Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr8
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: 56894857
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1173888 characters in sequence are not A, C, G, or T
File 2 of 185
Found at i:311738 original size:15 final size:15
Alignment explanation
Indices: 311718--311764 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
311708 AATAGTAATT
311718 ATAATTCTTTTATAA
1 ATAATTCTTTTATAA
* *
311733 ATAATT-TTTTGGTAG
1 ATAATTCTTTT-ATAA
311748 A-AATTCTTTTATAA
1 ATAATTCTTTTATAA
311762 ATA
1 ATA
311765 TTAAGTAGTG
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
14 11 0.44
15 14 0.56
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.51
Consensus pattern (15 bp):
ATAATTCTTTTATAA
Found at i:327242 original size:18 final size:18
Alignment explanation
Indices: 327219--327253 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
327209 AGTGAATGGA
327219 AAATAAAGAAAAATAAAG
1 AAATAAAGAAAAATAAAG
*
327237 AAATAAAGAAAATTAAA
1 AAATAAAGAAAAATAAA
327254 AGAACAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (18 bp):
AAATAAAGAAAAATAAAG
Found at i:327469 original size:29 final size:30
Alignment explanation
Indices: 327431--327500 Score: 90
Period size: 29 Copynumber: 2.3 Consensus size: 30
327421 CACGATAACG
327431 TAAGTGACTAAAATATAA-C-ATTTCAAACA
1 TAAGTGACTAAAATATAATCTA-TTCAAACA
*
327460 TAAGTGACTAAAATGTAATCTGATTCAAACA
1 TAAGTGACTAAAATATAATCT-ATTCAAACA
*
327491 AAAGTGACTA
1 TAAGTGACTA
327501 TTTTAATAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
29 17 0.47
30 1 0.03
31 17 0.47
32 1 0.03
ACGTcount: A:0.49, C:0.13, G:0.11, T:0.27
Consensus pattern (30 bp):
TAAGTGACTAAAATATAATCTATTCAAACA
Found at i:329153 original size:27 final size:24
Alignment explanation
Indices: 329080--329153 Score: 71
Period size: 25 Copynumber: 3.0 Consensus size: 24
329070 TATACCATAT
329080 ATAAAAAT-TATAAAAATA-AAAA
1 ATAAAAATATATAAAAATATAAAA
* *
329102 ATACAAATATATAAAAAAATTTAAAA
1 ATA-AAA-ATATATAAAAATATAAAA
329128 AGTAAAAATATATACAAAATGATAAA
1 A-TAAAAATATATA-AAAAT-ATAAA
329154 TTTTAACAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
22 3 0.07
23 3 0.07
24 2 0.05
25 14 0.34
26 13 0.32
27 6 0.15
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.24
Consensus pattern (24 bp):
ATAAAAATATATAAAAATATAAAA
Found at i:330925 original size:18 final size:18
Alignment explanation
Indices: 330904--330948 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
330894 TTTTTACAAC
* *
330904 TTTTTATATTTTTTATTT
1 TTTTTATATTTTTAATTA
330922 TTTTTATCA-TTTTAATTA
1 TTTTTAT-ATTTTTAATTA
330940 TTTTTATAT
1 TTTTTATAT
330949 AATTTTCTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 1 0.04
18 21 0.91
19 1 0.04
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTTATATTTTTAATTA
Found at i:330994 original size:40 final size:41
Alignment explanation
Indices: 330933--331038 Score: 105
Period size: 40 Copynumber: 2.7 Consensus size: 41
330923 TTTTATCATT
* *
330933 TTAATTAT-TTTTATATA-ATTTTCTATCATTTC-TAAC-TT
1 TTAATAATATTTTATA-ACATTTTCTATCATTTCATAACATA
* * *
330971 TTTATAATATTTATTTAACATTTTC-ATTATTTCATAACATA
1 TTAATAATATTT-TATAACATTTTCTATCATTTCATAACATA
*
331012 TTAATAATATTTTATAACATTTACTAT
1 TTAATAATATTTTATAACATTTTCTAT
331039 TTTTTATTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
38 6 0.11
39 11 0.20
40 23 0.43
41 14 0.26
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (41 bp):
TTAATAATATTTTATAACATTTTCTATCATTTCATAACATA
Found at i:331010 original size:19 final size:20
Alignment explanation
Indices: 330986--331033 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
330976 AATATTTATT
*
330986 TAACATTTTCAT-TATTTCA
1 TAACATTTTAATATATTTCA
* *
331005 TAACATATTAATAATATTTTA
1 TAACATTTTAAT-ATATTTCA
331026 TAACATTT
1 TAACATTT
331034 ACTATTTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 10 0.43
21 13 0.57
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (20 bp):
TAACATTTTAATATATTTCA
Found at i:331088 original size:10 final size:9
Alignment explanation
Indices: 331072--331113 Score: 50
Period size: 10 Copynumber: 4.6 Consensus size: 9
331062 ATGATATTTA
331072 ATAATTTTC
1 ATAATTTTC
331081 ATAGATTTTC
1 ATA-ATTTTC
331091 TATAATTTTC
1 -ATAATTTTC
*
331101 AAAATTTT-
1 ATAATTTTC
331109 ATAAT
1 ATAAT
331114 ATTTTAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
8 4 0.14
9 10 0.34
10 12 0.41
11 3 0.10
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.52
Consensus pattern (9 bp):
ATAATTTTC
Found at i:331474 original size:29 final size:29
Alignment explanation
Indices: 331406--331475 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
331396 TAATTTTGTG
*
331406 AAAATTGAATCAAAATAAAATTTCATGTAT
1 AAAATTGCA-CAAAATAAAATTTCATGTAT
** *
331436 AAAAAAGCACAAAATCAAAA-TTCGTGTAT
1 AAAATTGCACAAAAT-AAAATTTCATGTAT
*
331465 GAAATTGCACA
1 AAAATTGCACA
331476 GTTCATGTAT
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
29 22 0.69
30 10 0.31
ACGTcount: A:0.53, C:0.11, G:0.10, T:0.26
Consensus pattern (29 bp):
AAAATTGCACAAAATAAAATTTCATGTAT
Found at i:331561 original size:21 final size:22
Alignment explanation
Indices: 331535--331575 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
331525 ATTTTTTTTC
* *
331535 ATTTT-AGTTATTTTTATATAA
1 ATTTTAAGATATTTTAATATAA
331556 ATTTTAAGATATTTTAATAT
1 ATTTTAAGATATTTTAATAT
331576 TTTAAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (22 bp):
ATTTTAAGATATTTTAATATAA
Found at i:331587 original size:18 final size:19
Alignment explanation
Indices: 331551--331592 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
331541 GTTATTTTTA
* *
331551 TATAA-ATTTTAAGATATT
1 TATAATATTTTAAAAAATT
331569 T-TAATATTTTAAAAAATT
1 TATAATATTTTAAAAAATT
331587 TATAAT
1 TATAAT
331593 TTCTTGAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 3 0.15
18 13 0.65
19 4 0.20
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (19 bp):
TATAATATTTTAAAAAATT
Found at i:331664 original size:29 final size:30
Alignment explanation
Indices: 331617--331684 Score: 111
Period size: 29 Copynumber: 2.3 Consensus size: 30
331607 TATATAATCC
*
331617 TTAAAAATCAATTAAACCCTCTTAAAATAA
1 TTAAAAATCAATTAAACCCTCATAAAATAA
331647 TTAAAAATCAATT-AACCCTCATAAAATAA
1 TTAAAAATCAATTAAACCCTCATAAAATAA
*
331676 TAAAAAATC
1 TTAAAAATC
331685 CATTCACATC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
29 23 0.64
30 13 0.36
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (30 bp):
TTAAAAATCAATTAAACCCTCATAAAATAA
Found at i:334797 original size:23 final size:24
Alignment explanation
Indices: 334744--334798 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 24
334734 TTAAAATTTG
* *
334744 TATATATCAAATTTTAAATTTAAT
1 TATATATAAAATATTAAATTTAAT
* *
334768 AAT-TATAAAATATTAAA-TTATT
1 TATATATAAAATATTAAATTTAAT
334790 TATATATAA
1 TATATATAA
334799 TATTTTATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
22 6 0.24
23 17 0.68
24 2 0.08
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (24 bp):
TATATATAAAATATTAAATTTAAT
Found at i:335747 original size:7 final size:7
Alignment explanation
Indices: 335735--335763 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
335725 ATGTACCATT
335735 CCACTAC
1 CCACTAC
335742 CCACTAC
1 CCACTAC
335749 CCACTAC
1 CCACTAC
335756 CCACTAC
1 CCACTAC
335763 C
1 C
335764 GTCTATTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.59, G:0.00, T:0.14
Consensus pattern (7 bp):
CCACTAC
Found at i:338014 original size:25 final size:25
Alignment explanation
Indices: 337964--338021 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
337954 ATCCCTAACG
* *
337964 TCTGCTGCATCACCGTCGGTAGCCC
1 TCTGCTGCATCACCGTCAGCAGCCC
* * *
337989 TTTGCTGCATCTCCGTCAGCATCCC
1 TCTGCTGCATCACCGTCAGCAGCCC
338014 TCTGCTGC
1 TCTGCTGC
338022 TTCGCCTTGT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.10, C:0.40, G:0.21, T:0.29
Consensus pattern (25 bp):
TCTGCTGCATCACCGTCAGCAGCCC
Found at i:342441 original size:43 final size:44
Alignment explanation
Indices: 342375--342577 Score: 222
Period size: 43 Copynumber: 4.8 Consensus size: 44
342365 CGGTGTTTGC
* *
342375 GGGAAAAGCGCCACTAAAGGTCATGTTCTATAGCGGCATTTGT-
1 GGGAAAAGCGCCGCTAAAAGTCATGTTCTATAGCGGCATTTGTA
* * * *
342418 GGTAAAAGCGCCGCTAAAAGTCATGTTCTTTAGCTGCATTCGTA
1 GGGAAAAGCGCCGCTAAAAGTCATGTTCTATAGCGGCATTTGTA
** *
342462 GGGAAAA-CATCGCTAAACGTCATGTTCTATAGCGGCATTTGTA
1 GGGAAAAGCGCCGCTAAAAGTCATGTTCTATAGCGGCATTTGTA
* * *
342505 GGG---AGCGCCGCTAGAAGTCATGTTCTATAACGGCGTTTGT-
1 GGGAAAAGCGCCGCTAAAAGTCATGTTCTATAGCGGCATTTGTA
* *
342545 GGGAAAAGCGCCG-TTAAAGGCTATGTTCTATAG
1 GGGAAAAGCGCCGCTAAAAGTC-ATGTTCTATAG
342578 AGACGTTTTT
Statistics
Matches: 131, Mismatches: 23, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
40 4 0.03
41 29 0.22
42 5 0.04
43 87 0.66
44 6 0.05
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (44 bp):
GGGAAAAGCGCCGCTAAAAGTCATGTTCTATAGCGGCATTTGTA
Found at i:342571 original size:84 final size:84
Alignment explanation
Indices: 342362--342577 Score: 240
Period size: 84 Copynumber: 2.5 Consensus size: 84
342352 ACATGACTTT
* * *
342362 TAACGGTGTTTGCGGGAAAAGCGCCACTAAAGGTCATGTTCTATAGCGGCATTTGTGGTAAAAGC
1 TAACGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGTTCTATAGCGGCATTTGTGG--AAAGC
*
342427 GCCGCTAAAAGTCATGTTCTT
64 GCCGCTAAAAGTCATGTTCTA
* * * * ** * *
342448 TAGCTGCATTCGTAGGGAAAA-CATCGCTAAACGTCATGTTCTATAGCGGCATTTGTAGG-GAGC
1 TAACGGCGTTTGT-GGGAAAAGCGCCGCTAAAGGTCATGTTCTATAGCGGCATTTGT-GGAAAGC
*
342511 GCCGCTAGAAGTCATGTTCTA
64 GCCGCTAAAAGTCATGTTCTA
*
342532 TAACGGCGTTTGTGGGAAAAGCGCCGTTAAAGG-CTATGTTCTATAG
1 TAACGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTC-ATGTTCTATAG
342578 AGACGTTTTT
Statistics
Matches: 105, Mismatches: 21, Indels: 10
0.77 0.15 0.07
Matches are distributed among these distances:
83 8 0.08
84 50 0.48
86 38 0.36
87 9 0.09
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (84 bp):
TAACGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGTTCTATAGCGGCATTTGTGGAAAGCGC
CGCTAAAAGTCATGTTCTA
Found at i:343733 original size:25 final size:26
Alignment explanation
Indices: 343682--343738 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 26
343672 TTAAGATCCA
* * *
