Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167838.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_11, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 23775123
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 69000 characters in sequence are not A, C, G, or T
File 53 of 129
Found at i:10430621 original size:21 final size:21
Alignment explanation
Indices: 10430597--10430648 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
10430587 ATTAAGAGTA
10430597 GTTTGAATTTCTAAGCTTTAG
1 GTTTGAATTTCTAAGCTTTAG
* *
10430618 GTTTGAAGTTCTGAGCTTTAG
1 GTTTGAATTTCTAAGCTTTAG
10430639 GTTTGAATTT
1 GTTTGAATTT
10430649 TTGGGGTTGG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.08, G:0.23, T:0.48
Consensus pattern (21 bp):
GTTTGAATTTCTAAGCTTTAG
Found at i:10431052 original size:24 final size:24
Alignment explanation
Indices: 10431002--10431053 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
10430992 CCCTTGTGGG
* * *
10431002 TTTTCTTTTTTCTTTTTACTTTTA
1 TTTTCTATTTTCTTTTCAATTTTA
10431026 TTTTCTATTTT-TTTTCAATTTTCA
1 TTTTCTATTTTCTTTTCAATTTT-A
10431050 TTTT
1 TTTT
10431054 TTAAGCTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.77
Consensus pattern (24 bp):
TTTTCTATTTTCTTTTCAATTTTA
Found at i:10433020 original size:10 final size:11
Alignment explanation
Indices: 10432975--10433017 Score: 54
Period size: 10 Copynumber: 4.1 Consensus size: 11
10432965 AATTTTATTT
10432975 TTAATAATTAA
1 TTAATAATTAA
*
10432986 TT-TTAATTAA
1 TTAATAATTAA
*
10432996 TTAGT-ATTAA
1 TTAATAATTAA
10433006 TTAATAATTAA
1 TTAATAATTAA
10433017 T
1 T
10433018 AATGAGAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 18 0.67
11 9 0.33
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (11 bp):
TTAATAATTAA
Found at i:10433638 original size:44 final size:44
Alignment explanation
Indices: 10433583--10433671 Score: 124
Period size: 44 Copynumber: 2.0 Consensus size: 44
10433573 CGAATCTGGC
* * *
10433583 TCAACATATAAACACCTAAACATAATTATCACAAGATTGAAGAT
1 TCAACACATAAACAACTAAACATAATTATCAAAAGATTGAAGAT
* * *
10433627 TCAACACATAAATAACTAAACATAATTGTCAAAAGATTGACGAT
1 TCAACACATAAACAACTAAACATAATTATCAAAAGATTGAAGAT
10433671 T
1 T
10433672 GATTCTACTT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.49, C:0.17, G:0.08, T:0.26
Consensus pattern (44 bp):
TCAACACATAAACAACTAAACATAATTATCAAAAGATTGAAGAT
Found at i:10436378 original size:18 final size:18
Alignment explanation
Indices: 10436336--10436381 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
10436326 TTGAGTTATA
*
10436336 TTTAGGGTCTAGGGTTTGT
1 TTTAGGGT-TAGGGTTTGG
10436355 TTTAGGGTTAGAGG-TTGG
1 TTTAGGGTTAG-GGTTTGG
10436373 TTTAGGGTT
1 TTTAGGGTT
10436382 TAAACATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 15 0.60
19 10 0.40
ACGTcount: A:0.13, C:0.02, G:0.39, T:0.46
Consensus pattern (18 bp):
TTTAGGGTTAGGGTTTGG
Found at i:10437859 original size:143 final size:139
Alignment explanation
Indices: 10437432--10437876 Score: 367
Period size: 143 Copynumber: 3.1 Consensus size: 139
10437422 AATGTACAAA
* ** * * * *
10437432 AATCATAATAAAATCATAAAATAGTGCTTAATCATAATTTAGAGCTTTGCGTGAAAAATCGACAT
1 AATCATAA-AAAATCATAAAATAATATTTAATCATAATCTAGAGCTTTTCGTAAAAAAT-GACTT
* * * * *
10437497 CACAAAGGTAAAATTATAAAA-ACTCCCTTAAAGGATATTTTGGTAATGTTACA-CATTTCGAGG
64 GA-AAAGGTCAAATTAGAAAATAC-CCCTAAAAGG-TATTTTGATAAT-TTA-ATCATTTCGAGG
*
10437560 TGCACGATCAAGGTTTTT
124 AGCA--ATCAAGGTTTTT
* * ** * * * *
10437578 AATCTATCAAAAATCATGAAATAATATCAAAACATAATC-ATGAGATTTTCATGAAAAATTGATC
1 AATC-ATAAAAAATCATAAAATAATATTTAATCATAATCTA-GAGCTTTTCGT-AAAAAATGA-C
* * * ** * * * *
10437642 TCGAAAAAGTCAAATTATGAAAATACCACTAAAAGACATTTTGATAGTTTTATACCTTTTGA-GA
62 TTGAAAAGGTCAAATTA-GAAAATACCCCTAAAAGGTATTTTGATAATTTAAT-CATTTCGAGGA
**
10437706 TGTGATCAAGGTTTTT
125 -GCAATCAAGGTTTTT
10437722 AATACATAAAAAATCATAAAATAATATTTAATCATAATCTAGAGCTTTTCGTAAAAAATGACCTT
1 AAT-CATAAAAAATCATAAAATAATATTTAATCATAATCTAGAGCTTTTCGTAAAAAATGA-CTT
* *
10437787 GAAAAGGTCAAATTACGAAAATACCCCTAAAAGGTATTTTAATAATTTCAATCATCTCGAGGAGC
64 GAAAAGGTCAAATTA-GAAAATACCCCTAAAAGGTATTTTGATAATTT-AATCATTTCGAGGAGC
10437852 AATCAAGGTTTTT
127 AATCAAGGTTTTT
10437865 AATGCATAAAAA
1 AAT-CATAAAAA
10437877 TTATGAAATT
Statistics
Matches: 230, Mismatches: 56, Indels: 29
0.73 0.18 0.09
Matches are distributed among these distances:
143 80 0.35
144 58 0.25
145 6 0.03
146 63 0.27
147 21 0.09
148 2 0.01
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (139 bp):
AATCATAAAAAATCATAAAATAATATTTAATCATAATCTAGAGCTTTTCGTAAAAAATGACTTGA
AAAGGTCAAATTAGAAAATACCCCTAAAAGGTATTTTGATAATTTAATCATTTCGAGGAGCAATC
AAGGTTTTT
Found at i:10446839 original size:19 final size:21
Alignment explanation
Indices: 10446803--10446843 Score: 68
Period size: 19 Copynumber: 2.0 Consensus size: 21
10446793 AAAAAAATAT
10446803 ATATACAAAAAATAATACAAA
1 ATATACAAAAAATAATACAAA
10446824 ATAT-CAAAAAAT-ATACAAA
1 ATATACAAAAAATAATACAAA
10446843 A
1 A
10446844 CAAATAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 8 0.40
20 8 0.40
21 4 0.20
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.20
Consensus pattern (21 bp):
ATATACAAAAAATAATACAAA
Found at i:10446849 original size:33 final size:36
Alignment explanation
Indices: 10446776--10446859 Score: 99
Period size: 35 Copynumber: 2.5 Consensus size: 36
10446766 GAAAAAAAAT
* *
10446776 ACAAA-AATACGAAATA-CAAAAAAATATATATACA
1 ACAAATAATACAAAATATCAAAAAAATATACATACA
*
10446810 AAAAATAATACAAAATATC-AAAAAATATACA-A-A
1 ACAAATAATACAAAATATCAAAAAAATATACATACA
10446843 ACAAATAATA-AAAATAT
1 ACAAATAATACAAAATAT
10446860 AGAACAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
32 7 0.16
33 10 0.23
34 5 0.11
35 21 0.48
36 1 0.02
ACGTcount: A:0.70, C:0.10, G:0.01, T:0.19
Consensus pattern (36 bp):
ACAAATAATACAAAATATCAAAAAAATATACATACA
Found at i:10446852 original size:16 final size:15
Alignment explanation
Indices: 10446789--10446852 Score: 51
Period size: 16 Copynumber: 4.1 Consensus size: 15
10446779 AAAATACGAA
10446789 ATACAAAAAAATATAT
1 ATACAAAAAAATA-AT
10446805 ATAC-AAAAAATAAT
1 ATACAAAAAAATAAT
* *
10446819 ACA-AAATATCAAAAAAT
1 ATACAAA-A--AAATAAT
10446836 ATACAAAACAAATAAT
1 ATACAAAA-AAATAAT
10446852 A
1 A
10446853 AAAATATAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
14 6 0.15
15 9 0.23
16 12 0.31
17 9 0.23
18 3 0.08
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.20
Consensus pattern (15 bp):
ATACAAAAAAATAAT
Found at i:10446877 original size:22 final size:22
Alignment explanation
Indices: 10446829--10446879 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
10446819 ACAAAATATC
*
10446829 AAAAAATATACAAAACAAATAA
1 AAAAAATATACAAAACAAAAAA
* *
10446851 TAAAAATATAGAACAA-AAAAAA
1 AAAAAATATACAA-AACAAAAAA
10446873 AAAAAAT
1 AAAAAAT
10446880 TGAAGGTGGT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 22 0.92
23 2 0.08
ACGTcount: A:0.78, C:0.06, G:0.02, T:0.14
Consensus pattern (22 bp):
AAAAAATATACAAAACAAAAAA
Found at i:10446986 original size:29 final size:29
Alignment explanation
Indices: 10446914--10446975 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
10446904 TGGCACCACT
* *
10446914 ACCACCA-GCCCTACACC-CCACCCTTCTG
1 ACCACCATGCCCTAC-CCTCCACCCCTCTA
10446942 ACCACCATGCCCTACCCTCCACCCCTCTA
1 ACCACCATGCCCTACCCTCCACCCCTCTA
10446971 ACCAC
1 ACCAC
10446976 TATGGCTTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 9 0.30
29 21 0.70
ACGTcount: A:0.23, C:0.58, G:0.05, T:0.15
Consensus pattern (29 bp):
ACCACCATGCCCTACCCTCCACCCCTCTA
Found at i:10447195 original size:23 final size:23
Alignment explanation
Indices: 10447162--10447208 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
10447152 AGAGGAGGAG
*
10447162 ACACTGCAAAAAAAATGAAAAAA
1 ACACTGCAAAAAAAATAAAAAAA
*
10447185 ACACTGTAAAAAAAATAAAAAAA
1 ACACTGCAAAAAAAATAAAAAAA
10447208 A
1 A
10447209 ATACGCAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.72, C:0.11, G:0.06, T:0.11
Consensus pattern (23 bp):
ACACTGCAAAAAAAATAAAAAAA
Found at i:10447211 original size:10 final size:11
Alignment explanation
Indices: 10447169--10447210 Score: 50
Period size: 10 Copynumber: 3.8 Consensus size: 11
10447159 GAGACACTGC
10447169 AAAAAAAATGA
1 AAAAAAAATGA
* *
10447180 AAAAAACACTGT
1 AAAAAA-AATGA
10447192 AAAAAAAAT-A
1 AAAAAAAATGA
10447202 AAAAAAAAT
1 AAAAAAAAT
10447211 ACGCAATCCT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
10 9 0.35
11 8 0.31
12 9 0.35
ACGTcount: A:0.79, C:0.05, G:0.05, T:0.12
Consensus pattern (11 bp):
AAAAAAAATGA
Found at i:10447286 original size:20 final size:21
Alignment explanation
Indices: 10447255--10447306 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
10447245 AGCTTCCTGC
* *
10447255 ACAAAGAAAAAAAAAGTTAGTTT
1 ACAAA-AAAAAAAGAGTCAG-TT
10447278 A-AAAAAAAAAAGAGTCAGTT
1 ACAAAAAAAAAAGAGTCAGTT
10447298 ACAAAAAAA
1 ACAAAAAAA
10447307 TATCATTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 3 0.12
21 19 0.73
22 3 0.12
23 1 0.04
ACGTcount: A:0.67, C:0.06, G:0.12, T:0.15
Consensus pattern (21 bp):
ACAAAAAAAAAAGAGTCAGTT
Found at i:10449246 original size:23 final size:22
Alignment explanation
Indices: 10449214--10449257 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
10449204 AAATGTAAAA
10449214 AAAAAAAAAAAACAAAATAAATG
1 AAAAAAAAAAAACAAAA-AAATG
* *
10449237 AAAAATAAAAAGCAAAAAAAT
1 AAAAAAAAAAAACAAAAAAAT
10449258 TCGCATGCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.82, C:0.05, G:0.05, T:0.09
Consensus pattern (22 bp):
AAAAAAAAAAAACAAAAAAATG
Found at i:10459503 original size:8 final size:8
Alignment explanation
Indices: 10459487--10459528 Score: 59
Period size: 8 Copynumber: 5.4 Consensus size: 8
10459477 ATTTTGCTTG
*
10459487 AAAGAAAA
1 AAAGTAAA
10459495 AAAGTAAA
1 AAAGTAAA
*
10459503 AAAATAAA
1 AAAGTAAA
10459511 AAAGTAAA
1 AAAGTAAA
10459519 AAA-TAAA
1 AAAGTAAA
10459526 AAA
1 AAA
10459529 TAATGACTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
7 7 0.23
8 24 0.77
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.10
Consensus pattern (8 bp):
AAAGTAAA
Found at i:10459511 original size:7 final size:7
Alignment explanation
Indices: 10459501--10459531 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
10459491 AAAAAAAGTA
10459501 AAAAAAT
1 AAAAAAT
