 TATGATATAA
1 -AT-ATATAA
1768246 ATATATAA
1 ATATATAA
1768254 ATATATCAA
1 ATATAT-AA
* *
1768263 A-ATTTAT
1 ATATATAA
1768270 ATATTATAA
1 ATA-TATAA
*
1768279 AT-TATTA
1 ATATATAA
*
1768286 ATATTTTAAA
1 ATA-TAT-AA
1768296 ATTTATATAA
1 A--TATATAA
1768306 ATATA-AA
1 ATATATAA
1768313 ATATTATAA
1 ATA-TATAA
1768322 ATATAATTATA
1 ATAT-A-TA-A
1768333 ATATAATAAA
1 ATAT-AT-AA
1768343 ATATATAA
1 ATATATAA
1768351 ATAAAATATAA
1 AT---ATATAA
*
1768362 ATACATAA
1 ATATATAA
1768370 AT-TATTAA
1 ATATA-TAA
*
1768378 ATTTATA
1 ATATATA
1768385 TATAATTTTT
Statistics
Matches: 211, Mismatches: 25, Indels: 60
0.71 0.08 0.20
Matches are distributed among these distances:
6 8 0.04
7 22 0.10
8 111 0.53
9 30 0.14
10 20 0.09
11 18 0.09
12 2 0.01
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (8 bp):
ATATATAA
Found at i:1768270 original size:18 final size:17
Alignment explanation
Indices: 1768231--1768326 Score: 74
Period size: 18 Copynumber: 5.5 Consensus size: 17
1768221 AAAAAATAAA
*
1768231 ATAAATATGATATAAATAT
1 ATAAATAT-ATA-AAATTT
1768250 ATAAATATATCAAAATTT
1 ATAAATATAT-AAAATTT
*
1768268 ATATAT-TAT-AAA-TT
1 ATAAATATATAAAATTT
* *
1768282 ATTAATATTTTAAAATTT
1 ATAAATA-TATAAAATTT
1768300 ATATAA-ATATAAAATATT
1 ATA-AATATATAAAAT-TT
1768318 ATAAATATA
1 ATAAATATA
1768327 ATTATAATAT
Statistics
Matches: 62, Mismatches: 7, Indels: 17
0.72 0.08 0.20
Matches are distributed among these distances:
14 6 0.10
15 3 0.05
16 2 0.03
17 15 0.24
18 25 0.40
19 11 0.18
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (17 bp):
ATAAATATATAAAATTT
Found at i:1768322 original size:27 final size:28
Alignment explanation
Indices: 1768285--1768386 Score: 72
Period size: 27 Copynumber: 3.8 Consensus size: 28
1768275 ATAAATTATT
*
1768285 AATATTTTAAAAT-TTATATAAATATAA
1 AATATTATAAAATATTATATAAATATAA
*
1768312 AATATTATAAATATAATTATA-ATATAATAA
1 AATATTATAAA-AT-ATTATATAAAT-ATAA
** * *
1768342 AATA-TAT-AAATAAAATATAAATACAT
1 AATATTATAAAATATTATATAAATATAA
*
1768368 AA-ATTATTAAAT-TTATATA
1 AATATTATAAAATATTATATA
1768387 TAATTTTTTT
Statistics
Matches: 59, Mismatches: 9, Indels: 15
0.71 0.11 0.18
Matches are distributed among these distances:
25 1 0.02
26 16 0.27
27 19 0.32
28 4 0.07
29 6 0.10
30 13 0.22
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (28 bp):
AATATTATAAAATATTATATAAATATAA
Found at i:1768364 original size:29 final size:27
Alignment explanation
Indices: 1768300--1768364 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 27
1768290 TTTAAAATTT
* *
1768300 ATATAAATATAAAATATTATAAATATA
1 ATATAAATATAAAAAATTATAAATAAA
1768327 AT-TATAATATAATAAAATATATAAATAAA
1 ATATA-AATATAA-AAAAT-TATAAATAAA
1768356 ATATAAATA
1 ATATAAATA
1768365 CATAAATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 2 0.06
27 9 0.28
28 4 0.12
29 15 0.47
30 2 0.06
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (27 bp):
ATATAAATATAAAAAATTATAAATAAA
Found at i:1768373 original size:43 final size:45
Alignment explanation
Indices: 1768275--1768374 Score: 107
Period size: 43 Copynumber: 2.2 Consensus size: 45
1768265 TTTATATATT
** *
1768275 ATAAATTATTAATATTTTAAAATTTATATAAATATAAAATATTATAA
1 ATAAATTA-TAATATAATAAAA-TTATATAAATATAAAATATAATAA
*
1768322 ATATAATTATAATATAATAAAA-TATAT-AA-ATAAAATATAAATAC
1 ATA-AATTATAATATAATAAAATTATATAAATATAAAATAT-AATAA
1768366 ATAAATTAT
1 ATAAATTAT
1768375 TAAATTTATA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
43 15 0.32
44 8 0.17
45 5 0.11
47 14 0.30
48 5 0.11
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (45 bp):
ATAAATTATAATATAATAAAATTATATAAATATAAAATATAATAA
Found at i:1769395 original size:19 final size:19
Alignment explanation
Indices: 1769355--1769391 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1769345 ATGTTTAAAA