343682 TATTAA-ATTTAATTTAATATAATAAC
1 TATTAATA-TTAAATTAATAAAAAAAC
343708 T-TTAATATTAAATTAATAAAAAAAC
1 TATTAATATTAAATTAATAAAAAAAC
343733 TATTAA
1 TATTAA
343739 GATAAGTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 20 0.77
26 6 0.23
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (26 bp):
TATTAATATTAAATTAATAAAAAAAC
Found at i:345002 original size:51 final size:51
Alignment explanation
Indices: 344942--345042 Score: 193
Period size: 51 Copynumber: 2.0 Consensus size: 51
344932 AGAGCATAAG
*
344942 CCTCCACTTATATAAAAGCACATGAGTTACGTATGCATGGTTAATGACTAT
1 CCTCCACTTATATAAAAGCACATGAGTTACATATGCATGGTTAATGACTAT
344993 CCTCCACTTATATAAAAGCACATGAGTTACATATGCATGGTTAATGACTA
1 CCTCCACTTATATAAAAGCACATGAGTTACATATGCATGGTTAATGACTA
345043 ACTCGGAATT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.31
Consensus pattern (51 bp):
CCTCCACTTATATAAAAGCACATGAGTTACATATGCATGGTTAATGACTAT
Found at i:345157 original size:16 final size:16
Alignment explanation
Indices: 345136--345167 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
345126 CAGTCTAATT
345136 TATCATTTTTCCAATG
1 TATCATTTTTCCAATG
*
345152 TATCATTTTTCTAATG
1 TATCATTTTTCCAATG
345168 AATACATCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.06, T:0.53
Consensus pattern (16 bp):
TATCATTTTTCCAATG
Found at i:350722 original size:16 final size:19
Alignment explanation
Indices: 350701--350737 Score: 53
Period size: 16 Copynumber: 2.1 Consensus size: 19
350691 TTGTTTTAAG
350701 AACAAGA-AG-AAAAA-AA
1 AACAAGACAGTAAAAAGAA
350717 AACAAGACAGTAAAAAGAA
1 AACAAGACAGTAAAAAGAA
350736 AA
1 AA
350738 AAACGGAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.39
17 2 0.11
18 5 0.28
19 4 0.22
ACGTcount: A:0.76, C:0.08, G:0.14, T:0.03
Consensus pattern (19 bp):
AACAAGACAGTAAAAAGAA
Found at i:351125 original size:28 final size:29
Alignment explanation
Indices: 351085--351139 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
351075 GTTGAAATTG
*
351085 GCTATTGGGTTTTAATT-TT-ATTGGGCCT
1 GCTATTGGATTTT-ATTATTGATTGGGCCT
*
351113 GCTATTGTATTTTATTATTGATTGGGC
1 GCTATTGGATTTTATTATTGATTGGGC
351140 AGGGCAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 3 0.13
28 13 0.57
29 7 0.30
ACGTcount: A:0.16, C:0.09, G:0.24, T:0.51
Consensus pattern (29 bp):
GCTATTGGATTTTATTATTGATTGGGCCT
Found at i:351710 original size:112 final size:111
Alignment explanation
Indices: 351513--352067 Score: 806
Period size: 112 Copynumber: 5.0 Consensus size: 111
351503 ATTGAAAATA
* * * * *
351513 AAAAGGATATTTGGCTATTCGGTTAAATGAGAAAAATCGACACCCAGTACCTTAGGGCACGTTTT
1 AAAAGGATATTTAGCCATTTGGTTGAATGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTT
* * * **
351578 CTCGAATTTCTCAAACGCAAAACATTACCTTTTTTTGAATTTTTTTT
66 CTCGAATTTCCCAAACGCAAAACATTGCCTTATTTT-AAAATTTTTT
* * *
351625 AAAAGGATATTTAGCCATTTGGTTGAATGAAAAAAATCAACACCCAGCACCTTATGGCACGTTTT
1 AAAAGGATATTTAGCCATTTGGTTGAATGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTT
*
351690 CTCGAATTTCACAAACGCAAAACATTGCCTTATTTTAAAA-TTTTT
66 CTCGAATTTCCCAAACGCAAAACATTGCCTTATTTTAAAATTTTTT
* * * * * *
351735 AAAAGAATATTTAGCCATTTGGTTGAATGAGAAAAATCGACACTCAACACCTTAAGACATGTTTT
1 AAAAGGATATTTAGCCATTTGGTTGAATGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTT
* *
351800 CTCGAATTTCTCAAACGTAAAACATTGCCTTATTTTAAAATTTTTT
66 CTCGAATTTCCCAAACGCAAAACATTGCCTTATTTTAAAATTTTTT
* * *
351846 AAAAGGATATTTAGTCATTTGGTTGAACGAGAAAAATCGACACCGAGCACCTTAGGGCACGTTTT
1 AAAAGGATATTTAGCCATTTGGTTGAATGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTT
351911 CTCGAATTTCCCAAACGCAAAACATTGCCTTATTTTAAAAATTTTTT
66 CTCGAATTTCCCAAACGCAAAACATTGCCTTATTTT-AAAATTTTTT
* * * *
351958 AAAAGTATATTTAGCCATTTGGTTGAACGAGAAAAATCGACATCCAGCAGCTTAGGGCACGTTTT
1 AAAAGGATATTTAGCCATTTGGTTGAATGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTT
* *
352023 CTCGAATTTCCCAAACGCAAAACATTACCTTATTTTAAAAATTTT
66 CTCGAATTTCCCAAACGCAAAACATTGCCTTATTTTAAAATTTTT
352068 ATTCTTGATA
Statistics
Matches: 400, Mismatches: 41, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
110 100 0.25
111 105 0.26
112 195 0.49
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (111 bp):
AAAAGGATATTTAGCCATTTGGTTGAATGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTT
CTCGAATTTCCCAAACGCAAAACATTGCCTTATTTTAAAATTTTTT
Found at i:354511 original size:27 final size:27
Alignment explanation
Indices: 354477--354539 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
354467 GGTAATGGAA
*
354477 AGGCGGCACCAAAGGTTCC-TTTTCGAT
1 AGGCGGCACCAAAGGTGCCTTTTTC-AT
* * *
354504 AGGTGGCACCGATGGTGCCTTTTTCAT
1 AGGCGGCACCAAAGGTGCCTTTTTCAT
354531 AGGCGGCAC
1 AGGCGGCAC
354540 AGGACTAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 25 0.83
28 5 0.17
ACGTcount: A:0.19, C:0.25, G:0.30, T:0.25
Consensus pattern (27 bp):
AGGCGGCACCAAAGGTGCCTTTTTCAT
Found at i:356443 original size:19 final size:21
Alignment explanation
Indices: 356401--356450 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 21
356391 TTGATAAATA
356401 ATTTTTTATATATTATTTTGGT
1 ATTTTTT-TATATTATTTTGGT
*
356423 ATTTTTTTAT-TTCTTTT-GT
1 ATTTTTTTATATTATTTTGGT
*
356442 ATTATTTTA
1 ATTTTTTTA
356451 ATAAAAATCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 10 0.38
20 6 0.23
21 3 0.12
22 7 0.27
ACGTcount: A:0.20, C:0.02, G:0.06, T:0.72
Consensus pattern (21 bp):
ATTTTTTTATATTATTTTGGT
Found at i:357905 original size:21 final size:21
Alignment explanation
Indices: 357853--357905 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
357843 AAGCCAACCC
357853 ATATTATTTT-TTTAAATATT
1 ATATTATTTTATTTAAATATT
* *
357873 ATATTATATTATTTTAATATT
1 ATATTATTTTATTTAAATATT
357894 -TAATTATTTTAT
1 AT-ATTATTTTAT
357906 ACATTTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 10 0.36
21 18 0.64
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
ATATTATTTTATTTAAATATT
Found at i:363621 original size:24 final size:23
Alignment explanation
Indices: 363569--363611 Score: 63
Period size: 21 Copynumber: 1.9 Consensus size: 23
363559 ATAATAAAGT
363569 AATTATATAT-T-ATTTTTATAA
1 AATTATATATATGATTTTTATAA
363590 AATTATATATTATGATTTTTAT
1 AATTATATA-TATGATTTTTAT
363612 TAATTCATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.47
22 1 0.05
23 1 0.05
24 8 0.42
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (23 bp):
AATTATATATATGATTTTTATAA
Found at i:363882 original size:16 final size:16
Alignment explanation
Indices: 363861--363927 Score: 73
Period size: 16 Copynumber: 4.2 Consensus size: 16
363851 TGAATTACTG
363861 ATTACAACTCTA-TTC
1 ATTACAACTCTATTTC
*
363876 TATTACAGCTCTATTTC
1 -ATTACAACTCTATTTC
*
363893 ATTACAACTCTATTAC
1 ATTACAACTCTATTTC
* * *
363909 ATTATAGCTCTATTCC
1 ATTACAACTCTATTTC
363925 ATT
1 ATT
363928 CTCCCTAACC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
16 41 0.93
17 3 0.07
ACGTcount: A:0.30, C:0.24, G:0.03, T:0.43
Consensus pattern (16 bp):
ATTACAACTCTATTTC
Found at i:363902 original size:32 final size:32
Alignment explanation
Indices: 363861--363927 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
363851 TGAATTACTG
*
363861 ATTACAACTCTATT-CTATTACAGCTCTATTTC
1 ATTACAACTCTATTAC-ATTACAGCTCTATTCC
*
363893 ATTACAACTCTATTACATTATAGCTCTATTCC
1 ATTACAACTCTATTACATTACAGCTCTATTCC
363925 ATT
1 ATT
363928 CTCCCTAACC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 31 0.97
33 1 0.03
ACGTcount: A:0.30, C:0.24, G:0.03, T:0.43
Consensus pattern (32 bp):
ATTACAACTCTATTACATTACAGCTCTATTCC
Found at i:364157 original size:22 final size:23
Alignment explanation
Indices: 364127--364170 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
364117 TAATGTAATA
364127 TTTTATTTTATGAC-AATTTGAC
1 TTTTATTTTATGACAAATTTGAC
* *
364149 TTTTTTTTTATTACAAATTTGA
1 TTTTATTTTATGACAAATTTGA
364171 TCAGATTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.27, C:0.07, G:0.07, T:0.59
Consensus pattern (23 bp):
TTTTATTTTATGACAAATTTGAC
Found at i:375083 original size:16 final size:15
Alignment explanation
Indices: 375058--375103 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 15
375048 AGAAACAAAA
375058 ATAAAATAAAATTTC
1 ATAAAATAAAATTTC
375073 ATAATAAT-AAATTTC
1 ATAA-AATAAAATTTC
375088 ATAAAAATTAAAATTT
1 AT-AAAA-TAAAATTT
375104 TTCGACCAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 15 0.56
16 6 0.22
17 6 0.22
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (15 bp):
ATAAAATAAAATTTC
Found at i:383130 original size:29 final size:30
Alignment explanation
Indices: 383085--383145 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 30
383075 GGTTTGTACT
383085 ATGTAAAAAAAAACTAAAAGAACACTTATC
1 ATGTAAAAAAAAACTAAAAGAACACTTATC
383115 ATGT-AAAAAAAACTAAAAGAACACTTATC
1 ATGTAAAAAAAAACTAAAAGAACACTTATC
383144 AT
1 AT
383146 TGTACATATG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 27 0.87
30 4 0.13
ACGTcount: A:0.59, C:0.13, G:0.07, T:0.21
Consensus pattern (30 bp):
ATGTAAAAAAAAACTAAAAGAACACTTATC
Found at i:383507 original size:13 final size:14
Alignment explanation
Indices: 383486--383520 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
383476 CCTTTTTCAA
383486 TATTAATTATGATT
1 TATTAATTATGATT
*
383500 TA-TAATTATTATT
1 TATTAATTATGATT
383513 TATTAATT
1 TATTAATT
383521 TATTTTAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (14 bp):
TATTAATTATGATT
Found at i:383830 original size:34 final size:34
Alignment explanation
Indices: 383783--383855 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 34
383773 CATTCCTCCC
* * *
383783 ATAATCTTGCATTCTCGTAGTCCTATTATGAAAT
1 ATAATCTTACATTCTCGTAATCCTATTATAAAAT
* *
383817 GTAATCTTACATTCTTGTAATCCTATTATAAAAT
1 ATAATCTTACATTCTCGTAATCCTATTATAAAAT
383851 ATAAT
1 ATAAT
383856 ATTATATCCC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.42
Consensus pattern (34 bp):
ATAATCTTACATTCTCGTAATCCTATTATAAAAT
Found at i:397057 original size:49 final size:50
Alignment explanation
Indices: 396991--397120 Score: 140
Period size: 49 Copynumber: 2.6 Consensus size: 50
396981 GATAATAACA
* *
396991 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTT-TC-T-TGTAC
1 TGCCAATGCCATATCCCAGACATGGTCTTACATGGGA-GTTCTCATAT-TAC
* * * **
397040 TGCCAATGTCATATCCCAGATATAGTCTTACATGGGAGTTCTCATATTGG
1 TGCCAATGCCATATCCCAGACATGGTCTTACATGGGAGTTCTCATATTAC
* *