10459508 AAAAAAGT
1 AAAAAA-T
10459516 AAAAAAT
1 AAAAAAT
10459523 AAAAAAT
1 AAAAAAT
10459530 AA
1 AA
10459532 TGACTCATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.13
Consensus pattern (7 bp):
AAAAAAT
Found at i:10459519 original size:15 final size:16
Alignment explanation
Indices: 10459492--10459528 Score: 67
Period size: 15 Copynumber: 2.4 Consensus size: 16
10459482 GCTTGAAAGA
10459492 AAAAAAGTAAAAAAAT
1 AAAAAAGTAAAAAAAT
10459508 AAAAAAGT-AAAAAAT
1 AAAAAAGTAAAAAAAT
10459523 AAAAAA
1 AAAAAA
10459529 TAATGACTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.84, C:0.00, G:0.05, T:0.11
Consensus pattern (16 bp):
AAAAAAGTAAAAAAAT
Found at i:10460566 original size:50 final size:50
Alignment explanation
Indices: 10460306--10460932 Score: 581
Period size: 50 Copynumber: 12.8 Consensus size: 50
10460296 TTTTTCAATA
* * *
10460306 TTTTAAAGTTATTGAGCCTCTGTTGAGAGGAGC-TTTTCCAAGATGA-AA
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCCAAGATGAGAT
* ** *
10460354 TTTTAAAGTTGTTAAGCCTCTATTGAGATGAGCTTTTT-C-AGATGAGAT
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCCAAGATGAGAT
* * * * ** * *
10460402 TTTTAAAGTTATTGAGTCTCTGCTGAGAAGATCCCTTTCGAATATGAGA-
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCCAAGATGAGAT
* ** *
10460451 TTTTAAAGTTGTTGAGCCTCTACTGAGATAAGCTTTTT-CAA-AAGAGA-
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCCAAGATGAGAT
*
10460498 TTTTAAAGTTGTTGAGCCTCAGCTGAGAGGAGCTTTTTCCAAGATGAGAT
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCCAAGATGAGAT
* * * ** * *
10460548 TTTTAAAGTTGTTAAGCCTCTGCTGAAAGGAGTTTTTTTTAATATGGGAATT
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCCAAGATGAG-A-T
* * * * *
10460600 TTTTAAAGTTGATAAGCCTCTGTTGAGAGGAACTTTTT-CAA-ATAAGAT
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCCAAGATGAGAT
* ** *
10460648 TTTTAAAGAGTTGTTGAGCCTCTGCTAAGAGGAGCCCTTTCCAAGATGGGA-
1 TTTT-AA-AGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCCAAGATGAGAT
* * *
10460699 TTTTAAAGTTGCTGAGCCTCTGCTAAGAGGAACTTTTT-C---A--AGA-
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCCAAGATGAGAT
*
10460742 TTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAGC-TTTTCCAAGATGAGAT
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCCAAGATGAGAT
* * * * *
10460791 TTTTAAAGTTGTTGAGCCTCCGTTGAGAGGAACTTTTTTCAAGATGAAAAT
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCCAAGATG-AGAT
* * * ** *
10460842 TTTTAAAAATTGTTAAGCCTCTGCTGAGAGGAGTTTTTTTTAAGATGAAAT
1 TTTT-AAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCCAAGATGAGAT
* *
10460893 TTTTAAAATTGTTGAGCTTCTGCTGAGAGGAGTCTTTTTC
1 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTTC
10460933 AGATTTTAAA
Statistics
Matches: 475, Mismatches: 80, Indels: 45
0.79 0.13 0.08
Matches are distributed among these distances:
42 4 0.01
43 32 0.07
45 1 0.00
46 1 0.00
47 45 0.09
48 74 0.16
49 101 0.21
50 114 0.24
51 30 0.06
52 73 0.15
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (50 bp):
TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCCAAGATGAGAT
Found at i:10460863 original size:243 final size:242
Alignment explanation
Indices: 10460259--10460924 Score: 757
Period size: 243 Copynumber: 2.8 Consensus size: 242
10460249 AAGAAAAAAT
* * * * *
10460259 GAGATTTTAAAATTGTTGAGCCTCTGCTGAGAAGAGTTTTTTC-A-AT---A-TTTTAAAGTTAT
1 GAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATGAGATTTTTAAAGTTGT
* *
10460318 TGAGCCTCTGTTGAGAGGAGC-TTTTCCAAGATGAAA-TTTTAAAGTTGTTAAGCCTCTATTGAG
66 TGAGCCTCTGTTGAGAGGAGCTTTTTTCAAGATGAAATTTTTAAAGTTGTTAAGCCTCTGTTGAG
* * * * * * * * * *
10460381 ATGAGCTTTTTCAGATGAGATTTTT-AAAGTTATTGAGTCTCTGCTGAGAAGATCCCTTTCGAAT
131 AGGAACTTTTTCAAATAAGATTTTTAAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCCTTTCCAAG
* * *
10460445 ATGAGATTTTAAAGTTGTTGAGCCTCTACTGAGATAAGCTTTTTCAAAA
196 ATGAGATTTTAAAGTTGCTGAGCCTCTACTAAGAGAAGCTTTTTC--AA
*
10460494 GAGATTTTAAAGTTGTTGAGCCTCAGCTGAGAGGAGCTTTTTCCAAGATGAGATTTTTAAAGTTG
1 GAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGC-TTTTCCAAGATGAGATTTTTAAAGTTG
* * * * * * * *
10460559 TTAAGCCTCTGCTGAAAGGAGTTTTTTTTAATATGGGAATTTTTTAAAGTTGATAAGCCTCTGTT
65 TTGAGCCTCTGTTGAGAGGAGCTTTTTTCAAGAT--GAAATTTTTAAAGTTGTTAAGCCTCTGTT
*
10460624 GAGAGGAACTTTTTCAAATAAGATTTTTAAAGAGTTGTTGAGCCTCTGCTAAGAGGAGCCCTTTC
128 GAGAGGAACTTTTTCAAATAAGATTTTTAAA-AGTTGTTGAGCCTCTGCTGAGAGGAGCCCTTTC
* *
10460689 CAAGATGGGATTTTAAAGTTGCTGAGCCTCTGCTAAGAGGAA-CTTTTTC-A
192 CAAGATGAGATTTTAAAGTTGCTGAGCCTCTACTAAGA-GAAGCTTTTTCAA
*
10460739 -AGATTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAGCTTTTCCAAGATGAGATTTTTAAAGTTGT
1 GAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATGAGATTTTTAAAGTTGT
* * * *
10460803 TGAGCCTCCGTTGAGAGGAACTTTTTTCAAGATGAAAATTTTTAAAAATTGTTAAGCCTCTGCTG
66 TGAGCCTCTGTTGAGAGGAGCTTTTTTCAAGATG-AAATTTTT-AAAGTTGTTAAGCCTCTGTTG
** * *
10460868 AGAGGAGTTTTTTTTAAGATGAA-ATTTTTAAAA-TTGTTGAGCTTCTGCTGAGAGGAG
129 AGAGGA-ACTTTTTCAA-AT-AAGATTTTTAAAAGTTGTTGAGCCTCTGCTGAGAGGAG
10460925 TCTTTTTCAG
Statistics
Matches: 361, Mismatches: 51, Indels: 30
0.82 0.12 0.07
Matches are distributed among these distances:
235 33 0.09
236 5 0.01
237 1 0.00
238 2 0.01
241 2 0.01
242 35 0.10
243 107 0.30
244 42 0.12
245 15 0.04
246 48 0.13
247 2 0.01
248 67 0.19
249 2 0.01
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.37
Consensus pattern (242 bp):
GAGATTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATGAGATTTTTAAAGTTGT
TGAGCCTCTGTTGAGAGGAGCTTTTTTCAAGATGAAATTTTTAAAGTTGTTAAGCCTCTGTTGAG
AGGAACTTTTTCAAATAAGATTTTTAAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCCTTTCCAAG
ATGAGATTTTAAAGTTGCTGAGCCTCTACTAAGAGAAGCTTTTTCAA
Found at i:10460963 original size:102 final size:101
Alignment explanation
Indices: 10460742--10460964 Score: 254
Period size: 102 Copynumber: 2.2 Consensus size: 101
10460732 TTTTTCAAGA
* * *
10460742 TTTT-AAAGTTGTTGAGCCTCTGTTGAGAGGAGCTTTTCCAAGATGAGATTTTTAAAGTTGTTGA
1 TTTTAAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATGAAATTTTTAAAATTGTTGA
*
10460806 GCCTCCGTTGAGAGGAACTTTTTTCAAGATGAAAAT
66 GCCTCCGCTGAGAGGAACTTTTTTCAAGATGAAAAT
* * * **
10460842 TTTTAAAAATTGTTAAGCCTCTGCTGAGAGGAGTTTTTTTTAAGATGAAATTTTTAAAATTGTTG
1 TTTTAAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTCCAAGATGAAATTTTTAAAATTGTTG
* * * **
10460907 AGCTTCTGCTGAGAGG-AGTCTTTTTC-AGATTTTAAAT
65 AGCCTCCGCTGAGAGGAACT-TTTTTCAAGA-TGAAAAT
* *
10460944 TTTTAAAAGTTATCGAGCCTC
1 TTTTAAAAGTTGTTGAGCCTC
10460965 AAATGAGAAA
Statistics
Matches: 101, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
100 4 0.04
101 30 0.30
102 67 0.66
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.40
Consensus pattern (101 bp):
TTTTAAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTCCAAGATGAAATTTTTAAAATTGTTGA
GCCTCCGCTGAGAGGAACTTTTTTCAAGATGAAAAT
Found at i:10461167 original size:14 final size:14
Alignment explanation
Indices: 10461141--10461178 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
10461131 TTGTCTAGAA
10461141 AAAATATAAAAATAC
1 AAAATA-AAAAATAC
*
10461156 AAAATAAAAAATAT
1 AAAATAAAAAATAC
10461170 AAAA-AAAAA
1 AAAATAAAAA
10461179 TATATACCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 5 0.23
14 11 0.50
15 6 0.27
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.16
Consensus pattern (14 bp):
AAAATAAAAAATAC
Found at i:10461206 original size:19 final size:19
Alignment explanation
Indices: 10461182--10461222 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
10461172 AAAAAAATAT
10461182 ATACCAAAAATAATACAA-A
1 ATACCAAAAA-AATACAAGA
10461201 ATACCAAAAAAATACAAGA
1 ATACCAAAAAAATACAAGA
10461220 ATA
1 ATA
10461223 ATAATAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.68, C:0.15, G:0.02, T:0.15
Consensus pattern (19 bp):
ATACCAAAAAAATACAAGA
Found at i:10461374 original size:29 final size:29
Alignment explanation
Indices: 10461292--10461364 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
10461282 GGCACCATTG
* * *
10461292 CCACCAGGCCTTACACCT-CACCCTTCTGA
1 CCACCATGCCCTAC-CCTCCACCCCTCTGA
* *
10461321 CTACCATGCTCTACCCTCCACCCCTCTGA
1 CCACCATGCCCTACCCTCCACCCCTCTGA
10461350 CCACCATGCCCTACC
1 CCACCATGCCCTACC
10461365 ACCCATCCCT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
28 3 0.08
29 33 0.92
ACGTcount: A:0.19, C:0.52, G:0.08, T:0.21
Consensus pattern (29 bp):
CCACCATGCCCTACCCTCCACCCCTCTGA
Found at i:10465012 original size:13 final size:15
Alignment explanation
Indices: 10464994--10465027 Score: 54
Period size: 13 Copynumber: 2.4 Consensus size: 15
10464984 ATTTAAATAA
10464994 TATTTTAAT-AA-TT
1 TATTTTAATAAATTT
10465007 TATTTTAATAAATTT
1 TATTTTAATAAATTT
10465022 TATTTT
1 TATTTT
10465028 GTGCATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.47
14 2 0.11
15 8 0.42
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TATTTTAATAAATTT
Found at i:10466273 original size:31 final size:31
Alignment explanation
Indices: 10466235--10466324 Score: 135
Period size: 31 Copynumber: 2.9 Consensus size: 31
10466225 AAATTACCTA
*
10466235 TTCAATATAACATATCCCATTAGATAACATG
1 TTCAATATAACATATCTCATTAGATAACATG
* *
10466266 TTTAATATAACATATATCATTAGATAACATG
1 TTCAATATAACATATCTCATTAGATAACATG
* *
10466297 TTCAATATAACACATCTCATCAGATAAC
1 TTCAATATAACATATCTCATTAGATAAC
10466325 TTATACATTA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.43, C:0.18, G:0.06, T:0.33
Consensus pattern (31 bp):
TTCAATATAACATATCTCATTAGATAACATG
Found at i:10466808 original size:73 final size:74
Alignment explanation
Indices: 10466721--10466891 Score: 184
Period size: 74 Copynumber: 2.3 Consensus size: 74
10466711 ATTTCTAAAC
* * *
10466721 AAAAATGTAATCTTTGTTGAAAATATGAAAA-AATATATTTCTAAAATTTAATGAAGGCAACATT
1 AAAAATATAATCTTTGTTGAAAATATGAAAACAATATATTTCTAAAATTTAATAAAGACAACATT
10466785 TCTAAGATA
66 TCTAAGATA
* * * * * * * ** *
10466794 AAAAATATAATCTTTGCTAAAAATATGAAAACTATATTTTTTTAGAATTTAGTAAAGATGACGTT
1 AAAAATATAATCTTTGTTGAAAATATGAAAACAATATATTTCTAAAATTTAATAAAGACAACATT
10466859 TCTAAGATA
66 TCTAAGATA
*
10466868 AAAAA-ATGCAATCTTTATTGAAAA
1 AAAAATAT--AATCTTTGTTGAAAA
10466892 GATTATATTT
Statistics
Matches: 79, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
73 30 0.38
74 37 0.47
75 12 0.15
ACGTcount: A:0.47, C:0.07, G:0.11, T:0.35
