Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr14
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: 244914714
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 4503000 characters in sequence are not A, C, G, or T
File 2 of 770
Found at i:265693 original size:16 final size:16
Alignment explanation
Indices: 265672--265708 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
265662 ATGAGTGAGT
265672 AGAGCCAATATCAATG
1 AGAGCCAATATCAATG
265688 AGAGCCAATATCAATG
1 AGAGCCAATATCAATG
265704 AGAGC
1 AGAGC
265709 ATAATATGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.16
Consensus pattern (16 bp):
AGAGCCAATATCAATG
Found at i:268289 original size:62 final size:62
Alignment explanation
Indices: 268183--268361 Score: 211
Period size: 62 Copynumber: 2.9 Consensus size: 62
268173 GTGCCTTGGT
* * * * *
268183 TGTGTCGTTTTTA-AGCACAAACAATGAATTACACGGCTTGGGCACACGCCCGTGTCCC-GG-
1 TGTGTGGTTTTTATA-CCCAAACAGTGAGTTACATGGCTTGGGCACACGCCCGTGTCCCTGGC
* * * *
268243 TCGTGTGGTTTTTATACCCCAAACAGTGAGTTACATGGCCTAGGCACATGCCCATGTCCCTGGC
1 T-GTGTGGTTTTTATA-CCCAAACAGTGAGTTACATGGCTTGGGCACACGCCCGTGTCCCTGGC
* *
268307 TGTGTGGTTTTTATACCCAAATAGTAAGTTACATGGCTTGGGCACACGCCCGTGT
1 TGTGTGGTTTTTATACCCAAACAGTGAGTTACATGGCTTGGGCACACGCCCGTGT
268362 ATACATTGAG
Statistics
Matches: 99, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
60 1 0.01
61 11 0.11
62 70 0.71
63 16 0.16
64 1 0.01
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.28
Consensus pattern (62 bp):
TGTGTGGTTTTTATACCCAAACAGTGAGTTACATGGCTTGGGCACACGCCCGTGTCCCTGGC
Found at i:268592 original size:290 final size:290
Alignment explanation
Indices: 268072--268651 Score: 1133
Period size: 290 Copynumber: 2.0 Consensus size: 290
268062 TCAGTTATTC
268072 ATACATTGAGGAAACCAATATCAATGTTTAGTAATATTCTCAGCCCCAGAAGATAGTTCTCGGAC
1 ATACATTGAGGAAACCAATATCAATGTTTAGTAATATTCTCAGCCCCAGAAGATAGTTCTCGGAC
*
268137 CGAATATCCTGTAACACTTCCTGGCCACATGCCCTTGTGCCTTGGTTGTGTCGTTTTTAAGCACA
66 CGAATATCCTGTAACACTTCCTGGCCACATGCCCTTGTGCCTTGGTCGTGTCGTTTTTAAGCACA
*
268202 AACAATGAATTACACGGCTTGGGCACACGCCCGTGTCCCGGTCGTGTGGTTTTTATACCCCAAAC
131 AACAATGAATTACACGGCTTGGGCACACACCCGTGTCCCGGTCGTGTGGTTTTTATACCCCAAAC
268267 AGTGAGTTACATGGCCTAGGCACATGCCCATGTCCCTGGCTGTGTGGTTTTTATACCCAAATAGT
196 AGTGAGTTACATGGCCTAGGCACATGCCCATGTCCCTGGCTGTGTGGTTTTTATACCCAAATAGT
268332 AAGTTACATGGCTTGGGCACACGCCCGTGT
261 AAGTTACATGGCTTGGGCACACGCCCGTGT
268362 ATACATTGAGGAAACCAATATCAATGTTTAGTAATATTCTCAGCCCCAGAAGATAGTTCTCGGAC
1 ATACATTGAGGAAACCAATATCAATGTTTAGTAATATTCTCAGCCCCAGAAGATAGTTCTCGGAC
268427 CGAATATCCTGTAACACTTCCTGGCCACATGCCCTTGTGCCTTGGTCGTGTCGTTTTTAAGCACA
66 CGAATATCCTGTAACACTTCCTGGCCACATGCCCTTGTGCCTTGGTCGTGTCGTTTTTAAGCACA
*
268492 AACAGTGAATTACACGGCTTGGGCACACACCCGTGTCCCGGTCGTGTGGTTTTTATACCCCAAAC
131 AACAATGAATTACACGGCTTGGGCACACACCCGTGTCCCGGTCGTGTGGTTTTTATACCCCAAAC
268557 AGTGAGTTACATGGCCTAGGCACATGCCCATGTCCCTGGCTGTGTGGTTTTTATACCCAAATAGT
196 AGTGAGTTACATGGCCTAGGCACATGCCCATGTCCCTGGCTGTGTGGTTTTTATACCCAAATAGT
268622 AAGTTACATGGCTTGGGCACACGCCCGTGT
261 AAGTTACATGGCTTGGGCACACGCCCGTGT
268652 CCCTGGCCGT
Statistics
Matches: 287, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
290 287 1.00
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.28
Consensus pattern (290 bp):
ATACATTGAGGAAACCAATATCAATGTTTAGTAATATTCTCAGCCCCAGAAGATAGTTCTCGGAC
CGAATATCCTGTAACACTTCCTGGCCACATGCCCTTGTGCCTTGGTCGTGTCGTTTTTAAGCACA
AACAATGAATTACACGGCTTGGGCACACACCCGTGTCCCGGTCGTGTGGTTTTTATACCCCAAAC
AGTGAGTTACATGGCCTAGGCACATGCCCATGTCCCTGGCTGTGTGGTTTTTATACCCAAATAGT
AAGTTACATGGCTTGGGCACACGCCCGTGT
Found at i:268708 original size:63 final size:63
Alignment explanation
Indices: 268446--268727 Score: 309
Period size: 62 Copynumber: 4.5 Consensus size: 63
268436 TGTAACACTT
* * * * * * * * *
268446 CCTGGCCACATGCCCTTGTGCCTTGGTCGTGTCGTTTTTA-AGCACAAACAGTGAATTACACGG
1 CCTGGGCACACGCCCGTGT-CCCTGGCCGTGTGGTTTTTATACCCCAAACAGTGAGTTACACGG
* * * *
268509 CTTGGGCACACACCCGTGTCCC-GGTCGTGTGGTTTTTATACCCCAAACAGTGAGTTACATGG
1 CCTGGGCACACGCCCGTGTCCCTGGCCGTGTGGTTTTTATACCCCAAACAGTGAGTTACACGG
* * * * * * *
268571 CCTAGGCACATGCCCATGTCCCTGGCTGTGTGGTTTTTATA-CCCAAATAGTAAGTTACATGG
1 CCTGGGCACACGCCCGTGTCCCTGGCCGTGTGGTTTTTATACCCCAAACAGTGAGTTACACGG
* *
268633 CTTGGGCACACGCCCGTGTCCCTGGCCGTATGGTTTTTATACCCCAAACAGTGAGTTACACGG
1 CCTGGGCACACGCCCGTGTCCCTGGCCGTGTGGTTTTTATACCCCAAACAGTGAGTTACACGG
** *
268696 CCTGGGCACACGCTTGTGTCCCTGGCCATGTG
1 CCTGGGCACACGCCCGTGTCCCTGGCCGTGTG
268728 AACCCTGCAC
Statistics
Matches: 182, Mismatches: 34, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
61 15 0.08
62 92 0.51
63 75 0.41
ACGTcount: A:0.19, C:0.28, G:0.25, T:0.28
Consensus pattern (63 bp):
CCTGGGCACACGCCCGTGTCCCTGGCCGTGTGGTTTTTATACCCCAAACAGTGAGTTACACGG
Found at i:270511 original size:16 final size:16
Alignment explanation
Indices: 270471--270514 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 16
270461 TATTGAAAAC
*
270471 TTTAAAAATAAA-AAT
1 TTTAAAAATAAATATT
270486 TTT--AAA-AAATATT
1 TTTAAAAATAAATATT
270499 TTTAAAAATAAATATT
1 TTTAAAAATAAATATT
270515 AAACATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
12 3 0.12
13 8 0.33
15 6 0.25
16 7 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TTTAAAAATAAATATT
Found at i:270637 original size:17 final size:18
Alignment explanation
Indices: 270615--270658 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
270605 AGACAAAAAA
*
270615 TAATTATAATCAAT-ATT
1 TAATTATAATAAATAATT
*
270632 TAATTATATTAAATAAATT
1 TAATTATAATAAAT-AATT
270651 TAATTATA
1 TAATTATA
270659 TTTATTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 12 0.52
19 11 0.48
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
TAATTATAATAAATAATT
Found at i:283357 original size:19 final size:19
Alignment explanation
Indices: 283335--283379 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
283325 GGTTGGGGAT
283335 CGTTTTGACATCAAAGGCA
1 CGTTTTGACATCAAAGGCA
* *
283354 CGTTTTGATATCAAAGGGA
1 CGTTTTGACATCAAAGGCA
283373 CGTTTTG
1 CGTTTTG
283380 CAGGCTACCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (19 bp):
CGTTTTGACATCAAAGGCA
Found at i:283733 original size:21 final size:21
Alignment explanation
Indices: 283707--283777 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
283697 TTGTGCCCCA
*
283707 TCCACACGGGCGTGTGGGGCC
1 TCCACATGGGCGTGTGGGGCC
* * *
283728 TTCACATGGGTGTGTGTGGCC
1 TCCACATGGGCGTGTGGGGCC
* * *
283749 TCCATATGGGCGTGT-AGACC
1 TCCACATGGGCGTGTGGGGCC
283769 TCCACATGG
1 TCCACATGG
283778 CATGGGCAAT
Statistics
Matches: 40, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
20 11 0.28
21 29 0.73
ACGTcount: A:0.14, C:0.27, G:0.35, T:0.24
Consensus pattern (21 bp):
TCCACATGGGCGTGTGGGGCC
Found at i:285343 original size:26 final size:25
Alignment explanation
Indices: 285275--285344 Score: 63
Period size: 26 Copynumber: 2.7 Consensus size: 25
285265 TTTTACTTTG
*
285275 TTATATTTTTTCA-TTGTATATATTA
1 TTATATTTTTT-ATTTTTATATATTA
* *
285300 TT-TATTTTACTATGTTTTATCTATTA
1 TTATATTTT-TTAT-TTTTATATATTA
285326 TTATATTTTTTAATTTTTA
1 TTATATTTTTT-ATTTTTA
285345 AAATATATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
24 7 0.19
25 3 0.08
26 18 0.50
27 8 0.22
ACGTcount: A:0.26, C:0.04, G:0.03, T:0.67
Consensus pattern (25 bp):
TTATATTTTTTATTTTTATATATTA
Found at i:295223 original size:217 final size:218
Alignment explanation
Indices: 294842--295258 Score: 692
Period size: 217 Copynumber: 1.9 Consensus size: 218
294832 TACAGAACAC
* * * * *
294842 TTCCTCCACATATATATAAAACCTACTCCAGACCAAATGCAAATATCAGATACAGATTTATTAGA
1 TTCCTCCACATATATATAAAACCCACCCCAGAACAAATGCAAATATCAGATACAAATTTATCAGA
* * *
294907 CTAAACATGCTCAACATGCTTTATACAACTAATAGATACACATATATCAGTATAATCAGGCATAC
66 CTAAACATGCTCAAAATGCTTTATACAAATAACAGATACACATATATCAGTATAATCAGGCATAC
* *
294972 ATTAGTACCCTAATCAGATTAGTCTAATAGAATTTCATAGCATACAGATAGGAGTTTAATTAGCC
131 ATTAGTACCCTAATCAGATCAGTCTAACAGAATTTCATAGCATACAGATAGGAGTTTAATTAGCC
295037 CTTACTGACTCTAGAAGTGTGGG
196 CTTACTGACTCTAGAAGTGTGGG
* * *
295060 TTCCT-CACATATATATAAAACCCACCCCATAACAGATGCAGATATCAGATACAAATTTATCAGA
1 TTCCTCCACATATATATAAAACCCACCCCAGAACAAATGCAAATATCAGATACAAATTTATCAGA
295124 CTAAACATGCTCAAAATGCTTTATACAAATAACAGATACACATATATCAGTATAATCAGGCATAC
66 CTAAACATGCTCAAAATGCTTTATACAAATAACAGATACACATATATCAGTATAATCAGGCATAC
* *
295189 ATTAGTATCCTAATCAGATCAGTCTAACAGAATTTCATAGCATACAGATAGGGGTTTAATTAGCC
131 ATTAGTACCCTAATCAGATCAGTCTAACAGAATTTCATAGCATACAGATAGGAGTTTAATTAGCC
295254 CTTAC
196 CTTAC
295259 CGACCCTACA
Statistics
Matches: 184, Mismatches: 15, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
217 179 0.97
218 5 0.03
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (218 bp):
TTCCTCCACATATATATAAAACCCACCCCAGAACAAATGCAAATATCAGATACAAATTTATCAGA
CTAAACATGCTCAAAATGCTTTATACAAATAACAGATACACATATATCAGTATAATCAGGCATAC
ATTAGTACCCTAATCAGATCAGTCTAACAGAATTTCATAGCATACAGATAGGAGTTTAATTAGCC
CTTACTGACTCTAGAAGTGTGGG
Found at i:301681 original size:18 final size:18
Alignment explanation
Indices: 301638--301683 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
301628 GCAGTCCTGT
*
301638 TTTTAA-AAAAATCGTTG
1 TTTTAATAAAAACCGTTG
*
301655 -TTCACATAAAAACCGTTG
1 TTTTA-ATAAAAACCGTTG
301673 TTTTAATAAAA
1 TTTTAATAAAA
301684 CAATTTTACC
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
16 3 0.13
17 1 0.04
18 16 0.70
19 3 0.13
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (18 bp):
TTTTAATAAAAACCGTTG
Found at i:304314 original size:15 final size:16
Alignment explanation
Indices: 304288--304327 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
304278 TATTTTATAA
304288 ATTTTA-AAATA-TTT
1 ATTTTATAAATATTTT
304302 ATTTTATAAATATTTT
1 ATTTTATAAATATTTT
*
304318 ATTTTTTAAA
1 ATTTTATAAA
304328 ACTCCAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.26
15 5 0.22
16 12 0.52
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATTTTATAAATATTTT
Found at i:309731 original size:10 final size:10
Alignment explanation
Indices: 309712--309771 Score: 88
Period size: 10 Copynumber: 6.0 Consensus size: 10
309702 TGAAATTCTA
309712 AAAGATAAAT
1 AAAGATAAAT
309722 ACAA-ATAAAT
1 A-AAGATAAAT
309732 AAAGATAAAT
1 AAAGATAAAT
309742 AAAGATAAAT
1 AAAGATAAAT
309752 AAAGATAAAT
1 AAAGATAAAT
309762 GAAA-ATAAAT
1 -AAAGATAAAT
309772 CCTAAAATTA
Statistics
Matches: 47, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
9 2 0.04
10 40 0.85
11 5 0.11
ACGTcount: A:0.70, C:0.02, G:0.08, T:0.20
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:309893 original size:29 final size:29
Alignment explanation
Indices: 309860--309957 Score: 81
