Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 93 of 190
Found at i:27698647 original size:20 final size:20
Alignment explanation
Indices: 27698622--27698686 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
27698612 TACGAGATTT
*
27698622 ACACTTCGGTTTCCCTGTTC
1 ACACTTCGGTGTCCCTGTTC
* * *
27698642 ACACTTCAGTGCCCCTATAT-
1 ACACTTCGGTGTCCCTGT-TC
*
27698662 ACACTTCGGTGTCCTTGTTC
1 ACACTTCGGTGTCCCTGTTC
27698682 ACACT
1 ACACT
27698687 ACGATGCCCT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
19 1 0.03
20 33 0.94
21 1 0.03
ACGTcount: A:0.17, C:0.34, G:0.14, T:0.35
Consensus pattern (20 bp):
ACACTTCGGTGTCCCTGTTC
Found at i:27700122 original size:12 final size:13
Alignment explanation
Indices: 27700105--27700133 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
27700095 ATTTACACAA
27700105 CCTAGCACAT-GG
1 CCTAGCACATAGG
27700117 CCTAGCACATAGG
1 CCTAGCACATAGG
27700130 CCTA
1 CCTA
27700134 TGTGGTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.28, C:0.34, G:0.21, T:0.17
Consensus pattern (13 bp):
CCTAGCACATAGG
Found at i:27700225 original size:12 final size:12
Alignment explanation
Indices: 27700208--27700234 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
27700198 TCAGAGAGTT
27700208 ACACGGGTGAGG
1 ACACGGGTGAGG
27700220 ACACGGGTGAGG
1 ACACGGGTGAGG
27700232 ACA
1 ACA
27700235 GAAGCTAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.19, G:0.44, T:0.07
Consensus pattern (12 bp):
ACACGGGTGAGG
Found at i:27700367 original size:121 final size:121
Alignment explanation
Indices: 27700139--27700419 Score: 393
Period size: 121 Copynumber: 2.3 Consensus size: 121
27700129 GCCTATGTGG
** * *
27700139 TTATTTCGAGAGTTACACGACCTAGCGCACGGGCGTGTGGTTTGGCCGTGTGACCAAACTCAGAG
1 TTATTTCGATTGTTACACGGCCTGGCGCACGGGCGTGTGGTTTGGCCGTGTGACCAAACTCAGAG
* * *
27700204 AGTTACACGGGTGAGGACACGGGTGAGGACAGAAGCTAGGACATGAACATCTGTCC
66 AGTTACACGGGTGAGGACACGGATGAAGACACAAGCTAGGACATGAACATCTGTCC
*
27700260 TTATTTCGATTGTTACACGGCCTGGCGTACGGGCGTGTGGTTTGGCCGTGTGACCAAACTCAGAG
1 TTATTTCGATTGTTACACGGCCTGGCGCACGGGCGTGTGGTTTGGCCGTGTGACCAAACTCAGAG
* * * * * *
27700325 AGTTACATGGGTGAGGACTCGGATGAAGACACAAGTTGGGACATGAACGTGTGTCC
66 AGTTACACGGGTGAGGACACGGATGAAGACACAAGCTAGGACATGAACATCTGTCC
* * *
27700381 TTACTTCAATTGTTACACGGCCTGAG-ACACGGGCGTGTG
1 TTATTTCGATTGTTACACGGCCTG-GCGCACGGGCGTGTG
27700420 TCTCAACTGT
Statistics
Matches: 141, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
121 140 0.99
122 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.24
Consensus pattern (121 bp):
TTATTTCGATTGTTACACGGCCTGGCGCACGGGCGTGTGGTTTGGCCGTGTGACCAAACTCAGAG
AGTTACACGGGTGAGGACACGGATGAAGACACAAGCTAGGACATGAACATCTGTCC
Found at i:27702329 original size:26 final size:26
Alignment explanation
Indices: 27702293--27702369 Score: 93
Period size: 26 Copynumber: 2.9 Consensus size: 26
27702283 TTTGAGGTCA
27702293 GGCGAGCTGGTGTTCGTAGTAGGAC-T
1 GGCGAGCTGGTGTTCGTAGTAGG-CTT
* * *
27702319 GGCGAGTTGGTATTTGTAGTAGGCTT
1 GGCGAGCTGGTGTTCGTAGTAGGCTT
*
27702345 GACGAGCTGGTGTTCGTCAGTAGGC
1 GGCGAGCTGGTGTTCGT-AGTAGGC
27702370 CAGACAAGTA
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
25 1 0.02
26 34 0.81
27 7 0.17
ACGTcount: A:0.16, C:0.14, G:0.40, T:0.30
Consensus pattern (26 bp):
GGCGAGCTGGTGTTCGTAGTAGGCTT
Found at i:27705450 original size:18 final size:19
Alignment explanation
Indices: 27705427--27705466 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
27705417 TAAATGTTTC
27705427 TCATTTCACTT-TTTCTAT
1 TCATTTCACTTATTTCTAT
*
27705445 TCATTTCATTTATTTCTAT
1 TCATTTCACTTATTTCTAT
27705464 TCA
1 TCA
27705467 AACACACAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (19 bp):
TCATTTCACTTATTTCTAT
Found at i:27718619 original size:27 final size:26
Alignment explanation
Indices: 27718589--27718759 Score: 157
Period size: 27 Copynumber: 6.3 Consensus size: 26
27718579 CCCAATATTT
* * *
27718589 GTAAAATGACCGTAATCCCCCTGTAGG
1 GTAAAATGATCGAAAT-CCCCTGAAGG
* * * *
27718616 GTAAAATGACCAAAATACCCTAGAACG
1 GTAAAATGATCGAAATCCCCT-GAAGG
27718643 GTAAAATGATCGAAATACCCCTGAAGG
1 GTAAAATGATCGAAAT-CCCCTGAAGG
* *
27718670 GTAAAATGATCGAAATACCCTCAAAGG
1 GTAAAATGATCGAAATCCCCT-GAAGG
* *
27718697 GTAAAATGATCGAAATACCCTCAAAGG
1 GTAAAATGATCGAAATCCCCT-GAAGG
27718724 GTAAAATGATCGAAAAATCCCC--ATAGG
1 GTAAAATGATCG--AAATCCCCTGA-AGG
27718751 GTAAAATGA
1 GTAAAATGA
27718760 CTGTAATGCC
Statistics
Matches: 126, Mismatches: 12, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
26 9 0.07
27 106 0.84
28 4 0.03
29 7 0.06
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.19
Consensus pattern (26 bp):
GTAAAATGATCGAAATCCCCTGAAGG
Found at i:27718733 original size:54 final size:54
Alignment explanation
Indices: 27718589--27718759 Score: 195
Period size: 54 Copynumber: 3.2 Consensus size: 54
27718579 CCCAATATTT
* * * ** * * *
27718589 GTAAAATGACCGTAATCCCCCTGTAGGGTAAAATGACCAAAATACCCT-AGAACG
1 GTAAAATGATCGAAATACCCCTAAAGGGTAAAATGATCGAAATACCCTCA-AAGG
*
27718643 GTAAAATGATCGAAATACCCCTGAAGGGTAAAATGATCGAAATACCCTCAAAGG
1 GTAAAATGATCGAAATACCCCTAAAGGGTAAAATGATCGAAATACCCTCAAAGG
* *
27718697 GTAAAATGATCGAAATA-CCCTCAAAGGGTAAAATGATCGAAAAATCCC-CATAGG
1 GTAAAATGATCGAAATACCCCT-AAAGGGTAAAATGATCGAAATA-CCCTCAAAGG
27718751 GTAAAATGA
1 GTAAAATGA
27718760 CTGTAATGCC
Statistics
Matches: 104, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
53 4 0.04
54 96 0.92
55 4 0.04
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.19
Consensus pattern (54 bp):
GTAAAATGATCGAAATACCCCTAAAGGGTAAAATGATCGAAATACCCTCAAAGG
Found at i:27718782 original size:81 final size:79
Alignment explanation
Indices: 27718589--27718784 Score: 209
Period size: 81 Copynumber: 2.4 Consensus size: 79
27718579 CCCAATATTT
*
27718589 GTAAAATGACCGTAATCCCCCTGTAGGGTAAAATGACCAAAATACCCTAGAACGGTAAAATGATC
1 GTAAAATGACTGTAAT-CCCCTGTAGGGTAAAATGACCAAAATACCCTAGAACGGTAAAATGATC
*
27718654 GAAATACCCCTGAAGG
65 GAAAAACCCCT-AAGG
* * ** * * *
27718670 GTAAAATGA-TCGAAATACCCTCAAAGGGTAAAATGATCGAAATACCCTCA-AAGGGTAAAATGA
1 GTAAAATGACT-GTAATCCCCT-GTAGGGTAAAATGACCAAAATACCCT-AGAACGGTAAAATGA
27718733 TCGAAAAATCCCC-ATAGG
63 TCGAAAAA-CCCCTA-AGG
*
27718751 GTAAAATGACTGTAATGCCCCTGTAGAGTAAAAT
1 GTAAAATGACTGTAAT-CCCCTGTAGGGTAAAAT
27718785 CCCCATAGGG
Statistics
Matches: 94, Mismatches: 14, Indels: 14
0.77 0.11 0.11
Matches are distributed among these distances:
80 5 0.05
81 79 0.84
82 10 0.11
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.20
Consensus pattern (79 bp):
GTAAAATGACTGTAATCCCCTGTAGGGTAAAATGACCAAAATACCCTAGAACGGTAAAATGATCG
AAAAACCCCTAAGG
Found at i:27718825 original size:43 final size:43
Alignment explanation
Indices: 27718737--27718827 Score: 112
Period size: 43 Copynumber: 2.1 Consensus size: 43
27718727 AAATGATCGA
* ** *
27718737 AAAATCCCCATAGGGTAAAATGACTGTAATGCCCCTGTAGAGT
1 AAAATCCCCATAGGGTAAAATGACTGAAATAACCCTATAGAGT
* *
27718780 AAAATCCCCATAGGGTTAAATGACTGAAATAACCTTATA-AGGT
1 AAAATCCCCATAGGGTAAAATGACTGAAATAACCCTATAGA-GT
27718823 AAAAT
1 AAAAT
27718828 GTCTGTAATG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
42 1 0.02
43 40 0.98
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.24
Consensus pattern (43 bp):
AAAATCCCCATAGGGTAAAATGACTGAAATAACCCTATAGAGT
Found at i:27718904 original size:24 final size:24
Alignment explanation
Indices: 27718873--27718969 Score: 106
Period size: 24 Copynumber: 4.0 Consensus size: 24
27718863 ACCCCTCGAG
* *
27718873 TGTAAATGATTGATTTGTCCGTGA
1 TGTAAATGACTGATTTGTCTGTGA
* *
27718897 TGTAAATGAGTGATTTATCTGTGA
1 TGTAAATGACTGATTTGTCTGTGA
* *
27718921 TTTAAATGACTAATTTGTCTGTGA
1 TGTAAATGACTGATTTGTCTGTGA
* *
27718945 T-TAGTATAACTGATTTGTCTGTGA
1 TGTA-AATGACTGATTTGTCTGTGA
27718969 T
1 T
27718970 TTGTATTACT
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
23 2 0.03
24 60 0.97
ACGTcount: A:0.27, C:0.07, G:0.22, T:0.44
Consensus pattern (24 bp):
TGTAAATGACTGATTTGTCTGTGA
Found at i:27719200 original size:32 final size:32
Alignment explanation
Indices: 27719155--27719309 Score: 174
Period size: 32 Copynumber: 4.9 Consensus size: 32
27719145 GCTGCGATGC
**
27719155 TACTGATGGCTTTGTGTTGATCATATTATCGT
1 TACTGATGGCTTTGTGCCGATCATATTATCGT
*
27719187 TACTGATGACTTTGTGCCGATCATATTA-CTGT
1 TACTGATGGCTTTGTGCCGATCATATTATC-GT
*
27719219 TACTAATGGCTTTGTGCCGATCATATTATCG-
1 TACTGATGGCTTTGTGCCGATCATATTATCGT
* * * *
27719250 TACTGATAG-TTATGTGCCGGTCATATCA-CTGC
1 TACTGATGGCTT-TGTGCCGATCATATTATC-GT
*
27719282 TACTGATGGCTTTGTGCCAATCATATTA
1 TACTGATGGCTTTGTGCCGATCATATTA
27719310 CTGTACTTAT
Statistics
Matches: 104, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
30 3 0.03
31 23 0.22
32 75 0.72
33 3 0.03
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATATTATCGT
Found at i:27719291 original size:63 final size:64
Alignment explanation
Indices: 27719152--27719309 Score: 221
Period size: 63 Copynumber: 2.5 Consensus size: 64
27719142 TTTGCTGCGA
** *
27719152 TGCTACTGATGGCTTTGTGTTGATCATATTATCGTTACTGATGACTTTGTGCCGATCATATTAC
1 TGCTACTGATGGCTTTGTGCCGATCATATTATCGTTACTGATGACTTTGTGCCGATCATATCAC
* * * *
27719216 TGTTACTAATGGCTTTGTGCCGATCATATTATCG-TACTGAT-AGTTATGTGCCGGTCATATCAC
1 TGCTACTGATGGCTTTGTGCCGATCATATTATCGTTACTGATGACTT-TGTGCCGATCATATCAC
*
27719279 TGCTACTGATGGCTTTGTGCCAATCATATTA
1 TGCTACTGATGGCTTTGTGCCGATCATATTA
27719310 CTGTACTTAT
Statistics
Matches: 83, Mismatches: 10, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
62 3 0.04
63 50 0.60
64 30 0.36
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (64 bp):
TGCTACTGATGGCTTTGTGCCGATCATATTATCGTTACTGATGACTTTGTGCCGATCATATCAC
Found at i:27719341 original size:22 final size:22
Alignment explanation
Indices: 27719316--27719365 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
27719306 ATTACTGTAC
* *
27719316 TTATGGATTGTAGCCATTCTGT
1 TTATGGATTATAGCCATCCTGT
* * *
27719338 TTATAGCTTATAGCTATCCTGT
1 TTATGGATTATAGCCATCCTGT
27719360 TTATGG
1 TTATGG
27719366 CTCTTAGTCA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.20, C:0.14, G:0.20, T:0.46
Consensus pattern (22 bp):
TTATGGATTATAGCCATCCTGT
Found at i:27719609 original size:46 final size:46
Alignment explanation
Indices: 27719540--27719627 Score: 124
Period size: 46 Copynumber: 1.9 Consensus size: 46
27719530 ATTGTTGCAT
* * *
27719540 TTCTATTACTGATTCTGTCACTGTATTGGGCTTAGGCCCACATGTA
1 TTCTATTACTGATTCTGTCACTGTAATGGGCTAAGACCCACATGTA
*
27719586 TTCTATTTCTGATTCTGAT-ACTGTAATGGGCTAAGACCCACA
1 TTCTATTACTGATTCTG-TCACTGTAATGGGCTAAGACCCACA
27719628 CTACACTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
46 36 0.97
47 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.38
Consensus pattern (46 bp):
TTCTATTACTGATTCTGTCACTGTAATGGGCTAAGACCCACATGTA
Found at i:27740769 original size:20 final size:20
Alignment explanation
Indices: 27740717--27740769 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
27740707 ACATTTGTGC
*
27740717 CTCTATTTGCACTTTGGTGT
1 CTCTATTTGCACTTTGATGT
* *
27740737 CTCTACTTACACTTTGATGT
1 CTCTATTTGCACTTTGATGT
*
27740757 CTCTGTTTGCACT
1 CTCTATTTGCACT
27740770 ACAGTGCCTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.13, C:0.25, G:0.15, T:0.47
Consensus pattern (20 bp):
CTCTATTTGCACTTTGATGT
Found at i:27747882 original size:43 final size:42
Alignment explanation
Indices: 27747810--27747922 Score: 133
Period size: 43 Copynumber: 2.7 Consensus size: 42
27747800 TTTCGAGGTG
* * * *
27747810 TGATTTCGTGCAAGACCATGTCAGGGACATTGGCATCGGTATGA
1 TGATTACGTGTAAGACCATGTCTGGGACATTGGCA-CCGTAT-A
*
27747854 -GATTACGTGTAAGACCATGTCTGGGACATTGGCACCTTATA
1 TGATTACGTGTAAGACCATGTCTGGGACATTGGCACCGTATA
27747895 TGATCTA--TGTAAGACCATGTCTGGGACA
1 TGAT-TACGTGTAAGACCATGTCTGGGACA
27747923 AAGGCATTGA
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
41 22 0.35
42 7 0.11
43 33 0.53
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.28
Consensus pattern (42 bp):
TGATTACGTGTAAGACCATGTCTGGGACATTGGCACCGTATA
Found at i:27753854 original size:25 final size:25
Alignment explanation
Indices: 27753826--27753880 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
27753816 TTCCTGATAG