1769355 AAATTTAAATAAAAATATT
1 AAATTTAAATAAAAATATT
*
1769374 AAATTTAAA-AAATATATT
1 AAATTTAAATAAAAATATT
1769392 TAAAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATTTAAATAAAAATATT
Found at i:1769840 original size:2 final size:2
Alignment explanation
Indices: 1769835--1769864 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1769825 GCATACACAC
1769835 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
1769865 CTGTGTGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1770065 original size:3 final size:3
Alignment explanation
Indices: 1770057--1770105 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
1770047 ATTAGTTAAT
1770057 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1770105 T
1 T
1770106 CTAAGACAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1770686 original size:19 final size:19
Alignment explanation
Indices: 1770627--1770680 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
1770617 ATATTTATGG
1770627 TATTATATATAA-AT-TTTA
1 TATTATAT-TAATATATTTA
*
1770645 -A-TATATTTATATATTTA
1 TATTATATTAATATATTTA
1770662 TATTATATTAATATTATTT
1 TATTATATTAATA-TATTT
1770681 TTTTATGTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
15 2 0.07
16 7 0.24
17 5 0.17
18 1 0.03
19 9 0.31
20 5 0.17
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TATTATATTAATATATTTA
Found at i:1771626 original size:29 final size:29
Alignment explanation
Indices: 1771593--1771652 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
1771583 ATTATTGATT
**
1771593 AAATTTAAAATTTTAT-TTAATATTTAAAA
1 AAATTTAAAATTAAATATTAA-ATTTAAAA
1771622 AAATTTAAAATTAAATATTAAATTTAAAA
1 AAATTTAAAATTAAATATTAAATTTAAAA
1771651 AA
1 AA
1771653 TAAATTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 24 0.86
30 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (29 bp):
AAATTTAAAATTAAATATTAAATTTAAAA
Found at i:1771984 original size:22 final size:21
Alignment explanation
Indices: 1771959--1772112 Score: 67
Period size: 19 Copynumber: 7.2 Consensus size: 21
1771949 TTACAAATTC
1771959 ATATATATTAATTTATATATTT
1 ATATATATT-ATTTATATATTT
1771981 ATAT-TATT-TTTATATTATAATT
1 ATATATATTATTTATA-TAT--TT
**
1772003 ATA-ATTACAATATTATATATTT
1 ATATA-TATTAT-TTATATATTT
* *
1772025 ATATAAATT-TTAATATATTT
1 ATATATATTATTTATATATTT
**
1772045 -TATCAT-TTAAAT-TATATTT
1 ATAT-ATATTATTTATATATTT
1772064 ATAT-TATT-TTT-TATATTAT
1 ATATATATTATTTATATATT-T
*
1772083 ATTATATTTTATATTATATTATATT
1 A-TATATATTAT-TTATA-TAT-TT
1772108 ATATA
1 ATATA
1772113 ATATCTAAAG
Statistics
Matches: 99, Mismatches: 13, Indels: 38
0.66 0.09 0.25
Matches are distributed among these distances:
18 8 0.08
19 22 0.22
20 19 0.19
21 8 0.08
22 16 0.16
23 5 0.05
24 10 0.10
25 10 0.10
26 1 0.01
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (21 bp):
ATATATATTATTTATATATTT
Found at i:1771998 original size:5 final size:5
Alignment explanation
Indices: 1771962--1772116 Score: 82
Period size: 5 Copynumber: 32.0 Consensus size: 5
1771952 CAAATTCATA
*
1771962 TATAT TA-AT T-TA- TATATT TATAT TATTTT TATAT TATAAT TATAAT
1 TATAT TATAT TATAT TATA-T TATAT TA-TAT TATAT TAT-AT TAT-AT
* * * * * *
1772008 TACA- -ATAT TATA- TAT-T TATA- TAAAT TTTAA TATAT TTTAT CAT-T
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
*
1772052 TAAAT TATATT TATAT TAT-T T-T-T TATAT TATAT TATATTT TATAT
1 TATAT TATA-T TATAT TATAT TATAT TATAT TATAT TATA--T TATAT
*
1772097 TATAT TATAT TATAT AATAT
1 TATAT TATAT TATAT TATAT
1772117 CTAAAGTTAC
Statistics
Matches: 116, Mismatches: 17, Indels: 34
0.69 0.10 0.20
Matches are distributed among these distances:
3 6 0.05
4 20 0.17
5 62 0.53
6 23 0.20
7 5 0.04
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:1772064 original size:28 final size:27