Period size: 29 Copynumber: 3.3 Consensus size: 29
309850 AATCTCTTCT
309860 TTTGCATTTTAGTCCTTGGGTCTTCCGTG
1 TTTGCATTTTAGTCCTTGGGTCTTCCGTG
* * **** ** *
309889 TTTGCATTTTTGGCAC-CACTTCTCTCTTTC
1 TTTGCATTTTAGTC-CTTGGGTCT-TCCGTG
*
309919 ATTGCATTTTAGTCCTTGGGTCTTCCGTG
1 TTTGCATTTTAGTCCTTGGGTCTTCCGTG
309948 TTTGCATTTT
1 TTTGCATTTT
309958 TGGCACCACT
Statistics
Matches: 46, Mismatches: 20, Indels: 6
0.64 0.28 0.08
Matches are distributed among these distances:
29 28 0.61
30 18 0.39
ACGTcount: A:0.09, C:0.22, G:0.18, T:0.50
Consensus pattern (29 bp):
TTTGCATTTTAGTCCTTGGGTCTTCCGTG
Found at i:309944 original size:59 final size:59
Alignment explanation
Indices: 309861--309984 Score: 239
Period size: 59 Copynumber: 2.1 Consensus size: 59
309851 ATCTCTTCTT
309861 TTGCATTTTAGTCCTTGGGTCTTCCGTGTTTGCATTTTTGGCACCACTTCTCTCTTTCA
1 TTGCATTTTAGTCCTTGGGTCTTCCGTGTTTGCATTTTTGGCACCACTTCTCTCTTTCA
*
309920 TTGCATTTTAGTCCTTGGGTCTTCCGTGTTTGCATTTTTGGCACCACTTCTCTCTTTCT
1 TTGCATTTTAGTCCTTGGGTCTTCCGTGTTTGCATTTTTGGCACCACTTCTCTCTTTCA
309979 TTGCAT
1 TTGCAT
309985 GTTGGCCCAT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 64 1.00
ACGTcount: A:0.10, C:0.25, G:0.17, T:0.48
Consensus pattern (59 bp):
TTGCATTTTAGTCCTTGGGTCTTCCGTGTTTGCATTTTTGGCACCACTTCTCTCTTTCA
Found at i:309984 original size:30 final size:30
Alignment explanation
Indices: 309889--309984 Score: 79
Period size: 30 Copynumber: 3.2 Consensus size: 30
309879 GTCTTCCGTG
309889 TTTGCATTTTTGGCACCACTTCTCTCTTTC
1 TTTGCATTTTTGGCACCACTTCTCTCTTTC
* * * **** ** *
309919 ATTGCATTTTAGTC-CTTGGGTCT-TCCGTG
1 TTTGCATTTTTGGCAC-CACTTCTCTCTTTC
309948 TTTGCATTTTTGGCACCACTTCTCTCTTTC
1 TTTGCATTTTTGGCACCACTTCTCTCTTTC
309978 TTTGCAT
1 TTTGCAT
309985 GTTGGCCCAT
Statistics
Matches: 43, Mismatches: 20, Indels: 6
0.62 0.29 0.09
Matches are distributed among these distances:
29 18 0.42
30 25 0.58
ACGTcount: A:0.10, C:0.26, G:0.15, T:0.49
Consensus pattern (30 bp):
TTTGCATTTTTGGCACCACTTCTCTCTTTC
Found at i:310011 original size:59 final size:59
Alignment explanation
Indices: 309889--310019 Score: 138
Period size: 59 Copynumber: 2.2 Consensus size: 59
309879 GTCTTCCGTG
* * * * ***
309889 TTTGCATTTTTGGCACCACTTCTCTCTTTCATTGCATTTTAGTCCTTGGGTCTTCCGTG
1 TTTGCATTTTTGGCACCACTTCTCTCTTTCATTGCATGTTAGCCCTTAGATCTTCCAAA
* * * *
309948 TTTGCATTTTTGGCACCACTTCTCTCTTTCTTTGCATGTTGGCCCATTATATCTT-TAAA
1 TTTGCATTTTTGGCACCACTTCTCTCTTTCATTGCATGTTAGCCC-TTAGATCTTCCAAA
310007 TTTGCACTTTTTG
1 TTTGCA-TTTTTG
310020 CCCTTGAATT
Statistics
Matches: 59, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
59 47 0.80
60 12 0.20
ACGTcount: A:0.13, C:0.24, G:0.15, T:0.49
Consensus pattern (59 bp):
TTTGCATTTTTGGCACCACTTCTCTCTTTCATTGCATGTTAGCCCTTAGATCTTCCAAA
Found at i:311886 original size:41 final size:41
Alignment explanation
Indices: 311829--311910 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
311819 AAGGGCGAAT
311829 GATATCCTTTCATAAACATTGCATGGTTGATGGGAAACTAA
1 GATATCCTTTCATAAACATTGCATGGTTGATGGGAAACTAA
311870 GATATCCTTTCATAAACATTGCATGGTTGATGGGAAACTAA
1 GATATCCTTTCATAAACATTGCATGGTTGATGGGAAACTAA
311911 CATAGCCACT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.32
Consensus pattern (41 bp):
GATATCCTTTCATAAACATTGCATGGTTGATGGGAAACTAA
Found at i:326597 original size:16 final size:16
Alignment explanation
Indices: 326576--326610 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
326566 AACTAATTTG
326576 ATACTTAAATTTTACT
1 ATACTTAAATTTTACT
326592 ATACTTAAATTTTACT
1 ATACTTAAATTTTACT
326608 ATA
1 ATA
326611 TTACTAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (16 bp):
ATACTTAAATTTTACT
Found at i:332612 original size:39 final size:39
Alignment explanation
Indices: 332558--332637 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
332548 TGACTGTGTG
* *
332558 TATGATTCTGTATGTTTTGCATGTCTAATTTTGTTGGGT
1 TATGACTCTGTATGTTTTGCATGTCTAATTCTGTTGGGT
332597 TATGACTCTGTATGTTTTGCATGTCTAATTCTGTTGGGT
1 TATGACTCTGTATGTTTTGCATGTCTAATTCTGTTGGGT
332636 TA
1 TA
332638 CACACTGAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.16, C:0.10, G:0.23, T:0.51
Consensus pattern (39 bp):
TATGACTCTGTATGTTTTGCATGTCTAATTCTGTTGGGT
Found at i:346090 original size:25 final size:25
Alignment explanation
Indices: 346062--346109 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
346052 TTATACCATG
* * *
346062 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
346087 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
346110 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:346212 original size:20 final size:20
Alignment explanation
Indices: 346152--346212 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
346142 ATAAATATGG
*
346152 TATGTATGAGATGCACATGA
1 TATGTATGATATGCACATGA
*
346172 CATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
346192 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
346212 T
1 T
346213 GTAATCATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.33
Consensus pattern (20 bp):
TATGTATGATATGCACATGA
Found at i:346289 original size:24 final size:24
Alignment explanation
Indices: 346262--346404 Score: 209
Period size: 24 Copynumber: 6.0 Consensus size: 24
346252 GAGGAAGTGA
346262 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
346286 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
346310 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
346333 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* * *
346357 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
346381 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
346405 ATGATAAAGC
Statistics
Matches: 111, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
23 23 0.21
24 77 0.69
25 11 0.10
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:346355 original size:47 final size:47
Alignment explanation
Indices: 346262--346404 Score: 207
Period size: 47 Copynumber: 3.0 Consensus size: 47
346252 GAGGAAGTGA
346262 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATC
*
346310 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
* * *
346357 GAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCTTATGCC-CCAGTTAT
346405 ATGATAAAGC
Statistics
Matches: 88, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
47 43 0.49
48 34 0.39
49 11 0.12
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATC
Found at i:346378 original size:71 final size:72
Alignment explanation
Indices: 346262--346405 Score: 220
Period size: 71 Copynumber: 2.0 Consensus size: 72
346252 GAGGAAGTGA
*
346262 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAG-GGCTTATGCC-
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGC-TAGGCCT
346325 CCAGTTAT
65 CCAGTTAT
** * *
346333 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGCTAGGCCTC
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
346398 CAGTTAT
66 CAGTTAT
346405 A
1 A
346406 TGATAAAGCA
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
71 54 0.82
72 12 0.18
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (72 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGAGGCTAGGCCTC
CAGTTAT
Found at i:346631 original size:31 final size:31
Alignment explanation
Indices: 346596--346659 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
346586 CATTTACAGT
346596 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
** *
346627 AAAGGCTTCGGCCCAGTGTTATGGAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
346658 AA
1 AA
346660 CATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:354762 original size:21 final size:19
Alignment explanation
Indices: 354728--354789 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 19
354718 TAAGTTATAT
354728 ATAATAATATAATATGAATAAA
1 ATAATAA-A-AATAT-AATAAA
354750 AT-ATAAGGAAATATAATATAAA
1 ATAATAA--AAATAT-A-ATAAA
354772 ATAATAAAAATATAATAA
1 ATAATAAAAATATAATAA
354790 GTAATTTGCA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
19 4 0.11
20 1 0.03
21 16 0.46
22 10 0.29
23 4 0.11
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (19 bp):
ATAATAAAAATATAATAAA
Found at i:354839 original size:21 final size:22
Alignment explanation
Indices: 354813--354854 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
354803 AAAATATAGT
*
354813 AAAATAAATAGTATA-AAAAAC
1 AAAATAAATAATATATAAAAAC
354834 AAAATAAATAATATATAAAAA
1 AAAATAAATAATATATAAAAA
354855 TATAAGAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (22 bp):
AAAATAAATAATATATAAAAAC
Found at i:355203 original size:14 final size:14
Alignment explanation
Indices: 355173--355237 Score: 53
Period size: 14 Copynumber: 4.6 Consensus size: 14
355163 CAATTTTATA
355173 AAAATATAT-AAA-
1 AAAATATATAAAAT
*
355185 GAAATATATAAAAT
1 AAAATATATAAAAT
*
355199 AAAATATATAATAT
1 AAAATATATAAAAT
* * *
355213 AATATAATTTATAGAT
1 AAAAT-ATATA-AAAT
355229 AAAATATAT
1 AAAATATAT
355238 GATAAAATAA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
12 8 0.20
13 3 0.07
14 16 0.39
15 7 0.17
16 7 0.17
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (14 bp):
AAAATATATAAAAT
Found at i:355341 original size:28 final size:28
Alignment explanation
Indices: 355288--355343 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
355278 AATATTTATA
* *
355288 AAAATATATAAAGTATTTAAAGTAAATT
1 AAAATATAAAAAGTATTAAAAGTAAATT
*
355316 AAAATATAAAAACG-ATTAAAATTAAATT
1 AAAATATAAAAA-GTATTAAAAGTAAATT
355344 TAATTAGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 23 0.96
29 1 0.04
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (28 bp):
AAAATATAAAAAGTATTAAAAGTAAATT
Found at i:368903 original size:3 final size:3
Alignment explanation
Indices: 368895--369012 Score: 191
Period size: 3 Copynumber: 38.3 Consensus size: 3
368885 TTTGTTTACC
*
368895 TAT TAT TAT TAT TCATT TAT CTAT TAT TAT TGT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT T-A-T TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT
368943 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
368991 TAT TAT TAT TAT TAT TCT TAT T
1 TAT TAT TAT TAT TAT TAT TAT T
369013 CTTTATATTA
Statistics
Matches: 108, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
3 101 0.94
4 5 0.05
5 2 0.02
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:370178 original size:16 final size:16
Alignment explanation
Indices: 370154--370188 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
370144 GTTTAAAAAC
*
370154 ATTTATTTATAATTTT
1 ATTTATTTAAAATTTT
*
370170 ATTTTTTTAAAATTTT
1 ATTTATTTAAAATTTT
370186 ATT
1 ATT
370189 AAAACAACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
ATTTATTTAAAATTTT
Found at i:374697 original size:34 final size:33