27753826 GGCTCGCTTGAA-CTTCCCGA-TATAT
1 GGCTCGC-TGAAGCTTCCCGATTA-AT
**
27753851 GGCTATCTGAAGCTTCCCGATTAAT
1 GGCTCGCTGAAGCTTCCCGATTAAT
27753876 GGCTC
1 GGCTC
27753881 TTAGGAGTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
24 4 0.16
25 19 0.76
26 2 0.08
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.31
Consensus pattern (25 bp):
GGCTCGCTGAAGCTTCCCGATTAAT
Found at i:27756101 original size:2 final size:2
Alignment explanation
Indices: 27756094--27756133 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
27756084 AAGAAAACCA
27756094 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27756134 TAAGTTTATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27757828 original size:5 final size:5
Alignment explanation
Indices: 27757814--27757869 Score: 82
Period size: 5 Copynumber: 11.8 Consensus size: 5
27757804 TAAATATACA
*
27757814 ATAT- ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG -TA-C
1 ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG
27757861 ATATG ATAT
1 ATATG ATAT
27757870 ATGTATATAT
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
4 8 0.17
5 39 0.83
ACGTcount: A:0.41, C:0.02, G:0.16, T:0.41
Consensus pattern (5 bp):
ATATG
Found at i:27758245 original size:29 final size:30
Alignment explanation
Indices: 27758181--27758246 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 30
27758171 ATTTGGATTT
* * *
27758181 ATTTGATTCTTTTTAATAATATAAAAATTA
1 ATTTGATTCTATTTAATAATAGAAAAACTA
* **
27758211 AATTGATT-TATTTAATAATAGAATGACTA
1 ATTTGATTCTATTTAATAATAGAAAAACTA
27758240 ATTTGAT
1 ATTTGAT
27758247 CCAATTCTTA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
29 22 0.76
30 7 0.24
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (30 bp):
ATTTGATTCTATTTAATAATAGAAAAACTA
Found at i:27759299 original size:11 final size:11
Alignment explanation
Indices: 27759285--27759324 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
27759275 TATTTTCTTC
27759285 CTATTTTGCTA
1 CTATTTTGCTA
*
27759296 CTATTTTACTA
1 CTATTTTGCTA
* *
27759307 TTATGTTGCTA
1 CTATTTTGCTA
27759318 CTATTTT
1 CTATTTT
27759325 ATTGTTATTA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.20, C:0.15, G:0.07, T:0.57
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:27759422 original size:29 final size:30
Alignment explanation
Indices: 27759362--27759425 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 30
27759352 ACTTATTTTA
**
27759362 TTGTTAATTTTGTTATTATTTTAAAGGTAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
* *
27759392 TTGTTAA-TTTGTTATTATTTTAGATACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
27759421 TTGTT
1 TTGTT
27759426 TGTTAAGTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 23 0.77
30 7 0.23
ACGTcount: A:0.25, C:0.02, G:0.12, T:0.61
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:27767714 original size:7 final size:7
Alignment explanation
Indices: 27767667--27767713 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
27767657 TTTTTTGGTT
27767667 GTTTAGG
1 GTTTAGG
*
27767674 GTATTAGT
1 GT-TTAGG
27767682 GTATTAGG
1 GT-TTAGG
27767690 GTTTAGG
1 GTTTAGG
27767697 G-TTAGG
1 GTTTAGG
*
27767703 GTTTTGG
1 GTTTAGG
27767710 GTTT
1 GTTT
27767714 TAAATTGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
6 6 0.17
7 16 0.46
8 13 0.37
ACGTcount: A:0.15, C:0.00, G:0.38, T:0.47
Consensus pattern (7 bp):
GTTTAGG
Found at i:27774974 original size:30 final size:29
Alignment explanation
Indices: 27774896--27774983 Score: 94
Period size: 30 Copynumber: 3.1 Consensus size: 29
27774886 ATACATGTAC
*
27774896 ATATATAAA-AAAAATTAT-A-TACATAT
1 ATATATAAATAAAAATAATAATTACATAT
* *
27774922 ATATAGATTATAAAAA-AGATAATTACATAT
1 ATATATA-AATAAAAATA-ATAATTACATAT
27774952 ATATATAAATAAATAATAATAATTACATAT
1 ATATATAAATAAA-AATAATAATTACATAT
27774982 AT
1 AT
27774984 TAAAATTAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
26 6 0.12
27 1 0.02
28 7 0.14
29 6 0.12
30 29 0.58
31 1 0.02
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.35
Consensus pattern (29 bp):
ATATATAAATAAAAATAATAATTACATAT
Found at i:27775133 original size:17 final size:17
Alignment explanation
Indices: 27775113--27775147 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
27775103 AGGAAATAAA
*
27775113 AAAATATATATGTATAT
1 AAAATATAAATGTATAT
*
27775130 AAAATGTAAATGTATAT
1 AAAATATAAATGTATAT
27775147 A
1 A
27775148 TATGTATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (17 bp):
AAAATATAAATGTATAT
Found at i:27775284 original size:3 final size:3
Alignment explanation
Indices: 27775276--27775314 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
27775266 GTATATATAG
* * *
27775276 TAA TAA TAA TAA TGA TGA TAA TAA TAA CAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
27775315 CTTAATAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:27775322 original size:20 final size:20
Alignment explanation
Indices: 27775297--27775356 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
27775287 ATGATGATAA
27775297 TAATAACAATAATAATAACT
1 TAATAACAATAATAATAACT
* *
27775317 TAATAACAAGAA-AATCAAATT
1 TAATAACAATAATAAT--AACT
*
27775338 TAATAAAAATAAATAATAA
1 TAATAACAAT-AATAATAA
27775357 ATAAAAAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
19 3 0.09
20 11 0.34
21 13 0.41
22 2 0.06
23 3 0.09
ACGTcount: A:0.65, C:0.07, G:0.02, T:0.27
Consensus pattern (20 bp):
TAATAACAATAATAATAACT
Found at i:27775661 original size:23 final size:24
Alignment explanation
Indices: 27775631--27775677 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
27775621 AAATTAAATC
27775631 TCTAAGATTACA-AAATCATATCT
1 TCTAAGATTACATAAATCATATCT
* *
27775654 TCTAAGATTGCATATATCATATCT
1 TCTAAGATTACATAAATCATATCT
27775678 AAGATCATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.38
Consensus pattern (24 bp):
TCTAAGATTACATAAATCATATCT
Found at i:27775702 original size:14 final size:12
Alignment explanation
Indices: 27775669--27775694 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
27775659 GATTGCATAT
27775669 ATCATATCTAAG
1 ATCATATCTAAG
27775681 ATCATATCTAAG
1 ATCATATCTAAG
27775693 AT
1 AT
27775695 TGCATATCCT
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:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (12 bp):
ATCATATCTAAG
Found at i:27778428 original size:33 final size:33
Alignment explanation
Indices: 27778391--27778488 Score: 130
Period size: 32 Copynumber: 3.0 Consensus size: 33
27778381 CACACGGTTC
* * *
27778391 TGTGAAATGGTAACAAATATCAGCTTTTCATTT
1 TGTGAAATGATAACAAATATCAACTTTTAATTT
27778424 TGTGAAATGATAACAAAT-TACAAC-TTTAATTT
1 TGTGAAATGATAACAAATAT-CAACTTTTAATTT
*
27778456 TGTAAAATGATAACAAATATCAAC-TTTAATTT
1 TGTGAAATGATAACAAATATCAACTTTTAATTT
27778488 T
1 T
27778489 TTTTAAATGA
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
32 38 0.64
33 21 0.36
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (33 bp):
TGTGAAATGATAACAAATATCAACTTTTAATTT
Found at i:27780713 original size:50 final size:49
Alignment explanation
Indices: 27780585--27780713 Score: 120
Period size: 49 Copynumber: 2.6 Consensus size: 49
27780575 AATAATAACA
* * * *
27780585 TGCCAAAGTCATGTCCCAA-ACATGGTCTTACATGAGATGTTTCCTGTAC
1 TGCCAATGCCATGT-CCAAGACATGGTCTTACATGAGATGTTTCATATAC
* ** *
27780634 TGCCAATGCCATATCCCTGATATGGTCTTACATGAGA-GTTCTCATAT-C
1 TGCCAATGCCATGTCCAAGACATGGTCTTACATGAGATGTT-TCATATAC
*
27780682 GGTGCCCATGCCATGTCCAAGACATGGTCTTA
1 --TGCCAATGCCATGTCCAAGACATGGTCTTA
27780714 TGGGGGACCT
Statistics
Matches: 63, Mismatches: 13, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
48 6 0.10
49 32 0.51
50 25 0.40
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (49 bp):
TGCCAATGCCATGTCCAAGACATGGTCTTACATGAGATGTTTCATATAC
Found at i:27780734 original size:50 final size:50
Alignment explanation
Indices: 27780675--27780773 Score: 144
Period size: 50 Copynumber: 2.0 Consensus size: 50
27780665 ATGAGAGTTC
* *
27780675 TCATATCGGTGCCCATGCCATGTCCAAGACATGGTCTTATGGGGGACCTT
1 TCATATCGGTGCCAATGCCATGTCCAAGACACGGTCTTATGGGGGACCTT
* * * *
27780725 TCATCTCGGTGCGAATGCCATGTCCTAGACACGGTCTTATGTGGGACCT
1 TCATATCGGTGCCAATGCCATGTCCAAGACACGGTCTTATGGGGGACCT
27780774 CTTATAACCT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (50 bp):
TCATATCGGTGCCAATGCCATGTCCAAGACACGGTCTTATGGGGGACCTT
Found at i:27781198 original size:29 final size:29
Alignment explanation
Indices: 27781165--27781220 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
27781155 CCTTGACTCG
27781165 AACTTTGGCAAAATTACAATTTTCCCCTA
1 AACTTTGGCAAAATTACAATTTTCCCCTA
* * * *
27781194 AACTTTTGCATATTTACACTTTTCCCC
1 AACTTTGGCAAAATTACAATTTTCCCC
27781221 AAAGCTCGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.29, C:0.27, G:0.05, T:0.39
Consensus pattern (29 bp):
AACTTTGGCAAAATTACAATTTTCCCCTA
Found at i:27784073 original size:13 final size:13
Alignment explanation
Indices: 27784055--27784079 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27784045 AAATATTAAT
27784055 AATTAATTTTGAA
1 AATTAATTTTGAA
27784068 AATTAATTTTGA
1 AATTAATTTTGA
27784080 GAACAATTGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
AATTAATTTTGAA
Found at i:27785546 original size:21 final size:21
Alignment explanation
Indices: 27785520--27785561 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
27785510 TATGGTGTGG
27785520 ATGGAAGATGCTACCGAAACA
1 ATGGAAGATGCTACCGAAACA
27785541 ATGGAAGATGCTACCGAAACA
1 ATGGAAGATGCTACCGAAACA
27785562 TGTACAAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.14
Consensus pattern (21 bp):
ATGGAAGATGCTACCGAAACA
Found at i:27792678 original size:14 final size:14
Alignment explanation
Indices: 27792640--27792671 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
27792630 AAAATTAGAA
*
27792640 TTAGGAATTAGGAC
1 TTAGGACTTAGGAC
27792654 TTAGGACTTAGGAC
1 TTAGGACTTAGGAC
27792668 TTAG
1 TTAG
27792672 TATTTAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.31, C:0.09, G:0.28, T:0.31
Consensus pattern (14 bp):
TTAGGACTTAGGAC
Found at i:27799376 original size:50 final size:48
Alignment explanation
Indices: 27799273--27799442 Score: 135
Period size: 50 Copynumber: 3.4 Consensus size: 48
27799263 AGGTCCCACA
* * * * * **
27799273 TAAGACCGTGTCTAGGACATGGCGCTGGCACCGAGATGAAAGGTCCCCCG
1 TAAGACCATGTCTAGGACATGGC-ATGGCACTGACATGAAA-CTCCCATG
*
27799323 TAAGACCATGTCTAGGACATGGCATGGGCACTGATATGAGAACTCCCATG
1 TAAGACCATGTCTAGGACATGGCAT-GGCACTGACATGA-AACTCCCATG
* * * * * *
27799373 TAAGACCATATCTGGGATATGACATTGGCAGT-ACAAGAAACATCCCATG
1 TAAGACCATGTCTAGGACATGGCA-TGGCACTGACATGAAAC-TCCCATG
* *
27799422 TAAGACCATGTTTGGGACATG
1 TAAGACCATGTCTAGGACATG
27799443 ACTTTGGCAT
Statistics
Matches: 99, Mismatches: 17, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
48 3 0.03
49 30 0.30
50 63 0.64
51 3 0.03
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.21
Consensus pattern (48 bp):
TAAGACCATGTCTAGGACATGGCATGGCACTGACATGAAACTCCCATG
Found at i:27801066 original size:472 final size:472
Alignment explanation
Indices: 27799740--27802040 Score: 3659
Period size: 472 Copynumber: 4.9 Consensus size: 472
27799730 TCCATTTTAC
* * * *
27799740 GGGAGAATTTAACGAATTAACTGTGCTATTTGGCTAACCTAGAAATTCTAGAAATTTTATGATAA
1 GGGAGACTTTAACGAATTAACTGTACTATTTGGCTAACCCAAAAATTCTAGAAATTTTATGATAA
** * * *
27799805 GAAGATATATGAGTCTAGTTTTAGGAAAAATTTACTTATCTAAATTTAGAGTTTCGT-AACTCAA
66 GAAGATATATGAGTCTAGTTTTAGGAAAAATTTACGGATCTAAATTTCGAGTTT-TTAAACTCGA
*
27799869 GTTATAATTAAATTAGTGACTGTCACGCAAGTGGATAGTTTTATTATGAATAGTAAAATAAATTA
130 GTTATAATTAAATTAGTGACTGTCACGCAAGTGGATAGTTTTATTATGAATAGTGAAATAAATTA
* *
27799934 TTTTGATTTATTTAAGTATTCAGAAAATTTTTAATGTTCCTGGTTTGGACCTAAACCATTTTTGT
195 TTTTGATTTATTTAAGTATTCAGAAAATTTTTAATGTTCCCGGTTTGGACCTGAACCATTTTTGT
* *
27799999 TGCATGTTTTAGGGTCTTGAGGTCCCTTTTTAGGGACATATTGATTGAACGTGAGCGAATTAATT
260 TGCATGTTTTAGGGTCTCGAGGGCCCTTTTTAGGGACATATTGATTGAACGTGAGCGAATTAATT
* *
27800064 TTAAAAGCAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGGTAACGCATCATGTTCGACT-C
325 TTAAAAACAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGGTAACGCATCATGCTCGACTCC
* *