397090 TGCCAATGCCATGTCTCAGACATGGTCTTAC
1 TGCCAATGCCATATCCCAGACATGGTCTTAC
397121 GGGGGACCTC
Statistics
Matches: 66, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
48 3 0.05
49 34 0.52
50 28 0.42
51 1 0.02
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (50 bp):
TGCCAATGCCATATCCCAGACATGGTCTTACATGGGAGTTCTCATATTAC
Found at i:397118 original size:50 final size:49
Alignment explanation
Indices: 396991--397152 Score: 148
Period size: 50 Copynumber: 3.3 Consensus size: 49
396981 GATAATAACA
* **
396991 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTT-TC-TTGTAC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-GTTCTCATT-TGG
* * * *
397040 TGCCAATGTCATATCCCAGATATAGTCTTACATGGGAGTTCTCATATTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCAT-TTGG
* ** ** *
397090 TGCCAATGCCATGTCTCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCAT-TTGG
*
397140 TGCCAACGCCATG
1 TGCCAATGCCATG
397153 GTCTTACATG
Statistics
Matches: 91, Mismatches: 19, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
48 3 0.03
49 34 0.37
50 53 0.58
51 1 0.01
ACGTcount: A:0.22, C:0.26, G:0.23, T:0.29
Consensus pattern (49 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATTTGG
Found at i:398316 original size:13 final size:13
Alignment explanation
Indices: 398298--398328 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
398288 GCCCAAACGT
398298 CAAAATTTTCAAA
1 CAAAATTTTCAAA
398311 CAAAATTTTCAAA
1 CAAAATTTTCAAA
398324 -AAAAT
1 CAAAAT
398329 CATTCCGTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.28
13 13 0.72
ACGTcount: A:0.58, C:0.13, G:0.00, T:0.29
Consensus pattern (13 bp):
CAAAATTTTCAAA
Found at i:399850 original size:17 final size:17
Alignment explanation
Indices: 399819--399861 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
399809 ATTTTGTTTG
*
399819 TTTAGTTTTCTTTATTTA
1 TTTA-TTTTCGTTATTTA
*
399837 TTTCTTTTCGTTATTTA
1 TTTATTTTCGTTATTTA
399854 TTTATTTT
1 TTTATTTT
399862 TACTCCCTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 19 0.86
18 3 0.14
ACGTcount: A:0.14, C:0.07, G:0.05, T:0.74
Consensus pattern (17 bp):
TTTATTTTCGTTATTTA
Found at i:406899 original size:18 final size:17
Alignment explanation
Indices: 406834--406900 Score: 64
Period size: 17 Copynumber: 3.8 Consensus size: 17
406824 ATAATATATA
*
406834 AAAAATTAAAAAATTTT
1 AAAAATTAAAAATTTTT
*
406851 AAAAAGTAAAAATATTATAT
1 AAAAATTAAAAAT-TT-T-T
406871 AAAATATT-AAAATTTTT
1 AAAA-ATTAAAAATTTTT
*
406888 AAAAATTATAAAT
1 AAAAATTAAAAAT
406901 ATAATTTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
16 3 0.07
17 20 0.49
18 3 0.07
19 3 0.07
20 10 0.24
21 2 0.05
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (17 bp):
AAAAATTAAAAATTTTT
Found at i:414056 original size:16 final size:16
Alignment explanation
Indices: 414035--414066 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
414025 TGATTGAAAG
*
414035 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
414051 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
414067 GCAACAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:418141 original size:33 final size:30
Alignment explanation
Indices: 418090--418880 Score: 133
Period size: 31 Copynumber: 25.8 Consensus size: 30
418080 ATCCAATGCT
**
418090 CAAATCAATTCAACAATGTATATATTCATACA
1 CAAATCAATTCGGCAATGTATA-A-TCATACA
* *
418122 CAAATCAAATTCGGTAATGTATAATCATATA
1 CAAATC-AATTCGGCAATGTATAATCATACA
* * *
418153 CAAATCAATTTGGCAATGTATAA-CTGTATA
1 CAAATCAATTCGGCAATGTATAATC-ATACA
** * * *
418183 TGAATCAAGTTCAGAAATGTATAATCATATA
1 CAAATCAA-TTCGGCAATGTATAATCATACA
* * * *
418214 CAAATCAAATT-GACATTGTATAACCATATA
1 CAAATC-AATTCGGCAATGTATAATCATACA
* * * *
418244 CGAATTAATTCAGCAACT-TAT-ATCCATATA
1 CAAATCAATTCGGCAA-TGTATAAT-CATACA
*** * *
418274 CAAATCAATTTCAATAATGTATAACCATATA
1 CAAATCAA-TTCGGCAATGTATAATCATACA
* * * *
418305 CAAATAAATTTCAGCAATGTA-CATCCATATA
1 CAAATCAA-TTCGGCAATGTATAAT-CATACA
* **
418336 CGAATCAATTCGGCAACT-TAT-ATCCATTTA
1 CAAATCAATTCGGCAA-TGTATAAT-CATACA
** * * * *
418366 CAAATCAAATTCAACAATGAATGACCATATA
1 CAAATC-AATTCGGCAATGTATAATCATACA
* * * *
418397 CAAATAAATTTCAGCAATGTA-CATCCATATA
1 CAAATCAA-TTCGGCAATGTATAAT-CATACA
* **
418428 CGAATCAATTCGGCAACT-TAT-ATCCATTTA
1 CAAATCAATTCGGCAA-TGTATAAT-CATACA
** * * * *
418458 CAAATCAAATTCAACAATGAATGACCATATA
1 CAAATC-AATTCGGCAATGTATAATCATACA
* * * * *
418489 CAAATAAATTTCAGCAATGTACAACCATATA
1 CAAATCAA-TTCGGCAATGTATAATCATACA
* * * **
418520 CGAATTAATTCGACAACT-TAT-ATCCATTGA
1 CAAATCAATTCGGCAA-TGTATAAT-CATACA
** * *
418550 CAAATCAAATTCAACAATGAATAATCATATA
1 CAAATC-AATTCGGCAATGTATAATCATACA
* * * * *
418581 CAAATAAATTTCAGCAATGTACAACCATATA
1 CAAATCAA-TTCGGCAATGTATAATCATACA
* * * **
418612 CGAATTAATTCGACAACT-TAT-ATCCATTGA
1 CAAATCAATTCGGCAA-TGTATAAT-CATACA
** * *
418642 CAAATCAAATTCAACAATGAATAATCATATA
1 CAAATC-AATTCGGCAATGTATAATCATACA
* * * * *
418673 CAAATAAATTTCAGCAATGTACAACCATATA
1 CAAATCAA-TTCGGCAATGTATAATCATACA
* * * **
418704 CGAATTAATTCGACAACT-TAT-ATCCATTGA
1 CAAATCAATTCGGCAA-TGTATAAT-CATACA
** * *
418734 CAAATCAAATTCAACAATGAATAATCATATA
1 CAAATC-AATTCGGCAATGTATAATCATACA
* * * * * *
418765 CAAATAAATTTCAGCAATGGACAACCATATA
1 CAAATCAA-TTCGGCAATGTATAATCATACA
* * * ** *
418796 CGAATTAATTCGGCACCT-TATCTTCATATA
1 CAAATCAATTCGGCA-ATGTATAATCATACA
** *
418826 CAAATCAATTTCAACAATGTATAA-CTATAAA
1 CAAATCAA-TTCGGCAATGTATAATC-ATACA
* * *
418857 CAATTCAAATTAGGCAATATATAA
1 CAAATC-AATTCGGCAATGTATAA
418881 AACAATCAAA
Statistics
Matches: 566, Mismatches: 145, Indels: 97
0.70 0.18 0.12
Matches are distributed among these distances:
29 9 0.02
30 191 0.34
31 332 0.59
32 21 0.04
33 13 0.02
ACGTcount: A:0.45, C:0.18, G:0.07, T:0.29
Consensus pattern (30 bp):
CAAATCAATTCGGCAATGTATAATCATACA
Found at i:418210 original size:61 final size:61
Alignment explanation
Indices: 418137--418850 Score: 365
Period size: 61 Copynumber: 11.7 Consensus size: 61
418127 CAAATTCGGT
* ** *
418137 AATGTATAATCATATACAAATCAATTTGGCAATGTATAACTGTATATGAATCAAGTTCAG-A
1 AATGTATAATCATATACAAATCAATTTGACAATGTATAACCATATACGAATCAA-TTCAGCA
* * *
418198 AATGTATAATCATATACAAATCAAATTGACATTGTATAACCATATACGAATTAATTCAGCA
1 AATGTATAATCATATACAAATCAATTTGACAATGTATAACCATATACGAATCAATTCAGCA
* * * * *
418259 ACT-TAT-ATCCATATACAAATCAATTTCAATAATGTATAACCATATACAAATAAATTTCAGC-
1 AATGTATAAT-CATATACAAATCAATTT-GACAATGTATAACCATATACGAATCAA-TTCAGCA
* * * * * * * *
418320 AATGTA-CATCCATATACGAATCAATTCGGCAACT-TATATCCATTTACAAATCAAATTCAAC-
1 AATGTATAAT-CATATACAAATCAATTTGACAA-TGTATAACCATATACGAATC-AATTCAGCA
* * * * * * * *
418381 AATGAATGACCATATACAAATAAATTTCAGCAATGTACATCCATATACGAATCAATTCGGCA
1 AATGTATAATCATATACAAATCAATTTGA-CAATGTATAACCATATACGAATCAATTCAGCA
* * ** * * * *
418443 ACT-TAT-ATCCATTTACAAATCAAATTCAACAATGAATGACCATATACAAATAAATTTCAGC-
1 AATGTATAAT-CATATACAAATC-AATTTGACAATGTATAACCATATACGAATCAA-TTCAGCA
* * * * * * * *
418504 AATGTACAACCATATACGAATTAATTCGACAACT-TATATCCAT-TGACAAATCAAATTCAAC-
1 AATGTATAATCATATACAAATCAATTTGACAA-TGTATAACCATAT-ACGAATC-AATTCAGCA
* * * * *
418565 AATGAATAATCATATACAAATAAATTTCAGCAATGTACAACCATATACGAATTAATTC-GACA
1 AATGTATAATCATATACAAATCAATTTGA-CAATGTATAACCATATACGAATCAATTCAG-CA
* ** * * * *
418627 ACT-TAT-ATCCAT-TGACAAATCAAATTCAACAATGAATAATCATATACAAATAAATTTCAGC-
1 AATGTATAAT-CATAT-ACAAATC-AATTTGACAATGTATAACCATATACGAATCAA-TTCAGCA
* * * * * * * *
418688 AATGTACAACCATATACGAATTAATTCGACAACT-TATATCCAT-TGACAAATCAAATTCAAC-
1 AATGTATAATCATATACAAATCAATTTGACAA-TGTATAACCATAT-ACGAATC-AATTCAGCA
* * * * * * *
418749 AATGAATAATCATATACAAATAAATTTCAGCAATGGACAACCATATACGAATTAATTCGGCA
1 AATGTATAATCATATACAAATCAATTTGA-CAATGTATAACCATATACGAATCAATTCAGCA
** ** *
418811 CCT-TATCTTCATATACAAATCAATTTCAACAATGTATAAC
1 AATGTATAATCATATACAAATCAATTT-GACAATGTATAAC
418851 TATAAACAAT
Statistics
Matches: 493, Mismatches: 119, Indels: 82
0.71 0.17 0.12
Matches are distributed among these distances:
59 2 0.00
60 30 0.06
61 326 0.66
62 129 0.26
63 6 0.01
ACGTcount: A:0.45, C:0.18, G:0.07, T:0.29
Consensus pattern (61 bp):
AATGTATAATCATATACAAATCAATTTGACAATGTATAACCATATACGAATCAATTCAGCA
Found at i:418356 original size:92 final size:91
Alignment explanation
Indices: 418185--418849 Score: 985
Period size: 92 Copynumber: 7.2 Consensus size: 91
418175 ACTGTATATG
* * * * *
418185 AATCAAGTTCAGA-AATGTATAATCATATACAAATCAAA-TTGA-CATTGTATAACCATATACGA
1 AATCAAATTCA-ACAATGAATAATCATATACAAAT-AAATTTCAGCAATGTACAACCATATACGA
*
418247 ATTAATTCAGCAACTTATATCCATATACA
64 ATTAATTCGGCAACTTATATCCAT-TACA
* * * * *
418276 AATCAATTTCAATAATGTATAACCATATACAAATAAATTTCAGCAATGTACATCCATATACGAAT
1 AATCAAATTCAACAATGAATAATCATATACAAATAAATTTCAGCAATGTACAACCATATACGAAT
*
418341 CAATTCGGCAACTTATATCCATTTACA
66 TAATTCGGCAACTTATATCCA-TTACA
* * *
418368 AATCAAATTCAACAATGAATGACCATATACAAATAAATTTCAGCAATGTACATCCATATACGAAT
1 AATCAAATTCAACAATGAATAATCATATACAAATAAATTTCAGCAATGTACAACCATATACGAAT
*
418433 CAATTCGGCAACTTATATCCATTTACA
66 TAATTCGGCAACTTATATCCA-TTACA
* *
418460 AATCAAATTCAACAATGAATGACCATATACAAATAAATTTCAGCAATGTACAACCATATACGAAT
1 AATCAAATTCAACAATGAATAATCATATACAAATAAATTTCAGCAATGTACAACCATATACGAAT
*
418525 TAATTCGACAACTTATATCCATTGACA
66 TAATTCGGCAACTTATATCCATT-ACA
418552 AATCAAATTCAACAATGAATAATCATATACAAATAAATTTCAGCAATGTACAACCATATACGAAT
1 AATCAAATTCAACAATGAATAATCATATACAAATAAATTTCAGCAATGTACAACCATATACGAAT
*
418617 TAATTCGACAACTTATATCCATTGACA
66 TAATTCGGCAACTTATATCCATT-ACA
418644 AATCAAATTCAACAATGAATAATCATATACAAATAAATTTCAGCAATGTACAACCATATACGAAT
1 AATCAAATTCAACAATGAATAATCATATACAAATAAATTTCAGCAATGTACAACCATATACGAAT
*
418709 TAATTCGACAACTTATATCCATTGACA
66 TAATTCGGCAACTTATATCCATT-ACA
*
418736 AATCAAATTCAACAATGAATAATCATATACAAATAAATTTCAGCAATGGACAACCATATACGAAT
1 AATCAAATTCAACAATGAATAATCATATACAAATAAATTTCAGCAATGTACAACCATATACGAAT
* * *
418801 TAATTCGGCACCTTATCTTCATATACA
66 TAATTCGGCAACTTATATCCAT-TACA
* *
418828 AATCAATTTCAACAATGTATAA
1 AATCAAATTCAACAATGAATAA
418850 CTATAAACAA
Statistics
Matches: 544, Mismatches: 24, Indels: 11
0.94 0.04 0.02
Matches are distributed among these distances:
90 4 0.01
91 35 0.06
92 503 0.92
93 2 0.00
ACGTcount: A:0.45, C:0.19, G:0.07, T:0.29
Consensus pattern (91 bp):
AATCAAATTCAACAATGAATAATCATATACAAATAAATTTCAGCAATGTACAACCATATACGAAT
TAATTCGGCAACTTATATCCATTACA
Found at i:418899 original size:25 final size:26