Alignment explanation
Indices: 374654--374719 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 33
374644 TGCATATATG
* *
374654 CACTGTACTGTTACTG-AGATGGGCTCAGGCCCA
1 CACTGTACTGATACTGTA-ATGGGCTAAGGCCCA
374687 CACTGATACTGATACTGTAATGGGCTAAGGCCC
1 CACTG-TACTGATACTGTAATGGGCTAAGGCCC
374720 TGACTAAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 5 0.17
34 23 0.79
35 1 0.03
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.24
Consensus pattern (33 bp):
CACTGTACTGATACTGTAATGGGCTAAGGCCCA
Found at i:387664 original size:39 final size:39
Alignment explanation
Indices: 387616--387754 Score: 206
Period size: 39 Copynumber: 3.6 Consensus size: 39
387606 ATTTAATTAG
* *
387616 TAACAATCAATTATTCAGTACAGTAATTTAGTCATTCAA
1 TAACTATCAATTATTCAGTACAGTAATTTAGTTATTCAA
* * *
387655 TAACTATCAAATATTCAGTGCAGTAGTTTAGTTATTCAA
1 TAACTATCAATTATTCAGTACAGTAATTTAGTTATTCAA
* * *
387694 TAACTATCAATTATTCAATACAGCAATTTAGTTATTCAG
1 TAACTATCAATTATTCAGTACAGTAATTTAGTTATTCAA
387733 TAACTATCAATTATTCAGTACA
1 TAACTATCAATTATTCAGTACA
387755 TTAGTTTACC
Statistics
Matches: 88, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 88 1.00
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (39 bp):
TAACTATCAATTATTCAGTACAGTAATTTAGTTATTCAA
Found at i:387752 original size:18 final size:18
Alignment explanation
Indices: 387686--387749 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 18
387676 AGTAGTTTAG
387686 TTATTCAATAACTATCAA
1 TTATTCAATAACTATCAA
* * *
387704 TTATTCAATACAGCAATTTAG
1 TTATTCAATA-A-CTA-TCAA
*
387725 TTATTCAGTAACTATCAA
1 TTATTCAATAACTATCAA
387743 TTATTCA
1 TTATTCA
387750 GTACATTAGT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
18 19 0.53
19 3 0.08
20 3 0.08
21 11 0.31
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.41
Consensus pattern (18 bp):
TTATTCAATAACTATCAA
Found at i:389111 original size:30 final size:28
Alignment explanation
Indices: 389056--389117 Score: 97
Period size: 28 Copynumber: 2.1 Consensus size: 28
389046 ATTATTTAAT
389056 TAATAAATATCTTTTACTTAATAATAAA
1 TAATAAATATCTTTTACTTAATAATAAA
*
389084 TAATAAATATCTATTTACTTAAATAATAAG
1 TAATAAATATCT-TTTACTT-AATAATAAA
389114 TAAT
1 TAAT
389118 TTAAATCCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 12 0.39
29 7 0.23
30 12 0.39
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (28 bp):
TAATAAATATCTTTTACTTAATAATAAA
Found at i:392339 original size:18 final size:21
Alignment explanation
Indices: 392313--392353 Score: 61
Period size: 18 Copynumber: 2.1 Consensus size: 21
392303 TAGCCTAACC
392313 TAAATTAATAAAA-TAAA-AA
1 TAAATTAATAAAACTAAATAA
392332 TAAA-TAATAAAACTAAATAA
1 TAAATTAATAAAACTAAATAA
392352 TA
1 TA
392354 TCTTCTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 8 0.40
19 8 0.40
20 4 0.20
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (21 bp):
TAAATTAATAAAACTAAATAA
Found at i:392340 original size:13 final size:13
Alignment explanation
Indices: 392324--392353 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
392314 AAATTAATAA
392324 AATAAAAATAAAT
1 AATAAAAATAAAT
*
392337 AATAAAACTAAAT
1 AATAAAAATAAAT
392350 AATA
1 AATA
392354 TCTTCTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.23
Consensus pattern (13 bp):
AATAAAAATAAAT
Found at i:395788 original size:50 final size:48
Alignment explanation
Indices: 395660--395844 Score: 191
Period size: 50 Copynumber: 3.9 Consensus size: 48
395650 ACACTGCTGT
* **
395660 TATGTGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGC-TTG-A
1 TATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGCACCGAA
* *
395706 TAT--GTGTCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACCGACA
1 TATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATC-GCACCGA-A
* * *
395754 GATGAGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCG-ATCTCAATA
1 TATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGCA-C-CGA-A
* * *
395804 TATGACAGCCAGTGTAAGACCATATCTGGGATATGGCATCG
1 TATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCG
395845 GCATCGATAT
Statistics
Matches: 116, Mismatches: 15, Indels: 12
0.81 0.10 0.08
Matches are distributed among these distances:
44 33 0.28
45 2 0.02
46 4 0.03
48 4 0.03
49 2 0.02
50 71 0.61
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.24
Consensus pattern (48 bp):
TATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGCACCGAA
Found at i:418608 original size:20 final size:20
Alignment explanation
Indices: 418569--418614 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
418559 AGAAGCAAAG
*
418569 AAAA-AAAACAAAAGGGAGA
1 AAAAGAAAACAAAAGGAAGA
*
418588 AAAAGAAAACAAAAGTAAGA
1 AAAAGAAAACAAAAGGAAGA
*
418608 AGAAGAA
1 AAAAGAA
418615 GAAAGAAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.74, C:0.04, G:0.20, T:0.02
Consensus pattern (20 bp):
AAAAGAAAACAAAAGGAAGA
Found at i:424054 original size:18 final size:18
Alignment explanation
Indices: 424026--424061 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
424016 GAAAGTGAAA
424026 GTTATTATGAAATAGTTTT
1 GTTATTATGAAATA-TTTT
424045 GTTATT-TGAAATATTTT
1 GTTATTATGAAATATTTT
424062 CATAGCTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 7 0.41
19 6 0.35
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.56
Consensus pattern (18 bp):
GTTATTATGAAATATTTT
Found at i:438228 original size:24 final size:24
Alignment explanation
Indices: 438201--438286 Score: 68
Period size: 24 Copynumber: 3.5 Consensus size: 24
438191 TAAAGTTGAT
438201 TGAATGGATTGAAGTGATATATTA
1 TGAATGGATTGAAGTGATATATTA
* * *
438225 TGAATGTATT-AA-TTATTTCAATTGAA
1 TGAATGGATTGAAGTGATAT--ATT--A
* *
438251 AGAATGGATTGTAGTGATATATTA
1 TGAATGGATTGAAGTGATATATTA
*
438275 TGAATGTATTGA
1 TGAATGGATTGA
438287 TTATTTCAAT
Statistics
Matches: 45, Mismatches: 11, Indels: 12
0.66 0.16 0.18
Matches are distributed among these distances:
22 4 0.09
23 2 0.04
24 22 0.49
26 12 0.27
27 1 0.02
28 4 0.09
ACGTcount: A:0.37, C:0.01, G:0.21, T:0.41
Consensus pattern (24 bp):
TGAATGGATTGAAGTGATATATTA
Found at i:438260 original size:50 final size:51
Alignment explanation
Indices: 438201--438306 Score: 187
Period size: 50 Copynumber: 2.1 Consensus size: 51
438191 TAAAGTTGAT
438201 TGAATGGATTGAAGTGATATATTATGAATGTATTAATTATTTCAATTGAAA
1 TGAATGGATTGAAGTGATATATTATGAATGTATTAATTATTTCAATTGAAA
* *
438252 -GAATGGATTGTAGTGATATATTATGAATGTATTGATTATTTCAATTGAAA
1 TGAATGGATTGAAGTGATATATTATGAATGTATTAATTATTTCAATTGAAA
438302 TGAAT
1 TGAAT
438307 ATATATATGA
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
50 48 0.92
51 4 0.08
ACGTcount: A:0.38, C:0.02, G:0.19, T:0.42
Consensus pattern (51 bp):
TGAATGGATTGAAGTGATATATTATGAATGTATTAATTATTTCAATTGAAA
Found at i:438554 original size:41 final size:40
Alignment explanation
Indices: 438456--438566 Score: 138
Period size: 41 Copynumber: 2.8 Consensus size: 40
438446 CGACTTCGAG
* *
438456 TCGATGAGGCACTGGGTGCCAATTTACT--TT-GGTTTAA
1 TCGATGAGACACTGGGTGTCAATTTACTACTTCGGTTTAA
* * *
438493 CCGATGAGACATTGGGTGTCAATTTACTACTTCGGATTTAT
1 TCGATGAGACACTGGGTGTCAATTTACTACTTCGG-TTTAA
*
438534 TCGATGAGACACTGGTTGTCAATTTACTACTTC
1 TCGATGAGACACTGGGTGTCAATTTACTACTTC
438567 AAATTATCCG
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
37 24 0.39
39 2 0.03
40 2 0.03
41 34 0.55
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (40 bp):
TCGATGAGACACTGGGTGTCAATTTACTACTTCGGTTTAA
Found at i:439250 original size:2 final size:2
Alignment explanation
Indices: 439243--439283 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
439233 ATTGGCTTAG
439243 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
439284 CATGTGCTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:443560 original size:38 final size:38
Alignment explanation
Indices: 443508--443583 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 38
443498 GTTATGGTAG
*
443508 TTTAATGATCTATATTTTCTAGTGGTGTGCACATATTT
1 TTTAATGATCTATATTTTCTAGTGGTGTGCACACATTT
* * *
443546 TTTAATGATTTATATTTTTTAGTGGTTTGCACACATTT
1 TTTAATGATCTATATTTTCTAGTGGTGTGCACACATTT
443584 CTATCTATCA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.24, C:0.09, G:0.14, T:0.53
Consensus pattern (38 bp):
TTTAATGATCTATATTTTCTAGTGGTGTGCACACATTT
Found at i:456883 original size:30 final size:30
Alignment explanation
Indices: 456849--456909 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
456839 TCCTTAACTC
456849 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
456879 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
456909 A
1 A
456910 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:459783 original size:22 final size:23
Alignment explanation
Indices: 459735--459785 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
459725 TAGAACTTTA
* *
459735 TAATAACATACATACTACATGTT
1 TAATAACATAAATACTACATGCT
459758 TAATACACATAAATA-TA-ATGCT
1 TAATA-ACATAAATACTACATGCT
459780 TAATAA
1 TAATAA
459786 TAATTTATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 1 0.04
22 9 0.36
23 7 0.28
24 8 0.32
ACGTcount: A:0.49, C:0.14, G:0.04, T:0.33
Consensus pattern (23 bp):
TAATAACATAAATACTACATGCT
Found at i:459836 original size:17 final size:16
Alignment explanation
Indices: 459810--459850 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
459800 CATAATAGTG
*
459810 TAATAATATAT-TA-A
1 TAATAAAATATATATA
459824 TAATATAAATATATATA
1 TAATA-AAATATATATA
459841 TAATAAAATA
1 TAATAAAATA
459851 ACATATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 5 0.22
15 5 0.22
16 7 0.30
17 6 0.26
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAATAAAATATATATA
Found at i:459856 original size:17 final size:17
Alignment explanation
Indices: 459823--459866 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
459813 TAATATATTA
*
459823 ATAATATAAATATATAT
1 ATAATATAAATACATAT
459840 ATAATA-AAATAACATAT
1 ATAATATAAAT-ACATAT
*
459857 AAAATATAAA
1 ATAATATAAA
459867 AGAATAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 4 0.17
17 16 0.70
18 3 0.13
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (17 bp):
ATAATATAAATACATAT
Found at i:460031 original size:17 final size:17
Alignment explanation
Indices: 460003--460117 Score: 105
Period size: 17 Copynumber: 6.9 Consensus size: 17
459993 TATATGATAA
460003 AATATAA-A-ATAAAAT
1 AATATAATATATAAAAT
**
460018 AATATAATATATAATGT
1 AATATAATATATAAAAT
* * *
460035 -ATATTAAAACATAAGAT
1 AATA-TAATATATAAAAT
*
460052 AATATAATATATATAAT
1 AATATAATATATAAAAT
*
460069 AATATAAAATATAAAAT
1 AATATAATATATAAAAT
460086 AATAT-ATAT-TAATAAAT
1 AATATAATATAT-A-AAAT
460103 AATATAATATATAAA
1 AATATAATATATAAA
460118 TATACTTGAA
Statistics