27800128 TAGCAACGGTCTCGGGTAAGGGGTGTTATTTATGATAGTTGATTTCTAGTGAATAGAGGTCAGAA
390 GA-CAACGGTCTCGGGTAAGGGGTGTTATTTATGATAATTGATTTCTAGTGAATAGAGGTCAGAA
* * *
27800193 CAGTCGGACAGTGAAATAG
454 CCGTCAGACAGTGAAACAG
* * *
27800212 GGGAGAGTTTAACGAATTAACTTTACTATTTTGCTAACCCAAAAATTCTAGAAATTTTATGATAA
1 GGGAGACTTTAACGAATTAACTGTACTATTTGGCTAACCCAAAAATTCTAGAAATTTTATGATAA
* * *
27800277 GAAGACATGTGAGTCTAGTTTTAGGAAAAATTTACGGATCTAAATTTTGAGTTTTTAAACTCGAG
66 GAAGATATATGAGTCTAGTTTTAGGAAAAATTTACGGATCTAAATTTCGAGTTTTTAAACTCGAG
*
27800342 TTATAATTAAATTAGTGAATGTCACG-AAGTGGATAGTTTTATTATGAATAGTGAAATAAATTAT
131 TTATAATTAAATTAGTGACTGTCACGCAAGTGGATAGTTTTATTATGAATAGTGAAATAAATTAT
* *
27800406 TTTGATTTATTTAAGTATTTAGAAAATTTTTAATGTTCCAC-GTTTGGACCTAAACCATTTTTGT
196 TTTGATTTATTTAAGTATTCAGAAAATTTTTAATGTTCC-CGGTTTGGACCTGAACCATTTTTGT
* * * *
27800470 TGCATGTTTTAGGGTCTCGAGGTCCCTTTTTAGAGACATATTGATTGAGCGTGAGTGAATTAATT
260 TGCATGTTTTAGGGTCTCGAGGGCCCTTTTTAGGGACATATTGATTGAACGTGAGCGAATTAATT
* * *
27800535 TTAAAAATAAATTTTTATGCCCCGAACTAGTAAGTCAAGTCAGGTAACGCATCATGCTCGACTCC
325 TTAAAAACAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGGTAACGCATCATGCTCGACTCC
*
27800600 GACAATGGTCTCGGGTAAGGGGTGTTATTTATGATAATTGATTTCTAGTGAATAGAGGTCAGAAC
390 GACAACGGTCTCGGGTAAGGGGTGTTATTTATGATAATTGATTTCTAGTGAATAGAGGTCAGAAC
*
27800665 CGTCAGACAGTGAAACAA
455 CGTCAGACAGTGAAACAG
* * *
27800683 GGGAGACTTTAACGAATTAACTGTAGTATTTCGCAAACCCAAAAATTCTAGAAATTTTATGATAA
1 GGGAGACTTTAACGAATTAACTGTACTATTTGGCTAACCCAAAAATTCTAGAAATTTTATGATAA
* *
27800748 GAAGATATATGAGTCTAGTTTTAGGAAAAATTTACGAATCTAAATTTCAAGTTTTTAAACTCGAG
66 GAAGATATATGAGTCTAGTTTTAGGAAAAATTTACGGATCTAAATTTCGAGTTTTTAAACTCGAG
*
27800813 TTATAATGAAATTAGTGACTGTCACGCAAGTGGATAGTTTTATTATGAATAGTGAAATAAATTAT
131 TTATAATTAAATTAGTGACTGTCACGCAAGTGGATAGTTTTATTATGAATAGTGAAATAAATTAT
* * *
27800878 TTTGATTTATTTACGTATTCAGAAAATTTTTAATGTTCCCCGTTTGGACTTGAACCATTTTTGTT
196 TTTGATTTATTTAAGTATTCAGAAAATTTTTAATGTTCCCGGTTTGGACCTGAACCATTTTTGTT
27800943 GCATGTTTTAGGGTCTCGAGGGCCCTTTTTAGGGACATATTGATTGAACGTGAGCGAATTAATTT
261 GCATGTTTTAGGGTCTCGAGGGCCCTTTTTAGGGACATATTGATTGAACGTGAGCGAATTAATTT
*
27801008 TAAAAACAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGGTAACTCATCATGCTCGACTCCG
326 TAAAAACAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGGTAACGCATCATGCTCGACTCCG
* *
27801073 ACAATGGTCTCGGGTAAGGGGTGTTATTTATGATAATTGATTTCTAGTGAATAGAGGTCAAAACC
391 ACAACGGTCTCGGGTAAGGGGTGTTATTTATGATAATTGATTTCTAGTGAATAGAGGTCAGAACC
*
27801138 GTCAGACAGTGAAACAC
456 GTCAGACAGTGAAACAG
* * *
27801155 GGGAGACTTTAACAAATTAACTGTACTATTTGGCTAACCCAAAAATTCTGGAAATTTTATGATAT
1 GGGAGACTTTAACGAATTAACTGTACTATTTGGCTAACCCAAAAATTCTAGAAATTTTATGATAA
* *
27801220 GAAGATATATGAGTCTACTTTTAGGAAAAATTTACGGATCTCAATTTCGAGTTTTTAAACTCGAG
66 GAAGATATATGAGTCTAGTTTTAGGAAAAATTTACGGATCTAAATTTCGAGTTTTTAAACTCGAG
* *
27801285 TTATAATTAAATTAGTGACTGTAACACAAGTGGATAGTTTTATTATGAATAGTGAAATAAATTAT
131 TTATAATTAAATTAGTGACTGTCACGCAAGTGGATAGTTTTATTATGAATAGTGAAATAAATTAT
*
27801350 TTTGATTTATTTAAGTATTCAGAAATTTTTTAATGTTCCCGGTTTGGACCTGAACCATTTTTGTT
196 TTTGATTTATTTAAGTATTCAGAAAATTTTTAATGTTCCCGGTTTGGACCTGAACCATTTTTGTT
** * *
27801415 GCATGTTTTAGGGTCTTAAGGACCCTTTTTAGGGACATATTGATTGAACGTGAGAGAATTAATTT
261 GCATGTTTTAGGGTCTCGAGGGCCCTTTTTAGGGACATATTGATTGAACGTGAGCGAATTAATTT
* *
27801480 TAAAAGA-AAATTTTTATGCTCCAAACTAGTAAGTTAAGTCAAGTAACGCATCATGCTCGACTCC
326 TAAAA-ACAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGGTAACGCATCATGCTCGACTCC
*
27801544 GGCAACGGTCTCGGGTAAGGGGTGTTATTTATGATAATTGATTTCTAGTGAATAGAGGTCAGAAC
390 GACAACGGTCTCGGGTAAGGGGTGTTATTTATGATAATTGATTTCTAGTGAATAGAGGTCAGAAC
*
27801609 CGTCGGACAGTGAAACAG
455 CGTCAGACAGTGAAACAG
* *
27801627 GGGAGACTTTAACAAATTAACTGTACTATTTGGCTAACCCAAAAATTCTGGAAATTTTATGATAA
1 GGGAGACTTTAACGAATTAACTGTACTATTTGGCTAACCCAAAAATTCTAGAAATTTTATGATAA
*
27801692 GAAGATATATGAGTCTAGTTTTAGGAAAAATTTACGGATTTAAATTTCGAGTTTTTAAACTCGAG
66 GAAGATATATGAGTCTAGTTTTAGGAAAAATTTACGGATCTAAATTTCGAGTTTTTAAACTCGAG
* *
27801757 TTATAATTAAATTAGTGACTGTCATGCAAGTGGACT-GTTTTATTGTGAATAGTGAAATAAATTA
131 TTATAATTAAATTAGTGACTGTCACGCAAGTGGA-TAGTTTTATTATGAATAGTGAAATAAATTA
* * * ** **
27801821 TTTTGATTTATTTAAGTATTC-GAAAAAATTTTAATGTTCCCGGTTTAGATCTGAACTGTTTCCG
195 TTTTGATTTATTTAAGTATTCAG-AAAATTTTTAATGTTCCCGGTTTGGACCTGAACCATTTTTG
* * * *
27801885 TTGCATGTTTTAGTGTCTCGAGGGCCCTTTTTAAGGAC--ATTGATTGAACATGAGCAAATTAAT
259 TTGCATGTTTTAGGGTCTCGAGGGCCCTTTTTAGGGACATATTGATTGAACGTGAGCGAATTAAT
* * *
27801948 TTTAAAAGCAAATTTTTATGATCCGAACTAGTAAGTTAAGTCAGGTAACTGC-TCGTGCTCGACT
324 TTTAAAAACAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGGTAAC-GCATCATGCTCGACT
* * *
27802012 CTGGCAACGGTCTCGAGTAAGGGGTGTTA
388 CCGACAACGGTCTCGGGTAAGGGGTGTTA
27802041 CATCCCAGAA
Statistics
Matches: 1700, Mismatches: 119, Indels: 22
0.92 0.06 0.01
Matches are distributed among these distances:
470 104 0.06
471 441 0.26
472 1153 0.68
473 2 0.00
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (472 bp):
GGGAGACTTTAACGAATTAACTGTACTATTTGGCTAACCCAAAAATTCTAGAAATTTTATGATAA
GAAGATATATGAGTCTAGTTTTAGGAAAAATTTACGGATCTAAATTTCGAGTTTTTAAACTCGAG
TTATAATTAAATTAGTGACTGTCACGCAAGTGGATAGTTTTATTATGAATAGTGAAATAAATTAT
TTTGATTTATTTAAGTATTCAGAAAATTTTTAATGTTCCCGGTTTGGACCTGAACCATTTTTGTT
GCATGTTTTAGGGTCTCGAGGGCCCTTTTTAGGGACATATTGATTGAACGTGAGCGAATTAATTT
TAAAAACAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGGTAACGCATCATGCTCGACTCCG
ACAACGGTCTCGGGTAAGGGGTGTTATTTATGATAATTGATTTCTAGTGAATAGAGGTCAGAACC
GTCAGACAGTGAAACAG
Found at i:27801799 original size:944 final size:943
Alignment explanation
Indices: 27799740--27802040 Score: 3688
Period size: 943 Copynumber: 2.4 Consensus size: 943
27799730 TCCATTTTAC
* * * *
27799740 GGGAGAATTTAACGAATTAACTGTGCTATTTGGCTAACCTAGAAATTCTAGAAATTTTATGATAA
1 GGGAGACTTTAACGAATTAACTGTACTATTTGGCTAACCCAAAAATTCTAGAAATTTTATGATAA
** * * *
27799805 GAAGATATATGAGTCTAGTTTTAGGAAAAATTTACTTATCTAAATTTAGAGTTTCGT-AACTCAA
66 GAAGATATATGAGTCTAGTTTTAGGAAAAATTTACGAATCTAAATTTCGAGTTT-TTAAACTCGA
*
27799869 GTTATAATTAAATTAGTGACTGTCACGCAAGTGGATAGTTTTATTATGAATAGTAAAATAAATTA
130 GTTATAATTAAATTAGTGACTGTCACGCAAGTGGATAGTTTTATTATGAATAGTGAAATAAATTA
* * *
27799934 TTTTGATTTATTTAAGTATTCAGAAAATTTTTAATGTTCCTGGTTTGGACCTAAACCATTTTTGT
195 TTTTGATTTATTTAAGTATTCAGAAAATTTTTAATGTTCCCGGTTTGGACTTGAACCATTTTTGT
* *
27799999 TGCATGTTTTAGGGTCTTGAGGTCCCTTTTTAGGGACATATTGATTGAACGTGAGCGAATTAATT
260 TGCATGTTTTAGGGTCTCGAGGGCCCTTTTTAGGGACATATTGATTGAACGTGAGCGAATTAATT
* *
27800064 TTAAAAGCAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGGTAACGCATCATGTTCGACT-C
325 TTAAAAGCAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGGTAACTCATCATGCTCGACTCC
* * *
27800128 TAGCAACGGTCTCGGGTAAGGGGTGTTATTTATGATAGTTGATTTCTAGTGAATAGAGGTCAGAA
390 GA-CAACGGTCTCGGGTAAGGGGTGTTATTTATGATAATTGATTTCTAGTGAATAGAGGTCAAAA
* * * * * * *
27800193 CAGTCGGACAGTGAAATAGGGGAGAGTTTAACGAATTAACTTTACTATTTTGCTAACCCAAAAAT
454 CAGTCAGACAGTGAAACACGGGAGACTTTAACAAATTAACTGTACTATTTGGCTAACCCAAAAAT
* *
27800258 TCTAGAAATTTTATGATAAGAAGACATGTGAGTCTAGTTTTAGGAAAAATTTACGGATCTAAATT
519 TCTAGAAATTTTATGATAAGAAGACATATGAGTCTACTTTTAGGAAAAATTTACGGATCTAAATT
*
27800323 TTGAGTTTTTAAACTCGAGTTATAATTAAATTAGTGAATGTCACGAAGTGGATAGTTTTATTATG
584 TCGAGTTTTTAAACTCGAGTTATAATTAAATTAGTGAATGTCACGAAGTGGATAGTTTTATTATG
*
27800388 AATAGTGAAATAAATTATTTTGATTTATTTAAGTATTTAGAAAATTTTTAATGTTCCACGTTTGG
649 AATAGTGAAATAAATTATTTTGATTTATTTAAGTATTCAGAAAATTTTTAATGTTCCACGTTTGG
* *
27800453 ACCTAAACCATTTTTGTTGCATGTTTTAGGGTCTCGAGGTCCCTTTTTAGAGACATATTGATTGA
714 ACCTAAACCATTTTTGTTGCATGTTTTAGGGTCTCAAGGACCCTTTTTAGAGACATATTGATTGA
* * * *
27800518 GCGTGAGTGAATTAATTTTAAAAATAAATTTTTATGCCCCGAACTAGTAAGTCAAGTCAGGTAAC
779 ACGTGAGAGAATTAATTTTAAAAATAAATTTTTATGCCCCAAACTAGTAAGTCAAGTCAAGTAAC
*
27800583 GCATCATGCTCGACTCCGACAATGGTCTCGGGTAAGGGGTGTTATTTATGATAATTGATTTCTAG
844 GCATCATGCTCGACTCCGACAACGGTCTCGGGTAAGGGGTGTTATTTATGATAATTGATTTCTAG
27800648 TGAATAGAGGTCAGAACCGTCAGACAGTGAAACAA
909 TGAATAGAGGTCAGAACCGTCAGACAGTGAAACAA
* * *
27800683 GGGAGACTTTAACGAATTAACTGTAGTATTTCGCAAACCCAAAAATTCTAGAAATTTTATGATAA
1 GGGAGACTTTAACGAATTAACTGTACTATTTGGCTAACCCAAAAATTCTAGAAATTTTATGATAA
*
27800748 GAAGATATATGAGTCTAGTTTTAGGAAAAATTTACGAATCTAAATTTCAAGTTTTTAAACTCGAG
66 GAAGATATATGAGTCTAGTTTTAGGAAAAATTTACGAATCTAAATTTCGAGTTTTTAAACTCGAG
*
27800813 TTATAATGAAATTAGTGACTGTCACGCAAGTGGATAGTTTTATTATGAATAGTGAAATAAATTAT
131 TTATAATTAAATTAGTGACTGTCACGCAAGTGGATAGTTTTATTATGAATAGTGAAATAAATTAT
* *
27800878 TTTGATTTATTTACGTATTCAGAAAATTTTTAATGTTCCCCGTTTGGACTTGAACCATTTTTGTT
196 TTTGATTTATTTAAGTATTCAGAAAATTTTTAATGTTCCCGGTTTGGACTTGAACCATTTTTGTT
27800943 GCATGTTTTAGGGTCTCGAGGGCCCTTTTTAGGGACATATTGATTGAACGTGAGCGAATTAATTT
261 GCATGTTTTAGGGTCTCGAGGGCCCTTTTTAGGGACATATTGATTGAACGTGAGCGAATTAATTT
*
27801008 TAAAAACAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGGTAACTCATCATGCTCGACTCCG
326 TAAAAGCAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGGTAACTCATCATGCTCGACTCCG
* *
27801073 ACAATGGTCTCGGGTAAGGGGTGTTATTTATGATAATTGATTTCTAGTGAATAGAGGTCAAAACC
391 ACAACGGTCTCGGGTAAGGGGTGTTATTTATGATAATTGATTTCTAGTGAATAGAGGTCAAAACA
27801138 GTCAGACAGTGAAACACGGGAGACTTTAACAAATTAACTGTACTATTTGGCTAACCCAAAAATTC
456 GTCAGACAGTGAAACACGGGAGACTTTAACAAATTAACTGTACTATTTGGCTAACCCAAAAATTC
* * * *
27801203 TGGAAATTTTATGATATGAAGATATATGAGTCTACTTTTAGGAAAAATTTACGGATCTCAATTTC
521 TAGAAATTTTATGATAAGAAGACATATGAGTCTACTTTTAGGAAAAATTTACGGATCTAAATTTC
*
27801268 GAGTTTTTAAACTCGAGTTATAATTAAATTAGTGACTGTAACAC-AAGTGGATAGTTTTATTATG
586 GAGTTTTTAAACTCGAGTTATAATTAAATTAGTGAATGT--CACGAAGTGGATAGTTTTATTATG
*
27801332 AATAGTGAAATAAATTATTTTGATTTATTTAAGTATTCAGAAATTTTTTAATGTTCC-CGGTTTG
649 AATAGTGAAATAAATTATTTTGATTTATTTAAGTATTCAGAAAATTTTTAATGTTCCAC-GTTTG
* * *
27801396 GACCTGAACCATTTTTGTTGCATGTTTTAGGGTCTTAAGGACCCTTTTTAGGGACATATTGATTG
713 GACCTAAACCATTTTTGTTGCATGTTTTAGGGTCTCAAGGACCCTTTTTAGAGACATATTGATTG
* *
27801461 AACGTGAGAGAATTAATTTTAAAAGA-AAATTTTTATGCTCCAAACTAGTAAGTTAAGTCAAGTA
778 AACGTGAGAGAATTAATTTTAAAA-ATAAATTTTTATGCCCCAAACTAGTAAGTCAAGTCAAGTA
*
27801525 ACGCATCATGCTCGACTCCGGCAACGGTCTCGGGTAAGGGGTGTTATTTATGATAATTGATTTCT
842 ACGCATCATGCTCGACTCCGACAACGGTCTCGGGTAAGGGGTGTTATTTATGATAATTGATTTCT
* *
27801590 AGTGAATAGAGGTCAGAACCGTCGGACAGTGAAACAG
907 AGTGAATAGAGGTCAGAACCGTCAGACAGTGAAACAA
* *
27801627 GGGAGACTTTAACAAATTAACTGTACTATTTGGCTAACCCAAAAATTCTGGAAATTTTATGATAA
1 GGGAGACTTTAACGAATTAACTGTACTATTTGGCTAACCCAAAAATTCTAGAAATTTTATGATAA
* *
27801692 GAAGATATATGAGTCTAGTTTTAGGAAAAATTTACGGATTTAAATTTCGAGTTTTTAAACTCGAG
66 GAAGATATATGAGTCTAGTTTTAGGAAAAATTTACGAATCTAAATTTCGAGTTTTTAAACTCGAG
* *
27801757 TTATAATTAAATTAGTGACTGTCATGCAAGTGGACT-GTTTTATTGTGAATAGTGAAATAAATTA
131 TTATAATTAAATTAGTGACTGTCACGCAAGTGGA-TAGTTTTATTATGAATAGTGAAATAAATTA
* * ** **
27801821 TTTTGATTTATTTAAGTATTC-GAAAAAATTTTAATGTTCCCGGTTTAGA-TCTGAACTGTTTCC
195 TTTTGATTTATTTAAGTATTCAG-AAAATTTTTAATGTTCCCGGTTTGGACT-TGAACCATTTTT
* * * *
27801884 GTTGCATGTTTTAGTGTCTCGAGGGCCCTTTTTAAGGAC--ATTGATTGAACATGAGCAAATTAA
258 GTTGCATGTTTTAGGGTCTCGAGGGCCCTTTTTAGGGACATATTGATTGAACGTGAGCGAATTAA
* *
27801947 TTTTAAAAGCAAATTTTTATGATCCGAACTAGTAAGTTAAGTCAGGTAACTGC-TCGTGCTCGAC
323 TTTTAAAAGCAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGGTAACT-CATCATGCTCGAC
* * *
27802011 TCTGGCAACGGTCTCGAGTAAGGGGTGTTA
387 TCCGACAACGGTCTCGGGTAAGGGGTGTTA
27802041 CATCCCAGAA
Statistics
Matches: 1256, Mismatches: 92, Indels: 21
0.92 0.07 0.02
Matches are distributed among these distances:
942 108 0.09
943 578 0.46
944 565 0.45
945 5 0.00
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (943 bp):
GGGAGACTTTAACGAATTAACTGTACTATTTGGCTAACCCAAAAATTCTAGAAATTTTATGATAA
GAAGATATATGAGTCTAGTTTTAGGAAAAATTTACGAATCTAAATTTCGAGTTTTTAAACTCGAG
TTATAATTAAATTAGTGACTGTCACGCAAGTGGATAGTTTTATTATGAATAGTGAAATAAATTAT
TTTGATTTATTTAAGTATTCAGAAAATTTTTAATGTTCCCGGTTTGGACTTGAACCATTTTTGTT
GCATGTTTTAGGGTCTCGAGGGCCCTTTTTAGGGACATATTGATTGAACGTGAGCGAATTAATTT
TAAAAGCAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGGTAACTCATCATGCTCGACTCCG
ACAACGGTCTCGGGTAAGGGGTGTTATTTATGATAATTGATTTCTAGTGAATAGAGGTCAAAACA