Alignment explanation
Indices: 418854--418904 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
418844 GTATAACTAT
*
418854 AAACAATTCAAATTAGGCAATATATA
1 AAACAATTCAAATTAGACAATATATA
418880 AAACAA-TCAAATTCA-ACAATATATA
1 AAACAATTCAAATT-AGACAATATATA
418905 TCTATAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.57, C:0.14, G:0.04, T:0.25
Consensus pattern (26 bp):
AAACAATTCAAATTAGACAATATATA
Found at i:420499 original size:36 final size:36
Alignment explanation
Indices: 420452--420525 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
420442 CCCAATCAAA
420452 GAGTCAAAGCTTGAAACCCTTCCTATTATAGAAATG
1 GAGTCAAAGCTTGAAACCCTTCCTATTATAGAAATG
420488 GAGTCAAAGCTTGAAACCCTTCCTATTATAGAAATG
1 GAGTCAAAGCTTGAAACCCTTCCTATTATAGAAATG
420524 GA
1 GA
420526 AAAATCGGTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (36 bp):
GAGTCAAAGCTTGAAACCCTTCCTATTATAGAAATG
Found at i:421837 original size:23 final size:23
Alignment explanation
Indices: 421810--421871 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
421800 AAGTATGTAA
*
421810 TTTTTAAAAAAATTAATT-TTTT
1 TTTTTAAAAAAATTAATTATATT
*
421832 TATTTTAAACAAAA-AAATTATATT
1 T-TTTTAAA-AAAATTAATTATATT
*
421856 TTTATAAAAAAATTAA
1 TTTTTAAAAAAATTAA
421872 AATATATGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
22 5 0.16
23 19 0.59
24 8 0.25
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
TTTTTAAAAAAATTAATTATATT
Found at i:421857 original size:20 final size:19
Alignment explanation
Indices: 421832--421870 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
421822 TTAATTTTTT
421832 TATTTTAAACAAAAAAATTA
1 TATTTT-AACAAAAAAATTA
* *
421852 TATTTTTATAAAAAAATTA
1 TATTTTAACAAAAAAATTA
421871 AAATATATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (19 bp):
TATTTTAACAAAAAAATTA
Found at i:421883 original size:18 final size:18
Alignment explanation
Indices: 421862--421932 Score: 79
Period size: 19 Copynumber: 3.8 Consensus size: 18
421852 TATTTTTATA
* *
421862 AAAAAATTAAAATATATG
1 AAAAAATAAAAATATATT
*
421880 AAAAAATTAAAAAAATATT
1 AAAAAA-TAAAAATATATT
* *
421899 TAAAAATAAAAATATTTT
1 AAAAAATAAAAATATATT
421917 AAAAATATAAAAATAT
1 AAAAA-ATAAAAATAT
421933 TCATCTTATT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
18 20 0.45
19 24 0.55
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.30
Consensus pattern (18 bp):
AAAAAATAAAAATATATT
Found at i:421921 original size:37 final size:35
Alignment explanation
Indices: 421863--421933 Score: 88
Period size: 37 Copynumber: 2.0 Consensus size: 35
421853 ATTTTTATAA
*
421863 AAAAATTAAAATATATGAAAAAATTAAAAAAATATTT
1 AAAAATAAAAATATATG-AAAAA-TAAAAAAATATTT
* * *
421900 AAAAATAAAAATATTTTAAAAATATAAAAATATT
1 AAAAATAAAAATATATGAAAAATAAAAAAATATT
421934 CATCTTATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 11 0.37
36 5 0.17
37 14 0.47
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (35 bp):
AAAAATAAAAATATATGAAAAATAAAAAAATATTT
Found at i:421933 original size:19 final size:19
Alignment explanation
Indices: 421881--421933 Score: 67
Period size: 18 Copynumber: 2.9 Consensus size: 19
421871 AAATATATGA
*
421881 AAAAAT-TAAAAAAATATTT
1 AAAAATATAAAAATAT-TTT
421900 -AAAA-ATAAAAATATTTT
1 AAAAATATAAAAATATTTT
421917 AAAAATATAAAAATATT
1 AAAAATATAAAAATATT
421934 CATCTTATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
17 3 0.10
18 16 0.53
19 11 0.37
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAAATATAAAAATATTTT
Found at i:430330 original size:23 final size:23
Alignment explanation
Indices: 430262--430333 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 23
430252 ACCCTTTTTC
430262 TTTTGTCTCTATAATTTG-A-TT
1 TTTTGTCTCTATAATTTGAACTT
* * *
430283 TGTTTGTCCCTATAA-ATCAACCTT
1 T-TTTGTCTCTATAATTTGAA-CTT
*
430307 TTTTGTCTCTGTAATTTGAACTT
1 TTTTGTCTCTATAATTTGAACTT
430330 TTTT
1 TTTT
430334 TTATTTATTG
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
21 2 0.05
22 13 0.33
23 18 0.46
24 6 0.15
ACGTcount: A:0.19, C:0.15, G:0.10, T:0.56
Consensus pattern (23 bp):
TTTTGTCTCTATAATTTGAACTT
Found at i:441790 original size:42 final size:42
Alignment explanation
Indices: 441743--441854 Score: 136
Period size: 42 Copynumber: 2.7 Consensus size: 42
441733 TGCTAAACAG
* * **
441743 AAACCCATAAGGGTTGAACGGAAGCTCGTAAGAGCTGAACGA
1 AAACCCATAAGGGTTAAACGAAAGCTCAAAAGAGCTGAACGA
** *
441785 AAACCCATAAGGGTTAAATTAAAGCTCAAAAGAGCTGAACGG
1 AAACCCATAAGGGTTAAACGAAAGCTCAAAAGAGCTGAACGA
*
441827 AAACCCATAAAGGTTAAACAGAAA-CTCA
1 AAACCCATAAGGGTTAAAC-GAAAGCTCA
441855 TATGAGTTAA
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 56 0.95
43 3 0.05
ACGTcount: A:0.45, C:0.19, G:0.21, T:0.15
Consensus pattern (42 bp):
AAACCCATAAGGGTTAAACGAAAGCTCAAAAGAGCTGAACGA
Found at i:441795 original size:21 final size:21
Alignment explanation
Indices: 441743--441836 Score: 53
Period size: 21 Copynumber: 4.5 Consensus size: 21
441733 TGCTAAACAG
* * *
441743 AAACCCATAAGGGTTGAACGG
1 AAACCCATAAGAGCTGAACGA
* * *
441764 AAGCTCGTAAGAGCTGAACGA
1 AAACCCATAAGAGCTGAACGA
* * * **
441785 AAACCCATAAGGGTTAAATTA
1 AAACCCATAAGAGCTGAACGA
* * * *
441806 AAGCTCAAAAGAGCTGAACGG
1 AAACCCATAAGAGCTGAACGA
441827 AAACCCATAA
1 AAACCCATAA
441837 AGGTTAAACA
Statistics
Matches: 47, Mismatches: 26, Indels: 0
0.64 0.36 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.15
Consensus pattern (21 bp):
AAACCCATAAGAGCTGAACGA
Found at i:444518 original size:99 final size:100
Alignment explanation
Indices: 444383--444602 Score: 307
Period size: 99 Copynumber: 2.2 Consensus size: 100
444373 CCAAACACAC
* *
444383 CAGTATACAGTAATCAGTAACGGTAGTAGTAACAGTATTCAACACACAAAGTGCTGAATCTGTAA
1 CAGTA-ACAGTAA-CAGTAAC-G-AGTAGTAACAGTATTCAACACACAAAGTGCCGAATCGGTAA
* *
444448 CAGTAACGGTAACAGTATTCAACACACAAAGCGCCGAGT
62 CAGTAACAGTAACAGTATTCAACACACAAAGCGCCGAAT
* ** *
444487 CGGTAACAGTAACAGTAAC-AGTAGTAACAGTATTTGACACACAAAGTGCCGAGTCGGTAACAGT
1 CAGTAACAGTAACAGTAACGAGTAGTAACAGTATTCAACACACAAAGTGCCGAATCGGTAACAGT
* *
444551 AACAGTAACAGTATTCGACACACAAAGTGCCGAAT
66 AACAGTAACAGTATTCAACACACAAAGCGCCGAAT
444586 CAGTAACAGTAACAGTA
1 CAGTAACAGTAACAGTA
444603 GTCGGCACAT
Statistics
Matches: 105, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
99 87 0.83
102 7 0.07
103 7 0.07
104 4 0.04
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (100 bp):
CAGTAACAGTAACAGTAACGAGTAGTAACAGTATTCAACACACAAAGTGCCGAATCGGTAACAGT
AACAGTAACAGTATTCAACACACAAAGCGCCGAAT
Found at i:444527 original size:54 final size:54
Alignment explanation
Indices: 444389--444563 Score: 197
Period size: 54 Copynumber: 3.3 Consensus size: 54
444379 ACACCAGTAT
* * *
444389 ACAGTAATCAGTAACGGTAGTAGTAACAGTATTCAACACACAAAGTGCTGAATC--T-
1 ACAGTAA-CAGTAAC---AGTAGTAACAGTATTCAACACACAAAGCGCCGAGTCGGTA
444444 ---GTAACAGTAAC-G--GTAACAGTATTCAACACACAAAGCGCCGAGTCGGTA
1 ACAGTAACAGTAACAGTAGTAACAGTATTCAACACACAAAGCGCCGAGTCGGTA
** *
444492 ACAGTAACAGTAACAGTAGTAACAGTATTTGACACACAAAGTGCCGAGTCGGTA
1 ACAGTAACAGTAACAGTAGTAACAGTATTCAACACACAAAGCGCCGAGTCGGTA
444546 ACAGTAACAGTAACAGTA
1 ACAGTAACAGTAACAGTA
444564 TTCGACACAC
Statistics
Matches: 105, Mismatches: 6, Indels: 19
0.81 0.05 0.15
Matches are distributed among these distances:
45 29 0.28
47 2 0.02
51 18 0.17
52 5 0.05
54 51 0.49
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.20
Consensus pattern (54 bp):
ACAGTAACAGTAACAGTAGTAACAGTATTCAACACACAAAGCGCCGAGTCGGTA
Found at i:444590 original size:39 final size:39
Alignment explanation
Indices: 444509--444629 Score: 127
Period size: 45 Copynumber: 3.0 Consensus size: 39
444499 CAGTAACAGT
* *
444509 AGTAACAGTATTTGACACACAAAGTGCCGAGTCGGTAACAGTAAC
1 AGTAACAGTATTCGACACACAAAGTGCCGA------ATCAGTAAC
444554 AGTAACAGTATTCGACACACAAAGTGCCGAATCAGTAAC
1 AGTAACAGTATTCGACACACAAAGTGCCGAATCAGTAAC
* * * *
444593 AGTAACAGTAGTCGGCACA-TAAGTGCCTAATCAGTAA
1 AGTAACAGTATTCGACACACAAAGTGCCGAATCAGTAA
444630 GCCGGCAAAT
Statistics
Matches: 70, Mismatches: 6, Indels: 7
0.84 0.07 0.08
Matches are distributed among these distances:
38 16 0.23
39 25 0.36
45 29 0.41
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.20
Consensus pattern (39 bp):
AGTAACAGTATTCGACACACAAAGTGCCGAATCAGTAAC
Found at i:444599 original size:45 final size:45
Alignment explanation
Indices: 444394--444602 Score: 220
Period size: 45 Copynumber: 4.4 Consensus size: 45
444384 AGTATACAGT
* ** *
444394 AATCAGTAACGGTAGTAGTAACAGTATTCAACACACAAAGTGCTG
1 AATCAGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCG
* * *
444439 AATCTGTAACAGTAACGGTAACAGTATTCAACACACAAAGCGCCG
1 AATCAGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCG
* **
444484 AGTCGGTAACAGTAACAGTAACAGTAGTAACAGTATTTGACACACAAAGTGCCG
1 A------ATCAGTAACAGTAAC---AGTAACAGTATTCAACACACAAAGTGCCG
* * *
444538 AGTCGGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
1 AATCAGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCG
444583 AATCAGTAACAGTAACAGTA
1 AATCAGTAACAGTAACAGTA
444603 GTCGGCACAT
Statistics
Matches: 136, Mismatches: 19, Indels: 18
0.79 0.11 0.10
Matches are distributed among these distances:
45 85 0.62
48 12 0.09
51 13 0.10
54 26 0.19
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (45 bp):
AATCAGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCG
Found at i:444626 original size:38 final size:39
Alignment explanation
Indices: 444547--444629 Score: 123
Period size: 39 Copynumber: 2.2 Consensus size: 39
444537 GAGTCGGTAA
*
444547 CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
1 CAGTAACAGTAACAGTAGTCGACACACAAAGTGCCGAAT
* * *
444586 CAGTAACAGTAACAGTAGTCGGCACA-TAAGTGCCTAAT
1 CAGTAACAGTAACAGTAGTCGACACACAAAGTGCCGAAT
444624 CAGTAA
1 CAGTAA
444630 GCCGGCAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
38 16 0.40
39 24 0.60
ACGTcount: A:0.40, C:0.22, G:0.19, T:0.19
Consensus pattern (39 bp):
CAGTAACAGTAACAGTAGTCGACACACAAAGTGCCGAAT
Found at i:449966 original size:17 final size:18
Alignment explanation
Indices: 449941--449974 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
449931 ATTTTTCCTC
449941 TTGGACTTA-TTTGGGTG
1 TTGGACTTATTTTGGGTG
*
449958 TTGGGCTTATTTTGGGT
1 TTGGACTTATTTTGGGT
449975 TTATTGTGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.09, C:0.06, G:0.35, T:0.50
Consensus pattern (18 bp):