Matches: 79, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
15 8 0.10
16 8 0.10
17 54 0.68
18 8 0.10
19 1 0.01
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.35
Consensus pattern (17 bp):
AATATAATATATAAAAT
Found at i:460115 original size:34 final size:35
Alignment explanation
Indices: 459986--460117 Score: 136
Period size: 34 Copynumber: 3.9 Consensus size: 35
459976 ATGTAATAAG
*
459986 ATATAAATATATGATAA-AATAT-AAA-ATAAAATA
1 ATAT-AATATATAATAATAATATAAAATATAAAATA
* * *
460019 ATATAATATATAAT-GT-ATATTAAAACATAAGATA
1 ATATAATATATAATAATAATA-TAAAATATAAAATA
460053 ATATAATATAT-ATAATAATATAAAATATAAAATA
1 ATATAATATATAATAATAATATAAAATATAAAATA
*
460087 ATAT-ATAT-TAATAAATAATATAATATATAAA
1 ATATAATATATAAT-AATAATATAAAATATAAA
460118 TATACTTGAA
Statistics
Matches: 84, Mismatches: 7, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
31 3 0.04
32 11 0.13
33 15 0.18
34 52 0.62
35 3 0.04
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (35 bp):
ATATAATATATAATAATAATATAAAATATAAAATA
Found at i:460186 original size:20 final size:20
Alignment explanation
Indices: 460126--460201 Score: 57
Period size: 20 Copynumber: 3.6 Consensus size: 20
460116 AATATACTTG
* *
460126 AAAATAACAAAAATAATATAT
1 AAAATAA-ATAAATAATATGT
*
460147 -AAATAAATAAATTTTTATATGT
1 AAAATAAATAAA---TAATATGT
*
460169 ATAAAT-AATAAATAATATTT
1 A-AAATAAATAAATAATATGT
460189 AAAATAAATAAAT
1 AAAATAAATAAAT
460202 TTTAAAAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
19 8 0.18
20 20 0.45
22 6 0.14
23 6 0.14
24 4 0.09
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (20 bp):
AAAATAAATAAATAATATGT
Found at i:460196 original size:16 final size:16
Alignment explanation
Indices: 460175--460208 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
460165 ATGTATAAAT
460175 AATAAAT-AATATTTAA
1 AATAAATAAAT-TTTAA
460191 AATAAATAAATTTTAA
1 AATAAATAAATTTTAA
460207 AA
1 AA
460209 AATGATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.82
17 3 0.18
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AATAAATAAATTTTAA
Found at i:462050 original size:93 final size:93
Alignment explanation
Indices: 461932--462130 Score: 272
Period size: 93 Copynumber: 2.1 Consensus size: 93
461922 TACCAAATCA
** * * * *
461932 TCTTGGATCTACTTCGATGTGAAAACATCTGAAGGTTAGATCTGCTATGTCTTCGATCTGCTCTC
1 TCTTGGATCTGTTTCGATGTGAAAACATCCGAAGGTCAAATCTGCTATGTCTCCGATCTGCTCTC
* * *
461997 CATTGAATATGGAGATGCCAAATCTGTT
66 CATCGAATACGAAGATGCCAAATCTGTT
*
462025 TCTTGGATCTGTTTCGATGTGAAAACATCCGAAGGTCAAATCTGCTATGTCTCCGATCTGCTCTT
1 TCTTGGATCTGTTTCGATGTGAAAACATCCGAAGGTCAAATCTGCTATGTCTCCGATCTGCTCTC
* *
462090 CGTCGAATACGAAGATGCCAAATTTGTT
66 CATCGAATACGAAGATGCCAAATCTGTT
* *
462118 TCTTCGATTTGTT
1 TCTTGGATCTGTT
462131 CTCTGACAAT
Statistics
Matches: 92, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
93 92 1.00
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (93 bp):
TCTTGGATCTGTTTCGATGTGAAAACATCCGAAGGTCAAATCTGCTATGTCTCCGATCTGCTCTC
CATCGAATACGAAGATGCCAAATCTGTT
Found at i:474067 original size:22 final size:23
Alignment explanation
Indices: 474019--474069 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
474009 TAGAACTTTA
* *
474019 TAATAACATACATACTACATGTT
1 TAATAACATAAATACTACATGCT
474042 TAATACACATAAATA-TA-ATGCT
1 TAATA-ACATAAATACTACATGCT
474064 TAATAA
1 TAATAA
474070 TAATTTATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 1 0.04
22 9 0.36
23 7 0.28
24 8 0.32
ACGTcount: A:0.49, C:0.14, G:0.04, T:0.33
Consensus pattern (23 bp):
TAATAACATAAATACTACATGCT
Found at i:474298 original size:10 final size:10
Alignment explanation
Indices: 474285--474440 Score: 81
Period size: 10 Copynumber: 14.8 Consensus size: 10
474275 TATATGATAA
474285 AATATAAAAT
1 AATATAAAAT
*
474295 AATATAATAT
1 AATATAAAAT
*
474305 AATATATAAT
1 AATATAAAAT
*
474315 GTATATTAAAACAT
1 -AATA-T-AAA-AT
* *
474329 AAGATAATAT
1 AATATAAAAT
474339 AATATATATAAT
1 AATATA-A-AAT
474351 AATAT-AAA-
1 AATATAAAAT
474359 AATATAAAAT
1 AATATAAAAT
474369 AATATATATTAAT
1 AATATA-A--AAT
*
474382 AA-ATAATAT
1 AATATAAAAT
474391 AATATATAAAT
1 AATATA-AAAT
474402 -ATACTTGAAAAT
1 AATA--T-AAAAT
*
474414 AACA-AAAAT
1 AATATAAAAT
474423 AATATACAAAT
1 AATATA-AAAT
474434 AA-ATAAA
1 AATATAAA
474441 TTTTTATATG
Statistics
Matches: 113, Mismatches: 14, Indels: 39
0.68 0.08 0.23
Matches are distributed among these distances:
8 5 0.04
9 19 0.17
10 41 0.36
11 17 0.15
12 17 0.15
13 12 0.11
14 2 0.02
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.33
Consensus pattern (10 bp):
AATATAAAAT
Found at i:474301 original size:5 final size:5
Alignment explanation
Indices: 474268--474404 Score: 80
Period size: 5 Copynumber: 29.0 Consensus size: 5
474258 ATGTAATAAG
* * *
474268 ATATA A-AT- ATATG ATAAA ATATA AAATA ATATA ATATA ATAT- ATA-A
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
* * * * *
474314 TGTATA TTAAA ACATA AGATA ATATA ATATA TATAATA ATATA A-A-A
1 -ATATA ATATA ATATA ATATA ATATA ATATA -AT-ATA ATATA ATATA
* *
474360 ATATA AAATA ATAT- ATATT A-ATA A-ATA ATATA ATAT- ATA-A ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
474405 CTTGAAAATA
Statistics
Matches: 103, Mismatches: 16, Indels: 26
0.71 0.11 0.18
Matches are distributed among these distances:
3 3 0.03
4 26 0.25
5 66 0.64
6 5 0.05
7 3 0.03
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.36
Consensus pattern (5 bp):
ATATA
Found at i:474306 original size:22 final size:22
Alignment explanation
Indices: 474273--474400 Score: 74
Period size: 22 Copynumber: 5.9 Consensus size: 22
474263 ATAAGATATA
474273 AATAT-ATGATAAAATATAAAAT
1 AATATAAT-ATAAAATATAAAAT
*
474295 AATATAATAT--AATATATAAT
1 AATATAATATAAAATATAAAAT
* * *
474315 -GTAT-AT-TAAAACATAAGAT
1 AATATAATATAAAATATAAAAT
474334 AATATAATATATATAATAATATAAA-
1 AATATAATATA-A-AAT-ATA-AAAT
* * *
474359 AATATAAAATAATATATATTAAT
1 AATATAATATAAAATATA-AAAT
*
474382 AA-ATAATATAATATATAAA
1 AATATAATATAAAATATAAA
474401 TATACTTGAA
Statistics
Matches: 82, Mismatches: 13, Indels: 23
0.69 0.11 0.19
Matches are distributed among these distances:
17 1 0.01
18 2 0.02
19 10 0.12
20 12 0.15
21 3 0.04
22 29 0.35
23 7 0.09
24 3 0.04
25 13 0.16
26 2 0.02
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (22 bp):
AATATAATATAAAATATAAAAT
Found at i:474346 original size:27 final size:25
Alignment explanation
Indices: 474300--474486 Score: 88
Period size: 27 Copynumber: 7.4 Consensus size: 25
474290 AAAATAATAT
*
474300 AATATAAT-ATATAATGTATATTAAA
1 AATA-AATAATATAATATATATTAAA
474325 ACATAAGATAATATAATATATATAATAATA
1 A-ATAA-ATAATATAATATATAT--TAA-A
* *
474355 TAAAAATATAAAATAATATATATTAATA
1 -AATAA-ATAATATAATATATATTAA-A
* *
474383 AATAATATAATATATAAATATACTTGAA
1 AATAA-ATAATATA-ATATATA-TTAAA
* *
474411 AAT-AACAA-A-AATA-ATA-TACA
1 AATAAATAATATAATATATATTAAA
* * *
474431 AATAAATAA-AT-TTTTATATGTATA
1 AATAAATAATATAATATATAT-TAAA
*
474455 AATAAATAATA-AATA-ATATTTAA
1 AATAAATAATATAATATATATTAAA
474478 AATAAATAA
1 AATAAATAA
474487 ATTTTAAAAA
Statistics
Matches: 126, Mismatches: 20, Indels: 34
0.70 0.11 0.19
Matches are distributed among these distances:
20 5 0.04
21 6 0.05
22 6 0.05
23 13 0.10
24 17 0.13
25 5 0.04
26 8 0.06
27 25 0.20
28 15 0.12
29 6 0.05
30 19 0.15
31 1 0.01
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (25 bp):
AATAAATAATATAATATATATTAAA
Found at i:474413 original size:52 final size:55
Alignment explanation
Indices: 474327--474428 Score: 133
Period size: 52 Copynumber: 1.9 Consensus size: 55
474317 ATATTAAAAC
*
474327 ATAAGATAATATAATATATATAATAATATAAAAAT-A-TAAAATAATATATATTA
1 ATAAGATAATATAATATATATAATAATATAAAAATAACAAAAATAATATATATTA
*
474380 ATAA-ATAATATAATATATA-AAT-ATACTTGAAAATAACAAAAATAATATA
1 ATAAGATAATATAATATATATAATAATA--TAAAAATAACAAAAATAATATA
474429 CAAATAAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
50 3 0.07
51 3 0.07
52 21 0.49
53 5 0.12
54 11 0.26
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (55 bp):
ATAAGATAATATAATATATATAATAATATAAAAATAACAAAAATAATATATATTA
Found at i:474483 original size:16 final size:16
Alignment explanation
Indices: 474462--474499 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
474452 ATAAATAAAT
474462 AATAAAT-AATATTTAA
1 AATAAATAAAT-TTTAA
474478 AATAAATAAATTTTAA
1 AATAAATAAATTTTAA
474494 AA-AAAT
1 AATAAAT
474500 GATTAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.19
16 14 0.67
17 3 0.14
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AATAAATAAATTTTAA
Found at i:475772 original size:16 final size:17
Alignment explanation
Indices: 475751--475783 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
475741 TTTTATTCAA
475751 TATTTAT-TTAAATTTT
1 TATTTATATTAAATTTT
*
475767 TATTTATATTATATTTT
1 TATTTATATTAAATTTT
475784 ATTCGTTTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TATTTATATTAAATTTT
Found at i:478485 original size:42 final size:42
Alignment explanation
Indices: 478438--478544 Score: 196
Period size: 42 Copynumber: 2.5 Consensus size: 42
478428 TATTGGTCTC
478438 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
1 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
478480 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
1 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
* *
478522 GGCACTACGTGTGCGGGTTTAAA
1 GGCACTAAGTGTGCGGGTATAAA
478545 ATTGTACAGC
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.29, C:0.15, G:0.34, T:0.22
Consensus pattern (42 bp):
GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
Found at i:478600 original size:17 final size:17
Alignment explanation
Indices: 478578--478611 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
478568 ATTTGATTAT
*
478578 ATAGCACTATGTGTGCG
1 ATAGCACTAAGTGTGCG
478595 ATAGCACTAAGTGTGCG
1 ATAGCACTAAGTGTGCG
478612 GATTCACTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.26
Consensus pattern (17 bp):
ATAGCACTAAGTGTGCG
Found at i:486428 original size:42 final size:42
Alignment explanation
Indices: 486381--486487 Score: 187
Period size: 42 Copynumber: 2.5 Consensus size: 42
486371 TATTGGTCTC
*
486381 GGCACTAAGTGTGCGGGTATAAATGGACATGGTGACAAGATT
1 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
486423 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
1 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
* *
486465 GGCACTACGTGTGCGGGTTTAAA
1 GGCACTAAGTGTGCGGGTATAAA
486488 ATTGTACAGC
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 62 1.00
ACGTcount: A:0.29, C:0.14, G:0.34, T:0.23
Consensus pattern (42 bp):
GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
Found at i:486552 original size:27 final size:28
Alignment explanation