Consensus pattern (74 bp):
AAAAATATAATCTTTGTTGAAAATATGAAAACAATATATTTCTAAAATTTAATAAAGACAACATT
TCTAAGATA
Found at i:10466987 original size:74 final size:73
Alignment explanation
Indices: 10466898--10467039 Score: 162
Period size: 74 Copynumber: 1.9 Consensus size: 73
10466888 AAAAGATTAT
* * * * *
10466898 ATTTTTAAGATAAAAACA-CAGTCTTTGTCGAAAACATGGAAAAAATATATTTT-TTAGAATTTA
1 ATTTCTAAGACAAAAA-AGCAGTCTTTATCAAAAACAT-GAAAAAATATATTTTCCTA-AATTTA
10466961 ACAAAAATAAC
63 ACAAAAATAAC
* * *
10466972 ATTTCTAAGACAAAAAATGTAGTCTTTATTAAAAATATGAAAAAATATATTTTCCTAAATTTAAC
1 ATTTCTAAGACAAAAAA-GCAGTCTTTATCAAAAACATGAAAAAATATATTTTCCTAAATTTAAC
10467037 AAA
65 AAA
10467040 GACTACATTT
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
73 1 0.02
74 40 0.70
75 16 0.28
ACGTcount: A:0.49, C:0.09, G:0.08, T:0.34
Consensus pattern (73 bp):
ATTTCTAAGACAAAAAAGCAGTCTTTATCAAAAACATGAAAAAATATATTTTCCTAAATTTAACA
AAAATAAC
Found at i:10468205 original size:464 final size:466
Alignment explanation
Indices: 10467335--10468252 Score: 1768
Period size: 464 Copynumber: 2.0 Consensus size: 466
10467325 ATGTTTTCAA
10467335 CATTTTCTATCTTAGAAATGTTGTCTTTGTTGTACTCTAAAAAATACATTTTTTTCATATTTTCA
1 CATTTTCTATCTTAGAAATGTTGTCTTTGTTGTACTCTAAAAAATACATTTTTTTCATATTTTCA
*
10467400 ACAAAAATTGTGTTTTTATCTTAGAAACTTCATTTTTGTAATAAAATTTGCATTTTCTATCTTAA
66 ACAAAAATTATGTTTTTATCTTAGAAACTTCATTTTTGTAATAAAATTTGCATTTTCTATCTTAA
10467465 AACATCATTTTTTGTTAAATTGTAAAAAATAATTTTTTTTTATATTTACAACAAAGATTGGGTTT
131 AACATCATTTTTTGTTAAATTGTAAAAAATAATTTTTTTTTATATTTACAACAAAGATTGGGTTT
10467530 TTATCTTAAAAATATTATTAATATTTTAGTTTAACTATTTACCTCTATTTTAAATCAATTTATTC
196 TTATCTTAAAAATATTATTAATATTTTAGTTTAACTATTTACCTCTATTTTAAATCAATTTATTC
*
10467595 AATTTTTAATGTATGTTTTATCTAATGAGATGTGTTATATTAAATAGGTAATTTAATAGATGGTT
261 AATTTTTAATGTATGTGTTATCTAATGAGATGTGTTATATTAAATAGGTAATTTAATAGATGGTT
10467660 TATAAATACAACATAATATAATGGATGTTTTATAAGCATACATTACTAAATAAAAATAACAAAGT
326 TATAAATACAACATAATATAATGGATGTTTTATAAGCATACATTACTAAATAAAAATAACAAAGT
*
10467725 TACAAAATCACTACCCACTCTACAGTATCAATACCTTATTGGCTTTCCTTCAGCTTCTTAAATCG
391 TACAAAATCACTACCCACTCCACAGTATCAATACCTTATTGGCTTTCCTTCAGCTTCTTAAATCG
10467790 AACAAAAATAG
456 AACAAAAATAG
10467801 CATTTTCTATCTTAGAAATGTTGTCTTTGTTGTACTCTAAAAAATACATTTTTTTCATATTTTCA
1 CATTTTCTATCTTAGAAATGTTGTCTTTGTTGTACTCTAAAAAATACATTTTTTTCATATTTTCA
10467866 ACAAAAATTATGTTTTTATCTTAGAAACTTCATTTTTGTAATAAAATTTGCATTTTCTATCTTAA
66 ACAAAAATTATGTTTTTATCTTAGAAACTTCATTTTTGTAATAAAATTTGCATTTTCTATCTTAA
**
10467931 AACATCATTTTTTGTTAAATTGTGGAAAAT-A-TTTTTTTTATATTTACAACAAAGATTGGGTTT
131 AACATCATTTTTTGTTAAATTGTAAAAAATAATTTTTTTTTATATTTACAACAAAGATTGGGTTT
*
10467994 TTATCTTAAAAATATTATTAATATTTTAGTTTAACTATTTACCTCTATTTTAAATCGATTTATTC
196 TTATCTTAAAAATATTATTAATATTTTAGTTTAACTATTTACCTCTATTTTAAATCAATTTATTC
10468059 AATTTTTAATGTATGTGTTATCTAATGAGATGTGTTATATTAAATAGGTAATTTAATAGATGGTT
261 AATTTTTAATGTATGTGTTATCTAATGAGATGTGTTATATTAAATAGGTAATTTAATAGATGGTT
10468124 TATAAATACAACATAATATAATGGATGTTTTATAAGCATACATTACTAAATAAAAATAACAAAGT
326 TATAAATACAACATAATATAATGGATGTTTTATAAGCATACATTACTAAATAAAAATAACAAAGT
10468189 TACAAAATCACTACCCACTCCACAGTATCAATACCTTATTGGCTTTCCTTCAGCTTCTTAAATC
391 TACAAAATCACTACCCACTCCACAGTATCAATACCTTATTGGCTTTCCTTCAGCTTCTTAAATC
10468253 AAATATATAC
Statistics
Matches: 446, Mismatches: 6, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
464 288 0.65
465 1 0.00
466 157 0.35
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.44
Consensus pattern (466 bp):
CATTTTCTATCTTAGAAATGTTGTCTTTGTTGTACTCTAAAAAATACATTTTTTTCATATTTTCA
ACAAAAATTATGTTTTTATCTTAGAAACTTCATTTTTGTAATAAAATTTGCATTTTCTATCTTAA
AACATCATTTTTTGTTAAATTGTAAAAAATAATTTTTTTTTATATTTACAACAAAGATTGGGTTT
TTATCTTAAAAATATTATTAATATTTTAGTTTAACTATTTACCTCTATTTTAAATCAATTTATTC
AATTTTTAATGTATGTGTTATCTAATGAGATGTGTTATATTAAATAGGTAATTTAATAGATGGTT
TATAAATACAACATAATATAATGGATGTTTTATAAGCATACATTACTAAATAAAAATAACAAAGT
TACAAAATCACTACCCACTCCACAGTATCAATACCTTATTGGCTTTCCTTCAGCTTCTTAAATCG
AACAAAAATAG
Found at i:10468424 original size:15 final size:15
Alignment explanation
Indices: 10468404--10468433 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
10468394 TAAGCTTTAA
10468404 AAAGCTTATGAAAGT
1 AAAGCTTATGAAAGT
*
10468419 AAAGCTTATGGAAGT
1 AAAGCTTATGAAAGT
10468434 GGATATTTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.23, T:0.27
Consensus pattern (15 bp):
AAAGCTTATGAAAGT
Found at i:10471078 original size:33 final size:34
Alignment explanation
Indices: 10471036--10471105 Score: 133
Period size: 33 Copynumber: 2.1 Consensus size: 34
10471026 TCAAATAAGC
10471036 TAAAGTAAGCTAAGGAAATCATAGAAGAAAAAGG
1 TAAAGTAAGCTAAGGAAATCATAGAAGAAAAAGG
10471070 TAAA-TAAGCTAAGGAAATCATAGAAGAAAAAGG
1 TAAAGTAAGCTAAGGAAATCATAGAAGAAAAAGG
10471103 TAA
1 TAA
10471106 GAAAATCTCC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 32 0.89
34 4 0.11
ACGTcount: A:0.57, C:0.06, G:0.21, T:0.16
Consensus pattern (34 bp):
TAAAGTAAGCTAAGGAAATCATAGAAGAAAAAGG
Found at i:10471884 original size:32 final size:32
Alignment explanation
Indices: 10471824--10471885 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
10471814 AAACTTAAAA
*
10471824 AAAATTTAAAAAATATAATTTATTTTAAATTG
1 AAAATTTAAAAAATATAATTCATTTTAAATTG
10471856 AAAATTTAAAAAA-A-AATTGCATTGTTAAAT
1 AAAATTTAAAAAATATAATT-CATT-TTAAAT
10471886 AATTTCAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 4 0.15
31 4 0.15
32 19 0.70
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (32 bp):
AAAATTTAAAAAATATAATTCATTTTAAATTG
Found at i:10471916 original size:27 final size:29
Alignment explanation
Indices: 10471875--10471930 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 29
10471865 AAAAAAATTG
*
10471875 CATTGTTAAATAATTTCAAAATTCTGAAA
1 CATTGTTAAATAATTTAAAAATTCTGAAA
*
10471904 CATT-TTAAA-AATTTAAAAATTTTGAAA
1 CATTGTTAAATAATTTAAAAATTCTGAAA
10471931 ATAAAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 16 0.64
28 5 0.20
29 4 0.16
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.39
Consensus pattern (29 bp):
CATTGTTAAATAATTTAAAAATTCTGAAA
Found at i:10481621 original size:31 final size:31
Alignment explanation
Indices: 10481564--10481622 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
10481554 TACACTGTCA
* * *
10481564 GTGAATCAGATTATGATAACTCATTAATGAG
1 GTGAATCAGATGATAATAACTAATTAATGAG
10481595 GTGAATCAGATGATAAT-ACATAATTAAT
1 GTGAATCAGATGATAATAAC-TAATTAAT
10481623 AAGTAAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 2 0.08
31 22 0.92
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.32
Consensus pattern (31 bp):
GTGAATCAGATGATAATAACTAATTAATGAG
Found at i:10491583 original size:21 final size:22
Alignment explanation
Indices: 10491559--10491609 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 22
10491549 TCTGAAATTA
10491559 ATAAAATATTATTTT-T-TAAAT
1 ATAAAATATT-TTTTATATAAAT
10491580 ATAAAATATTTTTTAATATAAAT
1 ATAAAATATTTTTT-ATATAAAT
10491603 ATAAAAT
1 ATAAAAT
10491610 TAAATAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.15
21 10 0.37
22 1 0.04
23 12 0.44
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATAAAATATTTTTTATATAAAT
Found at i:10491597 original size:17 final size:18
Alignment explanation
Indices: 10491568--10491601 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
10491558 AATAAAATAT
10491568 TATTTTTTAAATATAAAA
1 TATTTTTTAAATATAAAA
10491586 TATTTTTT-AATATAAA
1 TATTTTTTAAATATAAA
10491602 TATAAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TATTTTTTAAATATAAAA
Found at i:10491634 original size:18 final size:17
Alignment explanation
Indices: 10491595--10491642 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
10491585 ATATTTTTTA
10491595 ATATAAATATA-AAATT
1 ATATAAATATATAAATT
*
10491611 AAATAAATATATAAATAT
1 ATATAAATATATAAAT-T
*
10491629 ATATAAATAAATAA
1 ATATAAATATATAA
10491643 TTTAAAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 10 0.37
17 4 0.15
18 13 0.48
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATATAAATATATAAATT
Found at i:10492691 original size:30 final size:30
Alignment explanation
Indices: 10492655--10492723 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
10492645 TTTATTATAT
10492655 CTAAATAAATATTTAACATTTA-ATTTGTAC
1 CTAAATAAATATTTAAC-TTTATATTTGTAC
* * * *
10492685 CTAAATAAATTTTTAACTTTATTTTTTTAT
1 CTAAATAAATATTTAACTTTATATTTGTAC
10492715 CTAAATAAA
1 CTAAATAAA
10492724 CTCTTAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 4 0.12
30 30 0.88
ACGTcount: A:0.42, C:0.09, G:0.01, T:0.48
Consensus pattern (30 bp):
CTAAATAAATATTTAACTTTATATTTGTAC
Found at i:10493412 original size:2 final size:2
Alignment explanation
Indices: 10493405--10493513 Score: 128
Period size: 2 Copynumber: 54.5 Consensus size: 2
10493395 TACTATAATG
* * * * *
10493405 AT AT AT AT AT AT AT AT AC AA AT AT AT TT AC AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
10493447 GT AT AT AT AT AT AC AT AT AT AC AT AT AT AT TT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10493489 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 A
10493514 CACACACACA
Statistics
Matches: 88, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 88 1.00
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:10497353 original size:15 final size:16
Alignment explanation
Indices: 10497325--10497358 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
10497315 ACTTCTGTAA
*
10497325 ATTATAATTCTTTTAT
1 ATTATAAATCTTTTAT
10497341 ATTATAAAT-TTTTAT
1 ATTATAAATCTTTTAT
10497356 ATT
1 ATT
10497359 TTCAAACTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTATAAATCTTTTAT
Found at i:10497757 original size:17 final size:17
Alignment explanation
Indices: 10497735--10497777 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
10497725 ATGACAAATG
10497735 ATAAAATTACCTTAATA
1 ATAAAATTACCTTAATA
* * *
10497752 ATAAAACTATCTTGATA
1 ATAAAATTACCTTAATA
*
10497769 ATTAAATTA
1 ATAAAATTA
10497778 TTATGATGAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.51, C:0.09, G:0.02, T:0.37
Consensus pattern (17 bp):
ATAAAATTACCTTAATA
Found at i:10499174 original size:24 final size:22
Alignment explanation
Indices: 10499147--10499190 Score: 52
Period size: 24 Copynumber: 1.9 Consensus size: 22
10499137 TTAGTATAAA
10499147 TAAAAATATATTTTATTATATATT
