Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D05
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: 63323194
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1953226 characters in sequence are not A, C, G, or T
File 128 of 199
Found at i:42864982 original size:29 final size:30
Alignment explanation
Indices: 42864924--42864982 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
42864914 TAGCCCTTCC
* *
42864924 AAAAATGATAAAAAATTAATTTAATCTTTT
1 AAAAATGATAAAAAATTAATTCAATATTTT
* *
42864954 AAAAATTATAAAAATTTAATTCAA-ATTTT
1 AAAAATGATAAAAAATTAATTCAATATTTT
42864983 TTTTTTAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (30 bp):
AAAAATGATAAAAAATTAATTCAATATTTT
Found at i:42866349 original size:21 final size:23
Alignment explanation
Indices: 42866311--42866357 Score: 80
Period size: 21 Copynumber: 2.1 Consensus size: 23
42866301 ACCATATTAA
42866311 ATTTTACAACACGAAAATAGCAT
1 ATTTTACAACACGAAAATAGCAT
42866334 ATTTTACAA-A-GAAAATAGCAT
1 ATTTTACAACACGAAAATAGCAT
42866355 ATT
1 ATT
42866358 AAATTTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 14 0.58
22 1 0.04
23 9 0.38
ACGTcount: A:0.49, C:0.13, G:0.09, T:0.30
Consensus pattern (23 bp):
ATTTTACAACACGAAAATAGCAT
Found at i:42868389 original size:21 final size:21
Alignment explanation
Indices: 42868356--42868401 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
42868346 AGTATTTTAT
* *
42868356 TTAATTAATTTAATTAATCAA
1 TTAACTAAATTAATTAATCAA
**
42868377 TTAACTAAATTAATTTCTCAA
1 TTAACTAAATTAATTAATCAA
42868398 TTAA
1 TTAA
42868402 ATAATTTTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.46
Consensus pattern (21 bp):
TTAACTAAATTAATTAATCAA
Found at i:42879171 original size:18 final size:18
Alignment explanation
Indices: 42879148--42879184 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
42879138 CCGTACTTAA
*
42879148 GTATATAAGGATAGTGGT
1 GTATATAAGGATAGCGGT
42879166 GTATATAAGGATAGCGGT
1 GTATATAAGGATAGCGGT
42879184 G
1 G
42879185 GTCTTTTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.03, G:0.35, T:0.30
Consensus pattern (18 bp):
GTATATAAGGATAGCGGT
Found at i:42879927 original size:18 final size:18
Alignment explanation
Indices: 42879904--42879951 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
42879894 ATTCAGGACT
42879904 AATTTGAAACAAA-TAAGA
1 AATTTGAAA-AAATTAAGA
*
42879922 AATTTGAGAAAAATTTAGA
1 AATTTGA-AAAAATTAAGA
42879941 AATTTTGAAAA
1 AA-TTTGAAAA
42879952 TAGGGGTAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 10 0.38
19 11 0.42
20 5 0.19
ACGTcount: A:0.56, C:0.02, G:0.12, T:0.29
Consensus pattern (18 bp):
AATTTGAAAAAATTAAGA
Found at i:42881317 original size:43 final size:43
Alignment explanation
Indices: 42881254--42881338 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
42881244 CTGATAAGTG
* *
42881254 TTTTCGTATAAGACCATGTCTGGGAC-GTTGGCATCGACTTGTA
1 TTTTCGTACAAGACCATGTCTAGGACAG-TGGCATCGACTTGTA
* * *
42881297 TTTTCGTGCAAGACCCTGTCTAGGACAGTGGCATCGATTTGT
1 TTTTCGTACAAGACCATGTCTAGGACAGTGGCATCGACTTGT
42881339 GATTACATGT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
43 35 0.97
44 1 0.03
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (43 bp):
TTTTCGTACAAGACCATGTCTAGGACAGTGGCATCGACTTGTA
Found at i:42881353 original size:43 final size:43
Alignment explanation
Indices: 42881262--42881371 Score: 107
Period size: 43 Copynumber: 2.6 Consensus size: 43
42881252 TGTTTTCGTA
* * *
42881262 TAAGACCATGTCTGGGACGTTGGCATCGACTTGTATTTTCGTG
1 TAAGACCATGTCTAGGACGTTGGCATCGACTTGTATTTACATG
* * *
42881305 CAAGACCCTGTCTAGGACAG-TGGCATCGATTTGTGA-TTACATG
1 TAAGACCATGTCTAGGAC-GTTGGCATCGACTTGT-ATTTACATG
* * *
42881348 TAAGACCACGTTTGGGACGTTGGC
1 TAAGACCATGTCTAGGACGTTGGC
42881372 GTTGTACTAG
Statistics
Matches: 53, Mismatches: 11, Indels: 6
0.76 0.16 0.09
Matches are distributed among these distances:
42 1 0.02
43 50 0.94
44 2 0.04
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (43 bp):
TAAGACCATGTCTAGGACGTTGGCATCGACTTGTATTTACATG
Found at i:42883642 original size:30 final size:30
Alignment explanation
Indices: 42883601--42883660 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
42883591 GCACATGACA
* *
42883601 GTGTAGCCAGGCCGTGAGTGTTACACGGCC
1 GTGTAGCCAGGCCATGAGTGTCACACGGCC
* *
42883631 GTGTAGTCAGGCCATGTGTGTCACACGGCC
1 GTGTAGCCAGGCCATGAGTGTCACACGGCC
42883661 ATGAGACCGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.17, C:0.27, G:0.35, T:0.22
Consensus pattern (30 bp):
GTGTAGCCAGGCCATGAGTGTCACACGGCC
Found at i:42893346 original size:21 final size:20
Alignment explanation
Indices: 42893298--42893348 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
42893288 GTTATTATAA
* *
42893298 AAAAAATTATAAAAATTATT
1 AAAAAATTATAAAAATAAAT
*
42893318 AATTAAATTATAAAAATAAAAT
1 AA-AAAATTATAAAAAT-AAAT
42893340 AAAAAATTA
1 AAAAAATTA
42893349 AATAATATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 2 0.08
21 19 0.76
22 4 0.16
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAAAATTATAAAAATAAAT
Found at i:42894818 original size:18 final size:18
Alignment explanation
Indices: 42894766--42894826 Score: 95
Period size: 18 Copynumber: 3.4 Consensus size: 18
42894756 ATGATATCGA
**
42894766 TATTGATGATAGTGACAA
1 TATTGATGATAGTGACGC
*
42894784 TATTGATGCTAGTGACGC
1 TATTGATGATAGTGACGC
42894802 TATTGATGATAGTGACGC
1 TATTGATGATAGTGACGC
42894820 TATTGAT
1 TATTGAT
42894827 CGTGACCTTG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.30, C:0.10, G:0.25, T:0.36
Consensus pattern (18 bp):
TATTGATGATAGTGACGC
Found at i:42896833 original size:59 final size:59
Alignment explanation
Indices: 42896741--42896858 Score: 218
Period size: 59 Copynumber: 2.0 Consensus size: 59
42896731 TTCTTATCTC
* *
42896741 TTTCTAATAAGAAAATGATAAATCAGATTTTTCTTCCTAATTTTAGTATTTTTAGTTGG
1 TTTCTAATAAAAAAATGATAAATCAGATTTTTCTTCCTAATTTTAGCATTTTTAGTTGG
42896800 TTTCTAATAAAAAAATGATAAATCAGATTTTTCTTCCTAATTTTAGCATTTTTAGTTGG
1 TTTCTAATAAAAAAATGATAAATCAGATTTTTCTTCCTAATTTTAGCATTTTTAGTTGG
42896859 ATTTGGATTT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.33, C:0.09, G:0.11, T:0.47
Consensus pattern (59 bp):
TTTCTAATAAAAAAATGATAAATCAGATTTTTCTTCCTAATTTTAGCATTTTTAGTTGG
Found at i:42901576 original size:20 final size:19
Alignment explanation
Indices: 42901518--42901583 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 19
42901508 TAAAATATAA
*
42901518 ATTTTGCAATTTTTATAAA-T
1 ATTTTG-AA-TTTTAAAAATT
*
42901538 ATTTTTAATTTTAAAAATT
1 ATTTTGAATTTTAAAAATT
*
42901557 ATTTTGAATATTTGAAAATT
1 ATTTTGAAT-TTTAAAAATT
42901577 ATTTTGA
1 ATTTTGA
42901584 TTTCCTTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
18 8 0.20
19 11 0.28
20 21 0.52
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.55
Consensus pattern (19 bp):
ATTTTGAATTTTAAAAATT
Found at i:42908861 original size:27 final size:28
Alignment explanation
Indices: 42908825--42908889 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 28
42908815 TTGAACCTTT
42908825 AAATTTTCCT-ATT-TACATTTGACCCCA
1 AAATTTTCCTAATTATAC-TTTGACCCCA
42908852 AAATTTTCCTAAAATTATACTTTGACCCCA
1 AAATTTTCCT--AATTATACTTTGACCCCA
42908882 AAAGTTTT
1 AAA-TTTT
42908890 GCATCCTCTG
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
27 10 0.30
30 16 0.48
31 7 0.21
ACGTcount: A:0.34, C:0.22, G:0.05, T:0.40
Consensus pattern (28 bp):
AAATTTTCCTAATTATACTTTGACCCCA
Found at i:42916347 original size:17 final size:17
Alignment explanation
Indices: 42916325--42916358 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
42916315 TGTTAGTAAA
42916325 TATTGTCATTGCATTTT
1 TATTGTCATTGCATTTT
42916342 TATTGTCATTGCATTTT
1 TATTGTCATTGCATTTT
42916359 AATGTTAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.12, G:0.12, T:0.59
Consensus pattern (17 bp):
TATTGTCATTGCATTTT
Found at i:42921548 original size:27 final size:26
Alignment explanation
Indices: 42921487--42921553 Score: 73
Period size: 27 Copynumber: 2.6 Consensus size: 26
42921477 ACATGTGTGA
**
42921487 TCACACGAGCTGTG-AATCGGTTTGC
1 TCACACGAGCTGTGAAATCGGCCTGC
* * *
42921512 TTACATGAGCTGTGAAAATGGGCCTGC
1 TCACACGAGCTGTG-AAATCGGCCTGC
42921539 TCACACGAGCTGTGA
1 TCACACGAGCTGTGA
42921554 GACAGAACGT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
25 12 0.36
26 1 0.03
27 20 0.61
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (26 bp):
TCACACGAGCTGTGAAATCGGCCTGC
Found at i:42928813 original size:40 final size:41
Alignment explanation
Indices: 42928745--42928877 Score: 142
Period size: 41 Copynumber: 3.3 Consensus size: 41
42928735 GGCAGGGGTG
* * * *
42928745 TGTGCAATTTAGGGGTATCGAAGTACAAATAGGGGCACATA
1 TGTGCAATTCAGGAGTACCAAAGTACAAATAGGGGCACATA
* *
42928786 TGTGCAATTCA-GAGTACTAAAGTACAAACAGGGGCACATA
1 TGTGCAATTCAGGAGTACCAAAGTACAAATAGGGGCACATA
* * * * * *
42928826 TGTGCAATTTAGGGGTACCGAAGTACAAATAGGGACATACA
1 TGTGCAATTCAGGAGTACCAAAGTACAAATAGGGGCACATA
*
42928867 TGTGAAATTCA
1 TGTGCAATTCA
42928878 TCATTTTCCT
Statistics
Matches: 75, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
40 34 0.45
41 41 0.55
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (41 bp):
TGTGCAATTCAGGAGTACCAAAGTACAAATAGGGGCACATA
Found at i:42928870 original size:41 final size:41
Alignment explanation
Indices: 42928745--42928859 Score: 169
Period size: 40 Copynumber: 2.8 Consensus size: 41
42928735 GGCAGGGGTG
*
42928745 TGTGCAATTTAGGGGTATCGAAGTACAAATAGGGGCACATA
1 TGTGCAATTTAGGGGTACCGAAGTACAAATAGGGGCACATA
* * ** *
42928786 TGTGCAATTCA-GAGTACTAAAGTACAAACAGGGGCACATA
1 TGTGCAATTTAGGGGTACCGAAGTACAAATAGGGGCACATA
42928826 TGTGCAATTTAGGGGTACCGAAGTACAAATAGGG
1 TGTGCAATTTAGGGGTACCGAAGTACAAATAGGG
42928860 ACATACATGT
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
40 34 0.55
41 28 0.45
ACGTcount: A:0.36, C:0.14, G:0.28, T:0.23
Consensus pattern (41 bp):