Alignment explanation
Indices: 1772037--1772097 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 27
1772027 ATAAATTTTA
1772037 ATATATTTTATCAT-TTAAATTATATTT
1 ATATATTTT-TCATATTAAATTATATTT
* *
1772064 ATATTATTTTTTATATTATATTATATTT
1 ATA-TATTTTTCATATTAAATTATATTT
1772092 -TATATT
1 ATATATT
1772098 ATATTATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
26 4 0.13
27 8 0.27
28 18 0.60
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (27 bp):
ATATATTTTTCATATTAAATTATATTT
Found at i:1772105 original size:17 final size:17
Alignment explanation
Indices: 1771962--1772112 Score: 102
Period size: 17 Copynumber: 8.9 Consensus size: 17
1771952 CAAATTCATA
1771962 TATATTA-ATTTATATATT
1 TATATTATATTT-TATA-T
1771980 TATATTAT-TTTTATAT
1 TATATTATATTTTATAT
* *
1771996 TATAATTATA-ATTACA-
1 TAT-ATTATATTTTATAT
1772012 -ATATTATATATTTATAT
1 TATATTATAT-TTTATAT
* *
1772029 AAATTTTAATATATTT-TAT
1 -TATATT-ATAT-TTTATAT
* * *
1772048 CAT-TTAAATTATAT-T
1 TATATTATATTTTATAT
*
1772063 TATATTATTTTTTATAT
1 TATATTATATTTTATAT
1772080 TATATTATATTTTATAT
1 TATATTATATTTTATAT
*
1772097 TATATTATATTATATA
1 TATATTATATTTTATA
1772113 ATATCTAAAG
Statistics
Matches: 107, Mismatches: 14, Indels: 25
0.73 0.10 0.17
Matches are distributed among these distances:
14 6 0.06
15 7 0.07
16 20 0.19
17 47 0.44
18 12 0.11
19 7 0.07
20 8 0.07
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (17 bp):
TATATTATATTTTATAT
Found at i:1772112 original size:12 final size:12
Alignment explanation
Indices: 1771960--1772112 Score: 96
Period size: 12 Copynumber: 13.5 Consensus size: 12
1771950 TACAAATTCA
1771960 TATATATTA-ATT
1 TATATATTATA-T
1771972 TATATATTTATAT
1 TATATA-TTATAT
*
1771985 TAT-TTTTATAT
1 TATATATTATAT
1771996 TATA-ATTATA-
1 TATATATTATAT
**
1772006 -AT-TACAATAT
1 TATATATTATAT
1772016 TATATATT-TA-
1 TATATATTATAT
* * *
1772026 TATAAATTTTAA
1 TATATATTATAT
*
1772038 TATATTTTATCAT
1 TATATATTAT-AT
*
1772051 T-TAAATTATAT
1 TATATATTATAT
*
1772062 T-TATATTATTT
1 TATATATTATAT
*
1772073 TTTATATTATAT
1 TATATATTATAT
*
1772085 TATATTTTATA-
1 TATATATTATAT
1772096 T-TATATTATAT
1 TATATATTATAT
1772107 TATATA
1 TATATA
1772113 ATATCTAAAG
Statistics
Matches: 109, Mismatches: 19, Indels: 26
0.71 0.12 0.17
Matches are distributed among these distances:
9 6 0.06
10 15 0.14
11 34 0.31
12 44 0.40
13 9 0.08
14 1 0.01
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (12 bp):
TATATATTATAT
Found at i:1772505 original size:10 final size:10
Alignment explanation
Indices: 1772462--1772540 Score: 58
Period size: 10 Copynumber: 8.2 Consensus size: 10
1772452 TAATATTATA
*
1772462 TTATTTTAAT
1 TTATATTAAT
1772472 TT-T-TTAA-
1 TTATATTAAT
*
1772479 TTATATCAAT
1 TTATATTAAT
1772489 TTATATTAAT
1 TTATATTAAT
1772499 TTATATTAAT
1 TTATATTAAT
** *
1772509 CAATA-TCAT
1 TTATATTAAT
1772518 TTAATATTAAT
1 TT-ATATTAAT
* *
1772529 ATGTATTAAT
1 TTATATTAAT
1772539 TT
1 TT
1772541 GTTTCAATTA
Statistics
Matches: 53, Mismatches: 11, Indels: 10
0.72 0.15 0.14
Matches are distributed among these distances:
7 2 0.04
8 5 0.09
9 7 0.13
10 35 0.66
11 4 0.08
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.57
Consensus pattern (10 bp):
TTATATTAAT
Found at i:1772525 original size:30 final size:30
Alignment explanation
Indices: 1772481--1772538 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
1772471 TTTTTTAATT
*
1772481 ATATCAATTTATATTAATTTATATTAATCA
1 ATATCAATTTATATTAATATATATTAATCA
*
1772511 ATATC-ATTTAATATTAATATGTATTAAT
1 ATATCAATTT-ATATTAATATATATTAAT
1772539 TTGTTTCAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (30 bp):
ATATCAATTTATATTAATATATATTAATCA
Found at i:1772613 original size:26 final size:26
Alignment explanation