1 TAAAAATATA-TTTA-TATATATT
**
10499171 TAAATCTATATTTATATATA
1 TAAAAATATATTTATATATA
10499191 ATTTTATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 6 0.33
23 4 0.22
24 8 0.44
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
TAAAAATATATTTATATATATT
Found at i:10501477 original size:7 final size:6
Alignment explanation
Indices: 10501445--10501494 Score: 59
Period size: 6 Copynumber: 8.3 Consensus size: 6
10501435 TAATATAATA
*
10501445 TTAAAT TTAAAT TTAAAT TT-AAT TTAAAAT TTAAAAT TT-AAC TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TT-AAAT TT-AAAT TTAAAT TTAAAT
10501493 TT
1 TT
10501495 GATCAAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
5 9 0.23
6 18 0.46
7 12 0.31
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (6 bp):
TTAAAT
Found at i:10501693 original size:18 final size:17
Alignment explanation
Indices: 10501665--10501726 Score: 63
Period size: 18 Copynumber: 3.5 Consensus size: 17
10501655 TTATTAATTA
10501665 AAATAATAAAAATATATTT
1 AAAT-ATAAAAAT-TATTT
*
10501684 AAATATAAAAATTTAATT
1 AAATATAAAAA-TTATTT
* *
10501702 AAATTTATAAATTATTT
1 AAATATAAAAATTATTT
10501719 AAAT-TAAA
1 AAATATAAA
10501727 CATAAAAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
16 3 0.08
17 9 0.24
18 20 0.54
19 5 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATATAAAAATTATTT
Found at i:10507559 original size:3 final size:3
Alignment explanation
Indices: 10507551--10507612 Score: 58
Period size: 3 Copynumber: 20.3 Consensus size: 3
10507541 TTTTATTCTG
*
10507551 TAT TAT TAT TAT T-T TTT GTAT T-T TAT GTAT T-T TAT TATT TAT TAT
1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT -TAT TAT TAT TA-T TAT TAT
10507596 TAT TAT TAT TAT GTAT T
1 TAT TAT TAT TAT -TAT T
10507613 GAATATATGG
Statistics
Matches: 51, Mismatches: 1, Indels: 14
0.77 0.02 0.21
Matches are distributed among these distances:
2 6 0.12
3 34 0.67
4 11 0.22
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:10507691 original size:21 final size:20
Alignment explanation
Indices: 10507667--10507714 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
10507657 GATTTAAGTG
*
10507667 TATTTATTTAATATAGTTCTA
1 TATTTATTTAATATA-TTATA
10507688 TATTTA-TT-ATATATTATA
1 TATTTATTTAATATATTATA
10507706 -ATTTATTTA
1 TATTTATTTA
10507715 TTATTTTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
17 5 0.21
18 6 0.25
19 5 0.21
20 2 0.08
21 6 0.25
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (20 bp):
TATTTATTTAATATATTATA
Found at i:10508792 original size:18 final size:18
Alignment explanation
Indices: 10508749--10508905 Score: 61
Period size: 18 Copynumber: 8.3 Consensus size: 18
10508739 TTTTTTGAAT
10508749 TTTTTTTATTTTCATTTA
1 TTTTTTTATTTTCATTTA
* ** *
10508767 TTTGTTTATTTTTTTTTC
1 TTTTTTTATTTTCATTTA
* *
10508785 TTTTTTTATTTATTAGATTA
1 TTTTTTTATTT-TCA-TTTA
* * *
10508805 GGTTTATTTAATATTCTTTTA
1 --TTT-TTTTATTTTCATTTA
* *
10508826 TCCTAATTTTATTTTTA-TT-
1 T--T-TTTTTATTTTCATTTA
10508845 TTTTTTTACTTTTC-TTTA
1 TTTTTTTA-TTTTCATTTA
** *
10508863 TTTTCCTATTTTTATTTA
1 TTTTTTTATTTTCATTTA
10508881 TTTTTTTATTATTCTATTT-
1 TTTTTTTATT-TTC-ATTTA
10508900 TTTTTT
1 TTTTTT
10508906 AAATAAAAAT
Statistics
Matches: 99, Mismatches: 26, Indels: 27
0.65 0.17 0.18
Matches are distributed among these distances:
16 5 0.05
17 11 0.11
18 42 0.42
19 12 0.12
20 8 0.08
21 11 0.11
22 4 0.04
23 6 0.06
ACGTcount: A:0.17, C:0.06, G:0.03, T:0.75
Consensus pattern (18 bp):
TTTTTTTATTTTCATTTA
Found at i:10508862 original size:26 final size:25
Alignment explanation
Indices: 10508832--10508906 Score: 98
Period size: 26 Copynumber: 2.9 Consensus size: 25
10508822 TTTATCCTAA
10508832 TTTTATTTT-TATTTTTTTTTACTTT
1 TTTTATTTTCTATTTTTTTTTA-TTT
*
10508857 TCTTTATTTTCCTATTTTTATTTATTT
1 T-TTTATTTT-CTATTTTTTTTTATTT
10508884 TTTTATTATTCTATTTTTTTTTA
1 TTTTATT-TTCTATTTTTTTTTA
10508907 AATAAAAATC
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
25 1 0.02
26 26 0.59
27 6 0.14
28 11 0.25
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.79
Consensus pattern (25 bp):
TTTTATTTTCTATTTTTTTTTATTT
Found at i:10508906 original size:18 final size:17
Alignment explanation
Indices: 10508832--10508906 Score: 66
Period size: 18 Copynumber: 4.3 Consensus size: 17
10508822 TTTATCCTAA
10508832 TTTTATTTTTATT-TTT
1 TTTTATTTTTATTATTT
10508848 TTTTACTTTTCT-TTATTT
1 TTTTA-TTTT-TATTATTT
**
10508866 TCCTATTTTTATTTATTT
1 TTTTATTTTTA-TTATTT
10508884 TTTTATTATTCTATT-TTT
1 TTTTATT-TT-TATTATTT
10508902 TTTTA
1 TTTTA
10508907 AATAAAAATC
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
16 6 0.12
17 10 0.21
18 26 0.54
19 4 0.08
20 2 0.04
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTATTTTTATTATTT
Found at i:10509003 original size:57 final size:59
Alignment explanation
Indices: 10508909--10509025 Score: 193
Period size: 57 Copynumber: 2.0 Consensus size: 59
10508899 TTTTTTTAAA
10508909 TAAAAATCAAAATTTCCAAAAAAAATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTCCT
1 TAAAAAT-AAAATTTCC-AAAAAAATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTCCT
*
10508970 TAAAAAT-AAATTTCC-AAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCC
1 TAAAAATAAAATTTCCAAAAAAATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTCC
10509026 CCACACAAGA
Statistics
Matches: 55, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
57 40 0.73
59 8 0.15
61 7 0.13
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.33
Consensus pattern (59 bp):
TAAAAATAAAATTTCCAAAAAAATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTCCT
Found at i:10512209 original size:15 final size:15
Alignment explanation
Indices: 10512184--10512230 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
10512174 TTTGCATACA
10512184 TGCATTTCTCATTCAT
1 TGCA-TTCTCATTCAT
10512200 TGCATTCTCATTCAT
1 TGCATTCTCATTCAT
* *
10512215 TACATTCTTATTCAT
1 TGCATTCTCATTCAT
10512230 T
1 T
10512231 ACACTTAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
15 25 0.86
16 4 0.14
ACGTcount: A:0.21, C:0.23, G:0.04, T:0.51
Consensus pattern (15 bp):
TGCATTCTCATTCAT
Found at i:10512231 original size:15 final size:15
Alignment explanation
Indices: 10512189--10512233 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
10512179 ATACATGCAT
*
10512189 TTCTCATTCATTGCA
1 TTCTCATTCATTACA
10512204 TTCTCATTCATTACA
1 TTCTCATTCATTACA
*
10512219 TTCTTATTCATTACA
1 TTCTCATTCATTACA
10512234 CTTAACAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.24, C:0.24, G:0.02, T:0.49
Consensus pattern (15 bp):
TTCTCATTCATTACA
Found at i:10514559 original size:15 final size:16
Alignment explanation
Indices: 10514539--10514572 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
10514529 AATACTAGAT
*
10514539 AAGGCTAAA-AGGGAG
1 AAGGCTAAAGAAGGAG
10514554 AAGGCTAAAGAAGGAG
1 AAGGCTAAAGAAGGAG
10514570 AAG
1 AAG
10514573 NNNNNNNNNN
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.50, C:0.06, G:0.38, T:0.06
Consensus pattern (16 bp):
AAGGCTAAAGAAGGAG
Found at i:10515747 original size:9 final size:8
Alignment explanation
Indices: 10515728--10515752 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
10515718 TTAAAATGTA
10515728 TTTTTTAT
1 TTTTTTAT
10515736 TTTTTTAT
1 TTTTTTAT
10515744 TTTTTTAT
1 TTTTTTAT
10515752 T
1 T
10515753 AGATAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTTAT
Found at i:10516299 original size:24 final size:23
Alignment explanation
Indices: 10516240--10516305 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 23
10516230 GTATATATCA
10516240 AAAATATATATTT-TATTATTTATT
1 AAAATATATATTTATA-TA-TTATT
* *
10516264 AAATTCTATATTTATATATTATT
1 AAAATATATATTTATATATTATT
10516287 AAAATATATTATTTA-ATAT
1 AAAATATA-TATTTATATAT
10516306 CTTAATCTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
23 15 0.42
24 19 0.53
25 2 0.06
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
AAAATATATATTTATATATTATT
Found at i:10516305 original size:23 final size:22
Alignment explanation
Indices: 10516240--10516305 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 22
10516230 GTATATATCA
*
10516240 AAAATATATATTTTATTATTTATT
1 AAAATATATA-TTTAATA-TTATT
* *
10516264 AAATTCTATATTTATATATTATT
1 AAAATATATATTTA-ATATTATT
10516287 AAAATATATTATTTAATAT
1 AAAATATA-TATTTAATAT
10516306 CTTAATCTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
23 19 0.54
24 16 0.46
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
AAAATATATATTTAATATTATT
Found at i:10518302 original size:108 final size:108
Alignment explanation
Indices: 10518042--10518294 Score: 310
Period size: 108 Copynumber: 2.3 Consensus size: 108
10518032 TTATTAGGGC
* * * *
10518042 ATTTCATTGCAAAAATGCTTTAATTTATTATTAATTATGGTGTTTTTGTTGTAAAAATAATTTAT
1 ATTTCATTGCAAAAATACCTTAATTTATTATCAATTATGGTGTTTTTGTTGTAAAAATAACTTAT
* * *
10518107 TTGGAGCTTCACACTTTTATCAAAATCAACTGGCCATTAAGGT
66 TTGGAGCCTCAAACTTTTATCAAAATCAACTGGCCATCAAGGT
* * * * * **
10518150 ATTTTATTACAGAAATACCTTAATTGATTATCAATTATGGTGTTTTTGTTGTACAAATGCCTTAT
1 ATTTCATTGCAAAAATACCTTAATTTATTATCAATTATGGTGTTTTTGTTGTAAAAATAACTTAT
* * * *
10518215 TTGGTGCC-CTAAACTTTTATCAAATTCAAGTGGCTATCAAGGT
66 TTGGAGCCTC-AAACTTTTATCAAAATCAACTGGCCATCAAGGT
* *
10518258 GTTTCATTGCAAAAACACCTTAATTTATTATCAATTA
1 ATTTCATTGCAAAAATACCTTAATTTATTATCAATTA
10518295 CGATGTTTCA
Statistics
Matches: 120, Mismatches: 24, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
107 1 0.01
108 119 0.99
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (108 bp):
ATTTCATTGCAAAAATACCTTAATTTATTATCAATTATGGTGTTTTTGTTGTAAAAATAACTTAT
TTGGAGCCTCAAACTTTTATCAAAATCAACTGGCCATCAAGGT
Found at i:10524012 original size:22 final size:23
Alignment explanation
Indices: 10523970--10524012 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 23
10523960 GTTTCATATT
*
10523970 TTCATTTAATGAAGTTCATAATA
1 TTCATTTAATGAAGTTAATAATA
10523993 TTCATTT-ATG-AGTATAATAA
1 TTCATTTAATGAAGT-TAATAA
10524013 AAGTATTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 3 0.17
22 8 0.44
23 7 0.39
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (23 bp):
TTCATTTAATGAAGTTAATAATA
Found at i:10524837 original size:26 final size:25
Alignment explanation
Indices: 10524783--10524839 Score: 62
Period size: 26 Copynumber: 2.3 Consensus size: 25
