Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 97507971
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: 97507971
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 232 characters in sequence are not A, C, G, or T
File 2 of 328
Found at i:469640 original size:272 final size:273
Alignment explanation
Indices: 469151--469707 Score: 1080
Period size: 272 Copynumber: 2.0 Consensus size: 273
469141 GTATTAATTT
*
469151 ATGGGGACCGTATTTCATTTACTAACTTGACTCAAATTATACCGTTAAGAGGGGTGGCTTACTCT
1 ATGGGGACTGTATTTCATTTACTAACTTGACTCAAATTATACCGTTAAGAGGGGTGGCTTACTC-
469216 TGTTGTTGAAGTTGCATTACTAAGCCAACATCCCATCACCATCACAACAATTTAATAACCAAAAG
65 T-TTGTTGAAGTTGCATTACTAAGCCAACATCCCATCACCATCACAACAATTTAATAACCAAAAG
469281 GTTTTAGAAACTTGTTGAAAATTATGATATATTTAATTGTTGTGGTTAAAGTTATGACATGAAAT
129 GTTTTAGAAACTTGTTGAAAATTATGATATATTTAATTGTTGTGGTTAAAGTTATGACATGAAAT
469346 TTGGATCAAGGTTAATACGGACGGCGCGTGGGCCTGAAGTTGTCGACGTTCGTCTGTTGGAGGAG
194 TTGGATCAAGGTTAATACGGACGGCGCGTGGGCCTGAAGTTGTCGACGTTCGTCTGTTGGAGGAG
469411 TCTTGCGGGGCTCGG
259 TCTTGCGGGGCTCGG
469426 ATGGGGACTGTATTTCATTTACTAACTTGACTCAAATTATACCGTTAAGAGGGGTGGCTTACTC-
1 ATGGGGACTGTATTTCATTTACTAACTTGACTCAAATTATACCGTTAAGAGGGGTGGCTTACTCT
469490 TTGTTGAAGTTGCATTACTAAGCCAACATCCCATCACCATCACAACAATTTAATAACCAAAAGGT
66 TTGTTGAAGTTGCATTACTAAGCCAACATCCCATCACCATCACAACAATTTAATAACCAAAAGGT
469555 TTTAGAAACTTGTTGAAAATTATGATATATTTAATTGTTGTGGTTAAAGTTATGACATGAAATTT
131 TTTAGAAACTTGTTGAAAATTATGATATATTTAATTGTTGTGGTTAAAGTTATGACATGAAATTT
469620 GGATCAAGGTTAATACGGACGGCGCGTGGGCCTGAAGTTGTCGACGTTCGTCTGTTGGAGGAGTC
196 GGATCAAGGTTAATACGGACGGCGCGTGGGCCTGAAGTTGTCGACGTTCGTCTGTTGGAGGAGTC
469685 TTGCGGGGCTCGG
261 TTGCGGGGCTCGG
469698 ATGGGGACTG
1 ATGGGGACTG
469708 GCAGCTTTGA
Statistics
Matches: 281, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
272 218 0.78
275 63 0.22
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (273 bp):
ATGGGGACTGTATTTCATTTACTAACTTGACTCAAATTATACCGTTAAGAGGGGTGGCTTACTCT
TTGTTGAAGTTGCATTACTAAGCCAACATCCCATCACCATCACAACAATTTAATAACCAAAAGGT
TTTAGAAACTTGTTGAAAATTATGATATATTTAATTGTTGTGGTTAAAGTTATGACATGAAATTT
GGATCAAGGTTAATACGGACGGCGCGTGGGCCTGAAGTTGTCGACGTTCGTCTGTTGGAGGAGTC
TTGCGGGGCTCGG
Found at i:475405 original size:13 final size:13
Alignment explanation
Indices: 475387--475433 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
475377 ATTAATCTCG
*
475387 AATTTAAGTTTAA
1 AATTTAAATTTAA
475400 AATTTAAAATTT-A
1 AATTT-AAATTTAA
*
475413 AATTAAAATTTAA
1 AATTTAAATTTAA
475426 AATATTAA
1 AAT-TTAA
475434 TATTACAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 6 0.21
13 14 0.50
14 8 0.29
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (13 bp):
AATTTAAATTTAA
Found at i:475407 original size:7 final size:7
Alignment explanation
Indices: 475395--475433 Score: 55
Period size: 7 Copynumber: 5.7 Consensus size: 7
475385 CGAATTTAAG
475395 TTTAAAA
1 TTTAAAA
475402 TTTAAAA
1 TTTAAAA
475409 TTT-AAA
1 TTTAAAA
475415 -TTAAAA
1 TTTAAAA
475421 TTTAAAA
1 TTTAAAA
475428 TATTAA
1 T-TTAA
475434 TATTACAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
5 2 0.07
6 6 0.21
7 17 0.59
8 4 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TTTAAAA
Found at i:475420 original size:19 final size:21
Alignment explanation
Indices: 475396--475438 Score: 72
Period size: 19 Copynumber: 2.1 Consensus size: 21
475386 GAATTTAAGT
475396 TTAAAATTTAAAAT-TTAA-A
1 TTAAAATTTAAAATATTAATA
475415 TTAAAATTTAAAATATTAATA
1 TTAAAATTTAAAATATTAATA
475436 TTA
1 TTA
475439 CAAGAATGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 14 0.64
20 4 0.18
21 4 0.18
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TTAAAATTTAAAATATTAATA
Found at i:477443 original size:15 final size:15
Alignment explanation
Indices: 477425--477492 Score: 57
Period size: 15 Copynumber: 4.5 Consensus size: 15
477415 GAGGTGGGGA
477425 TGGAGGTGGTGGTGG
1 TGGAGGTGGTGGTGG
****
477440 TGGAGAGT-AAACTGG
1 TGGAG-GTGGTGGTGG
*
477455 TGGTGGTGGTGGTGG
1 TGGAGGTGGTGGTGG
* *
477470 TGGTGGTGGTGGAGG
1 TGGAGGTGGTGGTGG
477485 TGGAGGTG
1 TGGAGGTG
477493 AATAAACAGG
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
14 2 0.05
15 36 0.90
16 2 0.05
ACGTcount: A:0.12, C:0.01, G:0.60, T:0.26
Consensus pattern (15 bp):
TGGAGGTGGTGGTGG
Found at i:477458 original size:3 final size:3
Alignment explanation
Indices: 477452--477492 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
477442 GAGAGTAAAC
* *
477452 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG AGG TGG AGG TG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TG
477493 AATAAACAGG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.05, C:0.00, G:0.66, T:0.29
Consensus pattern (3 bp):
TGG
Found at i:483971 original size:39 final size:39
Alignment explanation
Indices: 483928--484062 Score: 114
Period size: 39 Copynumber: 3.4 Consensus size: 39
483918 ACCAATATGG
*
483928 CACCCAGTGCCTCATCGGATAGTTCGAAGTAATAATTGA
1 CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAATTGA
* * * *
483967 CACCCAGTGTCTCATCGGCCTAG-CCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-ATAGTCCGAAGTAATAATTGA
* * * * *
484005 TACCCAGTACCTCATCGAATCTA-TCCGAAGAAATATAGTGA
1 CACCCAGTGCCTCATCGGA--TAGTCCGAAGTAATA-ATTGA
*
484046 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
484063 ACTCGAGGTC
Statistics
Matches: 73, Mismatches: 17, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAATTGA
Found at i:485603 original size:17 final size:17
Alignment explanation
Indices: 485581--485615 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
485571 GAATGCTCTC
*
485581 TGTTTCTTATTCTTCTT
1 TGTTTCTTATTATTCTT
*
485598 TGTTTCTTTTTATTCTT
1 TGTTTCTTATTATTCTT
485615 T
1 T
485616 TTCTTCATTT
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:0.06, C:0.14, G:0.06, T:0.74
Consensus pattern (17 bp):
TGTTTCTTATTATTCTT
Found at i:485685 original size:13 final size:13
Alignment explanation
Indices: 485645--485678 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
485635 ACATATATAT
* *
485645 ATAATATTATTTA
1 ATAATAATAGTTA
485658 ATAATAATAGTTA
1 ATAATAATAGTTA
485671 ATAATAAT
1 ATAATAAT
485679 TTATAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (13 bp):
ATAATAATAGTTA
Found at i:490687 original size:39 final size:39
Alignment explanation
Indices: 490644--490778 Score: 114
Period size: 39 Copynumber: 3.4 Consensus size: 39
490634 ACCAATATGG
*
490644 CACCCAGTGCCTCATCGGATAGTTCGAAGTAATAATTGA
1 CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAATTGA
* * * *
490683 CACCCAGTGTCTCATCGGCCTAG-CCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-ATAGTCCGAAGTAATAATTGA
* * * * *
490721 TACCCAGTACCTCATCGAATCTA-TCCGAAGAAATATAGTGA
1 CACCCAGTGCCTCATCGGA--TAGTCCGAAGTAATA-ATTGA
*
490762 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
490779 ACTCGAGGTC
Statistics
Matches: 73, Mismatches: 17, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAATTGA
Found at i:492317 original size:17 final size:17
Alignment explanation
Indices: 492295--492329 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
492285 GAATGCTCTC
*
492295 TGTTTCTTATTCTTCTT
1 TGTTTCTTATTATTCTT
*
492312 TGTTTCTTTTTATTCTT
1 TGTTTCTTATTATTCTT
492329 T
1 T
492330 TTCTTCATTT
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:0.06, C:0.14, G:0.06, T:0.74
Consensus pattern (17 bp):
TGTTTCTTATTATTCTT
Found at i:492399 original size:13 final size:13
Alignment explanation
Indices: 492359--492392 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
492349 ACATATATAT
* *
492359 ATAATATTATTTA
1 ATAATAATAGTTA
492372 ATAATAATAGTTA
1 ATAATAATAGTTA
492385 ATAATAAT
1 ATAATAAT
492393 TTATAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (13 bp):
ATAATAATAGTTA
Found at i:496915 original size:27 final size:26
Alignment explanation
Indices: 496855--496916 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
496845 ACTCTATTTT
496855 ATTTTATTAGGATGATTAATATTAAG
1 ATTTTATTAGGATGATTAATATTAAG
* * *
496881 ATAATTATTAGGATTATTCAA-ATTTAGG
1 AT-TTTATTAGGATGATT-AATA-TTAAG
496909 ATTTTATT
1 ATTTTATT
496917 TTAATTATCT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
26 2 0.07
27 19 0.66
28 8 0.28
ACGTcount: A:0.37, C:0.02, G:0.13, T:0.48
Consensus pattern (26 bp):
ATTTTATTAGGATGATTAATATTAAG
Found at i:499093 original size:13 final size:13
Alignment explanation
Indices: 499075--499116 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
499065 ATTAATCTCG
499075 AATTTAGATTTAA
1 AATTTAGATTTAA
499088 AATTTAGAATTT-A
1 AATTTAG-ATTTAA
* *
499101 AATTAAAATTTAA
1 AATTTAGATTTAA
499114 AAT
1 AAT
499117 ATTAATATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 4 0.16
13 17 0.68
14 4 0.16
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (13 bp):
AATTTAGATTTAA
Found at i:499099 original size:20 final size:19
Alignment explanation
Indices: 499074--499126 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 19
499064 AATTAATCTC
*
499074 GAATTTAGATTTAAAATTTA
1 GAATTTA-AATTAAAATTTA
499094 GAATTTAAATTAAAATTTA
1 GAATTTAAATTAAAATTTA
*
499113 AAATATTAATATTA
1 GAAT-TTAA-ATTA
499127 CAATAACGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 14 0.48
20 11 0.38
21 4 0.14
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (19 bp):
GAATTTAAATTAAAATTTA
Found at i:500034 original size:5 final size:5
Alignment explanation
Indices: 500013--500064 Score: 68
Period size: 5 Copynumber: 10.0 Consensus size: 5
500003 TGTTAAAATA
* *
500013 TATAT TAAAT TATTAT TATAT TATAG TATAT TATAT TATTAT TATAT TATAT
1 TATAT TATAT TA-TAT TATAT TATAT TATAT TATAT TA-TAT TATAT TATAT
500065 AAATAAGTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
5 32 0.78
6 9 0.22
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:500042 original size:26 final size:26
Alignment explanation
Indices: 500013--500063 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
500003 TGTTAAAATA
500013 TATATTAAATTATTATTATATTATAG
1 TATATTAAATTATTATTATATTATAG
*
500039 TATATTATATTATTATTATATTATA
1 TATATTAAATTATTATTATATTATA
500064 TAAATAAGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (26 bp):
TATATTAAATTATTATTATATTATAG
Found at i:501768 original size:39 final size:39
Alignment explanation
Indices: 501658--501792 Score: 112
Period size: 39 Copynumber: 3.4 Consensus size: 39
501648 GACCTCGAGT
* * * *
501658 CGATGAGACACTGGGTGTCACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCA-AATATTACTTCGGCTAG-TC
** ** * *
501699 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
* *
501737 CGATGAGACACTGGGTGTCAAATATTGCTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAAATATTACTTCG-GCTAGTC
*
501776 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
501793 CCATATTGGT
Statistics
Matches: 73, Mismatches: 19, Indels: 6
0.74 0.19 0.06
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
Found at i:501936 original size:18 final size:19
Alignment explanation
Indices: 501915--501955 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
501905 AATGAAATGA