TTGGACTTATTTTGGGTG
Found at i:457071 original size:21 final size:21
Alignment explanation
Indices: 457032--457074 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
457022 GTGAAAATGG
*
457032 TTGAATATTTTGAGAAATTTA
1 TTGAATATTTTAAGAAATTTA
*
457053 TTGAATATTTTAATGAATTTTA
1 TTGAATATTTTAA-GAAATTTA
457075 GCTTTAGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (21 bp):
TTGAATATTTTAAGAAATTTA
Found at i:461246 original size:58 final size:58
Alignment explanation
Indices: 461117--461325 Score: 235
Period size: 58 Copynumber: 3.6 Consensus size: 58
461107 CACAAGCAAC
* * ** * * * **
461117 TTTATATTTAAGAAAATTTT-AGAAGATAATCAACTA-GGATGTGAATTCGCGAATTGT
1 TTTATACTTAAGAAAATTTTGA-AAGATAACCAGTTAGGGATGTGAATCCGTGACTCAT
* * *
461174 TTCATATTTAAGAAAATTTTGAAAGATAACCAGTTAGGGATGTGAATCTGTGAGCT-AT
1 TTTATACTTAAGAAAATTTTGAAAGATAACCAGTTAGGGATGTGAATCCGTGA-CTCAT
* * *
461232 TTTATACTTAAGAAAATTTTGAAAGATAACCAGCTAGGGATGTGAATCCGTGATTCGT
1 TTTATACTTAAGAAAATTTTGAAAGATAACCAGTTAGGGATGTGAATCCGTGACTCAT
461290 TTTATACTTAAGAAAATTTTGAAAGATAACACAGTT
1 TTTATACTTAAGAAAATTTTGAAAGATAAC-CAGTT
461326 GAGAGTTTTC
Statistics
Matches: 131, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
57 31 0.24
58 95 0.73
59 5 0.04
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (58 bp):
TTTATACTTAAGAAAATTTTGAAAGATAACCAGTTAGGGATGTGAATCCGTGACTCAT
Found at i:461469 original size:69 final size:69
Alignment explanation
Indices: 461341--461735 Score: 305
Period size: 69 Copynumber: 5.7 Consensus size: 69
461331 TTTTCAACTT
* * * * * *** * *
461341 TCGCTAACTATGTTAGAGGCTACGGTCTTTATCCTGTAAGCCTTAGTATGAAAATTGGGAGCTTT
1 TCGCTAATTGTGTTGGAGGCTGCGGTTTTTATCCTACGAGCCTAAGTATGAAAACTGGGAGCTTT
461406 GCTC
66 GCTC
** * * * * *
461410 TCATTAATTGTGTTGGAGGCTACGCTTTTTATCTTACGGGCCTAAGTATGACAACTGGGAGCTTT
1 TCGCTAATTGTGTTGGAGGCTGCGGTTTTTATCCTACGAGCCTAAGTATGAAAACTGGGAGCTTT
*
461475 GCTA
66 GCTC
* * * * * * * * * * *
461479 TTGCTAATTTTGTTGAAAGCTGTGGTTTTTATCCTACAATCCTTAGTATGATAGCTGGGAGTTTT
1 TCGCTAATTGTGTTGGAGGCTGCGGTTTTTATCCTACGAGCCTAAGTATGAAAACTGGGAGCTTT
461544 GCTC
66 GCTC
* * * * * * * *
461548 TCGCTAATTGTGTTAGA-GATACGGGTTTTATCCTACGAGCTTTAA-TATGACAATTGGGAGTTT
1 TCGCTAATTGTGTTGGAGGCTGCGGTTTTTATCCTACGAGC-CTAAGTATGAAAACTGGGAGCTT
461611 TGCTC
65 TGCTC
* * ** * * *
461616 TTGCTAATTATGTTGGAGGCTGCAATATTTATCCTGCGAGCTTTAA-TAT-AAAAGCTGGGAGCT
1 TCGCTAATTGTGTTGGAGGCTGCGGTTTTTATCCTACGAGC-CTAAGTATGAAAA-CTGGGAGCT
461679 TTGCTC
64 TTGCTC
* *
461685 TCGCTAACTGTGTTGGAGGCTGCGGTTTTTATCCTATGAGCCTTAA-TATGA
1 TCGCTAATTGTGTTGGAGGCTGCGGTTTTTATCCTACGAGCC-TAAGTATGA
461736 CATAAATGTT
Statistics
Matches: 250, Mismatches: 71, Indels: 9
0.76 0.22 0.03
Matches are distributed among these distances:
68 54 0.22
69 195 0.78
70 1 0.00
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.38
Consensus pattern (69 bp):
TCGCTAATTGTGTTGGAGGCTGCGGTTTTTATCCTACGAGCCTAAGTATGAAAACTGGGAGCTTT
GCTC
Found at i:461647 original size:137 final size:137
Alignment explanation
Indices: 461368--461737 Score: 400
Period size: 137 Copynumber: 2.7 Consensus size: 137
461358 GGCTACGGTC
** ** **
461368 TTTATCCTGTAAGCCTTAGTATGAAAATTGGGAGCTTTGCTCTCATTAATTGTGTTGGAGGCTAC
1 TTTATCCTACAAGCCTTAGTATGAAAGCTGGGAGCTTTGCTCTCGCTAATTGTGTTGGAGGCTAC
* * * * *
461433 GCTTTTTATCTTACGGGCCTAAGTATGACAACTGGGAGCTTTGCTATTGCTAATTTTGTTGAAAG
66 GGTTTTTATCCTACGAGCTTAA-TATGACAACTGGGAGCTTTGCTATTGCTAATTATGTTGAAAG
*** *
461498 CTGTGGTT
130 CTGCAATA
* * * * *
461506 TTTATCCTACAATCCTTAGTATGATAGCTGGGAGTTTTGCTCTCGCTAATTGTGTTAGA-GATAC
1 TTTATCCTACAAGCCTTAGTATGAAAGCTGGGAGCTTTGCTCTCGCTAATTGTGTTGGAGGCTAC
* * * * * *
461570 GGGTTTTATCCTACGAGCTTTAATATGACAATTGGGAGTTTTGCTCTTGCTAATTATGTTGGAGG
66 GGTTTTTATCCTACGAGC-TTAATATGACAACTGGGAGCTTTGCTATTGCTAATTATGTTGAAAG
461635 CTGCAATA
130 CTGCAATA
* * * * * * *
461643 TTTATCCTGCGAGCTTTAATATAAAAGCTGGGAGCTTTGCTCTCGCTAACTGTGTTGGAGGCTGC
1 TTTATCCTACAAGCCTTAGTATGAAAGCTGGGAGCTTTGCTCTCGCTAATTGTGTTGGAGGCTAC
*
461708 GGTTTTTATCCTATGAGCCTTAATATGACA
66 GGTTTTTATCCTACGAG-CTTAATATGACA
461738 TAAATGTTGT
Statistics
Matches: 189, Mismatches: 40, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
137 107 0.57
138 81 0.43
139 1 0.01
ACGTcount: A:0.22, C:0.16, G:0.23, T:0.38
Consensus pattern (137 bp):
TTTATCCTACAAGCCTTAGTATGAAAGCTGGGAGCTTTGCTCTCGCTAATTGTGTTGGAGGCTAC
GGTTTTTATCCTACGAGCTTAATATGACAACTGGGAGCTTTGCTATTGCTAATTATGTTGAAAGC
TGCAATA
Found at i:462381 original size:11 final size:13
Alignment explanation
Indices: 462365--462398 Score: 54
Period size: 11 Copynumber: 2.8 Consensus size: 13
462355 AATTTTACGA
462365 AAAAATTTCG-T-
1 AAAAATTTCGTTC
462376 AAAAATTTCGTTC
1 AAAAATTTCGTTC
462389 AAAAATTTCG
1 AAAAATTTCG
462399 ACGTTTGGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.48
12 1 0.05
13 10 0.48
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (13 bp):
AAAAATTTCGTTC
Found at i:473806 original size:117 final size:117
Alignment explanation
Indices: 473653--473882 Score: 415
Period size: 117 Copynumber: 2.0 Consensus size: 117
473643 CATGAATGGA
*
473653 GAACTAAAAGATTTATTGAATGCTAGAGACATGAAGCTTAATAGTGAGATTGATGAGCTGAAAGA
1 GAACTAAAAGATTTATTGAATGCTAGAGACATGAAGCTTAATAGTGAGATTGATGAACTGAAAGA
* *
473718 TGGGCTGTCTGAGCCAGGGAAATCTGTTGAAGAGACAGTTGCTTCTGCAGAT
66 TAGGCTGTCTGAGCCAAGGAAATCTGTTGAAGAGACAGTTGCTTCTGCAGAT
*
473770 GAACTAAAAGATTTATTGAATGCTAGGGACATGAAGCTTAATAGTGAGATTGATGAACTGAAAGA
1 GAACTAAAAGATTTATTGAATGCTAGAGACATGAAGCTTAATAGTGAGATTGATGAACTGAAAGA
*
473835 TAGGCTGTTTGAGCCAAGGAAATCTGTTGAAGAGACAGTTGCTTCTGC
66 TAGGCTGTCTGAGCCAAGGAAATCTGTTGAAGAGACAGTTGCTTCTGC
473883 TGATAGAAAC
Statistics
Matches: 108, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
117 108 1.00
ACGTcount: A:0.34, C:0.12, G:0.27, T:0.27
Consensus pattern (117 bp):
GAACTAAAAGATTTATTGAATGCTAGAGACATGAAGCTTAATAGTGAGATTGATGAACTGAAAGA
TAGGCTGTCTGAGCCAAGGAAATCTGTTGAAGAGACAGTTGCTTCTGCAGAT
Found at i:481973 original size:11 final size:10
Alignment explanation
Indices: 481950--481983 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
481940 ATTTTATGCA
481950 ATTTATATAT
1 ATTTATATAT
481960 ATTTATATTAT
1 ATTTATA-TAT
481971 ATTTA-ATAT
1 ATTTATATAT
481980 ATTT
1 ATTT
481984 TCATTGTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 7 0.30
10 8 0.35
11 8 0.35
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
ATTTATATAT
Found at i:482519 original size:62 final size:62
Alignment explanation
Indices: 482422--482544 Score: 219
Period size: 62 Copynumber: 2.0 Consensus size: 62
482412 ATTAGTCATG
482422 GGTGGAGAACGAGAATTGAACTCTATGAGATCTAATCCCCCGTTGTTCTTCAATAGATCAAA
1 GGTGGAGAACGAGAATTGAACTCTATGAGATCTAATCCCCCGTTGTTCTTCAATAGATCAAA
* * *
482484 GGTGGAGAACGAGAGTTGAACTCTATGAGATCTAATCTCCCGTTGTTCTTCAATAGCTCAA
1 GGTGGAGAACGAGAATTGAACTCTATGAGATCTAATCCCCCGTTGTTCTTCAATAGATCAA
482545 CAGTAGAGCG
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 58 1.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (62 bp):
GGTGGAGAACGAGAATTGAACTCTATGAGATCTAATCCCCCGTTGTTCTTCAATAGATCAAA
Found at i:491164 original size:12 final size:12
Alignment explanation
Indices: 491128--491166 Score: 55
Period size: 13 Copynumber: 3.3 Consensus size: 12
491118 GCCAAAAGAG
491128 TCAAAAAT-T-T
1 TCAAAAATATCT
491138 TCAAAAATATCCT
1 TCAAAAATAT-CT
491151 TCAAAAATATCT
1 TCAAAAATATCT
491163 TCAA
1 TCAA
491167 TCTCCTTTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 8 0.31
11 1 0.04
12 6 0.23
13 11 0.42
ACGTcount: A:0.49, C:0.18, G:0.00, T:0.33
Consensus pattern (12 bp):
TCAAAAATATCT
Found at i:491864 original size:29 final size:28
Alignment explanation
Indices: 491811--491885 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 28
491801 GAATTATGTG
* *
491811 AGCCTATATGTGAACCTAGGAACATG-A
1 AGCCTACATGCGAACCTAGGAACATGCA
* *
491838 GAGTCTACATGCGAACCATAGGTACATGCA
1 -AGCCTACATGCGAACC-TAGGAACATGCA
*
491868 AGCCTACATGCGAGCCTA
1 AGCCTACATGCGAACCTA
491886 TGTGTGAACC
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
28 15 0.38
29 23 0.59
30 1 0.03
ACGTcount: A:0.33, C:0.24, G:0.23, T:0.20
Consensus pattern (28 bp):
AGCCTACATGCGAACCTAGGAACATGCA
Found at i:495175 original size:12 final size:12
Alignment explanation
Indices: 495136--495189 Score: 51
Period size: 12 Copynumber: 4.7 Consensus size: 12
495126 ATTCATAAAT
495136 ATAAT-TTATTTA
1 ATAATATTA-TTA
*
495148 A-AATTTTATTA
1 ATAATATTATTA
495159 A-AATATTATTA
1 ATAATATTATTA
* *
495170 ATAATATAAATA
1 ATAATATTATTA
495182 ATAATATT
1 ATAATATT
495190 TGATGCACCA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
11 17 0.47
12 19 0.53
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATAATATTATTA
Found at i:495234 original size:24 final size:25
Alignment explanation
Indices: 495181--495236 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
495171 TAATATAAAT
*
495181 AATAATATTTGATGCACCATCAGTG
1 AATAATATTTCATGCACCATCAGTG
*
495206 CATAA-ATTTCATGCACCATC-GTTG
1 AATAATATTTCATGCACCATCAG-TG
495230 AATAATA
1 AATAATA
495237 ACATGACACG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 1 0.04
24 20 0.77
25 5 0.19
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (25 bp):
AATAATATTTCATGCACCATCAGTG
Found at i:495506 original size:21 final size:21
Alignment explanation
Indices: 495482--495534 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
495472 TTTCAGCTCT
* *
495482 ATTCCATTCCCACAGTATAAC
1 ATTCCATTCCAACACTATAAC
* * *
495503 ATTCCATTACAACTCTATTAC
1 ATTCCATTCCAACACTATAAC
495524 ATTCCATTCCA
1 ATTCCATTCCA
495535 GTTAACCAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.32, C:0.32, G:0.02, T:0.34
Consensus pattern (21 bp):
ATTCCATTCCAACACTATAAC
Found at i:496252 original size:14 final size:15
Alignment explanation
Indices: 496228--496256 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
496218 TTATTATTGC
496228 TTAATGATGATTAAG
1 TTAATGATGATTAAG
496243 TTAA-GATGATTAAG
1 TTAATGATGATTAAG
496257 GCTTAGTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (15 bp):
TTAATGATGATTAAG
Found at i:500694 original size:13 final size:12
Alignment explanation
Indices: 500667--500692 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
500657 TCTTTTATTC
500667 TTAACATAATTT
1 TTAACATAATTT
500679 TTAACATAATTT
1 TTAACATAATTT
500691 TT
1 TT