10524773 TAAAATTTAA
**
10524783 GAAAC-AAACCAATATGCAATACAC
1 GAAACAAAACCAATATAAAATACAC
* *
10524807 AAAACAAAACCAATAATAAAATACAT
1 GAAACAAAACCAAT-ATAAAATACAC
10524833 GAAACAA
1 GAAACAA
10524840 GCCATACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 4 0.15
25 8 0.31
26 14 0.54
ACGTcount: A:0.63, C:0.19, G:0.05, T:0.12
Consensus pattern (25 bp):
GAAACAAAACCAATATAAAATACAC
Found at i:10526375 original size:13 final size:13
Alignment explanation
Indices: 10526357--10526385 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
10526347 TCCATACATG
10526357 AATAAAAGAAAAA
1 AATAAAAGAAAAA
10526370 AATAAAAGAAAAA
1 AATAAAAGAAAAA
10526383 AAT
1 AAT
10526386 TTTACACTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.10
Consensus pattern (13 bp):
AATAAAAGAAAAA
Found at i:10526934 original size:179 final size:179
Alignment explanation
Indices: 10526700--10527027 Score: 496
Period size: 179 Copynumber: 1.8 Consensus size: 179
10526690 TGTGTGATTA
* * * *
10526700 AAAAAAAAATCAATTAAGGAATTTATATTAAACAAATGTCGTAAATGATGAGTTTTTTTAAATTC
1 AAAAAAAAATCAATTAAGGAATTTATATTAAACAAATATCATAAATGAGGAGTTTTTTCAAATTC
10526765 TAAAACAAAAGCAATTAAGGCATTCATATTAAACAAACACCATAATCGAGAGTTCTAAACAATTA
66 TAAAACAAAAGCAATTAAGGCATTCATATTAAACAAACACCATAATCGAGAGTTCTAAACAATTA
*
10526830 TAAAACTTGCCAATTAAGGTGTTTATCTGTTCCAAATATCGTAACTGAG
131 TAAAACATGCCAATTAAGGTGTTTATCTGTTCCAAATATCGTAACTGAG
*
10526879 AAAAAAAAATCAATTAA-GACATTTATATTAAACAAATATCATAAGTGAGGAGTTTTTTCAAATT
1 AAAAAAAAATCAATTAAGGA-ATTTATATTAAACAAATATCATAAATGAGGAGTTTTTTCAAATT
** * * * * * * *
10526943 CTAAAATGAAAGTAATTAAGGCATTCCTATTAAACAAACATCGTAATTGAGAGTTTTAAATAATT
65 CTAAAACAAAAGCAATTAAGGCATTCATATTAAACAAACACCATAATCGAGAGTTCTAAACAATT
*
10527008 ATAAAACATGTCAATTAAGG
130 ATAAAACATGCCAATTAAGG
10527028 CAATCATTTG
Statistics
Matches: 132, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
178 2 0.02
179 130 0.98
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.31
Consensus pattern (179 bp):
AAAAAAAAATCAATTAAGGAATTTATATTAAACAAATATCATAAATGAGGAGTTTTTTCAAATTC
TAAAACAAAAGCAATTAAGGCATTCATATTAAACAAACACCATAATCGAGAGTTCTAAACAATTA
TAAAACATGCCAATTAAGGTGTTTATCTGTTCCAAATATCGTAACTGAG
Found at i:10528112 original size:26 final size:26
Alignment explanation
Indices: 10528061--10528113 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
10528051 ATTAATATAT
* *
10528061 AAAAAAAAGCTCGATTTTTATACTCG
1 AAAAAAAAGCTCGATTATTAGACTCG
*
10528087 AAAAAAAA-CTCGATTATTCGAGCTCG
1 AAAAAAAAGCTCGATTATTAGA-CTCG
10528113 A
1 A
10528114 GCTCGAGATC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.26
Consensus pattern (26 bp):
AAAAAAAAGCTCGATTATTAGACTCG
Found at i:10531873 original size:25 final size:25
Alignment explanation
Indices: 10531836--10531889 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
10531826 TCCCCACAAT
* *
10531836 ATTCATAAGGGTATTTAATTTAGGC
1 ATTCATAAAGGTATTTAATTAAGGC
10531861 ATTCATAAAGGTATTTAATTAAGGC
1 ATTCATAAAGGTATTTAATTAAGGC
10531886 ATTC
1 ATTC
10531890 TTATTTAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.39
Consensus pattern (25 bp):
ATTCATAAAGGTATTTAATTAAGGC
Found at i:10532126 original size:32 final size:32
Alignment explanation
Indices: 10532084--10532157 Score: 139
Period size: 32 Copynumber: 2.3 Consensus size: 32
10532074 TTGAGGGATC
10532084 GGGTTCTGTTGAAGCTGCTGCAAACGTCGAAT
1 GGGTTCTGTTGAAGCTGCTGCAAACGTCGAAT
*
10532116 GGGTTTTGTTGAAGCTGCTGCAAACGTCGAAT
1 GGGTTCTGTTGAAGCTGCTGCAAACGTCGAAT
10532148 GGGTTCTGTT
1 GGGTTCTGTT
10532158 CAAGATCAGG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.19, C:0.16, G:0.32, T:0.32
Consensus pattern (32 bp):
GGGTTCTGTTGAAGCTGCTGCAAACGTCGAAT
Found at i:10532194 original size:46 final size:47
Alignment explanation
Indices: 10532132--10532247 Score: 180
Period size: 46 Copynumber: 2.4 Consensus size: 47
10532122 TGTTGAAGCT
* *
10532132 GCTGCAAACGTCGAATGGGTTCTGTTCAAGATCAGGTTCTATTGAA-
1 GCTGCAAACGTCGAATGGGTTCTATTCAAGATCAAGTTCTATTGAAC
*
10532178 GCTGCAAACGTCGAATGGGTTCTATTCAAGATCAAGTTCTGTTGAAGC
1 GCTGCAAACGTCGAATGGGTTCTATTCAAGATCAAGTTCTATTGAA-C
10532226 TGCTGCAAACGTCGAATGGGTT
1 -GCTGCAAACGTCGAATGGGTT
10532248 TTGTCTGCAA
Statistics
Matches: 64, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
46 43 0.67
49 21 0.33
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (47 bp):
GCTGCAAACGTCGAATGGGTTCTATTCAAGATCAAGTTCTATTGAAC
Found at i:10532263 original size:24 final size:24
Alignment explanation
Indices: 10532228--10532275 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
10532218 GTTGAAGCTG
*
10532228 CTGCAAACGTCGAATGGGTTTTGT
1 CTGCAAAAGTCGAATGGGTTTTGT
10532252 CTGCAAAAGTCGAATGGGTTTTGT
1 CTGCAAAAGTCGAATGGGTTTTGT
10532276 TCAAGATCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.23, C:0.15, G:0.29, T:0.33
Consensus pattern (24 bp):
CTGCAAAAGTCGAATGGGTTTTGT
Found at i:10532298 original size:73 final size:73
Alignment explanation
Indices: 10532179--10532320 Score: 248
Period size: 73 Copynumber: 1.9 Consensus size: 73
10532169 TCTATTGAAG
*
10532179 CTGCAAACGTCGAATGGGTTCTATTCAAGATCAAGTTCTGTTGAAGCTGCTGCAAACGTCGAATG
1 CTGCAAAAGTCGAATGGGTTCTATTCAAGATCAAGTTCTGTTGAAGCTGCTGCAAACGTCGAATG
10532244 GGTTTTGT
66 GGTTTTGT
* * *
10532252 CTGCAAAAGTCGAATGGGTTTTGTTCAAGATCAGGTTCTGTTGAAGCTGCTGCAAACGTCGAATG
1 CTGCAAAAGTCGAATGGGTTCTATTCAAGATCAAGTTCTGTTGAAGCTGCTGCAAACGTCGAATG
10532317 GGTT
66 GGTT
10532321 CTGTTCAAGA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 65 1.00
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (73 bp):
CTGCAAAAGTCGAATGGGTTCTATTCAAGATCAAGTTCTGTTGAAGCTGCTGCAAACGTCGAATG
GGTTTTGT
Found at i:10532386 original size:57 final size:57
Alignment explanation
Indices: 10532300--10532464 Score: 209
Period size: 57 Copynumber: 3.0 Consensus size: 57
10532290 TGTTGAAGCT
* *
10532300 GCTGCAAACGTCGAATGGGTTCTGTTCAAGATCTGTAAACTGTTGAAGCTGCTGCAA
1 GCTGCAAACGTCGAATGGGTTCTGTTCAAGATCTGCAAACTGTTGAAGCTACTGCAA
*
10532357 GCTGCAAAGGTCGAATGGGTTCTGTTCAAGATCTGCAAACTGTTGAAG---CT---A
1 GCTGCAAACGTCGAATGGGTTCTGTTCAAGATCTGCAAACTGTTGAAGCTACTGCAA
* * * *
10532408 -CTGCAAACGTCGAATGGGTTCTGTTGAAGCTACTGCAAACTGTTGAAGTTACCGCAA
1 GCTGCAAACGTCGAATGGGTTCTGTTCAAGAT-CTGCAAACTGTTGAAGCTACTGCAA
10532465 ACTGTTGAAG
Statistics
Matches: 95, Mismatches: 6, Indels: 14
0.83 0.05 0.12
Matches are distributed among these distances:
50 28 0.29
51 17 0.18
54 3 0.03
57 47 0.49
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.27
Consensus pattern (57 bp):
GCTGCAAACGTCGAATGGGTTCTGTTCAAGATCTGCAAACTGTTGAAGCTACTGCAA
Found at i:10532452 original size:19 final size:19
Alignment explanation
Indices: 10532428--10532502 Score: 114
Period size: 19 Copynumber: 3.9 Consensus size: 19
10532418 CGAATGGGTT
10532428 CTGTTGAAGCTACTGCAAA
1 CTGTTGAAGCTACTGCAAA
* *
10532447 CTGTTGAAGTTACCGCAAA
1 CTGTTGAAGCTACTGCAAA
*
10532466 CTGTTGAAGCTGCTGCAAA
1 CTGTTGAAGCTACTGCAAA
*
10532485 CTGTTGAAGCTGCTGCAA
1 CTGTTGAAGCTACTGCAA
10532503 GCTGCAAACG
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 51 1.00
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (19 bp):
CTGTTGAAGCTACTGCAAA
Found at i:10532511 original size:26 final size:26
Alignment explanation
Indices: 10532477--10532568 Score: 87
Period size: 26 Copynumber: 3.3 Consensus size: 26
10532467 TGTTGAAGCT
10532477 GCTGCAAACTGTTGAAGCTGCTGCAA
1 GCTGCAAACTGTTGAAGCTGCTGCAA
* * **
10532503 GCTGCAAAC-GTCGAATGGGTTTTGTTCAA
1 GCTGCAAACTGTTGAA--GCTGCTG--CAA
10532532 GATCTGCAAACTGTTGAAGCTGCTGCAA
1 G--CTGCAAACTGTTGAAGCTGCTGCAA
10532560 GCTGCAAAC
1 GCTGCAAAC
10532569 GTCGAATGGG
Statistics
Matches: 51, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
25 5 0.10
26 17 0.33
27 4 0.08
28 4 0.08
29 4 0.08
30 4 0.08
31 8 0.16
32 5 0.10
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (26 bp):
GCTGCAAACTGTTGAAGCTGCTGCAA
Found at i:10532539 original size:57 final size:57
Alignment explanation
Indices: 10532478--10532666 Score: 268
Period size: 57 Copynumber: 3.4 Consensus size: 57
10532468 GTTGAAGCTG
*
10532478 CTGCAAACTGTTGAAGCTGCTGCAAGCTGCAAACGTCGAATGGGTTTTGTTCAAGAT
1 CTGCAAACTGTTGAAGCTGCTGCAAGCTGCAAACGTCGAATGGGTTCTGTTCAAGAT
*
10532535 CTGCAAACTGTTGAAGCTGCTGCAAGCTGCAAACGTCGAATGGGTTCTGTTCAAGCT
1 CTGCAAACTGTTGAAGCTGCTGCAAGCTGCAAACGTCGAATGGGTTCTGTTCAAGAT
*
10532592 GCTTCAAACTGTTGAA---GCT---A-CTGCAAACGTCG-ATGGGTTCTGTTCAAGAT
1 -CTGCAAACTGTTGAAGCTGCTGCAAGCTGCAAACGTCGAATGGGTTCTGTTCAAGAT
* *
10532642 TTGCAAACTGTTGAAGCTACTGCAA
1 CTGCAAACTGTTGAAGCTGCTGCAA
10532667 ACGTAGAATG
Statistics
Matches: 118, Mismatches: 7, Indels: 16
0.84 0.05 0.11
Matches are distributed among these distances:
49 13 0.11
50 17 0.14
51 12 0.10
52 3 0.03
55 4 0.03
57 55 0.47
58 14 0.12
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.28
Consensus pattern (57 bp):
CTGCAAACTGTTGAAGCTGCTGCAAGCTGCAAACGTCGAATGGGTTCTGTTCAAGAT
Found at i:10532542 original size:146 final size:149
Alignment explanation
Indices: 10532336--10532619 Score: 448
Period size: 146 Copynumber: 1.9 Consensus size: 149
10532326 CAAGATCTGT
*
10532336 AAACTGTTGAAGCTGCTGCAAGCTGCAAAGGTCGAATGGGTTCTGTTCAAGATCTGCAAACTGTT
1 AAACTGTTGAAGCTGCTGCAAGCTGCAAACGTCGAATGGGTTCTGTTCAAGATCTGCAAACTGTT
* *
10532401 GAA-GCT-A-CTGCAAACGTCGAATGGGTTCTGTTGAAGCTACTGCAAACTGTTGAAGTTACCGC
66 GAACGCTAAGCTGCAAACGTCGAATGGGTTCTGTTCAAGCTACTGCAAACTGTTGAAGCTACCGC
10532463 AAACTGTTGAAGCTGCTGC
131 AAACTGTTGAAGCTGCTGC
*
10532482 AAACTGTTGAAGCTGCTGCAAGCTGCAAACGTCGAATGGGTTTTGTTCAAGATCTGCAAACTGTT
1 AAACTGTTGAAGCTGCTGCAAGCTGCAAACGTCGAATGGGTTCTGTTCAAGATCTGCAAACTGTT
* *
10532547 GAAGCTGCTGCAAGCTGCAAACGTCGAATGGGTTCTGTTCAAGCTGCTTCAAACTGTTGAAGCTA
66 GAA-C-GCT--AAGCTGCAAACGTCGAATGGGTTCTGTTCAAGCTACTGCAAACTGTTGAAGCTA
*
10532612 CTGCAAAC
127 CCGCAAAC
10532620 GTCGATGGGT
Statistics
Matches: 124, Mismatches: 7, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
146 66 0.53
149 3 0.02
152 1 0.01
153 54 0.44
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.27
Consensus pattern (149 bp):
AAACTGTTGAAGCTGCTGCAAGCTGCAAACGTCGAATGGGTTCTGTTCAAGATCTGCAAACTGTT
GAACGCTAAGCTGCAAACGTCGAATGGGTTCTGTTCAAGCTACTGCAAACTGTTGAAGCTACCGC
AAACTGTTGAAGCTGCTGC
Found at i:10532575 original size:203 final size:202
Alignment explanation