GTCAGACAGTGAAACACGGGAGACTTTAACAAATTAACTGTACTATTTGGCTAACCCAAAAATTC
TAGAAATTTTATGATAAGAAGACATATGAGTCTACTTTTAGGAAAAATTTACGGATCTAAATTTC
GAGTTTTTAAACTCGAGTTATAATTAAATTAGTGAATGTCACGAAGTGGATAGTTTTATTATGAA
TAGTGAAATAAATTATTTTGATTTATTTAAGTATTCAGAAAATTTTTAATGTTCCACGTTTGGAC
CTAAACCATTTTTGTTGCATGTTTTAGGGTCTCAAGGACCCTTTTTAGAGACATATTGATTGAAC
GTGAGAGAATTAATTTTAAAAATAAATTTTTATGCCCCAAACTAGTAAGTCAAGTCAAGTAACGC
ATCATGCTCGACTCCGACAACGGTCTCGGGTAAGGGGTGTTATTTATGATAATTGATTTCTAGTG
AATAGAGGTCAGAACCGTCAGACAGTGAAACAA
Found at i:27806258 original size:13 final size:13
Alignment explanation
Indices: 27806203--27806259 Score: 53
Period size: 13 Copynumber: 4.4 Consensus size: 13
27806193 TAATACTCGA
*
27806203 TTTTCAAGATATG
1 TTTTAAAGATATG
* *
27806216 TTTCT-AGGTTATG
1 TTT-TAAAGATATG
* *
27806229 TTTTTAAGTTATG
1 TTTTAAAGATATG
27806242 TTTTAAAGATATG
1 TTTTAAAGATATG
27806255 TTTTA
1 TTTTA
27806260 CGATGCTCCT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
12 1 0.03
13 35 0.95
14 1 0.03
ACGTcount: A:0.26, C:0.04, G:0.16, T:0.54
Consensus pattern (13 bp):
TTTTAAAGATATG
Found at i:27807559 original size:25 final size:23
Alignment explanation
Indices: 27807497--27807560 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 23
27807487 CGAACCCATG
*
27807497 TTTTTATGCGAACTCATATTTTA
1 TTTTTATGCGAACTCATATTGTA
* *
27807520 TGTTTTAGTGTGAACTCATGTTGTA
1 T-TTTTA-TGCGAACTCATATTGTA
27807545 CTTTTCTATGCGAACT
1 -TTTT-TATGCGAACT
27807561 ATAATAATAG
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
23 1 0.03
24 5 0.15
25 24 0.73
26 3 0.09
ACGTcount: A:0.22, C:0.14, G:0.16, T:0.48
Consensus pattern (23 bp):
TTTTTATGCGAACTCATATTGTA
Found at i:27813940 original size:43 final size:43
Alignment explanation
Indices: 27813893--27814017 Score: 132
Period size: 41 Copynumber: 3.0 Consensus size: 43
27813883 CCCAGATATT
* * *
27813893 GTCTTATATGTTAACGCATATCGATGCCATTGTCCCAGACAGG
1 GTCTTATACGTTAACTCATATCGATGCCAATGTCCCAGACAGG
* *
27813936 GTCTTATACG--AA-TCATATACGATGCCAATATCCCAGACATG
1 GTCTTATACGTTAACTCATAT-CGATGCCAATGTCCCAGACAGG
* **
27813977 GTCTTACACGTTTTCTCACT-TCGATGCCAATGTCCCAGACA
1 GTCTTATACGTTAACTCA-TATCGATGCCAATGTCCCAGACA
27814018 TGATCTTACA
Statistics
Matches: 68, Mismatches: 9, Indels: 10
0.78 0.10 0.11
Matches are distributed among these distances:
40 5 0.07
41 30 0.44
43 28 0.41
44 4 0.06
45 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (43 bp):
GTCTTATACGTTAACTCATATCGATGCCAATGTCCCAGACAGG
Found at i:27814280 original size:92 final size:92
Alignment explanation
Indices: 27814152--27814572 Score: 526
Period size: 92 Copynumber: 4.6 Consensus size: 92
27814142 ATCCAATGCT
* * * * *
27814152 CAAATCAATTC-AGCAGTATATATCCATATACGAATCAAATTTGGCAATGTATATTTATATACAA
1 CAAATCAATTCGA-CAATGTATATCCATATACAAATCAAATTCGGCAATGTATATCTATATACAA
* *
27814216 ATC-AATTCGGCAATGAATATCCATATA
65 ATCAAATTCGGCAATGTATATCTATATA
* * * * *
27814243 CAATTCAAATTTGACAATGTATAACCATATACAAATCAAATTCGACAATATATATCTATATACAA
1 CAAATC-AATTCGACAATGTATATCCATATACAAATCAAATTCGGCAATGTATATCTATATACAA
*
27814308 ATCAAATTCGACAATGTATATCTATATA
65 ATCAAATTCGGCAATGTATATCTATATA
* * *
27814336 CAAATCAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATAACCATATACAAA
1 CAAATCAATTCGACAATGTATATCCATATACAAATCAAATTCGGCAATGTATATCTATATACAAA
27814401 TCAAATTCGGCAATGTATATCTATATA
66 TCAAATTCGGCAATGTATATCTATATA
* * * * * *
27814428 CAAATCAATTCGGCAATGTATATCTATAAACAATTCAAATTCGACAATGTATATCTATAAACAAA
1 CAAATCAATTCGACAATGTATATCCATATACAAATCAAATTCGGCAATGTATATCTATATACAAA
* * *
27814493 TCAATTTCGTCAATGTATATCTATAAA
66 TCAAATTCGGCAATGTATATCTATATA
* **
27814520 GAAATCAAATTC-AGCAATGTATATCTTTATACAAATC-AATTCGGCAATGTATA
1 CAAATC-AATTCGA-CAATGTATATCCATATACAAATCAAATTCGGCAATGTATA
27814573 AAACATATAC
Statistics
Matches: 287, Mismatches: 38, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
91 5 0.02
92 230 0.80
93 52 0.18
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.32
Consensus pattern (92 bp):
CAAATCAATTCGACAATGTATATCCATATACAAATCAAATTCGGCAATGTATATCTATATACAAA
TCAAATTCGGCAATGTATATCTATATA
Found at i:27814295 original size:123 final size:122
Alignment explanation
Indices: 27814152--27814572 Score: 560
Period size: 123 Copynumber: 3.4 Consensus size: 122
27814142 ATCCAATGCT
* * * * *
27814152 CAAATC-AATTCAGCAGTATATATCCATATACGAATCAAATTTGGCAATGTATATTTATATACAA
1 CAAATCAAATTCAGCAATATATATCTATATACAAATC-AATTCGGCAATGTATATCTATATACAA
* *
27814216 ATCAATTCGGCAATGAATATCCATATACAATTCAAATTTGACAATGTATAACCATATA
65 ATCAATTCGGCAATGTATATCCATATACAAATCAAATTTGACAATGTATAACCATATA
*
27814274 CAAATCAAATTC-GACAATATATATCTATATACAAATCAAATTCGACAATGTATATCTATATACA
1 CAAATCAAATTCAG-CAATATATATCTATATACAAATC-AATTCGGCAATGTATATCTATATACA
* *
27814338 AATCAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATAACCATATA
64 AATCAATTCGGCAATGTATATCCATATACAAATCAAATTTGACAATGTATAACCATATA
* * * *
27814397 CAAATCAAATTCGGCAATGTATATCTATATACAAATCAATTCGGCAATGTATATCTATAAACAAT
1 CAAATCAAATTCAGCAATATATATCTATATACAAATCAATTCGGCAATGTATATCTATATACAAA
* * * * * * *
27814462 TCAAATTCGACAATGTATATCTATAAACAAATC-AATTTCGTCAATGTATATCTATAAA
66 TC-AATTCGGCAATGTATATCCATATACAAATCAAATTT-GACAATGTATAACCATATA
* * *
27814520 GAAATCAAATTCAGCAATGTATATCTTTATACAAATCAATTCGGCAATGTATA
1 CAAATCAAATTCAGCAATATATATCTATATACAAATCAATTCGGCAATGTATA
27814573 AAACATATAC
Statistics
Matches: 269, Mismatches: 25, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
122 38 0.14
123 230 0.86
124 1 0.00
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.32
Consensus pattern (122 bp):
CAAATCAAATTCAGCAATATATATCTATATACAAATCAATTCGGCAATGTATATCTATATACAAA
TCAATTCGGCAATGTATATCCATATACAAATCAAATTTGACAATGTATAACCATATA
Found at i:27814583 original size:31 final size:31
Alignment explanation
Indices: 27814152--27814572 Score: 537
Period size: 31 Copynumber: 13.7 Consensus size: 31
27814142 ATCCAATGCT
* * * *
27814152 CAAATC-AATTCAGCAGTATATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* * *
27814182 CGAATCAAATTTGGCAATGTATATTTATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* *
27814213 CAAATC-AATTCGGCAATGAATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* * * * *
27814243 CAATTCAAATTTGACAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* *
27814274 CAAATCAAATTCGACAATATATATCTATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
*
27814305 CAAATCAAATTCGACAATGTATATCTATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
*
27814336 CAAATC-AATTCGGCAATGTATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* *
27814366 CAAATCAAATTCGGCAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
27814397 CAAATCAAATTCGGCAATGTATATCTATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
*
27814428 CAAATC-AATTCGGCAATGTATATCTATAAA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* * *
27814458 CAATTCAAATTCGACAATGTATATCTATAAA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* * *
27814489 CAAATCAATTTCGTCAATGTATATCTATAAA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* * *
27814520 GAAATCAAATTCAGCAATGTATATCTTTATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
27814551 CAAATC-AATTCGGCAATGTATA
1 CAAATCAAATTCGGCAATGTATA
27814573 AAACATATAC
Statistics
Matches: 345, Mismatches: 42, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
30 101 0.29
31 244 0.71
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.32
Consensus pattern (31 bp):
CAAATCAAATTCGGCAATGTATATCTATATA
Found at i:27815600 original size:4 final size:4
Alignment explanation
Indices: 27815591--27815617 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
27815581 TTCTCATATA
27815591 TTAT TTAT TTAT TTAT TTAT TTAT TTA
1 TTAT TTAT TTAT TTAT TTAT TTAT TTA
27815618 AAGTATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:27821327 original size:26 final size:26
Alignment explanation
Indices: 27821291--27821359 Score: 120
Period size: 26 Copynumber: 2.7 Consensus size: 26
27821281 CCCGTTATAT
*
27821291 GGCTCTTTGTGAGCTTCTTGATTAAA
1 GGCTCTTTGTGAGCTTCTCGATTAAA
27821317 GGCTCTTTGTGAGCTTCTCGATTAAA
1 GGCTCTTTGTGAGCTTCTCGATTAAA
*
27821343 GGCTTTTTGTGAGCTTC
1 GGCTCTTTGTGAGCTTC
27821360 CCAATATTGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.16, C:0.17, G:0.25, T:0.42
Consensus pattern (26 bp):
GGCTCTTTGTGAGCTTCTCGATTAAA
Found at i:27825572 original size:10 final size:10
Alignment explanation
Indices: 27825557--27825584 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
27825547 TAATATAAAT
27825557 ATTATAAACA
1 ATTATAAACA
27825567 ATTATAAACA
1 ATTATAAACA
27825577 ATTATAAA
1 ATTATAAA
27825585 TTAGATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (10 bp):
ATTATAAACA
Found at i:27833784 original size:15 final size:15
Alignment explanation
Indices: 27833766--27833804 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
27833756 CGGTATCATT
27833766 TTGTTCGTGATAATA
1 TTGTTCGTGATAATA
* *
27833781 TTGTTCGTGGTGATA
1 TTGTTCGTGATAATA
27833796 TTGTT-GTGA
1 TTGTTCGTGA
27833805 GCAAAATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 3 0.14
15 18 0.86
ACGTcount: A:0.18, C:0.05, G:0.28, T:0.49
Consensus pattern (15 bp):
TTGTTCGTGATAATA
Found at i:27839298 original size:40 final size:40
Alignment explanation
Indices: 27839248--27839330 Score: 114
Period size: 40 Copynumber: 2.1 Consensus size: 40
27839238 AATTATGGAA
* *
27839248 TACTGAATATTGTTT-TGAGTACTGAATTGAATTGTGAAGT
1 TACTGAATATT-TTTATGAGTACTGAATTGAACTGTGAAAT
* *
27839288 TACTGAATATTTTTATGTGTACTGCATTGAACTGTGAAAT
1 TACTGAATATTTTTATGAGTACTGAATTGAACTGTGAAAT
27839328 TAC
1 TAC
27839331 GGAAGTAATG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
39 3 0.08
40 35 0.92
ACGTcount: A:0.30, C:0.08, G:0.19, T:0.42
Consensus pattern (40 bp):
TACTGAATATTTTTATGAGTACTGAATTGAACTGTGAAAT
Found at i:27839607 original size:45 final size:44
Alignment explanation
Indices: 27839538--27839642 Score: 147
Period size: 45 Copynumber: 2.3 Consensus size: 44
27839528 GCCGACTATT
* *
27839538 GTTACTGTTACTGATTCAATACTTTGTGTGTCGAATACTGTTAGC
1 GTTACTGTTACT-ATTCAACACTTTGTGTGTCGAATACTATTAGC
* **
27839583 GTTACTGTTACATATTCAACACTTTGTGTGTTGAATACTATTATT
1 GTTACTGTTAC-TATTCAACACTTTGTGTGTCGAATACTATTAGC
27839628 GTTACTGTTACTATT
1 GTTACTGTTACTATT
27839643 ACTGATACCG
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
44 4 0.07
45 49 0.91
46 1 0.02
ACGTcount: A:0.24, C:0.14, G:0.16, T:0.46
Consensus pattern (44 bp):
GTTACTGTTACTATTCAACACTTTGTGTGTCGAATACTATTAGC
Found at i:27839641 original size:18 final size:18
Alignment explanation
Indices: 27839618--27839667 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
27839608 GTGTGTTGAA
* *
27839618 TACTATTATTGTTACTGT
1 TACTATTACTGTTACCGT
*
27839636 TACTATTACTGATACCGT
1 TACTATTACTGTTACCGT
27839654 TACTGATTACTGTT
1 TACT-ATTACTGTT
27839668 TAGGTGCTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
18 19 0.70
19 8 0.30
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.48
Consensus pattern (18 bp):
TACTATTACTGTTACCGT
Found at i:27839644 original size:12 final size:13
Alignment explanation
Indices: 27839618--27839667 Score: 52
Period size: 12 Copynumber: 4.1 Consensus size: 13
27839608 GTGTGTTGAA
*
27839618 TACT-ATTATTGT
1 TACTGATTACTGT
*
27839630 TACTG-TTACTAT
1 TACTGATTACTGT
*
27839642 TACTGA-TACCGT
1 TACTGATTACTGT
27839654 TACTGATTACTGT
1 TACTGATTACTGT
27839667 T
1 T
27839668 TAGGTGCTGT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
12 24 0.80
13 6 0.20
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.48
Consensus pattern (13 bp):
TACTGATTACTGT
Found at i:27842421 original size:22 final size:22
Alignment explanation
Indices: 27842395--27842471 Score: 64
Period size: 22 Copynumber: 3.2 Consensus size: 22
27842385 CTAAATTAAG
27842395 AATAAAGAATATAATGTATATT
1 AATAAAGAATATAATGTATATT
* * *
27842417 AATAATGTCATATAAAGTTAATAACAATT
1 AATAAAG-AATATAATG-T-AT----ATT
27842446 AATAAAGAATATAATGTATATT
1 AATAAAGAATATAATGTATATT
27842468 AATA
1 AATA
27842472 TATTAATTGC
Statistics
Matches: 42, Mismatches: 6, Indels: 14
0.68 0.10 0.23
Matches are distributed among these distances:
22 13 0.31
23 7 0.17
24 1 0.02