500693 TATTACTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (12 bp):
TTAACATAATTT
Found at i:513891 original size:30 final size:30
Alignment explanation
Indices: 513855--513912 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
513845 ACAAATCCTA
* *
513855 TCTCAATTTTCTTCCAAAATTCTCTCAAAC
1 TCTCAATTTCCTTCCAAAATCCTCTCAAAC
513885 TCTCAATTTCCTTCCAAAATCCTCTCAA
1 TCTCAATTTCCTTCCAAAATCCTCTCAA
513913 TTTCCTTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.29, C:0.33, G:0.00, T:0.38
Consensus pattern (30 bp):
TCTCAATTTCCTTCCAAAATCCTCTCAAAC
Found at i:513909 original size:22 final size:22
Alignment explanation
Indices: 513884--513934 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 22
513874 TTCTCTCAAA
*
513884 CTCTCAATTTCC-TTCCAAAAT
1 CTCTCAATTTCCTTTCAAAAAT
513905 CCTCTCAATTTCCTTTCAAAAAT
1 -CTCTCAATTTCCTTTCAAAAAT
513928 CTCTCAA
1 CTCTCAA
513935 ATCCATATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 19 0.70
23 8 0.30
ACGTcount: A:0.29, C:0.33, G:0.00, T:0.37
Consensus pattern (22 bp):
CTCTCAATTTCCTTTCAAAAAT
Found at i:514002 original size:30 final size:31
Alignment explanation
Indices: 513964--514033 Score: 117
Period size: 31 Copynumber: 2.3 Consensus size: 31
513954 TTCCCCTCAA
*
513964 TTTA-ATTTTTTTAAAATAA-TTTAATTTTT
1 TTTATATTTTTTTAAAATAATTTTAAATTTT
513993 TTTATATTTTTTTAAAATAATTTTAAATTTT
1 TTTATATTTTTTTAAAATAATTTTAAATTTT
514024 TTTATATTTT
1 TTTATATTTT
514034 CATCAATGGC
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
29 4 0.11
30 15 0.39
31 19 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (31 bp):
TTTATATTTTTTTAAAATAATTTTAAATTTT
Found at i:516407 original size:29 final size:30
Alignment explanation
Indices: 516354--516593 Score: 371
Period size: 30 Copynumber: 8.1 Consensus size: 30
516344 ATAAAAATCT
* *
516354 TAATTTAATTAAAAATCGTAAACCCTAACC
1 TAATTTAATTAAAAACCCTAAACCCTAACC
516384 TAATTTAATTAAAAACCCT-AACCCTAACC
1 TAATTTAATTAAAAACCCTAAACCCTAACC
* *
516413 TAATTTAATT-AAAACCCTAAATCATAACC
1 TAATTTAATTAAAAACCCTAAACCCTAACC
*
516442 TAATTTAATTAAAAACCTTAAACCCTAACC
1 TAATTTAATTAAAAACCCTAAACCCTAACC
516472 TAATTTAATTAAAAACCCT-AACCCTAACC
1 TAATTTAATTAAAAACCCTAAACCCTAACC
* *
516501 TAATTTAATT-AAAACCCTAAATCATAACC
1 TAATTTAATTAAAAACCCTAAACCCTAACC
*
516530 TAATTTAATTAAAAACCTTAAACCCTAACC
1 TAATTTAATTAAAAACCCTAAACCCTAACC
*
516560 TAATTTAATTAAAAACCCTAAACCCTAACT
1 TAATTTAATTAAAAACCCTAAACCCTAACC
516590 TAAT
1 TAAT
516594 ATTTTATACT
Statistics
Matches: 191, Mismatches: 15, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
28 16 0.08
29 76 0.40
30 99 0.52
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (30 bp):
TAATTTAATTAAAAACCCTAAACCCTAACC
Found at i:516492 original size:88 final size:88
Alignment explanation
Indices: 516354--516593 Score: 444
Period size: 88 Copynumber: 2.7 Consensus size: 88
516344 ATAAAAATCT
* *
516354 TAATTTAATTAAAAATCGTAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTT
1 TAATTTAATTAAAAACCTTAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTT
516419 AATTAAAACCCTAAATCATAACC
66 AATTAAAACCCTAAATCATAACC
516442 TAATTTAATTAAAAACCTTAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTT
1 TAATTTAATTAAAAACCTTAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTT
516507 AATTAAAACCCTAAATCATAACC
66 AATTAAAACCCTAAATCATAACC
*
516530 TAATTTAATTAAAAACCTTAAACCCTAACCTAATTTAATTAAAAACCCTAAACCCTAACTTAAT
1 TAATTTAATTAAAAACCTTAAACCCTAACCTAATTTAATTAAAAACCCT-AACCCTAACCTAAT
516594 ATTTTATACT
Statistics
Matches: 148, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
88 135 0.91
89 13 0.09
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (88 bp):
TAATTTAATTAAAAACCTTAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTT
AATTAAAACCCTAAATCATAACC
Found at i:516879 original size:27 final size:28
Alignment explanation
Indices: 516840--516907 Score: 68
Period size: 30 Copynumber: 2.4 Consensus size: 28
516830 CGATTTCCTG
* *
516840 AAAAAT-GGACCATTCCGGTAAA-TAAA
1 AAAAATCGGCCCATTCCGATAAATTAAA
* *
516866 AAAAATCGGCCCATTTCGATAAATTTTGAA
1 AAAAATCGGCCCATTCCGATAAA--TTAAA
516896 AAAAATCGGCCC
1 AAAAATCGGCCC
516908 TGTTTTTGGT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
26 6 0.18
27 13 0.38
30 15 0.44
ACGTcount: A:0.44, C:0.19, G:0.15, T:0.22
Consensus pattern (28 bp):
AAAAATCGGCCCATTCCGATAAATTAAA
Found at i:517281 original size:19 final size:19
Alignment explanation
Indices: 517257--517314 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 19
517247 TGTGTATGTT
517257 TTATTAAATTTAAAAAAAA
1 TTATTAAATTTAAAAAAAA
*
517276 TTATTAAA--AAATAAAAAA
1 TTATTAAATTTAA-AAAAAA
* *
517294 TCA-TAATTTTAAAAAAAA
1 TTATTAAATTTAAAAAAAA
517312 TTA
1 TTA
517315 CATATCAAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
17 5 0.16
18 16 0.52
19 10 0.32
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (19 bp):
TTATTAAATTTAAAAAAAA
Found at i:518233 original size:15 final size:15
Alignment explanation
Indices: 518214--518262 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 15
518204 GTATATATAT
518214 ATATTTTAAAATGTA
1 ATATTTTAAAATGTA
* * *
518229 TTATTTT-TAATTTA
1 ATATTTTAAAATGTA
518243 ATATTTTAAAA--TA
1 ATATTTTAAAATGTA
518256 ATATTTT
1 ATATTTT
518263 TTTTTGGTGG
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
13 9 0.32
14 11 0.39
15 8 0.29
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (15 bp):
ATATTTTAAAATGTA
Found at i:541843 original size:52 final size:52
Alignment explanation
Indices: 541765--541868 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
541755 AACAGCTACA
*
541765 ACAAAATATTTTCAGAACTTATGTTATCCGTGGCTATCCAGAGCTCATTGGC
1 ACAAAATATTTTCAGAACTTATGTTATCCATGGCTATCCAGAGCTCATTGGC
541817 ACAAAATATTTTCAGAACTTATGTTATCCATGGCTATCCAGAGCTCATTGGC
1 ACAAAATATTTTCAGAACTTATGTTATCCATGGCTATCCAGAGCTCATTGGC
541869 TATCTATTAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (52 bp):
ACAAAATATTTTCAGAACTTATGTTATCCATGGCTATCCAGAGCTCATTGGC
Found at i:547853 original size:17 final size:18
Alignment explanation
Indices: 547831--547865 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
547821 ATTTAAGATG
*
547831 TAAAATTTTAAAA-ATAA
1 TAAAATTTCAAAATATAA
547848 TAAAATTTCAAAATATAA
1 TAAAATTTCAAAATATAA
547866 AAAGTACAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (18 bp):
TAAAATTTCAAAATATAA
Found at i:547868 original size:16 final size:16
Alignment explanation
Indices: 547831--547895 Score: 53
Period size: 16 Copynumber: 4.0 Consensus size: 16
547821 ATTTAAGATG
* *
547831 TAAAATTTTAAAAATA
1 TAAAAATTTCAAAATA
547847 -ATAAAATTTCAAAATA
1 TA-AAAATTTCAAAATA
* *
547863 TAAAAAGTACAAAA-A
1 TAAAAATTTCAAAATA
547878 TTAAAAATTATCAAAATA
1 -TAAAAATT-TCAAAATA
547896 AAATATAAAG
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
15 2 0.05
16 29 0.76
17 6 0.16
18 1 0.03
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.29
Consensus pattern (16 bp):
TAAAAATTTCAAAATA
Found at i:559549 original size:22 final size:21
Alignment explanation
Indices: 559505--559548 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
559495 ATTTACTACC
*
559505 AACAAATTATAAATTGTTAAA
1 AACAAATTATAAAATGTTAAA
559526 AACATAATTA-AAAATGTTAAA
1 AACA-AATTATAAAATGTTAAA
559547 AA
1 AA
559549 AATTTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.30
Consensus pattern (21 bp):
AACAAATTATAAAATGTTAAA
Found at i:559579 original size:33 final size:30
Alignment explanation
Indices: 559515--559594 Score: 79
Period size: 32 Copynumber: 2.5 Consensus size: 30
559505 AACAAATTAT
**
559515 AAATTGTTAAAAACATAATTAAAAATGTTAAAA
1 AAATT-TTAAAAA-ATAATTAAAAACATT-AAA
559548 AAATTTTAAAAAATAATTATAATAACATTAAA
1 AAATTTTAAAAAATAATTA-AA-AACATTAAA
**
559580 CTATTTTAAAAAATA
1 AAATTTTAAAAAATA
559595 CTAACAATTG
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
31 7 0.17
32 25 0.61
33 9 0.22
ACGTcount: A:0.60, C:0.04, G:0.03, T:0.34
Consensus pattern (30 bp):
AAATTTTAAAAAATAATTAAAAACATTAAA
Found at i:565427 original size:10 final size:10
Alignment explanation
Indices: 565406--565456 Score: 57
Period size: 10 Copynumber: 4.8 Consensus size: 10
565396 AGAAGAGAAT
565406 GAAAAAAGAAA
1 GAAAAAA-AAA
565417 GAAAAAAAAA
1 GAAAAAAAAA
565427 GAAAAATTAAAA
1 GAAAAA--AAAA
* *
565439 GAACATAAAA
1 GAAAAAAAAA
565449 GAAAAAAA
1 GAAAAAAA
565457 TTAAATTGCT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
10 19 0.56
11 7 0.21
12 8 0.24
ACGTcount: A:0.80, C:0.02, G:0.12, T:0.06
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:565432 original size:22 final size:21
Alignment explanation
Indices: 565406--565456 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
565396 AGAAGAGAAT
*
565406 GAAAAAAGAAAGAAAAAAAAA
1 GAAAAAAAAAAGAAAAAAAAA
* * *
565427 GAAAAATTAAAAGAACATAAAA
1 GAAAAA-AAAAAGAAAAAAAAA
565449 GAAAAAAA
1 GAAAAAAA
565457 TTAAATTGCT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.80, C:0.02, G:0.12, T:0.06
Consensus pattern (21 bp):
GAAAAAAAAAAGAAAAAAAAA
Found at i:571455 original size:2 final size:2
Alignment explanation
Indices: 571448--571479 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
571438 TGAATTGATA
571448 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
571480 CAAATATGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:572481 original size:13 final size:13
Alignment explanation
Indices: 572463--572488 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
572453 AATATGTTTG
572463 ATTGTGTTTTGAA
1 ATTGTGTTTTGAA
572476 ATTGTGTTTTGAA
1 ATTGTGTTTTGAA
572489 CTGGTTAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (13 bp):
ATTGTGTTTTGAA
Found at i:577600 original size:11 final size:11
Alignment explanation
Indices: 577586--577612 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
577576 AAAAATAAAT
577586 ACAAAAGTTTC
1 ACAAAAGTTTC
577597 ACAAAAGTTTC
1 ACAAAAGTTTC
577608 ACAAA
1 ACAAA
577613 CTAATTTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.52, C:0.19, G:0.07, T:0.22
Consensus pattern (11 bp):
ACAAAAGTTTC
Found at i:589658 original size:22 final size:21
Alignment explanation
Indices: 589630--589672 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
589620 TGGATTTAAA
589630 TAATTTTAAATTATAATAATTT
1 TAATTTTAAA-TATAATAATTT
*
589652 TAATTTTAAATGTAATAATTT