Indices: 10532300--10532668 Score: 623
Period size: 203 Copynumber: 1.8 Consensus size: 202
10532290 TGTTGAAGCT
*
10532300 GCTGCAAACGTCGAATGGGTTCTGTTCAAGATCTGTAAACTGTTGAAGCTGCTGCAAGCTGCAAA
1 GCTGCAAACGTCGAATGGGTTCTGTTCAAGATCTGCAAACTGTTGAAGCTGCTGCAAGCTGCAAA
*
10532365 GGTCGAATGGGTTCTGTTCAAGAT-CTGCAAACTGTTGAAGCTACTGCAAACGTCGAATGGGTTC
66 CGTCGAATGGGTTCTGTTCAAGATGCTGCAAACTGTTGAAGCTACTGCAAACGTCG-ATGGGTTC
* * *
10532429 TGTTGAAGCTACTGCAAACTGTTGAAGTTACCGCAAACTGTTGAAGCTGCTGCAAACTGTTGAAG
130 TGTTCAAGAT-CTGCAAACTGTTGAAGCTACCGCAAACTGTTGAAGCTGCTGCAAACTGTTGAAG
10532494 CTGCTGCAA
194 CTGCTGCAA
*
10532503 GCTGCAAACGTCGAATGGGTTTTGTTCAAGATCTGCAAACTGTTGAAGCTGCTGCAAGCTGCAAA
1 GCTGCAAACGTCGAATGGGTTCTGTTCAAGATCTGCAAACTGTTGAAGCTGCTGCAAGCTGCAAA
* *
10532568 CGTCGAATGGGTTCTGTTCAAGCTGCTTCAAACTGTTGAAGCTACTGCAAACGTCGATGGGTTCT
66 CGTCGAATGGGTTCTGTTCAAGATGCTGCAAACTGTTGAAGCTACTGCAAACGTCGATGGGTTCT
* *
10532633 GTTCAAGATTTGCAAACTGTTGAAGCTACTGCAAAC
131 GTTCAAGATCTGCAAACTGTTGAAGCTACCGCAAAC
10532669 GTAGAATGGG
Statistics
Matches: 155, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
202 24 0.15
203 101 0.65
204 30 0.19
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (202 bp):
GCTGCAAACGTCGAATGGGTTCTGTTCAAGATCTGCAAACTGTTGAAGCTGCTGCAAGCTGCAAA
CGTCGAATGGGTTCTGTTCAAGATGCTGCAAACTGTTGAAGCTACTGCAAACGTCGATGGGTTCT
GTTCAAGATCTGCAAACTGTTGAAGCTACCGCAAACTGTTGAAGCTGCTGCAAACTGTTGAAGCT
GCTGCAA
Found at i:10532618 original size:19 final size:19
Alignment explanation
Indices: 10532581--10532619 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
10532571 CGAATGGGTT
* *
10532581 CTGTTCAAGCTGCTTCAAA
1 CTGTTCAAGCTACTGCAAA
*
10532600 CTGTTGAAGCTACTGCAAA
1 CTGTTCAAGCTACTGCAAA
10532619 C
1 C
10532620 GTCGATGGGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (19 bp):
CTGTTCAAGCTACTGCAAA
Found at i:10532653 original size:49 final size:50
Alignment explanation
Indices: 10532358--10532685 Score: 307
Period size: 50 Copynumber: 6.5 Consensus size: 50
10532348 CTGCTGCAAG
* *
10532358 CTGCAAAGGTCGAATGGGTTCTGTTCAAGATCTGCAAACTGTTGAAGCTA
1 CTGCAAACGTCGAATGGGTTCTGTTCAAGATCTTCAAACTGTTGAAGCTA
* * * *
10532408 CTGCAAACGTCGAATGGGTTCTGTTGAAGCTACTGCAAACTGTTGAAGTTA
1 CTGCAAACGTCGAATGGGTTCTGTTCAAGAT-CTTCAAACTGTTGAAGCTA
* * * * * * * *
10532459 CCGCAAACTGTTGAA--GCTGCTG--CAA-ACTGTTGAAGCTGCTGCAAG---
1 CTGCAAAC-GTCGAATGGGTTCTGTTCAAGA-TCTTCAAACTGTTG-AAGCTA
* *
10532504 CTGCAAACGTCGAATGGGTTTTGTTCAAGATCTGCAAACTGTTGAAGCTGCTGCAA
1 CTGCAAACGTCGAATGGGTTCTGTTCAAGATCTTCAAACTGTTGAA---GCT---A
*
10532560 GCTGCAAACGTCGAATGGGTTCTGTTCAAGCTGCTTCAAACTGTTGAAGCTA
1 -CTGCAAACGTCGAATGGGTTCTGTTCAAGAT-CTTCAAACTGTTGAAGCTA
10532612 CTGCAAACGTCG-ATGGGTTCTGTTCAAGAT-TTGCAAACTGTTGAAGCTA
1 CTGCAAACGTCGAATGGGTTCTGTTCAAGATCTT-CAAACTGTTGAAGCTA
*
10532661 CTGCAAACGTAGAATGGGTTCTGTT
1 CTGCAAACGTCGAATGGGTTCTGTT
10532686 GAAGCTACTG
Statistics
Matches: 226, Mismatches: 30, Indels: 44
0.75 0.10 0.15
Matches are distributed among these distances:
44 5 0.02
45 7 0.03
46 4 0.02
47 10 0.04
48 20 0.09
49 28 0.12
50 63 0.28
51 37 0.16
52 6 0.03
55 3 0.01
57 29 0.13
58 14 0.06
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.28
Consensus pattern (50 bp):
CTGCAAACGTCGAATGGGTTCTGTTCAAGATCTTCAAACTGTTGAAGCTA
Found at i:10532690 original size:32 final size:32
Alignment explanation
Indices: 10532649--10532717 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
10532639 GATTTGCAAA
*
10532649 CTGTTGAAGCTACTGCAAACGTAGAATGGGTT
1 CTGTTGAAGCTACTGCAAACGTAGAATAGGTT
*
10532681 CTGTTGAAGCTACTGCAAACGTCGAATAGGTT
1 CTGTTGAAGCTACTGCAAACGTAGAATAGGTT
10532713 CTGTT
1 CTGTT
10532718 CAAGATCGGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.30
Consensus pattern (32 bp):
CTGTTGAAGCTACTGCAAACGTAGAATAGGTT
Found at i:10532959 original size:18 final size:17
Alignment explanation
Indices: 10532938--10532973 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
10532928 AAGTAATTTT
10532938 ATAAATAAAATAATAAAA
1 ATAAAT-AAATAATAAAA
*
10532956 ATAAATATATAATAAAA
1 ATAAATAAATAATAAAA
10532973 A
1 A
10532974 AGCTCGATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (17 bp):
ATAAATAAATAATAAAA
Found at i:10539033 original size:2 final size:2
Alignment explanation
Indices: 10539026--10539056 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
10539016 TAAAGGCTAT
10539026 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
10539057 GGGGGGGGGA
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:10539837 original size:17 final size:16
Alignment explanation
Indices: 10539815--10539873 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
10539805 AATTATCTTA
10539815 AATTAAATATAAAAATT
1 AATTAAA-ATAAAAATT
*
10539832 AATTAAAA-ACAAAAAT
1 AATTAAAATA-AAAATT
* *
10539848 AATTTAAATAAATATT
1 AATTAAAATAAAAATT
10539864 AATTATAAAT
1 AATTA-AAAT
10539874 TTATTAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
15 1 0.03
16 21 0.62
17 12 0.35
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (16 bp):
AATTAAAATAAAAATT
Found at i:10542110 original size:19 final size:21
Alignment explanation
Indices: 10542058--10542115 Score: 66
Period size: 19 Copynumber: 2.8 Consensus size: 21
10542048 AAAATTTACA
*
10542058 TTTTAAAATAAAAAACATAATC
1 TTTTAAAATAATAAA-ATAATC
*
10542080 TTTATTAAATAATAAAAT-AT-
1 TTT-TAAAATAATAAAATAATC
10542100 TTTTAAAATAATAAAA
1 TTTTAAAATAATAAAA
10542116 ACTACGTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
19 12 0.38
20 3 0.09
21 2 0.06
22 5 0.16
23 10 0.31
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (21 bp):
TTTTAAAATAATAAAATAATC
Found at i:10542178 original size:21 final size:23
Alignment explanation
Indices: 10542152--10542248 Score: 67
Period size: 23 Copynumber: 4.2 Consensus size: 23
10542142 GTTTTTAATA
*
10542152 ATATAAAG-ATCAT-GTTTTTTT
1 ATATAAAGAAACATAGTTTTTTT
10542173 ATAT-AAGAAACATAGTTTTTTT
1 ATATAAAGAAACATAGTTTTTTT
* * * *
10542195 TTATAAATAAAAAAAGCATTTTTTT
1 ATATAAAGAAACATAG--TTTTTTT
* *
10542220 ATAATAAAAAAACTTA-TGTTTTTT
1 AT-ATAAAGAAACATAGT-TTTTTT
10542244 ATATA
1 ATATA
10542249 GAAACGTAGT
Statistics
Matches: 59, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
20 3 0.05
21 8 0.14
22 11 0.19
23 12 0.20
24 8 0.14
25 8 0.14
26 9 0.15
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.46
Consensus pattern (23 bp):
ATATAAAGAAACATAGTTTTTTT
Found at i:10543561 original size:21 final size:20
Alignment explanation
Indices: 10543523--10543562 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
10543513 AATTTTGAAA
* *
10543523 AATTTTGGTGATTTTTGATC
1 AATTTTGATGATTCTTGATC
10543543 AATTTTGATAGATTCTTGAT
1 AATTTTGAT-GATTCTTGAT
10543563 ACATTTGGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.25, C:0.05, G:0.17, T:0.53
Consensus pattern (20 bp):
AATTTTGATGATTCTTGATC
Found at i:10546171 original size:24 final size:24
Alignment explanation
Indices: 10546144--10546197 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
10546134 TTGTATCTTG
* *
10546144 ATTTTGATCATTG-ATTGAAATTGT
1 ATTTGGAT-ATTGAATTGAAATTAT
*
10546168 ATTTGGATTTTGAATTGAAATTAT
1 ATTTGGATATTGAATTGAAATTAT
10546192 ATTTGG
1 ATTTGG
10546198 GTTTTGATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 3 0.12
24 23 0.88
ACGTcount: A:0.30, C:0.02, G:0.19, T:0.50
Consensus pattern (24 bp):
ATTTGGATATTGAATTGAAATTAT
Found at i:10546180 original size:23 final size:23
Alignment explanation
Indices: 10546154--10546207 Score: 81
Period size: 24 Copynumber: 2.3 Consensus size: 23
10546144 ATTTTGATCA
*
10546154 TTGATTGAAATTGTATTTGGATT
1 TTGATTGAAATTATATTTGGATT
*
10546177 TTGAATTGAAATTATATTTGGGTT
1 TTG-ATTGAAATTATATTTGGATT
10546201 TTGATTG
1 TTGATTG
10546208 TTCATTGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 7 0.25
24 21 0.75
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (23 bp):
TTGATTGAAATTATATTTGGATT
Found at i:10552253 original size:29 final size:28
Alignment explanation
Indices: 10552220--10552284 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 28
10552210 TGAAGTGAAA
*
10552220 AGAAATAATAAAAAAAATGAAAAAAAATG
1 AGAAA-AATAAAAAAAATGAAAAAAAAAG
* **
10552249 AGAAAGATATGAAAAATGAAAAAAAAAG
1 AGAAAAATAAAAAAAATGAAAAAAAAAG
10552277 AGAGAAAA
1 AGA-AAAA
10552285 GGAAAACTCA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 22 0.73
29 8 0.27
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.11
Consensus pattern (28 bp):
AGAAAAATAAAAAAAATGAAAAAAAAAG
Found at i:10553457 original size:21 final size:21
Alignment explanation
Indices: 10553433--10553496 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 21
10553423 TTTCAAATAA
*
10553433 GAATCTTTGAGTTTTAGATAT
1 GAATCTTTGAATTTTAGATAT
* *
10553454 GAATCTTTAAGACTTTTTGA-AT
1 GAATCTTT--GAATTTTAGATAT
10553476 GTTAATCTTTGAATTTTAGAT
1 G--AATCTTTGAATTTTAGAT
10553497 GTAAACCTCT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
21 8 0.24
22 11 0.32
23 8 0.24
24 7 0.21
ACGTcount: A:0.30, C:0.06, G:0.16, T:0.48
Consensus pattern (21 bp):
GAATCTTTGAATTTTAGATAT
Found at i:10553498 original size:21 final size:21
Alignment explanation
Indices: 10553433--10553498 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
10553423 TTTCAAATAA
* *
10553433 GAATCTTTGAGTTTTAGATAT
1 GAATCTTTGAATTTTAGATGT
* *
10553454 GAATCTTTAAGACTTTTTGAATGT
1 GAATCTTT--GAATTTTAG-ATGT
*
10553478 TAATCTTTGAATTTTAGATGT
1 GAATCTTTGAATTTTAGATGT
10553499 AAACCTCTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
21 12 0.33
22 7 0.19
23 7 0.19
24 10 0.28
ACGTcount: A:0.29, C:0.06, G:0.17, T:0.48
Consensus pattern (21 bp):
GAATCTTTGAATTTTAGATGT
Found at i:10553516 original size:45 final size:45
Alignment explanation
Indices: 10553432--10553530 Score: 117
Period size: 45 Copynumber: 2.2 Consensus size: 45
10553422 TTTTCAAATA
* * * *
10553432 AGAATCTTTGAGTTTTAGATATGAATCTTTAAGACTTTTTGAATG
1 AGAATCTTTGAATTTTAGATATAAACCTCTAAGACTTTTTGAATG
** * * *
10553477 TTAATCTTTGAATTTTAGATGTAAACCTCTATGATTTTTTGAATG
1 AGAATCTTTGAATTTTAGATATAAACCTCTAAGACTTTTTGAATG
10553522 AGAATCTTT
1 AGAATCTTT
10553531 AAAATCTTGT
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.30, C:0.08, G:0.15, T:0.46
Consensus pattern (45 bp):
AGAATCTTTGAATTTTAGATATAAACCTCTAAGACTTTTTGAATG
Found at i:10553600 original size:45 final size:46