501915 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
501933 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
501952 GAAA
1 GAAA
501956 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:504233 original size:27 final size:26
Alignment explanation
Indices: 504203--504264 Score: 61
Period size: 27 Copynumber: 2.3 Consensus size: 26
504193 ATAAACAGGT
* *
504203 GGAGGTGGAGATGGTGGCGGTGGAGGA
1 GGAGGTGGACA-GGTGGCGGCGGAGGA
** *
504230 GGAGAGTACACAGGTGGCGGCGGAGGT
1 GGAG-GTGGACAGGTGGCGGCGGAGGA
504257 GGAGGTGG
1 GGAGGTGG
504265 TGAAGGGGGA
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
26 2 0.07
27 21 0.78
28 4 0.15
ACGTcount: A:0.19, C:0.08, G:0.60, T:0.13
Consensus pattern (26 bp):
GGAGGTGGACAGGTGGCGGCGGAGGA
Found at i:504243 original size:42 final size:42
Alignment explanation
Indices: 504117--504266 Score: 138
Period size: 42 Copynumber: 3.6 Consensus size: 42
504107 GGGGGTGATA
* * * *
504117 GTGGAGGTGGGGATGGAGGTGGTGGTGGTGGAGAGTAAACTG
1 GTGGAGGTGGAGATGGTGGTGGTGGTGGAGGAGAGTAAACAG
* * * * * * *
504159 CTGGTGGTGGTGGTGGTGGTGGAGGTGGAGGTGAATAAACAG
1 GTGGAGGTGGAGATGGTGGTGGTGGTGGAGGAGAGTAAACAG
* * *
504201 GTGGAGGTGGAGATGGTGGCGGTGGAGGAGGAGAGTACACAG
1 GTGGAGGTGGAGATGGTGGTGGTGGTGGAGGAGAGTAAACAG
* * * *
504243 GTGGCGGCGGAGGTGGAGGTGGTG
1 GTGGAGGTGGAGATGGTGGTGGTG
504267 AAGGGGGAGA
Statistics
Matches: 83, Mismatches: 25, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
42 83 1.00
ACGTcount: A:0.19, C:0.05, G:0.57, T:0.19
Consensus pattern (42 bp):
GTGGAGGTGGAGATGGTGGTGGTGGTGGAGGAGAGTAAACAG
Found at i:504276 original size:42 final size:42
Alignment explanation
Indices: 504197--504277 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
504187 AGGTGAATAA
* * *
504197 ACAGGTGGAGGTGGAGATGGTGGCGGTGGAGGAGGAGAGTAC
1 ACAGGTGGAGGCGGAGATGGAGGCGGTGAAGGAGGAGAGTAC
* * * *
504239 ACAGGTGGCGGCGGAGGTGGAGGTGGTGAAGGGGGAGAG
1 ACAGGTGGAGGCGGAGATGGAGGCGGTGAAGGAGGAGAG
504278 GGAGGGGGAG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.22, C:0.07, G:0.58, T:0.12
Consensus pattern (42 bp):
ACAGGTGGAGGCGGAGATGGAGGCGGTGAAGGAGGAGAGTAC
Found at i:506966 original size:20 final size:20
Alignment explanation
Indices: 506941--506984 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
506931 TCCAAGTTAG
506941 AATTTAATGCTAAAACTGAT
1 AATTTAATGCTAAAACTGAT
506961 AATTTAATGCTAAAACTGAT
1 AATTTAATGCTAAAACTGAT
506981 AATT
1 AATT
506985 AAGTAACTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (20 bp):
AATTTAATGCTAAAACTGAT
Found at i:513941 original size:13 final size:13
Alignment explanation
Indices: 513923--513949 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
513913 TTTTAACTCT
513923 AAAAAGAAAAAGA
1 AAAAAGAAAAAGA
513936 AAAAAGAAAAAGA
1 AAAAAGAAAAAGA
513949 A
1 A
513950 GGTACAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAGA
Found at i:515696 original size:31 final size:31
Alignment explanation
Indices: 515661--515724 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
515651 ATTATTCGGG
515661 ATAGTTTGAAAGCTGCTTCTGATCGTAAAAA
1 ATAGTTTGAAAGCTGCTTCTGATCGTAAAAA
515692 ATAGTTTGAAAGCTGCTTCTGATCGTAAAAA
1 ATAGTTTGAAAGCTGCTTCTGATCGTAAAAA
515723 AT
1 AT
515725 CGTATGCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (31 bp):
ATAGTTTGAAAGCTGCTTCTGATCGTAAAAA
Found at i:516956 original size:40 final size:35
Alignment explanation
Indices: 516866--516981 Score: 160
Period size: 35 Copynumber: 3.2 Consensus size: 35
516856 CATGGCAAAG
*
516866 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATAATCCATACTGAGT
* *
516901 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATAATCCATACTGAGT
516936 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGG---TAT--AATCCATACTGAGT
516976 TGTGAA
1 TGTGAA
516982 TCGTGGCATT
Statistics
Matches: 72, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
35 51 0.71
38 3 0.04
40 18 0.25
ACGTcount: A:0.30, C:0.10, G:0.25, T:0.34
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATAATCCATACTGAGT
Found at i:516957 original size:35 final size:35
Alignment explanation
Indices: 516866--516960 Score: 172
Period size: 35 Copynumber: 2.7 Consensus size: 35
516856 CATGGCAAAG
* *
516866 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
516901 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
516936 TGTGAAATGTAGGTATGGTATTATC
1 TGTGAAATGTAGGTATGGTATTATC
516961 AAATCCATAC
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 58 1.00
ACGTcount: A:0.28, C:0.09, G:0.26, T:0.36
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
Found at i:523901 original size:39 final size:35
Alignment explanation
Indices: 523794--523887 Score: 145
Period size: 35 Copynumber: 2.7 Consensus size: 35
523784 CATGGCAAAG
* * *
523794 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAATGTAGATATGGTATTATCCATACTGAGC
*
523829 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGATATGGTATTATCCATACTGAGC
523864 TGTGAAATGTAGATAT-GTATTATC
1 TGTGAAATGTAGATATGGTATTATC
523888 AAATCCATAC
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
34 8 0.14
35 48 0.86
ACGTcount: A:0.30, C:0.10, G:0.24, T:0.36
Consensus pattern (35 bp):
TGTGAAATGTAGATATGGTATTATCCATACTGAGC
Found at i:523930 original size:73 final size:74
Alignment explanation
Indices: 523816--523962 Score: 183
Period size: 73 Copynumber: 2.0 Consensus size: 74
523806 GTATGGTATC
** * * **
523816 ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTATCCATACTGAGCTGTGAAATGTAGATAT-
1 ATCCATACTGAGTTGAAAAATGTAGGTATGGCATTATCCATACCGAGCTGAAAAATGTAGATATG
523880 GTATTATCAA
66 GTATT-TCAA
* *
523890 ATCCATACTGAGTT-AAAAATGTAGGTATGGCATT-TCCCATACCGAGTTGAAAAATGTAGGTAT
1 ATCCATACTGAGTTGAAAAATGTAGGTATGGCATTAT-CCATACCGAGCTGAAAAATGTAGATAT
523953 GGTATTTCAA
65 GGTATTTCAA
523963 TGAGGAAAAC
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
72 1 0.02
73 43 0.68
74 19 0.30
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.33
Consensus pattern (74 bp):
ATCCATACTGAGTTGAAAAATGTAGGTATGGCATTATCCATACCGAGCTGAAAAATGTAGATATG
GTATTTCAA
Found at i:523937 original size:34 final size:35
Alignment explanation
Indices: 523892--523960 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
523882 ATTATCAAAT
*
523892 CCATACTGAGTT-AAAAATGTAGGTATGGCATTTC
1 CCATACCGAGTTGAAAAATGTAGGTATGGCATTTC
*
523926 CCATACCGAGTTGAAAAATGTAGGTATGGTATTTC
1 CCATACCGAGTTGAAAAATGTAGGTATGGCATTTC
523961 AATGAGGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 11 0.34
35 21 0.66
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (35 bp):
CCATACCGAGTTGAAAAATGTAGGTATGGCATTTC
Found at i:530851 original size:234 final size:233
Alignment explanation
Indices: 530443--530909 Score: 792
Period size: 234 Copynumber: 2.0 Consensus size: 233
530433 TTCAATGACT
* * *
530443 GCTATCGATGCTGTTGTGGCTGAGGATGGTGCGGTTAAGGTGGATCTGAGAGTATTTTTGACTAA
1 GCTATCGATACTGTTGTGACTGAGGATGGTGCGGTTAAGGTAGATCTGAGAGTATTTTTGACTAA
*
530508 GATTAGAATTCTTTTGTTTCTTTATTTGTTGATCTTGGTTATTTGGTGGTGATTTTTTGGTGAGT
66 GATTAGAATTCTTTTGTTTCTTTATTTGTTGATCTTGGTTATTTGGTGGTGATTTCTTGGTGAGT
530573 TATTAAGGCATTGAGCCATTGGTCTATTCAAGCAATTTTTGCAGGCATGGTTTGAGATTTGTTAA
131 TATTAAGGCATTGAGCCATTGGTCTATTCAAGCAATTTTTGCAGGCATGGTTTGAGATTTGTTAA
*
530638 GGGCTGGAAACGTTGTTTTCTTGGTGGCAAATAAGAAA
196 GGGCTGGAAACGTTGTTTACTTGGTGGCAAATAAGAAA
* * *
530676 GCTATCGATACTGTTGTGACTGAGGCTGGTGTGGTTAAGGTAGATCT-ACGAGTATTTTTTACTA
1 GCTATCGATACTGTTGTGACTGAGGATGGTGCGGTTAAGGTAGATCTGA-GAGTATTTTTGACTA
*
530740 AGATTTAGAATTCTTTTGTTTTTTTATTTGTTGATCTTGGTTATTTGGTGGTGATTTCTTGGTGA
65 AGA-TTAGAATTCTTTTGTTTCTTTATTTGTTGATCTTGGTTATTTGGTGGTGATTTCTTGGTGA
530805 GTTATTAAGGCATTGAGCCATTGGTCTATTCAAGCAATTTTTGCAGGCATGGTTTGAGATTTGTT
129 GTTATTAAGGCATTGAGCCATTGGTCTATTCAAGCAATTTTTGCAGGCATGGTTTGAGATTTGTT
* * * *
530870 AGGGGCTGGAAATGTTGTTTACTTGGTGGTAGATAAGAAA
194 AAGGGCTGGAAACGTTGTTTACTTGGTGGCAAATAAGAAA
530910 AGTAACGAAT
Statistics
Matches: 219, Mismatches: 13, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
232 1 0.00
233 59 0.27
234 159 0.73
ACGTcount: A:0.22, C:0.09, G:0.28, T:0.42
Consensus pattern (233 bp):
GCTATCGATACTGTTGTGACTGAGGATGGTGCGGTTAAGGTAGATCTGAGAGTATTTTTGACTAA
GATTAGAATTCTTTTGTTTCTTTATTTGTTGATCTTGGTTATTTGGTGGTGATTTCTTGGTGAGT
TATTAAGGCATTGAGCCATTGGTCTATTCAAGCAATTTTTGCAGGCATGGTTTGAGATTTGTTAA
GGGCTGGAAACGTTGTTTACTTGGTGGCAAATAAGAAA
Found at i:534668 original size:2 final size:2
Alignment explanation
Indices: 534652--534683 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
534642 GCATGTATGC
534652 AT AT AT A- AT AT -T 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
534684 GTTTTTTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:538317 original size:29 final size:28
Alignment explanation
Indices: 538285--538350 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 28
538275 TTCTAATCTT
*
538285 TTTAAATTATTTATTCAAATT-GTTTCAAA
1 TTTAAATTATTT-TTCAAATTAATTT-AAA
* *
538314 TTTAAACTATTTTTTAAATTAATTTAAA
1 TTTAAATTATTTTTCAAATTAATTTAAA
538342 TTTAAATTA
1 TTTAAATTA
538351 AGTATATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 18 0.56
29 14 0.44
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.53
Consensus pattern (28 bp):
TTTAAATTATTTTTCAAATTAATTTAAA
Found at i:538361 original size:15 final size:16
Alignment explanation
Indices: 538326--538365 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
538316 TAAACTATTT
*
538326 TTTAAATTAATTTAAA
1 TTTAAATTAATGTAAA
*
538342 TTTAAATTAA-GTATA
1 TTTAAATTAATGTAAA
538357 TTTAAATTA
1 TTTAAATTA
538366 TTATTTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
TTTAAATTAATGTAAA
Found at i:539618 original size:40 final size:40
Alignment explanation
Indices: 539545--539623 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 40
539535 AAATCTAAAG
* * ** *
539545 GTTGAACAATTTGTATGCAAAGAATTAGTAAAAATCAATT
1 GTTGAACAACTTATATGCAAAGAATTACCAAAAACCAATT
539585 GTTGAACAACTTATATGCAATA-AATTACCAAAAACCAAT
1 GTTGAACAACTTATATGCAA-AGAATTACCAAAAACCAAT
539624 AGTTCAAGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
40 32 0.97
41 1 0.03
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.29
Consensus pattern (40 bp):
GTTGAACAACTTATATGCAAAGAATTACCAAAAACCAATT
Found at i:552975 original size:15 final size:18
Alignment explanation
Indices: 552934--552975 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
552924 ATTACTACAA
552934 TATTAAAATAATATATAT
1 TATTAAAATAATATATAT
*
552952 TATTTAAATAA-AT-TAT
1 TATTAAAATAATATATAT
552968 T-TTAAAAT
1 TATTAAAAT
552976 GGAGAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 6 0.27
16 4 0.18
17 2 0.09
18 10 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TATTAAAATAATATATAT
Found at i:554065 original size:16 final size:18
Alignment explanation
Indices: 554036--554071 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
554026 TTAATCTTTT
554036 AAAAATTAACTTTTTTAA
1 AAAAATTAACTTTTTTAA
554054 AAAAATT-A-TTTTTTAA
1 AAAAATTAACTTTTTTAA
554070 AA
1 AA
554072 TGGAAGACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
17 1 0.06
18 7 0.39