TGTGCAATTTAGGGGTACCGAAGTACAAATAGGGGCACATA
Found at i:42936013 original size:41 final size:40
Alignment explanation
Indices: 42935968--42936116 Score: 154
Period size: 41 Copynumber: 3.6 Consensus size: 40
42935958 TCTGAAGCCT
*
42935968 AAACAGGGGCACATGTGTGCAATTCAGCGGTACCGAAGTAC
1 AAACAGGGGCACATATGTGCAATTCAG-GGTACCGAAGTAC
* * *
42936009 AAACAGGGGCACATATTTGCAATTTAGGGGTACCGAAGTAT
1 AAACAGGGGCACATATGTGCAATTCA-GGGTACCGAAGTAC
** * * * * *
42936050 AGGCAAGGGCACGTATGTGTAATTTAAGGGTACTGAAGTAC
1 AAACAGGGGCACATATGTGCAA-TTCAGGGTACCGAAGTAC
* *
42936091 AAATAGGGGCACGTATGTGCAATTCA
1 AAACAGGGGCACATATGTGCAATTCA
42936117 TAATTTTTCT
Statistics
Matches: 87, Mismatches: 19, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
40 3 0.03
41 80 0.92
42 4 0.05
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.22
Consensus pattern (40 bp):
AAACAGGGGCACATATGTGCAATTCAGGGTACCGAAGTAC
Found at i:42939327 original size:51 final size:51
Alignment explanation
Indices: 42939251--42939539 Score: 262
Period size: 51 Copynumber: 5.7 Consensus size: 51
42939241 TATTGATGAA
* * ** **
42939251 CACATGTGTAGTATTGTGTGAAGGCTACTACGTGTATTGATAAAAAATGGT
1 CACATGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAATTTGGT
* * * * * **
42939302 CACATGTGTAGTACTAAGTGAAGGCTACAATGTGTACTGAGAAGCTTTGGT
1 CACATGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAATTTGGT
* * * * *
42939353 CACGTGTGTAGTACTGTGTGAAGGCTACTA-GTGAATCGAT-AAATGATGGT
1 CACATGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAAT-TTGGT
* * *
42939403 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGA-AAAGCTTTGGT
1 CACATGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAA-ATTTGGT
** * * *
42939454 CATGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAAACTTGAT
1 CACATGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAATTTGGT
** * *
42939504 CATGTGTTTAGTACTATGTGAACGCTACTACGTGTA
1 CACATGTGTAGTACTATGTGAAGGCTACTACGTGTA
42939540 TCAAATGATA
Statistics
Matches: 193, Mismatches: 40, Indels: 11
0.79 0.16 0.05
Matches are distributed among these distances:
49 2 0.01
50 74 0.38
51 116 0.60
52 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (51 bp):
CACATGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAATTTGGT
Found at i:42939516 original size:101 final size:102
Alignment explanation
Indices: 42939255--42939539 Score: 376
Period size: 101 Copynumber: 2.8 Consensus size: 102
42939245 GATGAACACA
* * *
42939255 TGTGTAGTATTGTGTGAAGGCTACTACGTGTATTGATAAAAAATGGTCACATGTGTAGTACTAAG
1 TGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAAAAATGGTCACATGTGTAGTACTAAG
* * *
42939320 TGAAGGCTACAATGTGTACTGAGAAGCTTTGGTCACG
66 TGAAGGCTACTATGTGTACCGAAAAGCTTTGGTCACG
**
42939357 TGTGTAGTACTGTGTGAAGGCTACTA-GTGAATCGATAAATGATGGTCACATGTGTAGTACTAAG
1 TGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAAAAATGGTCACATGTGTAGTACTAAG
*
42939421 TGAAGGCTACTATGTGTACCGAAAAGCTTTGGTCATG
66 TGAAGGCTACTATGTGTACCGAAAAGCTTTGGTCACG
* * ** * ** * *
42939458 TGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAAACTTGATCATGTGTTTAGTACTATG
1 TGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAAAAATGGTCACATGTGTAGTACTAAG
* *
42939522 TGAACGCTACTACGTGTA
66 TGAAGGCTACTATGTGTA
42939540 TCAAATGATA
Statistics
Matches: 161, Mismatches: 21, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
101 129 0.80
102 32 0.20
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (102 bp):
TGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAAAAATGGTCACATGTGTAGTACTAAG
TGAAGGCTACTATGTGTACCGAAAAGCTTTGGTCACG
Found at i:42945705 original size:16 final size:17
Alignment explanation
Indices: 42945684--42945716 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
42945674 TCTTTTAGTC
42945684 TCACAA-TCTATAGTTT
1 TCACAATTCTATAGTTT
42945700 TCACAATTCTATAGTTT
1 TCACAATTCTATAGTTT
42945717 CAAGGTCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.30, C:0.18, G:0.06, T:0.45
Consensus pattern (17 bp):
TCACAATTCTATAGTTT
Found at i:42947489 original size:20 final size:20
Alignment explanation
Indices: 42947460--42947501 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
42947450 TATGTGATGG
42947460 ATTAGCTAAGTTATGTGTTT
1 ATTAGCTAAGTTATGTGTTT
*
42947480 ATTAGTTAAGTTATGTGTTT
1 ATTAGCTAAGTTATGTGTTT
42947500 AT
1 AT
42947502 CACTAACTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.26, C:0.02, G:0.19, T:0.52
Consensus pattern (20 bp):
ATTAGCTAAGTTATGTGTTT
Found at i:42949745 original size:13 final size:13
Alignment explanation
Indices: 42949729--42949753 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42949719 ATTAAATTAC
42949729 CTTATTAACTTTG
1 CTTATTAACTTTG
42949742 CTTATTAACTTT
1 CTTATTAACTTT
42949754 AAAAATCACA
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:0.24, C:0.16, G:0.04, T:0.56
Consensus pattern (13 bp):
CTTATTAACTTTG
Found at i:42950884 original size:23 final size:23
Alignment explanation
Indices: 42950861--42950940 Score: 126
Period size: 23 Copynumber: 3.5 Consensus size: 23
42950851 GTGTTAAAAG
42950861 TTAATGTGATTTATGCTTAAA-A
1 TTAATGTGATTTATGCTTAAATA
*
42950883 GTTAATGTGCTTTATGCTTAAATA
1 -TTAATGTGATTTATGCTTAAATA
42950907 TTAATGTGATTTATGCTTAAATA
1 TTAATGTGATTTATGCTTAAATA
*
42950930 TTGATGTGATT
1 TTAATGTGATT
42950941 AAAGTATAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
23 52 0.98
24 1 0.02
ACGTcount: A:0.31, C:0.05, G:0.16, T:0.47
Consensus pattern (23 bp):
TTAATGTGATTTATGCTTAAATA
Found at i:42956783 original size:14 final size:17
Alignment explanation
Indices: 42956762--42956798 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
42956752 AAGTGTATTT
*
42956762 TAAAAAAATA-ATA-AA
1 TAAAAAATTACATATAA
42956777 TAAAAAATTACATATAA
1 TAAAAAATTACATATAA
42956794 TAAAA
1 TAAAA
42956799 TTTGAATCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 9 0.47
16 3 0.16
17 7 0.37
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
TAAAAAATTACATATAA
Found at i:42959130 original size:57 final size:58
Alignment explanation
Indices: 42959065--42959177 Score: 167
Period size: 57 Copynumber: 2.0 Consensus size: 58
42959055 TTTTCATGTC
* *
42959065 ATTTTCATTTTAGAGAAAATCATATTCATTTCCAAATGATTT-C-ATTTCTCCATTTTT
1 ATTTTCATTTTAGAGAAAACCATAATCATTTCCAAATG-TTTCCTATTTCTCCATTTTT
* *
42959122 ATTTTCATTTTGGAGAAAACCTTAATCATTTCCAAATGTTTCCTATTTCTCCATTT
1 ATTTTCATTTTAGAGAAAACCATAATCATTTCCAAATGTTTCCTATTTCTCCATTT
42959178 CACCATTTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
56 3 0.06
57 35 0.70
58 12 0.24
ACGTcount: A:0.28, C:0.18, G:0.06, T:0.48
Consensus pattern (58 bp):
ATTTTCATTTTAGAGAAAACCATAATCATTTCCAAATGTTTCCTATTTCTCCATTTTT
Found at i:42960433 original size:14 final size:14
Alignment explanation
Indices: 42960414--42960440 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
42960404 AAGTGTAGTG
42960414 TATTTGTAATTTTA
1 TATTTGTAATTTTA
42960428 TATTTGTAATTTT
1 TATTTGTAATTTT
42960441 TTTAATAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (14 bp):
TATTTGTAATTTTA
Found at i:42971724 original size:15 final size:15
Alignment explanation
Indices: 42971683--42971724 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
42971673 CGATTTTTAG
*
42971683 ATTTCTTAT-TTTTC
1 ATTTCTTATAATTTC
*
42971697 ATTTATT-TAATTTC
1 ATTTCTTATAATTTC
42971711 ATTTCTTATAATTT
1 ATTTCTTATAATTT
42971725 TTAGTATAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 1 0.04
14 16 0.70
15 6 0.26
ACGTcount: A:0.24, C:0.10, G:0.00, T:0.67
Consensus pattern (15 bp):
ATTTCTTATAATTTC
Found at i:42976760 original size:36 final size:36
Alignment explanation
Indices: 42976708--42976776 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
42976698 ATTACAAGAA
42976708 AGTTCTATTTACTTTCAGAAAATCTCCTCAATGGGG
1 AGTTCTATTTACTTTCAGAAAATCTCCTCAATGGGG
*
42976744 AGTTTTATTTACTTTCAGAAAATCTCCTCAATG
1 AGTTCTATTTACTTTCAGAAAATCTCCTCAATG
42976777 AGATCCACAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (36 bp):
AGTTCTATTTACTTTCAGAAAATCTCCTCAATGGGG
Found at i:42978251 original size:27 final size:27
Alignment explanation
Indices: 42978200--42978251 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
42978190 AAACTAAAGT
* *
42978200 CTTTGTGGCAATCTATGAGATGGAAGA
1 CTTTGTGGCAATCTAGGAGAAGGAAGA
42978227 CTTTGTGGCAATCTAAGGA-AAGGAA
1 CTTTGTGGCAATCT-AGGAGAAGGAA
42978252 AGCCCTTGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 19 0.86
28 3 0.14
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.27
Consensus pattern (27 bp):
CTTTGTGGCAATCTAGGAGAAGGAAGA
Found at i:42980989 original size:22 final size:24
Alignment explanation
Indices: 42980964--42981007 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
42980954 TCAATATTTT
*
42980964 TTTC-TATTTCCCA-AAAATAAAC
1 TTTCATATTTCCAATAAAATAAAC
42980986 TTTCATATTTCCAATAAAATAA
1 TTTCATATTTCCAATAAAATAA
42981008 TTTTCTCAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 8 0.42
24 7 0.37
ACGTcount: A:0.43, C:0.18, G:0.00, T:0.39
Consensus pattern (24 bp):
TTTCATATTTCCAATAAAATAAAC
Found at i:42981012 original size:23 final size:22
Alignment explanation
Indices: 42980963--42981013 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
42980953 CTCAATATTT
*
42980963 TTTTCTATTTCCCAAAAATAAA
1 TTTTCTATTTCCAAAAAATAAA
*
42980985 CTTTCATATTTCCAATAAAAT-AA
1 TTTTC-TATTTCCAA-AAAATAAA
42981008 TTTTCT
1 TTTTCT
42981014 CAACCCAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
22 5 0.21
23 14 0.58
24 5 0.21
ACGTcount: A:0.37, C:0.18, G:0.00, T:0.45
Consensus pattern (22 bp):
TTTTCTATTTCCAAAAAATAAA
Found at i:42981198 original size:7 final size:6
Alignment explanation
Indices: 42981164--42981221 Score: 55
Period size: 6 Copynumber: 9.3 Consensus size: 6
42981154 AAAGCGTATA
* *
42981164 TTCATTT TTCA-T GTCATT TTTATTT TTCATCT TTCATT TTCATT TTCATT