Alignment explanation
Indices: 10553510--10553605 Score: 108
Period size: 46 Copynumber: 2.1 Consensus size: 46
10553500 AACCTCTATG
10553510 ATTTTTTGAATGAGAATCTTTAAAATCTTGTATGTGAATTCCTAAA
1 ATTTTTTGAATGAGAATCTTTAAAATCTTGTATGTGAATTCCTAAA
* * * * *
10553556 GTTTTTTGAAT-AGAAGTTTTTAAATTTTTG-GTGTGAA-TCTCTAAA
1 ATTTTTTGAATGAGAA-TCTTTAAAATCTTGTATGTGAATTC-CTAAA
10553601 ATTTT
1 ATTTT
10553606 CAAATGTAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
44 2 0.05
45 19 0.45
46 21 0.50
ACGTcount: A:0.31, C:0.06, G:0.15, T:0.48
Consensus pattern (46 bp):
ATTTTTTGAATGAGAATCTTTAAAATCTTGTATGTGAATTCCTAAA
Found at i:10553722 original size:48 final size:46
Alignment explanation
Indices: 10553664--10553807 Score: 141
Period size: 48 Copynumber: 3.0 Consensus size: 46
10553654 TGAATCCCTG
* *
10553664 AATTTGTCAAACATGAACTTTTTGAATTTTAGATGTAAATTTCTCTAA
1 AATTT-TCAAATATGAAC-TTTTGAATTTTAGATGTGAATTTCTCTAA
* ** *
10553712 AATTTATCAAATGTGAAC-TTTGAATTTTAGATGTGAATCACTGACAAA
1 AATTT-TCAAATATGAACTTTTGAATTTTAGATGTGAATTTCT--CTAA
*
10553760 AATCTTTCAAATATGAA-TATTTGAATTTTAGATATGAATTTCT-TAA
1 AAT-TTTCAAATATGAACT-TTTGAATTTTAGATGTGAATTTCTCTAA
10553806 AA
1 AA
10553808 ATTACAATTG
Statistics
Matches: 79, Mismatches: 12, Indels: 12
0.77 0.12 0.12
Matches are distributed among these distances:
46 25 0.32
48 31 0.39
49 23 0.29
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (46 bp):
AATTTTCAAATATGAACTTTTGAATTTTAGATGTGAATTTCTCTAA
Found at i:10554038 original size:18 final size:17
Alignment explanation
Indices: 10554017--10554116 Score: 65
Period size: 18 Copynumber: 5.6 Consensus size: 17
10554007 CTAGCGAACT
10554017 TTTGAATTCTTGTGAATC
1 TTTGAATT-TTGTGAATC
* *
10554035 TTTGAGTTTTTGCGAATC
1 TTTGA-ATTTTGTGAATC
* * *
10554053 ATTGAAATTTTGTAAACC
1 TTTG-AATTTTGTGAATC
* ** *
10554071 TTTGAAATCTTACGAACC
1 TTTG-AATTTTGTGAATC
*
10554089 TTTGAAATTTTATGAATC
1 TTTG-AATTTTGTGAATC
10554107 TTTGAATTTT
1 TTTGAATTTT
10554117 TATAGATTTT
Statistics
Matches: 65, Mismatches: 15, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
17 6 0.09
18 56 0.86
19 3 0.05
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.47
Consensus pattern (17 bp):
TTTGAATTTTGTGAATC
Found at i:10554130 original size:18 final size:18
Alignment explanation
Indices: 10554029--10554119 Score: 74
Period size: 18 Copynumber: 5.1 Consensus size: 18
10554019 TGAATTCTTG
** *
10554029 TGAATCTTTGAGTTTTTG
1 TGAATCTTTGAAATTTTA
* * *
10554047 CGAATCATTGAAATTTTG
1 TGAATCTTTGAAATTTTA
* * *
10554065 TAAACCTTTGAAATCTTA
1 TGAATCTTTGAAATTTTA
* *
10554083 CGAACCTTTGAAATTTTA
1 TGAATCTTTGAAATTTTA
*
10554101 TGAATCTTTGAATTTTTA
1 TGAATCTTTGAAATTTTA
10554119 T
1 T
10554120 AGATTTTTGA
Statistics
Matches: 57, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 57 1.00
ACGTcount: A:0.30, C:0.11, G:0.13, T:0.46
Consensus pattern (18 bp):
TGAATCTTTGAAATTTTA
Found at i:10554222 original size:22 final size:21
Alignment explanation
Indices: 10554196--10554265 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 21
10554186 CTTTAAATTT
10554196 AATTGCAAATCCTTGAATTTCA
1 AATTGC-AATCCTTGAATTTCA
*
10554218 AATTGTTAA-CCTTTGAATTTCA
1 AATTG-CAATCC-TTGAATTTCA
* *
10554240 AGTTGGCAATTCTTGAATTTCA
1 AATT-GCAATCCTTGAATTTCA
10554262 AATT
1 AATT
10554266 ATGAATCTGC
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
21 2 0.05
22 35 0.90
23 2 0.05
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.41
Consensus pattern (21 bp):
AATTGCAATCCTTGAATTTCA
Found at i:10554262 original size:44 final size:42
Alignment explanation
Indices: 10554183--10554265 Score: 114
Period size: 44 Copynumber: 1.9 Consensus size: 42
10554173 GATTTTTACG
10554183 AACCTTTAAATTTAATTGCAAATCCTTGAATTTCAAATTGTT
1 AACCTTTAAATTTAATTGCAAATCCTTGAATTTCAAATTGTT
* *
10554225 AACCTTTGAATTTCAAGTTGGC-AATTCTTGAATTTCAAATT
1 AACCTTTAAATTT-AA-TT-GCAAATCCTTGAATTTCAAATT
10554266 ATGAATCTGC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
42 12 0.33
43 2 0.06
44 20 0.56
45 2 0.06
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (42 bp):
AACCTTTAAATTTAATTGCAAATCCTTGAATTTCAAATTGTT
Found at i:10559600 original size:94 final size:95
Alignment explanation
Indices: 10559451--10559626 Score: 273
Period size: 94 Copynumber: 1.9 Consensus size: 95
10559441 CTCTACTCCC
*** * *
10559451 TTTCTAAACAACCTAAATCTTTTTTTGACCTTTTAATAGTCTGAGCTCAGAGTGTAGCTCTAGCT
1 TTTCTAAACAACCTAAATCTTTTTCAAACCTTTTAATAGTCTAAGCTCAAAGTGTAGCTCTAGCT
10559516 CATCTTTTAAGTCTGAATTTCTCTACTTTT
66 CATCTTTTAAGTCTGAATTTCTCTACTTTT
*
10559546 TTTCTAAACAACCTAAA-CTTTTTCAAACCTTTTAATAGTCTAAGCTTAAAGTGTAGCTCTAGCT
1 TTTCTAAACAACCTAAATCTTTTTCAAACCTTTTAATAGTCTAAGCTCAAAGTGTAGCTCTAGCT
* *
10559610 CATTTTTTAAGTTTGAA
66 CATCTTTTAAGTCTGAA
10559627 AAGTTTTTTT
Statistics
Matches: 73, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
94 56 0.77
95 17 0.23
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.43
Consensus pattern (95 bp):
TTTCTAAACAACCTAAATCTTTTTCAAACCTTTTAATAGTCTAAGCTCAAAGTGTAGCTCTAGCT
CATCTTTTAAGTCTGAATTTCTCTACTTTT
Found at i:10570495 original size:16 final size:17
Alignment explanation
Indices: 10570466--10570499 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
10570456 ATTATTAAAT
*
10570466 AATCAAAGTCAAACATA
1 AATCAAAATCAAACATA
10570483 AATCAAAAT-AAACATA
1 AATCAAAATCAAACATA
10570499 A
1 A
10570500 TTATAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.65, C:0.15, G:0.03, T:0.18
Consensus pattern (17 bp):
AATCAAAATCAAACATA
Found at i:10572534 original size:8 final size:7
Alignment explanation
Indices: 10572504--10572568 Score: 58
Period size: 7 Copynumber: 8.9 Consensus size: 7
10572494 TTGGGCCAAT
*
10572504 TTTTTTT
1 TTTTTTA
10572511 TTTTTTA
1 TTTTTTA
*
10572518 TCTTTTA
1 TTTTTTA
10572525 TTTTTATA
1 TTTTT-TA
*
10572533 TTATTATA
1 TT-TTTTA
10572541 TTTTTTA
1 TTTTTTA
*
10572548 TATTTTA
1 TTTTTTA
*
10572555 TTATTATA
1 TT-TTTTA
10572563 TTTTTT
1 TTTTTT
10572569 GGTGTGTTTG
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
7 30 0.65
8 14 0.30
9 2 0.04
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (7 bp):
TTTTTTA
Found at i:10572553 original size:25 final size:22
Alignment explanation
Indices: 10572520--10572568 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
10572510 TTTTTTTATC
*
10572520 TTTTATTTTTATATTATTATATT
1 TTTTATATTT-TATTATTATATT
10572543 TTTTATATTTTATTATTATATT
1 TTTTATATTTTATTATTATATT
10572565 TTTT
1 TTTT
10572569 GGTGTGTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 16 0.64
23 9 0.36
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTTATATTTTATTATTATATT
Found at i:10573240 original size:18 final size:18
Alignment explanation
Indices: 10573217--10573253 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
10573207 CCGAGTTACT
10573217 TGAATGTAGTGATTGACC
1 TGAATGTAGTGATTGACC
10573235 TGAATGTAGTGATTGACC
1 TGAATGTAGTGATTGACC
10573253 T
1 T
10573254 TGACTCGAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.11, G:0.27, T:0.35
Consensus pattern (18 bp):
TGAATGTAGTGATTGACC
Found at i:10575734 original size:21 final size:19
Alignment explanation
Indices: 10575695--10575739 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
10575685 AAAATTATTA
10575695 AATTTAAAAATATTATTTT
1 AATTTAAAAATATTATTTT
10575714 AATTTAAATAA-ATTTAGTTTT
1 AATTTAAA-AATA-TTA-TTTT
10575735 AATTT
1 AATTT
10575740 TAATTAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.39
20 5 0.22
21 9 0.39
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
AATTTAAAAATATTATTTT
Found at i:10575801 original size:2 final size:2
Alignment explanation
Indices: 10575796--10575827 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
10575786 ATCTCGATTT
*
10575796 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10575828 GAGGCTAGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:10584293 original size:282 final size:279
Alignment explanation
Indices: 10583783--10584334 Score: 790
Period size: 282 Copynumber: 2.0 Consensus size: 279
10583773 GTAATTATTC
* *
10583783 TCATCAAAATGGAATAACTAAAAACTTAAAGGTCAAAGGAAAAAACTATTATTTGTTGAGCTTCA
1 TCATCAAAATGGAATAACTAAAAACTTAAAGATCAAAAGAAAAAACTATTATTTGTTGAGCTTCA
10583848 AATAATAATACTAAAAACATAAAGGTTAAAAAAGAAACAATAACAAACAAATGCATCTCATCTTA
66 AATAATAATACTAAAAACATAAAGGTTAAAAAAGAAACAATAACAAACAAATGCATCTCATCTTA
* * *
10583913 CAAAAAAATTAAATTAAATATCAAAGTAATTAGCTTTTACACTTCATCTATTTCAAAATCAAGTA
131 CAAAAAAATTAAATTAAATATAAAAGTAATTAACTTTTACACTTCATCTATTTCAAAATCAAATA
* * *
10583978 ATAAAAAGATTAAATATTAACACTTGATCATGTTTTTATTTCATACCAATATATATTCAACAATG
196 ATAAAAAGATCAAATATTAAAACTTGATCATGTTTTCATTTCATACCAATATATATTCAACAATG
10584043 ATTCTTTTTTCAATCATTG
261 ATTCTTTTTTCAATCATTG
* * *
10584062 TCATCAAAGTGGAATAACTAAAAACTTAACA-ATCAAAAGAAGAAATTATTATTTGTTGAGCTTT
1 TCATCAAAATGGAATAACTAAAAACTTAA-AGATCAAAAGAAAAAACTATTATTTGTTGAGC-TT
* ** *
10584126 TAAATTGTAA-AGCTAAAATCATAAAGGTTAAAGGAAA-AAACAATATA-AAACAAATGCATCTC
64 CAAATAATAATA-CTAAAAACATAAAGGTTAAA--AAAGAAACAATA-ACAAACAAATGCATCTC
* * * *
10584188 AT-TTGACATAAAAATTAAATTAAATATTAAAAGTAGTTAACTTTTCCACTTCATGTATTTCAAA
125 ATCTT-ACAAAAAAATTAAATTAAATA-TAAAAGTAATTAACTTTTACACTTCATCTATTTCAAA
* * * *
10584252 ATCAAATAATAAAAAGGTCAAATGTTAAAACTTGATCATGTTTTCATTTCATATCAATGTATATT
188 ATCAAATAATAAAAAGATCAAATATTAAAACTTGATCATGTTTTCATTTCATACCAATATATATT
10584317 CAACAATGATTCTTTTTT
253 CAACAATGATTCTTTTTT
10584335 TAATACTTGG
Statistics
Matches: 242, Mismatches: 23, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
279 55 0.23
280 31 0.13
281 45 0.19
282 111 0.46
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (279 bp):
TCATCAAAATGGAATAACTAAAAACTTAAAGATCAAAAGAAAAAACTATTATTTGTTGAGCTTCA
AATAATAATACTAAAAACATAAAGGTTAAAAAAGAAACAATAACAAACAAATGCATCTCATCTTA
CAAAAAAATTAAATTAAATATAAAAGTAATTAACTTTTACACTTCATCTATTTCAAAATCAAATA
ATAAAAAGATCAAATATTAAAACTTGATCATGTTTTCATTTCATACCAATATATATTCAACAATG
ATTCTTTTTTCAATCATTG
Found at i:10587299 original size:4 final size:4
Alignment explanation
Indices: 10587292--10587334 Score: 52
Period size: 4 Copynumber: 10.8 Consensus size: 4
10587282 ATATGTATAA
* *
10587292 AAAT AAAT AAAA AAAT AAAT ATAT AAA- AAATT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA-T AAAT AAAT AAA