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
AAAAATTAACTTTTTTAA
Found at i:557675 original size:21 final size:21
Alignment explanation
Indices: 557633--557675 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
557623 ATTAATTCCG
* *
557633 TTAAACAATAATTGATATTTT
1 TTAAACAATAAATGATAATTT
*
557654 TTAAACAATAAATGTTAATTT
1 TTAAACAATAAATGATAATTT
557675 T
1 T
557676 ATTCCAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.47
Consensus pattern (21 bp):
TTAAACAATAAATGATAATTT
Found at i:558662 original size:20 final size:20
Alignment explanation
Indices: 558605--558662 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
558595 GCTAAATATA
*
558605 TATATTAATAAATTTAAAAT
1 TATATTAATAAATTTATAAT
* **
558625 TTTA-TAATGAAAAATATAAT
1 TATATTAAT-AAATTTATAAT
558645 TATATTAATAAATTTATA
1 TATATTAATAAATTTATA
558663 CAGTTATACT
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
19 4 0.14
20 21 0.72
21 4 0.14
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
TATATTAATAAATTTATAAT
Found at i:564729 original size:19 final size:20
Alignment explanation
Indices: 564705--564748 Score: 81
Period size: 19 Copynumber: 2.2 Consensus size: 20
564695 ATAAGTGAAC
564705 TCGGACTCAACTCAACGAG-
1 TCGGACTCAACTCAACGAGT
564724 TCGGACTCAACTCAACGAGT
1 TCGGACTCAACTCAACGAGT
564744 TCGGA
1 TCGGA
564749 TGCCTAGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 19 0.79
20 5 0.21
ACGTcount: A:0.30, C:0.30, G:0.23, T:0.18
Consensus pattern (20 bp):
TCGGACTCAACTCAACGAGT
Found at i:564793 original size:47 final size:47
Alignment explanation
Indices: 564724--564845 Score: 153
Period size: 46 Copynumber: 2.6 Consensus size: 47
564714 ACTCAACGAG
*
564724 TCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-TCA-CGAAC
1 TCGGACTCAACTCAACGAGTTCGGATGCCTAG---CATCCATAAGCGAAC
* * *
564771 TCGGACTCAACTCAACGAGTTCGGACG-CTCGCATCCATAAGTGAAC
1 TCGGACTCAACTCAACGAGTTCGGATGCCTAGCATCCATAAGCGAAC
564817 TCGGACTCAACTCAACGAGTTCGGATGCC
1 TCGGACTCAACTCAACGAGTTCGGATGCC
564846 AACCATCCTA
Statistics
Matches: 66, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
43 3 0.05
44 1 0.02
45 2 0.03
46 33 0.50
47 27 0.41
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.21
Consensus pattern (47 bp):
TCGGACTCAACTCAACGAGTTCGGATGCCTAGCATCCATAAGCGAAC
Found at i:567543 original size:46 final size:48
Alignment explanation
Indices: 567421--567550 Score: 155
Period size: 46 Copynumber: 2.8 Consensus size: 48
567411 TGTAACCCGC
567421 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA--CCTAGTTACAT
* * * *
567471 --TTCA-CGAACTCGGACTCAACTCAACGAGTTCGGA-C-A-TTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACCTAGTT-ACAT
567514 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
567551 TGCTCAACCA
Statistics
Matches: 69, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
42 2 0.03
43 4 0.06
44 1 0.01
45 2 0.03
46 29 0.42
47 29 0.42
48 2 0.03
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (48 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACCTAGTTACAT
Found at i:570774 original size:46 final size:45
Alignment explanation
Indices: 570662--570775 Score: 131
Period size: 46 Copynumber: 2.5 Consensus size: 45
570652 GAATGTTATG
* *
570662 GTGTCTTTCAACCATGGTCTTATTCATTCCCAACTTGATGTCAGA
1 GTGTCTTTCAACCATGGTCTTATTCATTCCCAACGTGATGCCAGA
* ** * *
570707 GTGTCTTTCAACCATGATCTTATTCATT-TTATATCGTGTTGCCATA
1 GTGTCTTTCAACCATGGTCTTATTCATTCCCA-A-CGTGATGCCAGA
*
570753 GTGTCTTTCAACCGTGGTCTTAT
1 GTGTCTTTCAACCATGGTCTTAT
570776 CCGTCTGATT
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
44 1 0.02
45 28 0.48
46 29 0.50
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.42
Consensus pattern (45 bp):
GTGTCTTTCAACCATGGTCTTATTCATTCCCAACGTGATGCCAGA
Found at i:570816 original size:45 final size:45
Alignment explanation
Indices: 570746--570911 Score: 147
Period size: 45 Copynumber: 3.7 Consensus size: 45
570736 TATATCGTGT
* ** *
570746 TGCCATAGTGTCTTTCAACCGTGGTCTTA-TCCGTCT-GATTCATAA
1 TGCCATAGCGTCTTTCAACTATGGTCTTACT-CGT-TAGAATCATAA
* * *
570791 TGCCATAGCGTCTTTCAGCTATGGTCTTACTCGTTAGAATCGTGA
1 TGCCATAGCGTCTTTCAACTATGGTCTTACTCGTTAGAATCATAA
* * * * ****
570836 TGCCATAACGTCTTTCAACTATGATTTTACTCGTTAAAATTGGGA
1 TGCCATAGCGTCTTTCAACTATGGTCTTACTCGTTAGAATCATAA
* *
570881 TGCCATAACGTCTTTCAGCTATGGTCTTACT
1 TGCCATAGCGTCTTTCAACTATGGTCTTACT
570912 TGTTTTTGGT
Statistics
Matches: 102, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
44 1 0.01
45 100 0.98
46 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.37
Consensus pattern (45 bp):
TGCCATAGCGTCTTTCAACTATGGTCTTACTCGTTAGAATCATAA
Found at i:570928 original size:45 final size:45
Alignment explanation
Indices: 570790--571000 Score: 126
Period size: 45 Copynumber: 4.7 Consensus size: 45
570780 CTGATTCATA
* * * *
570790 ATGCCATAGCGTCTTTCAGCTATGGTCTTACTCG--TTAGAATCGTG
1 ATGCCATAGCGTCTTTCAACTATGGTCTTACTCGTTTTTG-GT-ATG
* * * *
570835 ATGCCATAACGTCTTTCAACTATGATTTTACTCGTTAAAATTGG---G
1 ATGCCATAGCGTCTTTCAACTATGGTCTTACTCGTT---TTTGGTATG
* * *
570880 ATGCCATAACGTCTTTCAGCTATGGTCTTACTTGTTTTTGGTATG
1 ATGCCATAGCGTCTTTCAACTATGGTCTTACTCGTTTTTGGTATG
** * * *** * * *
570925 ATGCCAATAGTTTCTTTCAACTATGATCTTATTTAATTCTAGTATA
1 ATGCC-ATAGCGTCTTTCAACTATGGTCTTACTCGTTTTTGGTATG
* *
570971 ATGCCATAGCGTGTTTCATCTATGGTCTTA
1 ATGCCATAGCGTCTTTCAACTATGGTCTTA
571001 ATCAATTCCT
Statistics
Matches: 129, Mismatches: 28, Indels: 18
0.74 0.16 0.10
Matches are distributed among these distances:
42 4 0.03
45 89 0.69
46 34 0.26
50 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.41
Consensus pattern (45 bp):
ATGCCATAGCGTCTTTCAACTATGGTCTTACTCGTTTTTGGTATG
Found at i:572207 original size:15 final size:17
Alignment explanation
Indices: 572176--572208 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
572166 ATTTATTCAT
572176 TCAAATAACATAAATTA
1 TCAAATAACATAAATTA
572193 TCAAATAA-A-AAATTA
1 TCAAATAACATAAATTA
572208 T
1 T
572209 TATAATATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 1 0.06
17 8 0.50
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (17 bp):
TCAAATAACATAAATTA
Found at i:573352 original size:2 final size:2
Alignment explanation
Indices: 573347--573380 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
573337 TTTTTGAAAT
*
573347 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
573381 GGGATGGTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:573579 original size:85 final size:84
Alignment explanation
Indices: 573372--573715 Score: 383
Period size: 85 Copynumber: 4.1 Consensus size: 84
573362 ATATATATAT
* * ** * * * * * *
573372 ATATATATAGGGATGGTCTTCTCCGGTTCATTTAGGAGGAAAGGAGTAAGATTTATTGGAACCTA
1 ATATATATAGGGATAGTCTACTCCGGTTTGTATAGGAGGAACGAAATATGATTTATTGAAACCTA
* * *
573437 AACTGTTCTTTTGGGAATT
66 AAATGTTCTTTTGGAAATC
* * * *
573456 ACATATATAGGGATAGTCTACTCCAGTTTGTATGGGAGGAACGAAATATGATTTATTGGAACCTA
1 ATATATATAGGGATAGTCTACTCCGGTTTGTATAGGAGGAACGAAATATGATTTATTGAAACCTA
573521 AAATGTTCTTTTTGGAAATC
66 AAATGTTC-TTTTGGAAATC
* * ** * *
573541 ATATATATAGGGATAGTCTTCTCTGGTTTGTATAGGAGGAACGAAATACAATCTATTGAAACATA
1 ATATATATAGGGATAGTCTACTCCGGTTTGTATAGGAGGAACGAAATATGATTTATTGAAACCTA
573606 AAATGTTCTTTTGGAAATTC
66 AAATGTTCTTTTGGAAA-TC
*
573626 -TATATCTAGGGGATAGTCTACTCCGGTTTGTATAGGAGTG---G-AATATGATTTATTGAAACC
1 ATATATATA-GGGATAGTCTACTCCGGTTTGTATAGGAG-GAACGAAATATGATTTATTGAAACC
*
573686 TAAAATGTTCTTTTGGAAATT
64 TAAAATGTTCTTTTGGAAATC
*
573707 GTATATATA
1 ATATATATA
573716 TCGTTTTTGT
Statistics
Matches: 221, Mismatches: 34, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
81 1 0.00
82 41 0.19
83 1 0.00
84 76 0.34
85 101 0.46
86 1 0.00
ACGTcount: A:0.32, C:0.10, G:0.22, T:0.36
Consensus pattern (84 bp):
ATATATATAGGGATAGTCTACTCCGGTTTGTATAGGAGGAACGAAATATGATTTATTGAAACCTA
AAATGTTCTTTTGGAAATC
Found at i:582793 original size:23 final size:23
Alignment explanation
Indices: 582759--582803 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
582749 GCACATTCTC
* * *
582759 TTAATTTGATATTTATAATTTTT
1 TTAATTTAATATCTAAAATTTTT
582782 TTAATTTAATATCTAAAATTTT
1 TTAATTTAATATCTAAAATTTT
582804 ATTTTGATCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (23 bp):
TTAATTTAATATCTAAAATTTTT
Found at i:583987 original size:18 final size:18
Alignment explanation
Indices: 583964--584000 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
583954 ATATCATCTC
583964 AGCTTAGTATTACTACAT
1 AGCTTAGTATTACTACAT
583982 AGCTTAGTATTACTACAT
1 AGCTTAGTATTACTACAT
584000 A
1 A
584001 ATACTCACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (18 bp):
AGCTTAGTATTACTACAT
Found at i:586750 original size:14 final size:14
Alignment explanation
Indices: 586731--586757 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
586721 AATTATGTCA
586731 AATTAAATTACAAG
1 AATTAAATTACAAG
586745 AATTAAATTACAA
1 AATTAAATTACAA
586758 ATTTGAACAT
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:0.59, C:0.07, G:0.04, T:0.30
Consensus pattern (14 bp):
AATTAAATTACAAG
Found at i:587297 original size:17 final size:17
Alignment explanation
Indices: 587275--587314 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
587265 GAAAAAGACT
*
587275 ATTTTATCATTATATTA
1 ATTTTATAATTATATTA
*
587292 ATTTTATAATTTTATTA
1 ATTTTATAATTATATTA
*
587309 TTTTTA
1 ATTTTA
587315 AAGGAGTAAG
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:0.03, G:0.00, T:0.65
Consensus pattern (17 bp):
ATTTTATAATTATATTA
Found at i:587411 original size:4 final size:4
Alignment explanation
Indices: 587402--587434 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
587392 ATGCCTAGAC
587402 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
587435 GGAAATCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:591237 original size:51 final size:51
Alignment explanation
Indices: 591170--591271 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 51
591160 TGAATATGAA
*
591170 GATCAAATTATTACTACATATCTCATGCAGCAGCAACTCAATATTCTACCT
1 GATCAAATTATCACTACATATCTCATGCAGCAGCAACTCAATATTCTACCT
591221 GATCAAATTATCACTACATATCTCATGCAGCAGCAACTCAATATTCTACCT
1 GATCAAATTATCACTACATATCTCATGCAGCAGCAACTCAATATTCTACCT
591272 TCTTTTTTAC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.35, C:0.26, G:0.08, T:0.30
Consensus pattern (51 bp):
GATCAAATTATCACTACATATCTCATGCAGCAGCAACTCAATATTCTACCT
Found at i:605708 original size:126 final size:133
Alignment explanation
Indices: 605406--605709 Score: 379
Period size: 126 Copynumber: 2.3 Consensus size: 133
605396 GATTGAACTG
* *
605406 ATTGGATAATTTTTAACTATATTATGATTATGATTGTTGTTATTTCGTTATTTTTACTCTTGTTT
1 ATTGGTTAATTTTTAACTATATTATGATTATGATTGTTGTTATTGCGTTATTTTTACTCTTGTTT
* *
605471 GACGCCTTCTACTTAATTTAAGTATTAGGGTTTAGGGTTTAATTCTCAGCTTAACTATTATCCAA
66 GACGCCTTCTACTTAACTTAAGTATTAGGGTTTAGGGTTTAATTCTCAGCTTAACTATTATCAAA
*
605536 TTC
131 ATC
* * ** *
605539 ACTGGTTAATTTTTAACTATAATATTTTTATGATTGTTTTTATTGCGTTA-TTTTACTCTTGTTT
1 ATTGGTTAATTTTTAACTATATTATGATTATGATTGTTGTTATTGCGTTATTTTTACTCTTGTTT
* * * *
605603 GATG-C-T-TAC-T-ACTT-AGTTTTAGGGTTTAGGGTTTAATTCTCAGTTTAACTATTATTAAA