Indices: 486495--486564 Score: 97
Period size: 27 Copynumber: 2.5 Consensus size: 28
486485 AAAATTGTAC
**
486495 AGCACTAAGTGTGCGAATTTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
* *
486523 AGCACTATGTGTGCG-AGCTGATTTTAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
486550 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
486565 GATTCACTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 23 0.62
28 14 0.38
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.33
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAAGCTGATTATAT
Found at i:493786 original size:14 final size:14
Alignment explanation
Indices: 493767--493793 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
493757 GTTTTTAATT
493767 TAATTTTTGTTTTC
1 TAATTTTTGTTTTC
493781 TAATTTTTGTTTT
1 TAATTTTTGTTTT
493794 GTTTGCTTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.04, G:0.07, T:0.74
Consensus pattern (14 bp):
TAATTTTTGTTTTC
Found at i:493793 original size:19 final size:17
Alignment explanation
Indices: 493749--493797 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 17
493739 TTTTATTGCA
493749 TTTTTTTTGTTTTTAAT
1 TTTTTTTTGTTTTTAAT
*
493766 TTAATTTTTGTTTTCTAAT
1 TT-TTTTTTGTTTT-TAAT
493785 TTTTGTTTTGTTT
1 TTTT-TTTTGTTT
493798 GCTTCTGGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 2 0.07
18 11 0.41
19 14 0.52
ACGTcount: A:0.12, C:0.02, G:0.08, T:0.78
Consensus pattern (17 bp):
TTTTTTTTGTTTTTAAT
Found at i:512200 original size:18 final size:17
Alignment explanation
Indices: 512174--512226 Score: 63
Period size: 18 Copynumber: 3.1 Consensus size: 17
512164 ACCCCCATTC
*
512174 TCTTCATTTATTTTACTT
1 TCTTTATTTATTTTA-TT
512192 TCTTTATTTTATTTTATT
1 TCTTTA-TTTATTTTATT
*
512210 TCTTTATTCA-TTTATT
1 TCTTTATTTATTTTATT
512226 T
1 T
512227 ATTTTGGTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 7 0.22
17 3 0.09
18 13 0.41
19 9 0.28
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.72
Consensus pattern (17 bp):
TCTTTATTTATTTTATT
Found at i:514082 original size:12 final size:11
Alignment explanation
Indices: 514033--514083 Score: 50
Period size: 12 Copynumber: 4.4 Consensus size: 11
514023 TTTAAGTCCA
514033 TTTATTTTATCT
1 TTTATTTTAT-T
514045 TTTATTTT-TCT
1 TTTATTTTAT-T
514056 CTTTATTTTTATT
1 -TTTA-TTTTATT
*
514069 TTTATTTTAGT
1 TTTATTTTATT
514080 TTTA
1 TTTA
514084 AGGACTTGTC
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
11 13 0.37
12 16 0.46
13 5 0.14
14 1 0.03
ACGTcount: A:0.16, C:0.06, G:0.02, T:0.76
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:514083 original size:6 final size:6
Alignment explanation
Indices: 514033--514076 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
514023 TTTAAGTCCA
* *
514033 TTTA-T TTTATCT TTTATT TTTCTC TTTATT TTTATT TTTATT TT
1 TTTATT TTTAT-T TTTATT TTTATT TTTATT TTTATT TTTATT TT
514077 AGTTTTAAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
5 4 0.12
6 23 0.70
7 6 0.18
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTATT
Found at i:518860 original size:6 final size:6
Alignment explanation
Indices: 518845--518906 Score: 72
Period size: 6 Copynumber: 10.5 Consensus size: 6
518835 ATTAAGTCCA
* * * *
518845 TTTA-T TTTATT TTTATT TTTATT TCTAGT TTTATT TCTATT TTTATG
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
*
518892 TTTATT GTTATT TTT
1 TTTATT TTTATT TTT
518907 TTAGACTTCT
Statistics
Matches: 46, Mismatches: 10, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
5 4 0.09
6 42 0.91
ACGTcount: A:0.16, C:0.03, G:0.05, T:0.76
Consensus pattern (6 bp):
TTTATT
Found at i:522161 original size:17 final size:17
Alignment explanation
Indices: 522139--522173 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
522129 GTAGACCACT
*
522139 TGTGTGCGGCACATGCC
1 TGTGTGCAGCACATGCC
*
522156 TGTGTGTAGCACATGCC
1 TGTGTGCAGCACATGCC
522173 T
1 T
522174 ATATGGGTTG
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:0.14, C:0.26, G:0.31, T:0.29
Consensus pattern (17 bp):
TGTGTGCAGCACATGCC
Found at i:522609 original size:93 final size:93
Alignment explanation
Indices: 522503--522690 Score: 367
Period size: 93 Copynumber: 2.0 Consensus size: 93
522493 CTATAAGAAA
*
522503 TTCAAAGAAAAACAAAACAAAATGATGGGTGAATAAGTATAGTGGTAAAAACAATAAAAATCTGA
1 TTCAAAGAAAAACAAAACAAAATGATGGGTGAATAAGTACAGTGGTAAAAACAATAAAAATCTGA
522568 AAATTGGGAAGAAGAAAACGAAACTGAT
66 AAATTGGGAAGAAGAAAACGAAACTGAT
522596 TTCAAAGAAAAACAAAACAAAATGATGGGTGAATAAGTACAGTGGTAAAAACAATAAAAATCTGA
1 TTCAAAGAAAAACAAAACAAAATGATGGGTGAATAAGTACAGTGGTAAAAACAATAAAAATCTGA
522661 AAATTGGGAAGAAGAAAACGAAACTGAT
66 AAATTGGGAAGAAGAAAACGAAACTGAT
522689 TT
1 TT
522691 GAGAGAGGGA
Statistics
Matches: 94, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 94 1.00
ACGTcount: A:0.54, C:0.08, G:0.19, T:0.19
Consensus pattern (93 bp):
TTCAAAGAAAAACAAAACAAAATGATGGGTGAATAAGTACAGTGGTAAAAACAATAAAAATCTGA
AAATTGGGAAGAAGAAAACGAAACTGAT
Found at i:525137 original size:14 final size:14
Alignment explanation
Indices: 525118--525144 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
525108 GAAAAACATG
525118 TATATAATTAAATA
1 TATATAATTAAATA
525132 TATATAATTAAAT
1 TATATAATTAAAT
525145 TTATTGACTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TATATAATTAAATA
Found at i:525313 original size:20 final size:20
Alignment explanation
Indices: 525288--525325 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
525278 TAGTAACGAT
525288 ATCAATTAAATTAAAAATCA
1 ATCAATTAAATTAAAAATCA
*
525308 ATCAATTAAATTACAAAT
1 ATCAATTAAATTAAAAAT
525326 TACAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.32
Consensus pattern (20 bp):
ATCAATTAAATTAAAAATCA
Found at i:527001 original size:35 final size:35
Alignment explanation
Indices: 526961--527027 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
526951 GAAAAAACAT
* *
526961 ATTATTCCAATTATTTCAAGAAA-TAAAATAAAATA
1 ATTATTACAATTATTCCAA-AAAGTAAAATAAAATA
* *
526996 ATTATTATAATTATTCCAAAAAGTAAATTAAA
1 ATTATTACAATTATTCCAAAAAGTAAAATAAA
527028 TATATATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 3 0.11
35 24 0.89
ACGTcount: A:0.54, C:0.07, G:0.03, T:0.36
Consensus pattern (35 bp):
ATTATTACAATTATTCCAAAAAGTAAAATAAAATA
Found at i:531870 original size:18 final size:18
Alignment explanation
Indices: 531847--531906 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
531837 TTACTTTCTT
531847 TATTTTTTATAACTATGA
1 TATTTTTTATAACTATGA
* **
531865 TATTTTATT-T-ACTTTCTT
1 TATTTT-TTATAACTAT-GA
531883 TATTTTTTATAACTATGA
1 TATTTTTTATAACTATGA
531901 TATTTT
1 TATTTT
531907 ATTTAAAGGA
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
17 6 0.19
18 20 0.62
19 6 0.19
ACGTcount: A:0.27, C:0.07, G:0.03, T:0.63
Consensus pattern (18 bp):
TATTTTTTATAACTATGA
Found at i:531873 original size:36 final size:36
Alignment explanation
Indices: 531833--531911 Score: 158
Period size: 36 Copynumber: 2.2 Consensus size: 36
531823 TATTTTGGGA
531833 TTATTTACTTTCTTTATTTTTTATAACTATGATATT
1 TTATTTACTTTCTTTATTTTTTATAACTATGATATT
531869 TTATTTACTTTCTTTATTTTTTATAACTATGATATT
1 TTATTTACTTTCTTTATTTTTTATAACTATGATATT
531905 TTATTTA
1 TTATTTA
531912 AAGGATATTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.25, C:0.08, G:0.03, T:0.65
Consensus pattern (36 bp):
TTATTTACTTTCTTTATTTTTTATAACTATGATATT
Found at i:537849 original size:27 final size:24
Alignment explanation
Indices: 537802--537852 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 24
537792 AAAAAATTGT
537802 ATTTTTTTAAAAAGTTTAAATATA
1 ATTTTTTTAAAAAGTTTAAATATA
*
537826 ATTTTTTCTATAAAATTTTAAAATATA
1 ATTTTTT-TA-AAAAGTTT-AAATATA
537853 TAATTATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 7 0.30
25 2 0.09
26 7 0.30
27 7 0.30
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (24 bp):
ATTTTTTTAAAAAGTTTAAATATA
Found at i:538221 original size:20 final size:20
Alignment explanation
Indices: 538198--538252 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
538188 TTATAAATTT
538198 TAAAAATTAAAAATAAT-ATA
1 TAAAAATTAAAAA-AATGATA
* *
538218 TAAAAATTAGAAAAATGTTA
1 TAAAAATTAAAAAAATGATA
538238 TAAAAATTAAAAAAA
1 TAAAAATTAAAAAAA
538253 GGTATTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 3 0.10
20 28 0.90
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (20 bp):
TAAAAATTAAAAAAATGATA
Found at i:538328 original size:15 final size:15
Alignment explanation
Indices: 538308--538338 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
538298 AATTTTTAGA
538308 ATTTTATAATTATAT
1 ATTTTATAATTATAT
*
538323 ATTTTATAATTTTAT
1 ATTTTATAATTATAT
538338 A
1 A
538339 AAAATTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
ATTTTATAATTATAT
Found at i:538329 original size:9 final size:8
Alignment explanation
Indices: 538301--538339 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
538291 TTAAACAAAT
*
538301 TTTTAGAA
1 TTTTATAA
538309 TTTTATAA
1 TTTTATAA
*
538317 TTATAT-A
1 TTTTATAA
538324 TTTTATAA
1 TTTTATAA
538332 TTTTATAA
1 TTTTATAA
538340 AAATTAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (8 bp):
TTTTATAA
Found at i:547128 original size:7 final size:7
Alignment explanation
Indices: 547116--547160 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
547106 GATCCTAACG
547116 CTAAACC
1 CTAAACC
*
547123 CTAAACT
1 CTAAACC
547130 CTAAACC
1 CTAAACC
*
547137 CTCAACC
1 CTAAACC
547144 CTAAACC
1 CTAAACC
547151 CTAAACC
1 CTAAACC
547158 CTA
1 CTA
547161 CGATACATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.40, C:0.42, G:0.00, T:0.18
Consensus pattern (7 bp):
CTAAACC
Found at i:555019 original size:21 final size:20
Alignment explanation
Indices: 554986--555033 Score: 78
Period size: 21 Copynumber: 2.4 Consensus size: 20
554976 AAAGCCTATA
554986 AGATAAAGAATAATAATAAT
1 AGATAAAGAATAATAATAAT
555006 AGATAAATGAATAATAATAAT
1 AGATAAA-GAATAATAATAAT
*
555027 AGGTAAA
1 AGATAAA
555034 CAAATTCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 7 0.27
21 19 0.73
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.25
Consensus pattern (20 bp):
AGATAAAGAATAATAATAAT
Found at i:555573 original size:172 final size:171
Alignment explanation
Indices: 555287--555631 Score: 600
Period size: 172 Copynumber: 2.0 Consensus size: 171
555277 GCAAATTAAA
* * * *
555287 TGATAGAATAATGAGTAAAATAAAAAATAGGTCAAAAGATATGAAGTTTATGTTGATATTAAGCA
1 TGATAGAATAATGAGCAAAATAAAAAAAAGGTCAAAAGATATGAAGTTTATGTTGACACTAAGCA
* * *
555352 TTAAAAATAAGTAAAACAGAAGTGAAATGAGTAAACAAACGCTAGGGAAGAGAGATTGAGCGTCA
66 TTAAAAATAAGCAAAACAGAAGTGAAAGGAGTAAACAAACGCTAGGGAAGAGAGATTGAGCATCA
* *
555417 AAATGGAGTGGGAAGTGGCGCACGGGCGTGGCAGGGAGGCAG