25 2 0.05
26 2 0.05
27 1 0.02
28 7 0.17
29 9 0.21
ACGTcount: A:0.55, C:0.03, G:0.08, T:0.35
Consensus pattern (22 bp):
AATAAAGAATATAATGTATATT
Found at i:27845777 original size:50 final size:50
Alignment explanation
Indices: 27845651--27845892 Score: 211
Period size: 50 Copynumber: 4.7 Consensus size: 50
27845641 GATAATAACA
* * ** * * *
27845651 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGTATGTTTCCTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGG
* * * **
27845700 TGCCAATGCCATATCACAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * *
27845750 TGCCCATGCCATGTCCCAGACATGGTCTTAC-GGAGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATG-GGACCTCTCATATCGG
* * **
27845800 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATAACCTCAATAA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
*
27845856 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
27845893 TCTCATTCCC
Statistics
Matches: 155, Mismatches: 28, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
48 1 0.01
49 38 0.25
50 79 0.51
51 1 0.01
53 2 0.01
56 34 0.22
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:27857875 original size:25 final size:25
Alignment explanation
Indices: 27857847--27857905 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 25
27857837 AGCTATAAAC
*
27857847 AGTAAGCTCATACAAGTTGAATATT
1 AGTAAGCTCATACAAGCTGAATATT
* * *
27857872 AGTAAGGTCATGCGAGCTGAATATT
1 AGTAAGCTCATACAAGCTGAATATT
* *
27857897 GGCAAGCTC
1 AGTAAGCTC
27857906 TCTCGAGTTG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (25 bp):
AGTAAGCTCATACAAGCTGAATATT
Found at i:27865816 original size:27 final size:28
Alignment explanation
Indices: 27865786--27866082 Score: 219
Period size: 27 Copynumber: 11.1 Consensus size: 28
27865776 TAAAAGTTAG
**
27865786 TTTACCCTAT-GGGGGCGTTTCGATAAT
1 TTTACCCTATCGGGGGTATTTCGATAAT
*
27865813 TTTACCC-ATCGAGGGTATTTCGATAAT
1 TTTACCCTATCGGGGGTATTTCGATAAT
* *
27865840 TTTACCCT-TCGGGGGTATTTTGGTAAT
1 TTTACCCTATCGGGGGTATTTCGATAAT
*
27865867 TTTA-CCAATCGGGGGTATTTCGATAAT
1 TTTACCCTATCGGGGGTATTTCGATAAT
27865894 TTTACCCT-TC-GGGGTATTTC-AGTAAT
1 TTTACCCTATCGGGGGTATTTCGA-TAAT
* * * *
27865920 TTTACCC-ATCGAGGGTATTTTGGTAGT
1 TTTACCCTATCGGGGGTATTTCGATAAT
* * ** * * *
27865947 TTTA-TCTACCAAGGGTATTTTGGTAAG
1 TTTACCCTATCGGGGGTATTTCGATAAT
* ** *
27865974 TTTACTC-ATC-GATGTATTTCGGTAAT
1 TTTACCCTATCGGGGGTATTTCGATAAT
* *
27866000 TTTACCC-ATCGAGGGTATTTCGGTAAT
1 TTTACCCTATCGGGGGTATTTCGATAAT
* *
27866027 TTTA-CCTATCGAGAGTATTTC-AGTAAT
1 TTTACCCTATCGGGGGTATTTCGA-TAAT
** *
27866054 TTTACCC-ATCAAGGGTATTTTGATAAT
1 TTTACCCTATCGGGGGTATTTCGATAAT
27866081 TT
1 TT
27866083 AGGCCCATTA
Statistics
Matches: 221, Mismatches: 34, Indels: 30
0.78 0.12 0.11
Matches are distributed among these distances:
25 1 0.00
26 50 0.23
27 163 0.74
28 7 0.03
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.41
Consensus pattern (28 bp):
TTTACCCTATCGGGGGTATTTCGATAAT
Found at i:27865868 original size:54 final size:54
Alignment explanation
Indices: 27865809--27866082 Score: 295
Period size: 54 Copynumber: 5.1 Consensus size: 54
27865799 GGCGTTTCGA
**
27865809 TAATTTTACCCATCGAGGGTATTTCGATAATTTTACCCTTCGGGGGTATTTTGG
1 TAATTTTACCCATCGAGGGTATTTCGATAATTTTACCCTTCAAGGGTATTTTGG
* * * **
27865863 TAATTTTACCAATCGGGGGTATTTCGATAATTTTACCCTTC-GGGGTATTTCAG
1 TAATTTTACCCATCGAGGGTATTTCGATAATTTTACCCTTCAAGGGTATTTTGG
* * * * *
27865916 TAATTTTACCCATCGAGGGTATTTTGGTAGTTTTA-TCTACCAAGGGTATTTTGG
1 TAATTTTACCCATCGAGGGTATTTCGATAATTTTACCCT-TCAAGGGTATTTTGG
* * * * * * *
27865970 TAAGTTTACTCATCGA-TGTATTTCGGTAATTTTACCCATCGAGGGTATTTCGG
1 TAATTTTACCCATCGAGGGTATTTCGATAATTTTACCCTTCAAGGGTATTTTGG
* * * *
27866023 TAATTTTACCTATCGAGAGTATTTC-AGTAATTTTACCCATCAAGGGTATTTTGA
1 TAATTTTACCCATCGAGGGTATTTCGA-TAATTTTACCCTTCAAGGGTATTTTGG
27866077 TAATTT
1 TAATTT
27866083 AGGCCCATTA
Statistics
Matches: 183, Mismatches: 32, Indels: 10
0.81 0.14 0.04
Matches are distributed among these distances:
52 2 0.01
53 81 0.44
54 100 0.55
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (54 bp):
TAATTTTACCCATCGAGGGTATTTCGATAATTTTACCCTTCAAGGGTATTTTGG
Found at i:27865939 original size:80 final size:79
Alignment explanation
Indices: 27865803--27866082 Score: 319
Period size: 80 Copynumber: 3.5 Consensus size: 79
27865793 TATGGGGGCG
* *
27865803 TTTCGATAATTTTACCCATCGAGGGTATTTCGATAATTTTACCCTTCGGGGGTATTTTGGTAATT
1 TTTCGATAATTTTACCCATCG-GGGTATTTCG-TAATTTTACCCATCGAGGGTATTTTGGTAATT
* *
27865868 TTACCAATCGGGGGTA
64 TTACCTATCGAGGGTA
* *
27865884 TTTCGATAATTTTACCCTTCGGGGTATTTCAGTAATTTTACCCATCGAGGGTATTTTGGTAGTTT
1 TTTCGATAATTTTACCCATCGGGGTATTTC-GTAATTTTACCCATCGAGGGTATTTTGGTAATTT
* * *
27865949 TATCTACCAAGGGTA
65 TACCTATCGAGGGTA
* * * * ** *
27865964 TTTTGGTAAGTTTACTCATCGATGTATTTCGGTAATTTTACCCATCGAGGGTATTTCGGTAATTT
1 TTTCGATAATTTTACCCATCGGGGTATTTC-GTAATTTTACCCATCGAGGGTATTTTGGTAATTT
*
27866029 TACCTATCGAGAGTA
65 TACCTATCGAGGGTA
* *
27866044 TTTC-AGTAATTTTACCCATCAAGGGTATTTTGATAATTT
1 TTTCGA-TAATTTTACCCATC-GGGGTATTTCG-TAATTT
27866083 AGGCCCATTA
Statistics
Matches: 164, Mismatches: 31, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
80 131 0.80
81 33 0.20
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (79 bp):
TTTCGATAATTTTACCCATCGGGGTATTTCGTAATTTTACCCATCGAGGGTATTTTGGTAATTTT
ACCTATCGAGGGTA
Found at i:27867297 original size:25 final size:25
Alignment explanation
Indices: 27867247--27867300 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
27867237 TGAACCTCTA
* *
27867247 ACCTCCTTACCACACCTGTGATGCC
1 ACCTCATTACCACACCTATGATGCC
*
27867272 ACCTCATTGCCACACCTATG-TCGCC
1 ACCTCATTACCACACCTATGAT-GCC
27867297 ACCT
1 ACCT
27867301 TGGCACTACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 1 0.04
25 24 0.96
ACGTcount: A:0.20, C:0.44, G:0.11, T:0.24
Consensus pattern (25 bp):
ACCTCATTACCACACCTATGATGCC
Found at i:27872284 original size:26 final size:26
Alignment explanation
Indices: 27872255--27872309 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
27872245 AACACACTAA
27872255 TATCGCAACAAAGCTACCAGTAACAG
1 TATCGCAACAAAGCTACCAGTAACAG
* * *
27872281 TATCGCAGCAAAGCTGCCAGTAATAG
1 TATCGCAACAAAGCTACCAGTAACAG
27872307 TAT
1 TAT
27872310 ACTTCCTCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (26 bp):
TATCGCAACAAAGCTACCAGTAACAG
Found at i:27874145 original size:41 final size:41
Alignment explanation
Indices: 27874088--27874412 Score: 452
Period size: 41 Copynumber: 7.9 Consensus size: 41
27874078 NNNNNNNNNA
*
27874088 AATCAGGTTATAAGCCTAGCAGGCTAAGTGCCGGTGAACTG
1 AATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAACTG
* **
27874129 AATCAGGCTATAAGCCTAGCAGGCTAAGTGCTGGTGATTTG
1 AATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAACTG
* * *
27874170 AATCAAGCTATAAGCCTAGCAGGCTAAGTGCCAGTGATCTG
1 AATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAACTG
* *
27874211 AATCAGGCTATAAACCTAGCAGGCTAAATGCCGGTGAACTG
1 AATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAACTG
* * * * *
27874252 GATTAGGCTATAAGTCTAGCAGGCTAAGTGCTGGTGATCTG
1 AATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAACTG
27874293 AATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAACTG
1 AATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAACTG
* * * *
27874334 GATTAGGCTATAAGCCTAGCAGGCTAAGTGCTGGTGATCTG
1 AATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAACTG
* * * *
27874375 AATCAGGCTTTAAGCCTAACAAGCTAAGTGCCAGTGAA
1 AATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAA
27874413 TCTGTTTATA
Statistics
Matches: 247, Mismatches: 37, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 247 1.00
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23
Consensus pattern (41 bp):
AATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAACTG
Found at i:27876544 original size:48 final size:48
Alignment explanation
Indices: 27876492--27876619 Score: 148
Period size: 48 Copynumber: 2.7 Consensus size: 48
27876482 TGTATATTTT
* * **
27876492 TTTCAAGCAACGAAAAGACTGGGAAAGAAAATGGACGGGAGTTTGGGA
1 TTTCAAGCAAAGAAAAGTCTGGGAAAGAAAATGGACAAGAGTTTGGGA
* * * * * *
27876540 TTTCAAGTAAAGAGAAGTCTGGGAAAAAAAAGGGACAAGATTTTGGGG
1 TTTCAAGCAAAGAAAAGTCTGGGAAAGAAAATGGACAAGAGTTTGGGA
* *
27876588 TTTCAGGCAAAGAAAAGTCTGAGAAAGAAAAT
1 TTTCAAGCAAAGAAAAGTCTGGGAAAGAAAAT
27876620 AATTTGTGCG
Statistics
Matches: 64, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
48 64 1.00
ACGTcount: A:0.43, C:0.09, G:0.30, T:0.19
Consensus pattern (48 bp):
TTTCAAGCAAAGAAAAGTCTGGGAAAGAAAATGGACAAGAGTTTGGGA
Found at i:27888279 original size:20 final size:20
Alignment explanation
Indices: 27888243--27888282 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
27888233 TACTGCTGAG
*
27888243 CAGAGGCACCGTGGTGCAAA
1 CAGAGGCACAGTGGTGCAAA
27888263 CAGAGGCACTAGT-GTGCAAA
1 CAGAGGCAC-AGTGGTGCAAA
27888283 AAGGGGCACC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.33, C:0.23, G:0.33, T:0.12
Consensus pattern (20 bp):
CAGAGGCACAGTGGTGCAAA
Found at i:27888299 original size:20 final size:20
Alignment explanation
Indices: 27888276--27888341 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 20
27888266 AGGCACTAGT
27888276 GTGCAAAAAGGGGCACCAAA
1 GTGCAAAAAGGGGCACCAAA
** * ***
27888296 GTGCAATGAGGGACATTGAA
1 GTGCAAAAAGGGGCACCAAA
* *
27888316 GTGCAAATAGAGGCACCAAA
1 GTGCAAAAAGGGGCACCAAA
27888336 GTGCAA
1 GTGCAA
27888342 TCTCGTACAA
Statistics
Matches: 33, Mismatches: 13, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.41, C:0.17, G:0.30, T:0.12
Consensus pattern (20 bp):
GTGCAAAAAGGGGCACCAAA
Found at i:27899895 original size:22 final size:21
Alignment explanation
Indices: 27899860--27899974 Score: 71
Period size: 19 Copynumber: 5.7 Consensus size: 21
27899850 AAAAGGTATC
* * *
27899860 TACAAATTAAATCTCTAATAT
1 TACAAATCATATCTCTAAGAT
27899881 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
27899904 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
27899923 TACATATCATA--TCTATGAT
1 TACAAATCATATCTCTAAGAT
* * *
27899942 TGCATATCATA--TCTAAGAG
1 TACAAATCATATCTCTAAGAT
*
27899961 TACATATCATATCT
1 TACAAATCATATCT
27899975 AAGATTGCAT
Statistics
Matches: 79, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
19 51 0.65
21 4 0.05
22 15 0.19
23 9 0.11
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.37
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:27899920 original size:19 final size:19
Alignment explanation
Indices: 27899896--27899987 Score: 148
Period size: 19 Copynumber: 4.8 Consensus size: 19
27899886 AATCATATCT
27899896 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
27899915 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
*
27899934 TCTATGATTGCATATCATA
1 TCTAAGATTGCATATCATA
* *
27899953 TCTAAGAGTACATATCATA
1 TCTAAGATTGCATATCATA
27899972 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
27899988 CTTGAAGATT
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 65 1.00
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:27899949 original size:38 final size:38
Alignment explanation
Indices: 27899889--27899987 Score: 166
Period size: 38 Copynumber: 2.7 Consensus size: 38
27899879 ATTACAAAAT
*
27899889 CATATC-T-TCTAAGATTGCATATCATATCTAAGATTA
1 CATATCATATCTAAGATTGCATATCATATCTAAGAGTA
*
27899925 CATATCATATCTATGATTGCATATCATATCTAAGAGTA
1 CATATCATATCTAAGATTGCATATCATATCTAAGAGTA
27899963 CATATCATATCTAAGATTGCATATC
1 CATATCATATCTAAGATTGCATATC
27899988 CTTGAAGATT
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
36 6 0.10
37 1 0.02
38 51 0.88
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.37
Consensus pattern (38 bp):
CATATCATATCTAAGATTGCATATCATATCTAAGAGTA
Found at i:27900120 original size:15 final size:14
Alignment explanation
Indices: 27900089--27900119 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
27900079 AATTTTGGAC
*
27900089 TTTGTTTTATTATT
1 TTTGGTTTATTATT
27900103 TTTGGTTTATTATT
1 TTTGGTTTATTATT
27900117 TTT
1 TTT
27900120 TTATGAGTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.00, G:0.10, T:0.77
Consensus pattern (14 bp):
TTTGGTTTATTATT