Indices: 1772556--1772630 Score: 73
Period size: 26 Copynumber: 2.8 Consensus size: 26
1772546 AATTAGCATG
1772556 ATTTTATTT-TTTATATTTTTAAAATA
1 ATTTTATTTATTTA-ATTTTTAAAATA
* *
1772582 AATTTATTTATTTAATTTTT-AATTA
1 ATTTTATTTATTTAATTTTTAAAATA
1772607 ATTTTTATTGTTATCTTAATTTTT
1 A-TTTTA-T-TTAT-TTAATTTTT
1772631 TATAATCATA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
25 5 0.12
26 18 0.44
27 5 0.12
28 4 0.10
29 9 0.22
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.67
Consensus pattern (26 bp):
ATTTTATTTATTTAATTTTTAAAATA
Found at i:1772884 original size:20 final size:20
Alignment explanation
Indices: 1772842--1772880 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1772832 AAATTTTATT
* *
1772842 TTAATTAGTATTATTAAATA
1 TTAATTAATATTATTAAAAA
1772862 TTAATTAATATT-TTAAAAA
1 TTAATTAATATTATTAAAAA
1772881 ATTATAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TTAATTAATATTATTAAAAA
Found at i:1773108 original size:2 final size:2
Alignment explanation
Indices: 1773101--1773131 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1773091 AAAATCTACA
1773101 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1773132 AAAGTAATCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1773298 original size:22 final size:21
Alignment explanation
Indices: 1773273--1773343 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 21
1773263 ATATTCTATC
1773273 TATATTATTTTTATATTATAAA
1 TATATT-TTTTTATATTATAAA
* *
1773295 TATATTTATTATATATT-TATA
1 TATATTT-TTTTATATTATAAA
1773316 TA-ATTTTTTATATATTAATAAA
1 TATATTTTTT-TATATT-ATAAA
1773338 T-TATTT
1 TATATTT
1773344 AATATAAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
19 2 0.05
20 10 0.25
21 6 0.15
22 22 0.55
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TATATTTTTTTATATTATAAA
Found at i:1773330 original size:42 final size:45
Alignment explanation
Indices: 1773231--1773362 Score: 141
Period size: 44 Copynumber: 3.0 Consensus size: 45
1773221 AGCAATGTCT
* * * *
1773231 TTTTTTATA-ATTTAATAAAAAAATTTATATTTATATTCTATCTATA
1 TTTTTTATATA-TTAATAAATATATTTATATATATATT-TATATATA
1773277 TTATTTT-TATATT-ATAAATATATTTAT-TATATATTTATATA-A
1 TT-TTTTATATATTAATAAATATATTTATATATATATTTATATATA
*
1773319 TTTTTTATATATTAATAAAT-TATTTAATATAAATATTTATATAT
1 TTTTTTATATATTAATAAATATATTT-ATATATATATTTATATAT
1773363 TTATGTATTT
Statistics
Matches: 74, Mismatches: 5, Indels: 15
0.79 0.05 0.16
Matches are distributed among these distances:
41 4 0.05
42 14 0.19
43 13 0.18
44 20 0.27
45 12 0.16
46 6 0.08
47 5 0.07
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (45 bp):
TTTTTTATATATTAATAAATATATTTATATATATATTTATATATA
Found at i:1773348 original size:18 final size:20
Alignment explanation
Indices: 1773282--1773354 Score: 71
Period size: 19 Copynumber: 3.8 Consensus size: 20
1773272 CTATATTATT
* *
1773282 TTTATATTATAAATATATTTA
1 TTTATA-TATTAATATAATTA
* *
1773303 -TTATATATTTATATAATTT
1 TTTATATATTAATATAATTA
1773322 TTTATATATTAATA-AATTA
1 TTTATATATTAATATAATTA
*
1773341 TTTA-ATATAAATAT
1 TTTATATATTAATAT
1773355 TTATATATTT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
18 8 0.19
19 18 0.42
20 17 0.40
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTATATATTAATATAATTA
Found at i:1773385 original size:28 final size:27
Alignment explanation
Indices: 1773253--1773392 Score: 79
Period size: 28 Copynumber: 4.9 Consensus size: 27
1773243 TAATAAAAAA
* *
1773253 ATTTATATTTATATTCTATCTATATTATT
1 ATTTATA-TTATATTTTATATAT-TTATT
** *
1773282 -TTTATATTATA-AATATATTTATTATAT
1 ATTTATATTATATTTTATATAT-TTAT-T
* *
1773309 ATTTATATAATTTTTTATATATTAATAAATT
1 ATTTATATTATATTTTATATATT--T--ATT
*
1773340 ATTTA-ATATAAATATTTATATATTTATGT
1 ATTTATAT-TATAT-TTTATATATTTAT-T
*
1773369 ATTTATATTATATTTTATTTATTT