1 TTCA-TT TTCATT TTCATT TTCA-TT TTCAT-T TTCATT TTCATT TTCATT
*
42981214 TTTATT TT
1 TTCATT TT
42981222 GGAGAAAACC
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
5 4 0.09
6 24 0.56
7 15 0.35
ACGTcount: A:0.16, C:0.14, G:0.02, T:0.69
Consensus pattern (6 bp):
TTCATT
Found at i:42985791 original size:30 final size:31
Alignment explanation
Indices: 42985752--42985811 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
42985742 GGAGGTGGGA
*
42985752 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
42985783 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
42985812 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:42986568 original size:17 final size:16
Alignment explanation
Indices: 42986546--42986577 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
42986536 TTTTTGGTAC
42986546 ATTTATATATAGATAAT
1 ATTTATATATA-ATAAT
42986563 ATTTATATATAATAA
1 ATTTATATATAATAA
42986578 GAAGGGGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATTTATATATAATAAT
Found at i:42988764 original size:20 final size:21
Alignment explanation
Indices: 42988731--42988783 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
42988721 ATTTTTAACT
* *
42988731 TCCATGTTAGCAAT-TTTCAA
1 TCCATGTCATCAATCTTTCAA
* * *
42988751 TTCATGTCATCAATCTTTTAG
1 TCCATGTCATCAATCTTTCAA
42988772 TCCATGTCATCA
1 TCCATGTCATCA
42988784 TCCCGTTTCA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.26, C:0.23, G:0.09, T:0.42
Consensus pattern (21 bp):
TCCATGTCATCAATCTTTCAA
Found at i:42993693 original size:31 final size:30
Alignment explanation
Indices: 42993658--42993717 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
42993648 GGAGGTGGGA
*
42993658 TGGGAAGAGAATAAAAGTTTTAGGGGAAAAG
1 TGGG-AGAGAATAAAAATTTTAGGGGAAAAG
* * *
42993689 TGGGAGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAGAGAATAAAAATTTTAGGGGAAAA
42993718 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (30 bp):
TGGGAGAGAATAAAAATTTTAGGGGAAAAG
Found at i:42993877 original size:21 final size:21
Alignment explanation
Indices: 42993853--42993893 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
42993843 AGGGGGAAGT
* *
42993853 GGGAAAGAGAAAAAGTTTTGA
1 GGGAAAAAGAAAAAGGTTTGA
*
42993874 GGGAAAAATAAAAAGGTTTG
1 GGGAAAAAGAAAAAGGTTTG
42993894 GGAATTTAGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.32, T:0.20
Consensus pattern (21 bp):
GGGAAAAAGAAAAAGGTTTGA
Found at i:42993945 original size:9 final size:9
Alignment explanation
Indices: 42993931--42993967 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
42993921 TATAGTTTGA
42993931 TATTCGAAT
1 TATTCGAAT
42993940 TATTCGAAT
1 TATTCGAAT
*
42993949 TATTCGAGT
1 TATTCGAAT
42993958 TATTCGAAT
1 TATTCGAAT
42993967 T
1 T
42993968 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:42994711 original size:68 final size:68
Alignment explanation
Indices: 42994602--42994737 Score: 272
Period size: 68 Copynumber: 2.0 Consensus size: 68
42994592 CTTGTTGCAG
42994602 TCTCTTTATCATGATAAAAGCATCTCTTTCAGTCTAGACTTGAGTGAAAACCATGTCTCGGGCTA
1 TCTCTTTATCATGATAAAAGCATCTCTTTCAGTCTAGACTTGAGTGAAAACCATGTCTCGGGCTA
42994667 ACT
66 ACT
42994670 TCTCTTTATCATGATAAAAGCATCTCTTTCAGTCTAGACTTGAGTGAAAACCATGTCTCGGGCTA
1 TCTCTTTATCATGATAAAAGCATCTCTTTCAGTCTAGACTTGAGTGAAAACCATGTCTCGGGCTA
42994735 ACT
66 ACT
42994738 CCTATTTTAA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (68 bp):
TCTCTTTATCATGATAAAAGCATCTCTTTCAGTCTAGACTTGAGTGAAAACCATGTCTCGGGCTA
ACT
Found at i:42996772 original size:23 final size:23
Alignment explanation
Indices: 42996742--42996785 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
42996732 ATTTTTCCTA
*
42996742 AATATTATCACTAATTAATTCTT
1 AATATTATCACTAAATAATTCTT
42996765 AATATTATCACTAAATAATTC
1 AATATTATCACTAAATAATTC
42996786 AAAATTTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (23 bp):
AATATTATCACTAAATAATTCTT
Found at i:42997431 original size:22 final size:20
Alignment explanation
Indices: 42997398--42997437 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
42997388 TTTGTAAATG
42997398 TAAAAAAATATTAAAAATCA
1 TAAAAAAATATTAAAAATCA
42997418 TAAAAAAATTTATTAAAAAT
1 TAAAAAAA--TATTAAAAAT
42997438 AAAAATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
22 10 0.56
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (20 bp):
TAAAAAAATATTAAAAATCA
Found at i:42997556 original size:11 final size:10
Alignment explanation
Indices: 42997514--42997567 Score: 56
Period size: 11 Copynumber: 5.2 Consensus size: 10
42997504 AATATATAAA
*
42997514 TTATAAATTT
1 TTATAATTTT
*
42997524 TTATATCTTTT
1 TTATA-ATTTT
42997535 TTAATAATTTT
1 TT-ATAATTTT
42997546 TTATAA-TTT
1 TTATAATTTT
42997555 TTATGAATTTT
1 TTAT-AATTTT
42997566 TT
1 TT
42997568 TAAAAAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
9 7 0.19
10 11 0.30
11 16 0.43
12 3 0.08
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (10 bp):
TTATAATTTT
Found at i:43000213 original size:20 final size:19
Alignment explanation
Indices: 43000175--43000236 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 19
43000165 TTGATATAAA
*
43000175 ATTATAAATATAATAAAATT
1 ATTATAAATATTAT-AAATT
43000195 ATTATTAAATATTATAAA-T
1 ATTA-TAAATATTATAAATT
*
43000214 ATTATAAAAATCTAATAAATT
1 ATTATAAATAT-T-ATAAATT
43000235 AT
1 AT
43000237 AAAAAAATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
18 6 0.17
19 6 0.17
20 12 0.33
21 12 0.33
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (19 bp):
ATTATAAATATTATAAATT
Found at i:43000265 original size:58 final size:57
Alignment explanation
Indices: 43000173--43000281 Score: 132
Period size: 58 Copynumber: 1.9 Consensus size: 57
43000163 AATTGATATA
* * * *
43000173 AAATTATAAATATAATAAAATTATTATTAAATA-TTATAAATATTATAAAAATCTAAT
1 AAATTATAAAAAAAATAAAATTACTATAAAATATTTA-AAATATTATAAAAATCTAAT
*
43000230 AAATTATAAAAAAATATAAAATTACTA-AAACATATTTAAAATTTTATAAAAA
1 AAATTATAAAAAAA-ATAAAATTACTATAAA-ATATTTAAAATATTATAAAAA
43000282 CAAATTGAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
57 14 0.32
58 27 0.61
59 3 0.07
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (57 bp):
AAATTATAAAAAAAATAAAATTACTATAAAATATTTAAAATATTATAAAAATCTAAT
Found at i:43000831 original size:9 final size:9
Alignment explanation
Indices: 43000811--43000908 Score: 60
Period size: 9 Copynumber: 10.7 Consensus size: 9
43000801 GACTTTTTAA
43000811 TTTTATATAT
1 TTTTATA-AT
43000821 TTTTATAAT
1 TTTTATAAT
*
43000830 TTATTA-GAT
1 TT-TTATAAT
*
43000839 TTTCAT-AT
1 TTTTATAAT
43000847 TTTTATAAT
1 TTTTATAAT
*
43000856 ATTTATAAGT
1 TTTTATAA-T
*
43000866 TTATATCAAT
1 TTTTAT-AAT
*
43000876 TTTAAT-AT
1 TTTTATAAT
*
43000884 TTTTATGAT
1 TTTTATAAT
43000893 ATTTT-TAAT
1 -TTTTATAAT
43000902 ATTTTAT
1 -TTTTAT
43000909 GAGAAAATAT
Statistics
Matches: 70, Mismatches: 10, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
8 16 0.23
9 27 0.39
10 25 0.36
11 2 0.03
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (9 bp):
TTTTATAAT
Found at i:43002784 original size:20 final size:20
Alignment explanation
Indices: 43002734--43002784 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 20
43002724 AATAGTTATG
*
43002734 TCTCTTGATGAACAGTTGTA
1 TCTCTTGATGAACAATTGTA
*
43002754 -C-CTT-TTGAACAATTGTA
1 TCTCTTGATGAACAATTGTA
*
43002771 TCTCTTGGTGAACA
1 TCTCTTGATGAACA
43002785 GATTCATTGC
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
17 11 0.44
18 4 0.16
19 4 0.16
20 6 0.24
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (20 bp):
TCTCTTGATGAACAATTGTA
Found at i:43005964 original size:39 final size:39
Alignment explanation
Indices: 43005825--43005969 Score: 146
Period size: 40 Copynumber: 3.6 Consensus size: 39
43005815 AGTGGCGCTT
* * *
43005825 TTAGCGGCGTTTGGACAAAAAATGCCACTAAAAATTGAGCA
1 TTAGCGGCGTTT-TACAAAAAACGCCAC-AAAAATCGAGCA
* * *
43005866 TTAGCGGCATTTTACGAAAAACGCCGCAAAATATCGAGCA
1 TTAGCGGCGTTTTACAAAAAACGCCACAAAA-ATCGAGCA
** * * * *
43005906 TTAGCGGCGTTACATAAAAAACGCCACGAAAACCAAGCA
1 TTAGCGGCGTTTTACAAAAAACGCCACAAAAATCGAGCA
*
43005945 TTAGCGGCGTTTTACAAAAAGCGCC
1 TTAGCGGCGTTTTACAAAAAACGCC
43005970 GCAATAGAGT
Statistics
Matches: 84, Mismatches: 19, Indels: 4
0.79 0.18 0.04
Matches are distributed among these distances:
39 31 0.37
40 42 0.50
41 11 0.13
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.19
Consensus pattern (39 bp):
TTAGCGGCGTTTTACAAAAAACGCCACAAAAATCGAGCA
Found at i:43008008 original size:16 final size:16
Alignment explanation
Indices: 43007984--43008014 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
43007974 ATTTTTCCTC
43007984 TTCTAAAATCCCTAAG
1 TTCTAAAATCCCTAAG
*
43008000 TTCTGAAATCCCTAA
1 TTCTAAAATCCCTAA
43008015 CTCCATTTAC
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:0.26, G:0.06, T:0.32
Consensus pattern (16 bp):
TTCTAAAATCCCTAAG
Found at i:43010495 original size:34 final size:34
Alignment explanation
Indices: 43010457--43010562 Score: 105
Period size: 34 Copynumber: 3.2 Consensus size: 34
43010447 ATCATATCTT
43010457 AACTTACATAGTGAAATAATACTTATAAGTGAAA
1 AACTTACATAGTGAAATAATACTTATAAGTGAAA
* * * ***
43010491 AACTTACCCTTGT-AAATATATA-TCAT-A-T-CTT
1 AACTTA-CATAGTGAAATA-ATACTTATAAGTGAAA
43010522 AACTTACATAGTGAAATAATACTTATAAGTGAAA
1 AACTTACATAGTGAAATAATACTTATAAGTGAAA
43010556 AACTTAC
1 AACTTAC
43010563 CCTTGTAATA
Statistics
Matches: 53, Mismatches: 12, Indels: 14
0.67 0.15 0.18
Matches are distributed among these distances:
30 7 0.13
31 14 0.26
32 2 0.04
33 2 0.04
34 21 0.40
35 7 0.13
ACGTcount: A:0.45, C:0.13, G:0.08, T:0.33
Consensus pattern (34 bp):
AACTTACATAGTGAAATAATACTTATAAGTGAAA
Found at i:43010510 original size:65 final size:65
Alignment explanation
Indices: 43010438--43010570 Score: 266
Period size: 65 Copynumber: 2.0 Consensus size: 65
43010428 ACATAATACA
43010438 TAAATATATATCATATCTTAACTTACATAGTGAAATAATACTTATAAGTGAAAAACTTACCCTTG