66 GACGCCTTCTACTTAACTTAAGTATTAGGGTTTAGGGTTTAATTCTCAGCTTAACTATTATCAAA
605662 ATC
131 ATC
* * * * * *
605665 TTTGGTTAATGTTTAGCTTTATTATGATTGTGACTGTTGTTATTG
1 ATTGGTTAATTTTTAACTATATTATGATTATGATTGTTGTTATTG
605710 TTTTGTTTTG
Statistics
Matches: 146, Mismatches: 25, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
126 77 0.53
127 3 0.02
128 1 0.01
129 3 0.02
130 1 0.01
131 1 0.01
132 17 0.12
133 43 0.29
ACGTcount: A:0.24, C:0.10, G:0.15, T:0.52
Consensus pattern (133 bp):
ATTGGTTAATTTTTAACTATATTATGATTATGATTGTTGTTATTGCGTTATTTTTACTCTTGTTT
GACGCCTTCTACTTAACTTAAGTATTAGGGTTTAGGGTTTAATTCTCAGCTTAACTATTATCAAA
ATC
Found at i:607477 original size:30 final size:30
Alignment explanation
Indices: 607443--607506 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
607433 TTGGACTTAT
* *
607443 TTGATTCC-TTCTAATATTATAGGGACTAAA
1 TTGATTCCATT-TAATAATAGAGGGACTAAA
*
607473 TTGA-TCCATTTAATAATAGAGGGACTAAC
1 TTGATTCCATTTAATAATAGAGGGACTAAA
607502 TTGAT
1 TTGAT
607507 ACTGTCCCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 23 0.79
30 6 0.21
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (30 bp):
TTGATTCCATTTAATAATAGAGGGACTAAA
Found at i:616922 original size:23 final size:22
Alignment explanation
Indices: 616849--616927 Score: 113
Period size: 22 Copynumber: 3.5 Consensus size: 22
616839 AGGAGGGGGG
*
616849 ATCGATGGTATTTTGAGGAAGA
1 ATCGATTGTATTTTGAGGAAGA
616871 ATCGATTGTATTTTGAGGAAGA
1 ATCGATTGTATTTTGAGGAAGA
*
616893 ATCGATTGTATTTTGGGGAGAGA
1 ATCGATTGTATTTTGAGGA-AGA
**
616916 AGAGATTGTATT
1 ATCGATTGTATT
616928 AGAGGGGGTT
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 39 0.75
23 13 0.25
ACGTcount: A:0.30, C:0.04, G:0.30, T:0.35
Consensus pattern (22 bp):
ATCGATTGTATTTTGAGGAAGA
Found at i:617607 original size:39 final size:38
Alignment explanation
Indices: 617531--617682 Score: 250
Period size: 39 Copynumber: 3.9 Consensus size: 38
617521 ATAAAGTATG
617531 GTTTTAATTAATAATAAAAACAAAATAGTATGAGGGAATA
1 GTTTTAATTAATAAT-AAAACAAAATAGTATG-GGGAATA
617571 GTTTTAATTAATAATAAAACAAAATAGTATAGGGGAATA
1 GTTTTAATTAATAATAAAACAAAATAGTAT-GGGGAATA
617610 GTTTTAATTAATAATAAAACAAAATAGTATGGGGAAATA
1 GTTTTAATTAATAATAAAACAAAATAGTATGGGG-AATA
* *
617649 GTTTTAATTAATAATAAAACAAAGTAGCATGGGG
1 GTTTTAATTAATAATAAAACAAAATAGTATGGGG
617683 GGAGTGGAAT
Statistics
Matches: 108, Mismatches: 2, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
38 4 0.04
39 88 0.81
40 16 0.15
ACGTcount: A:0.50, C:0.03, G:0.16, T:0.30
Consensus pattern (38 bp):
GTTTTAATTAATAATAAAACAAAATAGTATGGGGAATA
Found at i:618700 original size:16 final size:16
Alignment explanation
Indices: 618681--618715 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
618671 AACCTAACCC
*
618681 AAAAAAAAACAAAGAA
1 AAAAAAAAAAAAAGAA
618697 AAAAAAAAAAAAAGAA
1 AAAAAAAAAAAAAGAA
618713 AAA
1 AAA
618716 CTTACCCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.91, C:0.03, G:0.06, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAGAA
Found at i:618730 original size:16 final size:16
Alignment explanation
Indices: 618711--618747 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
618701 AAAAAAAAAG
*
618711 AAAAACTTACCCCAAA
1 AAAAACTAACCCCAAA
*
618727 AAAACCTAACCCCAAA
1 AAAAACTAACCCCAAA
618743 AAAAA
1 AAAAA
618748 AAAAAAAAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.62, C:0.30, G:0.00, T:0.08
Consensus pattern (16 bp):
AAAAACTAACCCCAAA
Found at i:618772 original size:29 final size:28
Alignment explanation
Indices: 618740--618795 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 28
618730 ACCTAACCCC
618740 AAAAAAAAAAAAAAAAAGAAGAAAAAAAG
1 AAAAAAAAAAAAAAAAAG-AGAAAAAAAG
* * * *
618769 AAAAACATAACAAAAAAGATAAAAAAA
1 AAAAAAAAAAAAAAAAAGAGAAAAAAA
618796 CCTAGCCACC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 8 0.35
29 15 0.65
ACGTcount: A:0.86, C:0.04, G:0.07, T:0.04
Consensus pattern (28 bp):
AAAAAAAAAAAAAAAAAGAGAAAAAAAG
Found at i:618783 original size:19 final size:19
Alignment explanation
Indices: 618742--618795 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
618732 CTAACCCCAA
*
618742 AAAAAAAAAAAAAAAGAAG
1 AAAAAAAAAAAAAAAGAAC
* * *
618761 AAAAAAAGAAAAACATAAC
1 AAAAAAAAAAAAAAAGAAC
618780 AAAAAAGATAAAAAAA
1 AAAAAA-A-AAAAAAA
618796 CCTAGCCACC
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
19 21 0.78
20 1 0.04
21 5 0.19
ACGTcount: A:0.85, C:0.04, G:0.07, T:0.04
Consensus pattern (19 bp):
AAAAAAAAAAAAAAAGAAC
Found at i:618842 original size:12 final size:12
Alignment explanation
Indices: 618825--618854 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
618815 TCCCACTTGC
618825 CCCATTTTTCCT
1 CCCATTTTTCCT
618837 CCCATTTTTCCT
1 CCCATTTTTCCT
618849 CCCATT
1 CCCATT
618855 GTCTACCACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.10, C:0.43, G:0.00, T:0.47
Consensus pattern (12 bp):
CCCATTTTTCCT
Found at i:619363 original size:39 final size:39
Alignment explanation
Indices: 619291--619365 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
619281 TTTATATATA
* * *
619291 TTATGTATATATTTTTTAATGCCATTAGTTATATATTTC
1 TTATGTATATATTCTTAAATACCATTAGTTATATATTTC
*
619330 TTATGTATATATTCTTAAATACTATTA-TATATATAT
1 TTATGTATATATTCTTAAATACCATTAGT-TATATAT
619366 ATATATTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 1 0.03
39 30 0.97
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (39 bp):
TTATGTATATATTCTTAAATACCATTAGTTATATATTTC
Found at i:621689 original size:12 final size:13
Alignment explanation
Indices: 621671--621708 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
621661 TCTCTTGTAA
621671 ATTTATAATTTTT
1 ATTTATAATTTTT
621684 -TTTAT-ATTTTT
1 ATTTATAATTTTT
621695 ATTTATATATTTTT
1 ATTTATA-ATTTTT
621709 GAATAATACA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 6 0.27
12 10 0.45
14 6 0.27
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
ATTTATAATTTTT
Found at i:622796 original size:29 final size:31
Alignment explanation
Indices: 622764--622826 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 31
622754 AATAGGTCAG
* *
622764 TGACTAAATTAT-AATTTTTTAA-AATTAAA
1 TGACTAAAATATAAATTTATTAATAATTAAA
*
622793 TGACTAAAATATAAATTTATTAATAATTTAA
1 TGACTAAAATATAAATTTATTAATAATTAAA
622824 TGA
1 TGA
622827 TCTTTAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 11 0.38
30 9 0.31
31 9 0.31
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (31 bp):
TGACTAAAATATAAATTTATTAATAATTAAA
Found at i:626559 original size:29 final size:29
Alignment explanation
Indices: 626520--626681 Score: 92
Period size: 31 Copynumber: 5.2 Consensus size: 29
626510 ATTTTACGTG
* *
626520 TATATATAATTACACTAAATCAAAATTCA
1 TATATAAAATTACACTAAATCAAAATTTA
*
626549 TATATAAAATTACATATTAAATCAAAATTTA
1 TATATAAAATTAC--ACTAAATCAAAATTTA
* * * ** *
626580 TTTATATATTTAGTCAACAAT-AAAAGTTTTA
1 TATATAAAATTACACTA-AATCAAAA--TTTA
* * *
626611 TGTGTATATATAATTACACTAAATTAAAATTCA
1 ----TATATAAAATTACACTAAATCAAAATTTA
*
626644 TATATAAAATTACACATAAAATTAAAATTTA
1 TATATAAAATTACAC-T-AAATCAAAATTTA
*
626675 TGTATAA
1 TATATAA
626682 TTTTGAGATT
Statistics
Matches: 102, Mismatches: 19, Indels: 22
0.71 0.13 0.15
Matches are distributed among these distances:
29 31 0.30
30 4 0.04
31 45 0.44
33 3 0.03
34 3 0.03
35 16 0.16
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.39
Consensus pattern (29 bp):
TATATAAAATTACACTAAATCAAAATTTA
Found at i:626633 original size:95 final size:95
Alignment explanation
Indices: 626481--626684 Score: 313
Period size: 95 Copynumber: 2.2 Consensus size: 95
626471 AAATTGAAGT
*
626481 TTTATGTATATATTTGATCTACAATAAAAATTTTACGTGTATATATAATTACACTAAATCAAAAT
1 TTTATGTATATATTTGATCAACAATAAAAATTTTACGTGTATATATAATTACACTAAATCAAAAT
* *
626546 TCATATATAAAATTACATATTAAATCAAAA
66 TCATATATAAAATTACACATAAAATCAAAA
* * * *
626576 TTTATTTATATATTT-AGTCAACAATAAAAGTTTTATGTGTATATATAATTACACTAAATTAAAA
1 TTTATGTATATATTTGA-TCAACAATAAAAATTTTACGTGTATATATAATTACACTAAATCAAAA
*
626640 TTCATATATAAAATTACACATAAAATTAAAA
65 TTCATATATAAAATTACACATAAAATCAAAA
626671 TTTATGTATA-ATTT
1 TTTATGTATATATTT
626685 TGAGATTTAT
Statistics
Matches: 99, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
94 5 0.05
95 94 0.95
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (95 bp):
TTTATGTATATATTTGATCAACAATAAAAATTTTACGTGTATATATAATTACACTAAATCAAAAT
TCATATATAAAATTACACATAAAATCAAAA
Found at i:626683 original size:29 final size:28
Alignment explanation
Indices: 626615--626683 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 28
626605 GTTTTATGTG
626615 TATATATAATTACACTAAATTAAAATTCA
1 TATATATAATTACACTAAATTAAAATT-A
*
626644 TATATAAAATTACACATAAAATTAAAATT-
1 TATATATAATTACAC-T-AAATTAAAATTA
*
626673 TATGTATAATT
1 TATATATAATT
626684 TTGAGATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 23 0.66
30 1 0.03
31 11 0.31
ACGTcount: A:0.52, C:0.07, G:0.01, T:0.39
Consensus pattern (28 bp):
TATATATAATTACACTAAATTAAAATTA
Found at i:628107 original size:19 final size:21
Alignment explanation
Indices: 628075--628122 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 21
628065 AATGTATGGT
628075 AAAATTATAGTTTAACTTTAA
1 AAAATTATAGTTTAACTTTAA
* *
628096 AAAATTA-A-TTT-ATTTTTA
1 AAAATTATAGTTTAACTTTAA
628114 AAAATTATA
1 AAAATTATA
628123 AAAATATAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 12 0.50
19 4 0.17
20 1 0.04
21 7 0.29
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (21 bp):
AAAATTATAGTTTAACTTTAA
Found at i:628958 original size:19 final size:20
Alignment explanation
Indices: 628914--628958 Score: 51
Period size: 19 Copynumber: 2.3 Consensus size: 20
628904 GACTTATTTT
628914 ATATCATTTTTAATTATTTAA
1 ATAT-ATTTTTAATTATTTAA
628935 A-ATATTTTT-A-TATTTATA
1 ATATATTTTTAATTATTTA-A
628953 ATATAT
1 ATATAT
628959 AATAAATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
17 6 0.27
18 3 0.14
19 10 0.45
20 2 0.09
21 1 0.05
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
ATATATTTTTAATTATTTAA
Found at i:632394 original size:24 final size:22
Alignment explanation
Indices: 632367--632411 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
632357 CGATCTGAGT
632367 TATTATTTAATATACAAAATTTAA
1 TATTATTT-A-ATACAAAATTTAA
*
632391 TATTCTTTAATACAAAATTTA
1 TATTATTTAATACAAAATTTA
632412 TTAATTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 12 0.60
23 1 0.05
24 7 0.35
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (22 bp):
TATTATTTAATACAAAATTTAA
Found at i:634598 original size:2 final size:2
Alignment explanation
Indices: 634593--634643 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
634583 TAAGACACAC
*
634593 AT AT AT AT TT 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 AT
634635 AT AT AT AT A
1 AT AT AT AT A
634644 AAAGTAGGGA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:637236 original size:3 final size:3
Alignment explanation
Indices: 637223--637308 Score: 65
Period size: 3 Copynumber: 28.3 Consensus size: 3
637213 GAGGGCATAT
637223 ATA AT- ATA ATA ATA AT- ATAA ATA ATA ATA TATA CATGA GA-A ATA
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA -ATA -AT-A -ATA ATA