1 ATTTATATTATATTTTATATATTT
1773393 TTCTTATTAT
Statistics
Matches: 86, Mismatches: 14, Indels: 23
0.70 0.11 0.19
Matches are distributed among these distances:
26 10 0.12
27 6 0.07
28 28 0.33
29 16 0.19
30 6 0.07
31 8 0.09
32 12 0.14
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (27 bp):
ATTTATATTATATTTTATATATTTATT
Found at i:1773391 original size:20 final size:20
Alignment explanation
Indices: 1773273--1773392 Score: 70
Period size: 20 Copynumber: 6.0 Consensus size: 20
1773263 ATATTCTATC
*
1773273 TATATTAT-TTTTATAT-TA
1 TATATTATATTTTATATATT
*
1773291 TA-AATATATTTATTATATATT
1 TATATTATA-TT-TTATATATT
* *
1773312 TATATAATTTTTTATATATT
1 TATATTATATTTTATATATT
* * * **
1773332 AATA-AATTATTTAATATAAA
1 TATATTA-TATTTTATATATT
*
1773352 TAT-TTATATATTTATGTATT
1 TATATTATAT-TTTATATATT
*
1773372 TATATTATATTTTATTTATT
1 TATATTATATTTTATATATT
1773392 T
1 T
1773393 TTCTTATTAT
Statistics
Matches: 76, Mismatches: 17, Indels: 16
0.70 0.16 0.15
Matches are distributed among these distances:
17 4 0.05
18 2 0.03
19 7 0.09
20 49 0.64
21 11 0.14
22 3 0.04
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (20 bp):
TATATTATATTTTATATATT
Found at i:1773505 original size:16 final size:16
Alignment explanation
Indices: 1773483--1773529 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
1773473 TGTGGCATTT
1773483 ATATTATAT-TTTAATA
1 ATATTATATATTTAA-A
*
1773499 TTATTATTATATTTAAA
1 ATATTA-TATATTTAAA
1773516 ATATTATATATTTA
1 ATATTATATATTTA
1773530 TATAAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 13 0.48
17 9 0.33
18 5 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATATTATATATTTAAA
Found at i:1773508 original size:19 final size:21
Alignment explanation
Indices: 1773482--1773532 Score: 70
Period size: 19 Copynumber: 2.5 Consensus size: 21
1773472 GTGTGGCATT
*
1773482 TATATTATATTT-TAATATTA
1 TATATTATATTTAAAATATTA
1773502 T-TATTATATTTAAAATATTA
1 TATATTATATTTAAAATATTA
1773522 TATATTTATAT
1 TATA-TTATAT
1773533 AAATTTTGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 10 0.37
20 9 0.33
21 2 0.07
22 6 0.22
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TATATTATATTTAAAATATTA
Found at i:1773535 original size:20 final size:20
Alignment explanation
Indices: 1773495--1773535 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1773485 ATTATATTTT
*
1773495 AATATTATTATTATATTTAA
1 AATATTATTATTATATATAA
1773515 AATATTATATATT-TATATAA
1 AATATTAT-TATTATATATAA
1773535 A
1 A
1773536 TTTTGATACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AATATTATTATTATATATAA
Found at i:1773849 original size:240 final size:243
Alignment explanation
Indices: 1773479--1773917 Score: 541
Period size: 240 Copynumber: 1.8 Consensus size: 243
1773469 CCCGTGTGGC
*
1773479 ATTTATATTATATTTTAATATTATTATTATATTTAAAATATTATATATTTATATAAATTTTGATA
1 ATTTATATTATATTTTAATATTATGATTATATTTAAAATATTATATATTTATATAAATTTTGATA
* * * ** *
1773544 CAATAATAATTCATTTATGTAAAATTTGATAAGTTCATATATTCATGTTGTGTTCATACTATTTT
66 CAATAATAATTCATTTATATAAAATTTAAAAAGTTCATATATTCATGTCATATTCATACTATTTT
* * *
1773609 T-ATATTGTGTTATATTTTGA-ATTTTT-TATGTTATAT-TCGTATTGTATAATCATATTATATT
131 TCATATTGTATTATATTTTAATATTTTTCTAT-TTATATCT-GTATTGTATAATCATATTATATC
1773670 TAAAATCATCATATCTAATTAATACTATTTAAATAACAATTCTGTGTTAT
194 TAAAATCATCATATCTAATTAATACTATTTAAATAACAATTCTGTGTTAT
* * * *
1773720 ATTTATGTTAT-TTTTTATTTTATGATTATATTTAAAATATTATATA-TTATATAGATTTTGATA
1 ATTTATATTATATTTTAATATTATGATTATATTTAAAATATTATATATTTATATAAATTTTGATA
* * * * * * * * * *
1773783 -AGTTATTAATTTATTTTATATAAATTTTAAAAATTTTATCTATTTATGTCATATTTATATTATT
66 CA-ATAATAATTCA-TTTATATAAAATTTAAAAAGTTCATATATTCATGTCATATTCATACTATT
* * *
1773847 TTTCTTATTGTATTATATTTTAATTATTTTTCTATTTGTATCTGTGTTGTATAATCATATTATAT