1 TAAATATATATCATATCTTAACTTACATAGTGAAATAATACTTATAAGTGAAAAACTTACCCTTG
43010503 TAAATATATATCATATCTTAACTTACATAGTGAAATAATACTTATAAGTGAAAAACTTACCCTTG
1 TAAATATATATCATATCTTAACTTACATAGTGAAATAATACTTATAAGTGAAAAACTTACCCTTG
43010568 TAA
1 TAA
43010571 TATCTGCTGA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 68 1.00
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.35
Consensus pattern (65 bp):
TAAATATATATCATATCTTAACTTACATAGTGAAATAATACTTATAAGTGAAAAACTTACCCTTG
Found at i:43010539 original size:31 final size:31
Alignment explanation
Indices: 43010439--43010539 Score: 89
Period size: 31 Copynumber: 3.2 Consensus size: 31
43010429 CATAATACAT
43010439 AAATATATATCATATCTTAACTTACATAGTG
1 AAATATATATCATATCTTAACTTACATAGTG
* *** * *
43010470 AAATA-ATACTTATAAGTGAAAAACTTACCCTTGT-
1 AAATATATA-TCAT-A-T-CTTAACTTA-CATAGTG
43010504 AAATATATATCATATCTTAACTTACATAGTG
1 AAATATATATCATATCTTAACTTACATAGTG
43010535 AAATA
1 AAATA
43010540 ATACTTATAA
Statistics
Matches: 51, Mismatches: 12, Indels: 14
0.66 0.16 0.18
Matches are distributed among these distances:
30 7 0.14
31 19 0.37
32 2 0.04
33 2 0.04
34 14 0.27
35 7 0.14
ACGTcount: A:0.45, C:0.13, G:0.07, T:0.36
Consensus pattern (31 bp):
AAATATATATCATATCTTAACTTACATAGTG
Found at i:43016086 original size:21 final size:21
Alignment explanation
Indices: 43016062--43016102 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
43016052 AGCAAATGCG
43016062 GCAGCGAGAGAAGCAGAGGTA
1 GCAGCGAGAGAAGCAGAGGTA
*
43016083 GCAGCGAGAGAAGCTGAGGT
1 GCAGCGAGAGAAGCAGAGGT
43016103 TCAATGAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.15, G:0.44, T:0.07
Consensus pattern (21 bp):
GCAGCGAGAGAAGCAGAGGTA
Found at i:43016175 original size:21 final size:21
Alignment explanation
Indices: 43016149--43016207 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
43016139 AGTAGATCCG
**
43016149 GCAGCGAAAGAAGCAGAGGCT
1 GCAGCGAGGGAAGCAGAGGCT
* *
43016170 GTAGCGAGGGAAGTAGAGGCT
1 GCAGCGAGGGAAGCAGAGGCT
43016191 GCAGCGAGGGAAGCAGA
1 GCAGCGAGGGAAGCAGA
43016208 ACAGCTTAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.34, C:0.15, G:0.44, T:0.07
Consensus pattern (21 bp):
GCAGCGAGGGAAGCAGAGGCT
Found at i:43016177 original size:87 final size:87
Alignment explanation
Indices: 43016001--43016167 Score: 239
Period size: 87 Copynumber: 1.9 Consensus size: 87
43015991 AGGCAACATT
* *
43016001 GAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAACTACAACTTAAAGCAAATGCGGCAG
1 GAGAGAAGCTGAGGTTCAAAAAAGATATGAACAACTCCAACTACAACTTAAAGCAAATCCGGCAG
*
43016066 CGAGAGAAGCAGAGGTAGCAGC
66 CGAAAGAAGCAGAGGTAGCAGC
* * * *
43016088 GAGAGAAGCTGAGGTTCAATGAAAG-TATGAACAACTCCAGC-AGCAACTTAAAGTAGATCCGGC
1 GAGAGAAGCTGAGGTTCAA-AAAAGATATGAACAACTCCAACTA-CAACTTAAAGCAAATCCGGC
43016151 AGCGAAAGAAGCAGAGG
64 AGCGAAAGAAGCAGAGG
43016168 CTGTAGCGAG
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
86 1 0.01
87 66 0.93
88 4 0.06
ACGTcount: A:0.41, C:0.17, G:0.28, T:0.13
Consensus pattern (87 bp):
GAGAGAAGCTGAGGTTCAAAAAAGATATGAACAACTCCAACTACAACTTAAAGCAAATCCGGCAG
CGAAAGAAGCAGAGGTAGCAGC
Found at i:43017654 original size:11 final size:11
Alignment explanation
Indices: 43017638--43017735 Score: 73
Period size: 11 Copynumber: 9.3 Consensus size: 11
43017628 TCAATTATTT
43017638 TCTCAATTTCC
1 TCTCAATTTCC
43017649 TCTCAATTTCC
1 TCTCAATTTCC
* *
43017660 TCTCAAATTGC
1 TCTCAATTTCC
43017671 TCTCAATTTCC
1 TCTCAATTTCC
43017682 T-TCCAAATTT-C
1 TCT-C-AATTTCC
*
43017693 TCTCAA-ATCC
1 TCTCAATTTCC
* **
43017703 -AT--ATTTAA
1 TCTCAATTTCC
*
43017711 TCTCAATTTGC
1 TCTCAATTTCC
43017722 TCTCAATTTCC
1 TCTCAATTTCC
43017733 TCT
1 TCT
43017736 TAAATTTCTC
Statistics
Matches: 66, Mismatches: 13, Indels: 16
0.69 0.14 0.17
Matches are distributed among these distances:
7 1 0.02
8 1 0.02
9 3 0.05
10 4 0.06
11 51 0.77
12 6 0.09
ACGTcount: A:0.23, C:0.31, G:0.02, T:0.44
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:43017676 original size:33 final size:33
Alignment explanation
Indices: 43017638--43017700 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
43017628 TCAATTATTT
43017638 TCTCAATTTCC-TCTC-AATTTCCTCTCAAATTGC
1 TCTCAATTTCCTTC-CAAATTT-CTCTCAAATTGC
43017671 TCTCAATTTCCTTCCAAATTTCTCTCAAAT
1 TCTCAATTTCCTTCCAAATTTCTCTCAAAT
43017701 CCATATTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 21 0.75
34 7 0.25
ACGTcount: A:0.24, C:0.32, G:0.02, T:0.43
Consensus pattern (33 bp):
TCTCAATTTCCTTCCAAATTTCTCTCAAATTGC
Found at i:43017715 original size:51 final size:51
Alignment explanation
Indices: 43017660--43017759 Score: 148
Period size: 51 Copynumber: 2.0 Consensus size: 51
43017650 CTCAATTTCC
43017660 TCTCAAATTGCTCTCAATTTCCT-TCCAAATTTCTCTCAAATCCATATTTAA
1 TCTCAAATTGCTCTCAATTTCCTCT-CAAATTTCTCTCAAATCCATATTTAA
* * * *
43017711 TCTCAATTTGCTCTCAATTTCCTCTTAAATTTCTCTTAAATCCCTATTT
1 TCTCAAATTGCTCTCAATTTCCTCTCAAATTTCTCTCAAATCCATATTT
43017760 TTAATTATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 43 0.98
52 1 0.02
ACGTcount: A:0.26, C:0.27, G:0.02, T:0.45
Consensus pattern (51 bp):
TCTCAAATTGCTCTCAATTTCCTCTCAAATTTCTCTCAAATCCATATTTAA
Found at i:43019593 original size:18 final size:18
Alignment explanation
Indices: 43019562--43019604 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
43019552 TGCCAGGTGC
*
43019562 GTATCCTAGCCCTTTTAT
1 GTATCCTAGCCCTTATAT
43019580 GTATCCTAAG-CCTTATAT
1 GTATCCT-AGCCCTTATAT
*
43019598 GTTTCCT
1 GTATCCT
43019605 TTTTCTAGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.19, C:0.26, G:0.12, T:0.44
Consensus pattern (18 bp):
GTATCCTAGCCCTTATAT
Found at i:43020095 original size:49 final size:50
Alignment explanation
Indices: 43020025--43020151 Score: 222
Period size: 50 Copynumber: 2.6 Consensus size: 50
43020015 GTTTATATTA
43020025 ATGTAAT-AAATACAAAATAGTTTA-ATTTGAATATTTTGATATTATTTG
1 ATGTAATAAAATACAAAATAGTTTATATTTGAATATTTTGATATTATTTG
*
43020073 ATGTAATAAAATACAAAATAGTTTATTTTTGAATATTTTGATATTATTTG
1 ATGTAATAAAATACAAAATAGTTTATATTTGAATATTTTGATATTATTTG
*
43020123 ATGTAATAAAATACAAAATAGTTAATATT
1 ATGTAATAAAATACAAAATAGTTTATATT
43020152 CTTAATAATA
Statistics
Matches: 74, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
48 7 0.09
49 17 0.23
50 50 0.68
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.44
Consensus pattern (50 bp):
ATGTAATAAAATACAAAATAGTTTATATTTGAATATTTTGATATTATTTG
Found at i:43020169 original size:50 final size:50
Alignment explanation
Indices: 43020025--43020171 Score: 158
Period size: 50 Copynumber: 3.0 Consensus size: 50
43020015 GTTTATATTA
* * ** *
43020025 ATGTAAT-AAATACAAAATAGTTTAAT-TTGAATATTTTGATATTATTTG
1 ATGTAATAAAATACAAAATAGTTTATTCTTGAATATATAAAAATTATTTG
* * ** *
43020073 ATGTAATAAAATACAAAATAGTTTATTTTTGAATATTTTGATATTATTTG
1 ATGTAATAAAATACAAAATAGTTTATTCTTGAATATATAAAAATTATTTG
43020123 ATGTAATAAAATACAAAATAGTTAATATTCTT-AATA-ATAAAAATTATTT
1 ATGTAATAAAATACAAAATAGTT--TATTCTTGAATATATAAAAATTATTT
43020172 TAAATAATTC
Statistics
Matches: 89, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
48 7 0.08
49 18 0.20
50 54 0.61
51 4 0.04
52 6 0.07
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (50 bp):
ATGTAATAAAATACAAAATAGTTTATTCTTGAATATATAAAAATTATTTG
Found at i:43022773 original size:19 final size:19
Alignment explanation
Indices: 43022751--43022789 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
43022741 AAGAAATTAT
43022751 AAAATTTA-TTAAAATTAAC
1 AAAATTTATTTAAAA-TAAC
43022770 AAAATTTATTTAAAATAAC
1 AAAATTTATTTAAAATAAC
43022789 A
1 A
43022790 TCCAGAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAATTTATTTAAAATAAC
Found at i:43033737 original size:60 final size:60
Alignment explanation
Indices: 43033640--43033766 Score: 146
Period size: 60 Copynumber: 2.1 Consensus size: 60
43033630 CTTAAATATA
* ** * * * * * *
43033640 AAAAATTCATCAAATTTAGCCCTTAATGTTTAAAAAATTTTTCATTTTAGTTCTAATTCT
1 AAAAATTCATCAAATTTAGCCCTCAAAATTTAAAAAATCTATCAATTTACTCCTAACTCT
* * *
43033700 AAAAATTCATTAAATTTGGCCCTCAAAATTTATAAAATCTATCAATTTACTCCTAACTCT
1 AAAAATTCATCAAATTTAGCCCTCAAAATTTAAAAAATCTATCAATTTACTCCTAACTCT
43033760 AAAAATT
1 AAAAATT
43033767 TTAAAAATAA
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.40, C:0.16, G:0.04, T:0.40
Consensus pattern (60 bp):
AAAAATTCATCAAATTTAGCCCTCAAAATTTAAAAAATCTATCAATTTACTCCTAACTCT
Found at i:43035840 original size:12 final size:12
Alignment explanation
Indices: 43035823--43035888 Score: 86
Period size: 12 Copynumber: 5.8 Consensus size: 12
43035813 AACTAATCCT
43035823 CTCTCAAATTTC
1 CTCTCAAATTTC
43035835 CTCTCAAATTTC
1 CTCTCAAATTTC
43035847 CTCTCAAA-TTC
1 CTCTCAAATTTC
43035858 CTCTC-AATTTC
1 CTCTCAAATTTC
*
43035869 CT-TCCAAAATT-
1 CTCT-CAAATTTC
43035880 CTCTCAAAT
1 CTCTCAAAT
43035889 CCATATTTAA
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
10 3 0.06
11 20 0.42
12 25 0.52
ACGTcount: A:0.27, C:0.33, G:0.00, T:0.39
Consensus pattern (12 bp):
CTCTCAAATTTC
Found at i:43035862 original size:23 final size:23
Alignment explanation
Indices: 43035823--43035888 Score: 84
Period size: 23 Copynumber: 2.9 Consensus size: 23
43035813 AACTAATCCT
43035823 CTCTCAAATTTCCTCTCAAATTTC
1 CTCTCAAA-TTCCTCTCAAATTTC
43035847 CTCTCAAATTCCTCTC-AATTTC
1 CTCTCAAATTCCTCTCAAATTTC
43035869 CT-TCCAAAATT-CTCTCAAAT
1 CTCT-C-AAATTCCTCTCAAAT
43035889 CCATATTTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
21 1 0.03
22 14 0.36
23 16 0.41
24 8 0.21
ACGTcount: A:0.27, C:0.33, G:0.00, T:0.39
Consensus pattern (23 bp):
CTCTCAAATTCCTCTCAAATTTC
Found at i:43035869 original size:22 final size:22
Alignment explanation
Indices: 43035823--43035886 Score: 78
Period size: 22 Copynumber: 2.8 Consensus size: 22
43035813 AACTAATCCT
43035823 CTCTCAAATTTCCTCTCAAATTTC
1 CTCTCAAA-TTCCTCTC-AATTTC
43035847 CTCTCAAATTCCTCTCAATTTC