* *
637267 ATA ATA ATA AT- ATAA ATA ATA GTA AAA ATA ATA A-A ATA ATA A
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA A
637309 AACAAAGCTC
Statistics
Matches: 68, Mismatches: 6, Indels: 18
0.74 0.07 0.20
Matches are distributed among these distances:
2 9 0.13
3 48 0.71
4 9 0.13
5 2 0.03
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:637247 original size:12 final size:12
Alignment explanation
Indices: 637223--637305 Score: 73
Period size: 12 Copynumber: 6.8 Consensus size: 12
637213 GAGGGCATAT
637223 ATAATAT-AATA
1 ATAATATAAATA
637234 ATAATATAAATA
1 ATAATATAAATA
637246 ATAATATATACATGA
1 ATAATATA-A-AT-A
637261 GA-AATA-ATAATA
1 -ATAATATA-AATA
637273 ATAATATAAATA
1 ATAATATAAATA
* *
637285 ATAGTAAAAATA
1 ATAATATAAATA
*
637297 ATAAAATAA
1 ATAATATAA
637306 TAAAACAAAG
Statistics
Matches: 60, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
11 8 0.13
12 37 0.62
13 4 0.07
14 5 0.08
15 5 0.08
16 1 0.02
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (12 bp):
ATAATATAAATA
Found at i:637267 original size:21 final size:18
Alignment explanation
Indices: 637228--637308 Score: 76
Period size: 18 Copynumber: 4.4 Consensus size: 18
637218 CATATATAAT
*
637228 ATAATAATAATATAAATA
1 ATAATAATAATAGAAATA
637246 ATAATATATACATGAGAAATA
1 ATAATA-ATA-AT-AGAAATA
*
637267 ATAATAATAATATAAATA
1 ATAATAATAATAGAAATA
* *
637285 ATAGTAAAAATA-ATAA-A
1 ATAATAATAATAGA-AATA
637302 ATAATAA
1 ATAATAA
637309 AACAAAGCTC
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
17 8 0.15
18 24 0.44
19 5 0.09
20 5 0.09
21 12 0.22
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (18 bp):
ATAATAATAATAGAAATA
Found at i:637296 original size:27 final size:27
Alignment explanation
Indices: 637223--637309 Score: 78
Period size: 27 Copynumber: 3.4 Consensus size: 27
637213 GAGGGCATAT
* *
637223 ATAATAT-AATAATAATATAAATAATA
1 ATAATATAAATAATAGTAAAAATAATA
* *
637249 AT-ATATACAT--GAG-AAATAATAATA
1 ATAATATAAATAATAGTAAA-AATAATA
637273 ATAATATAAATAATAGTAAAAATAATA
1 ATAATATAAATAATAGTAAAAATAATA
637300 A-AATAATAAA
1 ATAAT-ATAAA
637310 ACAAAGCTCT
Statistics
Matches: 48, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
23 2 0.04
24 10 0.21
25 11 0.23
26 7 0.15
27 15 0.31
28 3 0.06
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (27 bp):
ATAATATAAATAATAGTAAAAATAATA
Found at i:637721 original size:23 final size:22
Alignment explanation
Indices: 637608--637715 Score: 89
Period size: 21 Copynumber: 4.7 Consensus size: 22
637598 AACTAGCCTT
*
637608 TCCAAGAAACAAAAACAACCTTCTT
1 TCCAA-AAACAAAAACAACC-TC-C
*
637633 TCCAAAAAAACAAAAA-AA-CACC
1 TCC--AAAAACAAAAACAACCTCC
637655 TCCAAAAAACAAAAA-AACCTCC
1 TCC-AAAAACAAAAACAACCTCC
637677 TCC-AAAACAAAGAACAATCCTCC
1 TCCAAAAACAAA-AACAA-CCTCC
637700 TCCAAAAACCAAAAAC
1 TCCAAAAA-CAAAAAC
637716 CCCCTCTTAA
Statistics
Matches: 72, Mismatches: 3, Indels: 17
0.78 0.03 0.18
Matches are distributed among these distances:
20 8 0.11
21 16 0.22
22 11 0.15
23 9 0.12
24 8 0.11
25 9 0.12
26 9 0.12
27 2 0.03
ACGTcount: A:0.56, C:0.31, G:0.02, T:0.11
Consensus pattern (22 bp):
TCCAAAAACAAAAACAACCTCC
Found at i:638265 original size:44 final size:44
Alignment explanation
Indices: 638217--639029 Score: 690
Period size: 44 Copynumber: 18.5 Consensus size: 44
638207 ATCTTCGATC
*
638217 TGTTCCCTATAAGCACAGGGATGCCAAATCTGATGTTTTCAACT
1 TGTTCCCTATAAGCACAGGGATGCCAAATCTGATATTTTCAACT
*
638261 TGTTCCCTATAAGCACAGGGATGCCAAATCTGATGTTTTCAACT
1 TGTTCCCTATAAGCACAGGGATGCCAAATCTGATATTTTCAACT
* * *
638305 TGTTCCCTATAAGCACAGGGATGCC--ATGCTGAAATCTTTGATC-
1 TGTTCCCTATAAGCACAGGGATGCCAAAT-CTGATAT-TTTCAACT
* * * * * * *
638348 TGCTTCACTATAAGCACAGGAATGTCAGATCTGTTATCTTT-GATT
1 TG-TTCCCTATAAGCACAGGGATGCCAAATCTGATAT-TTTCAACT
* *
638393 TGTTCCATATAAGCACAGGGATGCCAAATCTGATGTTTTCAACT
1 TGTTCCCTATAAGCACAGGGATGCCAAATCTGATATTTTCAACT
* *
638437 TGTTCCCTATAAGCACAGGGATGTCAAATCTGATGTTTTCAACT
1 TGTTCCCTATAAGCACAGGGATGCCAAATCTGATATTTTCAACT
* * *
638481 TGTTCCCTATAAGCACAGGGATGCC--ATGCTGAAATCTTTGATC-
1 TGTTCCCTATAAGCACAGGGATGCCAAAT-CTGATAT-TTTCAACT
* * * * * * * * *
638524 TGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCGATT
1 TG-TTCCCTATAAGCACAGGGATGCCAAATCTGATATTTTCAACT
* *
638569 TGTTCCCTATAAGCACAGGGATGCCAAATCTGCTGTTTTCAACT
1 TGTTCCCTATAAGCACAGGGATGCCAAATCTGATATTTTCAACT
* * *
638613 TGTTCCCTATAAGCACAGGGATGCC--ATGCTGAAATCTTCGA-T
1 TGTTCCCTATAAGCACAGGGATGCCAAAT-CTGATATTTTCAACT
* * * * * * * * *
638655 CTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCGATT
1 -TG-TTCCCTATAAGCACAGGGATGCCAAATCTGATATTTTCAACT
* *
638701 TGTTCCCTATAAGCACAGGGATGCCAAATCTGCTGTTTTCAACT
1 TGTTCCCTATAAGCACAGGGATGCCAAATCTGATATTTTCAACT
* * *
638745 TGTTCCCTATAAGCACAGGGATGCC--ATGCTGAAATCTTCGA-T
1 TGTTCCCTATAAGCACAGGGATGCCAAAT-CTGATATTTTCAACT
* * * * * * * * * *
638787 CTGCTTCACTGTAA--ATAGGAATGTCAGATCTGCTATCTTCGATT
1 -TG-TTCCCTATAAGCACAGGGATGCCAAATCTGATATTTTCAACT
* *
638831 TGTTCCCTATAAGCACAGGGATGCCAAATCTGCTGTTTTCAACT
1 TGTTCCCTATAAGCACAGGGATGCCAAATCTGATATTTTCAACT
* * *
638875 TGTTCCCTATAAGCACAGGGATGCC--ATGCTGAAATCTTTGATC-
1 TGTTCCCTATAAGCACAGGGATGCCAAAT-CTGATAT-TTTCAACT
* * * * * * * * *
638918 TGCTTCACTGTAAGCACAGGAATGTCACATCTGCTATCTTCGATT
1 TG-TTCCCTATAAGCACAGGGATGCCAAATCTGATATTTTCAACT
* * *
638963 TGTTCCCTATAAGCACAAGGATGCCAAATCTGCTGTTTTCAACT
1 TGTTCCCTATAAGCACAGGGATGCCAAATCTGATATTTTCAACT
639007 TGTTCCCTATAAGCACAGGGATG
1 TGTTCCCTATAAGCACAGGGATG
639030 TCATGCTGAA
Statistics
Matches: 619, Mismatches: 117, Indels: 66
0.77 0.15 0.08
Matches are distributed among these distances:
42 28 0.05
43 56 0.09
44 488 0.79
45 38 0.06
46 9 0.01
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (44 bp):
TGTTCCCTATAAGCACAGGGATGCCAAATCTGATATTTTCAACT
Found at i:638456 original size:176 final size:176
Alignment explanation
Indices: 638162--639089 Score: 979
Period size: 176 Copynumber: 5.3 Consensus size: 176
638152 GATATCCGCT
* * * *
638162 ATCTTTGATCTGCTTCACTGTAAGCACAGGAATGTCAGATTTGCTATCTTCGATCTGTTCCCTAT
1 ATCTTTGATCTGCTTCACTATAAGCACAGGAATGTCAGATCTGCTATCTTTGATTTGTTCCCTAT
638227 AAGCACAGGGATGCCAAATCTGATGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCAAATCT
66 AAGCACAGGGATGCCAAATCTGATGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCAAATCT
638292 GATGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGAA
131 GATGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGAA
* *
638338 ATCTTTGATCTGCTTCACTATAAGCACAGGAATGTCAGATCTGTTATCTTTGATTTGTTCCATAT
1 ATCTTTGATCTGCTTCACTATAAGCACAGGAATGTCAGATCTGCTATCTTTGATTTGTTCCCTAT
*
638403 AAGCACAGGGATGCCAAATCTGATGTTTTCAACTTGTTCCCTATAAGCACAGGGATGTCAAATCT
66 AAGCACAGGGATGCCAAATCTGATGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCAAATCT
638468 GATGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGAA
131 GATGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGAA
* *
638514 ATCTTTGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCGATTTGTTCCCTAT
1 ATCTTTGATCTGCTTCACTATAAGCACAGGAATGTCAGATCTGCTATCTTTGATTTGTTCCCTAT
*
638579 AAGCACAGGGATGCCAAATCTGCTGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCC--ATGC
66 AAGCACAGGGATGCCAAATCTGATGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCAAAT-C
** * * * * * * **
638642 TGAAATCTTCGA-TCTGCTTCACTGTAAGCACAGGAATGTCA-GATCTGCT
130 TGATGTTTTCAACT-TG-TTCCCTATAAGCACAGGGATGCCATG--CTGAA
* * * * * * * * *
638691 ATCTTCGATTTG-TTCCCTATAAGCACAGGGATGCCAAATCTGCTGT-TTTCAACTTGTTCCCTA
1 ATCTTTGATCTGCTTCACTATAAGCACAGGAATGTCAGATCTGCTATCTTT-GATTTGTTCCCTA
** * * * * * * * *
638754 TAAGCACAGGGATGCC--ATGCTGAAATCTTCGA-TCTGCTTCACTGTAA--ATAGGAATGTCAG
65 TAAGCACAGGGATGCCAAAT-CTGATGTTTTCAACT-TG-TTCCCTATAAGCACAGGGATGCCAA
* * * * * **
638814 ATCTGCTATCTTCGATTTGTTCCCTATAAGCACAGGGATGCCAAAT-CTGCT
127 ATCTGATGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCC--ATGCTGAA
* * * * * * ** * *
638865 GT-TTTCAACTTG-TTCCCTATAAGCACAGGGATG-C-CATGCTGAAATCTTTGATCTGCTTCAC
1 ATCTTTGATC-TGCTTCACTATAAGCACAGGAATGTCAGAT-CTGCTATCTTTGATTTG-TTCCC
* * * * * * * * * *
638926 TGTAAGCACAGGAATGTCACATCTGCTATCTTCGATTTGTTCCCTATAAGCACAAGGATGCCAAA
63 TATAAGCACAGGGATGCCAAATCTGATGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCAAA
* *
638991 TCTGCTGTTTTCAACTTGTTCCCTATAAGCACAGGGATGTCATGCTGAA
128 TCTGATGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGAA
* * *
639040 ATCTTCGATCTGCTTCATTGTAAGCACAGGAATGTCAGATCTGCTATCTT
1 ATCTTTGATCTGCTTCACTATAAGCACAGGAATGTCAGATCTGCTATCTT
639090 CGGTCTGCTC
Statistics
Matches: 630, Mismatches: 93, Indels: 57
0.81 0.12 0.07
Matches are distributed among these distances:
172 2 0.00
173 11 0.02
174 94 0.15
175 56 0.09
176 443 0.70
177 22 0.03
178 2 0.00
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (176 bp):
ATCTTTGATCTGCTTCACTATAAGCACAGGAATGTCAGATCTGCTATCTTTGATTTGTTCCCTAT
AAGCACAGGGATGCCAAATCTGATGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCAAATCT
GATGTTTTCAACTTGTTCCCTATAAGCACAGGGATGCCATGCTGAA
Found at i:638491 original size:132 final size:132
Alignment explanation
Indices: 638436--639091 Score: 1208
Period size: 132 Copynumber: 5.0 Consensus size: 132
638426 TGTTTTCAAC
* *
638436 TTGTTCCCTATAAGCACAGGGATGTCAAATCTGATGTTTTCAACTTGTTCCCTATAAGCACAGGG
1 TTGTTCCCTATAAGCACAGGGATGCCAAATCTGCTGTTTTCAACTTGTTCCCTATAAGCACAGGG
638501 ATGCCATGCTGAAATCTTTGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCG
66 ATGCCATGCTGAAATCTTTGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCG
638566 AT
131 AT
638568 TTGTTCCCTATAAGCACAGGGATGCCAAATCTGCTGTTTTCAACTTGTTCCCTATAAGCACAGGG
1 TTGTTCCCTATAAGCACAGGGATGCCAAATCTGCTGTTTTCAACTTGTTCCCTATAAGCACAGGG
*
638633 ATGCCATGCTGAAATCTTCGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCG
66 ATGCCATGCTGAAATCTTTGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCG
638698 AT
131 AT
638700 TTGTTCCCTATAAGCACAGGGATGCCAAATCTGCTGTTTTCAACTTGTTCCCTATAAGCACAGGG
1 TTGTTCCCTATAAGCACAGGGATGCCAAATCTGCTGTTTTCAACTTGTTCCCTATAAGCACAGGG
* *
638765 ATGCCATGCTGAAATCTTCGATCTGCTTCACTGTAA--ATAGGAATGTCAGATCTGCTATCTTCG
66 ATGCCATGCTGAAATCTTTGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCG
638828 AT
131 AT
638830 TTGTTCCCTATAAGCACAGGGATGCCAAATCTGCTGTTTTCAACTTGTTCCCTATAAGCACAGGG
1 TTGTTCCCTATAAGCACAGGGATGCCAAATCTGCTGTTTTCAACTTGTTCCCTATAAGCACAGGG
*
638895 ATGCCATGCTGAAATCTTTGATCTGCTTCACTGTAAGCACAGGAATGTCACATCTGCTATCTTCG
66 ATGCCATGCTGAAATCTTTGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCG
638960 AT
131 AT
*
638962 TTGTTCCCTATAAGCACAAGGATGCCAAATCTGCTGTTTTCAACTTGTTCCCTATAAGCACAGGG
1 TTGTTCCCTATAAGCACAGGGATGCCAAATCTGCTGTTTTCAACTTGTTCCCTATAAGCACAGGG
* * *
639027 ATGTCATGCTGAAATCTTCGATCTGCTTCATTGTAAGCACAGGAATGTCAGATCTGCTATCTTCG
66 ATGCCATGCTGAAATCTTTGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCG
639092 GTCTGCTCCT
Statistics
Matches: 510, Mismatches: 12, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
130 128 0.25
132 382 0.75
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.32
Consensus pattern (132 bp):
TTGTTCCCTATAAGCACAGGGATGCCAAATCTGCTGTTTTCAACTTGTTCCCTATAAGCACAGGG