1 TAATTTTAAATATAATAATTT
589673 ATTTAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
TAATTTTAAATATAATAATTT
Found at i:603113 original size:19 final size:19
Alignment explanation
Indices: 603089--603139 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
603079 GGAAATTATT
*
603089 TAAAAATTATTAAGATTTA-
1 TAAAAATTATTAA-ACTTAC
*
603108 TAAAAA-TATTGAACTTAC
1 TAAAAATTATTAAACTTAC
603126 TAAAAATTATTAAA
1 TAAAAATTATTAAA
603140 AACATCCATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 4 0.15
18 11 0.41
19 12 0.44
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (19 bp):
TAAAAATTATTAAACTTAC
Found at i:618475 original size:16 final size:16
Alignment explanation
Indices: 618454--618523 Score: 104
Period size: 16 Copynumber: 4.4 Consensus size: 16
618444 ATTTTTTCGC
* *
618454 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
* *
618470 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
618486 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
618502 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
618518 TGTAAT
1 TGTAAT
618524 AGCAAATCAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 52 1.00
ACGTcount: A:0.31, C:0.00, G:0.36, T:0.33
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:618991 original size:26 final size:28
Alignment explanation
Indices: 618962--619022 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
618952 TATGAATTTG
*
618962 TATAATTTAA-AATAAT-TATTATTACA
1 TATAATTTAATAATAATATATAATTACA
*
618988 TATAATTTAATAATAATATATAATTTCA
1 TATAATTTAATAATAATATATAATTACA
*
619016 TAAAATT
1 TATAATT
619023 ATTGATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (28 bp):
TATAATTTAATAATAATATATAATTACA
Found at i:619024 original size:91 final size:91
Alignment explanation
Indices: 618928--619107 Score: 272
Period size: 91 Copynumber: 2.0 Consensus size: 91
618918 AATTTAAAAT
* * * *
618928 AATTA-TAACTAATAAATTATCTTATATGAATTTGTATAATTTAAAATAATTATTATTACATATA
1 AATTATTAA-TAATAAATTATCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATA
618992 ATTTAATAATAATATATAATTTCATAA
65 ATTTAATAATAATATATAATTTCATAA
* * *
619019 AATTATTGATAATAATTTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAA
1 AATTATTAATAATAAATTATCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAA
*
619084 TTTAATAATGATATATAATTTCAT
66 TTTAATAATAATATATAATTTCAT
619108 TAATCAGATT
Statistics
Matches: 80, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
91 78 0.98
92 2 0.03
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (91 bp):
AATTATTAATAATAAATTATCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAA
TTTAATAATAATATATAATTTCATAA
Found at i:619025 original size:44 final size:42
Alignment explanation
Indices: 618962--619104 Score: 119
Period size: 44 Copynumber: 3.2 Consensus size: 42
618952 TATGAATTTG
618962 TATAATTTAAAATAATTATTATTACATATAATTTAATAATAATA
1 TATAATTTAAAATAATTATTATTA-ATATAATTTAATAAT-ATA
* ** *
619006 TATAATTTCATAA-AATTATTGA-TAATAATTTTTCTTATATGAATTTA
1 TATAATTT-AAAATAATTATT-ATTAAT-A-TAAT-TTA-AT-AATATA
* *
619053 TACAATTTAAAATAATTAATATTAAATATAATTTAATAATGATA
1 TATAATTTAAAATAATTATTATT-AATATAATTTAATAAT-ATA
619097 TATAATTT
1 TATAATTT
619105 CATTAATCAG
Statistics
Matches: 77, Mismatches: 11, Indels: 22
0.70 0.10 0.20
Matches are distributed among these distances:
43 5 0.06
44 29 0.38
45 9 0.12
46 9 0.12
47 19 0.25
48 6 0.08
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (42 bp):
TATAATTTAAAATAATTATTATTAATATAATTTAATAATATA
Found at i:624161 original size:27 final size:28
Alignment explanation
Indices: 624122--624180 Score: 102
Period size: 27 Copynumber: 2.1 Consensus size: 28
624112 AAAACCTAAG
624122 TTGATTCAGTTGTCAAATATGAAGCGAC
1 TTGATTCAGTTGTCAAATATGAAGCGAC
*
624150 TTGA-TCAGTTGTCAAATATTAAGCGAC
1 TTGATTCAGTTGTCAAATATGAAGCGAC
624177 TTGA
1 TTGA
624181 ACAAGTCGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 26 0.87
28 4 0.13
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (28 bp):
TTGATTCAGTTGTCAAATATGAAGCGAC
Found at i:624558 original size:31 final size:32
Alignment explanation
Indices: 624523--624584 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
624513 AATAAAAAAA
624523 TGCTCCTAGGCACAAGCTTAAACTG-TCACAT
1 TGCTCCTAGGCACAAGCTTAAACTGTTCACAT
* * *
624554 TGCTCCTAGTCACGAGCTTAAATTGTTCACA
1 TGCTCCTAGGCACAAGCTTAAACTGTTCACA
624585 CATAATAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 22 0.81
32 5 0.19
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.29
Consensus pattern (32 bp):
TGCTCCTAGGCACAAGCTTAAACTGTTCACAT
Found at i:625064 original size:14 final size:15
Alignment explanation
Indices: 625045--625074 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
625035 TATAATAATG
625045 ATAATAGTTA-TATA
1 ATAATAGTTAGTATA
625059 ATAATAGTTAGTATA
1 ATAATAGTTAGTATA
625074 A
1 A
625075 AAAAAAGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (15 bp):
ATAATAGTTAGTATA
Found at i:626881 original size:6 final size:6
Alignment explanation
Indices: 626870--626896 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
626860 CTATTAATAC
626870 GACTCG GACTCG GACTCG GACTCG GAC
1 GACTCG GACTCG GACTCG GACTCG GAC
626897 GGATACACAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.33, G:0.33, T:0.15
Consensus pattern (6 bp):
GACTCG
Found at i:627023 original size:37 final size:40
Alignment explanation
Indices: 626927--627066 Score: 124
Period size: 40 Copynumber: 3.5 Consensus size: 40
626917 AACACACCAG
* **
626927 TTTGGCACCCAGTGCCTCATCAGATAATTCGAAGTAATAA
1 TTTGGCACCCAGTGCCTCATCGGATAAACCGAAGTAATAA
* * *
626967 TTTGACACCCAGTGTCTCATCGGTTAAACCGAAGT-A-AA
1 TTTGGCACCCAGTGCCTCATCGGATAAACCGAAGTAATAA
* * * * *
627005 -TTGGCACCCAATGCCTCATCGAATTAATCTGAAGTAGTAA
1 TTTGGCACCCAGTGCCTCATCGGA-TAAACCGAAGTAATAA
* * *
627045 ATTGACACCCAGTGTCTCATCG
1 TTTGGCACCCAGTGCCTCATCG
627067 ACTCGAAGTA
Statistics
Matches: 79, Mismatches: 17, Indels: 7
0.77 0.17 0.07
Matches are distributed among these distances:
37 18 0.23
38 11 0.14
39 1 0.01
40 31 0.39
41 18 0.23
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (40 bp):
TTTGGCACCCAGTGCCTCATCGGATAAACCGAAGTAATAA
Found at i:628073 original size:7 final size:7
Alignment explanation
Indices: 628063--628122 Score: 54
Period size: 7 Copynumber: 8.7 Consensus size: 7
628053 TTCTTATATA
628063 ATATAAT
1 ATATAAT
628070 ATATAAT
1 ATATAAT
*
628077 ATATACT
1 ATATAAT
*
628084 -TA-AAC
1 ATATAAT
*
628089 AT-TAAG
1 ATATAAT
628095 ATATAAT
1 ATATAAT
628102 ATTATAAT
1 A-TATAAT
628110 ATTATAAT
1 A-TATAAT
628118 ATATA
1 ATATA
628123 TTTTAACTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
5 1 0.02
6 7 0.16
7 21 0.48
8 15 0.34
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (7 bp):
ATATAAT
Found at i:635043 original size:23 final size:22
Alignment explanation
Indices: 634992--635043 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
634982 CTTTGTCTTT
*
634992 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
635014 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
635037 TTCTTTT
1 TTCTTTT
635044 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:641007 original size:44 final size:44
Alignment explanation
Indices: 640958--641212 Score: 351
Period size: 44 Copynumber: 5.9 Consensus size: 44
640948 ATAAATCGAG
* * *
640958 AGGATAGATACATGGCAAAAACGGGAGCAAGATAACTTTTAATC
1 AGGATAGATACAAGGCAAAAACTGGAGCAAGATAGCTTTTAATC
* *
641002 AGGATAGACACAAGGCAAAAACTGGAGCAAGATGGCTTTTAATC
1 AGGATAGATACAAGGCAAAAACTGGAGCAAGATAGCTTTTAATC
*
641046 AGGATAGACACAAGGC--AAACTGGAGCAAGATAGCTTTTAATC
1 AGGATAGATACAAGGCAAAAACTGGAGCAAGATAGCTTTTAATC
* *
641088 GGGATAGATACATA-GCAAAAACTGGAGCAAGATTGCTTTTAATC
1 AGGATAGATACA-AGGCAAAAACTGGAGCAAGATAGCTTTTAATC
* *
641132 AGGATAGATACAAGGC--AAAGTAGAGCAAGATAGCTTTTAATC
1 AGGATAGATACAAGGCAAAAACTGGAGCAAGATAGCTTTTAATC
*
641174 AGGATAGATACATA-GCAAAAACTGGAGCAAGATTGCTTT
1 AGGATAGATACA-AGGCAAAAACTGGAGCAAGATAGCTTT
641213 AAACCAAAGA
Statistics
Matches: 188, Mismatches: 16, Indels: 14
0.86 0.07 0.06
Matches are distributed among these distances:
42 74 0.39
43 3 0.02
44 111 0.59
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.21
Consensus pattern (44 bp):
AGGATAGATACAAGGCAAAAACTGGAGCAAGATAGCTTTTAATC
Found at i:641083 original size:86 final size:86
Alignment explanation
Indices: 640958--641212 Score: 395
Period size: 86 Copynumber: 2.9 Consensus size: 86
640948 ATAAATCGAG
* * * *
640958 AGGATAGATACATGGCAAAAACGGGAGCAAGATAACTTTTAATCAGGATAGACACA-AGGCAAAA
1 AGGATAGATACAAGGC--AAACTGGAGCAAGATAGCTTTTAATCAGGATAGATACATA-GCAAAA
*
641022 ACTGGAGCAAGATGGCTTTTAATC
63 ACTGGAGCAAGATTGCTTTTAATC
* *
641046 AGGATAGACACAAGGCAAACTGGAGCAAGATAGCTTTTAATCGGGATAGATACATAGCAAAAACT
1 AGGATAGATACAAGGCAAACTGGAGCAAGATAGCTTTTAATCAGGATAGATACATAGCAAAAACT
641111 GGAGCAAGATTGCTTTTAATC
66 GGAGCAAGATTGCTTTTAATC
* *
641132 AGGATAGATACAAGGCAAAGTAGAGCAAGATAGCTTTTAATCAGGATAGATACATAGCAAAAACT
1 AGGATAGATACAAGGCAAACTGGAGCAAGATAGCTTTTAATCAGGATAGATACATAGCAAAAACT
641197 GGAGCAAGATTGCTTT
66 GGAGCAAGATTGCTTT
641213 AAACCAAAGA
Statistics
Matches: 155, Mismatches: 11, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
86 140 0.90
87 1 0.01
88 14 0.09
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.21
Consensus pattern (86 bp):
AGGATAGATACAAGGCAAACTGGAGCAAGATAGCTTTTAATCAGGATAGATACATAGCAAAAACT
GGAGCAAGATTGCTTTTAATC
Found at i:641196 original size:130 final size:129
Alignment explanation
Indices: 640959--641212 Score: 368
Period size: 130 Copynumber: 2.0 Consensus size: 129
640949 TAAATCGAGA
*
640959 GGATAGATACATGGCAAAAACGGGAGCAAGATAACTTTTAATCAGGATAGACACAAGGCAAAAAC
1 GGATAGATACATAGCAAAAACGGGAGCAAGATAACTTTTAATCAGGATAGACACAAGGC-AAAAC
* *
641024 TGGAGCAAGATGGCTTTTAATCAGGATAGACACAAGGCAAACTGGAGCAAGATAGCTTTTAATCG
65 TAGAGCAAGATAGCTTTTAATCAGGATAGACACAAGGCAAACTGGAGCAAGATAGCTTTTAATCG
* ** * *
641089 GGATAGATACATAGCAAAAACTGGAGCAAGATTGCTTTTAATCAGGATAGATACAAGGC-AAAGT
1 GGATAGATACATAGCAAAAACGGGAGCAAGATAACTTTTAATCAGGATAGACACAAGGCAAAACT
* *
641153 AGAGCAAGATAGCTTTTAATCAGGATAGATACATA-GCAAAAACTGGAGCAAGATTGCTTT
66 AGAGCAAGATAGCTTTTAATCAGGATAGACACA-AGGC--AAACTGGAGCAAGATAGCTTT
641213 AAACCAAAGA
Statistics
Matches: 111, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