1 CTCTCAAATTCCTCTCAATTTC
43035869 CT-TCCAAAATT-CTCTCAA
1 CTCT-C-AAATTCCTCTCAA
43035887 ATCCATATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
21 1 0.03
22 16 0.42
23 13 0.34
24 8 0.21
ACGTcount: A:0.27, C:0.34, G:0.00, T:0.39
Consensus pattern (22 bp):
CTCTCAAATTCCTCTCAATTTC
Found at i:43036917 original size:21 final size:20
Alignment explanation
Indices: 43036878--43036915 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
43036868 TAACGAGGTA
43036878 AATTTTATAATAGATTTTAC
1 AATTTTATAATAGATTTTAC
43036898 AATTATTAT-ATAGATTTT
1 AATT-TTATAATAGATTTT
43036916 TAAAAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (20 bp):
AATTTTATAATAGATTTTAC
Found at i:43038099 original size:45 final size:45
Alignment explanation
Indices: 43038050--43038137 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
43038040 ATATTTTGAA
* *
43038050 TATTTTGATATTATTTTATGTAATAAAATAGAAA-TTTTTTTGAGT
1 TATTTTGATATTATTTGATGTAATAAAATA-AAAGTTTATTTGAGT
43038095 TATTTTGATATTATTTGATGTAATAAAATAAAAGTTTATTTGA
1 TATTTTGATATTATTTGATGTAATAAAATAAAAGTTTATTTGA
43038138 TGTAATAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
44 3 0.08
45 37 0.93
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (45 bp):
TATTTTGATATTATTTGATGTAATAAAATAAAAGTTTATTTGAGT
Found at i:43041538 original size:125 final size:125
Alignment explanation
Indices: 43041316--43041694 Score: 614
Period size: 125 Copynumber: 3.0 Consensus size: 125
43041306 CTCAAACATG
*
43041316 CTACTGTAGCAAAAGCGCATCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* *
43041381 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAGAAATTACTTCTTCTATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAAAAACGTCAAAAAGAAATTATTTCTTCTATGAC
43041441 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* **
43041506 TAGAAGCGATTTTATACTATTTGCTCAAAAACGTCAAAAAAAAAATTATTTCTTCCGTGAC
66 TAGAAGCGATTTTATACTATTTGCTCAAAAACGTC-AAAAAGAAATTATTTCTTCTATGAC
* * *
43041567 CTACTGTAGCAAAAGCGCGTCCACGAGAGCGCAATTTCACAAATTCTTCTCAAATAGCATCCTAC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* * *** *
43041632 TAGAAGCGATTTTATACTATTTGATCACAAACGTCAACTTGAAATTATTTCTTCTAGGAC
66 TAGAAGCGATTTTATACTATTTGCTCAAAAACGTCAAAAAGAAATTATTTCTTCTATGAC
43041692 CTA
1 CTA
43041695 AAAACCCTAG
Statistics
Matches: 235, Mismatches: 18, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
125 119 0.51
126 116 0.49
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.28
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TAGAAGCGATTTTATACTATTTGCTCAAAAACGTCAAAAAGAAATTATTTCTTCTATGAC
Found at i:43041637 original size:126 final size:126
Alignment explanation
Indices: 43041316--43041668 Score: 600
Period size: 126 Copynumber: 2.8 Consensus size: 126
43041306 CTCAAACATG
*
43041316 CTACTGTAGCAAAAGCGCATCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* * *
43041381 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTC-AAAAAGAAATTACTTCTTCTATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAAAAACGTCAAAAAAAAAATTACTTCTTCCATGAC
43041441 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* *
43041506 TAGAAGCGATTTTATACTATTTGCTCAAAAACGTCAAAAAAAAAATTATTTCTTCCGTGAC
66 TAGAAGCGATTTTATACTATTTGCTCAAAAACGTCAAAAAAAAAATTACTTCTTCCATGAC
* * *
43041567 CTACTGTAGCAAAAGCGCGTCCACGAGAGCGCAATTTCACAAATTCTTCTCAAATAGCATCCTAC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* *
43041632 TAGAAGCGATTTTATACTATTTGATCACAAACGTCAA
66 TAGAAGCGATTTTATACTATTTGCTCAAAAACGTCAA
43041669 CTTGAAATTA
Statistics
Matches: 216, Mismatches: 11, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
125 98 0.45
126 118 0.55
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (126 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TAGAAGCGATTTTATACTATTTGCTCAAAAACGTCAAAAAAAAAATTACTTCTTCCATGAC
Found at i:43044355 original size:8 final size:8
Alignment explanation
Indices: 43044342--43044371 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
43044332 ATCTGCTCTA
43044342 ATTATTTT
1 ATTATTTT
43044350 ATTATTTT
1 ATTATTTT
43044358 ATTATTTT
1 ATTATTTT
43044366 ATTATT
1 ATTATT
43044372 CTGAATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (8 bp):
ATTATTTT
Found at i:43052831 original size:248 final size:252
Alignment explanation
Indices: 43052389--43052893 Score: 910
Period size: 248 Copynumber: 2.0 Consensus size: 252
43052379 TTTTGGTTAA
43052389 CATTAGCCTCAAAATTTGACATTTTTTTTACTGTGTTAATACCTGAAAAAATAATATATATATAT
1 CATTAGCCTCAAAATTTGACA-TTTTTTTACTGTGTTAATACCTGAAAAAATAATATATATATAT
* *
43052454 ATACATAAATTATTAAAAATAAATAAATTAAAACAATTAAATGAGATGTGACAATTTAAATGGAA
65 ATACATAAATTATTAAAAACAAATAAATTAAAACAATTAAATGAGATGTGACAATTTAAATGAAA
43052519 TCTAAATTCAAGGATCAAAATAGAAAAAAAAAACTAAGGCTAATGGAGATAAAGAAGTTCAAAGA
130 TCTAAATTCAAGGATCAAAATAGAAAAAAAAAACTAAGGCTAATGGAGATAAAGAAGTTCAAAGA
* *
43052584 CCAAGTTAATCGTTTTAAATATATTATTTTACATTTAAATAAAAGTAA-TTTTATTAT
195 CCAAGTTAATCATTTTAAATATATTATTTCACATTTAAATAAAAGTAATTTTTATTAT
43052641 CATTAGCCTCAAAATTTGACA-TTTTTTACTGTGTTAATACCTGAAAAAAT-A-ATATATATATA
1 CATTAGCCTCAAAATTTGACATTTTTTTACTGTGTTAATACCTGAAAAAATAATATATATATATA
* *
43052703 TACATAAATTATTAAAAACATATAAATTAAAACAATTAAATGAGATGTGACAATTTAAGTGAAAT
66 TACATAAATTATTAAAAACAAATAAATTAAAACAATTAAATGAGATGTGACAATTTAAATGAAAT
*
43052768 CTAAATTCAAGTATCAAAATAGAAAAAAAAAACTAAGGCTAATGGAGATAAAGAAGTTCAAAGAC
131 CTAAATTCAAGGATCAAAATAGAAAAAAAAAACTAAGGCTAATGGAGATAAAGAAGTTCAAAGAC
43052833 CAAGTTAATCATTTTAAATATATTATTTCACATTTAAATAAAAGTAATTTTTATTAT
196 CAAGTTAATCATTTTAAATATATTATTTCACATTTAAATAAAAGTAATTTTTATTAT
43052890 CATT
1 CATT
43052894 TAAATATTTT
Statistics
Matches: 245, Mismatches: 7, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
248 181 0.74
249 14 0.06
250 29 0.12
252 21 0.09
ACGTcount: A:0.48, C:0.09, G:0.10, T:0.34
Consensus pattern (252 bp):
CATTAGCCTCAAAATTTGACATTTTTTTACTGTGTTAATACCTGAAAAAATAATATATATATATA
TACATAAATTATTAAAAACAAATAAATTAAAACAATTAAATGAGATGTGACAATTTAAATGAAAT
CTAAATTCAAGGATCAAAATAGAAAAAAAAAACTAAGGCTAATGGAGATAAAGAAGTTCAAAGAC
CAAGTTAATCATTTTAAATATATTATTTCACATTTAAATAAAAGTAATTTTTATTAT
Found at i:43057056 original size:33 final size:33
Alignment explanation
Indices: 43057019--43057081 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
43057009 ATTTCCCTTT
43057019 GTACAATGTTTCAAAAAATTGTGGAGTTAGTGC
1 GTACAATGTTTCAAAAAATTGTGGAGTTAGTGC
43057052 GTACAATGTTTCAAAAAATTGTGGAGTTAG
1 GTACAATGTTTCAAAAAATTGTGGAGTTAG
43057082 CACTAACTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.35, C:0.08, G:0.24, T:0.33
Consensus pattern (33 bp):
GTACAATGTTTCAAAAAATTGTGGAGTTAGTGC
Found at i:43057740 original size:61 final size:63
Alignment explanation
Indices: 43057626--43057758 Score: 189
Period size: 61 Copynumber: 2.1 Consensus size: 63
43057616 AGCTCTTTCA
* * *
43057626 AAGAGGATATATACATAGGTTATGGAGTCACAATAAAATAAGATTATAGTATGTACCAGTGAT
1 AAGAAGATATATAAATAGGTTATGGAGTCACAATAAAATAAGATTATACTATGTACCAGTGAT
* **
43057689 AAGAAGATA-ATAAATAGGTTCTGGAGTCA-AATAAAATAAGATTATACTATGTATTAGTGAT
1 AAGAAGATATATAAATAGGTTATGGAGTCACAATAAAATAAGATTATACTATGTACCAGTGAT
*
43057750 ACGAAGATA
1 AAGAAGATA
43057759 GTGAGTGAAC
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
61 37 0.59
62 18 0.29
63 8 0.13
ACGTcount: A:0.45, C:0.07, G:0.20, T:0.29
Consensus pattern (63 bp):
AAGAAGATATATAAATAGGTTATGGAGTCACAATAAAATAAGATTATACTATGTACCAGTGAT
Found at i:43068928 original size:20 final size:20
Alignment explanation
Indices: 43068905--43068950 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
43068895 CCCACATGCT
43068905 CGTGTGGACAGGCACACGCC
1 CGTGTGGACAGGCACACGCC
* *
43068925 CGTGCGGATAGGCACACGCC
1 CGTGTGGACAGGCACACGCC
43068945 CGTGTG
1 CGTGTG
43068951 AAAACCACTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.17, C:0.33, G:0.37, T:0.13
Consensus pattern (20 bp):
CGTGTGGACAGGCACACGCC
Found at i:43071780 original size:102 final size:102
Alignment explanation
Indices: 43071665--43071865 Score: 305
Period size: 102 Copynumber: 2.0 Consensus size: 102
43071655 GAATATAAAG
* * *
43071665 GGGGTTGCTAAGTGCTGATTCCCC-AATTCATTGGTGGTTGCTAAGTGTTGATTCCACCGTATTT
1 GGGGTTGCTAAGTGCTGATTCCCCGAA-TCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCT
* *
43071729 TAAATATGAAGGGGGTTGCTACGTGCTGATTCCCCCAA
65 TAAATATGAAAGGGGTTGCTAAGTGCTGATTCCCCCAA
* *
43071767 GGGGTTGCTAAGTGTTGATTCCCCGAATCATTGGTGGTTGTTAAGTGCTGATCCCACCGTATCTT
1 GGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCTT
* *
43071832 AAATGTGAAAGGGGTTGCTAAGTGTTGATTCCCC
66 AAATATGAAAGGGGTTGCTAAGTGCTGATTCCCC
43071866 GATTCATTGG
Statistics
Matches: 89, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
102 87 0.98
103 2 0.02
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.33
Consensus pattern (102 bp):
GGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCTT
AAATATGAAAGGGGTTGCTAAGTGCTGATTCCCCCAA
Found at i:43071942 original size:77 final size:75
Alignment explanation
Indices: 43071765--43071977 Score: 336
Period size: 75 Copynumber: 2.8 Consensus size: 75
43071755 TGATTCCCCC
* *
43071765 AAGGGGTTGCTAAGTGTTGATTCCCCGAATCATTGGTGGTTGTTAAGTGCTGATCCCACCGTATC
1 AAGGGGTTGCTAAGTGTTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
43071830 TTAAATGTGA
66 TTAAATGTGA
* * *
43071840 AAGGGGTTGCTAAGTGTTGATTCCCCGATTCATTGGTGGTTGCTAAGTGTTGATTCCACTGTATT
1 AAGGGGTTGCTAAGTGTTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTA-T
* *
43071905 TTTTAATGTGAA
65 CTTAAATGTG-A
*
43071917 AAGGGGTTGCTAAGTGTTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGAATCCACCG
1 AAGGGGTTGCTAAGTGTTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCG
43071978 ATAACGGATA
Statistics
Matches: 125, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
75 58 0.46
76 9 0.07
77 58 0.46
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.35