10587335 ACAAATTGAC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
3 3 0.09
4 27 0.82
5 3 0.09
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:10587311 original size:16 final size:16
Alignment explanation
Indices: 10587292--10587340 Score: 71
Period size: 16 Copynumber: 3.0 Consensus size: 16
10587282 ATATGTATAA
10587292 AAATAAATAAAAAAAT
1 AAATAAATAAAAAAAT
* *
10587308 AAATATATAAAAAATT
1 AAATAAATAAAAAAAT
10587324 AAATAAATAAAACAAAT
1 AAATAAATAAAA-AAAT
10587341 TGACAAATTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
16 25 0.89
17 3 0.11
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (16 bp):
AAATAAATAAAAAAAT
Found at i:10587313 original size:28 final size:28
Alignment explanation
Indices: 10587270--10587340 Score: 83
Period size: 26 Copynumber: 2.6 Consensus size: 28
10587260 TACATTTTGA
* * *
10587270 AAATAAAAATATATATGTAT-AAAAA-T
1 AAATAAAAAAATAAATATATAAAAAATT
10587296 AAATAAAAAAATAAATATATAAAAAATT
1 AAATAAAAAAATAAATATATAAAAAATT
*
10587324 AAATAAATAAAACAAAT
1 AAATAAA-AAAATAAAT
10587341 TGACAAATTG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 17 0.45
27 5 0.13
28 8 0.21
29 8 0.21
ACGTcount: A:0.72, C:0.01, G:0.01, T:0.25
Consensus pattern (28 bp):
AAATAAAAAAATAAATATATAAAAAATT
Found at i:10588404 original size:5 final size:5
Alignment explanation
Indices: 10588387--10588430 Score: 61
Period size: 5 Copynumber: 8.8 Consensus size: 5
10588377 AACAAAAATA
* * *
10588387 ATAAT AAAAT ATATT ATATT ATAAT ATAAT ATAAT ATAAT ATAA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAA
10588431 AAATAAATTG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATAAT
Found at i:10599728 original size:19 final size:20
Alignment explanation
Indices: 10599704--10599744 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
10599694 AATACACAAA
*
10599704 AAAAATTAGGGAGAG-AGTC
1 AAAAATTAGGGAAAGTAGTC
10599723 AAAAATTAGGGAAAGTAGTC
1 AAAAATTAGGGAAAGTAGTC
10599743 AA
1 AA
10599745 GAAAAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.51, C:0.05, G:0.27, T:0.17
Consensus pattern (20 bp):
AAAAATTAGGGAAAGTAGTC
Found at i:10600036 original size:15 final size:14
Alignment explanation
Indices: 10600009--10600050 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
10599999 TTAAATTTTA
10600009 AAAAATTAA-AAAATT
1 AAAAA-TAATAAAA-T
10600024 AAAAATAATAAAAT
1 AAAAATAATAAAAT
10600038 AATAAATAATAAA
1 AA-AAATAATAAA
10600051 TTTTGAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 6 0.24
15 19 0.76
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
AAAAATAATAAAAT
Found at i:10600445 original size:25 final size:26
Alignment explanation
Indices: 10600417--10600467 Score: 61
Period size: 24 Copynumber: 2.0 Consensus size: 26
10600407 ATAATTATTC
*
10600417 AATGATGAGATTTTTAA-AAAT-TTTA
1 AATGAT-AAATTTTTAAGAAATCTTTA
*
10600442 AATGGTAAATTTTTAAGAAATCTTTA
1 AATGATAAATTTTTAAGAAATCTTTA
10600468 TGTGAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 9 0.41
25 9 0.41
26 4 0.18
ACGTcount: A:0.43, C:0.02, G:0.12, T:0.43
Consensus pattern (26 bp):
AATGATAAATTTTTAAGAAATCTTTA
Found at i:10600656 original size:52 final size:50
Alignment explanation
Indices: 10600587--10600782 Score: 144
Period size: 52 Copynumber: 3.7 Consensus size: 50
10600577 AGAGAAAGAT
*
10600587 ATTTCTAAATTA-ACCCAAATAGTAAAAAATTTAAAAATCCAACATAAAAAAA
1 ATTTCTAAA-TAGGCCCAAAT-GTAAAAAATTTAAAAATCCAACA-AAAAAAA
* * * * *
10600639 ATTTTTAAATAGGCCCAAATTGTGAAAACTTTAGAAATTTCAA-AAAAAAAA
1 ATTTCTAAATAGGCCCAAA-TGTAAAAAATTTA-AAAATCCAACAAAAAAAA
* ** * *
10600690 TATTTCTAAATTGATCAAAATGATAAAAATTTTAAAAATCCAACAAAAAAAAAGA
1 -ATTTCTAAATAGGCCCAAATG-TAAAAAATTTAAAAATCCAAC--AAAAAAA-A
** * *
10600745 ATTTCTAAATAGGTTCAAATGGTGAAAAATTTAGAAAT
1 ATTTCTAAATAGGCCCAAAT-GTAAAAAATTTAAAAAT
10600783 TAAAAAATAT
Statistics
Matches: 112, Mismatches: 22, Indels: 18
0.74 0.14 0.12
Matches are distributed among these distances:
51 18 0.16
52 48 0.43
53 8 0.07
54 36 0.32
55 2 0.02
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.29
Consensus pattern (50 bp):
ATTTCTAAATAGGCCCAAATGTAAAAAATTTAAAAATCCAACAAAAAAAA
Found at i:10600696 original size:104 final size:106
Alignment explanation
Indices: 10600585--10600783 Score: 278
Period size: 104 Copynumber: 1.9 Consensus size: 106
10600575 AAAGAGAAAG
* * *
10600585 ATATTTCTAAATTAACCCAAAT-AGTAAAAAATTTAAAAATCCAAC-ATAAAAAA-AATTTTTAA
1 ATATTTCTAAATTAACCAAAATGA-TAAAAAATTTAAAAATCCAACAAAAAAAAAGAATTTCTAA
* *
10600647 ATAGGCCCAAATTGTGAAAACTTTAGAAATTTCAAAAAAAAA
65 ATAGGCCCAAATGGTGAAAAATTTAGAAATTTCAAAAAAAAA
* * *
10600689 ATATTTCTAAATTGATCAAAATGATAAAAATTTTAAAAATCCAACAAAAAAAAAGAATTTCTAAA
1 ATATTTCTAAATTAACCAAAATGATAAAAAATTTAAAAATCCAACAAAAAAAAAGAATTTCTAAA
**
10600754 TAGGTTCAAATGGTGAAAAATTTAGAAATT
66 TAGGCCCAAATGGTGAAAAATTTAGAAATT
10600784 AAAAAATATA
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
104 39 0.48
105 8 0.10
106 35 0.43
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.29
Consensus pattern (106 bp):
ATATTTCTAAATTAACCAAAATGATAAAAAATTTAAAAATCCAACAAAAAAAAAGAATTTCTAAA
TAGGCCCAAATGGTGAAAAATTTAGAAATTTCAAAAAAAAA
Found at i:10600810 original size:106 final size:104
Alignment explanation
Indices: 10600609--10600819 Score: 266
Period size: 106 Copynumber: 2.0 Consensus size: 104
10600599 ACCCAAATAG
* * * *
10600609 TAAAAAATTTAAAAATCCAACATAAAAAAAATTTTTAAATAGGCCCAAATTGTGAAAACTTTAGA
1 TAAAAAATTTAAAAATCCAACAAAAAAAAAATTTCTAAATAGGCCCAAATGGTGAAAAATTTAGA
*
10600674 AATTTCAAAAAAAAAATATTTCTAAATTGA-TCAAAATGA
66 AATTTCAAAAAAAAAATATTTATAAATTGATTC-AAATGA
* **
10600713 TAAAAATTTTAAAAATCCAACAAAAAAAAAGAATTTCTAAATAGGTTCAAATGGTGAAAAATTTA
1 TAAAAAATTTAAAAATCCAAC-AAAAAAAA-AATTTCTAAATAGGCCCAAATGGTGAAAAATTTA
* *
10600778 GAAA-TT-AAAAAATATATATATTTATAATTTGATTCAAATGA
64 GAAATTTCAAAAAA-A-AAATATTTATAAATTGATTCAAATGA
10600819 T
1 T
10600820 GGAATAATTA
Statistics
Matches: 92, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
104 26 0.28
105 10 0.11
106 54 0.59
107 2 0.02
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (104 bp):
TAAAAAATTTAAAAATCCAACAAAAAAAAAATTTCTAAATAGGCCCAAATGGTGAAAAATTTAGA
AATTTCAAAAAAAAAATATTTATAAATTGATTCAAATGA
Found at i:10601356 original size:20 final size:21
Alignment explanation
Indices: 10601330--10601378 Score: 66
Period size: 19 Copynumber: 2.4 Consensus size: 21
10601320 ACAATTACTA
*
10601330 ATAAAAAAATATTTT-TTTCT
1 ATAAAAAAATATTTTATTTAT
*
10601350 -TTAAAAAATATTTTATTTAT
1 ATAAAAAAATATTTTATTTAT
10601370 ATAAAAAAA
1 ATAAAAAAA
10601379 GTCAAATCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 13 0.54
20 4 0.17
21 7 0.29
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
ATAAAAAAATATTTTATTTAT
Found at i:10601459 original size:24 final size:23
Alignment explanation
Indices: 10601425--10601498 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 23
10601415 ATTTAAAATA
10601425 TTTTAATTTTTTAAAAAATCATAT
1 TTTTAATTTTTT-AAAAATCATAT
*
10601449 TTTTGAATTTTTTTAAAATCA-AT
1 TTTT-AATTTTTTAAAAATCATAT
*
10601472 TTTTAATTTTTTAAAATTCTATAT
1 TTTTAATTTTTTAAAAATC-ATAT
10601496 TTT
1 TTT
10601499 GAAATTTGTA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
22 13 0.30
23 7 0.16
24 16 0.36
25 8 0.18
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.59
Consensus pattern (23 bp):
TTTTAATTTTTTAAAAATCATAT
Found at i:10601498 original size:23 final size:21
Alignment explanation
Indices: 10601422--10601498 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 21
10601412 ATAATTTAAA
10601422 ATATTTTAATTTTTTAAAAAATC
1 ATATTTTAATTTTTT--AAAATC
10601445 ATATTTTTGAATTTTTTTAAAATC
1 ATA-TTTT-AA-TTTTTTAAAATC
10601469 A-ATTTTTAATTTTTTAAAATTC
1 ATA-TTTTAATTTTTTAAAA-TC
10601491 TATATTTT
1 -ATATTTT
10601499 GAAATTTGTA
Statistics
Matches: 48, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
21 10 0.21
22 4 0.08
23 14 0.29
24 12 0.25
25 2 0.04
26 6 0.12
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.58
Consensus pattern (21 bp):
ATATTTTAATTTTTTAAAATC
Found at i:10601570 original size:15 final size:15
Alignment explanation
Indices: 10601552--10601581 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
10601542 GCTTTTTATA
10601552 ATATTTTTAATTTTT
1 ATATTTTTAATTTTT
*
10601567 ATATTTTTTATTTTT
1 ATATTTTTAATTTTT
10601582 TCAAAATTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
ATATTTTTAATTTTT
Found at i:10601672 original size:15 final size:16
Alignment explanation
Indices: 10601652--10601683 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
10601642 TTTTATAAAA
10601652 ATTTTTAT-TTTTTTT
1 ATTTTTATGTTTTTTT
10601667 ATTTTTATGTTTTTTT
1 ATTTTTATGTTTTTTT
10601683 A
1 A
10601684 GAAAATTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (16 bp):
ATTTTTATGTTTTTTT
Found at i:10602081 original size:21 final size:20
Alignment explanation
Indices: 10602048--10602115 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
10602038 AAAACTTCCT
*
10602048 AAAATGAAATTAAAATATTAA
1 AAAAT-AAATTAAAATATTTA
* *
10602069 AAAATAAATTTAATATTTTTA
1 AAAATAAA-TTAAAATATTTA
* *
10602090 AAAAT-TATTAAAAAATTTA
1 AAAATAAATTAAAATATTTA
10602109 AAAATAA
1 AAAATAA
10602116 TAAATTTTTA
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
19 14 0.38
20 4 0.11
21 19 0.51
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.35
Consensus pattern (20 bp):
AAAATAAATTAAAATATTTA
Found at i:10602941 original size:16 final size:17
Alignment explanation
Indices: 10602920--10602959 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
10602910 TGAAGGGTAG
10602920 AAAAAAAAC-AAATTAT
1 AAAAAAAACTAAATTAT
**
10602936 AAAAAAAACTTTATTAT
1 AAAAAAAACTAAATTAT
10602953 AAAAAAA
1 AAAAAAA
10602960 TTTCTTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (17 bp):
AAAAAAAACTAAATTAT
Found at i:10611417 original size:32 final size:33
Alignment explanation
Indices: 10611381--10611445 Score: 123
Period size: 32 Copynumber: 2.0 Consensus size: 33
10611371 CATTGATAGC
10611381 ATTTTAAATAAAGTTT-TTACATAAAGATTCTT
1 ATTTTAAATAAAGTTTCTTACATAAAGATTCTT
10611413 ATTTTAAATAAAGTTTCTTACATAAAGATTCTT
1 ATTTTAAATAAAGTTTCTTACATAAAGATTCTT
10611446 GAAGAATCAC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 16 0.50
33 16 0.50
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (33 bp):
ATTTTAAATAAAGTTTCTTACATAAAGATTCTT
Done.