Found at i:27901139 original size:19 final size:19
Alignment explanation
Indices: 27901117--27901157 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
27901107 TGGCCTCTCC
27901117 TTTTCCTCTTCTTCTTTCT
1 TTTTCCTCTTCTTCTTTCT
* * *
27901136 TTTTCTTTTTCTTTTTTCT
1 TTTTCCTCTTCTTCTTTCT
27901155 TTT
1 TTT
27901158 CTTTTTCTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTCCTCTTCTTCTTTCT
Found at i:27901148 original size:12 final size:12
Alignment explanation
Indices: 27901125--27901168 Score: 63
Period size: 12 Copynumber: 3.6 Consensus size: 12
27901115 CCTTTTCCTC
27901125 TTCTTCTTTCTTT
1 TTCTT-TTTCTTT
27901138 TTCTTTTTCTTT
1 TTCTTTTTCTTT
27901150 TT-TCTTTTCTTT
1 TTCT-TTTTCTTT
27901162 TTCTTTT
1 TTCTTTT
27901169 CCCTTTTTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 1 0.03
12 22 0.76
13 6 0.21
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (12 bp):
TTCTTTTTCTTT
Found at i:27901157 original size:18 final size:19
Alignment explanation
Indices: 27901125--27901168 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 19
27901115 CCTTTTCCTC
*
27901125 TTCTTCTTTCTTTTTCTTT
1 TTCTTTTTTCTTTTTCTTT
27901144 TTCTTTTTTC-TTTTCTTT
1 TTCTTTTTTCTTTTTCTTT
27901162 TTCTTTT
1 TTCTTTT
27901169 CCCTTTTTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (19 bp):
TTCTTTTTTCTTTTTCTTT
Found at i:27901174 original size:18 final size:18
Alignment explanation
Indices: 27901136--27901175 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
27901126 TCTTCTTTCT
**
27901136 TTTTCTTTTTCTTTTTTC
1 TTTTCTTTTTCTTTTCCC
27901154 TTTTCTTTTTCTTTTCCC
1 TTTTCTTTTTCTTTTCCC
27901172 TTTT
1 TTTT
27901176 TCCATCATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTCTTTTTCTTTTCCC
Found at i:27901175 original size:24 final size:23
Alignment explanation
Indices: 27901116--27901177 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 23
27901106 TTGGCCTCTC
*
27901116 CTTTTCCTCTTCTTCTTTCTTTTT
1 CTTTTCC-CTTTTTCTTTCTTTTT
* *
27901140 CTTTTTCTTTTTTCTTTTCTTTTT
1 CTTTTCCCTTTTTC-TTTCTTTTT
27901164 CTTTTCCCTTTTTC
1 CTTTTCCCTTTTTC
27901178 CATCATCATT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 5 0.16
24 27 0.84
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (23 bp):
CTTTTCCCTTTTTCTTTCTTTTT
Found at i:27905541 original size:19 final size:19
Alignment explanation
Indices: 27905516--27905568 Score: 79
Period size: 19 Copynumber: 2.8 Consensus size: 19
27905506 ATCATATCTT
*
27905516 CTAAGATTGCATATCATAT
1 CTAAGATTGCATATCATAC
* *
27905535 TTAAGATTACATATCATAC
1 CTAAGATTGCATATCATAC
27905554 CTAAGATTGCATATC
1 CTAAGATTGCATATC
27905569 CTTGAATATT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (19 bp):
CTAAGATTGCATATCATAC
Found at i:27906855 original size:16 final size:16
Alignment explanation
Indices: 27906834--27906875 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
27906824 TGTTTGGCTC
** *
27906834 GCTGTAATGGAATAGA
1 GCTGTAATAAAATAAA
27906850 GCTGTAATAAAATAAA
1 GCTGTAATAAAATAAA
27906866 GCTGTAATAA
1 GCTGTAATAA
27906876 GTAATTCAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.45, C:0.07, G:0.21, T:0.26
Consensus pattern (16 bp):
GCTGTAATAAAATAAA
Found at i:27908851 original size:15 final size:15
Alignment explanation
Indices: 27908831--27908862 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
27908821 ATTGCACAAC
27908831 TTAATAGTAAAGCAT
1 TTAATAGTAAAGCAT
27908846 TTAATAGTAAAGCAT
1 TTAATAGTAAAGCAT
27908861 TT
1 TT
27908863 TCCTCCATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (15 bp):
TTAATAGTAAAGCAT
Found at i:27920887 original size:15 final size:15
Alignment explanation
Indices: 27920867--27920896 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
27920857 ATTGAGGAGT
27920867 CAATTAATAATTAAC
1 CAATTAATAATTAAC
27920882 CAATTAATAATTAAC
1 CAATTAATAATTAAC
27920897 AAATGGACCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.33
Consensus pattern (15 bp):
CAATTAATAATTAAC
Found at i:27923774 original size:9 final size:9
Alignment explanation
Indices: 27923760--27923796 Score: 74
Period size: 9 Copynumber: 4.1 Consensus size: 9
27923750 TATAGTTTGA
27923760 TATTCGAAT
1 TATTCGAAT
27923769 TATTCGAAT
1 TATTCGAAT
27923778 TATTCGAAT
1 TATTCGAAT
27923787 TATTCGAAT
1 TATTCGAAT
27923796 T
1 T
27923797 CGAAAACTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:27925273 original size:10 final size:10
Alignment explanation
Indices: 27925260--27925290 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
27925250 TAGATGAAAT
*
27925260 TTGAATTGAA
1 TTGAATCGAA
27925270 TTGAATCGAA
1 TTGAATCGAA
27925280 TTGAATCGAA
1 TTGAATCGAA
27925290 T
1 T
27925291 ATATTTGTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.35
Consensus pattern (10 bp):
TTGAATCGAA
Found at i:27925489 original size:1 final size:1
Alignment explanation
Indices: 27925485--27925512 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
27925475 AGCAAAAGTC
27925485 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
27925513 CTAAACCAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:27933430 original size:16 final size:16
Alignment explanation
Indices: 27933409--27933442 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
27933399 AGGAGGAGTG
*
27933409 TTGAGAATCTTTGATA
1 TTGAGAATCTTTCATA
27933425 TTGAGAATCTTTCATA
1 TTGAGAATCTTTCATA
27933441 TT
1 TT
27933443 ATTAAATAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.09, G:0.15, T:0.47
Consensus pattern (16 bp):
TTGAGAATCTTTCATA
Found at i:27935243 original size:82 final size:82
Alignment explanation
Indices: 27935106--27935262 Score: 260
Period size: 82 Copynumber: 1.9 Consensus size: 82
27935096 TCTCCGCCAA
* * *
27935106 TGATCACGAAGCAACTCAATTGTCTATTTATTACACCATTGGACATATTATTACCGAAAAATACA
1 TGATCACGAAGCAACTCAACTGTCTATTTATTACACCATTGGAAATATCATTACCGAAAAATACA
27935171 CAAAAAGAAACCACTAG
66 CAAAAAGAAACCACTAG
* * *
27935188 TGATCACGAAGCAACTCAACTGTCTATTTATTCCACCATTGGAAATATCATTACCGGAAAATGCA
1 TGATCACGAAGCAACTCAACTGTCTATTTATTACACCATTGGAAATATCATTACCGAAAAATACA
27935253 CAAAAAGAAA
66 CAAAAAGAAA
27935263 ACATTCAAAT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
82 69 1.00
ACGTcount: A:0.42, C:0.21, G:0.12, T:0.25
Consensus pattern (82 bp):
TGATCACGAAGCAACTCAACTGTCTATTTATTACACCATTGGAAATATCATTACCGAAAAATACA
CAAAAAGAAACCACTAG
Found at i:27937152 original size:5 final size:5
Alignment explanation
Indices: 27937142--27937170 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
27937132 CACACTTCCA
27937142 TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
27937171 ACTCTTTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (5 bp):
TTTTG
Found at i:27946552 original size:23 final size:24
Alignment explanation
Indices: 27946522--27946629 Score: 150
Period size: 24 Copynumber: 4.6 Consensus size: 24
27946512 CATTATTGGG
*
27946522 AAAGGATGAATTGACGG-AAATGT
1 AAAGGATGAATTGAAGGAAAATGT
27946545 AAAGGATGAATTGAAGGAAAATGT
1 AAAGGATGAATTGAAGGAAAATGT
* *
27946569 AAAGGA-GAAACTGACGGAAAATGT
1 AAAGGATG-AATTGAAGGAAAATGT
*
27946593 AAAGGATGAATTGAAGG-TAATGT
1 AAAGGATGAATTGAAGGAAAATGT
27946616 AAAGGATGAATTGA
1 AAAGGATGAATTGA
27946630 TGACAAATTG
Statistics
Matches: 76, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
23 36 0.47
24 39 0.51
25 1 0.01
ACGTcount: A:0.47, C:0.03, G:0.30, T:0.20
Consensus pattern (24 bp):
AAAGGATGAATTGAAGGAAAATGT
Found at i:27949245 original size:91 final size:92
Alignment explanation
Indices: 27949078--27949258 Score: 283
Period size: 91 Copynumber: 2.0 Consensus size: 92
27949068 TTTTTTTTTC
* ** *
27949078 TTTTTAATGGAATGTATTGAACCTTTTAACGTGAAGAGGGATGACAACCCAAGCACCCCACCCCG
1 TTTTTAA-GGAATGTATCGAACCTTTTAACAAGAAGAGAGATGACAACCCAAGCACCCCACCCCG
*
27949143 GTTACTGAGCCCAACACACTCTTAATTA
65 GTTACTCAGCCCAACACACTCTTAATTA
* *
27949171 TTTTTAA-GAATGTATCGAACCTTTTGACAAGAAGAGAGATGACAACCCAAGCACCCCACCTCGG
1 TTTTTAAGGAATGTATCGAACCTTTTAACAAGAAGAGAGATGACAACCCAAGCACCCCACCCCGG
27949235 TTACTCAGCCCAACACACTCTTAA
66 TTACTCAGCCCAACACACTCTTAA
27949259 AATAATTTAT
Statistics
Matches: 81, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
91 74 0.91
93 7 0.09
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (92 bp):
TTTTTAAGGAATGTATCGAACCTTTTAACAAGAAGAGAGATGACAACCCAAGCACCCCACCCCGG
TTACTCAGCCCAACACACTCTTAATTA
Found at i:27955425 original size:21 final size:19
Alignment explanation
Indices: 27955399--27955445 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 19
27955389 TCATTTTTAG
27955399 CAACTTCCTCTTCTTCAGCAA
1 CAACTT-CTC-TCTTCAGCAA
*
27955420 CAACTT-TCTCTTCTGCAA
1 CAACTTCTCTCTTCAGCAA
27955438 CAACTTCT
1 CAACTTCT
27955446 GCTTTTGCAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 15 0.62
19 3 0.12
21 6 0.25
ACGTcount: A:0.23, C:0.36, G:0.04, T:0.36
Consensus pattern (19 bp):
CAACTTCTCTCTTCAGCAA
Found at i:27968442 original size:40 final size:41
Alignment explanation
Indices: 27968366--27968470 Score: 108
Period size: 40 Copynumber: 2.6 Consensus size: 41
27968356 GCTTAGATAA
*
27968366 AAAATACCGCTAAAAATCAAGCATTACCGGCGCTTTTA-AG
1 AAAATACCGCTAAAAATCAAGCATTACCGGCACTTTTAGAG
* * * * *
27968406 AAAATGCCGCTAAAGATCGAGTATTAGCGGCACTTTTAGAG
1 AAAATACCGCTAAAAATCAAGCATTACCGGCACTTTTAGAG
* * *
27968447 -AAACACTGCTAAAAAT-GAGCATTA
1 AAAATACCGCTAAAAATCAAGCATTA
27968471 GCGGTGTTTT
Statistics
Matches: 53, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
39 7 0.13
40 44 0.83
41 2 0.04
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.23
Consensus pattern (41 bp):
AAAATACCGCTAAAAATCAAGCATTACCGGCACTTTTAGAG
Found at i:27968590 original size:41 final size:41
Alignment explanation
Indices: 27968531--27968881 Score: 513
Period size: 41 Copynumber: 8.6 Consensus size: 41
27968521 TATTTGAGTT
* * *
27968531 CTCGGGTCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAGTT
1 CTCGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATG
* * *
27968572 TTCGGGTCTTTAGTGGCGTTTTTGAAGAAGAGCCGCTAATG
1 CTCGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATG
* * *
27968613 TTTGGGTCTTTAGTGGCGTTTTTGAAGAAGCGCCGCTAATG
1 CTCGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATG
* *
27968654 CTCGGGTCTTTAGCGGCGTTTTTGGAGAATCGCCGCTAATG
1 CTCGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATG
*
27968695 CTCGGGTCTTTAGCGGCATTTTTGAAGAAGCGCCGCTAATG
1 CTCGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATG
* * * *
27968736 CTCGGGTCTTTAGCGGTGTTTTTAAAGAAGCACTGCTAATG
1 CTCGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATG
* * *
27968777 CTCGGGTCTTTAGAGGCATTTTTGAAGAAGCGCTGCTAATG
1 CTCGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATG
* *
27968818 CTCAGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATT
1 CTCGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATG
27968859 CTCGGGTCTTTAGCGGCGTTTTT
1 CTCGGGTCTTTAGCGGCGTTTTT
27968882 AAAAAAGCTT
Statistics
Matches: 278, Mismatches: 32, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 278 1.00
ACGTcount: A:0.18, C:0.19, G:0.30, T:0.33
Consensus pattern (41 bp):
CTCGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATG
Found at i:27974684 original size:43 final size:43
Alignment explanation
Indices: 27974637--27974929 Score: 302
Period size: 43 Copynumber: 6.8 Consensus size: 43
27974627 TTTTTAATAG
* * ** *
27974637 AAGCGCCGCTAAAGCTCATGACCTTTAGCGGCGTTTGTAGGAA
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAA
** * * * * *** *
27974680 AAGCGTAGCTGAAGGTCTTGTTCTTTAGCAGCGTTTTTAATAG
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAA
* * **
27974723 AAGCGCCGCTAAAGCTCATGACCTTTAGCGGCGTTTGTGGGAA
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAA
** * * * *
27974766 AAGCGTAGCTGAAGGTCTTGTTCTTTAGCAGCGTTTTTGGGAA
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAA
* *
27974809 AAGCGCCGCTAAAAGTCTTGGTCTTTAGCGGCGTTTGTGGGAG
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAA
*
27974852 AA-CGCCGCTAAAGGTCTTGGTCTTTAG-GGACATTTGTGGGAA
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGG-CGTTTGTGGGAA
*
27974894 AAGGGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTT
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTT
27974930 TTTCTGGCGC
Statistics
Matches: 200, Mismatches: 47, Indels: 6
0.79 0.19 0.02
Matches are distributed among these distances:
41 2 0.01
42 36 0.18
43 160 0.80
44 2 0.01
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.29
Consensus pattern (43 bp):
AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAA
Found at i:27974719 original size:86 final size:86
Alignment explanation
Indices: 27974619--27974878 Score: 371
Period size: 86 Copynumber: 3.0 Consensus size: 86
27974609 GTCAATGTTA
* *
27974619 TAGCGGCGTTTTTAATAGAAGCGCCGCTAAAGCTCATGACCTTTAGCGGCGTTTGTAGGAAAAGC
1 TAGCAGCGTTTTTAATAGAAGCGCCGCTAAAGCTCATGACCTTTAGCGGCGTTTGTGGGAAAAGC
27974684 GTAGCTGAAGGTCTTGTTCTT
66 GTAGCTGAAGGTCTTGTTCTT
27974705 TAGCAGCGTTTTTAATAGAAGCGCCGCTAAAGCTCATGACCTTTAGCGGCGTTTGTGGGAAAAGC
1 TAGCAGCGTTTTTAATAGAAGCGCCGCTAAAGCTCATGACCTTTAGCGGCGTTTGTGGGAAAAGC
27974770 GTAGCTGAAGGTCTTGTTCTT
66 GTAGCTGAAGGTCTTGTTCTT
*** * * ** *
27974791 TAGCAGCGTTTTTGGGAAAAGCGCCGCTAAAAG-TCTTGGTCTTTAGCGGCGTTTGTGGGAGAA-
1 TAGCAGCGTTTTTAATAGAAGCGCCGCT-AAAGCTCATGACCTTTAGCGGCGTTTGTGGGAAAAG
** * *
27974854 CGCCGCTAAAGGTCTTGGTCTT
65 CGTAGCTGAAGGTCTTGTTCTT
27974876 TAG
1 TAG
27974879 GGACATTTGT
Statistics
Matches: 159, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
85 21 0.13
86 134 0.84
87 4 0.03
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.30
Consensus pattern (86 bp):
TAGCAGCGTTTTTAATAGAAGCGCCGCTAAAGCTCATGACCTTTAGCGGCGTTTGTGGGAAAAGC
GTAGCTGAAGGTCTTGTTCTT
Found at i:27976107 original size:19 final size:19
Alignment explanation
Indices: 27976084--27976135 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
27976074 AAAAAAACTT
*
27976084 AAAAATCATTAAAATTTA-
1 AAAAATCATTAAAAATTAC
**
27976102 ATAAAAAAATTAAAAATTAC
1 A-AAAATCATTAAAAATTAC
27976122 AAAAATCA-TAAAAA
1 AAAAATCATTAAAAA
27976136 AAACTATAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
18 7 0.26
19 19 0.70
20 1 0.04
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (19 bp):
AAAAATCATTAAAAATTAC
Found at i:27976126 original size:29 final size:30
Alignment explanation
Indices: 27976071--27976127 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
27976061 AATTATAAAA
**
27976071 AATAAAAAAACTTAAAAATCATTAAAATTT
1 AATAAAAAAACTTAAAAATCACAAAAATTT
*
27976101 AATAAAAAAA-TTAAAAATTACAAAAAT
1 AATAAAAAAACTTAAAAATCACAAAAAT
27976128 CATAAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 14 0.58
30 10 0.42
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.26
Consensus pattern (30 bp):
AATAAAAAAACTTAAAAATCACAAAAATTT
Found at i:27976187 original size:30 final size:28
Alignment explanation
Indices: 27976102--27976175 Score: 96
Period size: 30 Copynumber: 2.6 Consensus size: 28
27976092 TTAAAATTTA
27976102 ATAAAAAAATTA-AAAATTACAAAAATC
1 ATAAAAAAATTATAAAATTACAAAAATC
* *
27976129 ATAAAAAAAACTATAAAATTTTATAAAAATC
1 AT-AAAAAAATTATAAAA--TTACAAAAATC
27976160 ATAAAAAAATTATAAA
1 ATAAAAAAATTATAAA
27976176 CTTCACCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
27 2 0.05
28 9 0.22
29 4 0.10
30 13 0.32
31 12 0.30
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (28 bp):
ATAAAAAAATTATAAAATTACAAAAATC
Found at i:27976415 original size:21 final size:22
Alignment explanation
Indices: 27976358--27976415 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 22
27976348 TTGGTATGAT
27976358 AATTTTTATAATTTAT-TTTACG
1 AATTTTTATAATTT-TCTTTACG
*
27976380 AA-TCTTAT-A-TTTCTTTAC-
1 AATTTTTATAATTTTCTTTACG
27976398 AATTTTTATAATTTTCTT
1 AATTTTTATAATTTTCTT
27976416 ATGACTTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
18 3 0.10
19 12 0.40
20 2 0.07
21 11 0.37
22 2 0.07
ACGTcount: A:0.29, C:0.09, G:0.02, T:0.60
Consensus pattern (22 bp):
AATTTTTATAATTTTCTTTACG
Found at i:27979307 original size:138 final size:138
Alignment explanation
Indices: 27978962--27979655 Score: 1097
Period size: 138 Copynumber: 5.0 Consensus size: 138
27978952 TAGAAAACTA
*
27978962 AATTATATTCTTTCCAAAA-ACTATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
* *
27979026 TATAATTGTTTATATTAATAAATTTGGCAAAATATATACAATTAATATTTTGAATGAATCAAATT
66 TATAATTGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGAATCAAA-T
*
27979091 TATATATATT
130 T-CATATATT
* * *
27979101 AATTATATTCTTTCCAAATGAATATTAATTTCTATATCTTTTATATTTTGACCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
* * * *
27979166 TATAATTGTTTGTATTAATAAATTCGATAAAATATATACAATTAACATTTTGTATGAATCAAATT
66 TATAATTGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
27979231 CATATATT
131 CATATATT
* * *
27979239 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCCTTTATATTTTCAACGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
* * *
27979304 TATAACTATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
66 TATAATTGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
27979369 CATATATT
131 CATATATT
* *
27979377 AATTATATTCTTTCCAAAAAAATATTAGTTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
*
27979442 TATAATT-TTTATATTAATAAATTTGGTAAAATGTATACAATTAATATTTTGTATGAATCAAATT
66 TATAATTGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
27979506 CATATATT
131 CATATATT
* * * *
27979514 AATTATATTATTTCAAAAAGAATATTAATTTCCATGCCTTTTATATTTTGACTGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
* * *
27979579 TAT-ATCTGTTTATATTAATAAATTTGGTAAAATATATATAATTAATATTTTGTATGAACCACAT
66 TATAAT-TGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGAATCAAAT
27979643 TCATATATT
130 TCATATATT
27979652 AATT
1 AATT
27979656 TTATCTATGT
Statistics
Matches: 512, Mismatches: 40, Indels: 7
0.92 0.07 0.01
Matches are distributed among these distances:
136 2 0.00
137 126 0.25
138 265 0.52
139 20 0.04
140 99 0.19
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.45
Consensus pattern (138 bp):
AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
TATAATTGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
CATATATT
Found at i:27979559 original size:275 final size:275
Alignment explanation
Indices: 27978962--27979655 Score: 1079
Period size: 275 Copynumber: 2.5 Consensus size: 275
27978952 TAGAAAACTA
* * *
27978962 AATTATATTCTTTCCAAAA-ACTATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGCCTTTTATATTTT-AACGAAATTAATTAA
* * *
27979026 TATAATTGTTTATATTAATAAATTTGGCAAAATATATACAATTAATATTTTGAATGAATCAAATT
65 TATAACTGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGAATCAAA-T
* ** *
27979091 TATATATATTAATTATATTCTTTCCAAATGAATATTAATTTCTATATCTTTTATATTTTGACCGA
129 T-CATATATTAATTATATTCTTTCCAAAAAAATATTAATTTCCATATCTTTTATATTTTGACCGA
*
27979156 AATTAATTAATATAATTGTTTGTATTAATAAATTCGATAAAATATATACAATTAACATTTTGTAT
193 AATTAATTAATATAATTGTTTATATTAATAAATTCGATAAAATATATACAATTAACATTTTGTAT
27979221 GAATCAAATTCATATATT
258 GAATCAAATTCATATATT
27979239 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCC-TTTATATTTTCAACGAAATTAATTA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATG-CCTTTTATATTTT-AACGAAATTAATTA
* *
27979303 ATATAACTATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAAT
64 ATATAACTGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGAATCAAAT
* *
27979368 TCATATATTAATTATATTCTTTCCAAAAAAATATTAGTTTCCATGTCTTTTATATTTTGACCGAA
129 TCATATATTAATTATATTCTTTCCAAAAAAATATTAATTTCCATATCTTTTATATTTTGACCGAA
* * * *
27979433 ATTAATTAATATAATT-TTTATATTAATAAATTTGGTAAAATGTATACAATTAATATTTTGTATG
194 ATTAATTAATATAATTGTTTATATTAATAAATTCGATAAAATATATACAATTAACATTTTGTATG
27979497 AATCAAATTCATATATT
259 AATCAAATTCATATATT
* * *
27979514 AATTATATTATTTCAAAAAGAATATTAATTTCCATGCCTTTTATATTTTGACTGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGCCTTTTATATTTTAAC-GAAATTAATTAA
* * * *
27979579 TATATCTGTTTATATTAATAAATTTGGTAAAATATATATAATTAATATTTTGTATGAACCACATT
65 TATAACTGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
27979644 CATATATTAATT
130 CATATATTAATT
27979656 TTATCTATGT
Statistics
Matches: 384, Mismatches: 29, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
274 4 0.01
275 187 0.49
276 74 0.19
277 21 0.05
278 97 0.25
279 1 0.00
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.45
Consensus pattern (275 bp):
AATTATATTCTTTCCAAAAGAATATTAATTTCCATGCCTTTTATATTTTAACGAAATTAATTAAT
ATAACTGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGAATCAAATTC
ATATATTAATTATATTCTTTCCAAAAAAATATTAATTTCCATATCTTTTATATTTTGACCGAAAT
TAATTAATATAATTGTTTATATTAATAAATTCGATAAAATATATACAATTAACATTTTGTATGAA
TCAAATTCATATATT
Found at i:27979582 original size:71 final size:71
Alignment explanation
Indices: 27979365--27979583 Score: 161
Period size: 71 Copynumber: 3.2 Consensus size: 71
27979355 GTATGAATCA
* * * *
27979365 AATTCATATATTAATTATATTCTTTCCAAAAA-AATATTAGTTTCCATGTCTTTTATATTTTGAC
1 AATTAATATATTAATTATATTATTT-CAAAAAGAATATTAATTTCCATGCCTTTTATATTTTGAC
*
27979429 CGAAATT
65 TGAAATT
* * ** * * * * ** *
27979436 AATTAATATAATT-TTTATATTA-AT-AAATTTG-GTA-AAATGT--ATACAATTAATATTTTGT
1 AATTAATAT-ATTAATTATATTATTTCAAA-AAGAATATTAATTTCCATGCCTTTTATATTTTG-
*
27979494 A-TG-AATCA
63 ACTGAAAT-T
*
27979502 AATTCATATATTAATTATATTATTTCAAAAAGAATATTAATTTCCATGCCTTTTATATTTTGACT
1 AATTAATATATTAATTATATTATTTCAAAAAGAATATTAATTTCCATGCCTTTTATATTTTGACT
27979567 GAAATT
66 GAAATT
27979573 AATTAATATAT
1 AATTAATATAT
27979584 CTGTTTATAT
Statistics
Matches: 103, Mismatches: 31, Indels: 28
0.64 0.19 0.17
Matches are distributed among these distances:
65 6 0.06
66 29 0.28
67 3 0.03
68 11 0.11
69 6 0.06
70 2 0.02
71 40 0.39
72 6 0.06
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (71 bp):
AATTAATATATTAATTATATTATTTCAAAAAGAATATTAATTTCCATGCCTTTTATATTTTGACT
GAAATT
Found at i:27979741 original size:17 final size:17
Alignment explanation
Indices: 27979721--27979753 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
27979711 TTTAACTATC
27979721 AAATTAAAT-TAATTCAA
1 AAATT-AATCTAATTCAA
27979738 AAATTAATCTAATTCA
1 AAATTAATCTAATTCA
27979754 TGTGACAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATTAATCTAATTCAA
Found at i:27984358 original size:18 final size:18
Alignment explanation
Indices: 27984314--27984358 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
27984304 GCAATAAGAA
27984314 AACGTTTTGAAATTGAAT
1 AACGTTTTGAAATTGAAT
*
27984332 AACGATTTGTAAA-TGAAT
1 AACGTTTTG-AAATTGAAT
*
27984350 AATGTTTTG
1 AACGTTTTG
27984359 GAAAAGAACG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 20 0.87
19 3 0.13
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40
Consensus pattern (18 bp):
AACGTTTTGAAATTGAAT
Found at i:27987024 original size:27 final size:27
Alignment explanation
Indices: 27986970--27987033 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
27986960 TTTATCCCTA
*
27986970 GTAAAATTTT-GACCATTTTACCAGTG
1 GTAAAATTTTGGACCATTTTACCACTG
** *
27986996 GTAAAATTTTGGATGATTTTACCTCTG
1 GTAAAATTTTGGACCATTTTACCACTG
27987023 GTAAAATTTTG
1 GTAAAATTTTG
27987034 AGAAAATATG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
26 10 0.30
27 23 0.70
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.42
Consensus pattern (27 bp):
GTAAAATTTTGGACCATTTTACCACTG
Found at i:27988757 original size:23 final size:23
Alignment explanation
Indices: 27988727--27988775 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
27988717 TACGGAAGGA
27988727 AAACTTGTATTAGTAAATAAACT
1 AAACTTGTATTAGTAAATAAACT
*
27988750 AAACTTGTATTAGTAGATAAACT
1 AAACTTGTATTAGTAAATAAACT
27988773 AAA
1 AAA
27988776 TAAGATCATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.49, C:0.08, G:0.10, T:0.33
Consensus pattern (23 bp):
AAACTTGTATTAGTAAATAAACT
Found at i:27990706 original size:24 final size:24
Alignment explanation
Indices: 27990679--27990726 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
27990669 AATTGATGTG
27990679 CAAATCAGTGAGTTAAAGGGAGCT
1 CAAATCAGTGAGTTAAAGGGAGCT
27990703 CAAATCAGTGAGTTAAAGGGAGCT
1 CAAATCAGTGAGTTAAAGGGAGCT
27990727 GAGGTGGTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.12, G:0.29, T:0.21
Consensus pattern (24 bp):
CAAATCAGTGAGTTAAAGGGAGCT
Found at i:27992418 original size:33 final size:33