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGTTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
TTAAATGTGA
Found at i:43076329 original size:61 final size:61
Alignment explanation
Indices: 43076264--43076666 Score: 210
Period size: 61 Copynumber: 6.6 Consensus size: 61
43076254 TTTGATTGTT
* *
43076264 TTATATATTGTCGAATTAATTCGTATATAATTATACATTGCTAAAATTAATTTGTATATAG
1 TTATACATTGTCGAATTAATTCGTATATGATTATACATTGCTAAAATTAATTTGTATATAG
* * *
43076325 TTATACATTGTTGAAATTGAATT-GTATATGGA-TATA-AGTTGCT-GAATTAATTTGTATATGG
1 TTATACATTGTCG-AATT-AATTCGTATAT-GATTATACA-TTGCTAAAATTAATTTGTATATAG
* * * * * * * *
43076386 TTGTAAATTG-CTGAAATTTATTTGTATATGGTTATACATT-ATCGAAATTGATTTGTATATGAA
1 TTATACATTGTC-G-AATTAATTCGTATATGATTATACATTGCT-AAAATTAATTTGTATAT--A
43076449 G
61 G
* * * * *
43076450 --ATA-AGTTG-CAGAATTGACTCGTATATGATTATACTTTGCAAAAATTAATTTGTATATGG
1 TTATACA-TTGTC-GAATTAATTCGTATATGATTATACATTGCTAAAATTAATTTGTATATAG
* * * ** *
43076509 TTATACATTGTTGAATTTCAATT-GTATATG--GATACAAGTTAC-CGAATTAATTCGTATAT-G
1 TTATACATTGTCGAA-TT-AATTCGTATATGATTATAC-A-TTGCTAAAATTAATTTGTATATAG
* * * * * * *
43076569 ATTATACATTGTCGAACTTGATTCATATATGGTTATACATTGC-CAATTTGATTTGCATAT-G
1 -TTATACATTGTCGAA-TTAATTCGTATATGATTATACATTGCTAAAATTAATTTGTATATAG
* * *
43076630 ATTATACATTGCCGAATTTGATTCGTATATGAATATA
1 -TTATACATTGTCGAA-TTAATTCGTATATGATTATA
43076667 TATATTGTTG
Statistics
Matches: 265, Mismatches: 51, Indels: 52
0.72 0.14 0.14
Matches are distributed among these distances:
59 1 0.00
60 13 0.05
61 184 0.69
62 55 0.21
63 11 0.04
64 1 0.00
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.43
Consensus pattern (61 bp):
TTATACATTGTCGAATTAATTCGTATATGATTATACATTGCTAAAATTAATTTGTATATAG
Found at i:43076376 original size:92 final size:92
Alignment explanation
Indices: 43076276--43076610 Score: 402
Period size: 92 Copynumber: 3.6 Consensus size: 92
43076266 ATATATTGTC
* *
43076276 GAATTAATTCGTATATAATTATACATTGCTAAAATTAATTTGTATATAGTTATACATTGTTGAAA
1 GAATTAATTCGTATATGATTATACATTGCTAAAATTAATTTGTATATGGTTATACATTGTTGAAA
*
43076341 TTGAATTGTATATGGATATAAGTTGCT
66 TTGAATTGTATATGGATATAAGTTGCA
* * * * * * * *
43076368 GAATTAATTTGTATATGGTTGTAAATTGCTGAAATTTATTTGTATATGGTTATACATTATCGAAA
1 GAATTAATTCGTATATGATTATACATTGCTAAAATTAATTTGTATATGGTTATACATTGTTGAAA
* * *
43076433 TTGATTTGTATATGAAGATAAGTTGCA
66 TTGAATTGTATATGGATATAAGTTGCA
* * * * *
43076460 GAATTGACTCGTATATGATTATACTTTGCAAAAATTAATTTGTATATGGTTATACATTGTTGAAT
1 GAATTAATTCGTATATGATTATACATTGCTAAAATTAATTTGTATATGGTTATACATTGTTGAAA
* * * *
43076525 TTCAATTGTATATGGATACAAGTTACC
66 TTGAATTGTATATGGATATAAGTTGCA
* * * **
43076552 GAATTAATTCGTATATGATTATACATTG-TCGAACTTGATTCATATATGGTTATACATTG
1 GAATTAATTCGTATATGATTATACATTGCT-AAAATTAATTTGTATATGGTTATACATTG
43076611 CCAATTTGAT
Statistics
Matches: 199, Mismatches: 43, Indels: 2
0.82 0.18 0.01
Matches are distributed among these distances:
92 199 1.00
ACGTcount: A:0.34, C:0.07, G:0.16, T:0.43
Consensus pattern (92 bp):
GAATTAATTCGTATATGATTATACATTGCTAAAATTAATTTGTATATGGTTATACATTGTTGAAA
TTGAATTGTATATGGATATAAGTTGCA
Found at i:43076651 original size:31 final size:31
Alignment explanation
Indices: 43076264--43076666 Score: 186
Period size: 31 Copynumber: 13.2 Consensus size: 31
43076254 TTTGATTGTT
* * * *
43076264 TTATATATTGTCGAA-TTAATTCGTATATAA
1 TTATACATTGCCGAATTTGATTCGTATATGA
** * * *
43076294 TTATACATTGCTAAAATTAATTTGTATAT-A
1 TTATACATTGCCGAATTTGATTCGTATATGA
** *
43076324 GTTATACATTGTTGAAATTGAATT-GTATATGGA
1 -TTATACATTGCCGAATTTG-ATTCGTATAT-GA
* * * *
43076357 -TATA-AGTTGCTGAA-TTAATTTGTATATGG
1 TTATACA-TTGCCGAATTTGATTCGTATATGA
* * * * *
43076386 TTGTAAATTGCTGAAATTT-ATTTGTATATGG
1 TTATACATTGCCG-AATTTGATTCGTATATGA
** * *
43076417 TTATACATTATCGAAATTGATTTGTATATGA
1 TTATACATTGCCGAATTTGATTCGTATATGA
** * *
43076448 AGATA-AGTTGCAGAA-TTGACTCGTATATGA
1 TTATACA-TTGCCGAATTTGATTCGTATATGA
* ** * * * *
43076478 TTATACTTTGCAAAAATTAATTTGTATATGG
1 TTATACATTGCCGAATTTGATTCGTATATGA
** *
43076509 TTATACATTGTTGAATTTCAATT-GTATATG-
1 TTATACATTGCCGAATTT-GATTCGTATATGA
* * *
43076539 -GATACAAGTTACCGAA-TTAATTCGTATATGA
1 TTATAC-A-TTGCCGAATTTGATTCGTATATGA
* * * *
43076570 TTATACATTGTCGAACTTGATTCATATATGG
1 TTATACATTGCCGAATTTGATTCGTATATGA
* *
43076601 TTATACATTGCC-AATTTGATTTGCATATGA
1 TTATACATTGCCGAATTTGATTCGTATATGA
43076631 TTATACATTGCCGAATTTGATTCGTATATGA
1 TTATACATTGCCGAATTTGATTCGTATATGA
*
43076662 ATATA
1 TTATA
43076667 TATATTGTTG
Statistics
Matches: 292, Mismatches: 58, Indels: 45
0.74 0.15 0.11
Matches are distributed among these distances:
29 12 0.04
30 99 0.34
31 167 0.57
32 13 0.04
33 1 0.00
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.43
Consensus pattern (31 bp):
TTATACATTGCCGAATTTGATTCGTATATGA
Found at i:43076654 original size:92 final size:90
Alignment explanation
Indices: 43076275--43076684 Score: 274
Period size: 92 Copynumber: 4.4 Consensus size: 90
43076265 TATATATTGT
* * ** * ** * *
43076275 CGAATTAATTCGTATATAATTATACATTGCTAAAATTAATTTGTATATAGTTATACATTGTTGAA
1 CGAATTGATTCGTATATGATTATACATTG-TCGAATTGATTCATATATGGTTATACATTG-CGAA
* * *
43076340 ATTGAATTGTATATG-GATATAAGTTGC
64 TTTGATTTGTATATGAGATA-CAGTTGC
* * * * * * * ** *
43076367 TGAATTAATTTGTATATGGTTGTAAATTG-CTGAAATTTATTTGTATATGGTTATACATTATCGA
1 CGAATTGATTCGTATATGATTATACATTGTC-G-AATTGATTCATATATGGTTATACATT-GCGA
*
43076431 AATTGATTTGTATATGAAGATA-AGTTGC
63 ATTTGATTTGTATATG-AGATACAGTTGC
* * * * * ** *
43076459 AGAATTGACTCGTATATGATTATACTTTG-CAAAAATTAATTTGTATATGGTTATACATTGTTGA
1 CGAATTGATTCGTATATGATTATACATTGTC--GAATTGATTCATATATGGTTATACATTG-CGA
* * *
43076523 ATTTCAATTGTATATG-GATACAAGTTAC
63 ATTTGATTTGTATATGAGATAC-AGTTGC
* *
43076551 CGAATTAATTCGTATATGATTATACATTGTCGAACTTGATTCATATATGGTTATACATTGCCAAT
1 CGAATTGATTCGTATATGATTATACATTGTCGAA-TTGATTCATATATGGTTATACATTGCGAAT
* *
43076616 TTGATTTGCATATGATTATACA-TTGC
65 TTGATTTGTATATGA-GATACAGTTGC
* *
43076642 CGAATTTGATTCGTATATGAATATATATATTGTTGAATTGATT
1 CGAA-TTGATTCGTATATG-AT-TATACATTGTCGAATTGATT
43076685 TGAGCATTGG
Statistics
Matches: 254, Mismatches: 48, Indels: 31
0.76 0.14 0.09
Matches are distributed among these distances:
90 4 0.02
91 23 0.09
92 198 0.78
93 13 0.05
94 16 0.06
ACGTcount: A:0.34, C:0.08, G:0.16, T:0.43
Consensus pattern (90 bp):
CGAATTGATTCGTATATGATTATACATTGTCGAATTGATTCATATATGGTTATACATTGCGAATT
TGATTTGTATATGAGATACAGTTGC
Found at i:43088277 original size:21 final size:21
Alignment explanation
Indices: 43088252--43088302 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
43088242 GACACATAGA
43088252 TGCCTGAAACAACACACGAGG
1 TGCCTGAAACAACACACGAGG
* *
43088273 TGCCTGATACGACACACGAGG
1 TGCCTGAAACAACACACGAGG
43088294 TGCCTGAAA
1 TGCCTGAAA
43088303 TACGACACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.33, C:0.27, G:0.25, T:0.14
Consensus pattern (21 bp):
TGCCTGAAACAACACACGAGG
Found at i:43088305 original size:23 final size:22
Alignment explanation
Indices: 43088238--43088334 Score: 101
Period size: 23 Copynumber: 4.5 Consensus size: 22
43088228 CCTAATTAGT
* *
43088238 ATACGACACA-TAGATGCCTGA
1 ATACGACACACGAGGTGCCTGA
*
43088259 A-ACAACACACGAGGTGCCTG-
1 ATACGACACACGAGGTGCCTGA
43088279 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACGAGGTGCCTG-A
** *
43088302 ATACGACACATAAAGTGCCTGA
1 ATACGACACACGAGGTGCCTGA
43088324 TATACGACACA
1 -ATACGACACA
43088335 TAAAGTGTCT
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
20 8 0.12
21 27 0.42
22 1 0.02
23 28 0.44
ACGTcount: A:0.38, C:0.26, G:0.21, T:0.15
Consensus pattern (22 bp):
ATACGACACACGAGGTGCCTGA
Found at i:43088335 original size:23 final size:23
Alignment explanation
Indices: 43088237--43088347 Score: 97
Period size: 23 Copynumber: 5.0 Consensus size: 23
43088227 ACCTAATTAG
*
43088237 TATACGACACATAGA-TGCCTGA
1 TATACGACACATAAAGTGCCTGA
* ** *
43088259 -A-ACAACACACGAGGTGCCTG-
1 TATACGACACATAAAGTGCCTGA
** *
43088279 -ATACGACACACGAGGTGCCTGA
1 TATACGACACATAAAGTGCCTGA
*
43088301 AATACGACACATAAAGTGCCTGA
1 TATACGACACATAAAGTGCCTGA
*
43088324 TATACGACACATAAAGTGTCTGA
1 TATACGACACATAAAGTGCCTGA
43088347 T
1 T
43088348 CGGCAAAGCC
Statistics
Matches: 74, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
20 8 0.11
21 25 0.34
23 41 0.55
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (23 bp):
TATACGACACATAAAGTGCCTGA
Found at i:43089074 original size:19 final size:19
Alignment explanation
Indices: 43089050--43089100 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
43089040 GCTTCTCCTG
*
43089050 TTCTTTTTGTTTCTTTTAT
1 TTCTTTTTGTTTATTTTAT
*
43089069 TTCTTTAT-TTTATTTTAT
1 TTCTTTTTGTTTATTTTAT
43089087 TTACTTTATTGTTT
1 TT-CTTT-TTGTTT
43089101 TAATTACTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 11 0.42
19 11 0.42
20 1 0.04
21 3 0.12
ACGTcount: A:0.12, C:0.08, G:0.04, T:0.76
Consensus pattern (19 bp):
TTCTTTTTGTTTATTTTAT
Found at i:43092399 original size:16 final size:16
Alignment explanation
Indices: 43092362--43092416 Score: 62
Period size: 15 Copynumber: 3.6 Consensus size: 16
43092352 ATTCAATTAT
43092362 TCAATTCATAAATACA
1 TCAATTCATAAATACA
*
43092378 TC-ATTCATACCATAC-
1 TCAATTCATA-AATACA
*
43092393 TCAATTCATGAATACA
1 TCAATTCATAAATACA
43092409 -CAATTCAT
1 TCAATTCAT
43092417 GTGTCTCAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
15 21 0.64
16 12 0.36
ACGTcount: A:0.42, C:0.24, G:0.02, T:0.33
Consensus pattern (16 bp):
TCAATTCATAAATACA
Found at i:43092662 original size:37 final size:39
Alignment explanation
Indices: 43092567--43092670 Score: 113
Period size: 37 Copynumber: 2.7 Consensus size: 39
43092557 ACACACCAGC
***
43092567 TTGGCACCTAGTGCCTCATCGGATAATTTGAAGTAGTAAA
1 TTGGCACCTAGTGCCTCATCGGATAAACCGAAG-AGTAAA
* * * *
43092607 TTGACACCCAGTGTCTCATCGGTTAAACCG-A-AGTAAA
1 TTGGCACCTAGTGCCTCATCGGATAAACCGAAGAGTAAA
*
43092644 TTGGCACCTAGTGCCTCATCGAATAAA