131 AAATGGAGTGGGAAGCGGCGCAC-GGCGTGGCAAGGAGGCAG
555459 TGATAGAATAATGAGCAAAATAAAAAAAAGGTCAAAAGATATGAAGTTTATGTTGACACTAAGCA
1 TGATAGAATAATGAGCAAAATAAAAAAAAGGTCAAAAGATATGAAGTTTATGTTGACACTAAGCA
555524 TTAAAAATAAGCAAAACAGAAGTGAAAGGAGTAAACAAACGCTAGGGAAGAGAGATTGAGCATCA
66 TTAAAAATAAGCAAAACAGAAGTGAAAGGAGTAAACAAACGCTAGGGAAGAGAGATTGAGCATCA
555589 AAATGGAGTGGGAAGCGGCGCACGGCGTGGCAAGGAGGCAG
131 AAATGGAGTGGGAAGCGGCGCACGGCGTGGCAAGGAGGCAG
555630 TG
1 TG
555632 TGAACTTGCA
Statistics
Matches: 164, Mismatches: 9, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
171 19 0.12
172 145 0.88
ACGTcount: A:0.44, C:0.10, G:0.29, T:0.18
Consensus pattern (171 bp):
TGATAGAATAATGAGCAAAATAAAAAAAAGGTCAAAAGATATGAAGTTTATGTTGACACTAAGCA
TTAAAAATAAGCAAAACAGAAGTGAAAGGAGTAAACAAACGCTAGGGAAGAGAGATTGAGCATCA
AAATGGAGTGGGAAGCGGCGCACGGCGTGGCAAGGAGGCAG
Found at i:569237 original size:2 final size:2
Alignment explanation
Indices: 569230--569258 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
569220 CAACGATGAA
569230 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
569259 ATCAAGTTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:570793 original size:20 final size:20
Alignment explanation
Indices: 570770--570810 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
570760 CATAGAAAAC
570770 AATTAATTAAATTCTAATTT
1 AATTAATTAAATTCTAATTT
570790 AATTAATTAAATTCTAATTT
1 AATTAATTAAATTCTAATTT
570810 A
1 A
570811 GGTAAAACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (20 bp):
AATTAATTAAATTCTAATTT
Found at i:573251 original size:2 final size:2
Alignment explanation
Indices: 573244--573275 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
573234 TCACTTCAAA
573244 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
573276 TGTAAATTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:573946 original size:19 final size:19
Alignment explanation
Indices: 573908--573946 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
573898 GGGAGAAGGT
* * *
573908 GAAAAAAATAAGAAAGAAA
1 GAAAAAAAGAAAAAAAAAA
573927 GAAAAAAAGAAAAAAAAAA
1 GAAAAAAAGAAAAAAAAAA
573946 G
1 G
573947 GAAACGAGAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (19 bp):
GAAAAAAAGAAAAAAAAAA
Found at i:581675 original size:3 final size:3
Alignment explanation
Indices: 581667--581720 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
581657 AGTAGTTATG
581667 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
581715 ATA ATA
1 ATA ATA
581721 TTTTAGACAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:585848 original size:23 final size:25
Alignment explanation
Indices: 585814--585860 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
585804 TGATTATATG
585814 CATGACATTATG-TG-ATAGCATGC
1 CATGACATTATGTTGCATAGCATGC
585837 CATGAC-TGTATGTTGCATAGCATG
1 CATGACAT-TATGTTGCATAGCATG
585861 GGGATGGGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 1 0.05
23 10 0.48
24 2 0.10
25 8 0.38
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (25 bp):
CATGACATTATGTTGCATAGCATGC
Found at i:598885 original size:595 final size:593
Alignment explanation
Indices: 597733--599514 Score: 2974
Period size: 595 Copynumber: 3.0 Consensus size: 593
597723 CTGGGATTTC
* *
597733 TTTAATATTACTTTCCAGGGGAAGTATGTGGGGGCCAATTATGTGGATGCCCGTAGGAGAGAGTT
1 TTTAAGATTGCTTTCCAGGGGAAGTATGT-GGGGCCAATTATGTGGATGCCCGTAGGAGAGAGTT
* * * * *
597798 TCTACATTTAACCCAGGGTGATAGATCAGTGGTCGAGAATGAGGCTAAATTTCTTAGATTGAGCC
65 TCTAAATTTGACCCAGGGTGATAGATCAGTGGTCGAGAATGAGGCTGAATTTCTAAGACTGAGCC
*
597863 ACTATGCGCGAGGTATGATGGCGACTGAGTACGAGCGATGTGTTCACTTCGAGGATAGCCTCAAG
130 ACTATGCGCGAGGTATGATGGCGACTGAGTACGAGCGATGTGTTCACTTCGAGGATGGCCTCAAG
*
597928 GATAATCTGAGGGTTTTGATAGCTCCACAGACGGAGCGAGACTTTACTGCACTGGTTGATAAGAT
195 GATAATCTGAGGGTTTTGATAGCTCCACAGAGGGAGCGAGACTTTACTGCACTGGTTGATAAGAT
*
597993 GAAGATCACCGAGGAAGTGAAGCACGCTGAGCTCCAGAACCGGGAAAGAGGTAAGAGCAAGAGGG
260 GAAGATCACCGAGGAAGTGAAGCGCGCTGAGCTCCAGAACCGGGAAAGAGGTAAGAGCAAGAGGG
* * * *
598058 ATTTGGAGCCCTCGAGTTCTATTTAGAGGCTTAAGACAAAGGCCAAAGCGGATAAGCCGATCAGA
325 ATTTAGAGCCCTCGAGTTCTATTTAGAGGCTTAAGAAAAAGGCCAGAGCGGATAGGCCGATCAGA
* *
598123 GTTAGGGCTCCTATAGCTGCTGCTGGATAGCTGCCGTGTATTGACTGTGGTAGACGCCATCAGGG
390 GTTAGGGCTCCTATAGCTGCTGCTGGATAGCCGCCGTGTACTGACTGTGGTAGACGCCATCAGGG
*
598188 CGAGTGTTGGAAAAGAACTAGGGTTGGTTTGAAGTGCGGTTCATTAGGGCACCGTATTAGGGATT
455 CGAGTGTTGGAAAAGAACTAGGGTTGGTTTGAAGTGCGATTCATTAGGGCACCGTATTAGGGATT
* * * *
598253 ATCCACTGAGGTCCGACAAGATACAAGCCCCGGGTACTGGTATTACACCACCACTGAGCAGCCTT
520 ATCCGCGGAGGTCCGACAAGATGCAAG-CCCGGGTACTGGTATTGCACCACCACTGAGCAGCCTT
598318 CGAGAGGCCA
584 CGAGAGGCCA
* *
598328 TTTAAGATTGCTTTCTAGGGGAAGTATGTGGGGACCAATTATGTGGATGCCCGTAGGAAAGAGTT
1 TTTAAGATTGCTTTCCAGGGGAAGTATGTGGGG-CCAATTATGTGGATGCCCGTAGGAGAGAGTT
* * *
598393 TCTAAATTTGACCCAGGGTGATAGATCAATGGTCGAGGATGAGGCTGAATTTCTGAGACTGAGCC
65 TCTAAATTTGACCCAGGGTGATAGATCAGTGGTCGAGAATGAGGCTGAATTTCTAAGACTGAGCC
*
598458 ACTATGCGCGAGGTATGATGGCGACTGAGTACGAGCGATGTGTTCACTTCGAGAATGGCCTCAAG
130 ACTATGCGCGAGGTATGATGGCGACTGAGTACGAGCGATGTGTTCACTTCGAGGATGGCCTCAAG
598523 GATAATCTGAGGGTTTTGATAGCTCCACAGAGGGAGCGAGACTTTACTGCACTGGTTGATAAGAT
195 GATAATCTGAGGGTTTTGATAGCTCCACAGAGGGAGCGAGACTTTACTGCACTGGTTGATAAGAT
*
598588 GAAGATCACCGAGGAAGTGAAGCGCGCTGAGCTCCAGAACCGGGAAAGAGTTAAGAGCAAGAGGG
260 GAAGATCACCGAGGAAGTGAAGCGCGCTGAGCTCCAGAACCGGGAAAGAGGTAAGAGCAAGAGGG
* * *
598653 ATTTTGAGCCCTCGAGTTTTATTTAGAGGCTTAAGAAAAAGGCCAGAGCGGATAGGCCGATTAGA
325 ATTTAGAGCCCTCGAGTTCTATTTAGAGGCTTAAGAAAAAGGCCAGAGCGGATAGGCCGATCAGA
* * *
598718 GTTAGGGCTCCTATAGCTGCTGCTGGATAGCCGCTGTGTACTGACTGTGCTAGACGCTATCAGGG
390 GTTAGGGCTCCTATAGCTGCTGCTGGATAGCCGCCGTGTACTGACTGTGGTAGACGCCATCAGGG
**
598783 CGAGTGTTGGAAAAGAACTAGGGTTGGTTTGAAGTGCGATTCATTAGGGCACTATATTAGGGATT
455 CGAGTGTTGGAAAAGAACTAGGGTTGGTTTGAAGTGCGATTCATTAGGGCACCGTATTAGGGATT
598848 ATCCGCGGAGGTCCGACAAGATGCAAGCCCTGGGTACTGGTATTGCACCACCACTGAGCAGCCTT
520 ATCCGCGGAGGTCCGACAAGATGCAAGCCC-GGGTACTGGTATTGCACCACCACTGAGCAGCCTT
598913 CGAGAGGCCA
584 CGAGAGGCCA
* *
598923 TTTAAGATTGCTTTCCAGGGGAAGTATG-GGGGCAAATTATGTGGATGCTCGTAGGAGAGAGTTT
1 TTTAAGATTGCTTTCCAGGGGAAGTATGTGGGGCCAATTATGTGGATGCCCGTAGGAGAGAGTTT
*
598987 CTAAATTTGACCCAGGGTGATAGATCAGTGGTCGAGAATGAGGCTGAATTTCTAAGACTGAGCCG
66 CTAAATTTGACCCAGGGTGATAGATCAGTGGTCGAGAATGAGGCTGAATTTCTAAGACTGAGCCA
* * * *
599052 CTATACGCGAAGTATGATGGCGACTGAGTACGAGCGATGTGTTCACTTTGAGGATGGCCTTAAGG
131 CTATGCGCGAGGTATGATGGCGACTGAGTACGAGCGATGTGTTCACTTCGAGGATGGCCTCAAGG
599117 ATAATCTGAGGGTTTTGATAGCTCCACAGAGGGAGCGAGACTTTACTGCACTGGTTGATAAGATG
196 ATAATCTGAGGGTTTTGATAGCTCCACAGAGGGAGCGAGACTTTACTGCACTGGTTGATAAGATG
* * * *
599182 AAGATCAGCGAGGAAGTGAAGCGCGCTGAGCTCTAGAATCGGGAAAGAGGTAATAGCAAGAGGGA
261 AAGATCACCGAGGAAGTGAAGCGCGCTGAGCTCCAGAACCGGGAAAGAGGTAAGAGCAAGAGGGA
* * * *
599247 TTCAGAGCCCTCGAGTTCTATTTAGAGGCTTAAGAAAAAGGCCAGAACAGATAGGCCGATCAAAG
326 TTTAGAGCCCTCGAGTTCTATTTAGAGGCTTAAGAAAAAGGCCAGAGCGGATAGGCCGATCAGAG
* *
599312 TTAAGGG-TCCTATAGCTACTGCTGGACAGCCGCCGTGTACTGACTGTGGTAGACGCCATCAGGG
391 TT-AGGGCTCCTATAGCTGCTGCTGGATAGCCGCCGTGTACTGACTGTGGTAGACGCCATCAGGG
*
599376 CGAGTGTTGGAAAAGAACTAGGGTTGGTTTGAAGTGCGATTCATTAGGGCACCGTATTAAGGATT
455 CGAGTGTTGGAAAAGAACTAGGGTTGGTTTGAAGTGCGATTCATTAGGGCACCGTATTAGGGATT
** * *
599441 ATCCGCGGAGGTCTAACAAGATGCAAGTCCCAGGTACTGGTATTGCACCACCACTGAGCAGCTTT
520 ATCCGCGGAGGTCCGACAAGATGCAAG-CCCGGGTACTGGTATTGCACCACCACTGAGCAGCCTT
599506 CGAGAGGCC
584 CGAGAGGCC
599515 GTGGTTAGGC
Statistics
Matches: 1112, Mismatches: 71, Indels: 10
0.93 0.06 0.01
Matches are distributed among these distances:
593 515 0.46
594 18 0.02
595 579 0.52
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (593 bp):
TTTAAGATTGCTTTCCAGGGGAAGTATGTGGGGCCAATTATGTGGATGCCCGTAGGAGAGAGTTT
CTAAATTTGACCCAGGGTGATAGATCAGTGGTCGAGAATGAGGCTGAATTTCTAAGACTGAGCCA
CTATGCGCGAGGTATGATGGCGACTGAGTACGAGCGATGTGTTCACTTCGAGGATGGCCTCAAGG
ATAATCTGAGGGTTTTGATAGCTCCACAGAGGGAGCGAGACTTTACTGCACTGGTTGATAAGATG
AAGATCACCGAGGAAGTGAAGCGCGCTGAGCTCCAGAACCGGGAAAGAGGTAAGAGCAAGAGGGA
TTTAGAGCCCTCGAGTTCTATTTAGAGGCTTAAGAAAAAGGCCAGAGCGGATAGGCCGATCAGAG
TTAGGGCTCCTATAGCTGCTGCTGGATAGCCGCCGTGTACTGACTGTGGTAGACGCCATCAGGGC
GAGTGTTGGAAAAGAACTAGGGTTGGTTTGAAGTGCGATTCATTAGGGCACCGTATTAGGGATTA
TCCGCGGAGGTCCGACAAGATGCAAGCCCGGGTACTGGTATTGCACCACCACTGAGCAGCCTTCG
AGAGGCCA
Found at i:602536 original size:38 final size:38
Alignment explanation
Indices: 602461--602536 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 38
602451 TCTGGAAAAG
602461 AAATAAAAAAAAACAGAATTAAAAGTTTTGATCTGGAA
1 AAATAAAAAAAAACAGAATTAAAAGTTTTGATCTGGAA
* * *
602499 AAATAAAATAAAAATAGAATTAAAATTTTTTAT-TGGAA
1 AAATAAAA-AAAAACAGAATTAAAAGTTTTGATCTGGAA
602537 TTGCGAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 13 0.38
39 21 0.62
ACGTcount: A:0.58, C:0.03, G:0.11, T:0.29
Consensus pattern (38 bp):
AAATAAAAAAAAACAGAATTAAAAGTTTTGATCTGGAA
Found at i:603277 original size:10 final size:10
Alignment explanation
Indices: 603259--603307 Score: 57
Period size: 10 Copynumber: 4.9 Consensus size: 10
603249 TAAATTCTAT
603259 AAGATAAATA
1 AAGATAAATA
603269 CAA-ATAAATA
1 -AAGATAAATA
*
603279 AAGATAATTA
1 AAGATAAATA
603289 AAGATAAATGA
1 AAGATAAAT-A
603300 AA-ATAAAT
1 AAGATAAAT
603308 CTTAAAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
9 2 0.06
10 27 0.79
11 5 0.15
ACGTcount: A:0.67, C:0.02, G:0.08, T:0.22
Consensus pattern (10 bp):
AAGATAAATA
Found at i:604126 original size:96 final size:96
Alignment explanation
Indices: 603962--604159 Score: 326
Period size: 96 Copynumber: 2.1 Consensus size: 96
603952 GAATATATCG
*
603962 AACACACTCCTAATTTTTATTTTTCTTGAGAACATATCGAACCTTTTGACGCGAAGAAAAATGAC
1 AACACACTCCTAATTTTTATTTTTCTTAAGAACATATCGAACCTTTTGACGCGAAGAAAAATGAC
* *
604027 AGCCAAGCACCCCACCCCAGTTACTTAGCCC
66 AGCCAAGCACCCCACCCCAGTTACTCAACCC
*
604058 AACACACTCCTAATTTTTATTTTTCTTAAGAACATATCGAACCTTTTGACGCGAA-AAGAGATGA
1 AACACACTCCTAATTTTTATTTTTCTTAAGAACATATCGAACCTTTTGACGCGAAGAA-AAATGA
* *
604122 CAGCCAAGCACCTCACCCCGGTTACTCAACCC
65 CAGCCAAGCACCCCACCCCAGTTACTCAACCC
604154 AACACA
1 AACACA
604160 TTCTTAAAAA
Statistics
Matches: 95, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
95 2 0.02
96 93 0.98
ACGTcount: A:0.33, C:0.29, G:0.12, T:0.25
Consensus pattern (96 bp):
AACACACTCCTAATTTTTATTTTTCTTAAGAACATATCGAACCTTTTGACGCGAAGAAAAATGAC
AGCCAAGCACCCCACCCCAGTTACTCAACCC
Found at i:606065 original size:4 final size:4
Alignment explanation
Indices: 606053--606111 Score: 63
Period size: 4 Copynumber: 15.0 Consensus size: 4
606043 AAAAAAAAAG
606053 TAAA T-AA TAAA T-AA TAAA TAAA TAAA TAAA T-AA TATAA TATAA TATAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TA-AA TA-AA TA-AA