ATGCCATGCTGAAATCTTTGATCTGCTTCACTGTAAGCACAGGAATGTCAGATCTGCTATCTTCG
AT
Found at i:639064 original size:44 final size:43
Alignment explanation
Indices: 638159--639096 Score: 531
Period size: 44 Copynumber: 21.3 Consensus size: 43
638149 GGCGATATCC
* * * * * *
638159 GCTATCTTTGATCTGCTTCACTGTAAGCACAGGAATGTCA-GATTT
1 GCTATCTTCGATCTG-TTCCCTATAAGCACAGGGATGCCATG--CT
638204 GCTATCTTCGATCTGTTCCCTATAAGCACAGGGATGCCAAAT-CT
1 GCTATCTTCGATCTGTTCCCTATAAGCACAGGGATGCC--ATGCT
* * * *
638248 GATGTTTTC-AACTTGTTCCCTATAAGCACAGGGATGCCAAAT-CT
1 GCTATCTTCGATC-TGTTCCCTATAAGCACAGGGATGCC--ATGCT
* * * *
638292 GATGTTTTC-AACTTGTTCCCTATAAGCACAGGGATGCCATGCT
1 GCTATCTTCGATC-TGTTCCCTATAAGCACAGGGATGCCATGCT
** * * * *
638335 GAAATCTTTGATCTGCTTCACTATAAGCACAGGAATGTCA-GATCT
1 GCTATCTTCGATCTG-TTCCCTATAAGCACAGGGATGCCATG--CT
* * * *
638380 GTTATCTTTGATTTGTTCCATATAAGCACAGGGATGCCAAAT-CT
1 GCTATCTTCGATCTGTTCCCTATAAGCACAGGGATGCC--ATGCT
* * * * *
638424 GATGTTTTC-AACTTGTTCCCTATAAGCACAGGGATGTCAAAT-CT
1 GCTATCTTCGATC-TGTTCCCTATAAGCACAGGGATG-C-CATGCT
* * * *
638468 GATGTTTTC-AACTTGTTCCCTATAAGCACAGGGATGCCATGCT
1 GCTATCTTCGATC-TGTTCCCTATAAGCACAGGGATGCCATGCT
** * * * * *
638511 GAAATCTTTGATCTGCTTCACTGTAAGCACAGGAATGTCA-GATCT
1 GCTATCTTCGATCTG-TTCCCTATAAGCACAGGGATGCCATG--CT
*
638556 GCTATCTTCGATTTGTTCCCTATAAGCACAGGGATGCCAAAT-CT
1 GCTATCTTCGATCTGTTCCCTATAAGCACAGGGATGCC--ATGCT
* * *
638600 GCTGTTTTC-AACTTGTTCCCTATAAGCACAGGGATGCCATGCT
1 GCTATCTTCGATC-TGTTCCCTATAAGCACAGGGATGCCATGCT
** * * * *
638643 GAAATCTTCGATCTGCTTCACTGTAAGCACAGGAATGTCA-GATCT
1 GCTATCTTCGATCTG-TTCCCTATAAGCACAGGGATGCCATG--CT
*
638688 GCTATCTTCGATTTGTTCCCTATAAGCACAGGGATGCCAAAT-CT
1 GCTATCTTCGATCTGTTCCCTATAAGCACAGGGATGCC--ATGCT
* * *
638732 GCTGTTTTC-AACTTGTTCCCTATAAGCACAGGGATGCCATGCT
1 GCTATCTTCGATC-TGTTCCCTATAAGCACAGGGATGCCATGCT
** * * * * *
638775 GAAATCTTCGATCTGCTTCACTGTAA--ATAGGAATGTCA-GATCT
1 GCTATCTTCGATCTG-TTCCCTATAAGCACAGGGATGCCATG--CT
*
638818 GCTATCTTCGATTTGTTCCCTATAAGCACAGGGATGCCAAAT-CT
1 GCTATCTTCGATCTGTTCCCTATAAGCACAGGGATGCC--ATGCT
* * *
638862 GCTGTTTTC-AACTTGTTCCCTATAAGCACAGGGATGCCATGCT
1 GCTATCTTCGATC-TGTTCCCTATAAGCACAGGGATGCCATGCT
** * * * *
638905 GAAATCTTTGATCTGCTTCACTGTAAGCACAGGAATGTCACAT-CT
1 GCTATCTTCGATCTG-TTCCCTATAAGCACAGGGATG-C-CATGCT
* *
638950 GCTATCTTCGATTTGTTCCCTATAAGCACAAGGATGCCAAAT-CT
1 GCTATCTTCGATCTGTTCCCTATAAGCACAGGGATGCC--ATGCT
* * * *
638994 GCTGTTTTC-AACTTGTTCCCTATAAGCACAGGGATGTCATGCT
1 GCTATCTTCGATC-TGTTCCCTATAAGCACAGGGATGCCATGCT
** ** * * *
639037 GAAATCTTCGATCTGCTTCATTGTAAGCACAGGAATGTCA-GATCT
1 GCTATCTTCGATCTG-TTCCCTATAAGCACAGGGATGCCATG--CT
*
639082 GCTATCTTCGGTCTG
1 GCTATCTTCGATCTG
639097 CTCCTCTGTA
Statistics
Matches: 704, Mismatches: 132, Indels: 114
0.74 0.14 0.12
Matches are distributed among these distances:
41 1 0.00
42 30 0.04
43 80 0.11
44 501 0.71
45 84 0.12
46 8 0.01
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.32
Consensus pattern (43 bp):
GCTATCTTCGATCTGTTCCCTATAAGCACAGGGATGCCATGCT
Found at i:639253 original size:68 final size:66
Alignment explanation
Indices: 639144--639342 Score: 292
Period size: 68 Copynumber: 3.0 Consensus size: 66
639134 TCTTCTTCCG
* * * *
639144 CTGAAACTTCAAGGAGATCTGTTGTGGCTTTTAGCCTCTCCAATGCCATTTCTGGAAGAAGAGGT
1 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAATGCCATTTCAGGAAGAA-AAG-
*
639209 TTC
64 ATC
*
639212 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGAAGAAAAGAT
1 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAATGCCATTTCAGGAAGAAAAGAT
639277 C
66 C
*
639278 CTTTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAATGCCATTTCAGGGA-AAAAG
1 C--TGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAATGCCATTTCAGGAAGAAAAG
639342 A
64 A
639343 AATTTGAAAT
Statistics
Matches: 121, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
66 3 0.02
67 8 0.07
68 110 0.91
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (66 bp):
CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAATGCCATTTCAGGAAGAAAAGAT
C
Found at i:639511 original size:45 final size:44
Alignment explanation
Indices: 639414--639780 Score: 249
Period size: 43 Copynumber: 8.4 Consensus size: 44
639404 CTATTTCCCA
*
639414 ACTGCTTCA-GGGGTTAAGATCTGTAAA--TTCAACCTGTTACCCT
1 ACTGCTT-AGGGGGTTAAGATCTGTAAATCTTC-GCCTGTTACCCT
* *
639457 ACTGGTTAGGGGGTTAAGATTTGTAAATCTTCAGCCTGTTACCCT
1 ACTGCTTAGGGGGTTAAGATCTGTAAATCTTC-GCCTGTTACCCT
* * * * *
639502 ACTGCTTAGGGGTTTAAGGTTTGTAAA--TTCGGCTTGTTACCCA
1 ACTGCTTAGGGGGTTAAGATCTGTAAATCTTC-GCCTGTTACCCT
* ** * * *
639545 ACTGCTTAGGGGGTTAA-AGC-CCATCATCTTCGATCTGTTTCCCT
1 ACTGCTTAGGGGGTTAAGATCTGTA-AATCTTCG-CCTGTTACCCT
* * *
639589 ACTGCTTAGGGGGTTAAGATCT-T-CATCTTCGATCTGTTTCCCT
1 ACTGCTTAGGGGGTTAAGATCTGTAAATCTTCG-CCTGTTACCCT
* * * * *
639632 ACTGCTTAGGGAGATAAGATCTG-CAA--TTCGGTCTGTTACCTT
1 ACTGCTTAGGGGGTTAAGATCTGTAAATCTTC-GCCTGTTACCCT
* * * * ** * *
639674 ACCGATTAGGGGTTTAAGACCCT-T-CGTCTTCGATCTGTTTCCCT
1 ACTGCTTAGGGGGTTAAGA-TCTGTAAATCTTCG-CCTGTTACCCT
639718 ACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCT
1 ACTGCTTAGGGGGTTAAGATCTGTAAATCTTC-GCCTGTTACCCT
* *
639763 ATTGCTTAGGGGCTTAAG
1 ACTGCTTAGGGGGTTAAG
639781 GCTTGTGAAT
Statistics
Matches: 257, Mismatches: 47, Indels: 38
0.75 0.14 0.11
Matches are distributed among these distances:
41 1 0.00
42 28 0.11
43 99 0.39
44 57 0.22
45 71 0.28
46 1 0.00
ACGTcount: A:0.21, C:0.22, G:0.23, T:0.35
Consensus pattern (44 bp):
ACTGCTTAGGGGGTTAAGATCTGTAAATCTTCGCCTGTTACCCT
Found at i:639594 original size:44 final size:43
Alignment explanation
Indices: 639360--639780 Score: 235
Period size: 43 Copynumber: 9.7 Consensus size: 43
639350 AATTTCCAGC
* * * * *
639360 CTGTTACCCTACTACTTAGGGGTTTAAGGCCCATCATCTTCGAT
1 CTGTTTCCCTACTGCTTAGGGGGTTAA-GACCTTCATCTTCGAT
* * * ** * *
639404 CTATTTCCCAACTGCTTCA-GGGGTTAAGATCTGT-AAATTCAAC
1 CTGTTTCCCTACTGCTT-AGGGGGTTAAGACCT-TCATCTTCGAT
* * ** * *
639447 CTGTTACCCTACTGGTTAGGGGGTTAAGATTTGTAAATCTTC-AGC
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGACCT-T-CATCTTCGA-T
* * ** * ** *
639492 CTGTTACCCTACTGCTTAGGGGTTTAAG-GTTTGTAAATTCG-G
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGACCTT-CATCTTCGAT
* * * *
639534 CTTGTTACCCAACTGCTTAGGGGGTTAAAGCCCATCATCTTCGAT
1 C-TGTTTCCCTACTGCTTAGGGGGTT-AAGACCTTCATCTTCGAT
*
639579 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTTCATCTTCGAT
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGACCTTCATCTTCGAT
* * * * * *
639622 CTGTTTCCCTACTGCTTAGGGAGATAAGATCTGCA-ATTCGGT
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGACCTTCATCTTCGAT
* * * * * *
639664 CTGTTACCTTACCGATTAGGGGTTTAAGACCCTTCGTCTTCGAT
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGA-CCTTCATCTTCGAT
* * *
639708 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTC-AGC
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGACCT-T-CATCTTCGA-T
* * *
639753 CTGTTACCCTATTGCTTAGGGGCTTAAG
1 CTGTTTCCCTACTGCTTAGGGGGTTAAG
639781 GCTTGTGAAT
Statistics
Matches: 291, Mismatches: 70, Indels: 31
0.74 0.18 0.08
Matches are distributed among these distances:
42 29 0.10
43 113 0.39
44 85 0.29
45 64 0.22
ACGTcount: A:0.21, C:0.23, G:0.22, T:0.35
Consensus pattern (43 bp):
CTGTTTCCCTACTGCTTAGGGGGTTAAGACCTTCATCTTCGAT
Found at i:639706 original size:129 final size:132
Alignment explanation
Indices: 639447--639774 Score: 409
Period size: 129 Copynumber: 2.5 Consensus size: 132
639437 TAAATTCAAC
* * *
639447 CTGTTACCCTACTGGTTAGGGGGTTAAGATTTGTAAATCTTCAGCCTGTTACCCTACTGCTTAGG
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTGCTTAGG
* * * * *
639512 GGTTTAAGGTTTGTAAATTCGGCTTGTTACCCAACTGCTTAGGGGGTTAAAGCCCATCATCTTCG
66 GGTATAAGATCTGTAAATTCGGCTTGTTACCCAACCGATTAGGGGGTTAAAGCCCATCATCTTCG
639577 AT
131 AT
* * *
639579 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCT-T-CATCTTC-GATCTGTTTCCCTACTGCTTAG
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAG-CCTGTTACCCTACTGCTTAG
* ** * * *
639641 GGAG-ATAAGATCTG-CAATTCGG-TCTGTTACCTTACCGATTA-GGGGTTTAAGACCCTTCGTC
65 GG-GTATAAGATCTGTAAATTCGGCT-TGTTACCCAACCGATTAGGGGGTTAAAG-CCCATCATC
639702 TTCGAT
127 TTCGAT
*
639708 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTATTGCTTAGG
1 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTGCTTAGG
639773 GG
66 GG
639775 CTTAAGGCTT
Statistics
Matches: 168, Mismatches: 21, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
128 10 0.06
129 66 0.39
130 35 0.21
131 27 0.16
132 30 0.18
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.36
Consensus pattern (132 bp):
CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTGCTTAGG
GGTATAAGATCTGTAAATTCGGCTTGTTACCCAACCGATTAGGGGGTTAAAGCCCATCATCTTCG
AT
Found at i:639950 original size:66 final size:66
Alignment explanation
Indices: 639844--639970 Score: 227
Period size: 66 Copynumber: 1.9 Consensus size: 66
639834 TCAATGCTTA
* *
639844 TGTCAAATGATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTCACTAGATGTGTTATGAAT
1 TGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTGTTATGAAT
639909 G
66 G
*
639910 TGTCAAATAATTAGGATGCTATGATTGAAATGAATCAAATGCTCCTAACTAGATGTGTTAT
1 TGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTGTTAT
639971 TATATGAATG
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 58 1.00
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.33
Consensus pattern (66 bp):
TGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTGTTATGAAT
G
Found at i:641126 original size:20 final size:20
Alignment explanation
Indices: 641101--641148 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
641091 TTTTCCGCTT
*
641101 TTTTTTTTAGAATTTTTTTG
1 TTTTTTTTAGAATTTTTGTG
* **
641121 TTTTTTTTTGTGTTTTTGTG
1 TTTTTTTTAGAATTTTTGTG
641141 TTTTTTTT
1 TTTTTTTT
641149 TTTTTGCCTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.06, C:0.00, G:0.12, T:0.81
Consensus pattern (20 bp):
TTTTTTTTAGAATTTTTGTG
Found at i:643973 original size:19 final size:20
Alignment explanation
Indices: 643949--643995 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
643939 AGTGAAAGTT
643949 TAATGCAAATGT-TGCAATG
1 TAATGCAAATGTATGCAATG
*
643968 TAATGCAAATGTATGGAATG
1 TAATGCAAATGTATGCAATG
643988 -AATGCAAA
1 TAATGCAAA
643996 AGAAAGGAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 20 0.77
20 6 0.23
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.28
Consensus pattern (20 bp):
TAATGCAAATGTATGCAATG
Found at i:646821 original size:3 final size:3
Alignment explanation
Indices: 646808--646893 Score: 65
Period size: 3 Copynumber: 28.3 Consensus size: 3
646798 GAGGGCATAT
646808 ATA AT- ATA ATA ATA AT- ATAA ATA ATA ATA TATA CATGA GA-A ATA
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA -ATA -AT-A -ATA ATA
* *
646852 ATA ATA ATA AT- ATAA ATA ATA GTA AAA ATA ATA A-A ATA ATA A
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA A
646894 AACAAAGCTC
Statistics
Matches: 68, Mismatches: 6, Indels: 18
0.74 0.07 0.20
Matches are distributed among these distances:
2 9 0.13
3 48 0.71
4 9 0.13
5 2 0.03