1 TTGGCACCTAGTGCCTCATCGGATAAA
43092671 TCTGAAGTAA
Statistics
Matches: 52, Mismatches: 12, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
37 28 0.54
39 1 0.02
40 23 0.44
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (39 bp):
TTGGCACCTAGTGCCTCATCGGATAAACCGAAGAGTAAA
Found at i:43093568 original size:4 final size:4
Alignment explanation
Indices: 43093554--43093612 Score: 57
Period size: 4 Copynumber: 13.8 Consensus size: 4
43093544 GCCTTGTCAT
43093554 TTTC ATTTC TTTC TTTC -TTC TTTC TGTTTC GTTTC TATTC TTTC TTTC
1 TTTC -TTTC TTTC TTTC TTTC TTTC --TTTC -TTTC T-TTC TTTC TTTC
*
43093602 TTTA TTTC TTT
1 TTTC TTTC TTT
43093613 TTATTACTTA
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
3 3 0.06
4 28 0.58
5 13 0.27
6 4 0.08
ACGTcount: A:0.05, C:0.20, G:0.03, T:0.71
Consensus pattern (4 bp):
TTTC
Found at i:43093680 original size:40 final size:41
Alignment explanation
Indices: 43093622--43093698 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 41
43093612 TTTATTACTT
* *
43093622 ATTTTATTATTATCATATA-ATATATATACTTAAACATTAAG
1 ATTTTATTATTATAATATATATA-ATAAACTTAAACATTAAG
*
43093663 ATTTTA-TATTATAATATATATAATAAACTTACACAT
1 ATTTTATTATTATAATATATATAATAAACTTAAACAT
43093699 ATTTTAACCT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
40 23 0.72
41 9 0.28
ACGTcount: A:0.45, C:0.08, G:0.01, T:0.45
Consensus pattern (41 bp):
ATTTTATTATTATAATATATATAATAAACTTAAACATTAAG
Found at i:43102317 original size:20 final size:20
Alignment explanation
Indices: 43102292--43102339 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
43102282 GCAAAAATCA
*
43102292 AAAGTATTGATA-CTCTTAAC
1 AAAGTATCGATACCT-TTAAC
*
43102312 AAAGTATCGATACCTTTCAC
1 AAAGTATCGATACCTTTAAC
43102332 AAAGTATC
1 AAAGTATC
43102340 AATATCATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 23 0.92
21 2 0.08
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (20 bp):
AAAGTATCGATACCTTTAAC
Found at i:43104258 original size:42 final size:42
Alignment explanation
Indices: 43104212--43104319 Score: 121
Period size: 42 Copynumber: 2.6 Consensus size: 42
43104202 AAGTCAAATA
* *
43104212 GGCAAGGACATAGGCATTTGTCCAGACCA-TATGAGCTACACG
1 GGCAAGGACATAGGCATGTGTCCAGA-CAGTATGAGCCACACG
* * * *
43104254 GGCAAGGACATGGGCGTGTGTCCAGACAGTGTGAGCCATACG
1 GGCAAGGACATAGGCATGTGTCCAGACAGTATGAGCCACACG
*
43104296 GGCAAGGACAT-GAGCGTGTGTCCA
1 GGCAAGGACATAG-GCATGTGTCCA
43104320 AGTTGTGTGG
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
41 3 0.05
42 55 0.95
ACGTcount: A:0.27, C:0.22, G:0.33, T:0.18
Consensus pattern (42 bp):
GGCAAGGACATAGGCATGTGTCCAGACAGTATGAGCCACACG
Found at i:43105929 original size:104 final size:105
Alignment explanation
Indices: 43105784--43106030 Score: 311
Period size: 105 Copynumber: 2.4 Consensus size: 105
43105774 AGTGCAGGGT
* * * * * * *
43105784 TCACACGGGCAAAGGACACGAGCGTTTGTCTAGGCCATGTAACTCACTATTTGTGACTTAGTACC
1 TCACACGGGC-AAGGACACGGGCGTGTGTCCAGACCGTGTAACTCACTATTTATGACTTAGAACC
*
43105849 ACACGGC-CAG-GGACATGGGCGTGTGCCCAGGCCGTGTGAGG
65 ACAC-GCACAGAGGACATGGGCGTGTGCCCAGGCCGTGT-AAG
* **
43105890 T-ATACGGGCAAGGACACGGGCGTGTGTCCAGACCGTGTAACTCACTATTTATGTTTTAGAACCA
1 TCACACGGGCAAGGACACGGGCGTGTGTCCAGACCGTGTAACTCACTATTTATGACTTAGAACCA
43105954 CACGCACAGAGGACATGGGCGTGTGCCCAGGCCGTGTAAG
66 CACGCACAGAGGACATGGGCGTGTGCCCAGGCCGTGTAAG
** **
43105994 TCACAAAGGCAAGGACATAGGCGTGTGTCCAGACCGT
1 TCACACGGGCAAGGACACGGGCGTGTGTCCAGACCGT
43106031 ATGAGCTACA
Statistics
Matches: 122, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
103 2 0.02
104 55 0.45
105 64 0.52
106 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.30, T:0.20
Consensus pattern (105 bp):
TCACACGGGCAAGGACACGGGCGTGTGTCCAGACCGTGTAACTCACTATTTATGACTTAGAACCA
CACGCACAGAGGACATGGGCGTGTGCCCAGGCCGTGTAAG
Found at i:43106047 original size:42 final size:40
Alignment explanation
Indices: 43106001--43106117 Score: 110
Period size: 42 Copynumber: 2.8 Consensus size: 40
43105991 AAGTCACAAA
*
43106001 GGCAAGGACATAGGCGTGTGTCCAGACCGTATGAGCTACACG
1 GGCAAGGACAT-GGC-TGTGTCCAGACCGTATGAGCCACACG
* * * * *
43106043 GGCAAGGACATGTACATGTGTCCAGGCCATGTGAGCCATACG
1 GGCAAGGACATG-GC-TGTGTCCAGACCGTATGAGCCACACG
43106085 GGCAAGGACATGGGCTAGTGTCCA-AGCCGTATG
1 GGCAAGGACAT-GGCT-GTGTCCAGA-CCGTATG
43106118 GTATATAAAT
Statistics
Matches: 60, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
41 2 0.03
42 57 0.95
43 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.33, T:0.18
Consensus pattern (40 bp):
GGCAAGGACATGGCTGTGTCCAGACCGTATGAGCCACACG
Found at i:43107935 original size:54 final size:54
Alignment explanation
Indices: 43107877--43108004 Score: 152
Period size: 54 Copynumber: 2.4 Consensus size: 54
43107867 TCGTGTGTCT
*
43107877 CAAGTCCA-TGAGTTACACAGG-CTAGCACACGACCTACGACATGGCTGTGTGAGC
1 CAAGT-CAGTGAGTTACAC-GGACTAGCACACGACCTACGACACGGCTGTGTGAGC
* * * * * *
43107931 CAAGTCAGTGGGTTACACGGACTAGCACACGGCTTGCGACACGGTTGTGTGAGT
1 CAAGTCAGTGAGTTACACGGACTAGCACACGACCTACGACACGGCTGTGTGAGC
*
43107985 CAAGTTAGTGAGTTACACGG
1 CAAGTCAGTGAGTTACACGG
43108005 TCTATGAGAT
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
53 4 0.06
54 59 0.94
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.21
Consensus pattern (54 bp):
CAAGTCAGTGAGTTACACGGACTAGCACACGACCTACGACACGGCTGTGTGAGC
Found at i:43110291 original size:14 final size:14
Alignment explanation
Indices: 43110269--43110298 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
43110259 CAGAAAGAAG
43110269 TCTTCTTTTTTTTT
1 TCTTCTTTTTTTTT
43110283 TCTT-TTTTTTTTT
1 TCTTCTTTTTTTTT
43110296 TCT
1 TCT
43110299 GTAAATACAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (14 bp):
TCTTCTTTTTTTTT
Found at i:43112169 original size:3 final size:3
Alignment explanation
Indices: 43112161--43112187 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
43112151 ACTATCTTAT
43112161 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
43112188 ACAAGTTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:43122588 original size:28 final size:28
Alignment explanation
Indices: 43122554--43122610 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
43122544 CTGATATAAG
43122554 ATAAAATAATATATAATGTACTTAAGAT
1 ATAAAATAATATATAATGTACTTAAGAT
43122582 ATAAAATAATATATAATGTACTTAAGAT
1 ATAAAATAATATATAATGTACTTAAGAT
43122610 A
1 A
43122611 AATAGCTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.35
Consensus pattern (28 bp):
ATAAAATAATATATAATGTACTTAAGAT
Found at i:43124671 original size:57 final size:58
Alignment explanation
Indices: 43124572--43124707 Score: 186
Period size: 58 Copynumber: 2.3 Consensus size: 58
43124562 ATAGAAATAG
* *
43124572 TGAAAATGGAGAAATGAGAAACGTTTGGAAATGACTATGGTTTTCTCCAAAAT-AAAAA
1 TGAAAATGGAGAAATGA-AAACATTTGGAAATGAATATGGTTTTCTCCAAAATGAAAAA
* * *
43124630 TGAAAATGGAGAAATGAAATCATTTGGAAATGAATGTGGTTTTCTCCAAAATGGAAAA
1 TGAAAATGGAGAAATGAAAACATTTGGAAATGAATATGGTTTTCTCCAAAATGAAAAA
*
43124688 TGAAAAAT-GAAAAATGAAAA
1 TG-AAAATGGAGAAATGAAAA
43124708 ATGAAAAAGA
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
57 31 0.45
58 33 0.48
59 5 0.07
ACGTcount: A:0.48, C:0.07, G:0.21, T:0.25
Consensus pattern (58 bp):
TGAAAATGGAGAAATGAAAACATTTGGAAATGAATATGGTTTTCTCCAAAATGAAAAA
Found at i:43124681 original size:51 final size:52
Alignment explanation
Indices: 43124572--43124700 Score: 136
Period size: 57 Copynumber: 2.4 Consensus size: 52
43124562 ATAGAAATAG
* *
43124572 TGAAAATGGAGAAATGAGAAACGTTTGGAAATGACTATGGTTTTCTCCAAAATAAAAA
1 TGAAAATGGAGAAATGA-AAACATTTGGAAATGAATATGGTTTTCTCC-----AAAAA
* *
43124630 TGAAAATGGAGAAATGAAATCATTTGGAAATGAATGTGGTTTTCTCC-AAAA
1 TGAAAATGGAGAAATGAAAACATTTGGAAATGAATATGGTTTTCTCCAAAAA
*
43124681 TGGAAAAT-GAAAAATGAAAA
1 T-GAAAATGGAGAAATGAAAA
43124701 ATGAAAAATG
Statistics
Matches: 64, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
51 15 0.23
52 6 0.09
57 26 0.41
58 17 0.27
ACGTcount: A:0.47, C:0.07, G:0.21, T:0.26
Consensus pattern (52 bp):
TGAAAATGGAGAAATGAAAACATTTGGAAATGAATATGGTTTTCTCCAAAAA
Found at i:43124689 original size:7 final size:7
Alignment explanation
Indices: 43124677--43124715 Score: 69
Period size: 7 Copynumber: 5.6 Consensus size: 7
43124667 GGTTTTCTCC
*
43124677 AAAATGG
1 AAAATGA
43124684 AAAATGA
1 AAAATGA
43124691 AAAATGA
1 AAAATGA
43124698 AAAATGA
1 AAAATGA
43124705 AAAATGA
1 AAAATGA
43124712 AAAA
1 AAAA
43124716 GACCTGGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.13
Consensus pattern (7 bp):
AAAATGA
Found at i:43128179 original size:36 final size:35
Alignment explanation
Indices: 43128109--43128179 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 35
43128099 ATGACTAAAC
*
43128109 AATTCAATAATATAAATAATATAAAATCTGAAATTT
1 AATTCAATAATATAAATAATATAAAA-CTAAAATTT
*
43128145 AATTTAATAATATAAATAAATATATAAA-TAAAATT
1 AATTCAATAATATAAAT-AATATA-AAACTAAAATT
43128180 ATTACTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 22 0.71
37 6 0.19
38 3 0.10
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (35 bp):
AATTCAATAATATAAATAATATAAAACTAAAATTT
Found at i:43128429 original size:29 final size:30
Alignment explanation
Indices: 43128390--43128447 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
43128380 GGGGGTGGGA
*
43128390 TGGGAAGGGAGTAAAAGTTTTAGGGGAAAG
1 TGGGAAGGGAGTAAAAATTTTAGGGGAAAG
*
43128420 TGGG-AGGGAGTAAAAATTTTGGGGGAAA
1 TGGGAAGGGAGTAAAAATTTTAGGGGAAA
43128448 ATAAAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.36, C:0.00, G:0.43, T:0.21
Consensus pattern (30 bp):
TGGGAAGGGAGTAAAAATTTTAGGGGAAAG
Found at i:43128523 original size:30 final size:30
Alignment explanation
Indices: 43128489--43128554 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
43128479 ATTTTGTTTA
* *
43128489 GGGGAGGAAGTGGGAAGGAGTAAAAATTTT
1 GGGGAGAAACTGGGAAGGAGTAAAAATTTT
43128519 GGGGAGAAACTGGGAAGGAGTAAAAATTTT