606101 TAAA T-AA TAAA
1 TAAA TAAA TAAA
606112 AGAAAAAAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
3 12 0.24
4 24 0.48
5 14 0.28
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (4 bp):
TAAA
Found at i:606065 original size:7 final size:7
Alignment explanation
Indices: 606053--606111 Score: 70
Period size: 7 Copynumber: 8.6 Consensus size: 7
606043 AAAAAAAAAG
606053 TAAATAA
1 TAAATAA
606060 TAAATAA
1 TAAATAA
606067 TAAATAA
1 TAAATAA
*
606074 -ATA-AA
1 TAAATAA
606079 TAAATAA
1 TAAATAA
606086 TATAAT-A
1 TA-AATAA
606093 TAATATAA
1 TAA-ATAA
606101 TAAATAA
1 TAAATAA
606108 TAAA
1 TAAA
606112 AGAAAAAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
5 2 0.04
6 5 0.11
7 31 0.69
8 7 0.16
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (7 bp):
TAAATAA
Found at i:606081 original size:22 final size:22
Alignment explanation
Indices: 606053--606130 Score: 83
Period size: 25 Copynumber: 3.5 Consensus size: 22
606043 AAAAAAAAAG
606053 TAAATAATAAATAATAAATAAA
1 TAAATAATAAATAATAAATAAA
606075 TAAATAAATAATATAATATAATATAA
1 TAAAT-AATAA-ATAATA-AATA-AA
606101 TAAATAATAAA-AGA-AAA-AAA
1 TAAATAATAAATA-ATAAATAAA
606121 TAAA-AATAAA
1 TAAATAATAAA
606131 AATTGGGTTG
Statistics
Matches: 51, Mismatches: 0, Indels: 13
0.80 0.00 0.20
Matches are distributed among these distances:
19 6 0.12
20 6 0.12
21 1 0.02
22 7 0.14
23 7 0.14
24 8 0.16
25 9 0.18
26 7 0.14
ACGTcount: A:0.73, C:0.00, G:0.01, T:0.26
Consensus pattern (22 bp):
TAAATAATAAATAATAAATAAA
Found at i:606095 original size:26 final size:26
Alignment explanation
Indices: 606053--606107 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 26
606043 AAAAAAAAAG
606053 TAAATAATAAATAATAA-ATAAATAAA
1 TAAATAATAAATAATAATAT-AATAAA
606079 TAAATAATATAAT-ATAATATAATAAA
1 TAAATAATA-AATAATAATATAATAAA
606105 TAA
1 TAA
606108 TAAAAGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
26 22 0.81
27 5 0.19
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (26 bp):
TAAATAATAAATAATAATATAATAAA
Found at i:611084 original size:15 final size:15
Alignment explanation
Indices: 611061--611091 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
611051 ATATGTAGGG
611061 GACCAAGGCTATAAA
1 GACCAAGGCTATAAA
*
611076 GACCTAGGCTATAAA
1 GACCAAGGCTATAAA
611091 G
1 G
611092 CCTTTCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.19, G:0.23, T:0.16
Consensus pattern (15 bp):
GACCAAGGCTATAAA
Found at i:612254 original size:34 final size:35
Alignment explanation
Indices: 612178--612257 Score: 89
Period size: 34 Copynumber: 2.4 Consensus size: 35
612168 TGATTTATTT
**
612178 TTTATTC-TATATTACCTTTTATATATATGTTATG
1 TTTATTCATATATTACCAATTATATATATGTTATG
612212 --TATCTCATATATTACCAATTATAT-TAT-TTATG
1 TTTAT-TCATATATTACCAATTATATATATGTTATG
612244 TTTATATCATATAT
1 TTTAT-TCATATAT
612258 ATTATTTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
32 8 0.21
33 5 0.13
34 26 0.67
ACGTcount: A:0.31, C:0.10, G:0.04, T:0.55
Consensus pattern (35 bp):
TTTATTCATATATTACCAATTATATATATGTTATG
Found at i:614042 original size:13 final size:13
Alignment explanation
Indices: 614024--614049 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
614014 TTATTTATTG
614024 ATATCATGTGATA
1 ATATCATGTGATA
614037 ATATCATGTGATA
1 ATATCATGTGATA
614050 CTGACTATCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (13 bp):
ATATCATGTGATA
Found at i:616288 original size:15 final size:15
Alignment explanation
Indices: 616254--616301 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
616244 ATATTCTTTA
616254 TGCAT-TCATGCATT
1 TGCATCTCATGCATT
616268 TGCATCTCATGGCATT
1 TGCATCTCAT-GCATT
*
616284 T-CATCACAT-CATT
1 TGCATCTCATGCATT
616297 TGCAT
1 TGCAT
616302 TCAAGGTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
13 5 0.17
14 8 0.27
15 11 0.37
16 6 0.20
ACGTcount: A:0.23, C:0.25, G:0.12, T:0.40
Consensus pattern (15 bp):
TGCATCTCATGCATT
Found at i:624478 original size:120 final size:120
Alignment explanation
Indices: 624266--625104 Score: 1360
Period size: 120 Copynumber: 7.0 Consensus size: 120
624256 AATAGGCCGC
*
624266 AATATAGCAGATCTAGCCTTCAGATGTTTACACTGAAGC-AGATCCAAGATGATTTGGTATTCTT
1 AATATAGCAGATCTAGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGATTTGGTATTCTT
* *
624330 GTGTTTACAAGAAACAAATCGAGGACATAGTAGATTTGACTCTCAGATGTTGTCA
66 GTGTTTACAAGAAACAAATCGAGGACATAGCAGATTTGACTCTCAGATGTTCTCA
624385 AATATAGCAGATCTAGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGATTTGGTATTCTT
1 AATATAGCAGATCTAGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGATTTGGTATTCTT
624450 GTGTTTACAAGAAACAAATCGAGGACATAGCAGATTTGACTCTCAGATGTTCTCA
66 GTGTTTACAAGAAACAAATCGAGGACATAGCAGATTTGACTCTCAGATGTTCTCA
*
624505 AATATAGCAGATCTAGCTTTCAGATGTTTATACTGAAGCAAGATCCAAGATGATTTGGTATTCTT
1 AATATAGCAGATCTAGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGATTTGGTATTCTT
*
624570 GTGTTTATAAGAAACAAATCGAGGACATAGCAGATTTGACTCTCAGATGTTCTCA
66 GTGTTTACAAGAAACAAATCGAGGACATAGCAGATTTGACTCTCAGATGTTCTCA
*
624625 AATATAGCAGATCTAGCTTTCAGATGTTTATACTGAAGC-AGATCCAAGATGATTTGGTATTCTT
1 AATATAGCAGATCTAGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGATTTGGTATTCTT
* *
624689 GTGTTTACAAGGAACAAATCGAGAACATAGCAGATTTGACTCTCAGATGTTCTCA
66 GTGTTTACAAGAAACAAATCGAGGACATAGCAGATTTGACTCTCAGATGTTCTCA
* * *
624744 AACATGGCAGATCTAGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGATTTGATATTCTT
1 AATATAGCAGATCTAGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGATTTGGTATTCTT
* *
624809 GTGTTTACAAGGAACAAATCAAGGACATAGCAGATTTGACTCTCAGATGTTCTCA
66 GTGTTTACAAGAAACAAATCGAGGACATAGCAGATTTGACTCTCAGATGTTCTCA
* * * * * **
624864 GACATAGTAGGTCTAGCCTTCAGAGGTTTATACTGAAGCAAGATCCAAGATGATTTGACATTCTT
1 AATATAGCAGATCTAGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGATTTGGTATTCTT
* * *
624929 ATGTTTACAAGGAACAAATCAAGGACATAGCAGATTTGACTCTCAGATGTTCTCA
66 GTGTTTACAAGAAACAAATCGAGGACATAGCAGATTTGACTCTCAGATGTTCTCA
* * * * **
624984 GACATGGCAGATCTAGCCTTCAGAGGTTTATACTGAAGCAAG-TCCAAGATGATTTGACATTCTT
1 AATATAGCAGATCTAGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGATTTGGTATTCTT
* * * *
625048 ATGTTTACAAAAAACAAATCAAGGAAATAGCAGATTTGACTCTCAGATGTTCTCA
66 GTGTTTACAAGAAACAAATCGAGGACATAGCAGATTTGACTCTCAGATGTTCTCA
625103 AA
1 AA
625105 CAGACTCAAA
Statistics
Matches: 690, Mismatches: 28, Indels: 4
0.96 0.04 0.01
Matches are distributed among these distances:
119 226 0.33
120 464 0.67
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.31
Consensus pattern (120 bp):
AATATAGCAGATCTAGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGATTTGGTATTCTT
GTGTTTACAAGAAACAAATCGAGGACATAGCAGATTTGACTCTCAGATGTTCTCA
Found at i:624698 original size:239 final size:240
Alignment explanation
Indices: 624269--625104 Score: 1372
Period size: 239 Copynumber: 3.5 Consensus size: 240
624259 AGGCCGCAAT
* *
624269 ATAGCAGATCTAGCCTTCAGATGTTTACACTGAAGC-AGATCCAAGATGATTTGGTATTCTTGTG
1 ATAGCAGATCTAGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGATTTGATATTCTTGTG
* * *
624333 TTTACAAGAAACAAATCGAGGACATAGTAGATTTGACTCTCAGATGTTGTCAAATATAGCAGATC
66 TTTACAAGAAACAAATCAAGGACATAGCAGATTTGACTCTCAGATGTTCTCAAATATAGCAGATC
*
624398 TAGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGATTTGGTATTCTTGTGTTTACAAGAA
131 TAGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGATTTGGTATTCTTGTGTTTACAAGGA
*
624463 ACAAATCGAGGACATAGCAGATTTGACTCTCAGATGTTCTCAAAT
196 ACAAATCGAGGACATAGCAGATTTGACTCTCAGATGTTCTCAAAC
* *
624508 ATAGCAGATCTAGCTTTCAGATGTTTATACTGAAGCAAGATCCAAGATGATTTGGTATTCTTGTG
1 ATAGCAGATCTAGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGATTTGATATTCTTGTG
* *
624573 TTTATAAGAAACAAATCGAGGACATAGCAGATTTGACTCTCAGATGTTCTCAAATATAGCAGATC
66 TTTACAAGAAACAAATCAAGGACATAGCAGATTTGACTCTCAGATGTTCTCAAATATAGCAGATC
*
624638 TAGCTTTCAGATGTTTATACTGAAGC-AGATCCAAGATGATTTGGTATTCTTGTGTTTACAAGGA
131 TAGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGATTTGGTATTCTTGTGTTTACAAGGA
*
624702 ACAAATCGAGAACATAGCAGATTTGACTCTCAGATGTTCTCAAAC
196 ACAAATCGAGGACATAGCAGATTTGACTCTCAGATGTTCTCAAAC
*
624747 ATGGCAGATCTAGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGATTTGATATTCTTGTG
1 ATAGCAGATCTAGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGATTTGATATTCTTGTG
* * * * *
624812 TTTACAAGGAACAAATCAAGGACATAGCAGATTTGACTCTCAGATGTTCTCAGACATAGTAGGTC
66 TTTACAAGAAACAAATCAAGGACATAGCAGATTTGACTCTCAGATGTTCTCAAATATAGCAGATC
* ** *
624877 TAGCCTTCAGAGGTTTATACTGAAGCAAGATCCAAGATGATTTGACATTCTTATGTTTACAAGGA
131 TAGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGATTTGGTATTCTTGTGTTTACAAGGA
* *
624942 ACAAATCAAGGACATAGCAGATTTGACTCTCAGATGTTCTCAGAC
196 ACAAATCGAGGACATAGCAGATTTGACTCTCAGATGTTCTCAAAC
* * * *
624987 ATGGCAGATCTAGCCTTCAGAGGTTTATACTGAAGCAAG-TCCAAGATGATTTGACATTCTTATG
1 ATAGCAGATCTAGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGATTTGATATTCTTGTG
* *
625051 TTTACAAAAAACAAATCAAGGAAATAGCAGATTTGACTCTCAGATGTTCTCAAA
66 TTTACAAGAAACAAATCAAGGACATAGCAGATTTGACTCTCAGATGTTCTCAAA
625105 CAGACTCAAA
Statistics
Matches: 561, Mismatches: 34, Indels: 4
0.94 0.06 0.01
Matches are distributed among these distances:
239 331 0.59
240 230 0.41
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (240 bp):
ATAGCAGATCTAGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGATTTGATATTCTTGTG
TTTACAAGAAACAAATCAAGGACATAGCAGATTTGACTCTCAGATGTTCTCAAATATAGCAGATC
TAGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGATTTGGTATTCTTGTGTTTACAAGGA
ACAAATCGAGGACATAGCAGATTTGACTCTCAGATGTTCTCAAAC
Found at i:624947 original size:359 final size:359
Alignment explanation
Indices: 624266--625106 Score: 1362
Period size: 359 Copynumber: 2.3 Consensus size: 359
624256 AATAGGCCGC
*
624266 AATATAGCAGATCTAGCCTTCAGATGTTTACACTGAAGCAGATCCAAGATGATTTGGTATTCTTG
1 AATATAGCAGATCTAGCCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTG
* * * *
624331 TGTTTACAAGAAACAAATCGAGGACATAGTAGATTTGACTCTCAGATGTTGTCAAATATAGCAGA
66 TGTTTACAAGAAACAAATCGAGAACATAGCAGATTTGACTCTCAGATGTTCTCAAACATAGCAGA
*
624396 TCTAGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGATTTGGTATTCTTGTGTTTACAAG
131 TCTAGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGATTTGATATTCTTGTGTTTACAAG
* * *
624461 AAACAAATCGAGGACATAGCAGATTTGACTCTCAGATGTTCTCAAATATAGCAGATCTAGCTTTC
196 AAACAAATCAAGGACATAGCAGATTTGACTCTCAGATGTTCTCAAACATAGCAGATCTAGCCTTC
* ** * * *
624526 AGATGTTTATACTGAAGCAAGATCCAAGATGATTTGGTATTCTTGTGTTTATAAGAAACAAATCG
261 AGAGGTTTATACTGAAGCAAGATCCAAGATGATTTGACATTCTTATGTTTACAAGAAACAAATCA
624591 AGGACATAGCAGATTTGACTCTCAGATGTTCTCA
326 AGGACATAGCAGATTTGACTCTCAGATGTTCTCA
*
624625 AATATAGCAGATCTAGCTTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTG
1 AATATAGCAGATCTAGCCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTG
* *
624690 TGTTTACAAGGAACAAATCGAGAACATAGCAGATTTGACTCTCAGATGTTCTCAAACATGGCAGA
66 TGTTTACAAGAAACAAATCGAGAACATAGCAGATTTGACTCTCAGATGTTCTCAAACATAGCAGA
624755 TCTAGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGATTTGATATTCTTGTGTTTACAAG
131 TCTAGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGATTTGATATTCTTGTGTTTACAAG
* * * *
624820 GAACAAATCAAGGACATAGCAGATTTGACTCTCAGATGTTCTCAGACATAGTAGGTCTAGCCTTC
196 AAACAAATCAAGGACATAGCAGATTTGACTCTCAGATGTTCTCAAACATAGCAGATCTAGCCTTC
*
624885 AGAGGTTTATACTGAAGCAAGATCCAAGATGATTTGACATTCTTATGTTTACAAGGAACAAATCA
261 AGAGGTTTATACTGAAGCAAGATCCAAGATGATTTGACATTCTTATGTTTACAAGAAACAAATCA
624950 AGGACATAGCAGATTTGACTCTCAGATGTTCTCA
326 AGGACATAGCAGATTTGACTCTCAGATGTTCTCA
* * * * **
624984 GACATGGCAGATCTAGCCTTCAGAGGTTTATACTGAAGCA-AGTCCAAGATGATTTGACATTCTT
1 AATATAGCAGATCTAGCCTTCAGATGTTTATACTGAAGCAGA-TCCAAGATGATTTGGTATTCTT
* * *
625048 ATGTTTACAAAAAACAAATCAAGGAA-ATAGCAGATTTGACTCTCAGATGTTCTCAAACA
65 GTGTTTACAAGAAACAAATCGA-GAACATAGCAGATTTGACTCTCAGATGTTCTCAAACA
625107 GACTCAAAGA
Statistics
Matches: 446, Mismatches: 34, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
358 1 0.00
359 442 0.99
360 3 0.01
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (359 bp):
AATATAGCAGATCTAGCCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTG
TGTTTACAAGAAACAAATCGAGAACATAGCAGATTTGACTCTCAGATGTTCTCAAACATAGCAGA
TCTAGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGATTTGATATTCTTGTGTTTACAAG
AAACAAATCAAGGACATAGCAGATTTGACTCTCAGATGTTCTCAAACATAGCAGATCTAGCCTTC
AGAGGTTTATACTGAAGCAAGATCCAAGATGATTTGACATTCTTATGTTTACAAGAAACAAATCA
AGGACATAGCAGATTTGACTCTCAGATGTTCTCA
Found at i:627221 original size:34 final size:35
Alignment explanation
Indices: 627145--627224 Score: 89
Period size: 34 Copynumber: 2.4 Consensus size: 35
627135 TGATTTATTT
**
627145 TTTATTC-TATATTACCTTTTATATATATGTTATG
1 TTTATTCATATATTACCAATTATATATATGTTATG
627179 --TATCTCATATATTACCAATTATAT-TAT-TTATG
1 TTTAT-TCATATATTACCAATTATATATATGTTATG
627211 TTTATATCATATAT
1 TTTAT-TCATATAT
627225 ATTATTTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
32 8 0.21
33 5 0.13
34 26 0.67
ACGTcount: A:0.31, C:0.10, G:0.04, T:0.55
Consensus pattern (35 bp):
TTTATTCATATATTACCAATTATATATATGTTATG
Found at i:630520 original size:10 final size:10
Alignment explanation
Indices: 630502--630550 Score: 57
Period size: 10 Copynumber: 4.9 Consensus size: 10
630492 TAAATTCTAT
630502 AAGATAAATA
1 AAGATAAATA
630512 CAA-ATAAATA
1 -AAGATAAATA
*
630522 AAGATAATTA
1 AAGATAAATA
630532 AAGATAAATGA
1 AAGATAAAT-A
630543 AA-ATAAAT
1 AAGATAAAT
630551 CCTAAAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
9 2 0.06
10 27 0.79
11 5 0.15
ACGTcount: A:0.67, C:0.02, G:0.08, T:0.22
Consensus pattern (10 bp):
AAGATAAATA
Found at i:632328 original size:54 final size:54
Alignment explanation
Indices: 632269--632575 Score: 213
Period size: 54 Copynumber: 5.7 Consensus size: 54
632259 ACAAATTATG
* * * * **
632269 AAAATCTTGTAAGTACAAGGTTACGATCGTAAATTAGTGAACTAAAAGATTCTA
1 AAAATCTTGTAAGTACAAGGTTGCAATTGTAAATCAGCAAACTAAAAGATTCTA
* * * *
632323 AAAATCTTAG-AAGTGCAAGGTTGCAATTGTAAATCGGCGAACCT-CAAGATTCTA
1 AAAATCTT-GTAAGTACAAGGTTGCAATTGTAAATCAGC-AAACTAAAAGATTCTA
* * * ** * * * * *
632377 AAAATCATGGAAGTGCAAGGTTGTGATTGTAAATCAACAAACCAGAAGTTTCTG
1 AAAATCTTGTAAGTACAAGGTTGCAATTGTAAATCAGCAAACTAAAAGATTCTA
* * **
632431 AAAATCTTGTAAGTACAGGGTTGCAATTGTAAATCGGCAAACTGTAAGATTCTA
1 AAAATCTTGTAAGTACAAGGTTGCAATTGTAAATCAGCAAACTAAAAGATTCTA
* * ** ** * ** *** *
632485 AAAATCTTGGAACTGTAAGGTTGTGATTATAAATCAATAAACCCGAAGATTGTGA
1 AAAATCTTGTAAGTACAAGGTTGCAATTGTAAATCAGCAAACTAAAAGATTCT-A
* * *
632540 AAAATCTTGTAAGTACAGGGTTGTAATCGTAAATCA
1 AAAATCTTGTAAGTACAAGGTTGCAATTGTAAATCA
632576 AAAAATCGTA
Statistics
Matches: 192, Mismatches: 56, Indels: 9
0.75 0.22 0.04
Matches are distributed among these distances:
53 4 0.02
54 155 0.81
55 33 0.17
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (54 bp):
AAAATCTTGTAAGTACAAGGTTGCAATTGTAAATCAGCAAACTAAAAGATTCTA
Found at i:632435 original size:108 final size:108
Alignment explanation
Indices: 632314--632574 Score: 346
Period size: 108 Copynumber: 2.4 Consensus size: 108
632304 AGTGAACTAA
* * * *
632314 AAGATTCTAAAAATCTTAG-AAGTGCAAGGTTGCAATTGTAAATCGGCGAACCT-CAAGATTCTA
1 AAGATTCTGAAAATCTT-GTAAGTACAGGGTTGCAATTGTAAATCGGC-AAACTGCAAGATTCTA
* *
632377 AAAATCATGGAAGTGCAAGGTTGTGATTGTAAATCAACAAACCAG
64 AAAATCATGGAACTGCAAGGTTGTGATTATAAATCAACAAACCAG
* *
632422 AAGTTTCTGAAAATCTTGTAAGTACAGGGTTGCAATTGTAAATCGGCAAACTGTAAGATTCTAAA
1 AAGATTCTGAAAATCTTGTAAGTACAGGGTTGCAATTGTAAATCGGCAAACTGCAAGATTCTAAA
* * * *
632487 AATCTTGGAACTGTAAGGTTGTGATTATAAATCAATAAACCCG
66 AATCATGGAACTGCAAGGTTGTGATTATAAATCAACAAACCAG
* * *
632530 AAGATTGTGAAAAATCTTGTAAGTACAGGGTTGTAATCGTAAATC
1 AAGATTCTG-AAAATCTTGTAAGTACAGGGTTGCAATTGTAAATC
632575 AAAAAATCGT
Statistics
Matches: 134, Mismatches: 16, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
107 5 0.04
108 96 0.72
109 33 0.25
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.28
Consensus pattern (108 bp):
AAGATTCTGAAAATCTTGTAAGTACAGGGTTGCAATTGTAAATCGGCAAACTGCAAGATTCTAAA
AATCATGGAACTGCAAGGTTGTGATTATAAATCAACAAACCAG
Found at i:634632 original size:26 final size:27
Alignment explanation
Indices: 634603--634660 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
634593 GCGCGACTCT
* *
634603 TTTTTTATATTAAAT-TT-TTTTTTTGA
1 TTTTTTAAATAAAATATTATTTTTTT-A
634629 TTTTTTAAATAAAATATTATTTTTTTA
1 TTTTTTAAATAAAATATTATTTTTTTA
634656 TTTTT
1 TTTTT
634661 ATTAAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 13 0.46
27 8 0.29
28 7 0.25
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.71
Consensus pattern (27 bp):
TTTTTTAAATAAAATATTATTTTTTTA
Found at i:635469 original size:30 final size:29
Alignment explanation
Indices: 635434--635530 Score: 74
Period size: 30 Copynumber: 3.2 Consensus size: 29
635424 TAATTTTAAA
635434 ATTAATTTGTTAGTAATTTAGAATTATGTT
1 ATTAATTT-TTAGTAATTTAGAATTATGTT
* *
635464 ATTAATTTTT-GT-GTTT-GTAATTATTTT
1 ATTAATTTTTAGTAATTTAG-AATTATGTT
* *
635491 AAAATTAATTTATTAGTAATTTAGGATTAAGTT
1 ---ATTAATTT-TTAGTAATTTAGAATTATGTT
*
635524 ATAAATT
1 ATTAATT
635531 GTTGCGTTTA
Statistics
Matches: 52, Mismatches: 7, Indels: 16
0.69 0.09 0.21
Matches are distributed among these distances:
26 1 0.02
27 11 0.21
28 2 0.04
29 2 0.04
30 22 0.42
31 2 0.04
32 2 0.04
33 9 0.17
34 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (29 bp):
ATTAATTTTTAGTAATTTAGAATTATGTT
Found at i:635507 original size:60 final size:60
Alignment explanation
Indices: 635421--635539 Score: 175
Period size: 60 Copynumber: 2.0 Consensus size: 60
635411 TTGTTTTTTA
* * * * *
635421 TAATAATTTTAAAATTAATTTGTTAGTAATTTAGAATTATGTTATTAATTTTTGTGTTTG
1 TAATAATTTTAAAATTAATTTATTAGTAATTTAGAATTAAGTTATAAATTGTTGCGTTTG
* *
635481 TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAATTGTTGCGTTT
1 TAATAATTTTAAAATTAATTTATTAGTAATTTAGAATTAAGTTATAAATTGTTGCGTTT
635540 AGTTTAGTAT
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.34, C:0.01, G:0.12, T:0.53
Consensus pattern (60 bp):
TAATAATTTTAAAATTAATTTATTAGTAATTTAGAATTAAGTTATAAATTGTTGCGTTTG
Found at i:635654 original size:20 final size:19
Alignment explanation
Indices: 635629--635674 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
635619 CAGAAAATAA
635629 TTTCTGGAAAATGATTTAAT
1 TTTCTGG-AAATGATTTAAT
*
635649 TTTCTGGAAATGATTTACT
1 TTTCTGGAAATGATTTAAT
635668 TTTCTGG
1 TTTCTGG
635675 TGTTTGGATG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.26, C:0.09, G:0.17, T:0.48
Consensus pattern (19 bp):
TTTCTGGAAATGATTTAAT
Found at i:636093 original size:27 final size:27
Alignment explanation
Indices: 636052--636125 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
636042 CACCATTTGT
* *
636052 GCCTCCGAGATAGGCACAATTAGTCGC
1 GCCTCAGAGATAGGCACAACTAGTCGC
* * * *
636079 GCCTCTGAGAAAGGCTCAACTAGTCGT
1 GCCTCAGAGATAGGCACAACTAGTCGC
*
636106 GCCTCAGAGATAGGCGCAAC
1 GCCTCAGAGATAGGCACAAC
636126 GTATTCGTAT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.27, C:0.28, G:0.27, T:0.18
Consensus pattern (27 bp):
GCCTCAGAGATAGGCACAACTAGTCGC
Found at i:639027 original size:170 final size:170
Alignment explanation
Indices: 638745--639087 Score: 578
Period size: 170 Copynumber: 2.0 Consensus size: 170
638735 ACGAAATCTT
* *
638745 CCTTGAATGCTAAGTGGAACAAATGCACGAATATGAGATCCATCTAATGCTCCAATACAATCTTT
1 CCTTGAATGCTAAGTGGAACAAATGCACAAACATGAGATCCATCTAATGCTCCAATACAATCTTT
* * * *
638810 AAAATAAAGATAAAACCTTGGATTGTTTCTGATTTCACTAGGAGTTGACTTATTAGGTAATCTAA
66 AAAATAAAGATAAAACATTGGATTGTTTCTGATTTCACTAGGAGTTGACTCATCAAGTAATCTAA
638875 TAACTAGCTTATACAATTTCAAAATAGCTCTAAATACAAC
131 TAACTAGCTTATACAATTTCAAAATAGCTCTAAATACAAC
*** *
638915 CCTTGAATGCTAAGTGGAATGGATGCACAAACATGAGTTCCATCTAATGCTCCAATACAATCTTT
1 CCTTGAATGCTAAGTGGAACAAATGCACAAACATGAGATCCATCTAATGCTCCAATACAATCTTT
*
638980 AAAATAAGGATAAAACATTGGATTGTTTCTGATTTCACTAGGAGTTGACTCATCAAGTAATCTAA
66 AAAATAAAGATAAAACATTGGATTGTTTCTGATTTCACTAGGAGTTGACTCATCAAGTAATCTAA
*
639045 TAACTAGTTTATACAATTTCAAAATAGCTCTAAATACAAC
131 TAACTAGCTTATACAATTTCAAAATAGCTCTAAATACAAC
639085 CCT
1 CCT
639088 AAAGTAACAA
Statistics
Matches: 161, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
170 161 1.00
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (170 bp):
CCTTGAATGCTAAGTGGAACAAATGCACAAACATGAGATCCATCTAATGCTCCAATACAATCTTT
AAAATAAAGATAAAACATTGGATTGTTTCTGATTTCACTAGGAGTTGACTCATCAAGTAATCTAA
TAACTAGCTTATACAATTTCAAAATAGCTCTAAATACAAC
Found at i:642382 original size:2 final size:2
Alignment explanation
Indices: 642370--642401 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
642360 AGATTTAATG
*
642370 AT AT GT 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
642402 CAGGGTGATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:642881 original size:26 final size:25
Alignment explanation
Indices: 642845--642928 Score: 132
Period size: 26 Copynumber: 3.2 Consensus size: 25
642835 TGATACAAAT
642845 TGATAATAGGTTAGGTAAATGTTCAA
1 TGATAATAGGTTAGGTAAATGTTC-A
642871 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTT-CA
*
642897 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATG-TTCA
642923 TGATAA
1 TGATAA
642929 GAATTTCATG
Statistics
Matches: 55, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
26 52 0.95
27 3 0.05
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.36
Consensus pattern (25 bp):
TGATAATAGGTTAGGTAAATGTTCA
Done.