129 TTTCATATTGTATTATATTTTAA-TATTTTTCTATTTATATCTGTATTGTATAATCATATTATAT
1773912 CTAAAA
193 CTAAAA
1773918 ATGATCAAGT
Statistics
Matches: 164, Mismatches: 27, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
238 1 0.01
239 24 0.15
240 72 0.44
241 26 0.16
243 37 0.23
244 4 0.02
ACGTcount: A:0.35, C:0.05, G:0.06, T:0.55
Consensus pattern (243 bp):
ATTTATATTATATTTTAATATTATGATTATATTTAAAATATTATATATTTATATAAATTTTGATA
CAATAATAATTCATTTATATAAAATTTAAAAAGTTCATATATTCATGTCATATTCATACTATTTT
TCATATTGTATTATATTTTAATATTTTTCTATTTATATCTGTATTGTATAATCATATTATATCTA
AAATCATCATATCTAATTAATACTATTTAAATAACAATTCTGTGTTAT
Found at i:1774044 original size:12 final size:13
Alignment explanation
Indices: 1774028--1774069 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 13
1774018 ATTTTTATAT
1774028 TTTATTTTAAAAA
1 TTTATTTTAAAAA
1774041 -TTATTTTAAATAA
1 TTTATTTTAAA-AA
*
1774054 TTTAATTT-AAAA
1 TTTATTTTAAAAA
1774066 TTTA
1 TTTA
1774070 AGTTTAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 16 0.62
13 4 0.15
14 6 0.23
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TTTATTTTAAAAA
Found at i:1775167 original size:3 final size:3
Alignment explanation
Indices: 1775161--1775202 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1775151 TTTAATTTTT
1775161 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1775203 CTTTTAATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1776690 original size:24 final size:24
Alignment explanation
Indices: 1776663--1776708 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
1776653 TTTATATTTT
*
1776663 ATAA-TTATACTTTTAAAATATAAA
1 ATAATTTATA-TTTAAAAATATAAA
1776687 ATAATTTATATTTAAAAATATA
1 ATAATTTATATTTAAAAATATA
1776709 TATTTACGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
ATAATTTATATTTAAAAATATAAA
Found at i:1777201 original size:28 final size:28
Alignment explanation
Indices: 1777170--1777226 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
1777160 TATATCAATT
1777170 TTATTTCA-AAAAAAATTATTTTTTA-AAA
1 TTATTT-ATAAAAAAA-TATTTTTTATAAA
*
1777198 TTATTTATCAAAAAATATTTTTTATAAA
1 TTATTTATAAAAAAATATTTTTTATAAA
1777226 T
1 T
1777227 AAATGAACTC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 10 0.38
28 16 0.62
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (28 bp):
TTATTTATAAAAAAATATTTTTTATAAA
Found at i:1777433 original size:12 final size:12
Alignment explanation
Indices: 1777416--1777454 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1777406 TTTAAAAATT
*
1777416 TTAAAATTAAAA
1 TTAAAATTTAAA
*
1777428 TTAAAATTTAAT
1 TTAAAATTTAAA
1777440 TTAAATATTTAAA
1 TTAAA-ATTTAAA
1777453 TT
1 TT
1777455 TATTATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 15 0.65
13 8 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
TTAAAATTTAAA
Found at i:1777479 original size:21 final size:22
Alignment explanation
Indices: 1777427--1777479 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
1777417 TAAAATTAAA
1777427 ATTAAAAT-TTAATTTAAATAT
1 ATTAAAATATTAATTTAAATAT
*
1777448 -TTAAATTTATT-ATTTAAATAT
1 ATTAAA-ATATTAATTTAAATAT
1777469 ATTAAAATATT
1 ATTAAAATATT
1777480 TAAAATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
20 5 0.19
21 15 0.56
22 7 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
ATTAAAATATTAATTTAAATAT
Found at i:1778278 original size:2 final size:2
Alignment explanation
Indices: 1778271--1778305 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1778261 TTCTGAGGCT
1778271 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1778306 TTTGTTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1779072 original size:6 final size:6
Alignment explanation
Indices: 1779063--1779087 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1779053 TGGTTGTGGT