128 36 0.32
129 1 0.01
130 74 0.67
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.21
Consensus pattern (129 bp):
GGATAGATACATAGCAAAAACGGGAGCAAGATAACTTTTAATCAGGATAGACACAAGGCAAAACT
AGAGCAAGATAGCTTTTAATCAGGATAGACACAAGGCAAACTGGAGCAAGATAGCTTTTAATCG
Found at i:641280 original size:18 final size:18
Alignment explanation
Indices: 641257--641303 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
641247 ATTTAAATTG
*
641257 CGGTCGCGGTCGCATTTT
1 CGGTCGCGGTCGCAGTTT
641275 CGGTCGC-GTCGC-GTTT
1 CGGTCGCGGTCGCAGTTT
641291 --GTCGCGGTCGCAG
1 CGGTCGCGGTCGCAG
641304 ACATAACGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 5 0.19
15 5 0.19
16 4 0.15
17 5 0.19
18 7 0.27
ACGTcount: A:0.04, C:0.30, G:0.38, T:0.28
Consensus pattern (18 bp):
CGGTCGCGGTCGCAGTTT
Found at i:642874 original size:22 final size:22
Alignment explanation
Indices: 642841--642896 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
642831 ATTTCCTCTC
642841 AATTCCTCTCAATTTCCTTCCAA
1 AATT-CTCTCAATTTCCTTCCAA
642864 AATTCTCTCAATTTCCTTCCAA
1 AATTCTCTCAATTTCCTTCCAA
642886 AATTCTCTCAA
1 AATTCTCTCAA
642897 ATCTATATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 29 0.88
23 4 0.12
ACGTcount: A:0.29, C:0.32, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTCTCTCAATTTCCTTCCAA
Found at i:642925 original size:51 final size:51
Alignment explanation
Indices: 642868--642983 Score: 205
Period size: 51 Copynumber: 2.3 Consensus size: 51
642858 TTCCAAAATT
* *
642868 CTCTCAATTTCCTTCCAAAATTCTCTCAAATCTATATTTAATTTCAATTTC
1 CTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
642919 CTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
1 CTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
*
642970 TTCTCAATTTCCTT
1 CTCTCAATTTCCTT
642984 TTTTAAAATA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 62 1.00
ACGTcount: A:0.28, C:0.26, G:0.00, T:0.46
Consensus pattern (51 bp):
CTCTCAATTTCCTTCAAAAATTCTCTCAAATCCATATTTAATTTCAATTTC
Found at i:644806 original size:18 final size:18
Alignment explanation
Indices: 644780--644814 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
644770 AGGTGTGTTT
*
644780 CCTAGCCCTTATATGTAC
1 CCTAACCCTTATATGTAC
644798 CCTAACCCTTATATGTA
1 CCTAACCCTTATATGTA
644815 TCCTTTTCCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.31, G:0.09, T:0.34
Consensus pattern (18 bp):
CCTAACCCTTATATGTAC
Found at i:645039 original size:29 final size:30
Alignment explanation
Indices: 644992--645091 Score: 98
Period size: 29 Copynumber: 3.7 Consensus size: 30
644982 CCCTAAACCC
644992 TTAATTAAAAACCCT-AACCTTAACCTAAT
1 TTAATTAAAAACCCTAAACCTTAACCTAAT
645021 TTAATT-AAAACCCTAAA-C----CC----
1 TTAATTAAAAACCCTAAACCTTAACCTAAT
*
645041 TTAATTAAAAACCCTAA-CCCTAACCTAAT
1 TTAATTAAAAACCCTAAACCTTAACCTAAT
*
645070 TCAATTAAAAACCCTAAACCTT
1 TTAATTAAAAACCCTAAACCTT
645092 TAACTTAAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 23
0.70 0.02 0.28
Matches are distributed among these distances:
20 6 0.11
21 11 0.19
24 2 0.04
25 2 0.04
28 9 0.16
29 24 0.42
30 3 0.05
ACGTcount: A:0.45, C:0.27, G:0.00, T:0.28
Consensus pattern (30 bp):
TTAATTAAAAACCCTAAACCTTAACCTAAT
Found at i:645051 original size:21 final size:19
Alignment explanation
Indices: 645021--645061 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
645011 TTAACCTAAT
645021 TTAATTAAAACCCTAAACCC
1 TTAATTAAAACCCT-AACCC
645041 TTAATTAAAAACCCTAACCC
1 TTAATT-AAAACCCTAACCC
645061 T
1 T
645062 AACCTAATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.44, C:0.29, G:0.00, T:0.27
Consensus pattern (19 bp):
TTAATTAAAACCCTAACCC
Found at i:645083 original size:23 final size:23
Alignment explanation
Indices: 645056--645269 Score: 344
Period size: 23 Copynumber: 9.3 Consensus size: 23
645046 TAAAAACCCT
*
645056 AACCCTAACCTAATTCAATTAAA
1 AACCCTAACCTAATTTAATTAAA
645079 AACCCTAAACC---TTTAACTTAAA
1 AACCCT-AACCTAATTTAA-TTAAA
645101 AACCCTAACCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
*
645124 AACCCTAGCCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
*
645147 AACCTTAACCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
645170 AACCCTAACCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
*
645193 AACCCTAGCCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
645216 AACCCTAACCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
*
645239 AACCCTAGCCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
645262 AACCCTAA
1 AACCCTAA
645270 ACCCTTAACT
Statistics
Matches: 177, Mismatches: 9, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.05
22 11 0.06
23 149 0.84
24 9 0.05
ACGTcount: A:0.46, C:0.23, G:0.01, T:0.29
Consensus pattern (23 bp):
AACCCTAACCTAATTTAATTAAA
Found at i:645183 original size:69 final size:69
Alignment explanation
Indices: 645007--645268 Score: 349
Period size: 69 Copynumber: 3.8 Consensus size: 69
644997 TAAAAACCCT
*
645007 AACCTTAACCTAATTTAATT-AAAACCCTAAACCCTTAA-TTAA--AAACCCTAACCCTAACCTA
1 AACCTTAACCTAATTTAATTAAAAACCCT-AA-CC-TAATTTAATTAAA----AACCCTAGCCTA
*
645068 ATTCAATTAAA
59 ATTTAATTAAA
*
645079 AACCCTAAACC---TTTAACTTAAAAACCCTAACCTAATTTAATTAAAAACCCTAGCCTAATTTA
1 AA-CCTTAACCTAATTTAA-TTAAAAACCCTAACCTAATTTAATTAAAAACCCTAGCCTAATTTA
645141 ATTAAA
64 ATTAAA
645147 AACCTTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAGCCTAATTTAAT
1 AACCTTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAGCCTAATTTAAT
645212 TAAA
66 TAAA
* *
645216 AACCCTAACCTAATTTAATTAAAAACCCTAGCCTAATTTAATTAAAAACCCTA
1 AACCTTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTA
645269 AACCCTTAAC
Statistics
Matches: 175, Mismatches: 6, Indels: 21
0.87 0.03 0.10
Matches are distributed among these distances:
67 7 0.04
68 23 0.13
69 105 0.60
70 16 0.09
71 4 0.02
72 13 0.07
73 7 0.04
ACGTcount: A:0.46, C:0.24, G:0.01, T:0.29
Consensus pattern (69 bp):
AACCTTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAGCCTAATTTAAT
TAAA
Found at i:645283 original size:23 final size:21
Alignment explanation
Indices: 645257--645299 Score: 68
Period size: 23 Copynumber: 2.0 Consensus size: 21
645247 CCTAATTTAA
645257 TTAAAAACCCTAAACCCTTAACT
1 TTAAAAACCCT-AA-CCTTAACT
645280 TTAAAAACCCTAACCTTAAC
1 TTAAAAACCCTAACCTTAAC
645300 GTAATGTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 7 0.35
22 2 0.10
23 11 0.55
ACGTcount: A:0.44, C:0.30, G:0.00, T:0.26
Consensus pattern (21 bp):
TTAAAAACCCTAACCTTAACT
Found at i:645284 original size:46 final size:46
Alignment explanation
Indices: 644967--645295 Score: 311
Period size: 46 Copynumber: 7.0 Consensus size: 46
644957 TCGCCGTTCT
** *
644967 TAATTTAATTAAAAACCCTAAACCCTTAATTAAAAACCCTAACCTTAACC
1 TAATTTAATTAAAAACCCTAAACCCTTAATTTTAAA----AACCCTAACC
**
645017 TAATTTAATT-AAAACCCTAAACCCTTAATTAAAAACCCTAACCCTAACC
1 TAATTTAATTAAAAACCCTAAACCCTTAATTTTAAA----AACCCTAACC
* * *
645066 TAATTCAATTAAAAACCCTAAACCTTTAA-CTTAAAAACCCTAACC
1 TAATTTAATTAAAAACCCTAAACCCTTAATTTTAAAAACCCTAACC
* *
645111 TAATTTAATTAAAAACCCT--AGCC-TAATTTAATTAAAAACCTTAACC
1 TAATTTAATTAAAAACCCTAAACCCTTAA-TT--TTAAAAACCCTAACC
*
645157 TAATTTAATTAAAAACCCT-AA-CC-TAATTTAATTAAAAACCCTAGCC
1 TAATTTAATTAAAAACCCTAAACCCTTAA-TT--TTAAAAACCCTAACC
*
645203 TAATTTAATTAAAAACCCT-AA-CC-TAATTTAATTAAAAACCCTAGCC
1 TAATTTAATTAAAAACCCTAAACCCTTAA-TT--TTAAAAACCCTAACC
*
645249 TAATTTAATTAAAAACCCTAAACCCTTAACTTTAAAAACCCTAACC
1 TAATTTAATTAAAAACCCTAAACCCTTAATTTTAAAAACCCTAACC
645295 T
1 T
645296 TAACGTAATG
Statistics
Matches: 255, Mismatches: 15, Indels: 22
0.87 0.05 0.08
Matches are distributed among these distances:
42 3 0.01
43 2 0.01
45 28 0.11
46 136 0.53
47 3 0.01
48 3 0.01
49 53 0.21
50 27 0.11
ACGTcount: A:0.46, C:0.24, G:0.01, T:0.29
Consensus pattern (46 bp):
TAATTTAATTAAAAACCCTAAACCCTTAATTTTAAAAACCCTAACC
Found at i:645284 original size:69 final size:69
Alignment explanation
Indices: 644967--645295 Score: 297
Period size: 69 Copynumber: 4.7 Consensus size: 69
644957 TCGCCGTTCT
** *
644967 TAATTTAATTAAAAACCCTAAACCCTTAAT-TAAAAACCCTAACCTTAACCTAATTTAATT-AAA
1 TAATTTAATTAAAAACCCT-AACCCTTAATCTTTAAA----AACCCTAACCTAATTTAATTAAAA
645030 ACCCTAAACC
61 ACCCT-AACC
* *
645040 ---CTTAATTAAAAACCCTAACCCTAACCTAATTCAATTAAAAACCCTAAACC---TTTAACTTA
1 TAATTTAATTAAAAACCCTAACCCT----TAA-TC-TTTAAAAACCCT-AACCTAATTTAA-TTA
645099 AAAACCCTAACC
58 AAAACCCTAACC
* * *
645111 TAATTTAATTAAAAACCCT-AGCC-TAATTTAATTAAAAACCTTAACCTAATTTAATTAAAAACC
1 TAATTTAATTAAAAACCCTAACCCTTAATCT--TTAAAAACCCTAACCTAATTTAATTAAAAACC
645174 CTAACC
64 CTAACC
* *
645180 TAATTTAATTAAAAACCCT-AGCC-TAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACC
1 TAATTTAATTAAAAACCCTAACCCTTAATCT--TTAAAAACCCTAACCTAATTTAATTAAAAACC
*
645243 CTAGCC
64 CTAACC
645249 TAATTTAATTAAAAACCCTAAACCCTTAA-CTTTAAAAACCCTAACCT
1 TAATTTAATTAAAAACCCT-AACCCTTAATCTTTAAAAACCCTAACCT
645296 TAACGTAATG
Statistics
Matches: 221, Mismatches: 14, Indels: 46
0.79 0.05 0.16
Matches are distributed among these distances:
67 5 0.02
68 13 0.06
69 123 0.56
70 25 0.11
71 10 0.05
72 16 0.07
73 10 0.05
74 16 0.07
76 3 0.01
ACGTcount: A:0.46, C:0.24, G:0.01, T:0.29
Consensus pattern (69 bp):
TAATTTAATTAAAAACCCTAACCCTTAATCTTTAAAAACCCTAACCTAATTTAATTAAAAACCCT
AACC
Found at i:645436 original size:116 final size:116
Alignment explanation
Indices: 645301--645518 Score: 391
Period size: 116 Copynumber: 1.9 Consensus size: 116
645291 AACCTTAACG
*
645301 TAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAAATAATAATTTTACATAATTTGATA
1 TAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAAATAATAATTGTACATAATTTGATA
* *
645366 ATTTTACTAACCATTAATATAATTTTTTGACTTAATAATTTTACATTCACA
66 ATTTTACTAACCATTAATACAATTTTTTGACGTAATAATTTTACATTCACA
* *
645417 TAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAATAATTGTATATAATTTGATA
1 TAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAAATAATAATTGTACATAATTTGATA
645482 ATTTTACTAACCATTAATACAATTTTTTGACGTAATA
66 ATTTTACTAACCATTAATACAATTTTTTGACGTAATA
645519 CAATTTATCA
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
116 97 1.00
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.43
Consensus pattern (116 bp):
TAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAAATAATAATTGTACATAATTTGATA
ATTTTACTAACCATTAATACAATTTTTTGACGTAATAATTTTACATTCACA
Done.