Alignment explanation
Indices: 27992391--27992466 Score: 116
Period size: 33 Copynumber: 2.3 Consensus size: 33
27992381 ATAACTCGGT
27992391 TATGGTCTTATCATCAGAATGCTATAACCCAGC
1 TATGGTCTTATCATCAGAATGCTATAACCCAGC
* * * *
27992424 TATGGTCTTATCATCAGTATGCCATAGCCCAAC
1 TATGGTCTTATCATCAGAATGCTATAACCCAGC
27992457 TATGGTCTTA
1 TATGGTCTTA
27992467 CATATATACA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.33
Consensus pattern (33 bp):
TATGGTCTTATCATCAGAATGCTATAACCCAGC
Found at i:28003927 original size:41 final size:41
Alignment explanation
Indices: 28003786--28003927 Score: 196
Period size: 41 Copynumber: 3.5 Consensus size: 41
28003776 TTTAAAATGA
* * *
28003786 TTCACTGGCATTAAGCCT-ACTAGACGTAAAGTCTAAAATAT
1 TTCACTAGCATTAAGCCTGA-TAGACGTAAAGTCTGAATTAT
* * *
28003827 TACACCAGCATTAAGCCTGCTAGACGTAAAGTCTGAATTAT
1 TTCACTAGCATTAAGCCTGATAGACGTAAAGTCTGAATTAT
**
28003868 TTCACTAGCATTAAGCCTGATAGGTGTAAAGTCTGAATTAT
1 TTCACTAGCATTAAGCCTGATAGACGTAAAGTCTGAATTAT
28003909 TTCACTAGCATTAAGCCTG
1 TTCACTAGCATTAAGCCTG
28003928 CTAAGCACAG
Statistics
Matches: 89, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
41 89 1.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (41 bp):
TTCACTAGCATTAAGCCTGATAGACGTAAAGTCTGAATTAT
Found at i:28003945 original size:41 final size:40
Alignment explanation
Indices: 28003786--28003946 Score: 146
Period size: 41 Copynumber: 3.9 Consensus size: 40
28003776 TTTAAAATGA
* * * *
28003786 TTCACTGGCATTAAGCCTACT-AGACGTAAAGTCTAAAATAT
1 TTCACTAGCATTAAGCCTGCTAAGAC--AAAGTCTGAATTAT
* *
28003827 TACACCAGCATTAAGCCTGCT-AGACGTAAAGTCTGAATTAT
1 TTCACTAGCATTAAGCCTGCTAAGAC--AAAGTCTGAATTAT
* * **
28003868 TTCACTAGCATTAAGCCTGATAGGTGTAAAGTCTGAATTAT
1 TTCACTAGCATTAAGCCTGCTAAG-ACAAAGTCTGAATTAT
* *
28003909 TTCACTAGCATTAAGCCTGCTAAGCACAGAGCCTGAAT
1 TTCACTAGCATTAAGCCTGCTAAG-ACAAAGTCTGAAT
28003947 AACTCAGATA
Statistics
Matches: 99, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
41 98 0.99
42 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (40 bp):
TTCACTAGCATTAAGCCTGCTAAGACAAAGTCTGAATTAT
Found at i:28007607 original size:13 final size:13
Alignment explanation
Indices: 28007589--28007613 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28007579 ACAAACGATA
28007589 AAATTTTCACACG
1 AAATTTTCACACG
28007602 AAATTTTCACAC
1 AAATTTTCACAC
28007614 ATATCAATTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:28009550 original size:24 final size:24
Alignment explanation
Indices: 28009503--28009551 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
28009493 GCCGCTATAG
**
28009503 AACATGACCTTTAGCGGTGCTTTT
1 AACATGACCTTTAGCGGCACTTTT
* *
28009527 AACATGACCTTTAGTGGCATTTTT
1 AACATGACCTTTAGCGGCACTTTT
28009551 A
1 A
28009552 TCACAAACGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.39
Consensus pattern (24 bp):
AACATGACCTTTAGCGGCACTTTT
Found at i:28009594 original size:43 final size:43
Alignment explanation
Indices: 28009527--28009751 Score: 312
Period size: 43 Copynumber: 5.2 Consensus size: 43
28009517 CGGTGCTTTT
* * * *
28009527 AACATGACCTTTAGTGGCATTTTTATCACAAACGCAGTTAAAG
1 AACATGACCTTTAGCGGCACTTTTATCACAAACGCCGCTAAAG
* *
28009570 AACATGATCTTTAGCGGCACTTTTATCACAAACGCCGCTAAAT
1 AACATGACCTTTAGCGGCACTTTTATCACAAACGCCGCTAAAG
* *
28009613 AACATG-CCATTTAGCGGCACTTTTATCATAAATGCCGCTAAAG
1 AACATGACC-TTTAGCGGCACTTTTATCACAAACGCCGCTAAAG
*
28009656 AACATGACCTTTAGCGGCGCTTCTT-TCACAAACGCCGCTAAAG
1 AACATGACCTTTAGCGGCACTT-TTATCACAAACGCCGCTAAAG
*
28009699 AACATGACCTTTAGCGGCGCTTCTT-TCACAAACGCCGCTAAAG
1 AACATGACCTTTAGCGGCACTT-TTATCACAAACGCCGCTAAAG
28009742 AACATGACCT
1 AACATGACCT
28009752 GACTCTCCGA
Statistics
Matches: 166, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
42 1 0.01
43 161 0.97
44 4 0.02
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (43 bp):
AACATGACCTTTAGCGGCACTTTTATCACAAACGCCGCTAAAG
Found at i:28014242 original size:21 final size:21
Alignment explanation
Indices: 28014217--28014264 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
28014207 AATTGAAGTA
*
28014217 ACAAATGATGTAAAGGCAGAG
1 ACAAATGATGCAAAGGCAGAG
* *
28014238 ACAAATGATGCAGAGGTAGAG
1 ACAAATGATGCAAAGGCAGAG
28014259 ACAAAT
1 ACAAAT
28014265 TTAATGATTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.48, C:0.10, G:0.27, T:0.15
Consensus pattern (21 bp):
ACAAATGATGCAAAGGCAGAG
Found at i:28016113 original size:15 final size:15
Alignment explanation
Indices: 28016068--28016115 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
28016058 CTAAACCCCT
* *
28016068 AACCCTTAACCCATA
1 AACCCATAATCCATA
28016083 AA-CCATAATCTC-TA
1 AACCCATAATC-CATA
28016097 AACCCATAATCCATA
1 AACCCATAATCCATA
28016112 AACC
1 AACC
28016116 TTAGAATAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
14 11 0.39
15 17 0.61
ACGTcount: A:0.44, C:0.35, G:0.00, T:0.21
Consensus pattern (15 bp):
AACCCATAATCCATA
Found at i:28016151 original size:14 final size:14
Alignment explanation
Indices: 28016132--28016164 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
28016122 TAGGAACTCT
*
28016132 TAAACCTTAAACCC
1 TAAACCATAAACCC
28016146 TAAACCATAAACCC
1 TAAACCATAAACCC
28016160 TAAAC
1 TAAAC
28016165 TATATAGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.48, C:0.33, G:0.00, T:0.18
Consensus pattern (14 bp):
TAAACCATAAACCC
Found at i:28016325 original size:7 final size:7
Alignment explanation
Indices: 28016283--28016352 Score: 63
Period size: 7 Copynumber: 10.0 Consensus size: 7
28016273 AACCCCTATC
28016283 CCATAAA
1 CCATAAA
*
28016290 CCCTAAA
1 CCATAAA
*
28016297 TCATAAA
1 CCATAAA
*
28016304 ACATAAA
1 CCATAAA
**
28016311 CCCGAAA
1 CCATAAA
28016318 CCATAAA
1 CCATAAA
28016325 CC-TCAAA
1 CCAT-AAA
28016332 CC-TAAAA
1 CCAT-AAA
28016339 CCATAAA
1 CCATAAA
28016346 CCATAAA
1 CCATAAA
28016353 GCTCGATCTA
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
6 1 0.02
7 49 0.96
8 1 0.02
ACGTcount: A:0.54, C:0.30, G:0.01, T:0.14
Consensus pattern (7 bp):
CCATAAA
Found at i:28016389 original size:17 final size:17
Alignment explanation
Indices: 28016364--28016403 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
28016354 CTCGATCTAT
*
28016364 AGCGACATTTTTCGAAA
1 AGCGACATTTTCCGAAA
*
28016381 AGCGGCATTTTCCGAAA
1 AGCGACATTTTCCGAAA
28016398 AGCGAC
1 AGCGAC
28016404 GCTAATGCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.23
Consensus pattern (17 bp):
AGCGACATTTTCCGAAA
Found at i:28016552 original size:40 final size:40
Alignment explanation
Indices: 28016461--28016606 Score: 175
Period size: 40 Copynumber: 3.6 Consensus size: 40
28016451 TTTTTTGTGA
* * *
28016461 CATTTTTCAAAAAGCGCCGCTAATGGTCGACCTATAGCGG
1 CATTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGTGG
** * * * *
28016501 TGTTTTGCAAAACGCACCGGTAATGCTCGATCTATAGTGG
1 CATTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGTGG
* *
28016541 CATTTTTCAAAAGGCGCCGCTAATGCTCGATCTATAGTAG
1 CATTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGTGG
* *
28016581 CATTTTTCAAAAAGTGCTGCTAATGC
1 CATTTTTCAAAAAGCGCCGCTAATGC
28016607 CACTAAAGCT
Statistics
Matches: 87, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 87 1.00
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.29
Consensus pattern (40 bp):
CATTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGTGG
Found at i:28016731 original size:40 final size:40
Alignment explanation
Indices: 28016652--28017017 Score: 183
Period size: 40 Copynumber: 9.3 Consensus size: 40
28016642 TAATTTTTTT
* * * *
28016652 GCGGCATTTTTCGAA-AAGTGCTGCTAATGGTCGACCTATA
1 GCGGCATTTTTC-AAGAAGCGCCGCTAATGCTCGATCTATA
* * *
28016692 GCGGCGTTTTTCAAGAAGCGCCGCTAGTGCTCTATCTATA
1 GCGGCATTTTTCAAGAAGCGCCGCTAATGCTCGATCTATA
* *
28016732 GCGGCATTTTTCATGAAGCGCCGCTAATTCTCGATCTATA
1 GCGGCATTTTTCAAGAAGCGCCGCTAATGCTCGATCTATA
* * * * *
28016772 ACGGTATTTTCCAAGAAACGCCGCTAATGC-C-A-CTAAA
1 GCGGCATTTTTCAAGAAGCGCCGCTAATGCTCGATCTATA
* *** * * * ** ** * * *
28016809 GC-TCA-ACAT-AAAATAGGGGCG-TTGTGCTTAATTTTTTT
1 GCGGCATTTTTCAAGA-AGCGCCGCTAATGCTCGA-TCTATA
** * * * *
28016847 GCGGTGTTTTTCAAAAAGAGCCGCTAATGGTCGACCTATA
1 GCGGCATTTTTCAAGAAGCGCCGCTAATGCTCGATCTATA
* * *
28016887 GCAGCGTTTTTCAAGAAGCGCCGCGAATGCTCGATCTATA
1 GCGGCATTTTTCAAGAAGCGCCGCTAATGCTCGATCTATA
* ** *
28016927 GAGGTGTTTTTCAA-AAGGCGCCACTAATGCTCGATCTATA
1 GCGGCATTTTTCAAGAA-GCGCCGCTAATGCTCGATCTATA
* * * * * * *
28016967 ACTGCATTTTTTAAAAAGCGTCACTAATGCTAGATCTATA
1 GCGGCATTTTTCAAGAAGCGCCGCTAATGCTCGATCTATA
* *
28017007 ACGGCGTTTTT
1 GCGGCATTTTT
28017018 TTATCCAAAC
Statistics
Matches: 238, Mismatches: 76, Indels: 24
0.70 0.22 0.07
Matches are distributed among these distances:
34 7 0.03
35 4 0.02
36 2 0.01
37 5 0.02
38 4 0.02
39 5 0.02
40 200 0.84
41 11 0.05
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.31
Consensus pattern (40 bp):
GCGGCATTTTTCAAGAAGCGCCGCTAATGCTCGATCTATA
Found at i:28016731 original size:195 final size:194
Alignment explanation
Indices: 28016385--28016996 Score: 764
Period size: 195 Copynumber: 3.1 Consensus size: 194
28016375 TCGAAAAGCG
* * * * *
28016385 GCATTTTCCGAAAAGCGACGCTAATGCCACTAAAGCTCAACATAAAATGATGGTGTTATGCTTAA
1 GCATTTTTCAAAAAGCGCCGCTAATGCCACTAAAGCTCAACATAAAATGACGGTGTTGTGCTTAA
* * * * *
28016450 TTTTTTTGTGACATTTTTCAAAAAGCGCCGCTAATGGTCGACCTATAGCGGTGTTTTGCAA-AAC
66 TTTTTTTGCGGCATTTTTCAAAAAGAGCCGCTAATGGTCGACCTATAGCGGCGTTTTTCAAGAA-
* * * *
28016514 GCACCGGTAATGCTCGATCTATAGTGGCATTTTTCAAAAGGCGCCGCTAATGCTCGATCTATAGT
130 GCGCCGCTAATGCTCGATCTATAGAGGCATTTTTCAAAAGGCGCCGCTAATGCTCGATCTATAAT
* * * *
28016579 AGCATTTTTCAAAAAGTGCTGCTAATGCCACTAAAGCTCAACATAAAATGACAGTGTTGCGCTTA
1 -GCATTTTTCAAAAAGCGCCGCTAATGCCACTAAAGCTCAACATAAAATGACGGTGTTGTGCTTA
* * *
28016644 ATTTTTTTGCGGCATTTTTCGAAAAGTGCTGCTAATGGTCGACCTATAGCGGCGTTTTTCAAGAA
65 ATTTTTTTGCGGCATTTTTCAAAAAGAGCCGCTAATGGTCGACCTATAGCGGCGTTTTTCAAGAA
* * * * *
28016709 GCGCCGCTAGTGCTCTATCTATAGCGGCATTTTTCATGAA-GCGCCGCTAATTCTCGATCTATAA
130 GCGCCGCTAATGCTCGATCTATAGAGGCATTTTTCA-AAAGGCGCCGCTAATGCTCGATCTATAA
*
28016773 CG
194 -T
* * * *
28016775 GTATTTTCCAAGAAA-CGCCGCTAATGCCACTAAAGCTCAACATAAAAT-AGGGGCGTTGTGCTT
1 GCATTTTTCAA-AAAGCGCCGCTAATGCCACTAAAGCTCAACATAAAATGA-CGGTGTTGTGCTT
** *
28016838 AATTTTTTTGCGGTGTTTTTCAAAAAGAGCCGCTAATGGTCGACCTATAGCAGCGTTTTTCAAGA
64 AATTTTTTTGCGGCATTTTTCAAAAAGAGCCGCTAATGGTCGACCTATAGCGGCGTTTTTCAAGA
* ** *
28016903 AGCGCCGCGAATGCTCGATCTATAGAGGTGTTTTTCAAAAGGCGCCACTAATGCTCGATCTATAA
129 AGCGCCGCTAATGCTCGATCTATAGAGGCATTTTTCAAAAGGCGCCGCTAATGCTCGATCTATAA
28016968 CT
194 -T
* * *
28016970 GCATTTTTTAAAAAGCGTCACTAATGC
1 GCATTTTTCAAAAAGCGCCGCTAATGC
28016997 TAGATCTATA
Statistics
Matches: 356, Mismatches: 54, Indels: 14
0.84 0.13 0.03
Matches are distributed among these distances:
194 6 0.02
195 343 0.96
196 7 0.02
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (194 bp):
GCATTTTTCAAAAAGCGCCGCTAATGCCACTAAAGCTCAACATAAAATGACGGTGTTGTGCTTAA
TTTTTTTGCGGCATTTTTCAAAAAGAGCCGCTAATGGTCGACCTATAGCGGCGTTTTTCAAGAAG
CGCCGCTAATGCTCGATCTATAGAGGCATTTTTCAAAAGGCGCCGCTAATGCTCGATCTATAAT
Found at i:28021910 original size:27 final size:27
Alignment explanation
Indices: 28021880--28021934 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
28021870 AAGCTATTGC
28021880 ATTTAAACATAACTCTTTTTGGAACTA
1 ATTTAAACATAACTCTTTTTGGAACTA
*
28021907 ATTTAAACATAATTCTTTTTGGAACTA
1 ATTTAAACATAACTCTTTTTGGAACTA
28021934 A
1 A
28021935 CCACATGATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (27 bp):
ATTTAAACATAACTCTTTTTGGAACTA
Found at i:28050124 original size:25 final size:24
Alignment explanation
Indices: 28050088--28050164 Score: 77
Period size: 25 Copynumber: 3.2 Consensus size: 24
28050078 TATCATTTCT
* *
28050088 GCTCTTTTGAGCTATGATCGGTAA
1 GCTCTTTCGAGCTATGAACGGTAA
*
28050112 GCTCATTTCGAGCTGAAGAACGGTAA
1 GCTC-TTTCGAGCT-ATGAACGGTAA
*
28050138 GCTCTATCGAG-T-TGAAACGGTAA
1 GCTCTTTCGAGCTATG-AACGGTAA
28050161 GCTC
1 GCTC
28050165 ATAAGAGCTG
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
22 1 0.02
23 12 0.27
24 5 0.11
25 14 0.31
26 13 0.29
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (24 bp):
GCTCTTTCGAGCTATGAACGGTAA
Done.