1779063 ATTGAG ATTGAG ATTGAG ATTGAG A
1 ATTGAG ATTGAG ATTGAG ATTGAG A
1779088 GATGAATTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (6 bp):
ATTGAG
Found at i:1780916 original size:39 final size:39
Alignment explanation
Indices: 1780856--1780935 Score: 115
Period size: 39 Copynumber: 2.1 Consensus size: 39
1780846 CCAGTCAGTC
* * * *
1780856 AACAAAATGGAAACTTTACCAGAATGCTTAGTGGGATTG
1 AACAAAATGGAAAATTAACCAGAATGCTCAGTGGGACTG
*
1780895 AACAAAATGGAAAATTAACCAGAATTCTCAGTGGGACTG
1 AACAAAATGGAAAATTAACCAGAATGCTCAGTGGGACTG
1780934 AA
1 AA
1780936 AGGCTTGGTC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.23
Consensus pattern (39 bp):
AACAAAATGGAAAATTAACCAGAATGCTCAGTGGGACTG
Found at i:1791527 original size:19 final size:20
Alignment explanation
Indices: 1791503--1791568 Score: 61
Period size: 19 Copynumber: 3.5 Consensus size: 20
1791493 GCTCGATTCA
1791503 AAAATTTATATTATTAT-TT
1 AAAATTTATATTATTATATT
*
1791522 AAAA--T-TATTAATATATT
1 AAAATTTATATTATTATATT
* *
1791539 AAAA-ATATATTTTTATATT
1 AAAATTTATATTATTATATT
*
1791558 AATATTTATAT
1 AAAATTTATAT
1791569 ATTTTTATAA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
16 8 0.21
17 7 0.18
18 1 0.03
19 17 0.45
20 5 0.13
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AAAATTTATATTATTATATT
Found at i:1791571 original size:22 final size:22
Alignment explanation
Indices: 1791543--1791587 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
1791533 TATATTAAAA
1791543 ATATATTTTTAT-ATTAATATTT
1 ATATATTTTTATAATTAA-ATTT
1791565 ATATATTTTTATAATTAAATTT
1 ATATATTTTTATAATTAAATTT
1791587 A
1 A
1791588 AATAAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATATATTTTTATAATTAAATTT
Found at i:1793221 original size:18 final size:18
Alignment explanation
Indices: 1793190--1793236 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
1793180 ATTTTATAAA
* *
1793190 ATTTTTAATATATTTATTT
1 ATTTTTTATAT-TTTAATT
1793209 ATTTGTTTATATTTTAATT
1 ATTT-TTTATATTTTAATT
1793228 ATTTTTTAT
1 ATTTTTTAT
1793237 GATGTATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 5 0.20
19 14 0.56
20 6 0.24
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (18 bp):
ATTTTTTATATTTTAATT
Found at i:1794261 original size:2 final size:2
Alignment explanation
Indices: 1794254--1794286 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1794244 AATAAGGGTT
1794254 TA TA TA TA TA TA TA TA TA TA TA TA T- TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1794287 GCATAATGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:1796311 original size:27 final size:27
Alignment explanation
Indices: 1796278--1796332 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 27
1796268 ATATATTGAT
* *
1796278 AATAAAAATAAATTTTTAA-TTTTAAA
1 AATAAAAAAAAATATTTAATTTTTAAA
1796304 AATAAAAAAAAATATTTAATTTTTAAA
1 AATAAAAAAAAATATTTAATTTTTAAA
1796331 AA
1 AA
1796333 AATTTTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 17 0.65
27 9 0.35
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (27 bp):
AATAAAAAAAAATATTTAATTTTTAAA
Found at i:1796337 original size:17 final size:18
Alignment explanation
Indices: 1796310--1796343 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1796300 TAAAAATAAA
1796310 AAAAAATATTTAATTTTT
1 AAAAAATATTTAATTTTT
*
1796328 AAAAAA-ATTTTATTTT
1 AAAAAATATTTAATTTT
1796344 ATTTTAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AAAAAATATTTAATTTTT
Found at i:1796930 original size:16 final size:16
Alignment explanation
Indices: 1796890--1796931 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
1796880 TGTGGTGTAT
*
1796890 ATATAGATATAATTTA
1 ATATAAATATAATTTA
* *
1796906 TTA-AAATATTATTTA
1 ATATAAATATAATTTA
1796921 ATATAAATATA
1 ATATAAATATA