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:646832 original size:12 final size:12
Alignment explanation
Indices: 646808--646890 Score: 73
Period size: 12 Copynumber: 6.8 Consensus size: 12
646798 GAGGGCATAT
646808 ATAATAT-AATA
1 ATAATATAAATA
646819 ATAATATAAATA
1 ATAATATAAATA
646831 ATAATATATACATGA
1 ATAATATA-A-AT-A
646846 GA-AATA-ATAATA
1 -ATAATATA-AATA
646858 ATAATATAAATA
1 ATAATATAAATA
* *
646870 ATAGTAAAAATA
1 ATAATATAAATA
*
646882 ATAAAATAA
1 ATAATATAA
646891 TAAAACAAAG
Statistics
Matches: 60, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
11 8 0.13
12 37 0.62
13 4 0.07
14 5 0.08
15 5 0.08
16 1 0.02
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (12 bp):
ATAATATAAATA
Found at i:646852 original size:21 final size:18
Alignment explanation
Indices: 646813--646893 Score: 76
Period size: 18 Copynumber: 4.4 Consensus size: 18
646803 CATATATAAT
*
646813 ATAATAATAATATAAATA
1 ATAATAATAATAGAAATA
646831 ATAATATATACATGAGAAATA
1 ATAATA-ATA-AT-AGAAATA
*
646852 ATAATAATAATATAAATA
1 ATAATAATAATAGAAATA
* *
646870 ATAGTAAAAATA-ATAA-A
1 ATAATAATAATAGA-AATA
646887 ATAATAA
1 ATAATAA
646894 AACAAAGCTC
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
17 8 0.15
18 24 0.44
19 5 0.09
20 5 0.09
21 12 0.22
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (18 bp):
ATAATAATAATAGAAATA
Found at i:646881 original size:27 final size:27
Alignment explanation
Indices: 646808--646894 Score: 78
Period size: 27 Copynumber: 3.4 Consensus size: 27
646798 GAGGGCATAT
* *
646808 ATAATAT-AATAATAATATAAATAATA
1 ATAATATAAATAATAGTAAAAATAATA
* *
646834 AT-ATATACAT--GAG-AAATAATAATA
1 ATAATATAAATAATAGTAAA-AATAATA
646858 ATAATATAAATAATAGTAAAAATAATA
1 ATAATATAAATAATAGTAAAAATAATA
646885 A-AATAATAAA
1 ATAAT-ATAAA
646895 ACAAAGCTCT
Statistics
Matches: 48, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
23 2 0.04
24 10 0.21
25 11 0.23
26 7 0.15
27 15 0.31
28 3 0.06
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (27 bp):
ATAATATAAATAATAGTAAAAATAATA
Found at i:647308 original size:23 final size:22
Alignment explanation
Indices: 647225--647302 Score: 83
Period size: 21 Copynumber: 3.5 Consensus size: 22
647215 TTCTTTCCAA
*
647225 AAAAACAAAAA-AA-CACCTCC
1 AAAAACAAAAACAACCTCCTCC
647245 AAAAAACAAAAA-AACCTCCTCC
1 -AAAAACAAAAACAACCTCCTCC
647267 -AAAACAAAGAACAATCCTCCTCC
1 AAAAACAAA-AACAA-CCTCCTCC
647290 AAAAACCAAAAAC
1 AAAAA-CAAAAAC
647303 CCCCTCTTAA
Statistics
Matches: 50, Mismatches: 1, Indels: 9
0.83 0.02 0.15
Matches are distributed among these distances:
20 8 0.16
21 15 0.30
22 8 0.16
23 8 0.16
24 7 0.14
25 4 0.08
ACGTcount: A:0.60, C:0.31, G:0.01, T:0.08
Consensus pattern (22 bp):
AAAAACAAAAACAACCTCCTCC
Found at i:650178 original size:3 final size:3
Alignment explanation
Indices: 650163--650207 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
650153 TAGTTACTAA
*
650163 CAT CAT CAA CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
650208 AGGCCATGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:659380 original size:116 final size:116
Alignment explanation
Indices: 659182--659407 Score: 319
Period size: 116 Copynumber: 1.9 Consensus size: 116
659172 AAGTTTTAGG
* * * ** *
659182 TACCTAATTGGATCAAAATAAACTTTGGGTACTAAATTAAACCTTAAAGTCAAGTTCAAGTGCCT
1 TACCTAATTGAACCAAAATAAACTTTGGGTACCAAATTAAACCTTAAAACCAAGTTCAAGTACCT
* *
659247 AATTGGAAAAAACTCTTAGGTACTGATTTGAACCTTGAAGCTAAGCTTAAT
66 AATTGGAAAAAACTCTTAGGTACCGATTTGAACCTTGAACCTAAGCTTAAT
* * * *
659298 TACCTAATTGAACCAAAATAAACTTTTGTTACCAAATTGACCCTTAAAACCAAGTTCAAGTACCT
1 TACCTAATTGAACCAAAATAAACTTTGGGTACCAAATTAAACCTTAAAACCAAGTTCAAGTACCT
*
659363 AATTGAGAAAAAA-TCTTAGGTGCCGATTTGAACCTTGAACCTAAG
66 AATTG-GAAAAAACTCTTAGGTACCGATTTGAACCTTGAACCTAAG
659408 TTCATGTACC
Statistics
Matches: 96, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
116 89 0.93
117 7 0.07
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (116 bp):
TACCTAATTGAACCAAAATAAACTTTGGGTACCAAATTAAACCTTAAAACCAAGTTCAAGTACCT
AATTGGAAAAAACTCTTAGGTACCGATTTGAACCTTGAACCTAAGCTTAAT
Found at i:661556 original size:10 final size:10
Alignment explanation
Indices: 661541--661565 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
661531 TTTTTTCAAG
661541 TTTATAATAT
1 TTTATAATAT
661551 TTTATAATAT
1 TTTATAATAT
661561 TTTAT
1 TTTAT
661566 TTTTATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
TTTATAATAT
Found at i:668567 original size:74 final size:74
Alignment explanation
Indices: 668477--668625 Score: 253
Period size: 74 Copynumber: 2.0 Consensus size: 74
668467 GAAGAACAGT
* *
668477 ATAGTTTGCGACCAATTTTGTTGTGAGCTTTCCCCATCTTTTGGGTTAATTATATCACACATCCC
1 ATAGTTTGCGACCAATTTTGTTGTGAGCTTCCCCCATCTTTTGGGTTAATTATAGCACACATCCC
668542 TAGAATATG
66 TAGAATATG
* *
668551 ATAGTTTGGGACCAATTTTGTTGTGAGCTTCCCCCATCTTTTGGGTTAATTATAGCACACATTCC
1 ATAGTTTGCGACCAATTTTGTTGTGAGCTTCCCCCATCTTTTGGGTTAATTATAGCACACATCCC
*
668616 TAGATTATG
66 TAGAATATG
668625 A
1 A
668626 CTTAGATTTA
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
74 70 1.00
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.39
Consensus pattern (74 bp):
ATAGTTTGCGACCAATTTTGTTGTGAGCTTCCCCCATCTTTTGGGTTAATTATAGCACACATCCC
TAGAATATG
Found at i:671847 original size:375 final size:378
Alignment explanation
Indices: 671211--671898 Score: 942
Period size: 375 Copynumber: 1.8 Consensus size: 378
671201 AAAATCTAAC
*
671211 CATAAATCAAGTTAACTTAAATCAATGAAATTGTAGAAAATATTTGTAAACCTGCTCAATTTACA
1 CATAAATCAAGTTAACTTAAATCAATGAAATTGTAGAAAATATTTGTAAACCTGCTCAATTAACA
* * *
671276 GTGAATGAATTACTTATTTTACTAGGATTATATGACAGCTGATGCTTCATGTCATTTGATCTAAT
66 GTGAATGAAATACTAATTTTACTAGGATTATATGA-AGCTGATGCTTCAAGTCATTTGATCTAAT
* *
671341 TCATAAGCTAGTGAAGTTACTTCGGAAATTCTGATGCTTTAGGTTGATGGGGTTCTTCTAATCAC
130 TCAT-A--TAGTGAAGTTACTTCGAAAATTCGGATGCTTTAGGTTGATGGGGTTCTTCTAATCAC
* * ** * *
671406 TGCATTATGTTTTTTTTTTCATCCAAATGCTGCGTTTTTAATCGCAGCTGAGGCTATGGAATTTG
192 TGCATTATGTGTTCTTTTTCATCCAAATGCAACGTTTTTAATCGCAGATGAGGCGATGGAATTTG
* * *
671471 CATTAGTTAAAAGGGTGTTGATGTTAAATTCTAATGGACTCTT-CATTTTTGTTGAAGTATACAG
257 CATTAGTT-AAAGGGTGTTGATGCTAAATTCTAATAGACTATTGCATTTTTGTTGAAGTATACAG
671535 ATGGATATACGGATATGACTGTAAAAATTTAAAAAAATCTAATCATATCCCCAAGTAA
321 ATGGATATACGGATATGACTGTAAAAATTTAAAAAAATCTAATCATATCCCCAAGTAA
* ** **
671593 CATAAATCGAGTTAACTTTGATCAATGGTCA-TGTAGCAAAA-ATTTGTAAACCTGCTCAATTAA
1 CATAAATCAAGTTAACTTAAATCAAT-GAAATTGTAG-AAAATATTTGTAAACCTGCTCAATTAA
* * *
671656 CAGTGTATGAAATACTAATTTTACTAGGATTACTA-G-AGCTGGTGCTTCAAGTCATTTGATCTG
64 CAGTGAATGAAATACTAATTTTACTAGGATTA-TATGAAGCTGATGCTTCAAGTCATTTGATCTA
* * *
671719 GTTCAT-T-GTGCAGTTACTTTGAAAATTCGGATGCTTTAGGTTGATGGGGTTCTTCTAATCACT
128 ATTCATATAGTGAAGTTACTTCGAAAATTCGGATGCTTTAGGTTGATGGGGTTCTTCTAATCACT
* * ** *
671782 TCATTATGTGTTCTTTTTCATCCAAATGCAATGTTTTTAATCTTAGATG-GGACGATGGCATTTG
193 GCATTATGTGTTCTTTTTCATCCAAATGCAACGTTTTTAATCGCAGATGAGG-CGATGGAATTTG
* *
671846 CATTAGTTAAAGGGTTTTGATGCTAAATTCTAATAGACTATTGCTTTTTTGTT
257 CATTAGTTAAAGGGTGTTGATGCTAAATTCTAATAGACTATTGCATTTTTGTT
671899 TGAATTGCTA
Statistics
Matches: 268, Mismatches: 33, Indels: 17
0.84 0.10 0.05
Matches are distributed among these distances:
374 32 0.12
375 119 0.44
376 1 0.00
380 29 0.11
382 79 0.29
383 8 0.03
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.39
Consensus pattern (378 bp):
CATAAATCAAGTTAACTTAAATCAATGAAATTGTAGAAAATATTTGTAAACCTGCTCAATTAACA
GTGAATGAAATACTAATTTTACTAGGATTATATGAAGCTGATGCTTCAAGTCATTTGATCTAATT
CATATAGTGAAGTTACTTCGAAAATTCGGATGCTTTAGGTTGATGGGGTTCTTCTAATCACTGCA
TTATGTGTTCTTTTTCATCCAAATGCAACGTTTTTAATCGCAGATGAGGCGATGGAATTTGCATT
AGTTAAAGGGTGTTGATGCTAAATTCTAATAGACTATTGCATTTTTGTTGAAGTATACAGATGGA
TATACGGATATGACTGTAAAAATTTAAAAAAATCTAATCATATCCCCAAGTAA
Found at i:676976 original size:24 final size:24
Alignment explanation
Indices: 676947--676998 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
676937 TTTCTAGATA
*
676947 ATTTAATATTTATTAGTATAATAT
1 ATTTAACATTTATTAGTATAATAT
*
676971 ATTTAACATTTATTAGTATAATTT
1 ATTTAACATTTATTAGTATAATAT
676995 ATTT
1 ATTT
676999 GACCTACGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (24 bp):
ATTTAACATTTATTAGTATAATAT
Found at i:679283 original size:16 final size:16
Alignment explanation
Indices: 679264--679305 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
679254 AGAGCTCTAG
679264 AGTGTTGGAGCACTGA
1 AGTGTTGGAGCACTGA
* *
679280 AGTGCTGGAGCAGTGA
1 AGTGTTGGAGCACTGA
*
679296 AGCGTTGGAG
1 AGTGTTGGAG
679306 TGAAAACACT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.24, C:0.12, G:0.43, T:0.21
Consensus pattern (16 bp):
AGTGTTGGAGCACTGA
Found at i:683849 original size:29 final size:30
Alignment explanation
Indices: 683809--683872 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 30
683799 TAAGGATCTC
* *
683809 ATCAATTTAGTCCCTCTACTATT-AAATGA
1 ATCAATTCAGTCCCTCTACTATTAAAAAGA
*
683838 ATCAATTCAGTCCCTGTACTATTAAAAAGA
1 ATCAATTCAGTCCCTCTACTATTAAAAAGA
683868 ATCAA
1 ATCAA
683873 ACAAGGCCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
29 21 0.68
30 10 0.32
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (30 bp):
ATCAATTCAGTCCCTCTACTATTAAAAAGA
Found at i:686192 original size:25 final size:26
Alignment explanation
Indices: 686164--686220 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 26
686154 TCTCATCTCT
*
686164 TATTTATTTATTT-TTTAATATTTAA
1 TATTTATATATTTGTTTAATATTTAA
* * *
686189 TATTTA-ATATTTGTTTTATGTTTTA
1 TATTTATATATTTGTTTAATATTTAA
686214 TATTTAT
1 TATTTAT
686221 GATTCCGCAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 5 0.19
25 21 0.81
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (26 bp):
TATTTATATATTTGTTTAATATTTAA
Found at i:690675 original size:32 final size:32
Alignment explanation
Indices: 690639--690707 Score: 77
Period size: 32 Copynumber: 2.2 Consensus size: 32
690629 AAATTGTTTA
690639 AAAAAGAATAAAGGTAAAATTGT-AAAAAATAT
1 AAAAAGAA-AAAGGTAAAATTGTAAAAAAATAT
** * * *
690671 AAAAATTAAAAGTTAAATTTTTAAAAAAATAT
1 AAAAAGAAAAAGGTAAAATTGTAAAAAAATAT
690703 AAAAA
1 AAAAA
690708 TGTATACTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 11 0.35
32 20 0.65
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (32 bp):
AAAAAGAAAAAGGTAAAATTGTAAAAAAATAT
Found at i:695519 original size:130 final size:124
Alignment explanation
Indices: 695341--695682 Score: 371
Period size: 125 Copynumber: 2.7 Consensus size: 124
695331 GGTGGATAAT
* * * * ** *
695341 ATTAATAAGTTAGGCAGAAAAGATTTCGGTTTGGATCTACTTTTAATAAATTTGTAGTTACAGTA
1 ATTAATAAGTTAGGCGGATAACATTTCGGTTTGGATCGA-TTTTAATAAATTTACAGTTACAATA
695406 TTTTAATTTTTGAAAAAACAAAGAACCATATAACATGAACCATAAACAACAGTGAAAACAAACAC
65 TTTTAATTTTTGAAAAAACAAAGAACC-----ACATGAACCATAAACAACAGTGAAAACAAACAC
* *
695471 ATTAATAAGTTAGGCGGATAACATTTCGGTTTGGATCGATTTTAAATAAATTTACGGTTACAATG
1 ATTAATAAGTTAGGCGGATAACATTTCGGTTTGGATCGATTTT-AATAAATTTACAGTTACAATA
* * * * *
695536 TTTTAGTTTTTGAAAAAGCAAAGAACCGCATGAATCATAAACAACAGTGAAAATAAACAC
65 TTTTAATTTTTGAAAAAACAAAGAACCACATGAACCATAAACAACAGTGAAAACAAACAC
* * * * * * * * * *
695596 ATCAATAACTTAGACGGATAACATTTTGATTTGGATCGATTTTGAACAAATTTACGGATATAGTA