1 GGGGAGAAACTGGGAAGGAGTAAAAATTTT
43128549 GAGGGA
1 G-GGGA
43128555 AAAATAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
30 29 0.88
31 4 0.12
ACGTcount: A:0.38, C:0.02, G:0.42, T:0.18
Consensus pattern (30 bp):
GGGGAGAAACTGGGAAGGAGTAAAAATTTT
Found at i:43128700 original size:9 final size:9
Alignment explanation
Indices: 43128686--43128718 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
43128676 ATTCGAGTTG
43128686 ACTCGAATA
1 ACTCGAATA
*
43128695 ACTCGATTA
1 ACTCGAATA
43128704 ACTCGAATA
1 ACTCGAATA
43128713 ACTCGA
1 ACTCGA
43128719 TTCGTTTAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.24
Consensus pattern (9 bp):
ACTCGAATA
Found at i:43128709 original size:18 final size:18
Alignment explanation
Indices: 43128686--43128720 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
43128676 ATTCGAGTTG
43128686 ACTCGAATAACTCGATTA
1 ACTCGAATAACTCGATTA
43128704 ACTCGAATAACTCGATT
1 ACTCGAATAACTCGATT
43128721 CGTTTAACTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.29
Consensus pattern (18 bp):
ACTCGAATAACTCGATTA
Found at i:43132419 original size:50 final size:50
Alignment explanation
Indices: 43132294--43132590 Score: 292
Period size: 50 Copynumber: 5.8 Consensus size: 50
43132284 ATTTGGGTAA
* *
43132294 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATG
* * * *
43132350 AGAGGTCCCACGTAAGACCATGTTTAGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
**
43132400 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * *
43132450 AGAGGTCCCCCGTAAGACTATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * * * *
43132500 AGAACTCCCATGTAAGACCATATCTGGGATATGACATTGGTA--GTACAGG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* ** *
43132549 AAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
43132591 TGTTATTATC
Statistics
Matches: 203, Mismatches: 37, Indels: 9
0.82 0.15 0.04
Matches are distributed among these distances:
48 1 0.00
49 37 0.18
50 124 0.61
53 3 0.01
55 1 0.00
56 37 0.18
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:43134256 original size:49 final size:50
Alignment explanation
Indices: 43134164--43134345 Score: 192
Period size: 49 Copynumber: 3.7 Consensus size: 50
43134154 GTCAGGCTGG
* *** * * *
43134164 TTAGCAACTAACATGCCTTACCAGAAACTCAGCA-CATATGCCAATTTGA
1 TTAGCAACTAACATGCCCTACCAGTGGCCCATCATCATACGCCAATTTGA
* * * *
43134213 TTAGCAACTAACATGTCCTACCAGTGGCCCATCATC-TTCGCCAACTTGG
1 TTAGCAACTAACATGCCCTACCAGTGGCCCATCATCATACGCCAATTTGA
* * * *
43134262 TTAGCAACTAGCACGCCCTACTAGTGGCCCAACA-CATACGCCAATTT-A
1 TTAGCAACTAACATGCCCTACCAGTGGCCCATCATCATACGCCAATTTGA
43134310 GTTAGCAACTAACATGCCCTACCAGTGGCCCATCAT
1 -TTAGCAACTAACATGCCCTACCAGTGGCCCATCAT
43134346 ATTCAGATAT
Statistics
Matches: 106, Mismatches: 23, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
48 1 0.01
49 104 0.98
50 1 0.01
ACGTcount: A:0.30, C:0.31, G:0.15, T:0.24
Consensus pattern (50 bp):
TTAGCAACTAACATGCCCTACCAGTGGCCCATCATCATACGCCAATTTGA
Found at i:43137606 original size:29 final size:28
Alignment explanation
Indices: 43137570--43137647 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
43137560 GTATGAGATT
43137570 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
43137600 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
43137627 TGGCACTAAGTGTGCGCGGTT
1 -GGCACTAAGTGTGCG-GGTT
43137648 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:43137921 original size:173 final size:174
Alignment explanation
Indices: 43137600--43137926 Score: 566
Period size: 173 Copynumber: 1.9 Consensus size: 174
43137590 AAATTGTACA
* *
43137600 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
* *
43137665 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
43137730 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
* * * *
43137774 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGTGGTTGATTACTAAACATTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
*
43137839 TGTGC-AACCCAGTATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
43137903 TTTTGGACAGCGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
43137927 ACCTTGAGTT
Statistics
Matches: 144, Mismatches: 9, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
173 80 0.56
174 64 0.44
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:43142805 original size:2 final size:2
Alignment explanation
Indices: 43142792--43142822 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
43142782 GAGTATAATG
*
43142792 TC TC TC TT 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 T
43142823 ATATATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (2 bp):
TC
Found at i:43142861 original size:4 final size:4
Alignment explanation
Indices: 43142837--43142880 Score: 61
Period size: 4 Copynumber: 11.0 Consensus size: 4
43142827 ATATATATAT
* * *
43142837 ATAG ATTG ATAG ATTG ATAG ATAG ACAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
43142881 GAGCATACTA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.45, C:0.02, G:0.25, T:0.27
Consensus pattern (4 bp):
ATAG
Found at i:43154561 original size:19 final size:19
Alignment explanation
Indices: 43154537--43154576 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
43154527 ATTAATTTTG
43154537 ATCAAATAAAATT-AAATTA
1 ATCAAAT-AAATTAAAATTA
*
43154556 ATCAAATCAATTAAAATTA
1 ATCAAATAAATTAAAATTA
43154575 AT
1 AT
43154577 ATGATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (19 bp):
ATCAAATAAATTAAAATTA
Found at i:43155299 original size:25 final size:26
Alignment explanation
Indices: 43155253--43155302 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
43155243 AGTTGTAGAG
*
43155253 AGAAAATTCTCTGAAGAGATTGTTCC
1 AGAAAATTCTCTAAAGAGATTGTTCC
*
43155279 AGAAAATT-TCTAAAGATATTGTTC
1 AGAAAATTCTCTAAAGAGATTGTTC
43155303 TGTTTTACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (26 bp):
AGAAAATTCTCTAAAGAGATTGTTCC
Found at i:43158563 original size:13 final size:13
Alignment explanation
Indices: 43158545--43158569 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43158535 AGTTCTTTAT
43158545 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
43158558 TGCTTTTGAGAA
1 TGCTTTTGAGAA
43158570 ATTTGAGTGT
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:0.24, C:0.08, G:0.28, T:0.40
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:43161160 original size:11 final size:11
Alignment explanation
Indices: 43161144--43161175 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
43161134 TCAAACTCTT
43161144 AATCAACAGCA
1 AATCAACAGCA
*
43161155 AATCAACAACA
1 AATCAACAGCA
43161166 AATCAACAGC
1 AATCAACAGC
43161176 TTCAAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.56, C:0.28, G:0.06, T:0.09
Consensus pattern (11 bp):
AATCAACAGCA
Found at i:43161658 original size:16 final size:16
Alignment explanation
Indices: 43161637--43161668 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
43161627 ACTTCCGGGA
43161637 CTTAGTTTAGTTTTGG
1 CTTAGTTTAGTTTTGG
43161653 CTTAGTTTAGTTTTGG
1 CTTAGTTTAGTTTTGG
43161669 TTGTAATTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.06, G:0.25, T:0.56
Consensus pattern (16 bp):
CTTAGTTTAGTTTTGG
Found at i:43164482 original size:36 final size:36
Alignment explanation
Indices: 43164435--43164508 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
43164425 AGCATATATG
*
43164435 CAACAAATTGGGCAGCATTTAAGCATCCAAATTGGA
1 CAACAAATTGGGCAGCATTTAAGCATCAAAATTGGA
43164471 CAACAAATTGGGCAGCATTTAAGCATCAAAATTGGA
1 CAACAAATTGGGCAGCATTTAAGCATCAAAATTGGA
43164507 CA
1 CA
43164509 GCATATATGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (36 bp):
CAACAAATTGGGCAGCATTTAAGCATCAAAATTGGA
Found at i:43164505 original size:24 final size:24
Alignment explanation
Indices: 43164475--43164559 Score: 100
Period size: 24 Copynumber: 3.6 Consensus size: 24
43164465 ATTGGACAAC
*
43164475 AAATTGGGCAGCATTTAAGCATCA
1 AAATTGGACAGCATTTAAGCATCA
* * * *
43164499 AAATTGGACAGCATATATGTAAC-
1 AAATTGGACAGCATTTAAGCATCA
**
43164522 AAATTGGGTAGCATTTAAGCATCA
1 AAATTGGACAGCATTTAAGCATCA
43164546 AAATTGGACAGCAT
1 AAATTGGACAGCAT
43164560 ATATGTAACA
Statistics
Matches: 47, Mismatches: 13, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
23 17 0.36
24 30 0.64
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (24 bp):
AAATTGGACAGCATTTAAGCATCA
Found at i:43164526 original size:47 final size:47
Alignment explanation
Indices: 43164472--43164575 Score: 199
Period size: 47 Copynumber: 2.2 Consensus size: 47
43164462 CAAATTGGAC
43164472 AACAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGCATATATGT
1 AACAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGCATATATGT
*
43164519 AACAAATTGGGTAGCATTTAAGCATCAAAATTGGACAGCATATATGT
1 AACAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGCATATATGT
43164566 AACAAATTGG
1 AACAAATTGG
43164576 TTCAACTCAT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 56 1.00
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.26
Consensus pattern (47 bp):
AACAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGCATATATGT
Found at i:43164534 original size:23 final size:23
Alignment explanation
Indices: 43164471--43164575 Score: 93
Period size: 24 Copynumber: 4.5 Consensus size: 23
43164461 CCAAATTGGA
* *
43164471 CAACAAATTGGGCAGCATTTAAG
1 CAACAAATTGGACAGCATATAAG
* *
43164494 CATCAAAATTGGACAGCATATATG
1 CAAC-AAATTGGACAGCATATAAG
* ** *
43164518 TAACAAATTGGGTAGCATTTAAG
1 CAACAAATTGGACAGCATATAAG
* *
43164541 CATCAAAATTGGACAGCATATATG
1 CAAC-AAATTGGACAGCATATAAG
*
43164565 TAACAAATTGG
1 CAACAAATTGG
43164576 TTCAACTCAT
Statistics
Matches: 62, Mismatches: 18, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
23 27 0.44
24 35 0.56
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (23 bp):
CAACAAATTGGACAGCATATAAG
Done.