1796932 TAATTTAAAA
Statistics
Matches: 20, Mismatches: 5, Indels: 2
0.74 0.19 0.07
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (16 bp):
ATATAAATATAATTTA
Found at i:1796937 original size:18 final size:18
Alignment explanation
Indices: 1796896--1797047 Score: 75
Period size: 20 Copynumber: 8.3 Consensus size: 18
1796886 GTATATATAG
1796896 ATATAATTT-AT-TAAA-
1 ATATAATTTAATATAAAT
*
1796911 ATATTATTTAATATAAAT
1 ATATAATTTAATATAAAT
**
1796929 ATATAATTTAA-A-ATTT
1 ATATAATTTAATATAAAT
*
1796945 ATATAATATAAATTATAAAT
1 ATATAAT-TTAA-TATAAAT
*
1796965 ATATTAAAGTTAATATAAAT
1 ATA-T-AATTTAATATAAAT
* *
1796985 ATAAAATATTTAAAATATAAT
1 AT-ATA-ATTTAATATA-AAT
**
1797006 -TATTAAAATAATA-AAAT
1 ATA-TAATTTAATATAAAT
* *
1797023 ATATGATTATAATAAAAAT
1 ATATAATT-TAATATAAAT
1797042 ATATAA
1 ATATAA
1797048 ATTATTAAAT
Statistics
Matches: 101, Mismatches: 20, Indels: 28
0.68 0.13 0.19
Matches are distributed among these distances:
15 8 0.08
16 11 0.11
17 13 0.13
18 18 0.18
19 17 0.17
20 24 0.24
21 8 0.08
22 2 0.02
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (18 bp):
ATATAATTTAATATAAAT
Found at i:1796953 original size:29 final size:29
Alignment explanation
Indices: 1796906--1796962 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
1796896 ATATAATTTA
*
1796906 TTAAAATATTATTTAATATAAATATATAAT
1 TTAAAATATTATATAATATAAAT-TATAAT
1796936 TTAAAAT-TTATATAATATAAATTATAA
1 TTAAAATATTATATAATATAAATTATAA
1796963 ATATATTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 5 0.19
29 14 0.54
30 7 0.27
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
TTAAAATATTATATAATATAAATTATAAT
Found at i:1796958 original size:22 final size:23
Alignment explanation
Indices: 1796921--1797015 Score: 77
Period size: 23 Copynumber: 3.9 Consensus size: 23
1796911 ATATTATTTA
1796921 ATATAAATATATAATTTAAAAT-TT
1 ATAT-AATATA-AATTTAAAATATT
1796945 ATATAATATAAATTATAAATATATT
1 ATATAATATAAATT-TAAA-ATATT
* *
1796970 AAAGTTAATATAAATATAAAATATT
1 ATA--TAATATAAATTTAAAATATT
* *
1796995 -TAAAATATAATTATTAAAATA
1 ATATAATATAAAT-TTAAAATA
1797016 ATAAAATATA
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
22 12 0.20
23 17 0.29
24 7 0.12
25 9 0.15
26 4 0.07
27 10 0.17
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (23 bp):
ATATAATATAAATTTAAAATATT
Found at i:1797031 original size:24 final size:23
Alignment explanation
Indices: 1796921--1797056 Score: 74
Period size: 21 Copynumber: 5.9 Consensus size: 23
1796911 ATATTATTTA
1796921 ATATAAATATATAA-T-TTAAAAT
1 ATATAAA-ATATAATTATTAAAAT
* *
1796943 TTATATAATATAA--ATTATAAAT
1 ATATAAAATATAATTATTA-AAAT
*
1796965 ATATTAAAGT-TAATATAAATATAAAAT
1 ATA-TAAAATATAAT-T--AT-TAAAAT
*
1796992 ATTTAAAATATAATTATTAAAAT
1 ATATAAAATATAATTATTAAAAT
* *
1797015 A-ATAAAATAT-ATGATTATAAT
1 ATATAAAATATAATTATTAAAAT
1797036 A-A-AAATATATAAATTATTAAA
1 ATATAAA-ATAT-AATTATTAAA
1797057 TTTAATTATA
Statistics
Matches: 89, Mismatches: 12, Indels: 25
0.71 0.10 0.20
Matches are distributed among these distances:
20 3 0.03
21 24 0.27
22 22 0.25
23 18 0.20
24 2 0.02
26 6 0.07
27 12 0.13
28 2 0.02
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (23 bp):
ATATAAAATATAATTATTAAAAT
Found at i:1797250 original size:29 final size:30
Alignment explanation
Indices: 1797218--1797282 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
1797208 TGGATGATCT
*
1797218 AAATTTAAT-TATTACTTTAA-TTTATATA
1 AAATTTAATGTATTAATTTAATTTTATATA
* * *
1797246 AAAATTAATGTTTTAATTTAATTTTTTATA
1 AAATTTAATGTATTAATTTAATTTTATATA
1797276 AAATTTA
1 AAATTTA
1797283 TATTGTTCTG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 8 0.27
29 9 0.30
30 13 0.43
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (30 bp):
AAATTTAATGTATTAATTTAATTTTATATA
Done.