1 ATTAATAAGTTAGGCGGATAACATTTCGGTTTGGATCGATTTT-AATAAATTTACAGTTACAATA
*
695661 GTTTAATTTTT-AAAAAAGCAAA
65 TTTTAATTTTTGAAAAAA-CAAA
695683 TCGATTCATA
Statistics
Matches: 182, Mismatches: 28, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
124 5 0.03
125 97 0.53
129 4 0.02
130 76 0.42
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (124 bp):
ATTAATAAGTTAGGCGGATAACATTTCGGTTTGGATCGATTTTAATAAATTTACAGTTACAATAT
TTTAATTTTTGAAAAAACAAAGAACCACATGAACCATAAACAACAGTGAAAACAAACAC
Found at i:699806 original size:30 final size:28
Alignment explanation
Indices: 699763--699835 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 28
699753 GATATCTCAG
* *
699763 TAAATTTAAAATTTAA-TTTTTATATTTT
1 TAAATTTAAAATTTAACATTTTAT-TTCT
699791 TAATATTTAAAAATTTAACATTTTATTTCT
1 TAA-ATTT-AAAATTTAACATTTTATTTCT
699821 TAAATTTTAAAATTT
1 TAAA-TTTAAAATTT
699836 TAGTTTAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
28 3 0.08
29 12 0.31
30 18 0.46
31 6 0.15
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (28 bp):
TAAATTTAAAATTTAACATTTTATTTCT
Found at i:699829 original size:37 final size:37
Alignment explanation
Indices: 699764--699835 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
699754 ATATCTCAGT
* *
699764 AAATTTAAAATTTAATTTTTATATTTTTAATATTTAA
1 AAATTTAAAATTTAATTTTTATAATTTTAAAATTTAA
* *
699801 AAATTTAACATTTTATTTCTTA-AATTTTAAAATTT
1 AAATTTAAAATTTAATTT-TTATAATTTTAAAATTT
699836 TAGTTTAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 27 0.90
38 3 0.10
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (37 bp):
AAATTTAAAATTTAATTTTTATAATTTTAAAATTTAA
Found at i:700604 original size:22 final size:23
Alignment explanation
Indices: 700579--700621 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
700569 CGCCGATTAG
*
700579 TTAAAATTTTTTTA-TATTAACA
1 TTAAAATATTTTTATTATTAACA
*
700601 TTAATATATTTTTATTATTAA
1 TTAAAATATTTTTATTATTAA
700622 AATTGATCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (23 bp):
TTAAAATATTTTTATTATTAACA
Found at i:703661 original size:2 final size:2
Alignment explanation
Indices: 703656--703682 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
703646 ATTTCATTTG
703656 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 A
703683 CATGTTTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:713091 original size:3 final size:3
Alignment explanation
Indices: 713083--713126 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
713073 TGGCTAAGTT
713083 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
713127 CCAAAATGCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:721692 original size:204 final size:196
Alignment explanation
Indices: 721261--721823 Score: 675
Period size: 198 Copynumber: 2.8 Consensus size: 196
721251 GAAGGAAATA
** *
721261 ATTAGCTTTCTTGTTCATAGATTGTAAAGCAAAAATTTGGAAAATGAGATTAGTGGTTTGCTTGG
1 ATTAGCTTTCTTGTTCATAGATTGTAAAGCAAAAA-TACGAAAACGAGATTAGTGGTTTGCTTGG
** * ** *
721326 CAGAGTAG-AAAAAA-GGGAAGAAATGGATATAGGATGGTGAAAAACCAAAAAAGAACATAAATG
65 CAGAGTAGAAAAAAACAAGAAG-AAT-GAAATAGGATGGTGAAAAACTGAAAAAGAACATGAATG
* * * * *
721389 TTTGAGTGTGTTAGGTAGGGAAGAAAATTCTCGCTCACTTAACTGCATTACAAAGATTAGCTTTG
128 TTTGAGCGTGTTTGGTA-GGAAAAAAATTCTCGCTCACTTAACTGCATTACAAAGATTAGCATCG
721454 TCTTC
192 TCTTC
* *
721459 ATTAGCTTTCTTGTTCATAGATAGTAAAGCAAAAATACGAAAACGAGTTTAGTGGTTTGCTTGGC
1 ATTAGCTTTCTTGTTCATAGATTGTAAAGCAAAAATACGAAAACGAGATTAGTGGTTTGCTTGGC
* * *
721524 AGAGTGAGAAAAAAAAACAACAGAAGAATGAACAAAAGATGGTGAAAAACTGAAAAAGAATATGA
66 AGAGT-AG--AAAAAAAC-A-AGAAGAATGAA-ATAGGATGGTGAAAAACTGAAAAAGAACATGA
* * * *
721589 ATGTTTGAGCGTGTTTGGTAGGAAAAAGAATTCTTGTTCATTTAGCTGCATTACAAAAGATTAGC
125 ATGTTTGAGCGTGTTTGGTAGGAAAAA-AATTCTCGCTCACTTAACTGCATTAC-AAAGATTAGC
721654 ATCGTCTTC
188 ATCGTCTTC
* * *
721663 ATTAGCTTTCTTGTTCATAGATTGTAAAGCAAAAATACGGAAACAAGATTAGTGGTTTGCTTAGC
1 ATTAGCTTTCTTGTTCATAGATTGTAAAGCAAAAATACGAAAACGAGATTAGTGGTTTGCTTGGC
* * * * * *
721728 AGAGT-G-AAAAATCTAGAAGAAATGGAATTAGGGTGGTGAAAAACTGAAAAAGAAGATGGATGT
66 AGAGTAGAAAAAAACAAGAAG-AAT-GAAATAGGATGGTGAAAAACTGAAAAAGAACATGAATGT
721791 TTGAGCGTGTTTGGTAGGAAAGAAAATTCTCGC
129 TTGAGCGTGTTTGGTAGGAAA-AAAATTCTCGC
721824 ACCTGTTTGT
Statistics
Matches: 314, Mismatches: 38, Indels: 26
0.83 0.10 0.07
Matches are distributed among these distances:
197 36 0.11
198 97 0.31
199 11 0.04
201 6 0.02
202 9 0.03
203 69 0.22
204 86 0.27
ACGTcount: A:0.39, C:0.10, G:0.23, T:0.28
Consensus pattern (196 bp):
ATTAGCTTTCTTGTTCATAGATTGTAAAGCAAAAATACGAAAACGAGATTAGTGGTTTGCTTGGC
AGAGTAGAAAAAAACAAGAAGAATGAAATAGGATGGTGAAAAACTGAAAAAGAACATGAATGTTT
GAGCGTGTTTGGTAGGAAAAAAATTCTCGCTCACTTAACTGCATTACAAAGATTAGCATCGTCTT
C
Found at i:734196 original size:23 final size:24
Alignment explanation
Indices: 734170--734215 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
734160 TAAATTTATC
*
734170 TCTTA-ATATTTAATTTATTTTGA
1 TCTTATATATTTAAATTATTTTGA
* *
734193 TCTTATTTTTTTAAATTATTTTG
1 TCTTATATATTTAAATTATTTTG
734216 GCTCTTAACC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.65
Consensus pattern (24 bp):
TCTTATATATTTAAATTATTTTGA
Found at i:734382 original size:22 final size:22
Alignment explanation
Indices: 734339--734384 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 22
734329 TGAACTCTTG
734339 TTTTTTTTATGAAATCTTATGTT
1 TTTTTTTTATGAAATC-TATGTT
734362 TTTTTTTTATGAAATAC-ATGTT
1 TTTTTTTTATGAAAT-CTATGTT
734384 T
1 T
734385 ATAAGCTACA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 6 0.27
23 15 0.68
24 1 0.05
ACGTcount: A:0.24, C:0.04, G:0.09, T:0.63
Consensus pattern (22 bp):
TTTTTTTTATGAAATCTATGTT
Found at i:735726 original size:306 final size:311
Alignment explanation
Indices: 735159--735785 Score: 989
Period size: 306 Copynumber: 2.0 Consensus size: 311
735149 TTTCTCGATT
* *
735159 TTTTGTTGTTAATTGGAGTCACCGTTGTGATTCAATTCGATTTGACTTGGTTTGCAGCTTTTTTT
1 TTTTGTTGTTAATTGGAGTCACCGTTGTGATTCAATTCAATTTGACTTGGTTTGCAGCTGTTTTT
* *
735224 GGTTAGTGGTTGTAAGATTTGATTTGAATTTTATAAATTAATAATACTCGTGCAATAGAGCTTAA
66 GGTTAGTAGTTGTAAGATTTGATTTGAATTTTATAAATT-ATAATACTCATGCAATAGAGCTTAA
* * *
735289 TGCGATTCAATAGTGGAAAAATTAGATGTTTCAAATTCATATTCGAGCTGGAAACTATTGATATT
130 TGCGATTCAATAGTAGAAAAATTAGATGGTTCAAATTCATATTCAAGCTGGAAACTATTGATATT
* *
735354 AGAAGAGGTATGGAAATTTGAACTGTTTTACTTGTGTTTTGACTTGGTTTTTTGATGTAGGAAGT
195 AGAAGAGGTATGGAAATTGGAACTGTTTTAATTGTGTTTTGACTTGGTTTTTTGATGTAGGAAGT
* *
735419 TGCAT-AATATACTGGAGCTATT-AAAATATGAGGAAATGGTTTTTCC-TTTG
260 TGCATAAATATACTGGAGCTATTAAAAAT-TAAGGAAATGGTTTTCCCTTTTG
* * *
735469 TTTTGTTGTTAATTGGAGTTACCTTTGTGATTTAATTCAATTTGACTTGGTTTGCAGCTGTTTTT
1 TTTTGTTGTTAATTGGAGTCACCGTTGTGATTCAATTCAATTTGACTTGGTTTGCAGCTGTTTTT
*
735534 GGTTAGTAGTTGTAAGATTTGATTTGAATTTTATAAA-T-TAATACTCATGGAATAGAGCTTAAT
66 GGTTAGTAGTTGTAAGATTTGATTTGAATTTTATAAATTATAATACTCATGCAATAGAGCTTAAT
* * * * *
735597 GCGATTTAATA-TAGAGAAATTAGATGGTTCAAATTCCTATTTAAGCTGGAAATTATTGATATTA
131 GCGATTCAATAGTAGAAAAATTAGATGGTTCAAATTCATATTCAAGCTGGAAACTATTGATATTA
735661 GAAGAGGTATGGAAATTGGAACTGTTTTAATTGTG-TTTGACTTGGTATTTTTGATGTAGGAAGT
196 GAAGAGGTATGGAAATTGGAACTGTTTTAATTGTGTTTTGACTTGGT-TTTTTGATGTAGGAAGT
735725 TGCATAAATATACTGGAGCTATTAAAAATTAAGGAAATGGTTTTCCCTTTTG
260 TGCATAAATATACTGGAGCTATTAAAAATTAAGGAAATGGTTTTCCCTTTTG
*
735777 TTTTCTTGT
1 TTTTGTTGT
735786 AAAATTGTTA
Statistics
Matches: 292, Mismatches: 21, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
305 11 0.04
306 101 0.35
307 66 0.23
308 17 0.06
309 1 0.00
310 96 0.33
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.42
Consensus pattern (311 bp):
TTTTGTTGTTAATTGGAGTCACCGTTGTGATTCAATTCAATTTGACTTGGTTTGCAGCTGTTTTT
GGTTAGTAGTTGTAAGATTTGATTTGAATTTTATAAATTATAATACTCATGCAATAGAGCTTAAT
GCGATTCAATAGTAGAAAAATTAGATGGTTCAAATTCATATTCAAGCTGGAAACTATTGATATTA
GAAGAGGTATGGAAATTGGAACTGTTTTAATTGTGTTTTGACTTGGTTTTTTGATGTAGGAAGTT
GCATAAATATACTGGAGCTATTAAAAATTAAGGAAATGGTTTTCCCTTTTG
Found at i:740305 original size:13 final size:14
Alignment explanation
Indices: 740270--740298 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
740260 CTTAAAATTA
740270 TACATAAATTTTGG
1 TACATAAATTTTGG
740284 TACATAAATTTTGG
1 TACATAAATTTTGG
740298 T
1 T
740299 GATAAATCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.45
Consensus pattern (14 bp):
TACATAAATTTTGG
Found at i:740353 original size:31 final size:29
Alignment explanation
Indices: 740315--740384 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
740305 TCTTAAAAAT
*
740315 TATATATGAACTATGGTTTAATGTGTAATTG
1 TATATATGAACTATGATTT--TGTGTAATTG
* *
740346 TATATATGAACTTTGATTTTGTGTAATTT
1 TATATATGAACTATGATTTTGTGTAATTG
*
740375 TATACATGAA
1 TATATATGAA
740385 ATTTTGATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 18 0.51
31 17 0.49
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (29 bp):
TATATATGAACTATGATTTTGTGTAATTG
Found at i:740368 original size:29 final size:30
Alignment explanation
Indices: 740315--740394 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 30
740305 TCTTAAAAAT
* *
740315 TATATATGAACTATGGTTTAATGTGTAATTG
1 TATATATGAACTTTGATTT-ATGTGTAATTG
*
740346 TATATATGAACTTTGATTT-TGTGTAATTT
1 TATATATGAACTTTGATTTATGTGTAATTG
* *
740375 TATACATGAAATTTTGATTT
1 TATATATG-AACTTTGATTT
740395 GATCTAATTC
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 16 0.37
30 10 0.23
31 17 0.40
ACGTcount: A:0.31, C:0.04, G:0.15, T:0.50
Consensus pattern (30 bp):
TATATATGAACTTTGATTTATGTGTAATTG
Found at i:740395 original size:29 final size:29
Alignment explanation
Indices: 740336--740394 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
740326 TATGGTTTAA
*
740336 TGTGTAATTGTATATATGAACTTTGATTT
1 TGTGTAATTGTATACATGAACTTTGATTT
* *
740365 TGTGTAATTTTATACATGAAATTTTGATTT
1 TGTGTAATTGTATACATG-AACTTTGATTT
740395 GATCTAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.29, C:0.03, G:0.15, T:0.53
Consensus pattern (29 bp):
TGTGTAATTGTATACATGAACTTTGATTT
Found at i:740611 original size:29 final size:31
Alignment explanation
Indices: 740565--740626 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 31
740555 ATATATCTGA
* **
740565 ACCACAATTATAGTTTCACGTATATAATTGC
1 ACCACAATTAAAGTTTCACACATATAATTGC
*
740596 ACCA-AATTAAAG-TTCATACATATAATTGC
1 ACCACAATTAAAGTTTCACACATATAATTGC
740625 AC
1 AC
740627 GTTAAATCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 16 0.59
30 7 0.26
31 4 0.15
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.32
Consensus pattern (31 bp):
ACCACAATTAAAGTTTCACACATATAATTGC
Found at i:742294 original size:18 final size:17
Alignment explanation
Indices: 742263--742317 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
742253 TAGGATTTCA
*
742263 TATTAAATAAAAATAAC
1 TATTTAATAAAAATAAC
*
742280 TA-TTATATAAAAAATAAG
1 TATTTA-AT-AAAAATAAC
*
742298 AATTTAATAAAAATAAC
1 TATTTAATAAAAATAAC
742315 TAT
1 TAT
742318 ATTGGTAGTT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
16 2 0.07
17 14 0.47
18 11 0.37
19 3 0.10
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.33
Consensus pattern (17 bp):
TATTTAATAAAAATAAC
Done.